Related papers: Discrete molecular dynamics simulations of peptide…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
Thermal properties of graphene monolayers are studied by path-integral molecular dynamics (PIMD) simulations, which take into account the quantization of vibrational modes in the crystalline membrane, and allow one to consider anharmonic…
Size segregation in bedload transport is studied numerically with a coupled fluid-discrete element model. Starting from an initial deposit of small spherical particles on top of a large particle bed, the segregation dynamics of the bed is…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Usage, manipulation, transport, delivery, and mixing of granular or particulate media, comprised of spherical or polyhedral particles, is commonly encountered in industrial sectors of construction (cement and rock fragments), pharmaceutics…
Direct growth of flat micrometer-sized bilayer graphene islands in between molybdenum disulfide sheets is achieved by chemical vapor deposition of ethylene at about 800 {\deg}C. The temperature assisted decomposition of ethylene takes place…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by…
The sedimentation process of granular materials exists ubiquitously in nature and many fields which involve the solid-liquid separation. This paper employs the coupled computational fluid dynamics and discrete element method (CFD-DEM) to…
In this paper we introduce 1-$D$ and 2-$D$ discrete models for the dynamic granular matter formation process in the form of a system of difference equations. This approach allows us to differentiate between the influx of the rolling layer…
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a…
Cell-cell adhesion is established by specific binding of receptor and ligand proteins. The adhesion bonds attract each other and often aggregate into large clusters that are central to many biological processes. One possible origin of…