Related papers: A toy model solved by statistical mechanics for te…
Equilibrium Statistical Mechanics is undoubtedly a cornerstone for the description of many particle systems. The common interpretation is based on ensemble theory as put forward by Gibbs, alongside the basic assumptions that different…
When at equilibrium, large-scale systems obey conventional thermodynamics because they belong to microscopic configurations (or states) that are typical. Crucially, the typical states usually represent only a small fraction of the total…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
A two-temperature linear spin model is presented that allows an easily understandable introduction to non-equilibrium statistical physics. The model is one that includes the concepts that are typical of more realistic non-equilibrium models…
We study the non-equilibrium thermodynamics of a single particle with two available energy levels, in contact with a classical (Maxwell-Boltzmann) or quantum (Bose-Einstein) heat bath. The particle can undergo transitions between the levels…
Chemical theories involving thermodynamical equilibrium states invariably utilize statistical mechanical equilibrium density distributions. Here, a definition of heat-work transformation termed thermo mechanical coherence is first made, and…
Recent numerical results show that non-Bayesian knowledge revision may be helpful in search engine training and optimization. In order to demonstrate how basic assumption about about the physical nature (and hence the observed statistics)…
Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
The predictive ability of stochastic chemical reactions is currently limited by the lack of closed form solutions to the governing chemical master equation. To overcome this limitation, this paper proposes a computational method capable of…
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…
Stochastic thermodynamics is the field of study relating fluctuations in stochastic systems to thermodynamic quantities. The total entropy production (EP), is central to the thermodynamic classification of systems. Non-equilibrium systems…
We introduce a toy model of the "rat race" in which individuals try to better themselves relative to the rest of the population. An individual is characterized by a real-valued fitness and each advances at a constant rate by an amount that…
Transition State Theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a…
Equilibrium thermodynamics describes the energy exchange of a body with its environment. Here, we describe the global energy exchange of an ideal gas in the Coutte flow in a thermodynamic-like manner. We derive a fundamental relation…
Reaction rates are a complicated function of molecular interactions, which can be selected from vast chemical design spaces. Seeking the design that optimizes a rate is a particularly challenging problem since the rate calculation for any…
The empirical laws of chemical kinetics are studied from a microscopic point of view. An analysis based on elementary probability theory and combinatorics is enough to explain the kinetics law observed in experiments. Thus, an out of…
The nonequilibrium response and fluctuations of Markovian systems, both near and far from equilibrium, are best understood by varying their parameters along dynamical equivalence classes. In this note, I illustrate this approach for an…
The cage effect is widely accepted as the basic microscopic mechanism underlying the physics of supercooled liquids in contrast with usual liquids which are governed by molecular interactions only. In this work we implement a new toy model…