Biomedical subjects

Keith E Gubbins

Publications and source records attributed to Keith E Gubbins.

15 recordsLinked to original sources

PubMed2006

Molecular modeling of porous carbons using the hybrid reverse Monte Carlo method.

We apply a simulation protocol based on the reverse Monte Carlo (RMC) method, which incorporates an energy constraint, to model porous carbons. This method is called hybrid reverse Monte Carlo (HRMC), since it combines the features of the Monte Carlo and reverse Monte Carlo methods. The use of the energy constraint term helps alleviate the problem of the presence of unrealistic features (such as three- and four-membered carbon rings), reported in previous RMC studies of carbons, and also correctly describes the local environment of carbon atoms. The HRMC protocol is used to develop molecular models of saccharose-based porous carbons in which hydrogen atoms are taken into account explicitly in addition to the carbon atoms. We find that the model reproduces the experimental pair correlation function with good accuracy. The local structure differs from that obtained with a previous model (Pikunic, J.; Clinard, C.; Cohaut, N.; Gubbins, K. E.; Guet, J. M.; Pellenq, R. J.-M.; Rannou, I.; Rouzaud, J. N. Langmuir 2003, 19 (20), 8565). We study the local structure by calculating the nearest neighbor distribution, bond angle distribution, and ring statistics.

Carbon↗

PubMed2006

Fast method for computing pore size distributions of model materials.

Recently developed atomistic models of highly disordered nanoporous materials offer hope for a much more realistic description of the pore morphology and topology in such materials; however, a factor limiting their application has been the computationally intensive characterization of the models, particularly determination of the pore size distribution. We report a new technique for fast computation of pore size distributions of model materials from knowledge of the molecular coordinates. The pore size distribution (PSD) is defined as the statistical distribution of the radius of the largest sphere that can be fitted inside a pore at a given point. Using constrained nonlinear optimization, we calculate the maximum radii of test particles at random points inside the pore cavity. The final pore size distribution is then obtained by sampling the test particle radii using Monte Carlo integration. The computation time depends on factors such as the number of atoms, the sampling resolution, and the desired accuracy. However, even for large systems, PSDs with very high accuracy (>99.9%) are obtained in less than 24 h on a 3 GHz Pentium IV processor. The technique is validated by applying it to model structures, whose pore size distributions are already known. We then apply this method to investigate the pore structures of several mesoporous silica models such as SBA-15 and mesostructured cellular foams.

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PubMed2006

Effect of confinement by porous carbons on the unimolecular decomposition of formaldehyde.

As part of an effort to understand the effect of confinement by porous carbons on chemical reactions, we have carried out density functional theory calculations on the unimolecular decomposition of formaldehyde within graphitic carbons. Our results show that the interactions with the carbon walls result in a lowering of the reaction barrier. For larger pores, there is also a shift of the equilibrium towards the formation of carbon monoxide and hydrogen at low temperatures. This trend is reversed for small pore sizes.

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PubMed2006

Mesoscale modeling of complex binary fluid mixtures: towards an atomistic foundation of effective potentials.

This paper is devoted to equilibrium molecular-dynamics (MD) simulations of a fully atomistic model of binary mixtures of water (component 1) and ethanol (component 2). We investigate ways to extract from these simulations effective, pairwise additive potentials suitable to describe the interactions between coarse-grained molecules (i.e., beads) in corresponding mesoscale dissipative particle-dynamics simulations. The fully atomistic model employed in MD simulations is mapped onto an implicit water model, where the internal degrees of freedom of ethanol and all the degrees of freedom of water are integrated out. This gives us an effective one-component system consisting only of ethanol beads. The effective interaction potential between a pair of ethanol beads, Phi(R), is approximated at three levels of sophistication. At the lowest one, we approximate Phi(R) by the potential of mean force between the centers of mass of two ethanol beads calculated in the fully atomistic MD simulations; at the second level, we take Phi(R) to be the potential linked to total and direct correlation functions in the hypernetted-chain closure of the Ornstein-Zernike equation. At the third level we approximate Phi(R) numerically by improving it iteratively through the Boltzmann inversion scheme. Our results indicate that the level-one approach works only at the lowest (8 wt %) concentration; the level-two approach works only up to intermediate ethanol concentrations (ca. 50 wt %). Only the Boltzmann inversion scheme works for all, up to the highest concentration considered (70 wt %).

