Probabilistic and maximum entropy modeling of chemical reaction systems: Characteristics and comparisons to mass action kinetic models

被引:0
|
作者
Cannon, William R. [1 ,2 ,3 ]
Britton, Samuel [2 ,3 ]
Banwarth-Kuhn, Mikahl [3 ,4 ]
Alber, Mark [2 ]
机构
[1] Pacific Northwest Natl Lab, Phys & Computat Sci Directorate, Richland, WA 99352 USA
[2] Univ Calif Riverside, Dept Math, Riverside, CA 92505 USA
[3] Univ Calif Riverside, Ctr Quantitat Modeling Biol, Riverside, CA 92505 USA
[4] Calif State Univ East Bay, Dept Math, Hayward, CA 94542 USA
来源
JOURNAL OF CHEMICAL PHYSICS | 2024年 / 160卷 / 21期
基金
美国国家科学基金会;
关键词
METABOLITE CONCENTRATIONS; THERMODYNAMICS; PRINCIPLE; OUTPUT; TIME;
D O I
10.1063/5.0180417
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with standard chemical potentials, we derive and compare the free energy dissipation and the entropy production rates. We express the relation between entropy production and the chemical master equation for modeling metabolism, which unifies chemical kinetics and chemical thermodynamics. Because prediction uncertainty with respect to parameter variability is frequently a concern with mass action models utilizing rate constants, we compare and contrast the maximum entropy model, which has its own set of rate parameters, to a population of standard mass action models in which the rate constants are randomly chosen. We show that a maximum entropy model is characterized by a high probability of free energy dissipation rate and likewise entropy production rate, relative to other models. We then characterize the variability of the maximum entropy model predictions with respect to uncertainties in parameters (standard free energies of formation) and with respect to ionic strengths typically found in a cell.
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页数:19
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