Related papers: Coarse grained molecular simulations of membrane a…
We study an intrinsic curvature model defined on fixed-connectivity triangulated lattices enclosing a spherical core by using the canonical Monte Carlo simulation technique. We find that the model undergoes a discontinuous transition of…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
We discuss the nonlinear dynamics and fluctuations of interfaces with bending rigidity under the competing attractions of two walls with arbitrary permeabilities. This system mimics the dynamics of confined membranes. We use a two-dimension…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
We present the first large-scale molecular dynamics simulations of hexane on graphite that completely reproduces all experimental features of the melting transition. The canonical ensemble simulations required and used the most realistic…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
Cell plasma membranes display a dramatically rich structural complexity characterized by functional sub-wavelength domains with specific lipid and protein composition. Under favorable experimental conditions, patterned morphologies can also…
The adhesion dynamics of a membrane confined between two permeable walls is studied using a two-dimensional hydrodynamic model. The membrane morphology decomposes into adhesion patches on the upper and the lower walls and obeys a nonlinear…
Tissue dynamics and collective cell motion are crucial biological processes. Their biological machinery is mostly known, and simulation models such as the "active vertex model" (AVM) exist and yield reasonable agreement with experimental…
In this paper we introduce 1-$D$ and 2-$D$ discrete models for the dynamic granular matter formation process in the form of a system of difference equations. This approach allows us to differentiate between the influx of the rolling layer…
High-finesse optical cavity allows the establishment of long-range interactions between bosons in an optical lattice when most cold atoms experiments are restricted to short-range interactions. Supersolid phases have recently been…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Within the framework of a discrete Gaussian model, we present analytical results for the interaction induced by a lamellar phase between small embedded colloids. We consider the two limits of particles strongly adherent to the adjacent…
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…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
We study the diffusion-driven kinetics of phase separation of a symmetric binary mixture (AB), confined in a thin-film geometry between two parallel walls. We consider cases where (a) both walls preferentially attract the same component…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
We study membrane-protein interactions and membrane-mediated protein-protein interactions by Monte Carlo simulations of a generic coarse-grained model for lipid bilayers with cylindrical hydrophobic inclusions. The strength of the…
The dynamics of dry active matter have implications for a diverse collection of biological phenomena spanning a range of length and time scales, such as animal flocking, cell tissue dynamics, and swarming of inserts and bacteria. Uniting…
We present a percolation model that is inspired by recent works on immiscible two-phase flow in a mixed-wet porous medium made of a mixture of grains with two different wettability properties. The percolation model is constructed on a dual…