Related papers: Molecular dynamics study of T=3 capsid assembly
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
Molecular dynamics has been widely used to numerically solve equation of motion of classical many-particle system. It can be used to simulate many systems including biophysics, whose complexity level is determined by the involved elements.…
Molecular dynamics refers to the computer simulation of a material at the atomic level. An open problem in numerical analysis is to explain the apparent reliability of molecular dynamics simulations. The difficulty is that individual…
Semi-empirical molecular dynamics is used to simulate several gaseous atomic hydrogen interactions with hydrocarbon grains in space: recoil, adsorption, diffusion, chemisorption and recombination into molecular hydrogen. Their probabilities…
Parallel Molecular Dynamics simulations are conducted for describing growth on surfaces with different kind of roughness: a perfect ordered crystalline flat graphite surface, a disordered rough graphite surface and flat surface with an…
Molecular dynamics simulation is used to study vacancy cluster formation in $\beta$- and $\alpha$-$Si_3N_4$ with varying vacancy contents (0 - 25.6 at%). Vacancies are randomly created in supercells, which were subsequently heat-treated for…
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 present a simple and efficient method to simulate three-dimensional, complex-shaped, interacting bodies. The particle shape is represented by Minkowski operators. A time-continuous interaction between these bodies is derived using simple…
We have carried out molecular dynamics simulations of the crystallization of hard spheres modelling colloidal systems that are studied in conventional and space-based experiments. We use microscopic probes to investigate the effects of…
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…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
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…
The filtration of fluid in 2D porous medium is simulated by the molecular dynamics technique. The high concentration of fluid is created at the initial point in time and the number of fluid particles is investigated in all porous. The…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
Discrete particle simulations are used to model segregation in granular mixtures of three different particle species in a horizontal rotating drum. Axial band formation is observed, with medium-size particles tending to be located between…
Tight binding molecular dynamics simulations, with a non orthogonal basis set, are performed to study the fragmentation of carbon fullerenes doped with up to six silicon atoms. Both substitutional and adsorbed cases are considered. The…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
We use molecular dynamic to simulate the directional growth of binary mixtures. our results compare very well with analitical and experimental results. This opens up the possibility to probe growth situations which are difficult to reach…
Polymers with both soluble and insoluble blocks typically self-assemble into micelles, aggregates of a finite number of polymers where the soluble blocks shield the insoluble ones from contact with the solvent. Upon increasing…