ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations.

Non-structural protein 3 (NS3) helicase from hepatitis C virus is an enzyme that unwinds and translocates along nucleic acids with an ATP-dependent mechanism and has a key role in the replication of the viral RNA. An inchworm-like mechanism for translocation has been proposed based on crystal structures and single molecule experiments. We here perform atomistic molecular dynamics in explicit solvent on the microsecond time scale of the available experimental structures.

The effect of anaesthetics on the properties of a lipid membrane in the biologically relevant phase: a computer simulation study.

Molecular dynamics simulations of the fully hydrated neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing four different general anaesthetic molecules, namely chloroform, halothane, diethyl ether and enflurane, have been simulated at two different pressures, i.e., at 1 bar and 1000 bar, at the temperature of 310 K.

Calculation of the intrinsic solvation free energy profile of an ionic penetrant across a liquid-liquid interface with computer simulations.

We introduce the novel concept of an intrinsic free energy profile, allowing one to remove the artificial smearing caused by thermal capillary waves, which renders difficulties for the calculation of free energy profiles across fluid interfaces in computer simulations. We apply this concept to the problem of a chloride ion crossing the interface between water and 1,2-dichloroethane and show that the present approach is able to reveal several important features of the free energy profile which are not detected with the usual, nonintrinsic calculations. Thus, in contrast to the nonintrinsic profile, a free energy barrier is found at the aqueous side of the (intrinsic) interface, which is attributed to the formation of a water "finger" the ion pulls with itself upon approaching the organic phase.

Immersion depth of surfactants at the free water surface: a computer simulation and ITIM analysis study.

The adsorption layer of five different surfactants, namely, pentanol, octanol, dodecanol, dodecyl trimethyl ammonium chloride, and sodium dodecyl sulfate, has been analyzed on the basis of molecular dynamics simulation results at two surface densities, namely, 1 and 4 μmol/m(2). The analyses have primarily focused on the question of how deeply, in terms of atomistic layers, the different surfactant molecules are immersed into the aqueous phase. The orientation and conformation of the surfactant molecules have also been analyzed.

Molecular dynamics simulations of the water adsorption around malonic acid aerosol models.

Water nucleation around a malonic acid aggregate has been studied by means of molecular dynamics simulations in the temperature and pressure range relevant for atmospheric conditions. Systems of different water contents have been considered and a large number of simulations have allowed us to determine the phase diagram of the corresponding binary malonic acid-water systems. Two phases have been evidenced in the phase diagrams corresponding either to water adsorption on a large malonic acid grain at low temperatures, or to the formation of a liquid-like mixed aggregate of the two types of molecules, at higher temperatures.

Lateral dynamics of surfactants at the free water surface: a computer simulation study.

Molecular dynamics simulations of the adsorption layer of five different surfactant molecules, i.e., pentyl alcohol, octyl alcohol, dodecyl alcohol, sodium dodecyl sulfate, and dodecyl trimethyl ammonium chloride are performed at the free surface of their aqueous solution at two surface densities, namely 1 and 4 μmol/m(2) at 298 K.

Anesthetic molecules embedded in a lipid membrane: a computer simulation study.

The effect of four general anesthetic molecules, i.e., chloroform, halothane, diethyl ether and enflurane, on the properties of a fully hydrated dipalmitoylphosphatidylcholine (DPPC) membrane is studied in detail by long molecular dynamics simulations.

Surface properties of the polarizable Baranyai-Kiss water model.

The water surface properties using the Baranyai-Kiss (BK) model [A. Baranyai and P. T.

Adsorption of acetaldehyde on ice as seen from computer simulation and infrared spectroscopy measurements.

Detailed investigation of the adsorption of acetaldehyde on I(h) ice is performed under tropospheric conditions by means of grand canonical Monte Carlo computer simulations and compared to infrared spectroscopy measurements. The experimental and simulation results are in a clear accordance with each other. The simulations indicate that the adsorption process follows Langmuir behavior in the entire pressure range of the vapor phase of acetaldehyde.

