Related papers: Coarse grained molecular simulations of membrane a…
We consider two- and three-dimensional lattice models of proteins which were characterized previously. We coarse grain their folding dynamics by reducing it to transitions between effective states. We consider two methods of selection of…
We perform extensive numerical simulations of a paradigmatic model glass former, the hard-sphere fluid with 10% polydispersity. We sample from the ensemble of trajectories with fixed observation time, whereby single trajectories are…
We introduce a family of two-dimensional lattice models of quasicrystals, using a range of square hard cores together with a soft interaction based on an aperiodic tiling set. Along a low temperature isotherm we find, by Monte Carlo…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…
A simulation model is presented, comprising elastic spheres with a short range attraction. Besides conservative forces, radial- and shear friction, and radial noise are added. The model can be used to simulate colloids, granular solids and…
Understanding interactions between membranes requires measurements on well-controlled systems close to natural conditions, in which fluctuations play an important role. We have determined, by grazing incidence X-ray scattering, the…
The quasistatic behavior of a simple 2D model of a cohesive powder under isotropic loads is investigated by Discrete Element simulations. The loose packing states, as studied in a previous paper, undergo important structural changes under…
We study the transition of a granular packing from liquid to solid bonding in the course of drying. The particles are initially wetted by a liquid brine and the cohesion of the packing is ensured by capillary forces, but the crystallization…
The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to…
We analyze the structural behavior of a single polymer chain grafted to an attractive, flexible surface. Our model is composed of a coarse-grained bead-and-spring polymer and a tethered membrane. By means of extensive parallel tempering…
Nonequilibrium membrane pattern formation is studied using meshless membrane simulation. We consider that molecules bind to either surface of a bilayer membrane and move to the opposite leaflet by flip--flop. When binding does not modify…
Moir\'e related physics in twisted bilayer two-dimensional (2D) materials has attracted widespread interest in condensed matter physics. Simulation of moir\'e related physics in cold atom platform is expected to outperform the 2D materials…
Multicomponent lipid mixtures exhibit complex phase behavior, including coexistence of nanoscopic fluid phases in ternary mixtures mimicking the composition of the outer leaflet of mammalian plasma membrane. The physical mechanisms…
The behavior of lipid bilayer is important to understand the functionality of cells like the trafficking of ions between cells. Standard procedures to explore the properties of lipid bilayer and hemifused states typically use either…
We describe a simple model of fermions in quasi-one dimension that features interaction induced deconfinement (a phase transition where the effective dimensionality of the system increases as interactions are turned on) and which can be…
A coarse-grained model is developed to allow large-scale molecular dynamics (MD) simulations of a branched polyetherimide derived from two backbone monomers [4,4'-bisphenol A dianhydride (BPADA) and m-phenylenediamine (MPD)], a chain…
Using a lattice model and a versatile thermodynamic integration scheme, we study the critical Casimir interactions between inclusions embedded in a two-dimensional critical binary mixtures. For single-domain inclusions we demonstrate that…
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not…
A common mechanism for intracellular transport is the use of controlled deformations of the membrane to create spherical or tubular buds. While the basic physical properties of homogeneous membranes are relatively well-known, the effects of…
We introduce a solid-on-solid growth process which evolves by random deposition of dimers, surface diffusion, and evaporation of monomers from the edges of plateaus. It is shown that the model exhibits a robust transition from a smooth to a…