https://www.math.wisc.edu/wiki/api.php?action=feedcontributions&user=Jdbrunner&feedformat=atomUW-Math Wiki - User contributions [en]2021-02-26T00:57:04ZUser contributionsMediaWiki 1.30.1https://www.math.wisc.edu/wiki/index.php?title=MMM&diff=13206MMM2017-02-01T20:06:49Z<p>Jdbrunner: /* T-shirts */</p>
<hr />
<div>== Mega Math Meet ==<br />
<br />
This page is for organisers of the Mega Math Meet, and in particular for storing logistics information, template TeX files, possibly past exams, etc. '''''As this is a public page, it should not be used for storing contestant data, non-public results information, nor as a repository for sharing the current year's draft problems as they are written.'''''<br />
<br />
== TeX Instructions ==<br />
<br />
The exam is divided into usually around 5 problems--3 to be done individually and 2 to be done by a team. Problems are often subdivided into separate questions, each worth a specified number of points. Individual problems are often worth, in total, around 10 points each, whereas team problems are each worth around 50 points in total. <br />
<br />
Each problem should go in its own separate TeX file, which should contain no headers and should be formatted like the following example: <br />
<br />
template_problem.tex: <br />
<nowiki><br />
\Pnum[Problem Name]<br />
<br />
Explanation of the problem's mathematics and story. <br />
<br />
\pnum<br />
<br />
Part 1 of the problem. Include some introduction text here<br />
<br />
\qnum[1] Part 1 question 1. How many kilometres in a metre?<br />
\answerbox[km]<br />
<br />
\qnum[1] Part 1 question 2. 1+1<br />
\answerbox[]<br />
<br />
\qnum[2] Part 1 question 3<br />
\answerbox[units]<br />
<br />
\pnum<br />
<br />
Part 2 introduction<br />
<br />
\qnum[2] Part 2 question 1<br />
\answerbox[mile(s)]<br />
<br />
\qnum[4] Part 2 question 2<br />
\answerbox[hour(s)]<br />
</nowiki><br />
<br />
As seen in this example, when you want a box at the end of a question for the students to write the answers into, use the \answerbox macro or the \answerboxn macro, depending on whether you want an extra newline after the answerbox. The answerbox macros take an argument which allows you to put some text at the right side of the answerbox, e.g. to specify the units expected for the answer. Some versions of TeX seem to have trouble with the answerbox macro; in the past using answerboxn instead has solved the issue.<br />
<br />
The qnum macro also takes an argument, specifying how many points the particular question is worth. <br />
<br />
The above will not compile on its own, as it is not a complete document. Rather, there is one master file that defines all these macros and includes each of the individual problem files, which looks like the following: <br />
<br />
template_all.tex: <br />
<nowiki><br />
\documentclass[12pt]{amsart}<br />
\usepackage{graphicx,amsmath,amssymb,amsfonts,mathrsfs,latexsym}<br />
\pagestyle{empty}<br />
\theoremstyle{definition}<br />
\newtheorem{prob}{Problem}[section]<br />
\newcounter{PROB}<br />
\newcounter{PN}[PROB]<br />
\newcounter{QN}[PROB]<br />
\setcounter{QN}{0}<br />
\setcounter{PN}{0}<br />
\setcounter{PROB}{-1}<br />
\newcommand{\Pnum}[1][]{\begin{center}\stepcounter{PROB}{\large\textbf{Problem \arabic{PROB}: #1}}\end{center}\par}<br />
\newcommand{\pnum}[1][]{\stepcounter{PN}{\large \textbf{Part \arabic{PN}: #1}}\newline\par}<br />
\newcommand{\qnumn}{\stepcounter{QN}\textbf{Question \arabic{PROB}.\arabic{QN}: }}<br />
\newcommand{\qnum}[1][]{\stepcounter{QN}\par\textbf{Question \arabic{PROB}.\arabic{QN}: }(#1 points) }<br />
\newcommand{\answerboxn}[1][]{\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
\newcommand{\answerbox}[1][]{\\\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
<br />
\begin{document}<br />
\Pnum[Mental Math (no calculators allowed)]<br />
\vspace{1cm}<br />
Example:\hfill\answerboxn\\<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
<br />
\newpage<br />
<br />
\include{template_problem}<br />
<br />
\end{document}<br />
</nowiki><br />
<br />
So if you put your problem in a folder called P/ and call the tex file my_problem.tex, then you add a line to the body of all.tex like <br />
<br />
<nowiki><br />
\include{P/myproblem}</nowiki><br />
<br />
Inside my_problem.tex, if you include any files (e.g. images), you should specify the full path like <br />
<br />
<nowiki><br />
\includegraphics{P/my_image.eps}</nowiki><br />
<br />
== Logistics ==<br />
<br />
===Email===<br />
There is an email account for the mega math meet: megamathmeet@math.wisc.edu. Sara Nagreen can link this account to your wisc account so that you can access it via the webmail browser interface. From there, you can set up forwarding to other accounts. I recommend CCing this account on emails sent about the MMM so that these emails are kept as records. <br />
<br />
===Budget===<br />
As of 2015, we are in the department budget! Our budget is $1000, although this should be confirmed with an administrator every year. This is a little less than what was spent pre 2015, but this difference is easily made up by not buying t-shirts for chaperons, and cutting down on extra t-shirts.<br />
<br />
===Problems and Copies===<br />
Get each problem copied separately. Stapled and one-sided is best. The top sheet shouldn't have any problems yet, only examples (it's easier to pass out that way, no worries about students starting early). BEFORE COPYING, PUT A LINE FOR THE STUDENT'S NAME ON EACH INDIVIDUAL PROBLEM. Same for team name on team problems. Collate the individual problems into groups of 8. Collate the two team problems into groups of 4+4.<br />
<br />
Write and copy an answer key for the graders. The graders will then put it in the team folder (see below).<br />
<br />
===Beamer File===<br />
We need access to the projector in the lecture hall (typically B102). You will also need a key from 2nd floor staff to get into the potium to get a mic. Check in advance that the faculty presenter (usually Dave Anderson) has a projector code that works. Throughout the event, we use a Beamer for the mental math problems, to introduce each problem and go over an easy example, and play charades (below). Get the previous year's Beamer file, update the mental math and charades. Once the problems are done, copy and paste the tex from the example problem to the slides; generally, have anything on the slides also on the paper problems.<br />
<br />
===Forms===<br />
The middle school contact, Lisa Nyenhuis (lisa_nyenhuis at mcfarland dot k12 dot wi dot us), gets in touch with all teams that are coming. A week or so before the event, she'll email you forms from each team including student names and t-shirt sizes. Fill in the names onto the grading roster (below) and use the t-shirt sizes to bag t-shirts in advance.<br />
<br />
===Trophies===<br />
We order trophies from Dinn Bros. Inc., and tend to order 8 medals each for the 1st-3rd place teams, a trophy each for those teams, and trophies for the 1st-3rd place individual. If you can get an order number from the previous year and call them, they have been willing to simply update the year on the engravings and reorder, which saves a lot of time. Try to order a month in advance; you can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
The financial spreadsheet has order details.<br />
<br />
===T-shirts/Giveaway===<br />
We order T-shirts from Sports Products Mfg. Inc. in Fitchburg/Oregon. They also have our orders on file, including the Bucky MMM graphic, and can easily reuse it and update the year. Call at least a month in advance. Once the shirts are done, someone will have to go get them. It's only about five-ten minutes south of Madison. You might be able to find faculty that live nearby who would be willing to stop.<br />
<br />
We tend to order some combination of Badger color shirts and ink: shirts in white, grey, red or black with contrasting ink. The colored shirts are more expensive and we order those only every few years. We need shirts for all the students, and a few extras. Since there are usually 20 teams we usually order 180 or so shirts. To cut back on buying unnecessary extras, get t-shirt orders from schools before buying the shirts. This is the easiest way to stay under budget.<br />
<br />
We've also used drawstring bags with the logo printed on them. This went over well and was cheaper.<br />
<br />
You can call and place the order, and then have an administrator call to provide payment info, or just have them call and place the order.<br />
<br />
===Time and Place===<br />
The meet is usually held on a Thursday in late May, on the week in between spring finals and the first summer session. We need to reserve in advance a big lecture hall (we've used B102, which is better suited than B130) as well as about 10 or 12 smaller rooms (we've gotten them on the B1 and 2 levels, and we need one room for every two teams). Joan Wendt has helped us reserve them in the past and may be able just ask for the same rooms as were used the previous year. We have used the Mathlab for grading. We have never had an issue with this, but it is probably a good idea to ask David Camacho and make sure it is free.<br />
<br />
The event typically starts around 9, with the teams arriving starting at 8:30. They register, pick up their t-shirts (bagged and labeled in advance) and go to their small room to drop off snacks, jackets, etc. before settling in the lecture hall. The hall should be prepared with row signs showing where each team should sit (with two chaperones each). You should also post signs on all entrances of VV telling the teams where to go in the building. Also post signs on the small rooms with team names. Get the "sign files" from last year to help you out.<br />
<br />
Try to be done by noon for the sake of the kids getting lunch and then back to school; this means the awards are usually given out at 11:30 or so. The problems are being graded as soon as they're completed, which means that after the final team problem there are a few minutes before we can present awards. In the past we have had the teachers come up front, split into two teams, and play "math charades" with each other. The kids just watch (not guess) to keep the chaos to a minimum, but it is generally hilarious and the kids love it.<br />
<br />
The department likes to have pictures of the event, and especially the awards ceremony. Sara Nagreen has been willing to take pictures. Be sure to pass out the folders to the teams after awards and as everyone is filing out; just ask a chaperone to come get them.<br />
<br />
===Graders===<br />
We need a lot of help in grading the problems as they come in, so that we can be done by noon. We generally bribe graduate students and undergrad math students, etc. by offering them pizza (see below). Send out an email to various department lists (graduate, the math club, etc -- ask Sara if need be). Two weeks in advance is good; sen reminders the day before. Be sure you have enough help, generally at least one person per two teams. There is a grading spreadsheet we have used to help tally the scores. <br />
<br />
[[Media:GradeRoster.xls]]<br />
<br />
Fill in the student names from the forms. Fill in individual score results; they will be tallied. Note that the team tallies always drop the lowest score per problem. The individuals and their scores are automatically placed in one sheet toward the beginning of the file. Copy and paste this sheet (values only) to the first sheet, where you can sort it to determine individual winners.<br />
<br />
Alternatively, use google sheets. This can be shared with all the graders so they can immediately enter information, alleviating a bottleneck. Doing this sped up grading immensely in 2015. The 2015 sheet can be used as a template:<br />
<br />
https://docs.google.com/spreadsheets/d/11OyiBQWinJVPn5vgxZHbQ_QYyFmZxdrZ_HFhxJ8uPYA/edit?usp=sharing<br />
<br />
This was also nice because it allowed the MC to immediately see the scores, and even monitor the scoring in real time.<br />
<br />
===Folders===<br />
<br />
At the end of the day, we also give to the teachers of the teams a packet with: a blank copy of all the problems, their students' work from that day, and a copy of the answer key. It helps to have the person grading a team compile this, and to have the folders available and labeled in advance.<br />
<br />
===Pizza===<br />
<br />
For the event, we order pizza for the graders, often from Ian's. Talk to Vicki at least a day in advance and she will place the order for you. In the past 5 large pizzas and 3 2-liters have been enough. Ask to have them bring plates, cups, napkins. Also, Ian's will cut the pizzas into smaller slices, which is nice because generally their slices are enormous.<br />
<br />
== Exams from Previous Years ==<br />
<br />
A tarball with the all of 2012's problems, TeX and PDF, is at [[Image:2012MMM.tar.gz.gif]]<br />
<br />
It is uploaded as a .gif because of mediawiki's restrictions, so delete the .gif from the end of the filename after downloading to get the actual tarball. If you are on Windows and cannot open the file, download 7zip from [http://www.7-zip.org/]. If you are on some flavour of Unix, you can simply use the command:<br />
<nowiki>tar -xzvf 2012MMM.tar.gz</nowiki></div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=MMM&diff=13205MMM2017-02-01T20:04:58Z<p>Jdbrunner: /* Budget */</p>
<hr />
<div>== Mega Math Meet ==<br />
<br />
This page is for organisers of the Mega Math Meet, and in particular for storing logistics information, template TeX files, possibly past exams, etc. '''''As this is a public page, it should not be used for storing contestant data, non-public results information, nor as a repository for sharing the current year's draft problems as they are written.'''''<br />
<br />
== TeX Instructions ==<br />
<br />
The exam is divided into usually around 5 problems--3 to be done individually and 2 to be done by a team. Problems are often subdivided into separate questions, each worth a specified number of points. Individual problems are often worth, in total, around 10 points each, whereas team problems are each worth around 50 points in total. <br />
<br />
Each problem should go in its own separate TeX file, which should contain no headers and should be formatted like the following example: <br />
