Biomedical subjects

Richard J Sadus

Publications and source records attributed to Richard J Sadus.

15 recordsLinked to original sources

PubMed2006

Relationships between three-body and two-body interactions in fluids and solids.

Molecular dynamics data are reported for two-body and three-body interactions in noble gases at densities covering the gas, liquid, and solid phases. The data indicate that simple relationships exist between three- and two-body interactions in both fluid and solid phases. The relationship for liquids has a simple density dependence with only one external parameter. In contrast, the solid phase relationship depends both on density and on the square of density and requires the evaluation of two parameters. The relationships are tested for both system-size and temperature dependences. The values of the relationship parameters are only sensitive to system size when a small number of atoms are involved. For 500 or more atoms, they remain nearly constant. The relationships are valid for both subcritical and slightly supercritical temperatures. A practical benefit of the relationships is that they enable the use of two-body intermolecular potentials for the prediction of the properties of real systems without the computational expense of three-body calculations.

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PubMed2006

Three-body interactions and solid-liquid phase equilibria: application of a molecular dynamics algorithm.

The effect of three-body interactions on the solid-liquid phase boundaries of argon, krypton, and xenon is investigated via a novel technique that combines both nonequilibrium and equilibrium molecular dynamics. The simulations involve the evaluation of two- and three-body forces using accurate two-body and three-body intermolecular potentials. The effect of three-body interactions is to substantially increase the coexistence pressure and to lower the densities of liquid and solid phases. Comparison with experiment indicates that three-body interactions are required to accurately determine the total pressure. In contrast to vapor-liquid phase equilibria, the relative contribution of three-body interactions to the freezing pressure exceeds the contribution of two-body interactions at all temperatures.

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PubMed2006

Influence of two-body and three-body interatomic forces on gas, liquid, and solid phases.

Accurate molecular dynamics simulations are reported which quantify the contributions of two- and three-body interactions in the gas, liquid, and solid phases of argon at both subcritical and supercritical conditions. The calculations use an accurate two-body potential in addition to contributions from three-body dispersion interactions from third-order triple-dipole interactions. The number dependence of three-body interactions is quantified, indicating that a system size of at least five hundred atoms is required for reliable calculations. The results indicate that, although the contribution of three-body interaction to the overall energy is small, three-body interactions significantly affect the pressure at which vapor-liquid and solid-liquid transitions are observed. In particular, three-body interactions substantially increase the pressure of the freezing point. Unlike two-body interactions, which vary with both density and temperature, for a given density, three-body interactions have a near-constant 'background' value irrespective of the temperature. Both two-body interactions and kinetic energy have an important role in vapor-liquid equilibria whereas solid-liquid equilibria are dominated by two-body interactions.

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PubMed2006

Dynamic and coordinating domain motions in the active subunits of the F1-ATPase molecular motor.

F1-ATPase is a rotary molecular motor crucial for various cellular functions. In F1-ATPase, the rotation of the gammadeltaepsilon subunits against the hexameric alpha(3)beta(3) subunits is highly coordinative, driven by ATP hydrolysis and structural changes at three beta subunits. However, the dynamical and coordinating structural transitions in the beta subunits are not fully understood at the molecular level. Here we examine structural transitions and domain motions in the active subunits of F1-ATPase via dynamical domain analysis of the alpha(3)beta(3)gammadeltaepsilon complex. The domain movement and hinge axes and bending residues have been identified and determined for various conformational changes of the beta-subunits. P-loop and the ATP-binding pocket are for the first time found to play essential mechanical functions additional to the catalytic roles. The cooperative conformational changes pertaining to the rotary mechanism of F1-ATPase appears to be more complex than Boyer's 'bi-site' activity. These findings provide unique molecular insights into dynamic and cooperative domain motions in F1-ATPase.

Adenosine Triphosphate↗

PubMed2006

Effect of three-body interactions on the vapor-liquid phase equilibria of binary fluid mixtures.

Gibbs-Duhem Monte Carlo simulations are reported for the vapor-liquid phase coexistence of binary argon+krypton mixtures at different temperatures. The calculations employ accurate two-body potentials in addition to contributions from three-body dispersion interactions resulting from third-order triple-dipole interactions. A comparison is made with experiment that illustrates the role of three-body interactions on the phase envelope. In all cases the simulations represent genuine predictions with input parameters obtained independently from sources other than phase equilibria data. Two-body interactions alone are insufficient to adequately describe vapor-liquid coexistence. In contrast, the addition of three-body interactions results in very good agreement with experiment. In addition to the exact calculation of three-body interactions, calculations are reported with an approximate formula for three-body interactions, which also yields good results.

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PubMed2006

Analysis of the shape of dendrimers under shear.

Nonequilibrium molecular-dynamics simulations are used to investigate the molecular shape of dendrimers and linear polymers in a melt and under shear. Molecules are modeled at the coarse-grained level using a finitely extensible nonlinear elastic bead-spring model. The shape of dendrimers and linear polymers at equilibrium and undergoing planar Couette flow is analyzed quantitatively and it is related to the shear viscosity. The shape of dendrimers responds differently to the influence of shear compared with linear polymers of equivalent molecular mass. However, in both cases the transition from Newtonian to non-Newtonian viscosity behavior corresponds to significant changes in molecular symmetry. This suggests that a shape analysis could be used to estimate the onset of shear thinning in polymers.

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PubMed2005

Cooperativity in the motor activities of the ATP-fueled molecular motors.

Kinesin, myosin and F1-ATPase are multi-domain molecular motors with multiple catalytic subunits. The motor mechanochemics are achieved via the conversion of ATP hydrolysis energy into forces and motions. We find that the catalysis of these molecular motors do not follow the simple Michaelis-Menten mechanism. The motor activities, such as the hydrolysis or processive rates, of kinesin, myosin and F1-ATPase have a complex ATP-dependent cooperativity. To understand this complexity in kinetics and mechanochemics, we develop a conformation correlation theory of cooperativity for the ATP-fueled motor proteins. The quantitative analysis and simulations indicate that cooperativity is induced by the conformational coupling of binding states of different subunits and prevails in the motor activities.

Adenosine Triphosphate↗

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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PubMed2005

Molecular simulation of dendrimers and their mixtures under shear: comparison of isothermal-isobaric (NpT) and isothermal-isochoric (NVT) ensemble systems.

Flow properties of dendrimers are studied with the aid of nonequilibrium molecular dynamics techniques. Simulations are performed in the NpT ensemble using the NpT-SLLOD algorithm [P. J. Davis and D. J. Evans, J. Chem. Phys. 100, 541 (1994)] and are compared to the results from simulations performed in the NVT ensemble reported earlier [J. T. Bosko, B. D. Todd, and R. J. Sadus, Chem. Phys. 121, 12050 (2004)]. Shear thickening observed at high strain rates vanishes in systems kept under constant pressure. Also the exponents in the power-law dependencies of the viscosity and the normal stress coefficients change. The variations are significant only at high strain rates and do not affect largely microscopic properties such as shape, alignment, or rotation of molecules. The NpT-SLLOD algorithm has been applied to study various systems including dendrimers in solution and their blends with linear chain molecules of the same molecular mass, and some results for these systems are presented.

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PubMed2005

Molecular simulation of the shear viscosity and the self-diffusion coefficient of mercury along the vapor-liquid coexistence curve.

In earlier work [G. Raabe and R. J. Sadus, J. Chem. Phys. 119, 6691 (2003)] we reported that the combination of an accurate two-body ab initio potential with an empirically determined multibody contribution enables the prediction of the phase coexistence properties, the heats of vaporization, and the pair distribution functions of mercury with reasonable accuracy. In this work we present molecular dynamics simulation results for the shear viscosity and self-diffusion coefficient of mercury along the vapor-liquid coexistence curve using our empirical effective potential. The comparison with experiment and calculations based on a modified Enskog theory shows that our multibody contribution yields reliable predictions of the self-diffusion coefficient at all densities. Good results are also obtained for the shear viscosity of mercury at low to moderate densities. Increasing deviations between the simulation and experimental viscosity data at high densities suggest that not only a temperature-dependent but also a density-dependent multibody contribution is necessary to account for the effect of intermolecular interactions in liquid metals. An analysis of our simulation data near the critical point yields a critical exponent of beta = 0.39, which is identical to the value obtained from the analysis of the experimental saturation densities.

