David F. Anderson
Department of Mathematics
Phone: (608) 263-4943
Office: Van Vleck 617.
Interests. My research lies at the interface of
mathematics and biology, and encompasses two distinct arenas of
exploration: (1) mathematical systems biology, and (2) algorithm
design and numerical analysis for the stochastic models arising
in systems biology.
- I was recently awarded the IMA
Prize in Mathematics from the Institute for Mathematics and
its Applications (IMA).
- My former graduate student, Masanori Koyama,
is now a postdoc at Kyoto University.
- My former graduate student, Beth Skubak
Wolf, is now an assistant professor at St. Mary's
Teaching (Fall 2015): Math 605 - Stochastic methods in
Office hours (Fall 2015):
- Advising: Monday 1:20-2:20pm, Tuesday
- Math 605: Monday 2:30-4:30pm.
- By appointment.
Current graduate Students:
Former graduate Students:
- David F. Anderson and Thomas G. Kurtz, Stochastic
Analysis of Biochemical Systems, Springer, 2015.
and book chapters
- David F. Anderson, Desmond J. Higham, and Yu
Monte Carlo for stochastic differential equations with small
noise, submitted, 2015.
- David F. Anderson, Gheorghe Craciun, Manoj
Gopalkrishnan, and Carsten Wiuf, Lyapunov functions,
stationary distributions, and non-equilibrium potential for
reaction networks, submitted, 2015.
- David F. Anderson and Elizabeth Skubak Wolf, Hybrid
Pathwise Sensitivity Methods for Discrete Stochastic Models
of Chemical Reaction Systems, Journal of Chemical
Physics, Vol. 142, 034103, 2015.
- David F. Anderson and Masanori Koyama, An
asymptotic relationship between coupling methods for
stochastically modeled population processes, accepted
for publication to IMA Journal of Numerical Analysis, 2014.
- David F. Anderson, Bard Ermentrout, and Peter
J. Thomas, Stochastic
Representations of Ion Channel Kinetics and Exact Stochastic
Simulation of Neuronal Dynamics, Journal for
Computational Neuroscience, Vol. 38, Issue 1, 67-82, 2015.
- David F. Anderson, Desmond J. Higham, and Yu
Sun, Complexity of
Multilevel Monte Carlo Tau-Leaping, SIAM Journal on
Numerical Analysis, Vol. 52, Issue 6, 3106–3127, 2014.
- David F. Anderson, Germán Enciso, and Matthew
D. Johnston, Stochastic
analysis of biochemical reaction networks with absolute
concentration robustness (official
web-link), with Supplementary
Material (including proofs, and statements of the most
general theorems), Journal of the
Royal Society Interface, Vol. 11, 20130943, February 12,
In Definition 3.1 of the Supplementary Material it should be
stated that the two complexes are not equal. The linked
Supplementary Material above has this error corrected. Thanks
Brijder for pointing this out.)
- David F. Anderson, Joke Blom, Michel Mandjes,
Halldora Thorsdottir, and Koen De Turck, A functional central
limit theorem for a Markov-modulated infinite-server queue,
Methodology and Computing in Applied Probability, Springer,
DOI 10.1007/s11009-014-9405-8, 2014.
- Rishi Srivastava, David F. Anderson, and James
B. Rawlings, Comparison
of finite difference based methods to obtain sensitivities
of stochastic chemical kinetic models, Journal of
Chemical Physics, Vol. 138, No. 7, 074110, 2013.
- Elizabeth Skubak Wolf and David F. Anderson, A finite difference method
for estimating second order parameter sensitivities of
discrete stochastic chemical reaction networks, Journal
of Chemical Physics, Vol. 137, No. 22, 224112, 2012.
- David F. Anderson, An Efficient Finite Difference
Method for Parameter Sensitivities of Continuous Time Markov
Chains, SIAM Journal on Numerical Analysis, Vol. 50,
Issue 5, 2237 - 2258, 2012.
