Simulation of pore formation in lipid bilayers by mechanical stress and electric fields

We describe computer simulations of pore formation and membrane rupture of phospholipid bilayers under mechanical and electrical stress. On the nanosecond simulation time scale, pores are induced by a lateral pressure exceeding -200 bar or by an applied electric field of 0.5 V/nm.     

Enantioselective Enzymes by Computational Design and In Silico Screening

Computational enzyme design holds great promise for providing new biocatalysts for synthetic chemistry. A strategy to design small mutant libraries of complementary enantioselective epoxide hydrolase variants for the production of highly enantioenriched (S,S)‐diols and (R,R)‐diols is developed. Key features of this strategy (CASCO, catalytic selectivity by computational design) are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high‐throughput molecular dynamics simulations. Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.     

Helfrich model of membrane bending: From Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers

Helfrich model of membrane bending elasticity has been most influential in establishment and development of Soft-Matter Physics of lipid bilayers and biological membranes. Recently, Helfrich theory has been extensively used in Cell Biology to understand the phenomena of shaping, fusion and fission of cellular membranes. The general background of Helfrich theory on the one hand, and the ways of specifying the model parameters on the other, are important for quantitative treatment of particular biologically relevant membrane phenomena. Here we present the origin of Helfrich model within the context of the general Gibbs theory of capillary interfaces, and review the strategies of computing the membrane elastic moduli based on considering a lipid monolayer as a three-dimensional thick layer characterized by trans-monolayer profiles of elastic parameters. We present the results of original computations of these profiles by a state-of-the-art numerical approach.     

Simulation studies of pore and domain formation in a phospholipid monolayer

Despite extensive study the phase behavior of phospholipid monolayers at an air-water interface is still not fully understood. In particular recent vibrational sum-frequency generation (VSFG) spectra of DPPC monolayers as a function of area density show a sharp transition in the order of the lipid chains at 1.10 nm2/molecule. This is in a region where the lateral pressure as a function of area is effectively constant. We have investigated the nature of this transition by studying the phase behavior of DPPC monolayers as a function of area density using molecular-dynamics simulations. The changes in order within the monolayer as a function of area density correlate well with the experimental signal. At 0.58 nm2/molecule we observe the onset of lateral separation of highly ordered and disordered lipids, indicating the coexistence of a gel-like liquid condensed and a fluidlike liquid expanded phase. At 0.97 nm2/molecule the monolayer ruptures, marking the onset of the liquid-gas (G) coexistence region. This is much earlier than suggested by fluorescence microscopy results and implies that at the point of rupture, the initial pores have an equilibrium size smaller than approximately 500 nm in diameter. The rupture of the monolayer leads to a sharp increase in the overall lipid order that explains the sharp transition observed in the VSFG measurements. VSFG measurements thus may represent a sensitive means to determine the onset of the liquid-gas (G) coexistence region for such systems.     

Definition of percolation thresholds on self-affine surfaces

We study the percolation transition on a two-dimensional substrate with long-range self-affine correlations. We find that the position of the percolation threshold on a correlated lattice is no longer unique and depends on the spanning rule employed. Numerical results are provided for spanning across the lattice in specified (horizontal or vertical), either or both directions.     

Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamics simulations

Control of the size and agglomeration of micellar systems is important for pharmaceutical applications such as drug delivery. Although shape-related transitions in surfactant solutions are studied experimentally, their molecular mechanisms are still not well understood. In this study, we use coarse-grained molecular dynamics simulations to describe micellar assemblies of pentaethylene glycol monododecyl ether (C(12)E(5)) in aqueous solution at different concentrations. The obtained size and aggregation numbers of the aggregates formed are in very good agreement with the available experimental data. Importantly, increase of the concentration leads to a second critical micelle concentration where a transition to rod-like aggregates is observed. This transition is quantified in terms of shape anisotropy, together with a detailed structural analysis of the micelles as a function of aggregation number.