Showing papers by "Peter T. Cummings published in 1998"
TL;DR: In this article, two sets of intermolecular potentials for a united atom model of linear perfluorinated alkanes in their fluid states have been proposed, and the critical densities are slightly too high for one model and slightly too low for the other.
94 citations
TL;DR: In the last 25 years, nonequilibrium molecular dynamics (NEMD) has developed from a largely empirical molecular simulation methodology based on reproducing planar Couette flow in brute force fashion to a fully developed subfield of molecular simulation, underpinned rigorously by linear and nonlinear response theory as discussed by the authors.
86 citations
TL;DR: In this paper, the performance of free-energy perturbation methods when applied to compute the chemical potential of the Lennard-Jones model by Monte Carlo simulation was examined, and it was shown that any single- or multi-stage approach that incorporates a ''deletion'' component shows greatly diminished accuracy and precision when compared to its ''insertion'' counterpart.
81 citations
TL;DR: In this article, new developments in the polarizable water model consisting of smeared charges and a self-consistent point dipole polarizability were discussed. But the structural and polarization results at ambient and a supercritical conditions with those obtained previously with the corresponding simple point charges counterpart were compared.
71 citations
TL;DR: It is proved that for shallow attractant gradients the lumped integrals involving the tumbling probability frequency distribution and bacterial density distribution in the $\theta$ direction can be explicitly expressed as a product of three quantities: the mean tumbling frequency, the bacterial subpopulation density, and a reversal probability.
Abstract: The cell balance equations of Alt are rigorously studied and perturbatively expanded into forms similar to Segel's one-dimensional phenomenological cell balance equations by considering the simplifying case of bacterial density possessing symmetry in the x and y directions responding to an attractant gradient present only in the z direction. We prove that for shallow attractant gradients the lumped integrals involving the tumbling probability frequency distribution and bacterial density distribution in the $\theta$ direction can be explicitly expressed as a product of three quantities: the mean tumbling frequency, the bacterial subpopulation density, and a reversal probability. We also derive expressions for the bacterial net flux in the Fickian form from which two macroscopic transport parameters, the random motility coefficient and the chemotactic velocity, are explicitly related to individual cell properties and chemical gradients.
58 citations
TL;DR: In this article, molecular dynamics calculations of the ionic mobility and limiting conductance of NaCl in supercritical water as a function of density along an isotherm 5% above the critical temperature were performed.
52 citations
TL;DR: In this paper, the authors present the result of long molecular dynamics simulation calculations of the shear viscosity of liquid n-decane and n-hexadecane using the Green-Kubo integration method.
Abstract: This short commentary presents the result of long molecular dynamics simulation calculations of the shear viscosity of liquid n-decane and n-hexadecane using the Green-Kubo integration method. The relaxation time of the stress-stress correlation function is compared with those of rotation and diffusion. The rotational and diffusional relaxation times, which are easy to calculate, provide useful guides for the required simulation time in viscosity calculations. Also, the computational time required for viscosity calculations of these systems by the Green-Kubo method is compared with the time required for previous non-equilibrium molecular dynamics calculations of the same systems. The method of choice for a particular calculation is determined largely by the properties of interest, since the efficiencies of the two methods are comparable for calculation of the zero strain rate viscosity.
48 citations
TL;DR: In this article, the relationship between the molecular architecture and the viscous behavior of liquid alkanes has been investigated using massively parallel supercomputers and an efficient parallel algorithm, and the authors have carried out systematic studies of the rheological properties of a variety of model liquid alkane ranging from linear to singly branched and multiplybranched alkanes.
Abstract: Liquid alkanes in the molecular weight range of C20–C40 are the main constituents of lubricant basestocks, and their rheological properties are therefore of great concern in industrial lubricant applications Using massively parallel supercomputers and an efficient parallel algorithm, we have carried out systematic studies of the rheological properties of a variety of model liquid alkanes ranging from linear to singly branched and multiply branched alkanes We aim to elucidate the relationship between the molecular architecture and the viscous behavior Nonequilibrium molecular dynamics simulations have been carried out for n-decane (C10H22), n-hexadecane (C16H34), n-tetracosane (C24H50), 10-n-hexylnonadecane (C25H52), and squalane (2, 6, 10, 15, 19, 23-hexamethyltetracosane, C30H62) At a high strain rate, the viscosity shows a power-law shear thinning behavior over several orders of magnitude in strain rate, with exponents ranging from −033 to −059 This power-law shear thinning is shown to be closely related to the ordering of the molecules The molecular architecture is shown to have a significant influence on the power-law exponent At a low strain rate, the viscosity behavior changes to a Newtonian plateau, whose accurate determination has been elusive in previous studies The molecular order in this regime is essentially that of the equilibrium system, a signature of the linear response The Newtonian plateau is verified by independent equilibrium molecular dynamics simulations using the Green–Kubo method The reliable determination of the Newtonian viscosity from non-equilibrium molecular simulation permits us to calculate the viscosity index for squalane The viscosity index is a widely used property to characterize the lubricant's temperature performance, and our studies represent the first approach towards its determination by molecular simulation
46 citations
TL;DR: In this article, a statistical analysis of the solvation effects on the kinetic rate constants of reactions in near and supercritical solvents is presented to understand the experimental findings regarding the thermodynamic pressure effects.
Abstract: A statistical mechanical analysis of the solvation effects on the kinetic rate constants of reactions in near and supercritical solvents is presented to understand the experimental findings regarding the thermodynamic pressure effects. This is an extension of the solvation formalism of Chialvo and Cummings to the analysis of the microscopic basis for the macroscopic pressure and temperature effects on the kinetic rate constants of reactions conducted in the compressible region of the solvent phase diagram. This analysis is illustrated with integral equations calculations involving Lennard–Jones infinitely dilute quaternary systems to describe the species in solution during the reaction of triplet benzophenone (3BP) with a cosolvent (either O2 or 1,4-cyclohexadiene) in supercritical CO2 along the supercritical isotherms Tr = 1.01 and 1.06. The role of the species molecular asymmetries and consequently their solvation behavior in determining the thermodynamic pressure and temperature effects on the kinetic rate constant of reactions at near-critical conditions are discussed.
40 citations
TL;DR: For three decades, molecular models for water, nature's most important liquid, have been developed and refined by fitting to structure measured by neutron scattering as discussed by the authors, leading to reevaluation of water structure at normal conditions.
Abstract: For three decades, molecular models for water, nature's most important liquid, have been developed and refined by fitting to structure measured by neutron scattering. The decade-old widely accepted structure of water at room temperature and pressure was recently revised as a byproduct of attempts to understand the structure of high-temperature/high-pressure water for which, in a remarkable reversal of roles, molecular models successfully pinpointed inaccuracies in scattering data. Subsequent improvements in analyzing scattering data have led to reevaluation of water structure at normal conditions. This remarkable interplay between molecular modeling and experiment suggests molecular methods can effectively complement scattering experiments.
37 citations
TL;DR: A theoretical model provides explicit equations that explain how bacterial transport in cylindrical tubes of diameter 10 micrometers remains in the mode of a dimensionally reduced diffusion, and shifts to a wave motion when the tube diameter decreases to 6 micrometer.
TL;DR: In this paper, a simulation of infinitely dilute NaCl aqueous solutions is performed to study the Na{sup +}/Cl{sup -} ion pairing in a polarizable and a nonpolarizable solvent at supercritical conditions.
01 Jan 1998
TL;DR: This research group is pursuing a long-range research program aimed at understanding the role of bacterial motility and chemotaxis in in situ bioremediation processes, and developing mathematical models for bacterial migration based on microscopic and macroscopic level information.
Abstract: Many bacterial species exhibit chemotactic behavior, the ability to bias their otherwise random motion in the direction toward increasing concentrations of nutrients (referred to as attractants) or away from increasing concentrations of metabolites or compounds toxic to the bacteria, which may be indicators of unfavorable conditions (referred to as repellents) Chemotaxis can provide a competitive advantage for bacteria because in their natural habitats they are continually exposed to changing environmental conditions, and their survival depends on their capacity to respond favorably to adverse circumstances Because their small size (1 to 2 μn) and simple structure limits their ability to modify their surroundings, they respond either by migration to a more desirable location or by adaptation of their internal metabolic processes (Macnab 1980) Actaptation occurs naturally through genetic modification, but is relatively slow Chemotactic bacteria can clearly respond much more quickly by moving to a more favorable environment Chemotaxis has many practical applications and is known to play important roles in nitrogen fixation in plants, the pathogenesis of disease, and the bioremediation of contaminated aquifers This last case is of particular interest in our research group because it has been shown that bacteria are capable of degrading many toxic organic materials—including halogenated hydrocarbons via anaerobic degradation (Bouwer 1992; Harvey 1991)—and additionally respond chemotactically to these compounds We are pursuing a long-range research program aimed at understanding the role of bacterial motility and chemotaxis in in situ bioremediation processes The objectives are to quantitatively measure bacterial migration at the macroscopic level (both in the presence and absence of one or more attractant and/or repellent species), understand the basis for the macroscopic behavior by measuring and analyzing the motion of individual bacteria, develop mathematical models for bacterial migration based on microscopic and macroscopic level information, and use the model to predict bacterial migration in natural processes, with particular emphasis on in situ bioremedia- tion processes
TL;DR: In this article, molecular dynamics simulations of liquid alkanes, squalane and tetracosane, confined between moving walls to which butane chains are tethered, effectively screening the details of the wall.
TL;DR: Analytical derivations that convert the local angular turning probability density distribution into a global one and applications of the reduced global turning probability and its integrated moments to a three-dimensional cell balance equation in an axisymmetric system are presented.
TL;DR: In this paper, the analytical solution of the Ornstein-Zernike equation in the mean-spherical approximation for a Yukawa fluid and adhesive hard sphere Yukawa fluids with factorizable coefficients is used to derive a simple form for the thermodynamic properties for both mixtures.
Abstract: The analytical solution of the Ornstein-Zernike equation in the mean-spherical approximation for a Yukawa fluid and adhesive hard sphere Yukawa fluid with factorizable coefficients is used to derive a simple form for the thermodynamic properties for both mixtures. The second system contains an additional interaction. However, the general thermodynamic expressions were obtained in similar form for both systems. Some particular cases are discussed in terms of Γ, the principal parameter to be calculated for these systems. These results complement the recent work of Yasutomi, M., and Ginoza, M., 1996, Molec. Phys., 89, 1755.
TL;DR: In this paper, the authors presented results of NEMD simulations of planar Couette flow for normal decane and 4-propyl heptane molecules using the same models.
Abstract: In a recent paper [Mol. Sim., 16, 229 (1996)], we reported non-equilibrium molecular dynamics (NEMD) simulation of planar Couette flow for normal (n-butane) and isomeric butane (i-butane) molecules using two collapsed atom models and an atomistically detailed model. It was found that the collapsed atom models predict the viscosity of the n-butane quite well, but the viscosity of i-butane by those models is underpredicted. It was also found that the atomistically detailed model does not yield quantitative agreement with the viscosity of either the n-butane or i-butane, but it does have the one positive feature that the calculated viscosity of i-butane is higher than that of n-butane (branching increases viscosity) as observed experimentally. In the present paper, we present results of NEMD simulations of observed experimentally. In the present paper, we present results of NEMD simulations of planar Couette flow for normal decane and 4-propyl heptane molecules using the same models. The results sho...
TL;DR: In this article, an improved electrofreezing of supercooled water by applying oscillatory shear along with a homogeneous electric field in non-equilibrium molecular dynamics simulations of simple water models is presented.
TL;DR: The issues related to efficient implementation of molecular dynamics and Monte Carlo simulations on massively parallel supercomputers are described and the application of these methods to the prediction of the rheology of lubricants, polymer blends and high temperature aqueous electrolyte systems are described.
TL;DR: A suite of message-passing codes for classical molecular simulation of these industrially-important systems on the Intel Paragon was developed in this article, and some of the results can be found in Table 1.
Abstract: Advances in parallel supercomputing now make possible molecular-based engineering and science calculations that will soon revolutionize many technologies, such as those involving polymers and those involving aqueous electrolytes. We have developed a suite of message-passing codes for classical molecular simulation of these industrially-important systems on the Intel Paragon and summarize some of the results. Nonequilibrium, multiple time step molecular dynamics lets us investigate the rheology of molecular fluids. Chain molecule Monte Carlo simulations in the Gibbs ensemble permit calculation of phase equilibrium of long-chain molecular systems. Complementary equilibrium molecular dynamics yields fundamental insight into the technologically-important problem of liquid-liquid phase separation in polymer blends. Parallel codes for quaternion dynamics using techniques for handling long-range Coulombic forces allow study of ion pairing in supercritical aqueous electrolyte solutions.
