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Diffusion in a `rough' potential parameterized by a reaction coordinate $q$ is relevant to a wide spectrum of problems ranging from protein folding and charge transport in complex media to colloidal stabilization and self-assembly. This…
Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
In the present paper, using a molecular dynamics simulation, we study a nature of melting of a two-dimensional ($2D$) system of classical particles interacting through a purely repulsive isotropic core-softened potential which is used for…
In a microcanonical ensemble (constant $NVE$, hard reflecting walls) and in a molecular dynamics ensemble (constant $NVE\mathbf{PG}$, periodic boundary conditions) with a number $N$ of smooth elastic hard spheres in a $d$-dimensional volume…
The autocorrelation functions for the force on a particle, the velocity of a particle, and the transverse momentum flux are studied for the power law potential $v(r)=\epsilon (\sigma /r)^{\nu}$ (soft spheres). The latter two correlation…
Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions 'apparent'. Here we demonstrate how zeta potentials that agree with measured values can be calculated by: (1)…
The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles,…
Using molecular dynamics simulations we investigate the thermodynamic of particles interacting with a continuous and a discrete versions of a core-softened (CS) intermolecular potential composed by a repulsive shoulder. Dynamic and…
Molecular dynamics (MD) simulations of successive collision cascades within the same simulation domain were performed using two different inter-atomic potentials (IAP) in tungsten, one EAM based and the other a `quantum accurate' machine…
Spatial and temporal variations in the electron-to-proton mass ratio, mu, and in the fine-structure constant, alpha, are predicted in non-Standard models aimed to explain the nature of dark energy. Among them the so-called chameleon-like…
The Earth's magnetosphere represents a natural plasma laboratory that allows us to study the behavior of particle distribution functions in the absence of Coulomb collisions, typically described by the Kappa distributions. We have…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We investigate the long time behavior of a passive particle evolving in a one-dimensional diffusive random environment, with diffusion constant $D$. We consider two cases: (a) The particle is pulled forward by a small external constant…
Perfectly conducting boundaries, and their Dirichlet counterparts for quantum scalar fields, predict nonintegrable energy densities. A more realistic model with a finite ultraviolet cutoff yields two inconsistent values for the force on a…
The unique properties of suspensions containing both active (self-propelling) and passive matter, arising from the nonequilibrium nature of these systems, have been widely studied (e.g., enhanced diffusion, phase separation, and directed…
Due to their remarkable properties, systems that exhibit self-organization of their components resulting from intrinsic microscopic activity have been extensively studied in the last two decades. In a generic class of active matter, the…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
The probability that a randomly accelerated particle in two dimensions has not yet left a simply connected domain ${\cal A}$ after a time $t$ decays as $e^{-E_0t}$ for long times. The same quantity $E_0$ also determines the confinement free…
We consider two models of deterministic active particles in an external potential. In the limit where the speed of a particle is fixed, both models coincide and can be formulated as a Hamiltonian system, but only if the potential is…