Elastic and dynamical properties of alkali-silicate glasses from computer simulations techniques

This paper shows recent progresses in the field of computer simulations of inorganic glasses. Molecular dynamics simulations and energy minimization methods have been applied to calculate the elastic and transport properties of alkali silicate glasses of compositions xM₂O · (100 ? x)SiO₂ (with x = 0, 10, 15, 20, 25, 30 % mol for M = Li, Na and K) and of a soda-lime glass with composition 15Na₂O · 10CaO · 75SiO₂, which has been employed to ascertain the effect of the replacement of CaO for Na₂O. The excellent agreement of the computed results with the experimental data highlights the important predictive and interpretative role reached by computer simulations techniques.     

A topology preserving method for generating equilibrated polymer melts in computer simulations

A new method for generating equilibrated configurations of polymer melts is presented. In this method, the molecular weight of an equilibrated melt of polymers is successively doubled by affinely scaling the simulation box and adding beads along the contour of the chains. At each stage of molecular weight doubling, compressive deformations are produced on all length scales, while the random walk nature of the polymers is preserved, thereby requiring relaxation times significantly smaller than the reptation time to fully equilibrate the melt. This method preserves the topological state of individual polymers in the melt and its effectiveness is demonstrated for linear polymers with molecular weight N up to 1024, and cyclic polymers with N up to 8192. For the range of N studied, the method requires simulation time that scales as N(2) and is thought to be applicable to a variety of polymer architectures.     

Estimation of the liquid-vapor spinodal from interfacial properties obtained from molecular dynamics and lattice Boltzmann simulations

Interfacial pressure and density profiles are calculated from molecular dynamics and lattice Boltzmann simulations of a liquid film in equilibrium with its vapor. The set of local values of tangential pressure and density along an interface exhibits a van der Waals-type loop; starting from the stable vapor bulk phase one passes through metastable and unstable states to the stable liquid bulk phase. The minimum and maximum values of the profile of tangential pressure are related to the liquid and vapor spinodal states, respectively. The spinodal pressures turn out to be linearly related to the extreme values of the tangential pressure in the interface. The comparison with equations of state shows good agreement with the simulation results of the spinodals. In addition the properties of the metastable region are obtained. Based on this investigation a method is proposed for the estimation of the liquid spinodal from experimentally obtained interfacial properties. Estimations for water and helium are presented.     

Estimation of protein folding probability from equilibrium simulations

The assumption that similar structures have similar folding probabilities (p(fold)) leads naturally to a procedure to evaluate p(fold) for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide or protein. The procedure utilizes a structurally homogeneous clustering and does not require any additional simulation. It can be used to detect multiple folding pathways as shown for a three-stranded antiparallel beta-sheet peptide investigated by implicit solvent molecular dynamics simulations.     

A new instrument for measuring the viscoelastic properties of dilute polymer solutions

A new oscillating capillary viscometer has been developed and used for measuring viscoelastic flow properties of dilute polymer solutions. These flow properties are determined from measurements of the pressure to volume flow relationships for sinusoidal flow in cylindrical glass capillaries. The theory for this measurement procedure is based upon the known theory for oscillatory flow of a viscoelastic fluid in circular tubes and which is presented with a few supplementations in this paper.The oscillatory flow is generated by a piezoelectric driver which is dipped directly into the aqueous solution. The advantage of this driver is that the excitation voltage for the piston is a direct measure of the motion of the piston. Changes in pressure are measured with a sensitive low-pressure quartz tranducer.The viscometer was tested with aqueous glycerol solutions and a gelatin gel. The viscoelastic flow properties of dilute polymer solutions (gelatin, gelatin/color-coupler, polyacrylamide) were then investigated in the frequency range 5 Hz to 150 Hz at very small volume flow amplitudes. The results presented illustrate the suitability of the method. The results are also evaluated with regard to the stabilizing action of slightly viscoelastic gelatinous coating liquids in the high-speed coating process in the manufacture of photographic materials.     

