Biomedical subjects

Kurt Binder

Publications and source records attributed to Kurt Binder.

15 recordsLinked to original sources

PubMed2006

Static and dynamic critical behavior of a symmetrical binary fluid: a computer simulation.

A symmetrical binary, A+B Lennard-Jones mixture is studied by a combination of semi-grand-canonical Monte Carlo (SGMC) and molecular dynamics (MD) methods near a liquid-liquid critical temperature T(c). Choosing equal chemical potentials for the two species, the SGMC switches identities (A-->B-->A) to generate well-equilibrated configurations of the system on the coexistence curve for T T(c). A finite-size scaling analysis of the concentration susceptibility above T(c) and of the order parameter below T(c) is performed, varying the number of particles from N=400 to 12 800. The data are fully compatible with the expected critical exponents of the three-dimensional Ising universality class. The equilibrium configurations from the SGMC runs are used as initial states for microcanonical MD runs, from which transport coefficients are extracted. Self-diffusion coefficients are obtained from the Einstein relation, while the interdiffusion coefficient and the shear viscosity are estimated from Green-Kubo expressions. As expected, the self-diffusion constant does not display a detectable critical anomaly. With appropriate finite-size scaling analysis, we show that the simulation data for the shear viscosity and the mutual diffusion constant are quite consistent both with the theoretically predicted behavior, including the critical exponents and amplitudes, and with the most accurate experimental evidence.

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PubMed2006

Critical dynamics in a binary fluid: simulations and finite-size scaling.

We report comprehensive simulations of the critical dynamics of a symmetric binary Lennard-Jones mixture near its consolute point. The self-diffusion coefficient exhibits no detectable anomaly. The data for the shear viscosity and the mutual-diffusion coefficient are fully consistent with the asymptotic power laws and amplitudes predicted by renormalization-group and mode-coupling theories provided finite-size effects and the background contribution to the relevant Onsager coefficient are suitably accounted for. This resolves a controversy raised by recent molecular simulations.

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PubMed2006

Spinodal decomposition in thin films: molecular-dynamics simulations of a binary Lennard-Jones fluid mixture.

We use molecular dynamics (MD) to simulate an unstable homogeneous mixture of binary fluids (AB), confined in a slit pore of width D. The pore walls are assumed to be flat and structureless and attract one component of the mixture (A) with the same strength. The pairwise interactions between the particles are modeled by the Lennard-Jones potential, with symmetric parameters that lead to a miscibility gap in the bulk. In the thin-film geometry, an interesting interplay occurs between surface enrichment and phase separation. We study the evolution of a mixture with equal amounts of A and B, which is rendered unstable by a temperature quench. We find that A-rich surface enrichment layers form quickly during the early stages of the evolution, causing a depletion of A in the inner regions of the film. These surface-directed concentration profiles propagate from the walls towards the center of the film, resulting in a transient layered structure. This layered state breaks up into a columnar state, which is characterized by the lateral coarsening of cylindrical domains. The qualitative features of this process resemble results from previous studies of diffusive Ginzburg-Landau-type models [S. K. Das, S. Puri, J. Horbach, and K. Binder, Phys. Rev. E 72, 061603 (2005)], but quantitative aspects differ markedly. The relation to spinodal decomposition in a strictly two-dimensional geometry is also discussed.

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PubMed2005

Calculation of local pressure tensors in systems with many-body interactions.

Local pressures are important in the calculation of interface tensions and in analyzing micromechanical behavior. The calculation of local pressures in computer simulations has been limited to systems with pairwise interactions between the particles, which is not sufficient for chemically detailed systems with many-body potentials such as angles and torsions. We introduce a method to calculate local pressures in systems with n-body interactions (n=2,3,4,) based on a micromechanical definition of the pressure tensor. The local pressure consists of a kinetic contribution from the linear momentum of the particles and an internal contribution from dissected many-body interactions by infinitesimal areas. To define dissection by a small area, respective n-body interactions are divided into two geometric centers, effectively reducing them to two-body interactions. Consistency with hydrodynamics-derived formulas for systems with two-body interactions [J. H. Irving and J. G. Kirkwood, J. Chem. Phys. 18, 817 (1950)], for average cross-sectional pressures [B. D. Todd, D. J. Evans, and P. J. Daivis, Phys. Rev. E 52, 1627 (1995)], and for volume averaged pressures (virial formula) is shown. As a simple numerical example, we discuss liquid propane in a cubic box. Local, cross-sectional, and volume-averaged pressures as well as relative contributions from two-body and three-body forces are analyzed with the proposed method, showing full numerical equivalence with the existing approaches. The method allows computing local pressures in the presence of many-body interactions in atomistic simulations of complex materials and biological systems.

