Related papers: Discrete molecular dynamics simulations of peptide…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
We investigate the aggregation transition of theta polymers in spherical confinement with multicanonical simulations. This allows for a systematic study of the effect of density on the aggregation transition temperature for up to 24…
We present a theoretical study of the dynamics of H atoms adsorbed on graphene bilayers with Bernal stacking. First, through extensive density functional theory calculations, including van der Waals interactions, we obtain the activation…
Using molecular dynamics computer simulations we investigate the aging dynamics of a gel. We start from a fractal structure generated by the DLCA-DEF algorithm, onto which we then impose an interaction potential consisting of a short-range…
Molecular dynamics simulations are used to study the spreading of binary polymer nanodroplets in a cylindrical geometry. The polymers, described by the bead-spring model, spread on a flat surface with a surface-coupled Langevin thermostat…
We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…
We consider a model of bilayer lipid membrane with interdigitation, in which the lipid tails of the opposite monolayers interpenetrate. The interdigitation is modeled by linking tails of the hydrophobic chains in the opposite monolayers…
The need to understand the assembly kinetics of fibril formation has become urgent because of the realization that soluble oligomers of amyloidogenic peptides may be even more neurotoxic than the end product, namely, the amyloid fibrils. In…
We investigate the behavior of colloidal suspensions with different volume fractions confined between parallel walls under a range of steady shears. We model the particles using molecular dynamics (MD) with full hydrodynamic interactions…
We use a coarse grained molecular model of supported lipid bilayers to study the formation of adhesion domains. We find that this process is a first order phase transition, triggered by a combination of pairwise short range attractive…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
We examine the geometry of the spaces between particles in diffusion-limited cluster aggregation, a numerical model of aggregating suspensions. Computing the distribution of distances from each point to the nearest particle, we show that it…
We use Monte Carlo simulation and the Reference Interaction Site Model (RISM) theory of molecular fluids to investigate a simple model of colloidal mixture consisting of dimers, made up of two tangent hard monomers of different size, and…
Intrinsic localized modes or discrete breathers are investigated by molecular dynamics simulations in free-standing graphene. Discrete breathers are generated either through thermal quenching of the graphene lattice or by proper…
A molecular model is proposed of a bilayer consisting of fully saturated DPPC and mono unsaturated DOPC. The model not only encompasses the constant density within the hydrophobic core of the bilayer, but also the tendency of chain segments…
Due to neutron irradiation, solid breeder blankets are subjected to complex thermo-mechanical conditions. Within one breeder unit, the ceramic breeder bed is composed of spherical-shaped lithium orthosilicate pebbles, and as a type of…
Discrete pedestrian simulation models are viable alternatives to particle based approaches based on a continuous spatial representation. The effects of discretisation, however, also imply some difficulties in modelling certain phenomena…
This paper deals with the vibration of granular materials due to cyclic external excitation. It highlights the effect of the acceleration on the settlement speed and proves the existence of a relationship between settlement and loss of…
We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic…