Related papers: Computer Simulations of a Heterogeneous Membrane w…
Stochastic nonlinear dynamical systems can undergo rapid transitions relative to the change in their forcing, for example due to the occurrence of multiple equilibrium solutions for a specific interval of parameters. In this paper, we…
Direct simulation results for stationary gas transport through pure silica zeolite membranes (MFI, LTA and DDR types) are presented using a hybrid, non-equilibrium molecular dynamics simulation methodology introduced recently. The…
Based on multiple parallel short molecular dynamics simulation trajectories, we designed the reweighted ensemble dynamics (RED) method to more efficiently sample complex (biopolymer) systems, and to explore their hierarchical metastable…
The disordered microphases that develop in the high-temperature phase of systems with competing short-range attractive and long-range repulsive (SALR) interactions result in a rich array of distinct morphologies, such as cluster, void…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
Simulating the irreversible quantum dynamics of exciton and electron transfer problems poses a nontrivial challenge. Because the irreversibility of the system dynamics is a result of quantum thermal activation and dissipation caused by the…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
Biological tissues are complex structures composed of many elements which make light-based tissue diagnostics challenging. Over the past decades, Monte Carlo technique has been used as a fundamental and versatile approach toward modeling…
In this paper, we derive multicontinuum poroelasticity models using the multicontinuum homogenization method. Poroelasticity models are widely used in many areas of science and engineering to describe coupled flow and mechanics processes in…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Aims. Linear magnetohydrostatic (MHS) models of solar magnetic fields balance plasma pressure gradients, gravity and Lorentz forces where the current density is composed of a linear force-free component and a cross-field component that…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
From the Ising model and the Lennard-Jones fluid, to water and the iron-carbon system, phase diagrams are an indispensable tool to understand phase equilibria. In spite of the effort of the simulation community the calculation of a large…
Fluid flow simulation is a highly active area with applications in a wide range of engineering problems and interactive systems. Meshless methods like the Moving Particle Semi-implicit (MPS) are a great alternative to deal efficiently with…
In experimental systems, colloidal particles are virtually always at least somewhat polydisperse, which can have profound effects on their ability to crystallize. Unfortunately, accurately predicting the effects of polydispersity on phase…
Stochastic modeling has become a popular approach to quantify uncertainty in flows through heterogeneous porous media. The uncertainty in heterogeneous structure properties is often parameterized by a high-dimensional random variable. This…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…