- David F. Anderson and Masanori Koyama, Weak error analysis of numerical
methods for stochastic models of population processes,
SIAM: Multiscale Modeling and Simulation, Vol. 10, No. 4, 1493
- 1524, 2012.
- David F. Anderson and Desmond J. Higham, Multilevel Monte Carlo for
continuous time Markov chains, with applications in
biochemical kinetics, SIAM: Multiscale Modeling and
Simulation, Vol. 10, No. 1, 146 - 179, 2012.
Matlab files for the implementation of MLMC on the
dimerization model given on page 169 of the MLMC paper can be
found here: MLMC_DIMER_public.zip.
- David F. Anderson, A proof of the Global
Attractor Conjecture in the single linkage class case,
SIAM J. Appl. Math., Vol. 71, No. 4, 1487-1508, 2011.
- David F. Anderson, Boundedness of
trajectories for weakly reversible, single linkage class
reaction systems, Journal of Mathematical Chemistry,
Vol. 49, No. 10, 2275 - 2290, 2011.
- David F. Anderson and Thomas G. Kurtz, Continuous time Markov
chain models for chemical reaction networks, chapter in
Design and Analysis of
Biomolecular Circuits: Engineering Approaches to Systems and
Synthetic Biology, H. Koeppl et al. (eds.),
- David F. Anderson and Jonathan C. Mattingly, A weak trapezoidal method for
a class of stochastic differential equations,
Communications in Mathematical Sciences, Vol. 9, No. 1, 301 -
318, March 2011.
(Links for MATLAB code that implements
the Weak Trapezoidal algorithm for Example
5.1 and Example
5.2 from the manuscript.)
- David F. Anderson, Arnab Ganguly, and Thomas
G. Kurtz, Error
analysis of tau-leap simulation methods, Annals of
Applied Probability, Vol. 21, No. 6, 2226 - 2262,
- David F. Anderson, Gheorghe Craciun, and
Thomas G. Kurtz, Product-form
stationary distributions for deficiency zero chemical
reaction networks, Bulletin of Mathematical Biology,
Vol. 72, No. 8, 1947
- 1970, 2010.
- David F. Anderson and Anne Shiu, The dynamics of weakly
reversible population processes near facets, SIAM J.
Appl. Math., Vol. 70, No. 6, 1840 - 1858, January 2010.
- David F. Anderson, Global asymptotic stability
for a class of nonlinear chemical equations, SIAM J.
Appl. Math., Vol. 68, No. 5, pgs. 1464 - 1476, May 2008.
- David F. Anderson, Incorporating postleap checks
in tau-leaping, Journal of Chemical Physics, Vol 128,
No. 5, 054103, February 2008.
- David F. Anderson, A modified Next Reaction Method for
simulating chemical systems with time dependent propensities
and delays, Journal of Chemical Physics, Vol. 127, No.
21, 214107, December 2007.
- David F. Anderson and Jonathan C. Mattingly,
of Fluctuations in Biochemical Reaction Systems, II:
Nonlinear Chains, IET Systems Biology, 1(6), 313
- 325, November 2007.
- David F. Anderson, Jonathan C. Mattingly, H.
Frederik Nijhout, Michael Reed, Propagation
of Fluctuations in Biochemical Systems, I: Linear SSC
Networks, Bulletin of Mathematical Biology, Vol. 69, No.
6, 1791 - 1813, August 2007.
- H. Frederik Nijhout, Michael C. Reed, David
F. Anderson, Jonathan C. Mattingly, S. Jill James, and
Cornelia M. Ulrich,
Long-Range Allosteric Interactions between the Folate and
Methionine Cycles Stabilize DNA Methylation Reaction Rate,
Epigenetics, 1(2), 81 - 87, April/May 2006.
- David F. Anderson, Stochastic Perturbations
of Biochemical Reaction Systems, PhD Thesis, 2005.
- A short note on the Lyapunov
function for complex-balanced chemical reaction networks,