Related papers: SiMPLISTIC: A Novel Pairwise Potential for Implici…
A lattice model for binary mixture of lipids and water is introduced and investigated. The orientational degrees of freedom of the amphiphilic molecules are taken into account in the same way as in the model for oil-water-surfactant…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
We introduce a novel approach to simulate the interaction between fluids and thin elastic solids without any penetration. Our approach is centered around an optimization system augmented with barriers, which aims to find a configuration…
The interaction between thin structures and incompressible Newtonian fluids is ubiquitous both in nature and in industrial applications. In this paper we present an isogeometric formulation of such problems which exploits a boundary…
There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…
Implicit solvation is an effective, highly coarse-grained approach in atomic-scale simulations to account for a surrounding liquid electrolyte on the level of a continuous polarizable medium. Originating in molecular chemistry with finite…
Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…
Lipolysis is a life-essential metabolic process, which supplies fatty acids stored in lipid droplets to the body in order to match the demands of building new cells and providing cellular energy. In this paper, we present a first…
A unified Smoothed Particle Hydrodynamics (SPH) framework is proposed to simulate interaction dynamics involving thin shells modeled by a reduced-dimensional, single-layer particle discretization, as opposed to full-dimensional SPH solids.…
Discrete particle simulations are widely used to study large-scale particulate flows in complex geometries where particle-particle and particle-fluid interactions require an adequate representation but the computational cost has to be kept…
Based on the particle-in-cell (PIC) plasma simulation method, the speed-limited PIC (SLPIC) method delivers faster kinetic plasma simulation in cases where the particle distributions evolve slowly compared with the maximum stable PIC…
Certain sequences of peptoid polymers (synthetic analogs of peptides) assemble into bilayer nanosheets via a nonequilibrium assembly pathway of adsorption, compression, and collapse at an air-water interface. As with other large-scale…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
We present a novel implicit porous flow solver using SPH, which maintains fluid incompressibility and is able to model a wide range of scenarios, driven by strongly coupled solid-fluid interaction forces. Many previous SPH porous flow…
A new method is proposed for integrating the equations of motion of an elastic filament. In the standard finite-difference and finite-element formulations the continuum equations of motion are discretized in space and time, but it is then…
This paper presents a novel particle method to compute strongly coupled incompressible fluid and rigid bodies. The method adopts a velocity-based formulation and utilizes the linear complementarity problem for the incompressibility…
A model of lipid bilayers made of a mixture of two lipids with different average compositions on both leaflets, is developed. A Landau hamiltonian describing the lipid-lipid interactions on each leaflet, with two lipidic fields $\psi_1$ and…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
We present Monte Carlo simulations of an ultra coarse-grained lipid bilayer with different number of lipids on both leaflets. In the simulations, we employ a new method for measuring the elastic parameters of the membrane, including the…
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane,…