Bulletin of the American Physical Society
APS March Meeting 2023
Volume 68, Number 3
Las Vegas, Nevada (March 5-10)
Virtual (March 20-22); Time Zone: Pacific Time
Session F13: Emerging Principles and New Developments in Non-Equilibrium Thermodynamics, Natural Selection and Chemical Reaction NetworksInvited
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Sponsoring Units: DBIO Chair: William Cannon, Pacific Northwest Natl Lab Room: Room 238 |
Tuesday, March 7, 2023 8:00AM - 8:36AM |
F13.00001: Statistical Thermodynamics and Data ad Infinitum Invited Speaker: Ying-Jen Yang Generalizing ideas of Szilard (1925), Mandelbrot (1964) and Hill (1964), we show that a statistical thermodynamic structure can emerge purely from the infinitely large data limit under a probabilistic framework independent upon their underlying mechanistic details. Systems with distinct values of a set of observables are identified as different thermodynamic states, which are parameterized by the entropic forces conjugated to the observables. The ground state with zero entropic forces corresponds to the prior probability equipped with a symmetry of interest. The entropic forces lead to symmetry breaking for each particular system that produces the data, emph{c.f.} emerging of time correlation and breakdown of detailed balance. Probabilistic models for the excited states are predicted by the Maximum Entropy Principle for sequences of i.i.d. and correlated Markov samples. |
Tuesday, March 7, 2023 8:36AM - 9:12AM |
F13.00002: Energy costs of coupled metabolic and genetic information processes in a living minimal bacterial cell: Life at the edge Invited Speaker: Zaida Luthey-Schulten We recently published a 4D whole cell model (4DWCM) of a minimal bacterial cell (with only 493 genes) growing in a rich medium. Time-dependent behaviors of concentrations and reaction fluxes from hybrid stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth. The ATP energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. Emergent imbalances in availability of nucleotides and amino acids can lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a 4DWCM from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that are compared to qPCR measurements, and the experimentally observed doubling behavior |
Tuesday, March 7, 2023 9:12AM - 9:48AM |
F13.00003: Predicting Cellular Regulation by Combining Statistical Thermodynamics, Control Theory, and Optimization Invited Speaker: Ethan King Metabolic networks of biological cells can be viewed as dissipative structures. In particular, metabolic networks operate far from thermodynamic equilibrium, and are typically assumed to be near steady state. In that light, we present methods for inference of the distribution of flux through metabolic networks using the principle of maximum entropy production. Metabolism is governed by enzyme mediated reactions with fluxes that are subject to regulation through control of abundance of enzymes as well as control of their catalytic activities -- through for example post-translational regulation. On the time-scale of evolution natural selection will favor those cells with metabolic regulation that acts most efficiently in shifting environments and nutrient conditions, thus the environment will shape regulation. Therefore we assume regulation will be such that entropy production is maximized to the extent possible, subject to maintaining the physio-chemical viability of the cell while also directing flux to achieve a high rate of growth. From these principles we formulate methods for inferring regulation of metabolism in cells in response to environmental conditions as solutions of associated optimization problems that can additionally incorporate known information and available metabolomics and proteomics data. Critically, this approach allows for prediction of metabolic fluxes, concentrations, energetics, associated rate parameters and regulation/control that are extremely difficult to measure experimentally, while taking advantage of more readily available abundance data for metabolites and proteins in the cell. |
Tuesday, March 7, 2023 9:48AM - 10:24AM |
F13.00004: Nonequilibrium thermodynamics of chemical reaction networks Invited Speaker: Massimiliano Esposito I will first briefly review the fundamentals of thermodynamics of open chemical reaction networks (CRNs). I will then present a circuit theory of CRNs which, like electrical circuit theory, can be used to descibe complex CRNs in terms of modules charaterized by the chemical analogues of a current-voltage charateristics and of Kirchhoff current and voltage laws. Energy transduction in central metaboIism will be discussed as an application. Finally, I will discuss recent progress on the energetic cost of chemical growth in CRNs. |
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