ORCID Profile
0000-0002-6044-0409
Current Organisation
Swinburne University of Technology
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Chemical Thermodynamics And Energetics | Physical Chemistry (Incl. Structural) | Theoretical And Computational Chemistry Not Elsewhere Classified | Chemical Thermodynamics and Energetics | Computer Software | Chemical Engineering | Chemical Engineering Not Elsewhere Classified | Thermodynamics and Statistical Physics | Software Engineering | Distributed and Grid Systems | Concurrent Programming
Expanding Knowledge in the Physical Sciences | Chemical sciences | Physical sciences | Climate Change Models | Application Software Packages (excl. Computer Games) | Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Information and Computing Sciences |
Publisher: American Chemical Society (ACS)
Date: 05-1989
DOI: 10.1021/J100346A080
Publisher: Elsevier BV
Date: 04-2000
Publisher: Elsevier BV
Date: 10-2006
DOI: 10.1016/J.BBAPAP.2006.08.005
Abstract: 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.
Publisher: American Physical Society (APS)
Date: 30-05-2012
Publisher: AIP Publishing
Date: 08-02-2004
DOI: 10.1063/1.1639901
Publisher: Elsevier BV
Date: 08-1995
Publisher: Informa UK Limited
Date: 06-2007
Publisher: American Chemical Society (ACS)
Date: 03-1995
DOI: 10.1021/J100012A058
Publisher: AIP Publishing
Date: 08-09-2016
DOI: 10.1063/1.4961682
Abstract: The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point. Lustig’s thermodynamic approach is formally extended for temperature-dependent intermolecular potentials. Quantum effects are incorporated using the Feynman-Hibbs quantum correction, which results in significant improvement in the accuracy of predicted thermodynamic properties. The new Feynman-Hibbs version of the Hellmann-Bich-Vogel potential predicts the isochoric heat capacity to an accuracy of 1.4% over the entire range of liquid densities. It also predicts other thermodynamic properties more accurately than alternative intermolecular potentials.
Publisher: American Physical Society (APS)
Date: 15-09-2006
Publisher: AIP Publishing
Date: 22-11-2001
DOI: 10.1063/1.1413971
Abstract: Nonequilibrium molecular dynamics (NEMD) simulations are performed for argon at different strain rates using accurate two-body and three-body intermolecular potentials. The contributions of two- and three-body interactions to the configurational energy of argon at different strain rates are reported. The NEMD data indicate that there is the same simple relationship between two- and three-body interactions as reported previously [Marcelli and Sadus, J. Chem. Phys. 112, 6382 (2000)] from equilibrium Monte Carlo simulations. The relationship is largely independent of strain rate. NEMD calculations using this relationship for shear viscosity at different strain rates indicate good agreement with full two-body+three-body calculations. This means that the effect of three-body interactions on transport properties might be achieved in a conventional two-body NEMD simulation without incurring the computational penalty of three-body calculations.
Publisher: Wiley
Date: 2000
Publisher: Elsevier BV
Date: 03-1999
Publisher: Association of Reptilian and Amphibian Veterinarians (ARAV)
Date: 02-08-2023
Abstract: This paper presents novel baseline health parameters on the Española lava lizard (Microlophus delanonis). Blood s les and morphological measurements were taken on 51 lizards (21 males, 30 females) captured from three locations on the island of Española. Morphologic parameters measured included body weight, snout-vent length, and temperature. Blood s les were analyzed approximately eight hours after collection using a portable blood analyzer (i-STAT) which measured hemoglobin, total CO2, glucose, lactate, sodium, potassium, and ionized calcium. Hematologic characterization data were obtained using standard laboratory techniques. There were significant differences found in snout-vent length, weight, heart rate, respiratory rate, total CO2, and heterophil percentage between males and females. The data presented here can be used to monitor the health of this population of lava lizards as well as help to understand the health of a related species, the San Cristóbal lava lizard (Microlophus bivittatus), which faces different evolutionary pressures including the presence of humans and feral cats. This study continues to widen our understanding of the Microlophus genus however, further research should be done to characterize the remaining species that inhabit the islands in the Galápagos archipelago.
Publisher: AIP Publishing
Date: 14-09-2012
DOI: 10.1063/1.4749382
Abstract: Molecular dynamics simulations for the shear viscosity and self-diffusion coefficient of pure water were performed to investigate the effect of including intramolecular degrees of freedom in simple point charge (SPC) models over a wide range of state points. Results are reported for the flexible SPC/Fw model, its rigid SPC counterpart, and the widely used SPC/E model. The simulations covered the liquid phase from 277.15 to 363.15 K and the supercritical phase at 673.15 K and pressures up to 200 MPa. The flexibility exhibited by the SPC/Fw model results in slowing down of the dynamics. That is, it results in higher shear viscosities and lower diffusion coefficients than can be obtained from the rigid model, resulting in better agreement with experimental data. Significantly, the SPC/Fw model can be used to adequately predict the diffusion coefficients at ambient and supercritical temperatures over a wide range of pressures.
Publisher: Informa UK Limited
Date: 10-06-2000
Publisher: American Physical Society (APS)
Date: 24-01-2001
Publisher: American Physical Society (APS)
Date: 24-06-2002
Publisher: AIP Publishing
Date: 27-06-2017
DOI: 10.1063/1.4986917
Abstract: The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.
Publisher: AIP Publishing
Date: 12-11-2009
DOI: 10.1063/1.3256004
Abstract: The solid-liquid phase equilibria of the Gaussian core model are determined using the GWTS [J. Ge, G.-W. Wu, B. D. Todd, and R. J. Sadus, J. Chem. Phys. 119, 11017 (2003)] algorithm, which combines equilibrium and nonequilibrium molecular dynamics simulations. This is the first reported use of the GWTS algorithm for a fluid system displaying a reentrant melting scenario. Using the GWTS algorithm, the phase envelope of the Gaussian core model can be calculated more precisely than previously possible. The results for the low-density and the high-density (reentrant melting) sides of the solid state are in good agreement with those obtained by Monte Carlo simulations in conjunction with calculations of the solid free energies. The common point on the Gaussian core envelope, where equal-density solid and liquid phases are in coexistence, could be determined with high precision.
Publisher: AIP Publishing
Date: 07-08-2012
DOI: 10.1063/1.4739853
Abstract: A new molecular simulation procedure is reported for determining the phase behavior of fluids and fluid mixtures, which closely follows the experimental synthetic method. The simulation procedure can be implemented using Monte Calro or molecular dynamics in either the microcanonical or canonical statistical ensembles. Microcanonical molecular dynamics simulations are reported for the phase behavior of both the pure Lennard-Jones fluid and a Lennard-Jones mixture. The vapor pressures for the pure fluid are in good agreement with Monte Carlo Gibbs ensemble and Gibbs-Duhem calculations. The Lennard-Jones mixture is composed of equal size particles, with dissimilar energy parameters (ɛ2/ɛ1 = 1/2, ɛ12/ɛ1 = 1/$\\sqrt 2$2). The binary Lennard-Jones mixture exhibits liquid-liquid equilibria at high pressures and the simulation procedure allows us to estimate the coordinates of the high-pressure branch of the critical curve.
Publisher: Wiley
Date: 11-1999
Publisher: AIP Publishing
Date: 30-11-2004
DOI: 10.1063/1.1811073
Abstract: We argue that the claim of a third, thermodynamical stable phase in monodisperse hard sphere system is based on a wrong interpretation of the simulation data. Configurations, made available by the authors, are used to demonstrate that it is an artificially, by periodic boundaries stabilized phase with fcc signature and some defects.
Publisher: Elsevier BV
Date: 03-2008
Publisher: Elsevier BV
Date: 05-2004
Publisher: AIP Publishing
Date: 08-06-2004
DOI: 10.1063/1.1739212
Abstract: 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.
Publisher: AIP Publishing
Date: 15-06-2011
DOI: 10.1063/1.3600337
Abstract: The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure–temperature–density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment.
Publisher: Elsevier BV
Date: 1988
Publisher: AIP Publishing
Date: 13-07-2017
DOI: 10.1063/1.4991012
Abstract: Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.
Publisher: AIP Publishing
Date: 21-05-2019
DOI: 10.1063/1.5086054
Abstract: Nonequilibrium molecular dynamics simulations are reported to investigate the influence of different atomistic water models on the predicted flow behavior in carbon nanotubes (CNTs) with diameters between 0.81 nm and 1.9 nm. The comparison was made using rigid three-site [simplified point charge (SPC), extended SPC (SCP/E), and transferable intermolecular potential three point (TIP3P)] and four-site (TIP4P and TIP4P/2005) models. In addition, a flexible three-site model (SPC/Fw) was also investigated. The effect of different simulation conditions was determined by generating a flux across the CNT using either a pressure gradient across a membrane separating two water reservoirs or a periodic CNT with a constant force applied to each water molecule. Simulations involving the two water reservoirs indicate that the flux is strongly dependent on the choice of water model, which confirms earlier work. By contrast, this strong model dependency is not a feature of the periodic CNT simulations. Instead, the flux depends mainly on the pore diameter and the molecular density of water inside the CNT. The influence of the water model becomes very small in the periodic CNT simulations, which eliminates distorting entrance/exit effects.
Publisher: AIP Publishing
Date: 24-09-2012
DOI: 10.1063/1.4753940
Abstract: The dielectric properties and molecular structure of water mixtures with different nonpolar solutes (methane and noble gases) are studied using molecular dynamics. The water-water, water-solute, and solute-solute interactions are calculated using the combination of a polarizable potential [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)10.1063/1.2786449] for water plus the Lennard-Jones potential. The effect of solute size and concentration on the solubility of the system, hydrogen bonding, dielectric constant, and dipole moment are investigated over a temperature range of 278–750 K and solute percentage mole fractions up to 30%. Solute particles affect the structure of water, resulting in the compression of oxygen-oxygen and oxygen-hydrogen radial distribution functions. The influence of the solute extends both to relatively low concentrations and high temperatures. The coordination numbers of aqueous solutions of the nonpolar solutes appear to be proportional to the size of the solute particles. Our study shows the destructive influence of the nonpolar solute on both the tetrahedral water structure and hydrogen bond formation at solute concentrations greater than 30%. The presence of nonpolar particles typically decreases both the dielectric constant and dipole moment. The decrease of dielectric constant and water dipole moment is directly proportional to the solute concentration and temperature.
Publisher: AIP Publishing
Date: 08-04-2000
DOI: 10.1063/1.481199
Abstract: Molecular simulation data are reported that indicate that there is a simple empirical relationship between two-body and three-body interaction energies. The significance of this relationship is that three-body interactions can be estimated accurately from two-body interactions without incurring the computational penalty of three-body calculations. The relationship is tested by performing Gibbs ensemble simulations for the vapor–liquid equilibria of argon. The results are in good agreement with calculations that explicitly evaluate all three-body interactions.
Publisher: Elsevier BV
Date: 1987
Publisher: AIP Publishing
Date: 07-12-2020
DOI: 10.1063/5.0033466
Abstract: The ability to combine intermolecular potentials without loss of information is investigated. Molecular simulation results for both vapor–liquid equilibria and supercritical isochoric heat capacities are reported for different combinations of n–m potentials. The role of both additional cohesion and repulsive terms is determined. The 12-8-6 potential obtained by adding an m = 6 contribution to the 12-8 potential significantly broadens the phase envelope, which remains inside of the 12-6 envelope. In contrast, the 12+9-6 potential that involves an additional n = 9 repulsive contribution lifts the phase envelope above the 12-6 values. The 12-8-6 potential significantly reduces the maximum and minimum observed for the isochoric heat capacity at supercritical conditions. In contrast, the additional repulsion of the 12+9-6 potential has a relatively small influence on the supercritical behavior of the isochoric heat capacity. Significantly, a comparison of vapor–liquid equilibria data for two-body only simulations for Ar, Kr, and Xe indicates that there is very good agreement with the 12-8-6 data. This means that the 12-8-6 potential may provide a useful description of two-body only interactions for the noble gases. The 12+9-8 potential at least partially reproduces vapor–liquid properties of noble gases interacting via two-body plus three-body interactions. In general, the combination of potentials provides a mechanism of simplifying the calculation of two-body and two-body plus three-body interactions.
Publisher: American Chemical Society (ACS)
Date: 09-1993
DOI: 10.1021/J100137A036
Publisher: AIP Publishing
Date: 10-12-2009
DOI: 10.1063/1.3273083
Abstract: Nonequilibrium molecular dynamics simulations are reported for the shear viscosity of the Gaussian core model (GCM) fluid over a wide range of densities, temperatures and strain rates. A transition from Newtonian and non-Newtonian behavior is observed in all cases for sufficiently high strain rates. On the high-density side of the solid region where re-entrant melting occurs, the shear viscosity decreases significantly when the density is increased at constant temperature and Newtonian behavior persists until very high strain rates. This behavior, which is attributed to particle overlap, is in contrast to the monotonic increase in shear viscosity with density observed for the Lennard-Jones potential. Contrary to the behavior of normal fluids, the viscosity is observed to increase with increasing temperatures at high densities. This reflects a peculiarity of the GCM, namely the approach to the “infinite-density ideal-gas limit.” The behavior is also consistent with viscosity measurements of cationic surfactant solutions. In contrast to other potentials, the shear viscosities for the Gaussian core potential at low to moderate strain rates are obtained with modest statistical uncertainties. Zero shear viscosities extrapolated from the nonequilibrium simulations are in good agreement with equilibrium Green–Kubo calculations.
Publisher: AIP Publishing
Date: 24-06-2004
DOI: 10.1063/1.1755659
Abstract: 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.
Publisher: American Chemical Society (ACS)
Date: 08-1995
DOI: 10.1021/J100032A048
Publisher: Informa UK Limited
Date: 2008
Publisher: Inderscience Publishers
Date: 2009
Publisher: American Chemical Society (ACS)
Date: 20-07-2018
Abstract: The importance of both the Boyle temperature ( T
Publisher: Mary Ann Liebert Inc
Date: 02-2023
Publisher: AIP Publishing
Date: 22-03-1996
DOI: 10.1063/1.471172
Abstract: Gibbs-ensemble molecular simulations are reported for the vapor–liquid phase coexistence of argon using the two-body Lennard-Jones potential. During the simulation, the possible effect of three-body interactions on the pressure and configurational energy of the vapor and liquid phases is estimated by performing calculations with three-body potentials. The intermolecular potentials used for the three-body calculations incorporate the influence of both three-body-dispersion and three-body-repulsion interactions. The results show that three-body repulsion makes a significant contribution to three-body interactions in the liquid phase. The effect of three-body dispersion is offset substantially by three-body repulsion.
Publisher: Old City Publishing, Inc
Date: 2001
DOI: 10.1068/HTWU244
Publisher: American Chemical Society (ACS)
Date: 03-1993
DOI: 10.1021/J100111A042
Publisher: Elsevier BV
Date: 12-2006
Publisher: AIP Publishing
Date: 17-09-2003
DOI: 10.1063/1.1605381
Abstract: The vapor–liquid coexistence properties of mercury are determined from molecular simulation using empirical intermolecular potentials, ab initio two-body potentials, and an effective multibody intermolecular potential. Comparison with experiment shows that pair-interactions alone are inadequate to account for the vapor–liquid coexistence properties of mercury. It is shown that very good agreement between theory and experiment can be obtained by combining an accurate two-body ab initio potential with the addition of an empirically determined multibody contribution. As a consequence of this multibody contribution, we can reliably predict mercury’s phase coexistence properties and the heats of vaporization. The pair distribution function of mercury can also be predicted with reasonable accuracy.