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PubMed2004

Viscoelastic properties of dendrimers in the melt from nonequlibrium molecular dynamics.

The viscoelastic properties of dendrimers of generation 1-4 are studied using nonequilibrium molecular dynamics. Flow properties of dendrimer melts under shear are compared to systems composed of linear chain polymers of the same molecular weight, and the influence of molecular architecture is discussed. Rheological material properties, such as the shear viscosity and normal stress coefficients, are calculated and compared for both systems. We also calculate and compare the microscopic properties of both linear chain and dendrimer molecules, such as their molecular alignment, order parameters and rotational velocities. We find that the highly symmetric shape of dendrimers and their highly constrained geometry allows for substantial differences in their material properties compared to traditional linear polymers of equivalent molecular weight.

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PubMed2004

Internal structure of dendrimers in the melt under shear: a molecular dynamics study.

The molecular structure of fluids composed of dendrimers of different generations is studied using nonequilibrium molecular dynamics (NEMD). NEMD results for dendrimer melts undergoing planar Couette flow are reported and analyzed with particular attention paid to the shear-induced changes in the internal structure of dendrimers. The radii of gyration, pair distribution functions and the fractal dimensionality of the dendrimers are determined at different strain rates. The location of the terminal groups is analyzed and found to be uniformly distributed throughout the space occupied by the molecules. The fractal dimension as a function of strain rate displays crossover behavior analogous to the Newtonian/non-Newtonian transition of shear viscosity.

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PubMed2004

New phase for one-component hard spheres.

A completely new phase for one-component hard spheres is reported in an unexpected region of the phase diagram. The new phase is observed at compressibility factors intermediate between the solid and the metastable branches. It can be obtained from either Monte Carlo simulations alone or a combination of Monte Carlo and molecular dynamics calculations. An analysis of the intermediate scattering function data shows that the new phase is in a stable equilibrium. Radial distribution function data, configurational snapshots, bond order parameters, and translational order parameters obtained from molecular simulations indicate that the new phase is significantly different from the isotropic liquid, metastable, or crystalline phases traditionally observed in hard sphere systems. This result significantly changes our previous understanding of the behavior of hard spheres.

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PubMed2004

Complex cooperativity of ATP hydrolysis in the F(1)-ATPase molecular motor.

F(1)-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F(1)-ATPase does not follow the widely believed Michaelis-Menten mechanism. Instead, the hydrolysis mechanism behaves in an ATP-dependent manner. We develop a model for enzyme kinetics and hydrolysis cooperativity of F(1)-ATPase which involves the binding-state changes to the coupling catalytic reactions. The quantitative analysis and modeling suggest the existence of complex cooperative hydrolysis between three different catalysis sites of F(1)-ATPase. This complexity may be taken into account to resolve the arguments on the binding change mechanism in F(1)-ATPase.

Adenosine Triphosphate↗

PubMed2003

Scaling behavior for the pressure and energy of shearing fluids.

Recent simulation work has established that the widely accepted mode-coupling theory for the strain rate dependence of the pressure and energy of simple fluids under shear (i.e., energy and pressure are functions of strain rate to the power 3 / 2) is observed in the vicinity of the triple point. Away from the triple point, the scaling exponent of the strain rate was seen to be closer to 2 than 3 / 2, suggesting a possible analytic behavior. In this paper, we accurately determine the scaling exponent behavior for a Lennard-Jones fluid in the dense fliud region and find that it varies continuously between approximately 1.2 and approximately 2 as a function of density and temperature, thus confirming its nonanalyticity. We furthermore find that the behavior is characterized by a simple linear function of density and temperature.

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