28 Jun 1998
TL;DR: An innovative approach to combining research and curriculum development for the field of chemical engineering has the potential to define a new paradigm for instruction in rapidly-evolving fields such as molecular simulation, computational chemistry, biochemical engineering, and materials science.
Abstract: In this paper, we describe an innovative approach to combining research and curriculum development for the field of chemical engineering. The methodology has the potential to define a new paradigm for instruction in rapidly-evolving fields such as molecular simulation, computational chemistry, biochemical engineering, and materials science. Our immediate aim has been to initiate a World Wide Web (WWW)-based “textbook” on molecular simulation, and to introduce it into the graduate and undergraduate chemical engineering curricula at our respective institutions. The textbook will have the additional role of a refereed electronic journal that elaborates on important new developments and applications as they appear in the research literature, presenting such work in a manner suitable for class instruction and for self-paced learning. Our broader goal is to see that molecular simulation and molecular concepts in general are finely woven into the undergraduate and graduate chemical engineering curricula nationwide. The development of the text is funded by a grant from the Comined Research and Curriculum Development program of the National Science Foundation. The effort to develop the web text is partially the outgrowth of the establishment a Molecular Modeling Task Force within CACHE (Computer Aids for Chemical Engineers). CACHE, Inc. is a not-for-profit organization whose purpose is to promote cooperation among universities, industry, and government in the development and distribution of computer-related educational materials for the chemical engineering profession. More about CACHE activities can be learned from their WWW site http://www.cache.org/.
07 Nov 1998
TL;DR: The design strategy and performance analysis of a large scale scientific application, GEOCORE, for the prediction of 3D Protein structures, predicts small ensembles of native-like peptide conformations from amino acid sequences using a very simple energy function and an extensive conformational search process.
Abstract: We present here the design strategy and performance analysis of a large scale scientific application, for the prediction of 3D Protein structures. The unique challenges which will be investigated are the primary objectives of a reduction in wall clock run time through the parallelization process, and the production of an application capable of running and scaling to a massively parallel configuration (currently 1024 nodes of the Intel Paragon) reliably for many non-contiguous days of supercomputer time. Enough flexibility to be reconfigured for a number of different parallel architectures including the CRAY T3E and IBM SP2 was included through the use of MPI as the parallel software layer. The application, GEOCORE, predicts small ensembles of native-like peptide conformations from amino acid sequences. GEOCORE uses a very simple energy function and an extensive conformational search process. The serial program has been tested on around 20 small peptides and is shown to be capable of discriminating native from non-native structures.
01 Jun 1998
Abstract: 'The objective of this research program is to provide fundamental scientific information on the physical and chemical properties of solutes in aqueous solutions at high temperatures needed to assess and enhance the applicability of hydrothermal oxidation (HTO) to the remediation of DOE hazardous and mixed wastes. Potential limitations to the use of HTO technology include formation of deposits (scale) from precipitation of inorganic solutes in the waste, corrosion arising from formation of strong acids on oxidation of some organic compounds (e.g., chlorinated hydrocarbons), and unknown effects of fluid density and phase behavior at high temperatures. Focus areas for this project include measurements of the solubility and speciation of actinides and surrogates in model HTO process streams at high temperatures, and the experimental and theoretical development of equations of state for aqueous mixtures under HTO process conditions ranging above the critical temperature of water. A predictive level of understanding of the chemical and physical properties of HTO process streams is being developed through molecular-level simulations of aqueous solutions at high temperatures. Advances in fundamental understanding of phase behavior, density, and solute speciation at high temperatures and pressures contribute directly to the ultimate applicability of this process for the treatment of DOE hazardous and mixed wastes. Research in this project has been divided into individual tasks, with each contributing to a unified understanding of HTO processing problems related to the treatment of DOE wastes. This report summarizes progress attained after slightly less than two years of this three-year project.'