Community detection in sequence similarity networks based on attribute clustering.

Networks are powerful tools for the presentation and analysis of interactions in multi-component systems. A commonly studied mesoscopic feature of networks is their community structure, which arises from grouping together similar nodes into one community and dissimilar nodes into separate communities. Here, the community structure of protein sequence similarity networks is determined with a new method: Attribute Clustering Dependent Communities (ACDC).

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Additive force fields are designed to account for induced electronic polarization in a mean-field average way, using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations.

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.

A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular dynamics simulations of bilayer and monolayer membranes. The hierarchical parametrization strategy involves the optimization of parameters for small molecules representative of lipid functional groups, followed by their application in larger model compounds and full lipids. The polar headgroup is based on molecular ions tetramethyl ammonium and dimethyl phosphate, the esterified glycerol backbone is based on methyl acetate, and the aliphatic lipid hydrocarbon tails are based on linear alkanes.

Molecular simulation study of water mobility in aerosol-OT reverse micelles.

In this work, we present results from molecular dynamics simulations on the single-molecule relaxation of water within reverse micelles (RMs) of different sizes formed by the surfactant aerosol-OT (AOT, sodium bis(2-ethylhexyl)sulfosuccinate) in isooctane. Results are presented for RM water content w(0) = [H(2)O]/[AOT] in the range from 2.0 to 7.

Molecular dynamics simulation of aerosol-OT reverse micelles.

Molecular dynamics simulations are performed for the reverse micelles (RMs) formed by the surfactant Aerosol-OT (AOT, sodium bis(2-ethylhexyl)sulfosuccinate) in isooctane. The appropriate simulation methodology is identified and applied to the study of the effect of RM size, as quantified by w0 = [H2O]/[AOT], on the structure of the reverse micelle. The radial and intrinsic density profiles, pair densities and pair orientations in the first solvation shell, and water-water hydrogen bonding profiles were constructed.

Vibrational spectroscopy and dynamics of water confined inside reverse micelles.

In this work, we combine atomistic molecular dynamics simulations with theoretical vibrational spectroscopy to study the properties of water confined inside bis(2-ethylhexyl)sulfosuccinate (AOT) reverse micelles. This approach is found to successfully reproduce the experimental spectra, rotational anisotropy decays, and spectral diffusion time-correlation functions as a function of micelle size. These results are interpreted in terms of water molecules in different hydrogen bonding environments.

Hydrogen bond dynamics at the water/hydrocarbon interface.

The dynamics of hydrogen bond formation and breakage for water in the vicinity of water/hydrocarbon liquid interfaces is studied using molecular dynamics simulations. Several liquid alkanes are considered as the hydrocarbon phase in order to determine the effects of their chain length and extent of branching on the properties of the adjacent water phase. In addition to defining the interface location in terms of the laboratory-frame density profiles, the effects of interfacial fluctuations are considered by locating the interface in terms of the proximity of the molecules of the other phase.

Surface fluctuations at the liquid-liquid interface.

Within the capillary-wave model (CWM), the liquid-vapor interface is a hypothetical two-dimensional surface whose deviations from planarity are represented as long wavelength capillary waves. We modify the CWM for liquid-liquid interfaces and treat them as two harmonically interacting surfaces (model 1). Corrections to the model are proposed to prevent the usual divergence of the capillary-wave broadening in the thermodynamic limit by introducing a surface-bulk coupling (model 2) and to incorporate the curvature of the two surfaces (model 3).

Water/hydrocarbon interfaces: effect of hydrocarbon branching on single-molecule relaxation.

Water/hydrocarbon interfaces are studied using molecular dynamics simulations in order to understand the effect of hydrocarbon branching on the dynamics of the system at and away from the interface. A recently proposed procedure for studying the intrinsic structure of the interface in such systems is utilized, and dynamics are probed in the usual laboratory frame as well as the intrinsic frame. The use of these two frames of reference leads to insight into the effect of capillary waves at the interface on dynamics.

Water-hydrocarbon interfaces: effect of hydrocarbon branching on interfacial structure.

Molecular dynamics simulation are performed for the water/hydrocarbon system to study the effect of hydrocarbon branching on interfacial properties. The following two series of hydrocarbons are considered: (1) n-pentane, 2-methyl pentane, and 2,2,4-trimethyl pentane (constant chain length) and (2) n-octane, 2-methyl heptane, and 2,2,4-trimethyl pentane (constant molecular mass). With a simple algorithm for identification of surface sites and mapping nonsurface sites to these surface sites, intrinsic profiles were constructed with respect to the surface layer.