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PubMed2005

Comparison of model potentials for molecular-dynamics simulations of silica.

Structural, thermomechanical, and dynamic properties of pure silica SiO2 are calculated with three different model potentials, namely, the potential suggested by van Beest, Kramer, and van Santen (BKS) [Phys. Rev. Lett. 64, 1955 (1990)], the fluctuating-charge potential with a Morse stretch term for the short-range interactions proposed by Demiralp, Cagin, and Goddard (DCG)[Phys. Rev. Lett. 82, 1708 (1999)], and a polarizable force field proposed by Tangney and Scandolo (TS) [J. Chem. Phys. 117, 8898 (2002)]. The DCG potential had to be modified due to flaws in the original treatment. While BKS reproduces many thermomechanical properties of different polymorphs rather accurately, it also shows qualitatively wrong trends concerning the phononic density of states, an absence of the experimentally observed anomaly in the c/a ratio at the quartz alpha-beta transition, pathological instabilities in the beta-cristobalite phase, and a vastly overestimated transition pressure for the stishovite I --> II transition. These shortcomings are only partially remedied by the modified DCG potential but greatly improved by the TS potential. DCG and TS both reproduce a pressure-induced transition from alpha-quartz to quartz II, predicted theoretically based on the BKS potential.

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PubMed2005

Artificial multiple criticality and phase equilibria: an investigation of the PC-SAFT approach.

The perturbed-chain statistical associating fluid theory (PC-SAFT) is studied for a wide range of temperature, T, pressure, p, and (effective) chain length, m, to establish the generic phase diagram of polymers according to this theory. In addition to the expected gas-liquid coexistence, two additional phase separations are found, termed "gas-gas" equilibrium (at very low densities) and "liquid-liquid" equilibrium (at densities where the system is expected to be solid already). These phase separations imply that in one-component polymer systems three critical points occur, as well as equilibria of three fluid phases at triple points. However, Monte Carlo simulations of the corresponding system yield no trace of the gas-gas and liquid-liquid equilibria, and we conclude that the latter are just artefacts of the PC-SAFT approach. Using PC-SAFT to correlate data for polybutadiene melts, we suggest that discrepancies in modelling the polymer density at ambient temperature and high pressure can be related to the presumably artificial liquid-liquid phase separation at lower temperatures. Thus, particular care is needed in engineering applications of the PC-SAFT theory that aims at predicting properties of macromolecular materials.

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PubMed2005

A global investigation of phase equilibria using the perturbed-chain statistical-associating-fluid-theory approach.

The recently developed perturbed-chain statistical-associating-fluid theory (PC-SAFT) is investigated for a wide range of model parameters including the parameter m representing the chain length and the thermodynamic temperature T and pressure p. This approach is based upon the first-order thermodynamic perturbation theory for chain molecules developed by Wertheim [M. S. Wertheim, J. Stat. Phys. 35, 19 (1984); ibid. 42, 459 (1986)] and Chapman et al. [G. Jackson, W. G. Chapman, and K. E. Gubbins, Mol. Phys. 65, 1 (1988); W. G. Chapman, G. Jackson, and K. E. Gubbins, ibid. 65, 1057 (1988)] and includes dispersion interactions via the second-order perturbation theory of Barker and Henderson [J. A. Barker and D. Henderson, J. Chem. Phys. 47, 4714 (1967)]. We systematically study a hierarchy of models which are based on the PC-SAFT approach using analytical model calculations and Monte Carlo simulations. For one-component systems we find that the analytical model in contrast with the simulation results exhibits two phase-separation regions in addition to the common gas-liquid coexistence region: One phase separation occurs at high density and low temperature. The second demixing takes place at low density and high temperature where usually the ideal-gas phase is expected in the phase diagram. These phenomena, which are referred to as "liquid-liquid" and "gas-gas" equilibria, give rise to multiple critical points in one-component systems, as well as to critical end points and equilibria of three fluid phases, which can usually be found in multicomponent mixtures only. Furthermore, it is shown that the liquid-liquid demixing in this model is not a consequence of a "softened" repulsive interaction as assumed in the theoretical derivation of the model. Experimental data for the melt density of polybutadiene with molecular mass Mw=45,000 gmol are correlated here using the PC-SAFT equation. It is shown that the discrepancies in modeling the polymer density at ambient temperature and high pressure can be traced back to the liquid-liquid phase separation predicted by the equation of state at low temperatures. This investigation provides a basis for understanding possible inaccuracies or even unexpected phase behavior which can occur in engineering applications of the PC-SAFT model aiming at predicting properties of macromolecular substances.

