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We explore the direct modification of the pseudo-spectral truncation of 2D, incompressible fluid dynamics to maintain a prescribed kinetic energy spectrum. The method provides a means of simulating fluid states with defined spectral…
A variety of enhanced statistical and numerical methods are now routinely used to extract comprehensible and relevant thermodynamic information from the vast amount of complex, high-dimensional data obtained from intensive molecular…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
Monte Carlo sampling for Bayesian posterior inference is a common approach used in machine learning. The Markov Chain Monte Carlo procedures that are used are often discrete-time analogues of associated stochastic differential equations…
A wide variety of numerical methods are evaluated and compared for solving the stochastic differential equations encountered in molecular dynamics. The methods are based on the application of deterministic impulses, drifts, and Brownian…
The thermodynamic properties of systems with long-range interactions is still an ongoing challenge, both from the point of view of theory as well as computer simulation. In this work we study a model system, a Coulomb gas confined inside a…
Statistical mechanics of the discrete nonlinear Schr\"odinger equation is studied by means of analytical and numerical techniques. The lower bound of the Hamiltonian permits the construction of standard Gibbsian equilibrium measures for…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
With the objective of demonstrating usefulness of thermostats in the study of dynamic critical phenomena in fluids, we present results for transport properties in a binary Lennard-Jones fluid that exhibits liquid-liquid phase transition.…
Nonequilibrium molecular dynamics simulations often use mechanisms called thermostats to regulate the temperature. A Hamiltonian is presented for the case of the isoenergetic (constant internal energy) thermostat corresponding to a tunable…
Optimization of cyclic stochastic heat engines, a topic spanning decades of research, commonly assumes fixed control or response parameters at discrete points in the cycle-a limitation that often leads to experimentally impractical…
Computational studies of the thermodynamic properties of materials at the mesoscopic and macroscopic scales -- involving lengths and times of at least $\mu$m and $\mu$s, respectively -- rely on a coarse-graining approximation such that only…
We set up a discrete space-time dynamical model of molecules with thermalised kinetic energy and repulsive cores, in an external potential. The state is specified by a probability on the sample space. One time-step is given by a…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
The model quantum system of fermions in a one dimensional harmonic oscillator potential is investigated by a molecular dynamics method at constant temperature. Although in quantum mechanics the equipartition theorem cannot be used like in…
Recently we proposed a new constant-pressure molecular dynamics method for finite systems. In this paper, we discuss the current understanding of this method and its technique details. We also review the recent theoretical advances of…
State-of-the-art quantum simulators permit local temporal control of interactions and midcircuit readout. These capabilities open the way towards the exploration of intriguing nonequilibrium phenomena. We illustrate this with a kinetically…
The Dynamic Monte Carlo (DMC) method is an established molecular simulation technique for the analysis of the dynamics in colloidal suspensions. An excellent alternative to Brownian Dynamics or Molecular Dynamics simulation, DMC is…
Cellular automata can simulate many complex physical phenomena using the power of simple rules. The presented methodological platform expresses the concept of programmable matter in which Newtons laws of motion are one of examples. Energy…