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We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Molecular dynamics simulations (mds) were carried out to investigate the reorientational motion of a rigid (fixed bond length), asymmetric diatomic molecule in the liquid and glassy states. In the latter the molecule reorients via…
Diffusion Policy has shown great performance in robotic manipulation tasks under stochastic perturbations, due to its ability to model multimodal action distributions. Nonetheless, its reliance on a computationally expensive reverse-time…
In this paper the investigation of the dynamical processes of liquid alkali metals is executed by analyzing the time scales of relaxation processes in liquids. The obtained theoretical dynamic structure factor $S(k,\omega)$ for the case of…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Molecular dynamics simulations are performed to study spatially heterogeneous dynamics in a model of viscous silica above and below the critical temperature of the mode coupling theory, $T_{MCT}$. Specifically, we follow the evolution of…
We present a direct numerical simulation method for investigating the dynamics of dispersed particles in a compressible solvent fluid. The validity of the simulation is examined by calculating the velocity relaxation of an impulsively…
An exact and efficient new method to simulate dynamics in dissipative quantum systems is presented. A stochastic Liouville equation, deduced from Feynman and Vernon's path-integral expression of the reduced density matrix, is used to…
The 1D Ising model is the simplest Hamiltonian-based model in statistical mechanics. The sim- plest interacting particle process is the Symmetric Exclusion Process (SEP), a 1D lattice gas of particles that hop symmetrically and cannot…
The Stokes-Einstein-Sutherland (SES) equation is at the foundation of statistical physics, relating a particle's diffusion coefficient and size with the fluid viscosity, temperature and the boundary condition for the particle-solvent…
The liquidus temperature is an important parameter in understanding the crystalline behavior of materials and in the operation of blast furnaces. Its modeling can be carried out by linear and nonlinear methods through data, considering the…
We extend the phase field crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of…
A roughly constant temperature over a wide range of densities is maintained in molecular clouds through radiative heating and cooling. An isothermal equation of state is therefore frequently employed in molecular cloud simulations. However,…
We study the relaxation process of two driven colloidal suspensions in diffusive contact to a steady state, similar to thermalization. We start by studying a single suspension, subjecting it to random driving forces via holographic optical…
The stochastic differential equations for a model of dissipative particle dynamics, with both total energy and total momentum conservation at every time-step, are presented. The algorithm satisfies detailed balance as well as the…
This work focuses on the thermodynamics of pseudo-elastic models which represent the Mullins effect. Two established models are analyzed theoretically, their thermomechanical properties are derived, and certain critical points are…
In diffusion processes of solid materials, such as in the classical thermal shock problem and the recent lithium ion battery, the maximum diffusion induced stress (DIS) is a very important quantity. However a widely accepted, accurate and…
Non-equilibrium molecular dynamics simulations, of crucial importance in sliding friction, are hampered by arbitrariness and uncertainties in the way Joule heat is removed. We implement in a realistic frictional simulation a parameter-free,…
Time-resolved mapping of lattice dynamics in real- and momentum-space is essential to understand better several ubiquitous phenomena such as heat transport, displacive phase transition, thermal conductivity, and many more. In this regard,…