Applied Algebra Ph.D. Student

dynerman@math.wisc.edu

My advisor is Shamgar Gurevich. I'm on the job market looking for a postdoctoral position starting in Summer or Fall 2015.

I organize the department's Applied Algebra Seminar - if you're interested in giving a talk, please get in touch!

Research Interests

I am interested in applications of algebra to problems outside mathematics. My thesis uses tools from real algebraic geometry, optimization and group theory to study the geometry and symmetry of datasets produced in cryo-electron microscopy (cryo-EM). Cryo-EM is a technique used in structural biology to produce 3D models of proteins from very noisy 2D projections.

In October 2014 I was awarded my department's John Nohel prize for outstanding thesis work in Applied Mathematics.

Future Research

In my postdoc I am interested in using the mathematical viewpoint I have developed to create algorithms that improve 2D to 3D reconstruction in cryo-EM. Please contact me for my research statement which outlines several specific projects along these lines.

An important goal of my research plan is to collaborate directly with cryo-EM experimentalists. I hope that working closely with scientists will help produce algorithms suitable for laboratory use and which address actual problems of the cryo-EM community.

Letters of recommendation are available on request. My letter writers are my advisor, Prof. Shamgar Gurevich (Math, UW-Madison), as well as Prof. Jonathan Hauenstein (Applied Math, Notre Dame), Prof. Yoel Shkolnisky (Applied Math, Tel-Aviv), Prof. Bernd Sturmfels (Math, UC - Berkeley), and Prof. Nigel Boston (Math, UW-Madison).

Prof. Eva Nogales (Molecular & Cell Biology, UC - Berkeley) has provided a letter giving her viewpoint as a cryo-EM experimentalist, and Prof. I. Martin Isaacs (Math, UW - Madison) has written a letter about my teaching ability.

Publications

  1. David Dynerman, Shamgar Gurevich, and Yoel Shkolnisky. A remark on detecting molecular symmetry from cryo-EM images. In preparation. 2014.
  2. David Dynerman. Semi-algebraic Geometry of Common Lines. Research in the Mathematical Sciences, December 2014.
  3. David Dynerman, Erick Butzlaff, and Julie C. Mitchell. CUSA and CUDE: GPU-Accelerated Methods for Estimating Solvent Accessible Surface Area and Desolvation. Journal of Computational Biology. 2009.

Software

  1. FlowSym: A flowchart algorithm for detecting molecular symmetry from cryo-EM images. In preparation.
  2. CUDESA: GPU accelerated code for calculating solvent accessible surface area and desolvation for protein-protein interfaces. Download. 2008.