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Evaluating accessible conformational space is computationally expensive and thermal motions are partly neglected in computer models of molecular interactions. This produces error into the estimates of binding strength. We introduce a method…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
In this paper we formulate the theory of nonlinear elasticity in a geometrically intrinsic manner using exterior calculus and bundle-valued differential forms. We represent kinematics variables, such as velocity and rate-of-strain, as…
We develop a formalism for the calculation of the flow of angular momentum carried by the fluctuating electromagnetic field within a cavity bounded by two flat anisotropic materials. By generalizing a procedure employed recently for the…
We describe here a model for inelastic collisions for electronic excitation and deexcitation processes in a general, multifluid plasma. The model is derived from kinetic theory, and applicable to any mixture and mass ratio. The principle of…
Since physical theories employ mathematical models to describe and predict physical phenomena, our knowledge depends on the models available to that end. To increase their scope we present a particular type of simplified models, serial…
Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and…
This perspective paper deals with an overview of particle-in-cell / Monte Carlo collision models applied to different plasma-propulsion configurations and scenarios, from electrostatic (E x B and pulsed arc) devices to electromagnetic (RF…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
We derive an analytical expression for the effective force between a pair of macrospheres immersed in a sea of microspheres, in the case where the interaction between the two unlike species is assumed to be a square well or a square…
The micromechanics of a variety of systems experiencing a structural arrest due to their high density could be unified by a thermodynamic framework governing their approach to 'jammed' configurations. The mechanism of supporting an applied…
Nonlinear waves are a robust phenomenon observed in complex systems ranging from mechanics to ecology. Fronts are fundamental due to their robustness against perturbations and capacity to propagate one state over another. Controlling and…
We show from experiments and simulations on vibration-activated granular matter that self-propelled polar rods in an elastic medium on a substrate turn and move towards each other. We account for this effective attraction through a…
Dynamics of systems of structured particles consisting of potentially interacting material points is considered in the framework of classical mechanics. Equations of interaction and motion of structured particles have been derived. The…
Molecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded…
The status of the literature is reviewed for several thermophysical properties of pure solid and liquid tungsten which constitute input for the modelling of intense plasma-surface interaction phenomena that are important for fusion…
The strengths and short-comings of the point-dipole model for polar fluids of spherical molecules are illustrated by considering the physically more relevant case of extended dipoles formed by two opposite charges $\pm q$ separated by a…