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PubMed2006

Simulated water adsorption in chemically heterogeneous carbon nanotubes.

Grand canonical Monte Carlo simulations are used to study the adsorption of water in single-walled (10:10), (12:12), and (20:20) carbon nanotubes at 298 K. Water is represented by the extended simple point charge model and the carbon atoms as Lennard-Jones spheres. The nanotubes are decorated with different amounts of oxygenated sites, represented as carbonyl groups. In the absence of carbonyl groups the simulated isotherms are characterized by negligible amounts of water uptake at low pressures, sudden and complete pore filling once a threshold pressure is reached, and wide adsorption-desorption hysteresis loops. In the presence of a few carbonyl groups the simulated adsorption isotherms are characterized by pore filling at lower pressures and by narrower adsorption-desorption hysteresis loops compared to the results obtained in the absence of carbonyl groups. Our results show that the distribution of the carbonyl groups has a strong effect on the adsorption isotherms. For carbonyl groups localized in a narrow section the adsorption of water may be gradual because a cluster of adsorbed water forms at low pressures and grows as the pressure increases. For carbonyl groups distributed along the nanotube the adsorption isotherm is of type V.

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PubMed2006

Adsorption of simple gases in MCM-41 materials: the role of surface roughness.

This paper reports the development and testing of atomistic models of silica MCM-41 pores. Model A is a regular cylindrical pore having a constant section. Model B has a surface disorder that reproduces the morphological features of a pore obtained from an on-lattice simulation that mimics the synthesis process of MCM-41 materials. Both models are generated using a similar procedure, which consists of carving the pore out of an atomistic silica block. The differences between the two models are analyzed in terms of small angle neutron scattering spectra as well as adsorption isotherms and isosteric heat curves for Ar at 87 K and Xe at 195 K. As expected for capillary condensation in regular nanopores, the Ar and Xe adsorption/desorption cycles for model A exhibit a large hysteresis loop having a symmetrical shape, i.e., with parallel adsorption and desorption branches. The features of the adsorption isotherms for model B strongly depart from those observed for model A. Both the Ar and Xe adsorption branches for model B correspond to a quasicontinuous pore filling that involves coexistence within the pore of liquid bridges and gas nanobubbles. As in the case of model A, the Ar adsorption isotherm for model B exhibits a significant hysteresis loop; however, the shape of the loop is asymmetrical with a desorption branch much steeper than the adsorption branch. In contrast, the adsorption/desorption cycle for Xe in model B is quasicontinuous and quasireversible. Comparison with adsorption and neutron scattering experiments suggests that model B is too rough at the molecular scale but reproduces reasonably the surface disorder of real MCM-41 at larger length scales. In contrast, model A is smooth at small length scales in agreement with experiments but seems to be too ordered at larger length scales.

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PubMed2005

Modeling triblock surfactant-templated mesostructured cellular foams.

Lattice Monte Carlo simulations are used to understand the role of surfactant self-assembly in the synthesis of templated mesoporous materials with ultralarge pores. Our system consists of model triblock surfactants in the presence of oil, water, and inorganic oxide. Depending on the temperature and component concentrations, these systems phase separate, and the surfactant-rich phase forms structures such as cylinders, lamellae, and spheres ordered in repetitive arrangements. In the absence of oil, the structures are cylindrical with diameters of 100 A, but increasing oil concentration produces ultralarge spheres with diameters above 500 A. Our results closely resemble the cylinder to sphere transition associated with the synthesis of the mesostructured cellular foams (MCFs). Pore size distributions of our model structures are qualitatively comparable with the pore size distributions of MCFs obtained from adsorption experiments. We also observe an increase in average pore size with oil concentration, which is consistent with the experimental reportings.

Journal Article↗

PubMed2005

An experimental study of melting of CCl4 in carbon nanotubes.