<br />
template_problem.tex: <br />
<nowiki><br />
\Pnum[Problem Name]<br />
<br />
Explanation of the problem's mathematics and story. <br />
<br />
\pnum<br />
<br />
Part 1 of the problem. Include some introduction text here<br />
<br />
\qnum[1] Part 1 question 1. How many kilometres in a metre?<br />
\answerbox[km]<br />
<br />
\qnum[1] Part 1 question 2. 1+1<br />
\answerbox[]<br />
<br />
\qnum[2] Part 1 question 3<br />
\answerbox[units]<br />
<br />
\pnum<br />
<br />
Part 2 introduction<br />
<br />
\qnum[2] Part 2 question 1<br />
\answerbox[mile(s)]<br />
<br />
\qnum[4] Part 2 question 2<br />
\answerbox[hour(s)]<br />
</nowiki><br />
<br />
As seen in this example, when you want a box at the end of a question for the students to write the answers into, use the \answerbox macro or the \answerboxn macro, depending on whether you want an extra newline after the answerbox. The answerbox macros take an argument which allows you to put some text at the right side of the answerbox, e.g. to specify the units expected for the answer. Some versions of TeX seem to have trouble with the answerbox macro; in the past using answerboxn instead has solved the issue.<br />
<br />
The qnum macro also takes an argument, specifying how many points the particular question is worth. <br />
<br />
The above will not compile on its own, as it is not a complete document. Rather, there is one master file that defines all these macros and includes each of the individual problem files, which looks like the following: <br />
<br />
template_all.tex: <br />
<nowiki><br />
\documentclass[12pt]{amsart}<br />
\usepackage{graphicx,amsmath,amssymb,amsfonts,mathrsfs,latexsym}<br />
\pagestyle{empty}<br />
\theoremstyle{definition}<br />
\newtheorem{prob}{Problem}[section]<br />
\newcounter{PROB}<br />
\newcounter{PN}[PROB]<br />
\newcounter{QN}[PROB]<br />
\setcounter{QN}{0}<br />
\setcounter{PN}{0}<br />
\setcounter{PROB}{-1}<br />
\newcommand{\Pnum}[1][]{\begin{center}\stepcounter{PROB}{\large\textbf{Problem \arabic{PROB}: #1}}\end{center}\par}<br />
\newcommand{\pnum}[1][]{\stepcounter{PN}{\large \textbf{Part \arabic{PN}: #1}}\newline\par}<br />
\newcommand{\qnumn}{\stepcounter{QN}\textbf{Question \arabic{PROB}.\arabic{QN}: }}<br />
\newcommand{\qnum}[1][]{\stepcounter{QN}\par\textbf{Question \arabic{PROB}.\arabic{QN}: }(#1 points) }<br />
\newcommand{\answerboxn}[1][]{\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
\newcommand{\answerbox}[1][]{\\\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
<br />
\begin{document}<br />
\Pnum[Mental Math (no calculators allowed)]<br />
\vspace{1cm}<br />
Example:\hfill\answerboxn\\<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
<br />
\newpage<br />
<br />
\include{template_problem}<br />
<br />
\end{document}<br />
</nowiki><br />
<br />
So if you put your problem in a folder called P/ and call the tex file my_problem.tex, then you add a line to the body of all.tex like <br />
<br />
<nowiki><br />
\include{P/myproblem}</nowiki><br />
<br />
Inside my_problem.tex, if you include any files (e.g. images), you should specify the full path like <br />
<br />
<nowiki><br />
\includegraphics{P/my_image.eps}</nowiki><br />
<br />
== Logistics ==<br />
<br />
===Email===<br />
There is an email account for the mega math meet: megamathmeet@math.wisc.edu. Sara Nagreen can link this account to your wisc account so that you can access it via the webmail browser interface. From there, you can set up forwarding to other accounts. I recommend CCing this account on emails sent about the MMM so that these emails are kept as records. <br />
<br />
===Budget===<br />
As of 2015, we are in the department budget! Our budget is $1000, although this should be confirmed with an administrator every year. This is a little less than what was spent pre 2015, but this difference is easily made up by not buying t-shirts for chaperons, and cutting down on extra t-shirts.<br />
<br />
===Problems and Copies===<br />
Get each problem copied separately. Stapled and one-sided is best. The top sheet shouldn't have any problems yet, only examples (it's easier to pass out that way, no worries about students starting early). BEFORE COPYING, PUT A LINE FOR THE STUDENT'S NAME ON EACH INDIVIDUAL PROBLEM. Same for team name on team problems. Collate the individual problems into groups of 8. Collate the two team problems into groups of 4+4.<br />
<br />
Write and copy an answer key for the graders. The graders will then put it in the team folder (see below).<br />
<br />
===Beamer File===<br />
We need access to the projector in the lecture hall (typically B102). You will also need a key from 2nd floor staff to get into the potium to get a mic. Check in advance that the faculty presenter (usually Dave Anderson) has a projector code that works. Throughout the event, we use a Beamer for the mental math problems, to introduce each problem and go over an easy example, and play charades (below). Get the previous year's Beamer file, update the mental math and charades. Once the problems are done, copy and paste the tex from the example problem to the slides; generally, have anything on the slides also on the paper problems.<br />
<br />
===Forms===<br />
The middle school contact, Lisa Nyenhuis (lisa_nyenhuis at mcfarland dot k12 dot wi dot us), gets in touch with all teams that are coming. A week or so before the event, she'll email you forms from each team including student names and t-shirt sizes. Fill in the names onto the grading roster (below) and use the t-shirt sizes to bag t-shirts in advance.<br />
<br />
===Trophies===<br />
We order trophies from Dinn Bros. Inc., and tend to order 8 medals each for the 1st-3rd place teams, a trophy each for those teams, and trophies for the 1st-3rd place individual. If you can get an order number from the previous year and call them, they have been willing to simply update the year on the engravings and reorder, which saves a lot of time. Try to order a month in advance; you can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
The financial spreadsheet has order details.<br />
<br />
===T-shirts===<br />
We order T-shirts from Sports Products Mfg. Inc. in Fitchburg/Oregon. They also have our orders on file, including the Bucky MMM graphic, and can easily reuse it and update the year. Call at least a month in advance. Once the shirts are done, someone will have to go get them. It's only about five-ten minutes south of Madison. You might be able to find faculty that live nearby who would be willing to stop.<br />
<br />
We tend to order some combination of Badger color shirts and ink: shirts in white, grey, red or black with contrasting ink. The colored shirts are more expensive and we order those only every few years. We need shirts for all the students, and a few extras. Since there are usually 20 teams we usually order 180 or so shirts. To cut back on buying unnecessary extras, get t-shirt orders from schools before buying the shirts. This is the easiest way to stay under budget.<br />
<br />
You can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
===Time and Place===<br />
The meet is usually held on a Thursday in late May, on the week in between spring finals and the first summer session. We need to reserve in advance a big lecture hall (we've used B102, which is better suited than B130) as well as about 10 or 12 smaller rooms (we've gotten them on the B1 and 2 levels, and we need one room for every two teams). Joan Wendt has helped us reserve them in the past and may be able just ask for the same rooms as were used the previous year. We have used the Mathlab for grading. We have never had an issue with this, but it is probably a good idea to ask David Camacho and make sure it is free.<br />
<br />
The event typically starts around 9, with the teams arriving starting at 8:30. They register, pick up their t-shirts (bagged and labeled in advance) and go to their small room to drop off snacks, jackets, etc. before settling in the lecture hall. The hall should be prepared with row signs showing where each team should sit (with two chaperones each). You should also post signs on all entrances of VV telling the teams where to go in the building. Also post signs on the small rooms with team names. Get the "sign files" from last year to help you out.<br />
<br />
Try to be done by noon for the sake of the kids getting lunch and then back to school; this means the awards are usually given out at 11:30 or so. The problems are being graded as soon as they're completed, which means that after the final team problem there are a few minutes before we can present awards. In the past we have had the teachers come up front, split into two teams, and play "math charades" with each other. The kids just watch (not guess) to keep the chaos to a minimum, but it is generally hilarious and the kids love it.<br />
<br />
The department likes to have pictures of the event, and especially the awards ceremony. Sara Nagreen has been willing to take pictures. Be sure to pass out the folders to the teams after awards and as everyone is filing out; just ask a chaperone to come get them.<br />
<br />
===Graders===<br />
We need a lot of help in grading the problems as they come in, so that we can be done by noon. We generally bribe graduate students and undergrad math students, etc. by offering them pizza (see below). Send out an email to various department lists (graduate, the math club, etc -- ask Sara if need be). Two weeks in advance is good; sen reminders the day before. Be sure you have enough help, generally at least one person per two teams. There is a grading spreadsheet we have used to help tally the scores. <br />
<br />
[[Media:GradeRoster.xls]]<br />
<br />
Fill in the student names from the forms. Fill in individual score results; they will be tallied. Note that the team tallies always drop the lowest score per problem. The individuals and their scores are automatically placed in one sheet toward the beginning of the file. Copy and paste this sheet (values only) to the first sheet, where you can sort it to determine individual winners.<br />
<br />
Alternatively, use google sheets. This can be shared with all the graders so they can immediately enter information, alleviating a bottleneck. Doing this sped up grading immensely in 2015. The 2015 sheet can be used as a template:<br />
<br />
https://docs.google.com/spreadsheets/d/11OyiBQWinJVPn5vgxZHbQ_QYyFmZxdrZ_HFhxJ8uPYA/edit?usp=sharing<br />
<br />
This was also nice because it allowed the MC to immediately see the scores, and even monitor the scoring in real time.<br />
<br />
===Folders===<br />
<br />
At the end of the day, we also give to the teachers of the teams a packet with: a blank copy of all the problems, their students' work from that day, and a copy of the answer key. It helps to have the person grading a team compile this, and to have the folders available and labeled in advance.<br />
<br />
===Pizza===<br />
<br />
For the event, we order pizza for the graders, often from Ian's. Talk to Vicki at least a day in advance and she will place the order for you. In the past 5 large pizzas and 3 2-liters have been enough. Ask to have them bring plates, cups, napkins. Also, Ian's will cut the pizzas into smaller slices, which is nice because generally their slices are enormous.<br />
<br />
== Exams from Previous Years ==<br />
<br />
A tarball with the all of 2012's problems, TeX and PDF, is at [[Image:2012MMM.tar.gz.gif]]<br />
<br />
It is uploaded as a .gif because of mediawiki's restrictions, so delete the .gif from the end of the filename after downloading to get the actual tarball. If you are on Windows and cannot open the file, download 7zip from [http://www.7-zip.org/]. If you are on some flavour of Unix, you can simply use the command:<br />
<nowiki>tar -xzvf 2012MMM.tar.gz</nowiki></div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11703Applied/GPS2016-03-30T15:06:15Z<p>Jdbrunner: /* Abstracts */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|-<br />
|March 2<br />
|Fan Yang<br />
|"Berry phase in quantum mechanics"<br />
|-<br />
|April 1<br />
|Will Mitchell<br />
|"An exercise in asymptotics for finding stagnation points in a Stokes flow"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 12: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: I will present an introduction to Mass Action Kinetic models of biochemical systems. Chemical reaction network theory draws on both the theory of dynamical systems as well as techniques from algebra, algebraic geometry and graph theory, so hopefully I will be able to convince even the more algebraically minded among us that dynamic models are interesting.<br />
<br />
===Friday, Feb 19: Xiaoqian Xu===<br />
"Mixing: A brief introduction from the PDE aspect"<br />
<br />
Abstract: I will discuss several definitions and examples of mixing, and introduce an interesting conjecture about mixing, and also talk about the way how we can use them for other complicated situations like social life of bacteria and reproducing of corals.<br />
<br />
===Friday, April 1: Will Mitchell===<br />
"An exercise in asymptotics for finding stagnation points in a Stokes flow"<br />
<br />
Abstract: In this two-part talk, I will describe the Stokes flow about a sphere which is held fixed in a background shear flow. The flow and associated tractions are known exactly. We wish to find where the tangential component of the traction vanishes. This leads to some fourth-order polynomial equations which are hard to solve and provides a seque into the second part of the talk, wherein we attempt to solve them approximately using a small parameter argument.<br />
<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11702Applied/GPS2016-03-30T15:00:32Z<p>Jdbrunner: /* Spring 2016 */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|-<br />
|March 2<br />
|Fan Yang<br />
|"Berry phase in quantum mechanics"<br />
|-<br />
|April 1<br />
|Will Mitchell<br />
|"An exercise in asymptotics for finding stagnation points in a Stokes flow"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 12: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: I will present an introduction to Mass Action Kinetic models of biochemical systems. Chemical reaction network theory draws on both the theory of dynamical systems as well as techniques from algebra, algebraic geometry and graph theory, so hopefully I will be able to convince even the more algebraically minded among us that dynamic models are interesting.<br />
