Biocomplexity

Publications

Nigel Goldenfeld and Carl R. Woese. Life is Physics: evolution as a collective phenomenon far from equilibrium. Ann. Rev. Cond. Matt. Phys. 2, 375-399 (2011). (PDF)

N. Chia and Nigel Goldenfeld. Statistical mechanics of horizontal gene transfer in evolutionary ecology. J. Stat. Phys. 10.1007/s10955-010-0112-8 (2011). (PDF)

N. Chia and Nigel Goldenfeld. Dynamics of gene duplication and transposons in microbial genomes following a sudden environmental change. Phys. Rev. E 83, 021906:1-10 (2011). (PDF)

T. Butler and Nigel Goldenfeld. Fluctuation-driven Turing patterns. Phys. Rev. E 84, 011112 (12 pages) (2011). (PDF)

Zhenyu Wang and Nigel Goldenfeld. Theory of cooperation in a micro-organismal snowdrift game. Phys. Rev. E. Rapid Communications, 84, 020902 (4 pages) (2011). (PDF)

Patricio Jeraldo, Nicholas Chia and Nigel Goldenfeld. On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys. Environmental Microbiology (2011). (PDF)

Liu, C., M. C. McKinney, Y.H. Chen, T. M. Earnest, X. Shi, Li. J. Lin, Y. Ishino, K.A. Dahmen, I. K.O. Cann and T. Ha, Reverse-Chaperoning Activity of an AAA+ Protein, Biophysical Journal 100, 1344 – 1352 (2011)

Nicholas Guttenberg and Nigel Goldenfeld. Emergence of heterogeneity and political organization in information exchange networks. Phys. Rev. E 81, 046111:1-8 (2010). (PDF)

Z. Wang and Nigel Goldenfeld. Fixed points and limit cycles in the population dynamics of lysogenic viruses and their hosts. Phys. Rev. E 82, 011918:1-18 (2010). (PDF)

Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, et al. (2010) Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function. PLoS ONE 5(3): e9773. doi:10.1371/journal.pone.0009773 (PDF)

Fouke BJ, 2010, Hot-spring Systems Geobiology: abiotic and biotic influences ontravertine formation at Mammoth Hot Springs, Yellowstone National Park,USA, Sedimentology, 58, 170–219, doi: 10.1111/j.1365-3091.2010.01209.x (PDF)

M. Sipos, P. Jeraldo, N. Chia, A. Qu, A. S. Dhillon, M. Konkel, K.E. Nelson, B.A. White and Nigel Goldenfeld. Robust computational analysis of rRNA hypervariable tag datasets. PLoS One 5, e15220 (8 pages) (2010). (PDF)

Y. Liu, J. Park, K. A. Dahmen Y. R. Chemla, T. Ha, A comparative study of multivariate and univariate hidden Markov modelings in time-binned single-molecule FRET data analysis, J. Phys. Chem. B 114, 5386-403 (2010).

C.R. Woese and Nigel Goldenfeld. How the microbial world saved evolution from the Scylla of molecular biology and the Charybdis of the modern synthesis. Microbiology and Molecular Biology Reviews. 73, 14-21 (2009). (PDF)

N. Chia, I. Golding and Nigel Goldenfeld. Lambda-prophage induction modeled as a cooperative failure mode of lytic repression. Phys. Rev. E. Rapid Communications, 80, 030901 (R):1-4 (2009). (PDF)

T. Butler and Nigel Goldenfeld. Optimality properties of a proposed precursor to the genetic code. Phys. Rev. E 80, 032901:1-4 (2009). (PDF)

T. Butler and Nigel Goldenfeld. Robust ecological pattern formation induced by demographic noise. Phys. Rev. E Rapid Communications 80, 030902 (R): 1-4 (2009). (PDF)

T. Butler, N. Goldenfeld, D. Mathew and Z. Luthey-Schulten. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys. Rev. E Rapid Communications 79, 060901(R):1-4 (2009). (PDF)

K. Vetsigian and N. Goldenfeld. Genome rhetoric and the emergence of compositional bias. Proc. Natl. Acad. Sci. (USA) 106, 215-220 (2009). (PDF)

A.R. Missel, and K.A. Dahmen, Phys. Rev. E, Hopping Transport in Hostile Reaction-Diffusion Systems, Physical Review E 79 21126/1-14 (2009).

N. Chia, C. Woese and N. Goldenfeld. A collective mechanism for phase variation in biofilms. Proc. Natl. Acad. Sci. (USA), 105, 14597-14602 (2008). (PDF)

J. Veysey, T.J. Schickel, B.W. Fouke, M. Kandianis, R. Johnson and Nigel Goldenfeld. Reconstruction of Water Temperature, pH, and Flux of Ancient Hot Springs from Travertine Depositional Facies. J. Sed. Res. 78, 69-76 (2008) (PDF)

J. Veysey and N. Goldenfeld. Watching rocks grow. Nature Physics, 4, 310-313 (2008) (PDF)

N. Guttenberg and N. Goldenfeld. Cascade of complexity in evolving predator-prey dynamics. Phys. Rev. Lett. 100, 058102:1-4 (2008) (PDF)

A.R. Missel and K. A. Dahmen, Hopping conduction and Bacteria: Transport in Disordered Reaction Diffusion Systems, Phys. Rev. Lett. 100, 058301/1-4 (2008).

N. Goldenfeld and C. Woese. Biology's next revolution. Nature 445, 369-369 (2007) (PDF)

H.G. Martin and Nigel Goldenfeld. Origin of the species-area relationship in ecology. Proc. Natl. Acad. Sci. (USA) 103, 10310-10315 (2006) (PDF)

H.G. Martin and Nigel Goldenfeld. Estimation of microbial cover distributions at Mammoth Hot Springs using a multiple clone library resampling method. Env. Micro. 8, 1145-1154 (2006) (PDF)

K. Vetsigian, C.R. Woese and Nigel Goldenfeld. Communal evolution of the genetic code. Proc. Natl. Acad. Sci. 103, 10696-10701 (2006) (PDF)