Biomedical subjects

Peter T Cummings

Publications and source records attributed to Peter T Cummings.

26 records · Page 2Linked to original sources

PubMed2005

From dimer to condensed phases at extreme conditions: accurate predictions of the properties of water by a Gaussian charge polarizable model.

Water exhibits many unusual properties that are essential for the existence of life. Water completely changes its character from ambient to supercritical conditions in a way that makes it possible to sustain life at extreme conditions, leading to conjectures that life may have originated in deep-sea vents. Molecular simulation can be very useful in exploring biological and chemical systems, particularly at extreme conditions for which experiments are either difficult or impossible; however this scenario entails an accurate molecular model for water applicable over a wide range of state conditions. Here, we present a Gaussian charge polarizable model (GCPM) based on the model developed earlier by Chialvo and Cummings [Fluid Phase Equilib. 150, 73 (1998)] which is, to our knowledge, the first that satisfies the water monomer and dimer properties, and simultaneously yields very accurate predictions of dielectric, structural, vapor-liquid equilibria, and transport properties, over the entire fluid range. This model would be appropriate for simulating biological and chemical systems at both ambient and extreme conditions. The particularity of the GCPM model is the use of Gaussian distributions instead of points to represent the partial charges on the water molecules. These charge distributions combined with a dipole polarizability and a Buckingham exp-6 potential are found to play a crucial role for the successful and simultaneous predictions of a variety of water properties. This work not only aims at presenting an accurate model for water, but also at proposing strategies to develop classical accurate models for the predictions of structural, dynamic, and thermodynamic properties.

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PubMed2005

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

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PubMed2005

Fluidity of hydration layers nanoconfined between mica surfaces.

We perform molecular dynamics simulations to investigate the shear dynamics of hydration water nanoconfined between two mica surfaces at 1 bar pressure and 298 K. Newtonian plateaus of shear viscosity comparable to the bulk value for different hydration layers D=0.92-2.44 nm are obtained. The origin of this persistent fluidity of the confined aqueous system is found to be closely associated with the rotational dynamics of water molecules, accompanied by fast translational diffusion under this confinement.

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PubMed2004

Equation of state and liquid-vapor equilibria of one- and two-Yukawa hard-sphere chain fluids: theory and simulation.

The accuracy of several theories for the thermodynamic properties of the Yukawa hard-sphere chain fluid are studied. In particular, we consider the polymer mean spherical approximation (PMSA), the dimer version of thermodynamic perturbation theory (TPTD), and the statistical associating fluid theory for potentials of variable attractive range (SAFT-VR). Since the original version of SAFT-VR for Yukawa fluids is restricted to the case of one-Yukawa tail, we have extended SAFT-VR to treat chain fluids with two-Yukawa tails. The predictions of these theories are compared with Monte Carlo (MC) simulation data for the pressure and phase behavior of the chain fluid of different length with one- and two-Yukawa tails. We find that overall the PMSA and TPTD give more accurate predictions than SAFT-VR, and that the PMSA is slightly more accurate than TPTD.

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PubMed2004

Phase coexistence in polydisperse charged hard-sphere fluids: mean spherical approximation.

Taking advantage of the availability of the analytic solution of the mean spherical approximation for a mixture of charged hard spheres with an arbitrary number of components we show that the polydisperse fluid mixture of charged hard spheres belongs to the class of truncatable free energy models, i.e., to those systems where the thermodynamic properties can be represented by a finite number of (generalized) moments of the distribution function that characterizes the mixture. Thus, the formally infinitely many equations that determine the parameters of the two coexisting phases can be mapped onto a system of coupled nonlinear equations in these moments. We present the formalism and demonstrate the power of this approach for two systems; we calculate the full phase diagram in terms of cloud and shadow curves as well as binodals and discuss the distribution functions of the coexisting daughter phases and their charge distributions.

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PubMed2003

Cell balance equation for chemotactic bacteria with a biphasic tumbling frequency.

Alt's three-dimensional cell balance equation characterizing the chemotactic bacteria was analyzed under the presence of one-dimensional spatial chemoattractant gradients. Our work differs from that of others who have developed rather general models for chemotaxis in the use of a non-smooth anisotropic tumbling frequency function that responds biphasically to the combined temporal and spatial chemoattractant gradients. General three-dimensional expressions for the bacterial transport parameters were derived for chemotactic bacteria, followed by a perturbation analysis under the planar geometry. The bacterial random motility and chemotaxis were summarized by a motility tensor and a chemotactic velocity vector, respectively. The consequence of invoking the diffusion-approximation assumption and using intrinsic one-dimensional models with modified cellular swimming speeds was investigated by numerical simulations. Characterizing the bacterial random orientation after tumbles by a turn angle probability distribution function, we found that only the first-order angular moment of this turn angle probability distribution is important in influencing the bacterial long-term transport.

Anisotropy↗

PubMed2003

Molecular simulations of liquid-liquid interfacial properties: water-n-alkane and water-methanol-n-alkane systems.

Direct molecular dynamics simulations of the liquid-liquid interface of water-n-alkane and water-methanol-n-alkane systems have been performed in order to study the interfacial properties of these systems. The simulations were carried out using the NERD revised force field of Nath et al. for the n-alkanes, the simple point charge extended model for water, and the optimized potential for liquid simulations model for methanol. In order to validate the model employed in this work for the n-alkanes we calculated the coexisting densities, surface tension, and thickness of the interface for pure n-pentane. For all the systems studied the interfacial tension and thickness were calculated at 298.15 K. Our results show that, by adjusting the number of molecules to reproduce the liquid densities in the direct simulation method of the liquid-liquid interface in multicomponent systems, we are able to reproduce available experimental data for interfacial tension. The interfacial thickness is underpredicted and a constant negative deviation of approximately 2.5 A from the experimental data is usually observed. We find that methanol acts like surfactant when it is added to the water-n-alkane mixtures, reducing the interfacial tension of the liquid-liquid ternary system. The interfacial tension results agree quantitatively well for the range of concentrations of methanol studied.

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PubMed2002

Comparison of nonequilibrium molecular dynamics with experimental measurements in the nonlinear shear-thinning regime.

Nonequilibrium molecular dynamics of a low-molecular-weight fluid (squalane) are compared with experimental measurements in both the linear (Newtonian) and nonlinear (non-Newtonian) regimes. The experimental and simulation data are shown to follow the same time-temperature superposition master curve. This represents the first comparison of the nonlinear rheology predicted by nonequilibrium molecular dynamics with experiment, and is thus the first experimental test of nonequilibrium molecular dynamics simulations in the nonlinear regime.

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