Biomedical subjects

D G Vlachos

Publications and source records attributed to D G Vlachos.

10 recordsLinked to original sources

PubMed2006

Potential of mean force for tetramethylammonium binding to cagelike oligosilicates in aqueous solution.

We have carried out free energy calculations to compute the potential of mean force for the cagelike silicate polyion-TMA+ cation ion pair interaction in aqueous solution. We also have studied solvent reorganization-related entropic effects. We conclude that the organocations, as opposed to, for example, alkali-metal ions, play a pivotal role in reorganizing the solvent around the cagelike silicates in a manner conducive to the formation of heteronetwork clathrates that are stable both thermodynamically and kinetically. In the case of stable cagelike polysilicate anions, this solvent reorganization correlates with entropic losses. We also infer that transient cagelike polysilicate species, that may indeed form but participate in floppy clathrates, eventually have to give way to cagelike polysilicates that lead to more rigid structures.

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PubMed2005

The role of molecular interactions and interfaces in diffusion: transport diffusivity and evaluation of the Darken approximation.

Kinetic Monte Carlo (KMC) simulations are carried out to directly study diffusion of benzene through thin (37-100 nm) NaX zeolite membranes under a gradient in chemical potential. Nonlinearities in adsorbate loading near the membrane boundaries are shown to arise from the difference in adsorbate density between the zeolite and adjacent fluid phase. Direct extraction of the transport diffusivity from gradient KMC simulations enables testing of the Darken approximation. This rigorous approach reveals limitations of the Darken approximation and, for the first time, the potentially complex nonunique functionality and multiplicity of the transport diffusivity for strongly interacting adsorbates. In the companion paper we explore these nonlinear interfacial effects in the context of permeation through both single-crystal and polycrystalline membranes.

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PubMed2005

The role of molecular interactions and interfaces in diffusion: permeation through single-crystal and polycrystalline microporous membranes.

In this second paper of a two part series, we investigate the implications of the interfacial phenomenon, caused by adsorbate-adsorbate interactions coupled with the difference in adsorbate density between the zeolite and the gas phase, upon benzene permeation through single-crystal and polycrystalline microporous NaX membranes. The high flux predicted for thin single-crystal membranes reveals that substantially enhanced flux should be expected in submicron films. Simulations also indicate that the standard local equilibrium assumption made for larger scale membranes is inapplicable at the submicron scale associated with nanometer size grains of thin and/or polycrystalline membranes. Apparent activation energies predicted for benzene permeation through NaX membranes via kinetic Monte Carlo (KMC) simulations are in good agreement with laboratory experiments. The simulations also uncover temperature-dependent flux pathways leading to non-Arrhenius behavior observed experimentally. The failure of the Darken approximation, especially in the presence of the interfacial phenomenon, leads to a substantial overprediction of the flux. Simulations of polycrystalline membranes suggest that this same interfacial phenomenon leads to resistance that can reduce flux by an order of a magnitude with only moderate polycrystallinity.

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PubMed2005

Overcoming stiffness in stochastic simulation stemming from partial equilibrium: a multiscale Monte Carlo algorithm.

In this paper the problem of stiffness in stochastic simulation of singularly perturbed systems is discussed. Such stiffness arises often from partial equilibrium or quasi-steady-state type of conditions. A multiscale Monte Carlo method is discussed that first assesses whether partial equilibrium is established using a simple criterion. The exact stochastic simulation algorithm (SSA) is next employed to sample among fast reactions over short time intervals (microscopic time steps) in order to compute numerically the proper probability distribution function for sampling the slow reactions. Subsequently, the SSA is used to sample among slow reactions and advance the time by large (macroscopic) time steps. Numerical examples indicate that not only long times can be simulated but also fluctuations are properly captured and substantial computational savings result.

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PubMed2005

Hierarchical multiscale mechanism development for methane partial oxidation and reforming and for thermal decomposition of oxygenates on Rh.