<br />
===Friday, Feb 19: Xiaoqian Xu===<br />
"Mixing: A brief introduction from the PDE aspect"<br />
<br />
Abstract: I will discuss several definitions and examples of mixing, and introduce an interesting conjecture about mixing, and also talk about the way how we can use them for other complicated situations like social life of bacteria and reproducing of corals.<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11576Applied/GPS2016-03-02T14:44:31Z<p>Jdbrunner: /* Friday, Feb 12: Jim Brunner */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|-<br />
|March 2<br />
|Fan Yang<br />
|"Berry phase in quantum mechanics"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 12: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: I will present an introduction to Mass Action Kinetic models of biochemical systems. Chemical reaction network theory draws on both the theory of dynamical systems as well as techniques from algebra, algebraic geometry and graph theory, so hopefully I will be able to convince even the more algebraically minded among us that dynamic models are interesting.<br />
<br />
===Friday, Feb 19: Xiaoqian Xu===<br />
"Mixing: A brief introduction from the PDE aspect"<br />
<br />
Abstract: I will discuss several definitions and examples of mixing, and introduce an interesting conjecture about mixing, and also talk about the way how we can use them for other complicated situations like social life of bacteria and reproducing of corals.<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11575Applied/GPS2016-03-02T14:43:59Z<p>Jdbrunner: /* Spring 2016 */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|-<br />
|March 2<br />
|Fan Yang<br />
|"Berry phase in quantum mechanics"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 12: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: i will present an introduction to Mass Action Kinetic models of biochemical systems. Chemical reaction network theory draws on both the theory of dynamical systems as well as techniques from algebra, algebraic geometry and graph theory, so hopefully I will be able to convince even the more algebraically minded among us that dynamic models are interesting. <br />
<br />
===Friday, Feb 19: Xiaoqian Xu===<br />
"Mixing: A brief introduction from the PDE aspect"<br />
<br />
Abstract: I will discuss several definitions and examples of mixing, and introduce an interesting conjecture about mixing, and also talk about the way how we can use them for other complicated situations like social life of bacteria and reproducing of corals.<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11519Applied/GPS2016-02-19T21:15:16Z<p>Jdbrunner: /* Graduate Applied Math Seminar */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 12: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: i will present an introduction to Mass Action Kinetic models of biochemical systems. Chemical reaction network theory draws on both the theory of dynamical systems as well as techniques from algebra, algebraic geometry and graph theory, so hopefully I will be able to convince even the more algebraically minded among us that dynamic models are interesting. <br />
<br />
===Friday, Feb 19: Xiaoqian Xu===<br />
"Mixing: A brief introduction from the PDE aspect"<br />
<br />
Abstract: I will discuss several definitions and examples of mixing, and introduce an interesting conjecture about mixing, and also talk about the way how we can use them for other complicated situations like social life of bacteria and reproducing of corals.<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11518Applied/GPS2016-02-19T21:11:50Z<p>Jdbrunner: /* Spring 2016 */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaoqian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|}<br />
<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=11517Applied/GPS2016-02-19T21:11:26Z<p>Jdbrunner: /* Graduate Applied Math Seminar */</p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Jim Brunner (jdbrunner (at) math.wisc.edu).<br />
<br />
The seminar schedule can be found here. We meet in Van Vleck 901 from 1:00 to 2:00 on Fridays.<br />
<br />
==Spring 2016==<br />
<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 12<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 19<br />
|Xiaogian Xu<br />
|"Mixing: A brief introduction from the PDE aspect"<br />
|}<br />
<br />
== Spring 2014 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 3<br />
|Jim Brunner<br />
|"Chemical reaction networks"<br />
|-<br />
|February 17<br />
|Peter Mueller<br />
|"Optimal swimming and evolution"<br />
|-<br />
|March 3<br />
|Zhennan Zhou<br />
|-<br />
|April 7<br />
|Will Mitchell<br />
|"Pade Approximants: How does your machine compute exp(A), with A a matrix?"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Monday, Feb 3: Jim Brunner===<br />
"Chemical reaction networks"<br />
<br />
Abstract: Jim will be using Jeremy Gunawardena's notes to introduce the topic: http://www.jeremy-gunawardena.com/papers/crnt.pdf and then transition into talking about what Prof. Craciun is looking at.<br />
<br />
===Monday, Feb 17: Peter Mueller===<br />
"Optimal swimming and evolution"<br />
<br />
Abstract: We will be going over Christophe Eloy's paper: "On the best results for undulatory swimming" (https://www.irphe.fr/~eloy/PDF/JFM2013a.pdf).<br />
<br />
===Monday, Mar 3: Zhennan Zhou===<br />
"Efficient computation of the semi-classical limit of the Schrödinger equation"<br />
<br />
Abstract: After looking at previous techniques, we will try using the Gaussian Wave Packet Transform on the semi-classical Schrödinger equation.<br />
<br />
== Fall 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|September 20<br />
|Peter Mueller<br />
|"Fluid dynamics crash course"<br />
|-<br />
|September 27<br />
|Peter Mueller<br />
|"Solutions to Stokes flow"<br />
|-<br />
|October 25<br />
|Zhennan Zhou<br />
|"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 1<br />
|Zhennan Zhou<br />
|Part 2: "Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
|-<br />
|November 8<br />
|Will Mitchell<br />
|"How do we make a mesh? Two fundamental schemes"<br />
|-<br />
|November 22<br />
|David Dynerman<br />
|"Semi-algebraic geometry of common lines"<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Sept 20: Peter Mueller===<br />
"Fluid dynamics crash course"<br />
<br />
Abstract: Deriving fundamental solutions to Stokes flow and using complex variable tricks to solve two-dimensional problems.<br />
<br />
===Friday, Sept 27: Peter Mueller===<br />
"Solutions to Stokes flow"<br />
<br />
Abstract: We will slowly traverse the steps to exactly solve flow past a cylinder (2D) or sphere (3D).<br />
<br />
===Friday, Oct 25 and Nov 1: Zhennan Zhou===<br />
"Numerical approximation of the Schrodinger equation with the electromagnetic field by the<br />
Hagedorn wave packets"<br />
<br />
Abstract: In this paper, we approximate the semi-classical Schrodinger equation in the<br />
presence of electromagnetic field by the Hagedorn wave packets approach. By operator<br />
splitting, the Hamiltonian is divided into the modified part and the residual part. The<br />
modified Hamiltonian, which is the main new idea of this paper, is chosen by the fact<br />
that Hagedorn wave packets are localized both in space and momentum so that a crucial<br />
correction term is added to the truncated Hamiltonian, and is treated by evolving the<br />
parameters associated with the Hagedorn wave packets. The residual part is treated by a<br />
Galerkin approximation. We prove that, with the modified Hamiltonian only, the Hagedorn<br />
wave packets dynamics gives the asymptotic solution with error O(eps^{1/2}), where eps is the the scaled Planck constant. We also prove that, the Galerkin<br />
approximation for the residual Hamiltonian can reduce the approximation error to O(<br />
eps^{k/2}), where k depends on the number of Hagedorn wave packets added to the dynamics.<br />
This approach is easy to implement, and can be naturally extended to the multidimensional<br />
cases. Unlike the high order Gaussian beam method, in which the non-constant cut-off<br />
function is necessary and some extra error is introduced, the Hagedorn wave packets<br />
approach gives a practical way to improve accuracy even when eps is not very small.<br />
<br />
===Friday, Nov 8: Will Mitchell===<br />
"How do we make a mesh? Two fundamental schemes"<br />
<br />
Abstract: Meshing a bounded 2D or 3D region using triangles or tetrahedra is a fundamental problem in numerical mathematics and an area of active research. In this talk I'll discuss two now-classical (although only 10-year-old) algorithms which can succeed in addressing the challenges of irregular boundaries and variable densities. For those wishing to read ahead, see:<br />
<br />
1) Persson and Strang, "A simple mesh generator in Matlab," SIAM Review, 2004<br />
<br />
2) Du et al, "Constrained centroidal Voronoi tesselations for surfaces," SIAM Journal on Scientific Computing, 2003.<br />
<br />
===Friday, Nov 22: David Dynerman===<br />
"Semi-algebraic geometry of common lines"<br />
<br />
Abstract: Cryo-electron microscopy (cryo-EM) is a technique for discovering<br />
the 3D structures of small molecules. To perform this 3D reconstruction a<br />
large number of 2D images taken from unknown microscope positions must be<br />
correctly positioned back in 3D space. Although these microscope positions<br />
are unknown, the common lines of intersection of the image planes can be<br />
detected and used in 3D reconstruction. A major difficulty in this process<br />
is large amounts of noise in the common line data.<br />
<br />
The set of all noiseless common lines forms a semi-algebraic set (a set<br />
defined by polynomial equalities and inequalities). We define and describe<br />
the geometry of this set, and briefly discuss applications.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 8<br />
|Peter Mueller<br />
|Mandelbrot's TED talk <br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|February 22<br />
|Leland Jefferis<br />
|Video lecture on intro quantum mechanics + The postulates of quantum mechanics + Spin 1/2 systems<br />
|-<br />
|February 29<br />
|Leland Jefferis<br />
|Topics in quantum mechanics: Spin 1/2 systems + Uncertainty relations + Quantum harmonic oscillators + ...<br />
|-<br />
|March 15<br />
|Will Mitchell<br />
|FEniCS, my favorite finite element software package<br />
|-<br />
|March 22<br />
|<br />
|<br />
|-<br />
|April 5<br />
|Bryan Crompton<br />
|TBD<br />
|-<br />
|April 26<br />
|Peter Mueller<br />
|Stokeslets, flagella, and stresslet swimmers<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
===Friday, Feb 22 & Feb 29: Leland Jefferis===<br />
"Topics in Quantum Mechanics"<br />
<br />
Abstract: I will introduce the key ideas of quantum mechanics and expose the fascinating mathematical framework behind the theory.<br />
<br />
===Friday, Mar 15: Will Mitchell===<br />
"FEniCS, my favorite finite element software"<br />
<br />
Abstract: The finite element method is mathematically elegant but can be thorny to code from scratch. The free, open-source FEniCS software takes care of the worst implementation details without constraining the freedom of the user to specify methods. I'll review the finite element method and then give some examples of FEniCS code.<br />
<br />
===Friday, Apr 6: Bryan Crompton===<br />
"Fractional Calculus and the Fractional Diffusion Wave Equation"<br />
<br />
Abstract: I'll talk about the equivalent formulations, the Grundwald-Letnikov and Riemann-Liouville, of fractional calculus. I will give some examples of fractional derivatives (and integrals) and then discuss the fundamental solutions to the fractional diffusion wave equation. Derivations will be done non-rigorously.<br />
<br />
===Friday, Apr 26: Peter Mueller===<br />
"Stokeslets, flagella, and stresslet swimmers"<br />
<br />
Abstract: I will be discussing time-dependent swimmers involving stokeslets as an approximation to flagella. We will then approximate the far-field by an oscillating stresslet and discuss some questionable results.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=MMM&diff=11392MMM2016-02-01T17:06:19Z<p>Jdbrunner: /* Logistics */</p>
<hr />
<div>== Mega Math Meet ==<br />
<br />
This page is for organisers of the Mega Math Meet, and in particular for storing logistics information, template TeX files, possibly past exams, etc. '''''As this is a public page, it should not be used for storing contestant data, non-public results information, nor as a repository for sharing the current year's draft problems as they are written.'''''<br />
<br />
== TeX Instructions ==<br />
<br />
The exam is divided into usually around 5 problems--3 to be done individually and 2 to be done by a team. Problems are often subdivided into separate questions, each worth a specified number of points. Individual problems are often worth, in total, around 10 points each, whereas team problems are each worth around 50 points in total. <br />
<br />
Each problem should go in its own separate TeX file, which should contain no headers and should be formatted like the following example: <br />
<br />
template_problem.tex: <br />
<nowiki><br />
\Pnum[Problem Name]<br />
<br />
Explanation of the problem's mathematics and story. <br />
<br />
\pnum<br />
<br />
Part 1 of the problem. Include some introduction text here<br />
<br />
\qnum[1] Part 1 question 1. How many kilometres in a metre?<br />
\answerbox[km]<br />
<br />
\qnum[1] Part 1 question 2. 1+1<br />
\answerbox[]<br />
<br />
\qnum[2] Part 1 question 3<br />
\answerbox[units]<br />
<br />
\pnum<br />
<br />
Part 2 introduction<br />
<br />
\qnum[2] Part 2 question 1<br />
\answerbox[mile(s)]<br />
<br />
\qnum[4] Part 2 question 2<br />
\answerbox[hour(s)]<br />
</nowiki><br />
<br />
