The David Reynolds Page

David Reynolds

Department of Physics
Loomis Laboratory
University of Illinois at Urbana-Champaign
1110 West Green Street
Urbana, IL 61801
USA

Tel: 217-333-4647 (IGB)
Tel: 217-244-3800 (Physics)

Email: dereynol [at] illinois [dot] edu

Basics

I am currently working as a postdoctoral researcher working at the University of Illinois at Urbana-Champaign under the guidance of Nigel Goldenfeld and Carl Woese. I am interested in a broad range of biological phenomena with emphasis on microbiology, ecology, and evolution. Part of my focus has been examining the role of collective effects and emergent properties in biological systems, with particular interest in the role of gene transfers and mobile genetic elements such as viruses, transposons, and plasmids.

I received my Ph.D. working under Jean Carlson in the Department of Physics at the University of California, Santa Barabara. My thesis work focused on trade-offs in complex systems, coarse-graining, and the renormalization group.

Abbreviated Curriculum Vitae

2006-2009: Postdoctoral Researcher at the Institute for Genomic Biology Fellow and the Department of Physics, University of Illinois at Urbana-Champaign
2004-2006: Institute for Computational Engineering and Sciences Fellow, University of Texas at Austin
2004: Ph.D. in Physics from University of California, Santa Barbara
2003: Awarded UCSB Affiliates Graduate Dissertation Fellowship
1998: B.S. in Physics and Math from The University of Iowa

Research Interests

Early Life
Collective Dynamics in Microbial Populations
The goal of this work is to explore the collective dynamics of microbial ecosystems, taking into account horizontal gene transfer via viruses or other gene transfer agents. Specific examples being studied include the coevolution of microbial-virus systems, of relevance to phenomena on as small a scale as biofilms and as large a scale as ocean phytoplankton blooms, and bacterial persistence. Our ongoing work is part of an effort to form a quantitative understanding of microbial ecology from the genome upto the global scale. This includes, but is not limited to, understanding the role of horizontal gene transfers, the distributed gene pool (a.k.a. pan-genome or supra-genome), and biodiversity.

Systems Biology
Stochastic Effects in Population Dynamics and Biochemical Networks
Multi-scale Modeling
Mathematical Aspects of the Renormalization Group

List of Publications

D.E. Reynolds, C. Woese, and N, Goldenfeld, Ambiguity resistance as a collective mode of genome repair, (in progress, to be submitted to PNAS or similar).

D.E. Reynolds, M. Marder, and J.T. Oden, Goal-oriented a posteriori error estimation meets the Ising model, (in progress, to be submitted to SIAM J. of Multiscale Modeling and Simulation).

D.E. Reynolds, Homeostasis in chemical networks via birth and death processes, (in preparation, to be submitted to PLOS Computational Biology or Phys. Rev. E).

D.E. Reynolds, Coarse-grained descriptions of the bacteriophage lambda repressor (to be submitted to Phys. Rev. E).

D.E. Reynolds, Predator-Prey Quasi-cycles from a Path Integral Formalism, (submitted to Phys. Rev. E).

D.E. Reynolds, Construction of coarse-grained order-parameters in non-equilibrium systems (submitted to Phys. Rev. E).

D. Reynolds, J.M. Carlson, and J. Doyle, Design degrees of freedom and mechanisms for complexity Phys. Rev. E 66 (2002) 016108.

M.E. Flatte and D.E. Reynolds, Local spectrum of a superconductor as a probe of interactions between magnetic impurities, Phys. Rev. B 61 (2000) 14810.

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