Liquid-phase structure of dialkylimidazolium ionic liquids from computer simulations

We present a detailed computational study of the structure of ionic liquids based on the imidazolium cation. Both imidazolium-ring stacking and hydrogen bonding behavior are investigated from radial and spatial orientational distribution functions, as well as orientational correlation functions. The alkyl chain size and anion effect on the liquid structure are provided and discussed. Our results support models for liquid organization comparable to those formulated on the basis of experimental observations.     

Monte Carlo simulations of single crystals from polymer solutions

A novel "anisotropic aggregation" model is proposed to simulate nucleation and growth of polymer single crystals as functions of temperature and polymer concentration in dilute solutions. Prefolded chains in a dilute solution are assumed to aggregate at a seed nucleus with an anisotropic interaction by a reversible adsorption/desorption mechanism, with temperature, concentration, and seed size being the control variables. The Monte Carlo results of this model resolve the long-standing dilemma regarding the kinetic and thermal roughenings, by producing a rough-flat-rough transition in the crystal morphology with increasing temperature. It is found that the crystal growth rate varies nonlinearly with temperature and concentration without any marked transitions among any regimes of polymer crystallization kinetics. The induction time increases with decreasing the seed nucleus size, increasing temperature, or decreasing concentration. The apparent critical nucleus size is found to increase exponentially with increasing temperature or decreasing concentration, leading to a critical nucleus diagram composed in the temperature-concentration plane with three regions of different nucleation barriers: no growth, nucleation and growth, and spontaneous growth. Melting temperatures as functions of the crystal size, heating rate, and concentration are also reported. The present model, falling in the same category of small molecular crystallization with anisotropic interactions, captures most of the phenomenology of polymer crystallization in dilute solutions.     

Phase equilibrium in polymer systems

The topological analysis of phase equilibria in polymer systems, which was developed by S.P. Papkov; the classification of the types of phase equilibrium; the principle of mutual independence of the two types of equilibrium; the concept of the generality of the phase equilibrium in polymer-solvent, polymer-plasticizer, polymer-oligomer, and polymer-polymer systems; and the processes of water sorption by polymers are considered. It is shown that the problems that Papkov dealt with remain topical and the concepts that he elaborated can underlie new studies in the field of phase equilibria in polymer systems.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Structures of neat and hydrated 1-octanol from computer simulations

Molecular dynamics computer simulations of 1-octanol and its mixtures with water have been performed. The liquid is composed of regions enriched in either hydrocarbons or hydroxyl groups. In neat octanol, the hydroxyl groups form clusters of long, thin chains. Upon the addition of water, the clusters become longer and more spherical, forming a structure that can be described as consisting of "overlapping elongated inverse micelles". The structures of the mixtures obtained at different hydration levels are consistent with those of experimental diffraction studies of water/octanol mixtures and previous computer simulations of neat and water-saturated octanol. The saturation point of the model has been calculated using the cavity-bias particle insertion method. The solubility of water in octanol is slightly too low compared to experimental results, and suggestions for possible improvements to the force field are made.     

Thermal conductivity of molten alkali halides from equilibrium molecular dynamics simulations

The thermal conductivity of molten sodium chloride and potassium chloride has been computed through equilibrium molecular dynamics Green-Kubo simulations in the microcanonical ensemble (N,V,E). In order to access the temperature dependence of the thermal conductivity coefficient of these materials, the simulations were performed at five different state points. The form of the microscopic energy flux for ionic systems whose Coulombic interactions are calculated through the Ewald method is discussed in detail and an efficient formula is used by analogy with the methods used to evaluate the stress tensor in Coulombic systems. The results show that the Born-Mayer-Huggins-Tosi-Fumi potential predicts a weak negative temperature dependence for the thermal conductivity of NaCl and KCl. The simulation results are in agreement with part of the experimental data available in the literature with simulation values generally overpredicting the thermal conductivity by 10%-20%.     

