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Molecular dynamics simulations are carried out to investigate the diffusion behavior of penetrable-sphere model fluids characterized by a finite energy barrier $\epsilon$. The self-diffusion coefficient is evaluated from the time-dependent…
We analyze the freezing and collapse transition of a simple model for flexible polymer chains on simple cubic and face-centered cubic lattices by means of sophisticated chain-growth methods. In contrast to bond-fluctuation polymer models in…
Model-based reinforcement learning methods often use learning only for the purpose of estimating an approximate dynamics model, offloading the rest of the decision-making work to classical trajectory optimizers. While conceptually simple,…
A one dimensional lattice model is formulated to study tapping dynamics and the long time steady distribution in granular media. The dynamics conserves the number of particles in the system, and density changes are associated to the…
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,…
Lattices with a circulant generator matrix represent a subclass of cyclic lattices. This subclass can be described by a basis containing a vector and its circular shifts. In this paper, we present certain conditions under which the norm…
Lattice diffusion and internal local magnetic field gradients in solids are investigated by numerical simulation of nuclear mangetic resonance(NMR) spin echo experiments. The Fourier-spectrum method is employed in order to solve the…
A lattice Boltzmann model is introduced which simulates oil-water-surfactant mixtures. The model is based on a Ginzburg-Landau free energy with two scalar order parameters. Diffusive and hydrodynamic transport is included. Results are…
We apply lattice Boltzmann method to study the phase separation of a two-dimensional binary fluid mixture in shear flow. The algorithm can simulate systems described by the Navier-Stokes and convection-diffusion equations. We propose a new…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
Metamaterial cloaking has been proposed and studied in recent years following several interesting approaches. One of them, the scattering-cancellation technique, or plasmonic cloaking, exploits the plasmonic effects of suitably designed…
We study the single file diffusion problem on a one-dimensional lattice with a self-similar distribution of hopping rates. We find that the time dependence of the mean-square displacement of both a tagged particle and the center of mass of…
In a number of experimental situations, single polymer molecules can be suspended in a vacuum. Here collisions between such molecules are considered. The limit of high collision velocity is investigated numerically for a variety of…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
We studied the single dimer dynamics in a lattice diffusive model as a function of particle density in the high densification regime. The mean square displacement is found to be subdiffusive both in one and two dimensions. The spatial…
Simulation of a multicomponent lipid bilayer having a fixed percentage of cholesterol is done to study phase transition leading to domain formation. The concept of random lattice has been used in simulation to account for the coupling…
We study by Monte Carlo simulations and scaling analysis two models of pairs of confined and dense ring polymers in two dimensions. The pair of ring polymers are modelled by squared lattice polygons confined within a square cavity and they…
We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the…
Colloidal patchy particles with divalent attractive interaction can self-assemble into linear polymer chains. Their equilibrium properties in 2D and 3D are well described by Wertheim's thermodynamic perturbation theory which predicts a…