As seen in this example, when you want a box at the end of a question for the students to write the answers into, use the \answerbox macro or the \answerboxn macro, depending on whether you want an extra newline after the answerbox. The answerbox macros take an argument which allows you to put some text at the right side of the answerbox, e.g. to specify the units expected for the answer. Some versions of TeX seem to have trouble with the answerbox macro; in the past using answerboxn instead has solved the issue.<br />
<br />
The qnum macro also takes an argument, specifying how many points the particular question is worth. <br />
<br />
The above will not compile on its own, as it is not a complete document. Rather, there is one master file that defines all these macros and includes each of the individual problem files, which looks like the following: <br />
<br />
template_all.tex: <br />
<nowiki><br />
\documentclass[12pt]{amsart}<br />
\usepackage{graphicx,amsmath,amssymb,amsfonts,mathrsfs,latexsym}<br />
\pagestyle{empty}<br />
\theoremstyle{definition}<br />
\newtheorem{prob}{Problem}[section]<br />
\newcounter{PROB}<br />
\newcounter{PN}[PROB]<br />
\newcounter{QN}[PROB]<br />
\setcounter{QN}{0}<br />
\setcounter{PN}{0}<br />
\setcounter{PROB}{-1}<br />
\newcommand{\Pnum}[1][]{\begin{center}\stepcounter{PROB}{\large\textbf{Problem \arabic{PROB}: #1}}\end{center}\par}<br />
\newcommand{\pnum}[1][]{\stepcounter{PN}{\large \textbf{Part \arabic{PN}: #1}}\newline\par}<br />
\newcommand{\qnumn}{\stepcounter{QN}\textbf{Question \arabic{PROB}.\arabic{QN}: }}<br />
\newcommand{\qnum}[1][]{\stepcounter{QN}\par\textbf{Question \arabic{PROB}.\arabic{QN}: }(#1 points) }<br />
\newcommand{\answerboxn}[1][]{\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
\newcommand{\answerbox}[1][]{\\\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
<br />
\begin{document}<br />
\Pnum[Mental Math (no calculators allowed)]<br />
\vspace{1cm}<br />
Example:\hfill\answerboxn\\<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
<br />
\newpage<br />
<br />
\include{template_problem}<br />
<br />
\end{document}<br />
</nowiki><br />
<br />
So if you put your problem in a folder called P/ and call the tex file my_problem.tex, then you add a line to the body of all.tex like <br />
<br />
<nowiki><br />
\include{P/myproblem}</nowiki><br />
<br />
Inside my_problem.tex, if you include any files (e.g. images), you should specify the full path like <br />
<br />
<nowiki><br />
\includegraphics{P/my_image.eps}</nowiki><br />
<br />
== Logistics ==<br />
<br />
===Email===<br />
There is an email account for the mega math meet: megamathmeet@math.wisc.edu. Sara Nagreen can link this account to your wisc account so that you can access it via the webmail browser interface. From there, you can set up forwarding to other accounts. I recommend CCing this account on emails sent about the MMM so that these emails are kept as records. <br />
<br />
===Budget===<br />
As of 2015, we are in the department budget! Our budget is $1000, although this should be confirmed with Vicki every year. This is a little less than what was spent pre 2015, but this difference is easily made up by not buying t-shirts for chaperons, and cutting down on extra t-shirts.<br />
<br />
===Problems and Copies===<br />
Get each problem copied separately. Stapled and one-sided is best. The top sheet shouldn't have any problems yet, only examples (it's easier to pass out that way, no worries about students starting early). BEFORE COPYING, PUT A LINE FOR THE STUDENT'S NAME ON EACH INDIVIDUAL PROBLEM. Same for team name on team problems. Collate the individual problems into groups of 8. Collate the two team problems into groups of 4+4.<br />
<br />
Write and copy an answer key for the graders. The graders will then put it in the team folder (see below).<br />
<br />
===Beamer File===<br />
We need access to the projector in the lecture hall (typically B102). You will also need a key from 2nd floor staff to get into the potium to get a mic. Check in advance that the faculty presenter (usually Dave Anderson) has a projector code that works. Throughout the event, we use a Beamer for the mental math problems, to introduce each problem and go over an easy example, and play charades (below). Get the previous year's Beamer file, update the mental math and charades. Once the problems are done, copy and paste the tex from the example problem to the slides; generally, have anything on the slides also on the paper problems.<br />
<br />
===Forms===<br />
The middle school contact, Lisa Nyenhuis (lisa_nyenhuis at mcfarland dot k12 dot wi dot us), gets in touch with all teams that are coming. A week or so before the event, she'll email you forms from each team including student names and t-shirt sizes. Fill in the names onto the grading roster (below) and use the t-shirt sizes to bag t-shirts in advance.<br />
<br />
===Trophies===<br />
We order trophies from Dinn Bros. Inc., and tend to order 8 medals each for the 1st-3rd place teams, a trophy each for those teams, and trophies for the 1st-3rd place individual. If you can get an order number from the previous year and call them, they have been willing to simply update the year on the engravings and reorder, which saves a lot of time. Try to order a month in advance; you can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
The financial spreadsheet has order details.<br />
<br />
===T-shirts===<br />
We order T-shirts from Sports Products Mfg. Inc. in Fitchburg/Oregon. They also have our orders on file, including the Bucky MMM graphic, and can easily reuse it and update the year. Call at least a month in advance. Once the shirts are done, someone will have to go get them. It's only about five-ten minutes south of Madison. You might be able to find faculty that live nearby who would be willing to stop.<br />
<br />
We tend to order some combination of Badger color shirts and ink: shirts in white, grey, red or black with contrasting ink. The colored shirts are more expensive and we order those only every few years. We need shirts for all the students, and a few extras. Since there are usually 20 teams we usually order 180 or so shirts. To cut back on buying unnecessary extras, get t-shirt orders from schools before buying the shirts. This is the easiest way to stay under budget.<br />
<br />
You can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
===Time and Place===<br />
The meet is usually held on a Thursday in late May, on the week in between spring finals and the first summer session. We need to reserve in advance a big lecture hall (we've used B102, which is better suited than B130) as well as about 10 or 12 smaller rooms (we've gotten them on the B1 and 2 levels, and we need one room for every two teams). Joan Wendt has helped us reserve them in the past and may be able just ask for the same rooms as were used the previous year. We have used the Mathlab for grading. We have never had an issue with this, but it is probably a good idea to ask David Camacho and make sure it is free.<br />
<br />
The event typically starts around 9, with the teams arriving starting at 8:30. They register, pick up their t-shirts (bagged and labeled in advance) and go to their small room to drop off snacks, jackets, etc. before settling in the lecture hall. The hall should be prepared with row signs showing where each team should sit (with two chaperones each). You should also post signs on all entrances of VV telling the teams where to go in the building. Also post signs on the small rooms with team names. Get the "sign files" from last year to help you out.<br />
<br />
Try to be done by noon for the sake of the kids getting lunch and then back to school; this means the awards are usually given out at 11:30 or so. The problems are being graded as soon as they're completed, which means that after the final team problem there are a few minutes before we can present awards. In the past we have had the teachers come up front, split into two teams, and play "math charades" with each other. The kids just watch (not guess) to keep the chaos to a minimum, but it is generally hilarious and the kids love it.<br />
<br />
The department likes to have pictures of the event, and especially the awards ceremony. Sara Nagreen has been willing to take pictures. Be sure to pass out the folders to the teams after awards and as everyone is filing out; just ask a chaperone to come get them.<br />
<br />
===Graders===<br />
We need a lot of help in grading the problems as they come in, so that we can be done by noon. We generally bribe graduate students and undergrad math students, etc. by offering them pizza (see below). Send out an email to various department lists (graduate, the math club, etc -- ask Sara if need be). Two weeks in advance is good; sen reminders the day before. Be sure you have enough help, generally at least one person per two teams. There is a grading spreadsheet we have used to help tally the scores. <br />
<br />
[[Media:GradeRoster.xls]]<br />
<br />
Fill in the student names from the forms. Fill in individual score results; they will be tallied. Note that the team tallies always drop the lowest score per problem. The individuals and their scores are automatically placed in one sheet toward the beginning of the file. Copy and paste this sheet (values only) to the first sheet, where you can sort it to determine individual winners.<br />
<br />
Alternatively, use google sheets. This can be shared with all the graders so they can immediately enter information, alleviating a bottleneck. Doing this sped up grading immensely in 2015. The 2015 sheet can be used as a template:<br />
<br />
https://docs.google.com/spreadsheets/d/11OyiBQWinJVPn5vgxZHbQ_QYyFmZxdrZ_HFhxJ8uPYA/edit?usp=sharing<br />
<br />
This was also nice because it allowed the MC to immediately see the scores, and even monitor the scoring in real time.<br />
<br />
===Folders===<br />
<br />
At the end of the day, we also give to the teachers of the teams a packet with: a blank copy of all the problems, their students' work from that day, and a copy of the answer key. It helps to have the person grading a team compile this, and to have the folders available and labeled in advance.<br />
<br />
===Pizza===<br />
<br />
For the event, we order pizza for the graders, often from Ian's. Talk to Vicki at least a day in advance and she will place the order for you. In the past 5 large pizzas and 3 2-liters have been enough. Ask to have them bring plates, cups, napkins. Also, Ian's will cut the pizzas into smaller slices, which is nice because generally their slices are enormous.<br />
<br />
== Exams from Previous Years ==<br />
<br />
A tarball with the all of 2012's problems, TeX and PDF, is at [[Image:2012MMM.tar.gz.gif]]<br />
<br />
It is uploaded as a .gif because of mediawiki's restrictions, so delete the .gif from the end of the filename after downloading to get the actual tarball. If you are on Windows and cannot open the file, download 7zip from [http://www.7-zip.org/]. If you are on some flavour of Unix, you can simply use the command:<br />
<nowiki>tar -xzvf 2012MMM.tar.gz</nowiki></div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=MMM&diff=11391MMM2016-02-01T16:57:45Z<p>Jdbrunner: </p>
<hr />
<div>== Mega Math Meet ==<br />
<br />
This page is for organisers of the Mega Math Meet, and in particular for storing logistics information, template TeX files, possibly past exams, etc. '''''As this is a public page, it should not be used for storing contestant data, non-public results information, nor as a repository for sharing the current year's draft problems as they are written.'''''<br />
<br />
== TeX Instructions ==<br />
<br />
The exam is divided into usually around 5 problems--3 to be done individually and 2 to be done by a team. Problems are often subdivided into separate questions, each worth a specified number of points. Individual problems are often worth, in total, around 10 points each, whereas team problems are each worth around 50 points in total. <br />
<br />
Each problem should go in its own separate TeX file, which should contain no headers and should be formatted like the following example: <br />
<br />
template_problem.tex: <br />
<nowiki><br />
\Pnum[Problem Name]<br />
<br />
Explanation of the problem's mathematics and story. <br />
<br />
\pnum<br />
<br />
Part 1 of the problem. Include some introduction text here<br />
<br />
\qnum[1] Part 1 question 1. How many kilometres in a metre?<br />
\answerbox[km]<br />
<br />
\qnum[1] Part 1 question 2. 1+1<br />
\answerbox[]<br />
<br />
\qnum[2] Part 1 question 3<br />
\answerbox[units]<br />
<br />
\pnum<br />
<br />
Part 2 introduction<br />
<br />
\qnum[2] Part 2 question 1<br />
\answerbox[mile(s)]<br />
<br />
\qnum[4] Part 2 question 2<br />
\answerbox[hour(s)]<br />
</nowiki><br />
<br />
As seen in this example, when you want a box at the end of a question for the students to write the answers into, use the \answerbox macro or the \answerboxn macro, depending on whether you want an extra newline after the answerbox. The answerbox macros take an argument which allows you to put some text at the right side of the answerbox, e.g. to specify the units expected for the answer. Some versions of TeX seem to have trouble with the answerbox macro; in the past using answerboxn instead has solved the issue.<br />
<br />
The qnum macro also takes an argument, specifying how many points the particular question is worth. <br />
<br />
The above will not compile on its own, as it is not a complete document. Rather, there is one master file that defines all these macros and includes each of the individual problem files, which looks like the following: <br />
<br />
template_all.tex: <br />
<nowiki><br />
\documentclass[12pt]{amsart}<br />
\usepackage{graphicx,amsmath,amssymb,amsfonts,mathrsfs,latexsym}<br />
\pagestyle{empty}<br />
\theoremstyle{definition}<br />
\newtheorem{prob}{Problem}[section]<br />
\newcounter{PROB}<br />
\newcounter{PN}[PROB]<br />
\newcounter{QN}[PROB]<br />
\setcounter{QN}{0}<br />
\setcounter{PN}{0}<br />
\setcounter{PROB}{-1}<br />
\newcommand{\Pnum}[1][]{\begin{center}\stepcounter{PROB}{\large\textbf{Problem \arabic{PROB}: #1}}\end{center}\par}<br />
\newcommand{\pnum}[1][]{\stepcounter{PN}{\large \textbf{Part \arabic{PN}: #1}}\newline\par}<br />
\newcommand{\qnumn}{\stepcounter{QN}\textbf{Question \arabic{PROB}.\arabic{QN}: }}<br />
\newcommand{\qnum}[1][]{\stepcounter{QN}\par\textbf{Question \arabic{PROB}.\arabic{QN}: }(#1 points) }<br />
