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A new approach is developed to integrate numerically the equations of motion for systems of interacting rigid polyatomic molecules. With the aid of a leapfrog framework, we directly involve principal angular velocities into the integration,…
Dissipative particle dynamics (DPD) does not conserve energy and this precludes its use in the study of thermal processes in complex fluids. We present here a generalization of DPD that incorporates an internal energy and a temperature…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient…
We formulate a canonical quantization of Equilibrium Thermodynamics by applying Dirac's theory of constrained systems. Thermodynamic variables are treated as conjugate pairs of coordinates and momenta, allowing extensive and intensive…
We expand on two previous developments in the modeling of discrete-time Langevin systems. One is the well-documented Gr{\o}nbech-Jensen Farago (GJF) thermostat, which has been demonstrated to give robust and accurate configurational…
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…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
Thermodynamics and information have intricate inter-relations. The justification of the fact that information is physical, is done by inter-linking information and thermodynamics - through Landauer's principle. This modern approach towards…
We study the classical dynamics of a particle in Snyder spacetime, adopting the formalism of constrained Hamiltonian systems introduced by Dirac. We show that the motion of a particle in a scalar potential is deformed with respect to…
A new Langevin-Verlet thermostat that preserves the fluctuation-dissipation relationship for discrete time steps, is applied to molecular modeling and tested against several popular suites (AMBER, GROMACS, LAMMPS) using a small molecule as…
We consider quantum nonlinear many-body systems with dissipation described within the Caldeira-Leggett model, i.e., by a nonlocal action in the path integral for the density matrix. Approximate classical-like formulas for thermodynamic…
A numerical model is built, simulating the principles of kinetic gas theory, to predict pressures of molecules in a spherical pressure vessel; the model tracks a single particle and multiplies the force on the spherical walls by a mole of…
The interplay of slow dynamics and thermodynamic features of dense liquids is studied by examinining how the glass transition changes depending on the presence or absence of Lennard-Jones-like attractions. Quite different thermodynamic…
The length-scale dependence of the dynamic entropy is studied in a molecular dynamics simulation of a binary Lennard-Jones liquid above the mode-coupling critical temperature $T_c$. A number of methods exist for estimating the entropy of…
Simulations at the atomic scale provide a direct and effective way to understand the mechanical properties of materials. In the regime of classical mechanics, simulations for the thermodynamic properties of metals and alloys can be done by…
In conventional micromagnetism magnetic domain configurations are calculated based on a continuum theory for the magnetization which is assumed to be of constant length in time and space. Dynamics is usually described with the…
A class of explicit numerical schemes is developed to solve for the relativistic dynamics and spin of particles in electromagnetic fields, using the Lorentz-BMT equation formulated in the Clifford algebra representation of Baylis. It is…
We systematically develop beneficial and practical velocity measures for accurate and efficient statistical simulations of the Langevin equation with direct applications to computational statistical mechanics and molecular dynamics…
The classical nucleation theory (CNT) and its modified versions provide a convenient framework for describing the nucleation process under the capillary approximation. However, these models often predict nucleation rates that depart…