Related papers: Discrete molecular dynamics simulations of peptide…
We use large-scale computer simulations to explore the non-equilibrium aging dynamics in a microscopic model for colloidal gels. We find that gelation resulting from a kinetically-arrested phase separation is accompanied by `anomalous'…
Particle beds are widely used in various systems and processes, such as particle heat exchangers, granular flow reactors, and additive manufacturing. Accurate modeling of thermal conductivity of particle beds and understanding of their heat…
The settling of colloidal particles with short-ranged attractions is investigated via highly resolved immersed boundary simulations. At modest volume fractions, we show that inter-colloid attractions lead to clustering that reduces the…
The adhesive behaviour of biological attachment structures such as spider web anchorages is usually studied using single or multiple peeling models involving "tapes", i.e. one-dimensional contacts elements. This is an oversimplification for…
We discuss variance reduced simulations for an individual-based model of chemotaxis of bacteria with internal dynamics. The variance reduction is achieved via a coupling of this model with a simpler process in which the internal dynamics…
Colloidal gels are a prototypical example of a heterogeneous network solid whose complex properties are governed by thermally-activated dynamics. In this Letter we experimentally establish the connection between the intermittent dynamics of…
While gradient-based discrete samplers are effective in sampling from complex distributions, they are susceptible to getting trapped in local minima, particularly in high-dimensional, multimodal discrete distributions, owing to the…
A new version of the nuclear shell model unifies the consideration of the discrete spectrum, where the results agree with the standard shell model, and continuum. The ingredients of the method are the non-Hermitian effective Hamiltonian,…
The aim of this paper is to further develop mathematical models for bleb formation in cells, including cell-membrane interactions with linker proteins. This leads to nonlinear reaction-diffusion equations on a surface coupled to fluid…
The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)$_n$(L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as…
The internal dynamics of active gels, both in artificial (in-vitro) model systems and inside the cytoskeleton of living cells, has been extensively studied by experiments of recent years. These dynamics are probed using tracer particles…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
We consider nucleation of amyloid fibrils in the case when the process occurs by the mechanism of direct polymerization of practically fully extended protein segments, i.e. beta-strands, into beta-sheets. Applying the classical nucleation…
In an effort to understand ``rafts'' in biological membranes, we propose phenomenological models for saturated and unsaturated lipid mixtures, and lipid-cholesterol mixtures. We consider simple couplings between the local composition and…
Granular impact -- the dynamic intrusion of solid objects into granular media -- is widespread across scientific and engineering applications including geotechnics. Existing approaches for simulating granular impact dynamics have relied on…
In this study, we present a comprehensive exploration of formation of different phases in lipid molecules using a coarse-grained implicit solvent model, where each lipid molecule is represented as a rigid, three-bead rod-like structure. Our…
Discrete Element Methods (DEM) are a useful tool to model the fracture of cohesive granular materials. For this kind of application, simple particle shapes (discs in 2D, spheres in 3D) are usually employed. However, dealing with more…
Membrane bending is an extensively studied problem from both modeling and experimental perspectives because of the wide implications of curvature generation in cell biology. Many of the curvature generating aspects in membranes can be…
We study the formation of a colloidal gel by means of Molecular Dynamics simulations of a model for colloidal suspensions. A slowing down with gel-like features is observed at low temperatures and low volume fractions, due to the formation…