We report dielectric relaxation spectroscopy measurements of the melting point of carbon tetrachloride confined within open-tip multi-walled carbon nanotubes with two different pore diameters, 4.0 and 2.8 nm. In both cases, a single transition temperature well above the bulk melting point was obtained for confined CCl4. These results contrast with what was obtained in our previous measurements using carbon nanotubes with a pore diameter of 5.0 nm, where multiple transition temperatures both above and below the bulk melting point of CCl4 were observed. Our experimental measurements are consistent with our recent molecular simulation results (F. R. Hung, B. Coasne, E. E. Santiso, K. E. Gubbins, F. R. Siperstein and M. Sliwinska-Bartkowiak, J. Chem. Phys., 2005, 122, 144706). Although the simulations overestimate the temperatures in which melting upon confinement occurs, both simulations and experiments suggest that all regions of adsorbate freeze at the same temperature, and that freezing occurs at higher temperatures upon reduction of the pore diameter.

Carbon Tetrachloride↗

PubMed2005

Argon and nitrogen adsorption in disordered nanoporous carbons: simulation and experiment.

We report experimental measurements of the isosteric heats of adsorption for argon and nitrogen in two microporous saccharose-based carbons, using a Tian-Calvet microcalorimeter. These data are used to test recently developed molecular models of these carbons, obtained by a constrained reverse Monte Carlo method. Grand canonical Monte Carlo simulation is used to calculate the adsorption isotherms and isosteric heats for these systems, and the results for the latter are compared to the experimental data. For argon, excellent quantitative agreement is obtained over the entire range of pore filling. In the case of nitrogen, very good agreement is obtained over the range of coverage 0.25 < or = gamma/gamma 0 < or = 0.85, but discrepancies are observed at lower and higher coverages. The discrepancy at low coverage may be due to the presence of oxygenated groups on the pore surfaces, which are not taken into account in the model. The differences at high coverage are believed to arise from the presence of a few mesopores, which again are not included in the model. Pair correlation functions (argon-carbon and argon-argon) are determined from the simulations and are discussed as a function of pore filling. Snapshots of the simulations are presented and provide a picture of the pore filling process.

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PubMed2005

Molecular modeling of freezing of simple fluids confined within carbon nanotubes.

We report Monte Carlo simulation results for freezing of Lennard-Jones carbon tetrachloride confined within model multiwalled carbon nanotubes of different diameters. The structure and thermodynamic stability of the confined phases, as well as the transition temperatures, were determined from parallel tempering grand canonical Monte Carlo simulations and free-energy calculations. The simulations show that the adsorbate forms concentric molecular layers that solidify into defective quasi-two-dimensional hexagonal crystals. Freezing in such concentric layers occurs via intermediate phases that show remnants of hexatic behavior, similar to the freezing mechanism observed for slit pores in previous works. The adsorbate molecules in the inner regions of the pore also exhibit changes in their properties upon reduction of temperature. The structural changes in the different regions of adsorbate occur at temperatures above or below the bulk freezing point, depending on pore diameter and distance of the adsorbate molecules from the pore wall. The simulations show evidence of a rich phase behavior in confinement; a number of phases, some of them inhomogeneous, were observed for the pore sizes considered. The multiple transition temperatures obtained from the simulations were found to be in good agreement with recent dielectric relaxation spectroscopy experiments for CCl(4) confined within multiwalled carbon nanotubes.

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PubMed2005

Cosurfactant and cosolvent effects on surfactant self-assembly in supercritical carbon dioxide.

The impact of alcohol additives on the self-assembly of surfactants in supercritical carbon dioxide is investigated using lattice Monte Carlo simulations. We observe that all studied (model) alcohols reduce the critical micelle concentration. The reduction is stronger the longer the hydrocarbon chain of the alcohol, and the higher the alcohol concentration. Short-chain alcohols are found to concentrate in the surfactant layer of the aggregates, replacing surfactant molecules and leading to a strong decrease of the aggregation number and a large increase of the number of aggregates. On the other hand, only a small number of alcohol molecules with longer chain length are found in the aggregates, leading to a slight increase in the aggregation number. However, structural properties such as size and density profiles of aggregates at the same aggregation number are not influenced markedly. Consequently, short-chain alcohols act as cosurfactants, directly influencing the properties of the aggregates, while alcohols with longer hydrocarbon chains work as cosolvents, altering the properties of the solvent. However, the transition between both extremes is gradual.

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PubMed2005

Vapor-liquid and vapor-liquid-liquid equilibria of carbon dioxide/n-perfluoroalkane/n-alkane ternary mixtures.

Perfluoroalkanes have numerous applications (e.g., in the medical field and the chemical industry), and their high affinity for carbon dioxide makes them attractive as surfactants and cosolvents. Although research in this area has grown in the past few years, very little phase-equilibrium data is available in the open literature for these systems. In this work, we present, for the first time, predictions of vapor-liquid and vapor-liquid-liquid equilibria of binary and ternary systems of carbon dioxide/n-perfluoroalkane/n-alkane. Our results are based on the SAFT-VR EOS (statistical associating fluid theory of variable range, equation of state), and we study the influence of temperature, pressure, composition, and chain length on the phase diagram. The predicted phase diagrams are based on temperature-independent binary interaction parameters, and no ternary parameters are introduced. Comparisons to the available experimental and molecular simulation data show that the predicted diagrams should provide a good representation of the phase equilibria.

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PubMed2004

Reaction ensemble molecular dynamics: direct simulation of the dynamic equilibrium properties of chemically reacting mixtures.

A molecular simulation method to study the dynamics of chemically reacting mixtures is presented. The method uses a combination of stochastic and dynamic simulation steps, allowing for the simulation of both thermodynamic and transport properties. The method couples a molecular dynamics simulation cell (termed dynamic cell) to a reaction mixture simulation cell (termed control cell) that is formulated upon the reaction ensemble Monte Carlo (RxMC) method, hence the term reaction ensemble molecular dynamics. Thermodynamic and transport properties are calculated in the dynamic cell by using a constant-temperature molecular dynamics simulation method. RxMC forward and reverse reaction steps are performed in the control cell only, while molecular dynamics steps are performed in both the dynamic cell and the control cell. The control cell, which acts as a sink and source reservoir, is maintained at reaction equilibrium conditions via the RxMC algorithm. The reaction ensemble molecular dynamics method is analogous to the grand canonical ensemble molecular dynamics technique, while using some elements of the osmotic molecular dynamics method, and so simulates conditions that directly relate to real, open systems. The accuracy and stability of the method is assessed by considering the ammonia synthesis reaction N2 +3 H2 <-->2N H3 . It is shown to be a viable method for predicting the effects of nonideal environments on the dynamic properties (particularly diffusion) as well as reaction equilibria for chemically reacting mixtures.

Journal Article↗

PubMed2004

Lattice Monte Carlo simulations of phase separation and micellization in supercritical CO2/surfactant systems: effect of CO2 density.

Lattice Monte Carlo simulations are used to study the effect of nonionic surfactant concentration and CO2 density on the micellization and phase equilibria of supercritical CO2/surfactant systems. The interaction parameter for carbon dioxide is obtained by matching the critical temperature of the model fluid with the experimental critical temperature. Various properties such as the critical micelle concentration and the size, shape, and structure ofmicelles are calculated, and the phase diagram in the surfactant concentration-CO2 density space is constructed. On increasing the CO2 density, we find an increase in the critical micelle concentration and a decrease in the micellar size; this is consistent with existing experimental results. The variation of the micellar shape and structure with CO2 density shows that the micelles are spherical and that the extension of the micellar core increases with increasing micellar size, while the extension of the micellar corona increases with increasing CO2 density. The predicted phase diagram is in qualitative agreement with experimental phase diagrams for nonionic surfactants in carbon dioxide.

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PubMed2002

Existence of a hexatic phase in porous media.

Molecular simulations for simple fluids in narrow slit-shaped carbon pores exhibit crystal-hexatic and hexatic-liquid transitions that are consistent with Kosterlitz-Thouless-Halperin-Nelson-Young theory. The temperature range over which the hexatic phase is stable is dramatically widened under confinement. Remarkably, the transitions, which are continuous for a single adsorbed layer, become weakly first order when the pore can accommodate two molecular layers. Nonlinear dielectric effect measurements for CCl4 and aniline in activated carbon fibers (pore width 1.4 nm) show divergence at these transitions, confirming the hexatic phase.

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