Related papers: A Simulation Study on Multicomponent Lipid Bilayer
We present a lattice Boltzmann algorithm based on an underlying free energy that allows the simulation of the dynamics of a multicomponent system with an arbitrary number of components. The thermodynamic properties, such as the chemical…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
We present a field theory to describe the composition of a surface spontaneously exchanging matter with its bulk environment. By only assuming matter conservation in the system, we show with extensive numerical simulations that, depending…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
Reconstituted nicotinic acetylcholine receptors (nAChRs) exhibit significant gain-of-function upon addition of cholesterol to reconstitution mixtures, and cholesterol affects organization of nAChRs within domain-forming membranes, but…
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…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Many coarse-grained models have been developed for equilibrium studies of lipid bilayer membranes. To achieve in simulations access to length-scales and time-scales difficult to attain in fully atomistic molecular dynamics, these…
We study, using dissipative particle dynamics simulations, the effect of active lipid flip-flop on model fluid bilayer membranes. We consider both cases of symmetric as well as asymmetric flip-flops. Symmetric flip-flop leads to a steady…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
Domain growth is a key process in many areas of biology, including embryonic development, the growth of tissue, and limb regeneration. As a result, mechanisms for incorporating it into traditional models for cell movement, interaction, and…
We use complexity theory to rigorously investigate the difficulty of classically simulating evolution under many-body localized (MBL) Hamiltonians. Using the defining feature that MBL systems have a complete set of quasilocal integrals of…
We study lipid translocation ("flip-flop") between the leaflets of a planar lipid bilayer with transition path sampling (TPS). Rare flip-flops compete with biological machineries that actively establish asymmetric lipid compositions.…
The paper contains a development of the previously proposed generalized lattice model (GLM). In contrast to usual lattice models, the difference of the specific atomic volumes of the components is taken in account in GLM. In addition to…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
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…
Here we review a hybrid lattice Boltzmann algorithm to solve the equations of motion of cholesteric liquid crystals. The method consists in coupling a lattice Boltzmann solver for the Navier-Stokes equation to a finite difference method to…
We report diffusion coeffcients of micron-scale liquid domains in giant unilamellar vesicles of phospholipids and cholesterol. The trajectory of each domain is tracked, and the mean square displacement grows linearly in time as expected for…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…