Lipid Diffusion, Free Area, and Molecular Dynamics Simulations

Microsecond Molecular Dynamics Simulations of Lipid Mixing

Molecular dynamics (MD) simulations of membranes are often hindered by the slow lateral diffusion of lipids and the limited time scale of MD. In order to study the dynamics of mixing and characterize the lateral distribution of lipids in converged mixtures, we report microsecond-long all-atom MD simulations performed on the special-purpose machine Anton. Two types of mixed bilayers, POPE:POPG (...

Molecular dynamics simulations of lipid bilayers.

During the past decade, computer simulations of bilayers have moved from the realm of model systems to realistic systems containing tens of phospholipids along with the requisite number of water molecules hydrating the entire molecular assembly. Concomitant with the ability to model larger and larger systems, simulators have also begun to utilize more accurate numerical tools to ensure that the...

Molecular Dynamics and Stochastic Simulations of Surface Diffusion

Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics

Accelerated molecular dynamics (aMD) is an enhanced sampling technique that expedites conformational space sampling by reducing the barriers separating various low-energy states of a system. Here, we present the first application of the aMD method on lipid membranes. Altogether, ∼1.5 μs simulations were performed on three systems: a pure POPC bilayer, a pure DMPC bilayer, and a mixed POPC:DMPC ...

Molecular dynamics simulations of a nucleosome and free DNA.

All atom molecular dynamics simulations (10ns) of a nucleosome and of its 146 basepairs of DNA free in solution have been conducted. DNA helical parameters (Roll, Tilt, Twist, Shift, Slide, Rise) were extracted from each trajectory to compare the conformation, effective force constants, persistence length measures, and fluctuations of nucleosomal DNA to free DNA. The conformation of DNA in the ...