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?

Adam04
Adami, C. (2004) Information theory in molecular biology. Physics of Life Reviews, 1(1), 3–22. DOI.
AGSB06
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.
Aoki87
Aoki, I. (1987) Entropy Balance in Lake Biwa. Ecological Modelling, 37, 235.
ANPP12
Apell, S. P., Neidrauer, M., Papazoglou, E. S., & Pizziconi, V. (2012) Physics of Wound Healing I: Energy Considerations. arXiv:1212.3778.
BaPo15
Baez, J. C., & Pollard, B. S.(2015) Relative Entropy in Biological Systems.
Clar04
Clarke, A. (2004) Is there a Universal Temperature Dependence of metabolism?. Functional Ecology, 18, 252–256. DOI.
Croo99
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.
Crut92
Crutchfield, J. P.(1992) Semantics and thermodynamics. In Nonlinear Modeling and Forecasting (pp. 317–359).
VlBa11
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.
Engl13
England, J. L.(2013) Statistical physics of self-replication. The Journal of Chemical Physics, 139(12), 121923. DOI.
FeCr98
Feldman, D. P., & Crutchfield, J. P.(1998) Measures of statistical complexity: Why?. Physics Letters A, 238(4-5), 244–252. DOI.
FNCT16
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.
Gall73
Gallucci, V. F.(1973) On the Principles of Thermodynamics in Ecology. Annual Review of Ecology and Systematics, 4(1), 329. DOI.
LaMa10
Lane, N., & Martin, W. (2010) The energetics of genome complexity. Nature, 467(7318), 929–934. DOI.
LFMM14
Lang, A. H., Fisher, C. K., Mora, T., & Mehta, P. (2014) Thermodynamics of statistical inference by cells. Physical Review Letters, 113(14). DOI.
PeME14
Perunov, N., Marsland, R., & England, J. (2014) Statistical Physics of Adaptation. arXiv:1412.1875 [cond-Mat, Physics:physics, Q-Bio].
Poll16
Pollard, B. S.(2016) Open Markov processes: A compositional perspective on non-equilibrium steady states in biology. arXiv:1601.00711 [cond-Mat, Physics:physics].
ReHM86
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.
Schw12
Schwab, D. J.(2012) The Energetic Costs of Cellular Computation. Proceedings of the National Academy of Sciences, 109(44), 17978–17982. DOI.
Smit06
Smith, D. E.(2006) Chemical Carnot Cycles, Landauer’s Principle, and the Thermodynamics of Natural Selection.
Smit08a
Smith, D. E.(2008a) Thermodynamics of natural selection I: Energy flow and the limits on organization. Journal of Theoretical Biology, 252, 185–197. DOI.
Smit08b
Smith, D. E.(2008b) Thermodynamics of natural selection II: Chemical Carnot cycles. Journal of Theoretical Biology, 252, 198–212. DOI.
Smit08c
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.
SAGH99
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.
SSBC12
Still, S., Sivak, D. A., Bell, A. J., & Crooks, G. E.(2012) Thermodynamics of Prediction. Physical Review Letters, 109(12), 120604. DOI.
Whit04
Whitfield, J. (2004) Ecology’s Big, Hot Idea. PloS Biology, 2, -440.