Related papers: Hydrodynamics of Diffusion in Lipid Membrane Simul…
Many lipid membrane-mediated transport processes--such as mechanically-gated channel activation and solute transport--involve structural and dynamical features on membrane thickness length scales. Most existing membrane models, however,…
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 extend the Saffman theory of membrane hydrodynamics to account for the correlated motion of membrane proteins, along with the effect of protein concentration on that correlation and on the response of the membrane to stresses.…
We present a numerical method to deal efficiently with large numbers of particles in incompressible fluids. The interactions between particles and fluid are taken into account by a physically motivated ansatz based on locally defined drag…
Water nanoconfinement is known to occur inside material void spaces, such as 2D confinement between surfaces, 1D confinement inside nanotubes, and variable-dimension confinement inside nanoporous materials. In the present work we…
When an ensemble of particles interact hydrodynamically, they generically display large-scale transient structures such as swirls in sedimenting particles [1], or colloidal strings in sheared suspensions [2]. Understanding these…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
In cell membranes, proteins and lipids diffuse in a highly crowded and heterogeneous landscape, where aggregates and dense domains of proteins or lipids obstruct the path of diffusing molecules. In general, hindered motion gives rise to…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Past work has shown that ions can pass through a membrane more readily in one direction than the other. We demonstrate here in a model and an experiment that for a mixture of small and large particles such asymmetric diffusion can arise…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
Via hydrodynamics preserving molecular dynamics simulations we study growth phenomena in a phase separating symmetric binary mixture model. We quench high-temperature homogeneous configurations to state points inside the miscibility gap,…
We present a hydrodynamic theory describing pair diffusion in systems with periodic boundary conditions, thereby generalizing earlier work on self-diffusion [D\"unweg and Kremer, J. Chem. Phys. 1993, 99, 6983-6997; Yeh and Hummer, J. Phys.…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Diffusion rates through a membrane can be asymmetric, if the diffusing particles are spatially extended and the pores in the membrane have asymmetric structure. This phenomenon is demonstrated here via a deterministic simulation of a…
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…
The quantitative understanding of membranes is still rooted in work performed in the 1970s by Helfrich and others, concerning amphiphilic bilayers. However, most biological membranes contain a wide variety of nonamphiphilic molecules too.…
In this paper we introduce a novel method to simulate lateral diffusion of inclusions in a fluctuating membrane. The regarded systems are governed by two dynamic processes: the height fluctuations of the membrane and the diffusion of the…
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are…
Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space,…