\newcommand{\answerboxn}[1][]{\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
\newcommand{\answerbox}[1][]{\\\phantom{.}\hfill\framebox[5cm]{\begin{minipage}{1px}\hfill\vspace{.4in}\end{minipage}\hfill#1\ }\newline\newline}<br />
<br />
\begin{document}<br />
\Pnum[Mental Math (no calculators allowed)]<br />
\vspace{1cm}<br />
Example:\hfill\answerboxn\\<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
\qnumn \hfill \answerboxn<br />
<br />
\newpage<br />
<br />
\include{template_problem}<br />
<br />
\end{document}<br />
</nowiki><br />
<br />
So if you put your problem in a folder called P/ and call the tex file my_problem.tex, then you add a line to the body of all.tex like <br />
<br />
<nowiki><br />
\include{P/myproblem}</nowiki><br />
<br />
Inside my_problem.tex, if you include any files (e.g. images), you should specify the full path like <br />
<br />
<nowiki><br />
\includegraphics{P/my_image.eps}</nowiki><br />
<br />
== Logistics ==<br />
<br />
===Budget===<br />
As of 2015, we are in the department budget! Our budget is $1000, although this should be confirmed with Vicki every year. This is a little less than what was spent pre 2015, but this difference is easily made up by not buying t-shirts for chaperons, and cutting down on extra t-shirts.<br />
<br />
===Problems and Copies===<br />
Get each problem copied separately. Stapled and one-sided is best. The top sheet shouldn't have any problems yet, only examples (it's easier to pass out that way, no worries about students starting early). BEFORE COPYING, PUT A LINE FOR THE STUDENT'S NAME ON EACH INDIVIDUAL PROBLEM. Same for team name on team problems. Collate the individual problems into groups of 8. Collate the two team problems into groups of 4+4.<br />
<br />
Write and copy an answer key for the graders. The graders will then put it in the team folder (see below).<br />
<br />
===Beamer File===<br />
We need access to the projector in the lecture hall (typically B102). You will also need a key from 2nd floor staff to get into the potium to get a mic. Check in advance that the faculty presenter (usually Dave Anderson) has a projector code that works. Throughout the event, we use a Beamer for the mental math problems, to introduce each problem and go over an easy example, and play charades (below). Get the previous year's Beamer file, update the mental math and charades. Once the problems are done, copy and paste the tex from the example problem to the slides; generally, have anything on the slides also on the paper problems.<br />
<br />
===Forms===<br />
The middle school contact, Lisa Nyenhuis (lisa_nyenhuis at mcfarland dot k12 dot wi dot us), gets in touch with all teams that are coming. A week or so before the event, she'll email you forms from each team including student names and t-shirt sizes. Fill in the names onto the grading roster (below) and use the t-shirt sizes to bag t-shirts in advance.<br />
<br />
===Trophies===<br />
We order trophies from Dinn Bros. Inc., and tend to order 8 medals each for the 1st-3rd place teams, a trophy each for those teams, and trophies for the 1st-3rd place individual. If you can get an order number from the previous year and call them, they have been willing to simply update the year on the engravings and reorder, which saves a lot of time. Try to order a month in advance; you can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
The financial spreadsheet has order details.<br />
<br />
===T-shirts===<br />
We order T-shirts from Sports Products Mfg. Inc. in Fitchburg/Oregon. They also have our orders on file, including the Bucky MMM graphic, and can easily reuse it and update the year. Call at least a month in advance. Once the shirts are done, someone will have to go get them. It's only about five-ten minutes south of Madison. You might be able to find faculty that live nearby who would be willing to stop.<br />
<br />
We tend to order some combination of Badger color shirts and ink: shirts in white, grey, red or black with contrasting ink. The colored shirts are more expensive and we order those only every few years. We need shirts for all the students, and a few extras. Since there are usually 20 teams we usually order 180 or so shirts. To cut back on buying unnecessary extras, get t-shirt orders from schools before buying the shirts. This is the easiest way to stay under budget.<br />
<br />
You can call and place the order, and then have Vicki call to provide payment info.<br />
<br />
===Time and Place===<br />
The meet is usually held on a Thursday in late May, on the week in between spring finals and the first summer session. We need to reserve in advance a big lecture hall (we've used B102, which is better suited than B130) as well as about 10 or 12 smaller rooms (we've gotten them on the B1 and 2 levels, and we need one room for every two teams). Joan Wendt has helped us reserve them in the past and may be able just ask for the same rooms as were used the previous year. We have used the Mathlab for grading. We have never had an issue with this, but it is probably a good idea to ask David Camacho and make sure it is free.<br />
<br />
The event typically starts around 9, with the teams arriving starting at 8:30. They register, pick up their t-shirts (bagged and labeled in advance) and go to their small room to drop off snacks, jackets, etc. before settling in the lecture hall. The hall should be prepared with row signs showing where each team should sit (with two chaperones each). You should also post signs on all entrances of VV telling the teams where to go in the building. Also post signs on the small rooms with team names. Get the "sign files" from last year to help you out.<br />
<br />
Try to be done by noon for the sake of the kids getting lunch and then back to school; this means the awards are usually given out at 11:30 or so. The problems are being graded as soon as they're completed, which means that after the final team problem there are a few minutes before we can present awards. In the past we have had the teachers come up front, split into two teams, and play "math charades" with each other. The kids just watch (not guess) to keep the chaos to a minimum, but it is generally hilarious and the kids love it.<br />
<br />
The department likes to have pictures of the event, and especially the awards ceremony. Sara Nagreen has been willing to take pictures. Be sure to pass out the folders to the teams after awards and as everyone is filing out; just ask a chaperone to come get them.<br />
<br />
===Graders===<br />
We need a lot of help in grading the problems as they come in, so that we can be done by noon. We generally bribe graduate students and undergrad math students, etc. by offering them pizza (see below). Send out an email to various department lists (graduate, the math club, etc -- ask Sara if need be). Two weeks in advance is good; sen reminders the day before. Be sure you have enough help, generally at least one person per two teams. There is a grading spreadsheet we have used to help tally the scores. <br />
<br />
[[Media:GradeRoster.xls]]<br />
<br />
Fill in the student names from the forms. Fill in individual score results; they will be tallied. Note that the team tallies always drop the lowest score per problem. The individuals and their scores are automatically placed in one sheet toward the beginning of the file. Copy and paste this sheet (values only) to the first sheet, where you can sort it to determine individual winners.<br />
<br />
Alternatively, use google sheets. This can be shared with all the graders so they can immediately enter information, alleviating a bottleneck. Doing this sped up grading immensely in 2015. The 2015 sheet can be used as a template:<br />
<br />
https://docs.google.com/spreadsheets/d/11OyiBQWinJVPn5vgxZHbQ_QYyFmZxdrZ_HFhxJ8uPYA/edit?usp=sharing<br />
<br />
This was also nice because it allowed the MC to immediately see the scores, and even monitor the scoring in real time.<br />
<br />
===Folders===<br />
<br />
At the end of the day, we also give to the teachers of the teams a packet with: a blank copy of all the problems, their students' work from that day, and a copy of the answer key. It helps to have the person grading a team compile this, and to have the folders available and labeled in advance.<br />
<br />
===Pizza===<br />
<br />
For the event, we order pizza for the graders, often from Ian's. Talk to Vicki at least a day in advance and she will place the order for you. In the past 5 large pizzas and 3 2-liters have been enough. Ask to have them bring plates, cups, napkins. Also, Ian's will cut the pizzas into smaller slices, which is nice because generally their slices are enormous.<br />
<br />
== Exams from Previous Years ==<br />
<br />
A tarball with the all of 2012's problems, TeX and PDF, is at [[Image:2012MMM.tar.gz.gif]]<br />
<br />
It is uploaded as a .gif because of mediawiki's restrictions, so delete the .gif from the end of the filename after downloading to get the actual tarball. If you are on Windows and cannot open the file, download 7zip from [http://www.7-zip.org/]. If you are on some flavour of Unix, you can simply use the command:<br />
<nowiki>tar -xzvf 2012MMM.tar.gz</nowiki></div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=10461Networks Seminar2015-10-13T22:18:17Z<p>Jdbrunner: </p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by James Brunner, Jinsu Kim, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
James Brunner<br><br />
<b>Email:</b> jdbrunner[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jdbrunner www.math.wisc.edu/~jdbrunner]<br />
<br />
Jinsu Kim<br><br />
<b>Email:</b> jskim[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jskim www.math.wisc.edu/~jskim]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Fall 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted.<br />
<br />
== Wednesday, October 14, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
We will be discussing thoughts from last week's mini-conference.<br />
<br />
= Past Seminars =<br />
<br />
= Spring 2015 = <br />
<br />
== January 30, February 4, and February 11 (2:00 p.m. in Van Vleck 901), [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Toric Differential Inclusions and a Proof of the Global Attractor Conjecture<br />
<br />
<b>Abstract:</b> The global attractor conjecture says that toric dynamical systems (i.e., a class of polynomial dynamical systems on the positive orthant) have a globally attracting point within each positive linear invariant subspace -- or, equivalently, complex balanced mass-action systems have a globally attracting point within each positive stoichiometric compatibility class. We introduce toric differential inclusions, and we show that each positive solution of a toric differential inclusion is contained in an invariant region that prevents it from approaching the origin. In particular, we show that similar invariant regions prevent positive solutions of weakly reversible k-variable polynomial dynamical systems from approaching the origin. We use this result to prove the global attractor conjecture.<br />
<br />
== Wednesday, March 11, [http://pages.stat.wisc.edu/~claudia/ Claudia Solis-Lemus] (UW-Madison statistics) ==<br />
<br />
<b>Title:</b> Statistical inference of phylogenetic networks<br />
<br />
<b>Abstract:</b> Bacteria and other organisms do not follow the paradigm of vertical inheritance of genetic material. Human beings, for example, inherit their DNA from their parents only (vertical transfer), but bacteria can share DNA between different species (horizontal transfer). Therefore, their evolution cannot be modeled by a tree. To incorporate these organisms to the tree of life, we need methods to infer phylogenetic networks. In this talk, I will present a statistical method to infer phylogenetic networks from DNA sequences. I will discuss the challenges and results on assessing the identifiability of the model. Our techniques to learn phylogenetic networks will enable scientists to incorporate organisms to the tree of life in parts that are more net-like than tree-like, and thus, complete a broader picture of evolution.<br />
<br />
== Wednesday, March 18, [http://www.math.wisc.edu/~jdbrunner/ James Brunner] (UW-Madison) ==<br />
<br />
<b>Title:</b> Predator-prey systems: non-robust permanence<br />
<br />
<b>Abstract:</b> The classic Lotka-Volterra predator-prey system can be thought of as a chemical reaction network which is persistent, but not k-variable persistent or permanent. A geometric argument for this inspires a small change that makes the system k-variable permanent. However, the resulting system is not robustly permanent. In fact, an infinitesimal perturbation will cause the system to lose even the property of persistence. Similar situations are very common in CRNT, arising whenever a reaction in a network does not involve one or more species. Determining permanence of such systems remains a challenge.<br />
<br />
== Wednesday, April 15, [http://banajim.myweb.port.ac.uk Murad Banaji], University of Portsmouth ==<br />
<br />
<b>Title:</b> Logarithmic norms, compound matrices, and applications to chemical reaction networks<br />
<br />
<b>Abstract:</b> I'll discuss some background from analysis and exterior algebra and how it might be applied to chemical reaction networks or other models in biology. Starting with basic calculus, we can write down differential/integral inequalities bounding the growth rates of (generalised) lengths of curves, areas of surfaces, etc. under the action of a semiflow. Local information - encoded in Jacobian matrices - can then be used to derive global conclusions about the nature of limit-sets, and the possibility of oscillation or chaos.<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=10460Networks Seminar2015-10-13T22:15:57Z<p>Jdbrunner: </p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by James Brunner, Jinsu Kim, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
James Brunner<br><br />
<b>Email:</b> jdbrunner[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jdbrunner www.math.wisc.edu/~jdbrunner]<br />
<br />
Jinsu Kim<br><br />
<b>Email:</b> jskim[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jskim www.math.wisc.edu/~jskim]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Fall 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted.<br />