A thermodynamically consistent C1 microkinetic model is developed for methane partial oxidation and reforming and for oxygenate (methanol and formaldehyde) decomposition on Rh via a hierarchical multiscale methodology. Sensitivity analysis is employed to identify the important parameters of the semiempirical unity bond index quadratic exponential potential (UBI-QEP) method and these parameters are refined using quantum mechanical density functional theory. With adjustment of only two pre-exponentials in the CH4 oxidation subset, the C1 mechanism captures a multitude of catalytic partial oxidation (CPOX) and reforming experimental data as well as thermal decomposition of methanol and formaldehyde. We validate the microkinetic model against high-pressure, spatially resolved CPOX experimental data. Distinct oxidation and reforming zones are predicted to exist, in agreement with experiments, suggesting that hydrogen is produced from reforming of methane by H2O formed in the oxidation zone. CO is produced catalytically by partial oxidation up to moderately high pressures, with water-gas shift taking place in the gas-phase at sufficiently high pressures resulting in reduction of CO selectivity.

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PubMed2005

Molecular valves actuated by intermolecular forces.

Phase behavior in nanostructured thin films under a gradient in chemical potential is studied via kinetic Monte Carlo simulation. Switching between saturated, partially saturated, and unsaturated states drives precipitous changes in permeation. This phenomenon could render nanostructured thin films as molecular valves, where adsorbate-adsorbate forces actuate the flow of molecules.

Computer Simulation↗

PubMed2005

Molecular dynamics studies on the role of tetramethylammonium cations in the stability of the silica octamers Si8O20(8-) in solution.

The stability of silica octamers, Si(8) observed in tetramethylammonium (TMA) solutions by Kinrade et al. is investigated in connection with the TMA concentration by performing equilibrium molecular dynamics simulations of Si(8)-TMA-water mixture at two concentrations. At the experimental concentration at which the silica octamers have been observed spectroscopically, we find that, on the average, six TMA molecules surround the silica octamer, coordinated so that each cation occupies a face of the cubic octamer. We also find that upon TMA adsorption, water molecules associated with the siloxane oxygens leave the silica surface, whereas the hydrogen-bond network of the silanol oxygens with water molecules remains intact. No TMA adsorption is observed at the concentration at which the octamers have not been observed.

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PubMed2005

Molecular sieve valves driven by adsorbate-adsorbate interactions: hysteresis in permeation of microporous membranes.

A recently derived mesoscopic framework describing activated micropore diffusion is employed to explore system criticality in microporous membranes under nonequilibrium conditions. Rapid exploration of parameter space, possible with this continuum framework, elucidates a novel temperature-induced ignition and extinction of the molecular flux under a macroscopic gradient in pressure (chemical potential). Deviation from equilibrium like phase behavior (i.e., shifting and narrowing of phase envelopes and double hysteresis) derives from asymmetry of the coupled boundaries of the nonequilibrium membrane. We confirm this new phase behavior, akin to "opening" and "closing" of a molecular valve, via gradient kinetic Monte Carlo simulations of thin one-dimensional and three-dimensional systems. The heat of adsorption, strength of adsorbate-adsorbate intermolecular forces, and chemical potential gradient are all shown to control 'valve' actuation, suggesting potential implications in chemical sensing and novel diffusion control.

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PubMed2005

Spatially adaptive grand canonical ensemble Monte Carlo simulations.

A spatially adaptive Monte Carlo method is introduced directly from the underlying microscopic mechanisms, which satisfies detailed balance, gives the correct noise, and describes accurately dynamic and equilibrium states for adsorption-desorption (grand canonical ensemble) processes. It enables simulations of large scales while capturing sharp gradients with molecular resolution at significantly reduced computational cost. A posteriori estimates, in the sense used in finite-elements methods, are developed for assessing errors (information loss) in coarse-graining and guiding mesh generation.

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PubMed2004

Bifurcation analysis of Liesegang ring pattern formation.

Bifurcation analysis is introduced to a prototype Liesegang ring (LR) model to explain pattern formation as an instability of a propagating plane reaction front. A theoretical criterion for the onset of patterning is derived and numerically tested. The uneven spacing law of LR bands is explained as a consequence of the time varying velocity of the moving reaction front. Suggestions for controlling pattern formation are provided.

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