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PubMed2004

Polymer nanodroplets forming liquid bridges in chemically structured slit pores: a computer simulation.

Using a coarse-grained bead-spring model of flexible polymer chains, the structure of a polymeric nanodroplet adsorbed on a chemically decorated flat wall is investigated by means of molecular dynamics simulation. We consider sessile drops on a lyophilic (attractive for the monomers) region of circular shape with radius R(D) while the remaining part of the substrate is lyophobic. The variation of the droplet shape, including its contact angle, with R(D) is studied, and the density profiles across these droplets also are obtained. In addition, the interaction of droplets adsorbed on two walls forming a slit pore with two lyophilic circular regions just opposite of one another is investigated, paying attention to the formation of a liquid bridge between both walls. A central result of our study is the measurement of the force between the two substrate walls at varying wall separation as well as the kinetics of droplet merging. Our results are compared to various phenomenological theories developed for liquid droplets of mesoscopic rather than nanoscopic size.

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PubMed2004

Polymer translocation through a nanopore induced by adsorption: Monte Carlo simulation of a coarse-grained model.

Dynamic Monte Carlo simulation of a bead-spring model of flexible macromolecules threading through a very narrow pore in a very thin rigid membrane are presented, assuming at the cis side of the membrane a purely repulsive monomer-wall interaction, while the trans side is attractive. Two choices of monomer-wall attraction epsilon are considered, one choice is slightly below and the other slightly above the "mushroom to pancake" adsorption threshold epsilon(c) for an infinitely long chain. Studying chain lengths N=32, 64, 128, and 256 and varying the number of monomers N(trans) (time t=0) that have already passed the pore when the simulation started, over a wide range, we find for epsilon epsilon(c) a finite number N(trans)(t=0) suffices that the translocation probability is close to unity. In the case epsilon epsilon(c), we find that the translocation time scales as tau proportional, variant N(1.65+/-0.08). We suggest a tentative scaling explanation for this result. Also the distribution of translocation times is obtained and discussed.

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PubMed2004

Stability of thin polymer films: influence of solvents.

The interface and surface properties and the wetting behavior of polymer-solvent mixtures are investigated using Monte Carlo simulations and self-consistent field calculations. We carry out Monte Carlo simulations in the framework of a coarse-grained bead-spring model using short chains (oligomers) of N(P)=5 beads and a monomeric solvent, N(S)=1. The self-consistent field calculations are based on a simple phenomenological equation of state for compressible binary mixtures and we employ Gaussian chain model. The bulk behavior of the polymer-solvent mixture belongs to type III in the classification of van Konynenburg and Scott [Phil. Trans. R. Soc. London, Ser. A 298, 495 (1980)]. It is characterized by a triple line on which the polymer-liquid coexists with solvent-vapor and a solvent-rich liquid. The solvent is not homogeneously distributed across the dense polymer film but tends to accumulate at the surface and the polymer-vapor interface. This solvent enrichment at the interface and surface becomes more pronounced upon increasing the vapor pressure and alters the surface and interface tensions. This effect gives rise to a nonmonotonic dependence of the contact angle on the vapor pressure and one might observe reentrant wetting. The results of the Monte Carlo simulations and the self-consistent field calculations qualitatively agree. The profiles of drops are investigated by Monte Carlo simulations and a pronounced solvent enrichment is observed at the wedge formed by the substrate and the liquid-vapor interface at the three-phase contact line.

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PubMed2004

The evaporation/condensation transition of liquid droplets.