<br />
= Past Seminars =<br />
<br />
= Spring 2015 = <br />
<br />
== January 30, February 4, and February 11 (2:00 p.m. in Van Vleck 901), [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Toric Differential Inclusions and a Proof of the Global Attractor Conjecture<br />
<br />
<b>Abstract:</b> The global attractor conjecture says that toric dynamical systems (i.e., a class of polynomial dynamical systems on the positive orthant) have a globally attracting point within each positive linear invariant subspace -- or, equivalently, complex balanced mass-action systems have a globally attracting point within each positive stoichiometric compatibility class. We introduce toric differential inclusions, and we show that each positive solution of a toric differential inclusion is contained in an invariant region that prevents it from approaching the origin. In particular, we show that similar invariant regions prevent positive solutions of weakly reversible k-variable polynomial dynamical systems from approaching the origin. We use this result to prove the global attractor conjecture.<br />
<br />
== Wednesday, March 11, [http://pages.stat.wisc.edu/~claudia/ Claudia Solis-Lemus] (UW-Madison statistics) ==<br />
<br />
<b>Title:</b> Statistical inference of phylogenetic networks<br />
<br />
<b>Abstract:</b> Bacteria and other organisms do not follow the paradigm of vertical inheritance of genetic material. Human beings, for example, inherit their DNA from their parents only (vertical transfer), but bacteria can share DNA between different species (horizontal transfer). Therefore, their evolution cannot be modeled by a tree. To incorporate these organisms to the tree of life, we need methods to infer phylogenetic networks. In this talk, I will present a statistical method to infer phylogenetic networks from DNA sequences. I will discuss the challenges and results on assessing the identifiability of the model. Our techniques to learn phylogenetic networks will enable scientists to incorporate organisms to the tree of life in parts that are more net-like than tree-like, and thus, complete a broader picture of evolution.<br />
<br />
== Wednesday, March 18, [http://www.math.wisc.edu/~jdbrunner/ James Brunner] (UW-Madison) ==<br />
<br />
<b>Title:</b> Predator-prey systems: non-robust permanence<br />
<br />
<b>Abstract:</b> The classic Lotka-Volterra predator-prey system can be thought of as a chemical reaction network which is persistent, but not k-variable persistent or permanent. A geometric argument for this inspires a small change that makes the system k-variable permanent. However, the resulting system is not robustly permanent. In fact, an infinitesimal perturbation will cause the system to lose even the property of persistence. Similar situations are very common in CRNT, arising whenever a reaction in a network does not involve one or more species. Determining permanence of such systems remains a challenge.<br />
<br />
== Wednesday, April 15, [http://banajim.myweb.port.ac.uk Murad Banaji], University of Portsmouth ==<br />
<br />
<b>Title:</b> Logarithmic norms, compound matrices, and applications to chemical reaction networks<br />
<br />
<b>Abstract:</b> I'll discuss some background from analysis and exterior algebra and how it might be applied to chemical reaction networks or other models in biology. Starting with basic calculus, we can write down differential/integral inequalities bounding the growth rates of (generalised) lengths of curves, areas of surfaces, etc. under the action of a semiflow. Local information - encoded in Jacobian matrices - can then be used to derive global conclusions about the nature of limit-sets, and the possibility of oscillation or chaos.<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=10459Networks Seminar2015-10-13T22:12:54Z<p>Jdbrunner: /* Fall 2015 */</p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by James Brunner, Jinsu Kim, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
James Brunner<br><br />
<b>Email:</b> jdbrunner[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jdbrunner www.math.wisc.edu/~jdbrunner]<br />
<br />
Jinsu Kim<br><br />
<b>Email:</b> jskim[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jskim www.math.wisc.edu/~jskim]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Fall 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted.<br />
<br />
= Past Seminars =<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=10259Networks Seminar2015-09-18T20:09:40Z<p>Jdbrunner: /* Organization and Contacts */</p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by James Brunner, Jinsu Kim, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
James Brunner<br><br />
<b>Email:</b> jdbrunner[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jdbrunner www.math.wisc.edu/~jdbrunner]<br />
<br />
Jinsu Kim<br><br />
<b>Email:</b> jskim[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jskim www.math.wisc.edu/~jskim]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Spring 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted. <br />
<br />
== January 30, February 4, and February 11 (2:00 p.m. in Van Vleck 901), [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Toric Differential Inclusions and a Proof of the Global Attractor Conjecture<br />
<br />
<b>Abstract:</b> The global attractor conjecture says that toric dynamical systems (i.e., a class of polynomial dynamical systems on the positive orthant) have a globally attracting point within each positive linear invariant subspace -- or, equivalently, complex balanced mass-action systems have a globally attracting point within each positive stoichiometric compatibility class. We introduce toric differential inclusions, and we show that each positive solution of a toric differential inclusion is contained in an invariant region that prevents it from approaching the origin. In particular, we show that similar invariant regions prevent positive solutions of weakly reversible k-variable polynomial dynamical systems from approaching the origin. We use this result to prove the global attractor conjecture.<br />
<br />
== Wednesday, March 11, [http://pages.stat.wisc.edu/~claudia/ Claudia Solis-Lemus] (UW-Madison statistics) ==<br />
<br />
<b>Title:</b> Statistical inference of phylogenetic networks<br />
<br />
<b>Abstract:</b> Bacteria and other organisms do not follow the paradigm of vertical inheritance of genetic material. Human beings, for example, inherit their DNA from their parents only (vertical transfer), but bacteria can share DNA between different species (horizontal transfer). Therefore, their evolution cannot be modeled by a tree. To incorporate these organisms to the tree of life, we need methods to infer phylogenetic networks. In this talk, I will present a statistical method to infer phylogenetic networks from DNA sequences. I will discuss the challenges and results on assessing the identifiability of the model. Our techniques to learn phylogenetic networks will enable scientists to incorporate organisms to the tree of life in parts that are more net-like than tree-like, and thus, complete a broader picture of evolution.<br />
<br />
== Wednesday, March 18, [http://www.math.wisc.edu/~jdbrunner/ James Brunner] (UW-Madison) ==<br />
<br />
<b>Title:</b> Predator-prey systems: non-robust permanence<br />
<br />
<b>Abstract:</b> The classic Lotka-Volterra predator-prey system can be thought of as a chemical reaction network which is persistent, but not k-variable persistent or permanent. A geometric argument for this inspires a small change that makes the system k-variable permanent. However, the resulting system is not robustly permanent. In fact, an infinitesimal perturbation will cause the system to lose even the property of persistence. Similar situations are very common in CRNT, arising whenever a reaction in a network does not involve one or more species. Determining permanence of such systems remains a challenge.<br />
<br />
== Wednesday, April 15, [http://banajim.myweb.port.ac.uk Murad Banaji], University of Portsmouth ==<br />
<br />
<b>Title:</b> Logarithmic norms, compound matrices, and applications to chemical reaction networks<br />
<br />
<b>Abstract:</b> I'll discuss some background from analysis and exterior algebra and how it might be applied to chemical reaction networks or other models in biology. Starting with basic calculus, we can write down differential/integral inequalities bounding the growth rates of (generalised) lengths of curves, areas of surfaces, etc. under the action of a semiflow. Local information - encoded in Jacobian matrices - can then be used to derive global conclusions about the nature of limit-sets, and the possibility of oscillation or chaos.<br />
<br />
= Past Seminars =<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=10258Networks Seminar2015-09-18T20:07:22Z<p>Jdbrunner: /* Organization and Contacts */</p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by Matthew D. Johnston, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
James Brunner<br><br />
<b>Email:</b> jdbrunner[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jdbrunner www.math.wisc.edu/~jdbrunner]<br />
<br />
Jinsu Kim<br><br />
<b>Email:</b> jskim[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~jskim www.math.wisc.edu/~jskim]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Spring 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted. <br />
<br />
== January 30, February 4, and February 11 (2:00 p.m. in Van Vleck 901), [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Toric Differential Inclusions and a Proof of the Global Attractor Conjecture<br />
<br />
<b>Abstract:</b> The global attractor conjecture says that toric dynamical systems (i.e., a class of polynomial dynamical systems on the positive orthant) have a globally attracting point within each positive linear invariant subspace -- or, equivalently, complex balanced mass-action systems have a globally attracting point within each positive stoichiometric compatibility class. We introduce toric differential inclusions, and we show that each positive solution of a toric differential inclusion is contained in an invariant region that prevents it from approaching the origin. In particular, we show that similar invariant regions prevent positive solutions of weakly reversible k-variable polynomial dynamical systems from approaching the origin. We use this result to prove the global attractor conjecture.<br />
<br />
== Wednesday, March 11, [http://pages.stat.wisc.edu/~claudia/ Claudia Solis-Lemus] (UW-Madison statistics) ==<br />
<br />
<b>Title:</b> Statistical inference of phylogenetic networks<br />
<br />
<b>Abstract:</b> Bacteria and other organisms do not follow the paradigm of vertical inheritance of genetic material. Human beings, for example, inherit their DNA from their parents only (vertical transfer), but bacteria can share DNA between different species (horizontal transfer). Therefore, their evolution cannot be modeled by a tree. To incorporate these organisms to the tree of life, we need methods to infer phylogenetic networks. In this talk, I will present a statistical method to infer phylogenetic networks from DNA sequences. I will discuss the challenges and results on assessing the identifiability of the model. Our techniques to learn phylogenetic networks will enable scientists to incorporate organisms to the tree of life in parts that are more net-like than tree-like, and thus, complete a broader picture of evolution.<br />
<br />
== Wednesday, March 18, [http://www.math.wisc.edu/~jdbrunner/ James Brunner] (UW-Madison) ==<br />
<br />
<b>Title:</b> Predator-prey systems: non-robust permanence<br />
<br />
<b>Abstract:</b> The classic Lotka-Volterra predator-prey system can be thought of as a chemical reaction network which is persistent, but not k-variable persistent or permanent. A geometric argument for this inspires a small change that makes the system k-variable permanent. However, the resulting system is not robustly permanent. In fact, an infinitesimal perturbation will cause the system to lose even the property of persistence. Similar situations are very common in CRNT, arising whenever a reaction in a network does not involve one or more species. Determining permanence of such systems remains a challenge.<br />
<br />
== Wednesday, April 15, [http://banajim.myweb.port.ac.uk Murad Banaji], University of Portsmouth ==<br />
<br />
<b>Title:</b> Logarithmic norms, compound matrices, and applications to chemical reaction networks<br />
<br />
<b>Abstract:</b> I'll discuss some background from analysis and exterior algebra and how it might be applied to chemical reaction networks or other models in biology. Starting with basic calculus, we can write down differential/integral inequalities bounding the growth rates of (generalised) lengths of curves, areas of surfaces, etc. under the action of a semiflow. Local information - encoded in Jacobian matrices - can then be used to derive global conclusions about the nature of limit-sets, and the possibility of oscillation or chaos.<br />
<br />
= Past Seminars =<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Networks_Seminar&diff=9518Networks Seminar2015-03-17T13:18:41Z<p>Jdbrunner: </p>
<hr />
<div>__NOTOC__<br />
<br />
= Introduction and Overview =<br />
<br />
Networks arise in many scientific applications, from resource allocation/transportation problems, to electrical engineering networks, to the study of biochemical reactions systems. While the intended applications and analytic techniques vary significantly in these disciplines, the core goal remains the same: to extract as much information as possible about the dynamical behaviors of the resulting systems from the structure of the network itself.<br />
<br />
= Organization and Contacts =<br />
<br />
The Networks Seminar is currently organized by Matthew D. Johnston, David F. Anderson, and Gheorghe Craciun. Contact information, including how to join the mailing list, is contained below:<br />
<br />
Matthew D. Johnston<br><br />
<b>Tel:</b> 608-263-2727<br><br />
<b>Email:</b> mjohnston3[at]wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~mjohnston3 www.math.wisc.edu/~mjohnston3]<br />
