Biomedical subjects

Karl P Travis

Publications and source records attributed to Karl P Travis.

5 recordsLinked to original sources

PubMed2006

Effect of solvation and confinement on the trans-gauche isomerization reaction in n-butane.

The effect of solvation and confinement on the conformational equilibria and kinetics of n-butane is examined using molecular dynamics simulations of the bulk and confined fluids and compared to appropriately chosen reference states. Clear evidence for a solvent shift of the preferred conformation in bulk n-butane is found. At a temperature of 292 K and a density of 6.05 nm-3 a small solvent shift in favor of gauche is observed (similar to previously reported values), and the shift increases substantially with an increase in density to 8.28 nm-3. The rate of torsional interconversion from the trans to the gauche state, calculated using the relaxation function method, was found to increase with increasing temperature and density. The rate constants kTG and kGT have an Arrhenius temperature dependence yielding activation energies significantly lower than the trans-gauche and gauche-trans barrier heights in the torsional potential for a free molecule, depending on the density. In the confined phase, we considered the same densities as simulated in the bulk phase, and for four different values of the physical pore width (approximately 1.5-4.0 nm). At the high density, we find that the position of the trans-gauche equilibrium is displaced towards excess trans compared with the bulk phase, reflecting the confinement and interactions of the molecules with the pore wall. The isomerization rate is found to decrease with decreasing pore width. Again, we find that the kinetics obeys an Arrhenius rate law and the activation energy for the trans-gauche and gauche-trans interconversions is slightly smaller than that of the bulk fluid at the same density.

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PubMed2006

Configurational constant pressure molecular dynamics.

We propose two new algorithms for generating isothermal-isobaric molecular dynamics. The algorithms are based on an extended phase space dynamics where two extra degrees of freedom, representing the thermostat and the barostat, are included. These new methods adopt a totally different approach towards molecular dynamics simulation in the isothermal-isobaric ensemble. They are fully configurational in the sense that only the particle positions are required in the control of the system temperature and pressure. Following on from the works of Delhommelle and Evans [Mol. Phys., 99, 1825 (2001)] and of Braga and Travis [J. Chem. Phys., 123, 134101 (2005)] concerning configurational canonical dynamics, these new algorithms can be seen as a natural extension to the isothermal-isobaric ensemble. We have validated both of our new configurational isothermal-isobaric schemes by conducting molecular dynamics simulations of a Lennard-Jones fluid and comparing the static and dynamic properties for a single state point. We find that both schemes generate similar results compared with schemes which use kinetic temperature and pressure control. We have also monitored the response of the system to a series of isothermal compressions and isobaric quenches. We find that the configurational schemes performed at least as well as the kinetic based scheme in bringing the system temperature and pressure into line with the set point values of these variables. These new methods will potentially play a significant role in simulations where the calculation of the kinetic temperature and pressure can be problematic. A well known example resides in the field of nonequilibrium simulations where the kinetic temperature and pressure require a knowledge of the streaming velocity of the fluid in order to calculate the true peculiar velocities (or momenta) that enter into their definitions. These are completely avoided by using our configurational thermostats and barostats, since these are independent of momenta. By extending the analysis of Kusnezov et al. [Ann. Phys., 204, 155 (1990)] in order to derive a set of generalized Nose-Hoover equations of motion which can generate isothermal-isobaric dynamics in a number of different ways, we are able to show that both of our new configurational barostats and Hoover's kinetic isothermal-isobaric scheme are special cases of this more general set of equations. This generalization can be very powerful in generating constant pressure dynamics for a variety of systems.

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PubMed2005

A configurational temperature Nosé-Hoover thermostat.

We propose two new thermostats which can be employed in computer simulations to ensure that two different variants of the configurational temperature fluctuate around their equilibrium values. These new thermostats differ from one previously introduced by Delhommelle and Evans [Mol. Phys. 99, 1825 (2001)] in several important ways. First, our thermostats are derived in the same spirit as the Nosé-Hoover thermostat and therefore generate the canonical phase-space distribution. Second, our thermostats involve simpler equations of motion, which do not involve spatial gradients of the configurational temperature. They do not suffer from problems stemming from stiff equations of motion and furthermore, in large temperature perturbation simulations, the measured temperature follows the set-point temperature without any overshoot, and with good damping of oscillations. We show that both of our configurational thermostats are special cases of a more general set of Nosé-Hoover equations proposed by Kusnezov et al. [Ann. Phys. 204, 155 (1990)]. The new thermostats are expected to be highly useful in nonequilibrium simulations, particularly those characterized by spatial inhomogeneities. They should also find applicability in simulations involving large changes in temperature over small time scales, such as temperature quench molecular dynamics and radiation damage modeling.

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PubMed2005

A molecular dynamics study of nitric oxide in water: diffusion and structure.

We present molecular dynamics simulations of the diffusion coefficients and structure of water-nitric oxide mixtures at ambient (298 K) and in vivo (310 K) conditions. A two-site rigid-body molecular model with partial charges and a Lennard-Jones potential on both sites is proposed for nitric oxide and used in conjunction with the extended simple point-charge model for liquid water in our simulations. The diffusion coefficients obtained from the simulations are in good agreement with experimental data. The results from intermolecular partial pair functions show that under these thermodynamic conditions, the existence of nitric oxide in liquid water has little impact on the structure of water and the tendency to form H bonds between water molecules. We also find that it is unlikely that H bonds form between the hydrogen atoms in water and either the nitrogen or the oxygen atom on the nitric oxide at the temperatures and densities examined in this study. This study suggests that in low concentrations nitric oxide molecules exist as free molecules in liquid water rather than forming complexes with water molecules.

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PubMed2004

Viscosity of confined inhomogeneous nonequilibrium fluids.

We use the nonlocal linear hydrodynamic constitutive model, proposed by Evans and Morriss [Statistical Mechanics of Nonequilibrium Liquids (Academic, London, 1990)], for computing an effective spatially dependent shear viscosity of inhomogeneous nonequilibrium fluids. The model is applied to a simple atomic fluid undergoing planar Poiseuille flow in a confined channel of several atomic diameters width. We compare the spatially dependent viscosity with a local generalization of Newton's law of viscosity and the Navier-Stokes viscosity, both of which are known to suffer extreme inaccuracies for highly inhomogeneous systems. The nonlocal constitutive model calculates effective position dependent viscosities that are free from the notorious singularities experienced by applying the commonly used local constitutive model. It is simple, general, and has widespread applicability in nanofluidics where experimental measurement of position dependent transport coefficients is currently inaccessible. In principle the method can be used to predict approximate flow profiles of any arbitrary inhomogeneous system. We demonstrate this by predicting the flow profile for a simple fluid undergoing planar Couette flow in a confined channel of several atomic diameters width.

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