The condensation of a supersaturated vapor enclosed in a finite system is considered. A phenomenological analysis reveals that the vapor is found to be stable at densities well above coexistence. The system size at which the supersaturated vapor condenses into a droplet is found to be governed by a typical length scale which depends on the coexistence densities, temperature and surface tension. When fluctuations are neglected, the chemical potential is seen to show a discontinuity at an effective spinodal point, where the inhomogeneous state becomes more stable than the homogeneous state. If fluctuations are taken into account, the transition is rounded, but the slope of the chemical potential versus density isotherm develops a discontinuity in the thermodynamic limit. In order to test the theoretical predictions, we perform a simulation study of droplet condensation for a Lennard-Jones fluid and obtain loops in the chemical potential versus density and pressure. By computing probability distributions for the cluster size, chemical potential, and internal energy, we confirm that the effective spinodal point may be identified with the occurrence of a first order phase transition, resulting in the condensation of a droplet. An accurate equation of state is employed in order to estimate the droplet size and the coexisting vapor density and good quantitative agreement with the simulation data is obtained. The results highlight the need of an accurate equation of state data for the Laplace equation to have predictive power.

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PubMed2004

Analysis of the phase transitions in alkyl-mica by density and pressure profiles.

In a previous work [Heinz, Castelijns, and Suter, J. Am. Chem. Soc. 115, 9500 (2003)], we developed an accurate force field and simulated the phase transitions in C18-mica (octadecyltrimethylammonium-mica) as well as the absence of such transitions in 2C18-mica (dioctadecyldimethylammonium-mica) between room temperature and 100 degrees C. Here we analyze (i) average z coordinates of the carbon atoms and interdigitation of the hydrocarbon bilayers, (ii) density profiles, and (iii) pressure profiles of the structures along all Cartesian axes. In C18-mica, the standard deviation in the z coordinate for the chain atoms is high and more than doubles in the disordered phase. The order-disorder transition is accompanied by a change in the orientation of the ammonium head group, as well as decreasing tensile and shear stress in the disordered phase. In 2C18-mica, the standard deviation in the z coordinate for the chain atoms is low and does not increase remarkably on heating. The backbones display a highly regular structure, which is slightly obscured by rotations in the C18 backbones and minor head group displacements at 100 degrees C. Close contacts between the bulky head groups with sidearms cause significant local pressure which is in part not relieved at 100 degrees C. An increase of the basal-plane spacing at higher temperature is found in both systems due to larger separation between the two hydrocarbon layers and an increased z spacing between adjacent chain atoms (=decreased tilt of the chains relative to the surface normal), and, in C18-mica only, a stronger upward orientation of the C18 chain at the ammonium head group. The likelihood for chain interdigitation between the two hydrocarbon layers is 24%-30% for C18-mica, and 65%-26% for 2C18-mica (for 20-100 degrees C).

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PubMed2004

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation.

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.

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PubMed2002

Surface-directed phase separation with off-critical composition: analytical and numerical results.

We study the interplay of wetting and phase separation in an unstable binary mixture (AB) with off-critical composition, placed in contact with a surface which prefers the component A. We consider surface potentials V(z) approximately z(-n), where z is the distance from the surface, and present analytical arguments and detailed numerical results to elucidate wetting-layer kinetics for arbitrary mixture compositions. If the preferred component is the minority phase, the wetting-layer thickness exhibits a potential-specific behavior at early times tau, R1 approximately tau(1/(n+2)), before crossing over to the universal growth law, R1 approximately tau(1/3). On the other hand, if the preferred component is the majority phase, there is a crossover from potential-specific growth (as before) to a slower growth regime.

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PubMed2002

Dynamics of sodium in sodium disilicate: channel relaxation and sodium diffusion.

We use molecular-dynamics computer simulations to study the dynamics of amorphous (Na2O)2(SiO2). We find that the Na ions move in channels embedded in a SiO2 matrix. The characteristic distance between these channels gives rise to a prepeak in the structure factor at q approximately equal to 0.95 A(-1). The dynamics of sodium is given by a fast process which can be seen in the incoherent scattering function and a slow process which is seen in the coherent function. The relaxation time of the latter coincides with the alpha-relaxation time of the matrix. The Kohlrausch exponent of the fast process for q>1.6 A(-1) is the same as the von Schweidler exponent for the slow one. Thus the two processes are closely related.

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