Related papers: Membrane simulation models from nm to $\mu$m scale
In order to describe two-dimensionally packed cells in epithelial tissues both mathematically and physically, there have been developed several sorts of geometrical models, such as the vertex model, the finite element model, the…
We report a numerical simulation for the phase diagram of a simple two dimensional model, similar to one proposed by Noro and Frenkel [J. Chem. Phys. \textbf{114}, 2477 (2001)] for membrane proteins, but one that includes the role of the…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
Quantum fluid (or hydrodynamic) models provide an attractive alternative for the modeling and simulation of the electron dynamics in nano-scale objects. Compared to more standard approaches, such as density functional theory or phase-space…
A substantial number of algorithms exists for the simulation of moving particles suspended in fluids. However, finding the best method to address a particular physical problem is often highly non-trivial and depends on the properties of the…
Shear-flow-induced structure formation in surfactant-water mixtures is investigated numerically using a meshless-membrane model in combination with a particle-based hydrodynamics simulation approach for the solvent. At low shear rates,…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Recent experiments have shown that when a near-hemispherical lipid vesicle attached to a solid surface is subjected to a simple shear flow it exhibits a pattern of membrane circulation much like a dipole vortex. This is in marked contrast…
To efficiently simulate very thin, inextensible materials like cloth or paper, it is tempting to replace force-based thin-plate dynamics with hard isometry constraints. Unfortunately, naive formulations of the constraints induce membrane…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
The study of vesicles in suspension is important to understand the complicated dynamics exhibited by cells in vivo and in vitro. We developed a computer simulation based on the boundary-integral method to model the three dimensional…
Dynamic bonding is an essential feature of many soft materials. Molecular simulations have proven to be a powerful tool for modeling bonding kinetics and thermodynamics in these materials, providing insights into their properties that…
In this paper we introduce a mesoscale continuum model for membranes made of two different types of amphiphilic lipids. The model extends work by Peletier and the second author [Arch. Ration. Mech. Anal. 193, 2009] for the one-phase case.…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
The motion of the three-phase contact line between two immiscible fluids and a solid surface arises in a variety of wetting phenomena and technological applications. One challenge in continuum theory is the effective representation of…
The dynamics of compressible liquid-vapor flow depends sensitively on the microscale behavior at the phase boundary. We consider a sharp-interface approach, and propose a multiscale model to describe liquid-vapor flow accurately, without…
We apply to a liquid of linear molecules the semischematic mode-coupling model, previously introduced to describe the center of mass (COM) slow dynamics of a network-forming molecular liquid. We compare the theoretical predictions and…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pharmaceutical applications. The elucidation of a comprehensive…