Atomistic Monte Carlo Simulation of Lipid Membranes

Abstract

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

Interactions between Beta-2-Glycoprotein-1 and Phospholipid Bilayer—A Molecular Dynamic Study

“…Based on this observation, we can say that longer simulations are needed to equilibrate the POPE than DPPC bilayers, but in both cases, 50 ns was enough to observe the interactions' formation. Similar results were obtained for the DPPC bilayer by Wustner et al [48], where the results come from Monte Carlo simulations of the bilayer self-organization. They present there the methods as a good indicator of equilibration of the system.…”

“…The mean value in angular brackets is an average of all positions of atoms i and j in Cartesian space (separately for the x, y, and z coordinates) calculated for a given time. The assumption needed for this computation is that fluctuations are normally distributed around the mean, allowing the covariances to be estimated from a multidimensional Gaussian distribution [48]. Otherwise, the covariance matrix does not yield all information tied to the cross-correlation of the data, and other measures such as higher-order moments or cumulants can be beneficial in a more detailed research.…”

Dynamic Mode Decomposition of Multiphoton and Stimulated Emission Depletion Microscopy Data for Analysis of Fluorescent Probes in Cellular Membranes

“…where A is a matrix which describes the advancement of the system from image x k to image x k+1 . This matrix resembles the Koopman or transfer operator for measurements g(x k ) = x k [29]. For the analysis of 3D microscopy and two-photon polarimetry data, one replaces ∆t by ∆z and ∆θ, respectively.…”

Using molecular simulation to understand the skin barrier

“…However, methods such as configw [ 111 ] and hybrid MC [ 112 ]. as well as more complex MC moves have made the simulation of lipid bilayer systems possible using MC methods [ 113 ]. The main barriers for adoption of these new MC methods is the difficulty in implementing these algorithms and the lack of available open-source and easy-to-use software for such simulations.…”