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Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
Three-body recombination is a prime example of the fundamental interaction between three particles. Due to the complexity of this process it has resisted a comprehensive description. Experimental investigations have mainly focussed on the…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
The Boltzmann kinetic theory for a model of a confined quasi-two dimensional granular mixture derived previously [Garz\'o, Brito and Soto, Phys. Fluids \textbf{33}, 023310 (2021)] is considered further to analyze two different problems.…
The kinetics of carbon condensation, or carbon clustering, in detonation of carbon-rich high explosives is modeled by solving a system of rate equations for concentrations of carbon particles. Unlike previous efforts, the rate equations…
Traditional stochastic modeling of reactive systems limits the domain of applicability of the associated path thermodynamics to systems involving a single elementary reaction at the origin of each observed change in composition. An…
This work presents a unified viscoelastic-viscoplastic continuum framework for modeling rate-dependent granular flows across regimes. The formulation incorporates two distinct rate-dependent mechanisms, namely micro-inertia and viscoelastic…
The quantum theory of coherent Ising machines, based on degenerate optical parametric oscillators and measurement-feedback circuits, is developed using the positive $P({\alpha},{\beta})$ representation of the density operator and the master…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
Multi-dimensional spectroscopy represents a particularly insightful tool for investigating the interplay of nuclear and electronic dynamics, which plays an important role in a number of photophysical processes and photochemical reactions.…
We develop a causal hydrodynamic model that provides an effective macroscopic description of the field-theoretic dynamics during the early stages of reheating. The inflaton condensate is treated as a homogeneous background coupled to a…
The local balance equations for the density, momentum, and energy of a dilute gas of elastic or inelastic hard spheres, strongly confined between two parallel hard plates are obtained. The starting point is a Boltzmann-like kinetic…
An isolated mixture of smooth, inelastic hard spheres supports a homogeneous cooling state with different kinetic temperatures for each species. This phenomenon is explored here by molecular dynamics simulation of a two component fluid,…
Photons excited into ground state modes at finite temperature display partitioning among photon phases, lifetimes and distances travelled since creation. These distributions set the distance from an interface a created photon has some…
In this article we deduce a mathematical model of Maxwell-Stefan type for a reactive mixture of polyatomic gases with a continuous structure of internal energy. The equations of the model are derived in the diffusive limit of a kinetic…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Cross-sections for dissociative recombination and electron-impact vibrational excitation of the BF$^+_2$ molecular ion are computed using a theoretical approach that combines the normal modes approximation for the vibrational states of the…
Simplified stochastic models are widely used in the study of frequency-resolved noise propagation in biochemical reaction networks, a common measure being the coherence between random fluctuations in molecule number trajectories. Such…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…