Molecular-dynamics simulations of the transport properties of a single polymer chain in two dimensions

Molecular-dynamics simulations are conducted to elucidate the critical factors affecting the transport properties of isolated polymer chains in strictly two dimensions. The relevance of surface inhomogeneity is critically examined. We unequivocally find that surface inhomogeneity is critical in obtaining transport behavior consistent with the recent measurements of surface diffusion for polymers adsorbed at the solid-liquid interface. For a systematic investigation of this point, heterogeneity was introduced by decorating the surface with impenetrable elements and we find that chain diffusivity crossed over from Rouse-type behavior to reptationlike with increasing surface coverage of obstacles. This transition in behavior occurred when the mean distance between obstacles is approximately equal to the end-to-end distance, Re, of the two-dimensional chain. Our results underscore the importance of surface disorder (not only literal obstacles but by reasonable extension also to other types of disorder) in determining the transport behavior of chains adsorbed to solids.     

The effects of Lowe-Andersen temperature controlling method on the polymer properties in mesoscopic simulations

Lowe-Andersen (LA) temperature controlling method [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] is applied in a series of mesoscopic polymer simulations to test its validity and efficiency. The method is an alternative for dissipative particle dynamics simulation (DPD) technique which is also Galilean invariant. It shows excellent temperature control and gives correct radial distribution function as that from DPD simulation. The efficiency of LA method is compared with other typical DPD integration schemes and is proved to be moderately efficient. Moreover, we apply this approach to diblock copolymer microphase separation simulations. With LA method, we are able to reproduce all the results from the conventional DPD simulations. The calculated structure factors of the microphases are consistent with the experiments. We also study the microphase evolution dynamics with increasing chiN and find that the bath collision frequency Gamma does not affect the order of appearing phases. Although the thermostat does not affect the surface tension, the order-disorder transition (ODT) is somewhat sensitive to the values of Gamma, i.e., the ODT is nonmonotonic with increasing Gamma. The dynamic scaling law is also tested, showing that the relation obeys the Rouse theory with various Gamma.     

Information about the biologically relevant properties of Clostridium pasteurianum rubredoxin obtained from modeling and dynamics simulations of molecular variants

Rubredoxins are small electron transfer proteins containing one iron atom at their active site. The rubredoxin from the anaerobic bacterium Clostridium pasteurianum has been subjected to molecular dynamics studies starting from the minimized solvated structure. The results of the simulations have been compared with identical ones carried out with selected mutated forms of the protein obtained by molecular modeling. Surface residues, which are highly conserved among rubredoxins and close to the cysteine ligands, can be replaced by glutamates, i.e. long chain carboxylates. The main structural consequence is a shift of the protein backbone bearing conserved aromatic residues. Reciprocally, substitution of the aromatic residue closest to the iron atom shifts the cysteine-containing peptide fragments. These observations have been related to the changes in electron transfer and redox properties previously measured for this set of rubredoxin molecular variants. Received: 16 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Charge transport through polyene self-assembled monolayers from multiscale computer simulations

We combine first-principles density-functional theory with matrix Green's function calculations to predict the structures and charge transport characteristics of self-assembled monolayers (SAMs) of four classes of systems in contact with Au(111) electrodes: conjugated polyene chains (n = 4, 8, 12, 16, and 30) thiolated at one or both ends and saturated alkane chains (n = 4, 8, 12, and 16) thiolated at one or both ends. For the polyene SAMs, we find no decay in the current as a function of chain length and conclude that these 1-3 nm long polyene SAMs act as metallic wires. We also find that the polyene-monothiolate leads to a contact resistance only 2.8 times higher than that for the polyene-dithiolate chains, indicating that the device conductance is dominated by the properties of the molecular connector with less importance in having a second molecule-electrode contact. For the alkane SAMs, we observe the normal exponential decay in the current as a function of the chain length with a decay constant of beta(n) = 0.82 for the alkane-monothiolate and 0.88 for the alkane-dithiolate. We find that the contact resistance for the alkane-monothiolate is 12.5 times higher than that for the alkane-dithiolate chains, reflecting the extra resistance due to the weak contact on the nonthiolated end. These contrasting charge transport characteristics of alkane and polyene SAMs and their contact dependence are explained in terms of the atomic projected density of states.     

