Light propagation in two-dimensional and three-dimensional slabs of reflective colloidal particles in solution: The effect of interfaces and interparticle correlations.

The propagation of light across 2D and 3D slabs of reflective colloidal particles in a fluidlike state has been investigated by simulation. The colloids are represented as hard spheres with and without an attractive square-well tail. Representative configurations of particles have been generated by Monte Carlo.

Effect of Organic Ions on The Formation and Collapse of Nanometric Bubbles in Ionic Liquid/Water Solutions: A Molecular Dynamics Study.

Molecular dynamics simulation is applied to investigate the effect of two ionic liquids (IL) on the nucleation and growth of (nano)cavities in water under tension and on the cavities' collapse following the release of tension. Simulations of the same phenomena in two pure water samples of different sizes are carried out for comparison. The first IL, i.

Effects of Degrees of Freedom on Calculating Diffusion Properties in Nanoporous Materials.

If one carries out a molecular simulation of particles using periodic boundary conditions, linear momentum is conserved, and hence, the number of degrees of freedom is set to 3 - 3. In most programs, this number of degrees of freedom is the default setting. However, if one carries out a molecular simulation in an external field, one needs to ensure that degrees of freedom are changed from this default setting to 3, as in an external field the velocity of the center of mass can change.

The role of pressure and defects in the wurtzite to rock salt transition in cadmium selenide.

Using molecular dynamics and path sampling techniques we investigated the effect of pressure and defects in the wurtzite to rock salt transition in cadmium selenide (CdSe). In the pressure range 2-10 GPa, rate constants of transition are in the order of 10 to 10 s for the transformation of a relatively small wurtzite crystal consisting of 1024 atoms with periodic boundary conditions. The transition paths predominantly evolve through an intermediate 5-coordinated structure, as reported before, though its typical lifetime within the transition paths is particularly long in the intermediate pressure range (4-6 GPa).

Precursors of fluidisation in the creep response of a soft glass.

Via extensive numerical simulations, we study the fluidisation process of dense amorphous materials subjected to an external shear stress, using a three-dimensional colloidal glass model. In order to disentangle possible boundary effects from finite size effects in the process of fluidisation, we implement a novel geometry-constrained protocol with periodic boundary conditions. We show that this protocol is well controlled and that the longtime fluidisation dynamics is, to a great extent, independent of the details of the protocol parameters.

Foundations and latest advances in replica exchange transition interface sampling.

Nearly 20 years ago, transition path sampling (TPS) emerged as an alternative method to free energy based approaches for the study of rare events such as nucleation, protein folding, chemical reactions, and phase transitions. TPS effectively performs Monte Carlo simulations with relatively short molecular dynamics trajectories, with the advantage of not having to alter the actual potential energy surface nor the underlying physical dynamics. Although the TPS approach also introduced a methodology to compute reaction rates, this approach was for a long time considered theoretically attractive, providing the exact same results as extensively long molecular dynamics simulations, but still expensive for most relevant applications.

Ice nucleation on carbon surface supports the classical theory for heterogeneous nucleation.

The prevalence of heterogeneous nucleation in nature was explained qualitatively by the classical theory for heterogeneous nucleation established over more than 60 years ago, but the quantitative validity and the key conclusions of the theory have remained unconfirmed. Employing the forward flux sampling method and the coarse-grained water model (mW), we explicitly computed the heterogeneous ice nucleation rates in the supercooled water on a graphitic surface at various temperatures. The independently calculated ice nucleation rates were found to fit well according to the classical theory for heterogeneous nucleation.

Confounding the paradigm: peculiarities of amyloid fibril nucleation.

Fibrils of amyloid proteins are currently of great interest because of their involvement in various amyloid-related diseases and nanotechnological products. In a recent kinetic Monte Carlo simulation study (Cabriolu, R.; Kashchiev, D.

Breakdown of nucleation theory for crystals with strongly anisotropic interactions between molecules.

We study the nucleation of model two-dimensional crystals in order to gain insight into the effect of anisotropic interactions between molecules on the stationary nucleation rate J. With the aid of kinetic Monte Carlo simulations, we determine J as a function of the supersaturation s. It turns out that with increasing degree of interaction anisotropy the dependence of ln J on s becomes step-like, with jumps at certain s values.

Size distribution of amyloid nanofibrils.

We consider the size distribution of amyloid nanofibrils (protofilaments) in nucleating protein solutions when the nucleation process occurs by the mechanism of direct polymerization of β-strands (extended peptides or protein segments) into β-sheets. Employing the atomistic nucleation theory, we derive a general expression for the stationary size distribution of amyloid nanofibrils constituted of successively layered β-sheets. The application of this expression to amyloid β(1-40) (Aβ(40)) fibrils allows us to determine the nanofibril size distribution as a function of the protein concentration and temperature.

Amyloid fibrillation kinetics: insight from atomistic nucleation theory.

We consider the nucleation of nanosized amyloid fibrils composed of successively layered β-sheets at the molecular level when this process takes place by direct polymerization of protein segments (β-strands) into β-sheets. Application of the atomistic nucleation theory (ANT) to amyloid nucleation of β(2)-microglobulin and amyloid β(40) allows us to predict the fibril nucleus size and the fibril nucleation rate as functions of the supersaturation of the protein solution. The ANT predictions are compared to recent time-resolved optical experiments where they measure the effect of the protein concentration and mutations on the initial lag time before amyloid fibrils form in the protein solution.

Atomistic theory of amyloid fibril nucleation.

We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution.