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Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
We present molecular dynamics simulations of mono- or bidisperse inelastic granular gases driven by vibrating walls, in two dimensions (without gravity). Because of the energy injection at the boundaries, a situation often met…
Biomolecular systems like molecular motors or pumps, transcription and translation machinery, and other enzymatic reactions can be described as Markov processes on a suitable network. We show quite generally that in a steady state the…
The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The…
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative…
Properties of transport of molecular motors are investigated. A simplified model based on the concept of Brownian ratchets is applied. We analyze a stochastic equation of motion by means of numerical methods. The transport is systematically…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Reversible bipolar nano-switches that can be set and read electronically in a solid-state two-terminal device are very promising for applications. We have performed molecular-dynamics simulations that mimic systems with oxygen vacancies…
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…
Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
We investigate a model of a stochastic engine operating cyclically at constant bath temperature, which consists of an overdamped Brownian harmonic oscillator that plays the role of working substance and is elastically coupled to an active…
We explore quantization of the response of a molecular motor to periodic modulation of control parameters. We formulate the Pumping-Quantization Theorem (PQT) that identifies the conditions for robust integer quantized behavior of a…
Molecular Dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size…
Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular…
Fluid phase equilibria involving nano-dispersed phases, where at least one of the coexisting phases is confined to a small volume, are investigated by molecular dynamics simulation. Complementing previous studies on nanoscopic droplets,…
Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather…