Related papers: Molecular dynamics study of T=3 capsid assembly
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to…
This paper introduces a new approach for simulating magnetic properties of nanocomposites comprising magnetic particles embedded in a non-magnetic matrix, taking into account the 3D structure of the system in which particles' positions…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
Gels in soft-matter systems are an important nonergodic state of matter. We study a colloid-polymer mixture which is quenched by increasing the polymer concentration, from a fluid to a gel. Using confocal microscopy, we study both the…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials…
We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…
The Monte Carlo simulation of the dynamics of complex molecules produces trajectories with a large number of different configurations to sample configuration space. It is expected that these configurations can be classified into a small…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
We study compressible fluid flow in narrow two-dimensional channels using a novel molecular dynamics simulation method. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream…
The interaction of mass-selected atomic clusters and nanoparticles with surfaces attracts strong interest in view of fundamental research and technological applications. Understanding dynamics of the deposition process is important for…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
A challenging and fundamental research problem is the better understanding and control of the turbulent transport of heat in present-day tokamak fusion experiments. Recent developments in numerical methods along with enormous gains in…
The most interesting step of condensation is the cluster formation up to the critical size. In a closed system, this is an instationary process, as the vapour is depleted by the emerging liquid phase. This imposes a limitation on direct…
Two different preparation methods (liquid-quenching and evaporation) of chalcogenide glasses have been investigated by molecular dynamics simulations. Our particular aim was to determine how the structural changes occur due to the different…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…