The structure of electrodeposits – a computer simulation study

Polycrystalline higher manganese silicide (MnSi_1.73) films with addition of chromium were prepared on thermally oxidized silicon substrates by magnetron sputtering. A cap layer of chromium disilicide was used as the doping source. Both the Seebeck coefficient and the resistivity were strongly dependent on the amount of chromium added to the film. When the thickness ratio of chromium disilicide to manganese silicide increased from 2.4% to 9.8%, the Seebeck coefficient at room temperature decreased from 121 to 100 μV/K. However, the temperature at which the maximum value of the Seebeck coefficient occurred increased from 343 to 633 K. When the thickness ratio was about 2.4%, the resistivity increased to 33×10^-3 Ω cm. Otherwise, the resistivity decreased from 13×10^-3 to 5.2×10^-3 Ω cm by increasing the thickness ratio. As a result, the thermoelectric power factor increased greatly at high temperatures. Several activation energies (0.021–0.383 eV) were observed from the curves of the logarithm of resistivity versus reciprocal temperature. PACS 72.20.Pa; 72.80.Ga; 72.15.Jf; 73.50.Lw; 73.61.Le     

A model phospholipid monolayer: a computer simulation study

A phospholipid monolayer is modelled by quasi two-dimensional hard dipoles. The dipole interactions are three-dimensional and the two continuous phases are characterized by their dielectric constants. A tendency of dipolar chain formation is observed for low temperatures and for equal dielectric constants. This tendency disappears when the two regions are slightly different.     

Rise transient dynamics of supercooled sec-butyl chloride — a computer simulation

The role of chiral discrimination in the R enantiomer and racemic mixture of sec butyl chloride is investigated by computer simulation in the glassy condition at 50K. The effect of left or right handedness on the molecular dynamics is clearly measurable at equilibrium in the appropriate frame of reference. The physical (lab. frame) effects of chiral discrimination are emphasized by the application of a strong, external electric field. This produces deeply oscillatory rise transients whose time dependence is clearly different for enantiomer and racemic mixture at the same nominal temperature (50K).     

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].     

Conformational properties of cyclooctane: a molecular dynamics simulation study

Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400 K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied (313 and 400 K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boat-chair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.     

Distinct conformational properties determined by implicit and explicit representation of protein-solvent interactions. An analytical and computer simulation study

In the protein folding problem, solvent-mediated forces are commonly represented by intra-chain pairwise contact energy. Although this approximation has proven to be useful in several circumstances, it is limited in some other aspects of the problem. Here we show that it is possible to achieve two models to represent the chain-solvent system, one of them with implicit and other with explicit solvent, such that both reproduce the same thermodynamic results. Firstly, lattice models treated by analytical methods, were used to show that the implicit and explicitly representation of solvent effects can be energetically equivalent only if local solvent properties are time and spatially invariant. Following, applying the same reasoning used for the lattice models, two inter-consistent Monte Carlo off-lattice models for implicit and explicit solvent are constructed, being that now in the latter the solvent properties are allowed to fluctuate. Then, it is shown that the chain configurational evolution as well as the globule equilibrium conformation are significantly distinct for implicit and explicit solvent systems. Actually, strongly contrasting with the implicit solvent version, the explicit solvent model predicts: (i) a malleable globule, in agreement with the estimated large protein-volume fluctuations; (ii) thermal conformational stability, resembling the conformational heat resistance of globular proteins, in which radii of gyration are practically insensitive to thermal effects over a relatively wide range of temperatures; and (iii) smaller radii of gyration at higher temperatures, indicating that the chain conformational entropy in the unfolded state is significantly smaller than that estimated from random coil configurations. Finally, we comment on the meaning of these results with respect to the understanding of the folding process.     

Hydration of nucleic acid components in dependence on nucleotide composition and relative humidity: a Monte Carlo simulation

What role does the nucleotide composition play in the process of formation of hydrated environment of nucleic acids? Can one estimate the hydration of nucleic acids on the level of their components? In order to resolve these questions we have completed an extensive computer simulation of the hydration of nucleic acids components - deoxynucleoside monophosphates distinguished by nucleotide composition. The energetic characteristics of systems containing deoxynucleoside monophosphates and water clusters of various dimensions are received. Our results demonstrate that deoxynucleoside monophosphates containing guanine and/or cytosine residues hydrated more strongly because of formation of more hydrogen bonds with water molecules in small water clusters, i.e. at low values of relative humidity. With increasing of number of water molecules in a water cluster the energetic preference of deoxynucleoside monophosphates containing guanine and/or cytosine residues decreases, and for water clusters corresponding to a state of a dilute aqueous solution the hydration of all types of deoxynucleoside monophosphates does not differ in a great degree. Deoxynucleoside monophosphates containing guanine and/or cytosine residues cause the greater destruction of the water structure compensated by the greater interaction with the nearest water molecules for all levels of relative humidity. Received 25 December 2001 and Received in final form 22 March 2002 Published online 13 September 2002     

有机添加剂柠檬酸与乙二胺四乙酸吸附在Mg(0001)表面的计算模拟研究

镁及镁合金具有良好的生物降解性, 生物相容性和优异的力学相容性, 作为新一代理想的可降解医用金属材料具有巨大的潜力, 但植入人体后, 极易腐蚀和降解. 本工作用密度泛函理论计算模拟方法研究了有机添加剂柠檬酸与乙二胺四乙酸在Mg(0001)表面的吸附. 通过吸附能, 分态密度, 差分电荷密度及布居电荷分析发现柠檬酸与乙二胺四乙酸在Mg(0001)表面存在强烈的Mg-O“单齿”和O-Mg-O“双齿”共价相互作用, 而乙二胺四乙酸平躺于Mg(0001)表面有最强的相互作用. 研究结论有望为在有机添加剂改善镁及镁合金生物医用材料的腐蚀及降解方面提供有用的理论指导.     

Femtosecond laser ablation of metals:a molecular dynamics simulation study

Using molecular dynamics (MD) methods combining with two-step radiation heating model, the mechanisms of ablation and the thermodynamic states at Ni surface under femtosecond laser irradiation are investigated. Simulation results show that the main mechanisms of ablation are evaporation and tensile stresses generated inside the target. The velocity of stress wave is predicted to be nearly equal to sound velocity. The rates of ablation at different fluences obtained from simulations are in good agreement with experimental data. Superheating phenomenon is also discovered.     

Hydration water in dynamics of a hydrated beta-lactoglobulin

Incoherent spin-echo signals of a hydrated β-lactoglobulin protein were investigated, at 275 and 293 K. The intermediate scattering functions I(Q,t) were divided in two contributions from surface water and protein, respectively. On one hand, the dynamics of the surface water follows a KWW stretched exponential function (the exponent is ~0.5), on the other hand, that of the protein follows a single exponential. The present results are consistent with our previous results of hydrated C-phycocyanin combining elastic and quasielastic neutron scattering and by molecular dynamics simulation.     

A computer simulation study of racemic mixtures

A simple model for a chiral molecule is proposed. The model consists of a central atom bonded to four different atoms in tetrahedral coordination. Two different potentials were used to describe the pair potentials between atoms: the hard sphere potential and the Lennard-Jones potential. For both the hard sphere and the Lennard-Jones chiral models, computer simulations have been performed for the pure enantiomers and also for the racemic mixture. The racemic mixture consisted of an equimolar mixture of the two optically active enantiomers. It is found that the equations of state are the same, within statistical uncertainty, for the pure enantiomer fluid and for the racemic mixture. Only at high pressures does the racemic mixture seem to have a higher density, for a given pressure, than the pure enantiomer. Concering the structure, no difference is found in the site-site correlation functions between like and unlike molecules in the racemic mixture either at low or at high densities. However, small differences are found for the site-site correlations of the pure enantiomer and those of the racemic mixtures. In the Lennard-Jones model, similar conclusions are drawn. The extension of Wertheim's first-order perturbation theory, denoted bonded hard sphere theory (ARCHER, A. L., and JACKSON, G., 1991, Molec. Phys., 73, 881; AMOS, M. D., and JACKSON, G., 1992, J. chem. Phys., 96, 4604), successfully reproduces the simulation results for the hard chiral model. Virial coefficients of the hard chiral model up to the fourth have also been evaluated. Again, no differences are found between virial coefficients of the pure fluid and of the racemic mixture. All the results of this work illustrate the quasi-ideal behaviour of racemic mixtures in the fluid phase.     

Hydration and protein dynamics: an ESR and ST-ESR spin labelling study of human serum albumin

Human serum albumin has been studied at low hydration level by the ESR spin labelling technique, under the assumption that a covalently bound spin-label is a reporter of the protein internal dynamics. At room temperature, the presence of a double component signal allowed us to monitor the influence of increasing hydration level on internal protein dynamics as well as on the superficial water dynamics. The ESR results have shown that the first 20 g of water per 100 g of protein activate the internal protein dynamics and that superficial water dynamics starts at higher hydration values. ESR experiments at low temperature have shown that at ?160°C ?T??80°C, the label experiences an increasing environmental polarity with increasing temperature in the samples with hydration values higher than about 20 g of water per 100 g of protein. The results are discussed in connection with both conformational substates of the protein and hydration water dynamics.     

Hydration and translocation of an excess proton in water clusters: Anab initio molecular dynamics study

The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite temperature quantum simulations. The simulations are performed by employing the method of Car-Parrinello molecular dynamics where the forces on the nuclei are obtained directly from ‘on the fly’ quantum electronic structure calculations. Since no predefined interaction potentials are used in this scheme, it is ideally suited to study proton translocation processes which proceed through breaking and formation of chemical bonds. The coordination number of the hydrated proton and the index of oxygen to which the excess proton is attached are calculated along the simulation trajectories for both the clusters.