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During a crossover via a switching mechanism from one 2-body potential to another as might be applied in modeling (chemical) reactions in the vicinity of bond formation, energy violations would occur due to finite step size which determines…
A new pairwise hybrid machine-learning/molecular mechanics (ML/MM) potential is introduced that is conceived for application to large, heterogeneous condensed-phase systems. The PhysNet ML method describes monomers and short-range dimer…
We generalize a recently investigated lattice model of semiflexible polymers formed under equilibrium polymerization in a solution and conduct a comprehensive investigation of its melting properties. The model is characterized by six…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…
We introduce a simple nonequilibrium model for a driven diffusive system with nonconservative reaction kinetics which exhibits ergodicity breaking and hysteresis in one dimension. These phenomena can be understood through a description of…
We consider the heat equation in a multidimensional domain with nonlocal hysteresis feedback control in a boundary condition. Thermostat is our prototype model. We construct all periodic solutions with exactly two switching on the period…
We have developed a thermodynamic theory in the non-equilibrium regime, which we describe as a thermodynamic system-bath model [S. Koyanagi and Y. Tanimura, J. Chem. Phys. \textbf{160}, 234112 (2024)]. Based on the dimensionless (DL)…
This work is devoted to the consistent modeling of a three-phase mixture of a gas, a liquid and its vapor. Since the gas and the vapor are mis-cible, the mixture is subjected to a non-symmetric constraint on the volume. Adopting the Gibbs…
One of the most striking many-body phenomena in nature is the sudden change of macroscopic properties as the temperature or energy reaches a critical value. Such equilibrium transitions have been predicted and observed in two and three…
Using as a starting point conservation of momentum, a multiphase mechanical energy balance equation is derived that accounts for multiple material phases and interfaces present within a moving control volume. This balance is applied to a…
Non-equilibrium thermodynamics can provide strong advantages when compared to more standard equilibrium situations. Here, we present a general framework to study its application to concrete problems, which is valid also beyond the…
We study a symmetry property of momentum distribution functions in the steady state of heat conduction. When the equation of motion is symmetric under change of signs for all dynamical variables, the distribution function is also symmetric.…
We review a dynamical approach to non-equilibrium MD (D-NEMD). We show how, using a proper simulation setup, is possible to treat interesting cases in which the initial condition is a stationary non-equilibrium state produced by a suitable…
We report the results of a numerical study of nonequilibrium steady states for a class of Hamiltonian models. In these models of coupled matter-energy transport, particles exchange energy through collisions with pinned-down rotating disks.…
Quantum simulations of photoexcited low-dimensional systems are pivotal for understanding how to functionalize and integrate novel two-dimensional (2D) materials in next-generation optoelectronic devices. First principles predictions are…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
Our study unveils the precise role of the underlying potential in regulating the fundamental processes of dynamic hysteresis, which manifests in numerous natural and designed systems. We identify that it is possible to induce symmetry…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…