Thermodynamics of life


Thermodynamics, of life.

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

Shinier and newer, Jeremy England is hip… others?

Apell, S. Peter, Michael Neidrauer, Elisabeth S. Papazoglou, and Vincent Pizziconi. 2012. “Physics of Wound Healing I: Energy Considerations,” December. http://arxiv.org/abs/1212.3778.

Baez, John C, and Blake S. Pollard. 2015. “Relative Entropy in Biological Systems.” https://johncarlosbaez.wordpress.com/2015/11/27/relative-entropy-in-biological-systems/.

Beretta, Gian Paolo. 2020. “The Fourth Law of Thermodynamics: Steepest Entropy Ascent.” Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 378 (2170): 20190168. https://doi.org/10.1098/rsta.2019.0168.

Boyd, A. B., J. P. Crutchfield, and M. Gu. 2020. “Thermodynamic Machine Learning Through Maximum Work Production,” June. https://arxiv.org/abs/2006.15416v1.

Clarke, A. 2004. “Is There a Universal Temperature Dependence of Metabolism?” Functional Ecology 18: 252–56. https://doi.org/10.1111/j.0269-8463.2004.00842.x.

Crooks, Gavin E. 1999. “The Entropy Production Fluctuation Theorem and the Nonequilibrium Work Relation for Free Energy Differences.” Physical Review E 60 (3): 2721–6. https://doi.org/10.1103/PhysRevE.60.2721.

Crutchfield, James P. 1992. “Semantics and Thermodynamics.” In Nonlinear Modeling and Forecasting, 317–59. Santa Fe Institute Studies in the Sciences of Complexity, XII.

England, Jeremy L. 2013. “Statistical Physics of Self-Replication.” The Journal of Chemical Physics 139 (12): 121923. https://doi.org/10.1063/1.4818538.

Fodor, Étienne, Cesare Nardini, Michael E. Cates, Julien Tailleur, Paolo Visco, and Frédéric van Wijland. 2016. “How Far from Equilibrium Is Active Matter?” Physical Review Letters 117 (3): 038103. https://doi.org/10.1103/PhysRevLett.117.038103.

Gallucci, Vincent F. 1973. “On the Principles of Thermodynamics in Ecology.” Annual Review of Ecology and Systematics 4 (1): 329. https://doi.org/10.1146/annurev.es.04.110173.001553.

Harvey, S. E., S. Lahiri, and S. Ganguli. 2020. “A Universal Energy Accuracy Tradeoff in Nonequilibrium Cellular Sensing,” February. https://arxiv.org/abs/2002.10567v1.

Judson, Olivia P. 2017. “The Energy Expansions of Evolution.” Nature Ecology & Evolution 1 (April): 0138. https://doi.org/10.1038/s41559-017-0138.

Krakauer, DAvid C, and Jessica C Flack. 2010. “Better Living Through Physics.” Nature 467: 661. https://doi.org/10.1038/467661a.

Lane, Nick, and William Martin. 2010. “The Energetics of Genome Complexity.” Nature 467 (7318): 929–34. https://doi.org/10.1038/nature09486.

Lang, Alex H., Charles K. Fisher, Thierry Mora, and Pankaj Mehta. 2014. “Thermodynamics of Statistical Inference by Cells.” Physical Review Letters 113 (14). https://doi.org/10.1103/PhysRevLett.113.148103.

Lotka, Alfred J. 1922. “Natural Selection as a Physical Principle.” PNAS 8: 151.

Martyushev, and Seleznev. 2006. “Maximum Entropy Production Principle in Physics, Chemistry and Biology.” Physics Reports 426: 1–45. https://doi.org/10.1016/j.physrep.2005.12.001.

McLeod, A. Ian. 1998. “Hyperbolic Decay Time Series.” Journal of Time Series Analysis 19 (4): 473–83. https://doi.org/10.1111/1467-9892.00104.

Morowitz, Harold, and D Eric Smith. 2007. “Energy Flow and the Organization of Life.” Complexity 13 (1): 51–59. https://doi.org/10.1002/cplx.20191.

Odum, Howard T. 1973. “Energy, Ecology, and Economics.” Ambio 2 (6): 220–27. http://www.jstor.org/stable/4312030.

Perunov, Nikolai, Robert Marsland, and Jeremy England. 2014. “Statistical Physics of Adaptation,” December. http://arxiv.org/abs/1412.1875.

Pollard, Blake S. 2016. “Open Markov Processes: A Compositional Perspective on Non-Equilibrium Steady States in Biology,” January. http://arxiv.org/abs/1601.00711.

Reiss, H, Audrey D Hammerich, and E W Montroll. 1986. “Thermodynamic Treatment of Nonphysical Systems: Formalism and an Example (Single-Lane Traffic).” Journal of Statistical Physics 42: 647–87. https://doi.org/10.1007/BF01127733.

Schneider, J J, and James J Kay. 1994. “Life as a Manifestation of the Second Law of Thermodynamics.” Mathematical and Computer Modelling 19 (6-8): 25–48.

Schwab, David J. 2012. “The Energetic Costs of Cellular Computation.” Proceedings of the National Academy of Sciences 109 (44): 17978–82. https://doi.org/10.1073/pnas.1207814109.

Smith, D Eric. 2008a. “Thermodynamics of Natural Selection I: Energy Flow and the Limits on Organization.” Journal of Theoretical Biology 252: 185–97. https://doi.org/10.1016/j.jtbi.2008.02.010.

———. 2008b. “Thermodynamics of Natural Selection III: Landauer’s Principle in Computation and Chemistry.” Journal of Theoretical Biology 252 (2): 213–20. https://doi.org/10.1016/j.jtbi.2008.02.013.

Stanley, H Eugene, Luís A Nunes Amaral, A L Goldberger, Shlomo Havlin, P Ch Ivanov, and C K Peng. 1999. “Statistical Physics and Physiology: Monofractal and Multifractal Approaches.” Physica A: Statistical and Theoretical Physics 270 (1-2): 309–24.

Still, Susanne, David A. Sivak, Anthony J. Bell, and Gavin E. Crooks. 2012. “Thermodynamics of Prediction.” Physical Review Letters 109 (12): 120604. https://doi.org/10.1103/PhysRevLett.109.120604.

Vinković, Dejan, and Alan Kirman. 2006. “A Physical Analogue of the Schelling Model.” Proceedings of the National Academy of Sciences 103 (51): 19261–5. https://doi.org/10.1073/pnas.0609371103.

Vladar, Harold P. de, and Nick H. Barton. 2011. “The Contribution of Statistical Physics to Evolutionary Biology.” Trends in Ecology & Evolution 26 (8): 424–32. https://doi.org/10.1016/j.tree.2011.04.002.

Whitfield, John. 2004. “Ecology’s Big, Hot Idea.” PloS Biology 2: –440.