Water adsorption around oxalic acid aggregates: a molecular dynamics simulation of water nucleation on organic aerosols.

The phase behaviour of binary oxalic acid-water mixtures has been investigated by means of computer simulation techniques. Such mixtures play an important role in atmospheric processes, since the hydrogen bonding ability of oxalic acid molecules allows them to form aerosol particles. Water can in turn be readily adsorbed on the surface of such aerosol particles, which results in the formation of small ice grains.

Molecular level properties of the free water surface and different organic liquid/water interfaces, as seen from ITIM analysis of computer simulation results.

Molecular dynamics simulations of the interface of water with four different apolar phases, namely water vapour, liquid carbon tetrachloride, liquid dichloromethane (DCM) and liquid dichloroethane (DCE) are performed on the canonical ensemble at 298 K. The resulting configurations are analysed using the novel method of identification of the truly interfacial molecules (ITIM). Properties of the first three molecular layers of the liquid phases (e.

Competitive adsorption of surfactants and polymers at the free water surface. A computer simulation study of the sodium dodecyl sulfate-poly(ethylene oxide) system.

Competitive adsorption of a neutral amphiphilic polymer, namely poly(ethylene oxide) (PEO) and an ionic surfactant, i.e., sodium dodecyl sulfate (SDS), is investigated at the free water surface by computer simulation methods at 298 K.

Adsorption of hydroxyacetone on pure ice surfaces.

The adsorption of hydroxyacetone molecules at the surface of ice is investigated by means of flow-tube reactor measurements in the temperature range: 213-253 K. The number of molecules adsorbed per surface unit is conventionally plotted as a function of the absolute gas concentration of hydroxyacetone and is compared to that previously obtained for acetone and ethanol. The enthalpy of adsorption and the monolayer capacity at the ice surface are determined.

Molecular dynamics simulation of the adsorption of oxalic acid on an ice surface.

The adsorption properties of oxalic acid molecules on the surface of hexagonal ice are investigated by means of molecular dynamics simulations performed at tropospheric temperatures. Although the oxalic acid-water interaction is strong at low coverage, due to the possible formation of a large number of hydrogen bonds between the adsorbed oxalic acid and the surface water molecules, the results of the simulations at finite coverage show the predominant role played by the oxalic acid-oxalic acid lateral interactions in the adsorption/desorption process. These interactions are even stronger than the water-water or water-oxalic acid interactions.

Adsorption of poly(ethylene oxide) at the free water surface. A computer simulation study.

Molecular dynamics simulation of poly(ethylene oxide) (PEO) adsorbed at the free water surface are reported on the canonical ensemble at 298 K. The obtained results are analyzed in terms of the novel Identification of the Truly Interfacial Molecules (ITIM) method. To obtain a deep, molecular level insight into the origin of the adsorption process, structural, dynamical, and energetic aspects have been investigated.

Molecular dynamics simulation and identification of the truly interfacial molecules (ITIM) analysis of the liquid-vapor interface of dimethyl sulfoxide.

The liquid-vapor interface of dimethyl sulfoxide (DMSO) is investigated by molecular dynamics computer simulation and by the novel method of the identification of the truly interfacial molecules (ITIM). With this method, it is possible to consider in the analysis specifically those molecules that are located right at the boundary of the two phases. The obtained results show that the orientation of the surface molecules is driven by the requirement that these molecules should be able to maintain their strong dipole-dipole and pi-pi interactions with each other, such as in the bulk liquid phase.

Free energy of mixing of pyridine and its methyl-substituted derivatives with water, as seen from computer simulations.

The free energies of mixing of pyridine, 2-methylpyridine, and 2,6-dimethylpyridine with water have been calculated at 298 K for systems containing 1, 5, and 50 mol % pyridine or its derivative by the method of thermodynamic integration. The obtained results show that the trend of the free energy of mixing of these compounds with water, observed previously at infinite dilution, clearly vanishes at 1 mol % and reverses at higher pyridine concentrations. Thus, in the 5 and 50 mol % systems, the free energy of mixing increases with increasing number of methyl groups.