<br />
David F. Anderson<br><br />
<b>Tel:</b> 608-263-4943<br><br />
<b>Email:</b> anderson[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~anderson www.math.wisc.edu/~anderson]<br />
<br />
Gheorghe Craciun<br><br />
<b>Tel:</b> 608-265-3391<br><br />
<b>Email:</b> craciun[at]math.wisc.edu<br><br />
<b>Webpage:</b> [http://www.math.wisc.edu/~craciun www.math.wisc.edu/~craciun]<br />
<br />
<b>Join Mailing List:</b> join-math-networks-seminar[at]lists.wisc.edu<br />
<br />
<b>Email Mailing List:</b> networksem[at]math.wisc.edu<br />
<br />
= Spring 2015 =<br />
<br />
The seminar will take place on <b>Wednesdays in 901 Van Vleck Hall at 2:25 PM</b>, unless otherwise noted. <br />
<br />
== January 30, February 4, and February 11 (2:00 p.m. in Van Vleck 901), [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Toric Differential Inclusions and a Proof of the Global Attractor Conjecture<br />
<br />
<b>Abstract:</b> The global attractor conjecture says that toric dynamical systems (i.e., a class of polynomial dynamical systems on the positive orthant) have a globally attracting point within each positive linear invariant subspace -- or, equivalently, complex balanced mass-action systems have a globally attracting point within each positive stoichiometric compatibility class. We introduce toric differential inclusions, and we show that each positive solution of a toric differential inclusion is contained in an invariant region that prevents it from approaching the origin. In particular, we show that similar invariant regions prevent positive solutions of weakly reversible k-variable polynomial dynamical systems from approaching the origin. We use this result to prove the global attractor conjecture.<br />
<br />
<br />
== Wednesday, March 11, [http://pages.stat.wisc.edu/~claudia/ Claudia Solis-Lemus] (UW-Madison statistics) ==<br />
<br />
<b>Title:</b> Statistical inference of phylogenetic networks<br />
<br />
<b>Abstract:</b> Bacteria and other organisms do not follow the paradigm of vertical inheritance of genetic material. Human beings, for example, inherit their DNA from their parents only (vertical transfer), but bacteria can share DNA between different species (horizontal transfer). Therefore, their evolution cannot be modeled by a tree. To incorporate these organisms to the tree of life, we need methods to infer phylogenetic networks. In this talk, I will present a statistical method to infer phylogenetic networks from DNA sequences. I will discuss the challenges and results on assessing the identifiability of the model. Our techniques to learn phylogenetic networks will enable scientists to incorporate organisms to the tree of life in parts that are more net-like than tree-like, and thus, complete a broader picture of evolution.<br />
<br />
== Wednesday, March 18, [http://www.math.wisc.edu/~jdbrunner/ James Brunner] (UW-Madison) ==<br />
<br />
<b>Title:</b> Predator-prey systems: non-robust permanence<br />
<br />
<b>Abstract:</b> The classic Lotka-Volterra predator-prey system can be thought of as a chemical reaction network which is persistent, but not k-variable persistent or permanent. A geometric argument for this inspires a small change that makes the system k-variable permanent. However, the resulting system is not robustly permanent. In fact, an infinitesimal perturbation will cause the system to lose even the property of persistence. Similar situations are very common in CRNT, arising whenever a reaction in a network does not involve one or more species. Determining permanence of such systems remains a challenge.<br />
<br />
== Wednesday, March 25 ==<br />
<br />
<b>Title:</b> TBD<br />
<br />
<b>Abstract:</b> TBD<br />
<br />
<br />
== Wednesday, April 1 ==<br />
<br />
<b>Title:</b> TBD<br />
<br />
<b>Abstract:</b> TBD<br />
<br />
<br />
== Wednesday, April 8 ==<br />
<br />
<b>Title:</b> TBD<br />
<br />
<b>Abstract:</b> TBD<br />
<br />
== Wednesday, April 15, [http://banajim.myweb.port.ac.uk Murad Banaji], University of Portsmouth ==<br />
<br />
<b>Title:</b> TBD<br />
<br />
<b>Abstract:</b> TBD<br />
<br />
= Past Seminars =<br />
<br />
= Fall 2014 =<br />
<br />
== Wednesday, September 17, [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> An Introduction to Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> There has been significant interest recently in the relationship between the kinetic of models of biochemical reaction networks and the underlying network structure. In this introductory talk, we will discuss the basic features of so-called Chemical Reaction Network Theory which has been an active area of research since the 1970s. In particular, graph-theoretic notions such as weak reversibility and network deficiency will be introduced. We will also discuss reasonable modeling choices---including deterministic and stochastic formulations---and summarize a few surprising results which hold for deterministically modeled mass action systems.<br />
<br />
== Monday, September 22 (2:25 p.m. in Van Vleck B105) [http://math.wvu.edu/~cpantea/ Casian Pantea] (WVU) ==<br />
<br />
<b>Title:</b> Injectivity and multistationarity in chemical reaction networks <br />
<br />
<b>Abstract:</b> Much attention has been paid recently to bistability and switch-like behavior that might be resident in important biochemical reaction networks. It turns out that large classes of extremely complex networks cannot give rise to multistationarity, no matter what their reaction rates might be. In turn, absence of multistationarity in a reaction network is often a consequence of the corresponding vector field being injective. In this talk I will give an overview of both older and newer injectivity results for vector fields associated with a biochemical reaction network. As much as possible, the matrix-theoretic techniques behind these results will also be discussed.<br />
<br />
== Wednesday, October 1 [http://www.math.wisc.edu/~anderson/ David F. Anderson] (UW-Madison) ==<br />
<br />
<b>Title:</b> Deficiency and stochastic models of biochemical reaction networks<br />
<br />
<b>Abstract:</b> The deficiency of a reaction network is central to many results from chemical reaction network theory. In this talk, I will explain what the deficiency of a reaction network is, and how it can be used to shed light on the behavior of the associated mathematical models. I will try to discuss results for both deterministic and stochastic models.<br />
<br />
== Wednesday, October 15, [http://www.math.ku.dk/english/about/news/phd-students/phd_cappelletti/ Daniele Cappelletti] (University of Copenhagen) ==<br />
<br />
<b>Title:</b> Elimination of intermediate species in biochemical reaction networks<br />
<br />
<b>Abstract:</b> Biochemical reactions often proceed through the formation of transient intermediate species. These species are usually more unstable than the other species and degraded at a faster rate. Due to the complexity and intractability of many reaction networks, intermediate species are therefore often ignored in the models. In this talk I will formally introduce stochastic reaction networks and unveil a connection with the deterministic ones. Further, I will show an asymptotic result giving some condition on when it is possible to safely ignore intermediate species, both in the stochastic and deterministic frameworks. I will finally show some further issues on intermediate species I am currently working on.<br />
<br />
== Wednesday, October 22; October 29; November 5, [http://www.math.wisc.edu/~craciun/ Gheorghe Craciun] (UW-Madison) ==<br />
<br />
<b>Title:</b> Persistence properties of mass action systems<br />
<br />
<b>Abstract:</b> A positive trajectory of a dynamical system is called persistent if, in the long run, it does not approach the boundary of the positive orthant. In biological applications, the persistence property is critical in deciding if a species in an ecosystem will become extinct, an infection will die off, or a chemical species will be completely consumed by a reaction network. We describe some classes of dynamical systems for which all positive trajectories are persistent. We also describe connections to the Global Attractor Conjecture, which says that a large class of mass-action systems (called complex balanced or toric dynamical systems) have a global attractor within any invariant subspace.<br />
<br />
== Wednesday, November 19 [http://www.math.wisc.edu/~mjohnston3 Matthew D. Johnston] (UW-Madison) ==<br />
<br />
<b>Title:</b> Recent Results in Chemical Reaction Network Theory<br />
<br />
<b>Abstract:</b> In this talk, I will present some recent results in two related areas of Chemical Reaction Network Theory. (1) I will present a method called network translation which is often capable of determinining characteristics of the steady state sets of deterministically modeled mass action systems. The method associates the original reaction network to a related non-physical network which is more strongly connected than the original one. (2) I will investigate differences in long-term behavior between traditional deterministic models of chemical reaction systems and the more physically realistic stochastic models. I will present a classification of systems for which the deterministic model often predicts positivity, but for which an extinction event necessarily occurs when modeled stochastically.<br />
<br />
== Friday, December 5 (11:00 a.m. in Van Vleck 901), [http://www4.ncsu.edu/~ncmeshka/ Nikki Meshkat] (NCSU) ==<br />
<br />
<b>Title:</b> Finding identifiable functions of linear and nonlinear biological models<br />
<br />
<b>Abstract:</b> Identifiability concerns finding which unknown parameters of a model can be quantified from given input-output data. Many linear ODE models, used primarily in Systems Biology, are unidentifiable, which means that parameters can take on an infinite number of values and yet yield the same input-output data. For a given unidentifiable model, the goal is then to find a set of identifiable functions, i.e. parameter combinations, and then attempt to find a scaling reparametrization so that the resulting model is identifiable. We examine this problem of finding a simple set of identifiable parameter combinations for both linear and nonlinear models. In particular, we use a graph-theoretic approach to find identifiable parameter combinations for linear compartment models and also demonstrate an algorithm using Grobner bases to find identifiable parameter combinations for nonlinear models. We demonstrate these results using our web implementation, COMBOS.</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied_and_Computational_Mathematics&diff=5047Applied and Computational Mathematics2013-02-12T21:21:10Z<p>Jdbrunner: </p>
<hr />
<div>__NOTOC__<br />
[[Image:jet.jpg|link=http://www.math.wisc.edu/~jeanluc|frame|jet striking an inclined plane]]<br />
<br />
= '''Applied Mathematics at UW-Madison''' =<br />
<br />
Welcome to the Applied Mathematics Group at the University of Wisconsin, Madison. Our faculty members, postdoctoral fellows, and students are involved in a variety of research projects, including fluid dynamics, partial and stochastic differential equations, scientific computing, biology, biochemistry, and topology.<br />
<br />
<br><br />
<br />
== News and opportunities ==<br />
<br />
* '''Sarah Tumasz''' (student of Jean-Luc Thiffeault) was awarded the 2012/13 John Nohel Prize in Applied Mathematics for her thesis, "Topological stirring."<br />
<br />
* '''Qiang Deng''' (student of Leslie Smith) graduated in Summer 2012 and has a postdoc at Courant Abu-Dhabi starting Sept 2012.<br />
<br />
* '''Hesam Dashti''' (student of Amir Assadi) received an MSc in Computational Mathematics in May 2012 and continues his PhD in Biophysics at UW Madison. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* '''Anakewit (Tete) Boonkasame''' (Ph.D. student of Paul Milewski) graduated in Summer 2012, and is now a postdoc with Leslie Smith and Fabian Waleffe. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* '''Zhan Wang''' (Ph.D. student of Paul Milewski) graduated in Summer 2012, and is now a postdoc with Jean-Marc Vanden-Broeck at UCL. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* '''Peng Qi''' (Ph.D. student of Shi Jin) graduated in Summer 2012 and took a Quantitative Associate position at Wells Fargo Bank in California. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* '''Li (Aug) Wang''' (Ph.D. student of Shi Jin) graduated in Summer 2012 and is now an postdoctoral Assistant Professor at University of Michigan-Ann Arbor. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* Research Projects in High Performance Computation and BIGDATA resources are available for graduate students taking courses or participating in [http://vv811a.math.wisc.edu/persepolis/index.php/hpc Persepolis research projects]. <!-- Added by jeanluc 2012-08-09 --><br />
<br />
* Funding opportunity for a '''postdoctoral researcher''' in the area of '''stochastic and statistical modeling of climate''' (contact [http://www.math.wisc.edu/~stechmann/ Sam Stechmann], supported by [http://www.onr.navy.mil/ ONR], apply at [http://www.mathjobs.org/jobs/jobs/3803 mathjobs.org]). <!-- Added by stechmann 2012-07-24 --><br />
<br />
* '''[http://www.math.msu.edu/~seal/ David Seal]''' (Ph.D. student with James Rossmanith) graduated in 2012 and is now a post-doc at [http://www.math.msu.edu/ Michigan State University]. <!-- Added by rossmani 2012-06-14 --><br />
<br />
* '''E. Alec Johnson''' (Ph.D. student with James Rossmanith) graduated and is now a post-doc at the [http://wis.kuleuven.be/cpa/index.php Centre for Plasma Astrophysics (KU-Leuven)]. <!-- Added by rossmani 2012-06-14 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study dynamics of large-scale molecular systems, such as cell membranes (contact [http://www.math.wisc.edu/~mitchell Julie Mitchell], supported by [http://nsf.gov NSF]). <!-- Added by mitchell 2012-06-11 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study mathematics of fluids - regularity and mixing, more for information check http://www.math.wisc.edu/~kiselev/graduate.html (contact [http://www.math.wisc.edu/~kiselev Sasha Kiselev], supported by [http://nsf.gov NSF]). <!-- Added by kiselev 2012-04-19 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study chemotaxis and applications in mathematical biology, more for information check http://www.math.wisc.edu/~kiselev/graduate.html (contact [http://www.math.wisc.edu/~kiselev Sasha Kiselev], supported by [http://nsf.gov NSF]). <!-- Added by kiselev 2012-04-19 --><br />
