The Living Thing / Notebooks : Thermodynamics of life

Thermodynamics, of life

What is happening in this area, since everyone got tired of handwaving about “dissipative systems”? Prigogene’s work seems to have sunk into… disregard? disrepute? But there is a revival, recycling some of the same terms.

Shinier and newer, Jeremy England is hip… others? Is there in fact a difference?

Adami, C. (2004) Information theory in molecular biology. Physics of Life Reviews, 1(1), 3–22. DOI.
Allen, A. P., Gillooly, J. F., Savage, V. M., & Brown, J. H.(2006) Kinetic effects of temperature on rates of genetic divergence and speciation. PNAS, 103, 9130–9135. DOI.
Aoki, I. (1987) Entropy Balance in Lake Biwa. Ecological Modelling, 37, 235.
Apell, S. P., Neidrauer, M., Papazoglou, E. S., & Pizziconi, V. (2012) Physics of Wound Healing I: Energy Considerations. arXiv:1212.3778.
Baez, J. C., & Pollard, B. S.(2015) Relative Entropy in Biological Systems.
Clarke, A. (2004) Is there a Universal Temperature Dependence of metabolism?. Functional Ecology, 18, 252–256. DOI.
Crooks, G. E.(1999) The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences. Physical Review E, 60(3), 2721–2726. DOI.
Crutchfield, J. P.(1992) Semantics and thermodynamics. In Nonlinear Modeling and Forecasting (pp. 317–359).
de Vladar, H. P., & Barton, N. H.(2011) The contribution of statistical physics to evolutionary biology. Trends in Ecology & Evolution, 26(8), 424–432. DOI.
England, J. L.(2013) Statistical physics of self-replication. The Journal of Chemical Physics, 139(12), 121923. DOI.
Feldman, D. P., & Crutchfield, J. P.(1998) Measures of statistical complexity: Why?. Physics Letters A, 238(4-5), 244–252. DOI.
Fodor, É., Nardini, C., Cates, M. E., Tailleur, J., Visco, P., & van Wijland, F. (2016) How Far from Equilibrium Is Active Matter?. Physical Review Letters, 117(3), 038103. DOI.
Gallucci, V. F.(1973) On the Principles of Thermodynamics in Ecology. Annual Review of Ecology and Systematics, 4(1), 329. DOI.
Lane, N., & Martin, W. (2010) The energetics of genome complexity. Nature, 467(7318), 929–934. DOI.
Lang, A. H., Fisher, C. K., Mora, T., & Mehta, P. (2014) Thermodynamics of statistical inference by cells. Physical Review Letters, 113(14). DOI.
Perunov, N., Marsland, R., & England, J. (2014) Statistical Physics of Adaptation. arXiv:1412.1875 [cond-Mat, Physics:physics, Q-Bio].
Pollard, B. S.(2016) Open Markov processes: A compositional perspective on non-equilibrium steady states in biology. arXiv:1601.00711 [cond-Mat, Physics:physics].
Reiss, H., Hammerich, A. D., & Montroll, E. W.(1986) Thermodynamic treatment of nonphysical systems: Formalism and an example (Single-lane traffic). Journal of Statistical Physics, 42, 647–687. DOI.
Schwab, D. J.(2012) The Energetic Costs of Cellular Computation. Proceedings of the National Academy of Sciences, 109(44), 17978–17982. DOI.
Smith, D. E.(2006) Chemical Carnot Cycles, Landauer’s Principle, and the Thermodynamics of Natural Selection.
Smith, D. E.(2008a) Thermodynamics of natural selection I: Energy flow and the limits on organization. Journal of Theoretical Biology, 252, 185–197. DOI.
Smith, D. E.(2008b) Thermodynamics of natural selection II: Chemical Carnot cycles. Journal of Theoretical Biology, 252, 198–212. DOI.
Smith, D. E.(2008c) Thermodynamics of natural selection III: Landauer’s principle in computation and chemistry. Journal of Theoretical Biology, 252(2), 213–220. DOI.
Stanley, H. E., Amaral, L. A. N., Goldberger, A. L., Havlin, S., Ivanov, P. C., & Peng, C. K.(1999) Statistical physics and physiology: monofractal and multifractal approaches. Physica A: Statistical and Theoretical Physics, 270(1-2), 309–324.
Still, S., Sivak, D. A., Bell, A. J., & Crooks, G. E.(2012) Thermodynamics of Prediction. Physical Review Letters, 109(12), 120604. DOI.
Whitfield, J. (2004) Ecology’s Big, Hot Idea. PloS Biology, 2, -440.