The photochromic properties of indoline spirooxazine-thermoplastic polymer systems obtained by supercritical fluid impregnation

The impregnation of thermoplastic polymers (polyethylene, polypropylene, polymethyl methacrylate, and polycarbonate) with photochromic compounds from the class of indoline spirooxazines in supercritical carbon dioxide (SC-CO₂) was studied. The concentration of the photochrome and the kinetics of decolorization of its colored form depended strongly on the type of the polymer matrix and the structure of spirooxazine. The introduction of 1,3′,3′-trimethylspiro(indoline-2′,3-3H-anthraceno[2,1-b][1,4]oxazine) (SAO) into polycarbonate caused anomalous stabilization (the prolonged conservation of the excited colored form of SAO in the polymer matrix). In contrast to other photochrome-polymer pairs, after supercritical impregnation into polycarbonate, at least 10% of all SAO molecules were in the colored form, which was highly stable and did not decolorize after 150 days; the rest of the impregnated SAO molecules were localized in the matrix as individual molecules, partially colorized after matrix relaxation, or nanocrystals of characteristic sizes ∼10–20 nm. The mechanisms of the anomalous stabilization of the colored SAO form in the polycarbonate matrix are discussed. Original Russian Text ? N.N. Glagolev, A.B. Solov’eva, A.V. Kotova, V.T. Shashkova, B.I. Zapadinskii, N.L. Zaichenko, L.S. Kol’tsova, A.I. Shienok, P.S. Timashev, V.N. Bagratashvili, 2009, published in Zhurnal Fizicheskoi Khimii, 2009, Vol. 83, No. 5, pp. 985–992.     

Driven polymer transport through a nanopore controlled by a rotating electric field: off-lattice computer simulations

The driven translocation kinetics of a single strand polynucleotide chain through a nanopore is studied using off-lattice Monte Carlo simulations, by which the authors demonstrate a novel method in controlling the driven polymer transport through a nanopore by a rotating electric field. The recorded time series of blockade current from the driven polynucleotide transport are used to determine the sequence of polynucleotides by implementing a modified Monte Carlo algorithm, in which the energy landscape paving technique is incorporated to avoid trapping at deep local minima. It is found that only six-time series of block current are required to completely determine the polynucleotide sequence if the average missing rate (AMR) of current signals in these time series is smaller than 20%. For those time series with AMR greater than 20%, the error rate in sequencing an unknown polynucleotide decreases rapidly by increasing the number of time series. To find the most appropriate experimental conditions, the authors have investigated the dependence of AMR of current signals and qualified rate of measured time series of blockade current on various controllable experimental variables.     

Shear viscosity of molten alkali halides from equilibrium and nonequilibrium molecular-dynamics simulations

The shear viscosity of molten NaCl and KCl was calculated through equilibrium (EMD) and nonequilibrium molecular-dynamics (NEMD) simulations in the canonical (N,V,T) ensemble. Two rigid-ion potentials were investigated, namely, the Born-Mayer-Huggins-Tosi-Fumi potential and the Michielsen-Woerlee-Graaf-Ketelaar potential with the parameters proposed by Ladd. The NEMD simulations were performed using the SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] with a Gaussian isokinetic thermostat and the results are compared with those obtained from Green-Kubo EMD (N,V,T) simulations and experimental shear viscosity data. The NEMD zero strain rate shear viscosity, eta(0), was obtained by fitting a simplified Carreau-type equation and by application of mode-coupling theory, i.e., a eta-gamma(1/2) linear relationship. The values obtained from the first method are found to be significantly lower than those predicted by the second. The agreement between the EMD and NEMD results with experimental data is satisfactory for the two potentials investigated. The ion-ion radial distribution functions obtained with the two rigid-ion potentials for both molten salts are discussed in terms of the differences between the two models.