Related papers: Discrete molecular dynamics simulations of peptide…
We consider the dynamic wetting and dewetting processes of films and droplets of complex liquids on planar surfaces, focusing on the case of colloidal suspensions, where the particle interactions can be sufficiently attractive to cause…
Understanding the coupled thermo-mechanical behaviour of compacted granular beds can benefit various industrial applications, such as pebble bed design in fusion reactors. In this study, a thermo-mechanical discrete element method based on…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
Elastin-like polypeptides (ELPs) undergo a sharp solubility transition from low temperature solvated phases to coacervates at elevated temperatures, driven by the increased strength of hydrophobic interactions at higher temperatures. The…
In this work we study the spreading dynamics of tiny liquid droplets on solid surfaces in the case where the ends of the molecules feel different interactions with respect to the surface. We consider a simple model of dimers and short…
We investigate diffusion of a peptide drug through Graphene Oxide (GO) membranes that are modeled as a porous layered laminate constructed from aligned flakes of GO. Our experiments using a peptide drug show a tunable non-linear dependence…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
Molecular dynamics simulations of a short-chain polymer melt between two brush-covered surfaces under shear have been performed. The end-grafted polymers which constitute the brush have the same chemical properties as the free chains in the…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
The microtubule assembly process has been extensively studied, but the underlying molecular mechanism remains poorly understood. The structure of an artificially generated sheet polymer that alternates two types of lateral contacts and that…
We investigate the aggregation kinetics of a simulated telechelic polymer gel. In the hybrid Molecular Dynamics (MD) / Monte Carlo (MC) algorithm, aggregates of associating end groups form and break according to MC rules, while the position…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…
Abeta is a disordered peptide central to Alzheimer's Disease. Aggregation of Abeta has been widely explored, but its molecular crowding less so. The synaptic cleft where Abeta locates only holds 60-70 water molecules along its width. We…