Related papers: SiMPLISTIC: A Novel Pairwise Potential for Implici…
Whether live cell membranes show miscibility phase transitions (MPTs), and if so, how they fluctuate near the transitions remain outstanding unresolved issues in physics and biology alike. Motivated by these questions we construct a generic…
We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ~25 nm^2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic…
(Abbreviated) In this paper we report on the development of a multiscale method for simulating complex liquid-liquid systems such as water in contact with oil containing asphaltenes. We consider simulations where water drops covered with…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
Correctly formulated continuum models for lipid-bilayer membranes present a significant challenge to computational mechanics. In particular, the mid-surface behavior is that of a 2-dimensional fluid, while the membrane resists bending much…
We propose a robust simulation method for phospholipid membranes. It is based on a mixed three-field formulation that accounts for tangential fluidity (Boussinesq-Scriven law), bending elasticity (Canham-Helfrich model) and inextensibility.…
We propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isothermal-isobaric ensembles. We also present a symplectic algorithm in the constant normal pressure and lateral…
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet, no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such…
We introduce a microscopic model of a lipid with a charged headgroup and flexible hydrophobic tails, a neutral solvent, and counter ions. Short-ranged interactions between hydrophilic and hydrophobic moieties are included as are the Coulomb…
Aqueous solid-liquid interfaces (SLI) are ubiquitous in nature and technology, often hosting molecular-level processes with macroscopic consequences. Molecular dynamics (MD) simulations offer a tool of choice to investigate interfacial…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
Implicit particle-in-cell codes offer advantages over their explicit counterparts in that they suffer weaker stability constraints on the need to resolve the higher frequency modes of the system. This feature may prove particularly valuable…
The paper presents a 1D2V electrostatic PIC model with a drift-kinetic description of all particle types aiming at simulating classical longitudinal plasma transport in axially symmetric open traps. The model generalizes the semi-implicit…
The great challenge with biological membrane systems is the wide range of scales involved, from nanometers and picoseconds for individual lipids, to the micrometers and beyond millisecond for cellular signalling processes. While…
We present a new asymptotic strategy for general micro-macro models which analyze complex viscoelastic fluids governed by coupled multiscale dynamics. In such models, the elastic stress appearing in the macroscopic continuum equation is…
This study presents an innovative direct numerical simulation approach for complex particle systems with irregular shapes and large numbers. Using partially saturated methods, it accurately models arbitrary shapes, albeit at considerable…
We develop theory and computational methods to investigate particle inclusions embedded within curved lipid bilayer membranes. We consider the case of spherical lipid vesicles where inclusion particles are coupled through (i) intramembrane…
We present a multiparticle collision dynamics (MPC) implementation of layered immiscible fluids $A$ and $B$ of different shear viscosities separated by planar interfaces. The simulated flow profile for imposed steady shear motion and the…