<br />
* '''[http://www.math.wisc.edu/~spagnolie/ Saverio Spagnolie]''' has accepted a position as a tenure-track assistant professor in our department. Saverio will join us this Fall. Welcome to the group, Saverio! <!-- Added by jeanluc 2012-03-15 --><br />
<br />
* '''Bokai Yan''' (PhD student with Shi Jin) graduated in Fall 2011 and is now a postdoc at UCLA. <!-- Added by jeanluc 2012-02-05 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study '''persistence and multistability in biological networks''' (contact [http://www.math.wisc.edu/~craciun Gheorghe Craciun], supported by [http://nih.gov NIH]). <!-- Added by craciun 2011-09-01 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study '''mathematical analysis of mass spectrometry data and proteomics''' (contact [http://www.math.wisc.edu/~craciun Gheorghe Craciun], supported by [http://nsf.gov NSF]). <!-- Added by craciun 2011-09-01 --><br />
<br />
* '''Li Wang''' (PhD student with Leslie Smith) graduated and has a job at [http://www.epic.com/ Epic]. <!-- Added by jeanluc 2011-09-01 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study '''waves in geophysical flows and tropical cyclogenesis''' (contact [http://www.math.wisc.edu/~lsmith Leslie Smith], supported by [http://nsf.gov NSF]). <!-- Added by jeanluc 2011-09-01 --><br />
<br />
* Funding opportunity for a '''graduate student''' to study '''nonlinear critical layers and exact coherent states in turbulent shear flows''' (contact [http://www.math.wisc.edu/~waleffe Fabian Waleffe], supported by [http://nsf.gov NSF]). <!-- Added by Wally 2011-09-02 --><br />
<br />
<br><br />
<br />
== Seminars ==<br />
<br />
''organized by Applied Math''<br />
<br />
* [http://www.math.wisc.edu/wiki/index.php/Applied/ACMS Applied and Computational Math Seminar] (Fridays at 2:25pm, VV 901)<br />
* [http://www.math.wisc.edu/wiki/index.php/Applied/GPS GPS Applied Math Seminar] (Fridays at 9:00am, VV 901)<br />
* Joint Math/Atmospheric & Oceanic Sciences Informal Seminar (Thursdays at 3:45 pm, AOS 811)<br />
<br />
<br />
''other seminar series of interest''<br />
<br />
* [http://www.math.wisc.edu/wiki/index.php/Colloquia Mathematics Colloquium] (Fridays at 4:00pm, VV B239)<br />
* [http://silo.ece.wisc.edu/web/content/seminars SILO Seminar] (Wednesdays at 12:30pm, 3rd floor WID)<br />
* [http://www.cs.wisc.edu/category/event-types/wid-dow-presentation-series WID-DOW Seminar] (Mondays at 4:00pm, 3rd floor WID)<br />
* [http://sprott.physics.wisc.edu/Chaos-Complexity/ Chaos and Complex Systems Seminar] (Tuesdays at 12:05pm, 4274 Chamberlin Hall)<br />
* [http://www.engr.wisc.edu/news/events/index.phtml?start=2011-09-02&range=3650&search=Rheology RRC Lecture] (Fridays at 12:05pm, 1800 Engineering Hall)<br />
* [http://www.physics.wisc.edu/twap/view.php?name=PDC Physics Department Colloquium] (Fridays at 3:30 pm; 2241 Chamberlin Hall)<br />
<br />
<br><br />
<br />
== Tenured and tenure-track faculty ==<br />
<br />
[http://www.math.wisc.edu/~anderson/ David Anderson:] (Duke, 2005) probability and stochastic processes, computational methods for stochastic processes, mathematical/systems biology.<br />
<br />
[http://www.math.wisc.edu/~angenent/ Sigurd Angenent:] (Leiden, 1986) partial differential equations.<br />
<br />
[http://www.math.wisc.edu/~assadi/ Amir Assadi:] (Princeton, 1978) computational & mathematical models in molecular biology & neuroscience.<br />
<br />
[http://www.math.wisc.edu/~boston/ Nigel Boston:] (Harvard, 1987) algebraic number theory, group theory, arithmetic geometry, computational algebra, coding theory, cryptography, and other applications of algebra to electrical engineering. <br />
<br />
[http://www.math.wisc.edu/~craciun/ Gheorghe Craciun:] (Ohio State, 2002) mathematical biology, biochemical networks, biological interaction networks.<br />
<br />
[http://www.math.wisc.edu/~shamgar/ Shamgar Gurevich:] (Tel Aviv, 2006) Representation theory of groups, algebraic geometry, applications to signal Processing, structural biology, mathematical physics.<br />
<br />
[http://www.math.wisc.edu/~jin/ Shi Jin:] (Arizona, 1991) applied & computational mathematics.<br />
<br />
[http://www.math.wisc.edu/~kiselev/ Alex (Sasha) Kiselev:] (CalTech, 1997) partial differential equations, Fourier analysis<br />
and applications in fluid mechanics, combustion, mathematical biology and Schr&ouml;dinger operators.<br />
<br />
[http://www.math.wisc.edu/~maribeff/ Gloria Mari-Beffa:] (Minnesota, 1991) differential geometry, applied math.<br />
<br />
[http://www.math.wisc.edu/~mitchell/ Julie Mitchell:] (Berkeley, 1998) computational mathematics, structural biology.<br />
<br />
[http://www.math.wisc.edu/~roch/ S&eacute;bastien Roch:] (Berkeley, 2007) applied probability, statistics and theoretical computer science, with emphasis on biological applications.<br />
<br />
[http://www.math.wisc.edu/~lsmith/ Leslie Smith:] (MIT, 1988) applied mathematics. Waves and coherent structures in oceanic and atmospheric flows. <br />
<br />
[http://www.math.wisc.edu/~spagnolie/ Saverio Spagnolie:] (Courant, 2008) fluid dynamics, biological locomotion, computational mathematics.<br />
<br />
[http://www.math.wisc.edu/~stechmann/ Sam Stechmann:] (Courant, 2008) fluid dynamics, atmospheric science, computational mathematics.<br />
<br />
[http://www.math.wisc.edu/~jeanluc/ Jean-Luc Thiffeault:] (Texas, 1998) fluid dynamics, mixing, biological swimming and mixing, topological dynamics.<br />
<br />
[http://www.math.wisc.edu/~waleffe/ Fabian Waleffe:] (MIT, 1989) applied and computational mathematics. Fluid dynamics, hydrodynamic instabilities. Turbulence and unstable coherent flows.<br />
<br />
[http://www.math.wisc.edu/~zlatos/ Andrej Zlatos:] (Caltech, 2003) partial differential equations, combustion, fluid dynamics, Schrödinger operators, orthogonal polynomials<br />
<br />
<br><br />
<br />
== Postdoctoral fellows and researchers ==<br />
<br />
<!-- [http://www.math.wisc.edu/~dwei/ Dongming Wei:] (Maryland, 2007) nonlinear partial differential equations, applied analysis, and numerical computation. --><br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/30-majid-arabgol Majid Arabgol:]<br />
HPC & Visualization Research Scholar<br />
<br />
[http://www.math.wisc.edu/~boonkasa Anakewit (Tete) Boonkasame:] (UW Madison, 2012)<br />
<br />
[http://www.math.wisc.edu/~caiy Yongyong Cai:] (National University of Singapore, 2012)<br />
<br />
[http://www.math.wisc.edu/~hernande Gerardo Hernandez-Duenas:] (Michigan, 2011) geophysical fluid dynamics<br />
<br />
[http://www.math.wisc.edu/~mjohnston3 Matthew Johnston:]<br />
(University of Waterloo, 2011) dynamical systems<br />
<br />
<br><br />
<br />
== Current Graduate Students ==<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/23-adel-ardalan Adel Ardalan:] Student of Amir Assadi.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/24-hamisha-ardalani Hamisha Ardalani:] Student of Amir Assadi.<br />
<br />
[http://www.math.wisc.edu/~blackman/ Claire Blackman:] Student of Jean-Luc Thiffeault.<br />
<br />
Yongtao Cheng: Student of James Rossmanith.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/26-alireza-fotuhi-siahpirani Alireza Fotuhi:] Student of Amir Assadi.<br />
<br />
[http://www.math.wisc.edu/~jefferis/ Leland Jefferis:] Student of Shi Jin.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/27-mohammad-khabazian Mohammad Khabbazian:] Student of Amir Assadi.<br />
<br />
[http://www.math.wisc.edu/~koyama/ Masanori (Maso) Koyama:] Student of David Anderson.<br />
<br />
[http://www.math.wisc.edu/~leili/ Lei Li:] Student of Shi Jin.<br />
<br />
[http://www.math.wisc.edu/~qinli/ Qin Li:] Student of Shi Jin.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/32-hasti-mirkia Hasti Mirkia:] Student of Amir Assadi.<br />
<br />
Peter Mueller: Student of Jean-Luc Thiffeault.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/28-arash-sangari Arash Sangari:] Student of Amir Assadi.<br />
<br />
[http://vv811a.math.wisc.edu/persepolis/index.php/members/10-members/29-ebru-selin-selen Ebru Selin Selen:] Student of Amir Assadi.<br />
<br />
Yun Sun: Student of Shi Jin.<br />
<br />
[http://www.math.wisc.edu/~matz/ Sarah Tumasz:] Student of Jean-Luc Thiffeault.<br />
<br />
[http://www.math.wisc.edu/~skubak/ Elizabeth Skubak Wolf:] Student of David Anderson.<br />
<br />
Qian You: Student of Sigurd Angenent.<br />
<br />
[http://www.math.wisc.edu/~zhou/ Zhennan Zhou:] Student of Shi Jin.<br />
<br />
<!-- Past students: --><br />
<!-- [http://www.math.wisc.edu/~hu/ Jingwei Hu:] Student of Shi Jin. --><br />
<!-- [http://www.math.wisc.edu/~yan/ Bokai Yan:] Student of Shi Jin. --><br />
<!--Zhan Wang: Student of Paul Milewski.--><br />
<!--Anekewit (Tete) Boonkasame: Student of Paul Milewski.--><br />
<!--Peng Qi: Student of Shi Jin. --><br />
<!--Li (Aug) Wang: Student of Shi Jin. --><br />
<!--Li Wang: Student of Leslie Smith. --><br />
<!--David Seal: Student of James Rossmanith. --><br />
<!--E. Alec Johnson: Student of James Rossmanith. --><br />
<!--Hesam Dashti: MSc Student of Amir Assadi.--><br />
<!--Qiang Deng: Student of Leslie Smith.--><br />
<br />
<br />
<br><br />
<br />
== Graduate course offerings ==<br />
<br />
<!-- === Spring 2012 ===<br />
* Math 714: [http://www.math.wisc.edu/math-714-scientific-computing Methods of Computational Math I] (S. Stechmann) --><br />
<br />
=== [http://www.math.wisc.edu/graduate/gcourses_fall Fall 2012] ===<br />
<br />
* Math 606: Mathematical Methods for Structural Biology (Julie Mitchell)<br />
* Math 632: Introduction to Stochastic Processes (David Anderson)<br />
* Math 703: Methods of Applied Mathematics 1 (Jean-Luc Thiffeault)<br />
* Math 705: Mathematical Fluid Dynamics (Saverio Spagnolie)<br />
* Math 714: Methods of Computational Math I (Shi Jin)<br />
* Math 833: Topics in Probability - Stochastic Processes in Evolution and Genetics (Sebastien Roch)<br />
* Math 842: Topics in Applied Algebra for EE/Math/CS students (Shamgar Gurevich)<br />
<br />
=== [http://www.math.wisc.edu/graduate/gcourses_spring Spring 2013] ===<br />
<br />
* Math 704: Methods of Applied Mathematics 2 (Sam Stechmann)<br />
* Math 715: Methods of Computational Math II (Saverio Spagnolie)<br />
* Math 801: Topics in Applied Mathematics -- Mathematical Aspects of Mixing (Jean-Luc Thiffeault)<br />
<br />
<!--<br />
=== [http://www.math.wisc.edu/graduate/gcourses_fall Fall 2011] ===<br />
<br />
* Math 605: [http://www.math.wisc.edu/math-727-calculus-variations-0 Stochastic Methods for Biology] (D. Anderson)<br />
* Math 703: [http://www.math.wisc.edu/math-703-methods-applied-mathematics-i Methods of Applied Mathematics II] (L. Smith)<br />
* Math 707: [http://www.math.wisc.edu/math707-ema700-theory-elasticity Theory of Elasticity] (F. Waleffe)<br />
* Math 714: [http://www.math.wisc.edu/math-714-scientific-computing Methods of Computational Math I] (J. Mitchell)<br />
* Math 801: [http://www.math.wisc.edu/801-waves-fluids Comp Math Applied to Biology] (A. Assadi)<br />
* Math 837: [http://www.math.wisc.edu/math-837-topics-numerical-analysis Topics in Numerical Analysis] (S. Jin)<br />
--><br />
<br />
<!--<br />
Spring 2011:<br />
* Math 609: [https://www.math.wisc.edu/609-mathematical-methods-systems-biology Mathematical Methods for Systems Biology] (G. Craciun)<br />
* Math 704: [https://www.math.wisc.edu/704-methods-applied-mathematics-2 Methods of Applied Mathematics II] (S. Stechmann)<br />
* Math/CS 715: [https://www.math.wisc.edu/715-methods-computational-math-ii Methods of Computational Math II] (S. Jin)<br />
* Math 801: [https://www.math.wisc.edu/math-801-hydrodynamic-instabilities-chaos-and-turbulence Hydrodynamic Instabilities, Chaos and Turbulence] (F. Waleffe)<br />
* Math 826: [https://www.math.wisc.edu/826-Functional-Analysis Partial Differential Equations in Fluids and Biology] (A. Kiselev)<br />
* Math/CS 837: [https://www.math.wisc.edu/837-Numerical-Analysis Numerical Methods for Hyperbolic PDEs] (J. Rossmanith)<br />
--><br />
<br />
<br><br />
<br />
----<br />
Return to the [http://www.math.wisc.edu/wiki/index.php Mathematics Department Wiki Page]<br />
<br />
[http://www3.clustrmaps.com/stats/maps-no_clusters/www.math.wisc.edu-wiki-index.php-Applied-thumb.jpg Locations of visitors to this page] ([http://www3.clustrmaps.com/user/195f39ef Clustermaps])</div>Jdbrunnerhttps://www.math.wisc.edu/wiki/index.php?title=Applied/GPS&diff=5046Applied/GPS2013-02-12T21:00:35Z<p>Jdbrunner: </p>
<hr />
<div>__NOTOC__<br />
= Graduate Applied Math Seminar =<br />
<br />
The Graduate Applied Math Seminar is one of the main tools for bringing together applied grad students in the department and building the community. You are encouraged to get involved! It is weekly seminar run by grad students for grad students. If you have any questions, please contact Bryan Crompton.<br />
<br />
The seminar schedule can be found here.<br />
<br />
== Spring 2013 ==<br />
<br />
{| cellpadding="5"<br />
!align="left" | date<br />
!align="left" | speaker<br />
!align="left" | title<br />
|-<br />
|February 1<br />
|Bryan Crompton<br />
|"The surprising math of cities and corporations"<br />
|-<br />
|February 15<br />
|Jim Brunner<br />
|"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
|-<br />
|<br />
|<br />
|<br />
|}<br />
<br />
== Abstracts ==<br />
<br />
Please add your abstracts here.<br />
<br />
===Friday, Feb 1: Bryan Cromtpon===<br />
"The surprising math of cities and corporations"<br />
<br />
Abstract: We'll watch Geoffrey West's TED talk and discuss some of the math in his papers.<br />
<br />
===Friday, Feb 15: Jim Brunner===<br />
"Logical Models, Polynomial Dynamical Systems, and Iron Metabolism"<br />
<br />
Abstract: I will introduce logical models and polynomial dynamical systems in the context of a model of iron metabolism in an epithelial cell.<br />
<br />
== Archived semesters ==<br />
*[[Applied/GPS/Fall2012|Fall 2012]]<br />
*[[Applied/GPS/Spring2012|Spring 2012]]<br />
*[[Applied/GPS/Fall2011|Fall 2011]]</div>Jdbrunner