Publisher: Elsevier BV
Date: 1991
Publisher: Elsevier BV
Date: 03-2002
Publisher: Elsevier BV
Date: 09-1992
Publisher: American Physical Society (APS)
Date: 10-07-2019
Publisher: Wiley
Date: 03-12-2010
DOI: 10.1002/AIC.12257
Publisher: Elsevier BV
Date: 03-1996
Publisher: Wiley
Date: 16-12-2004
DOI: 10.1002/AIC.10233
Publisher: American Physical Society (APS)
Date: 06-07-2010
Publisher: American Chemical Society (ACS)
Date: 1996
DOI: 10.1021/MA951613C
Publisher: American Physical Society (APS)
Date: 10-06-2003
Publisher: AIP Publishing
Date: 28-09-2010
DOI: 10.1063/1.3481102
Abstract: Molecular simulation results for the solid-liquid coexistence properties of untruncated, truncated, truncated and shifted, and truncated and shifted-force 12-6 Lennard-Jones potentials are reported. It is found that solid-liquid coexistence properties vary systematically with potential truncations, shifts, and cut-off values. Potential truncations and shifts have important consequences at low temperatures, particularly in the vicinity of the triple point. The main influence is on the coexistence pressure whereas both liquid and solid densities are less sensitive to the truncations and shifts. The data reported in this work indicate that the cut-off radius mainly affects the properties of the liquid phase whereas its influence on the solid phase is almost negligible. The data suggest a monotonic variation of the melting temperature as a function of cut-off radius, which contradicts the oscillatory behavior of the melting temperature reported elsewhere.
Publisher: American Chemical Society (ACS)
Date: 09-09-2019
Abstract: The phenomenological behavior of the Widom line above the vapor-liquid critical point for the Lennard-Jones (LJ) potential is investigated using four accurate equations of state (EoS) and a comparison with molecular dynamics (MD) simulation data. This involved calculating the supercritical maximum values of the isochoric heat capacity (
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/CH09449
Abstract: An essential aspect of protein science is to determine the deductive relationship between structure, dynamics, and various sets of functions. The role of dynamics is currently challenging our understanding of protein functions, both experimentally and theoretically. To verify the internal fluctuations and dynamics correlations in an enzyme protein undergoing conformational transitions, we have applied a coarse-grained dynamics algorithm using the elastic network model for adenylate kinase. Normal mode analysis reveals possible dynamical and allosteric pathways for the transition between the open and the closed states of adenylate kinase. As the ligands binding induces significant flexibility changes of the nucleotides monophosphate (NMP) domain and adenosine triphosphate (ATP) domain, the diagonalized correlation between different structural transition states shows that most correlated motions occur between the NMP domain and the helices surrounding the ATP domain. The simultaneous existence of positive and negative correlations indicates that the conformational changes of adenylate kinase take place in an allosteric manner. Analyses of the cumulated normal mode overlap coefficients and long-range correlated motion provide new insights of operating mechanisms and dynamics of adenylate kinase. They also suggest a quantitative dynamics criterion for determining the allosteric cooperativity, which may be applicable to other proteins.
Publisher: AIP Publishing
Date: 06-01-2010
DOI: 10.1063/1.3285596
Publisher: AIP Publishing
Date: 18-03-2014
DOI: 10.1063/1.4867898
Abstract: The coordination of Mg2+ with the triphosphate group of adenosine triphosphate (ATP) in motor proteins is investigated using data mining and molecular dynamics. The possible coordination structures available from crystal data for actin, myosin, RNA polymerase, DNA polymerase, DNA helicase, and F1-ATPase are verified and investigated further by molecular dynamics. Coordination states are evaluated using structural analysis and quantified by radial distribution functions, coordination numbers, and pair interaction energy calculations. The results reveal a erse range of both transitory and stable coordination arrangements between Mg2+ and ATP. The two most stable coordinating states occur when Mg2+ coordinates two or three oxygens from the triphosphate group of ATP. Evidence for five-site coordination is also reported involving water in addition to the triphosphate group. The stable states correspond to a pair interaction energy of either ∼−2750 kJ/mol or −3500 kJ/mol. The role of water molecules in the hydration shell surrounding Mg2+ is also reported.
Publisher: Elsevier BV
Date: 11-1991
Publisher: AIP Publishing
Date: 04-04-2019
DOI: 10.1063/1.5085420
Abstract: A new method is reported for developing accurate two-body interatomic potentials from existing ab initio data. The method avoids the computational complexity of alternative methods without sacrificing accuracy. Two-body potentials are developed for He, Ne, Ar, Kr, and Xe, which accurately reproduce the potential energy at all inter-atomic separations. Monte Carlo simulations of the pressure, radial distribution function, and isochoric heat capacity using the simplified potential indicate that the results are in very close, and sometimes almost indistinguishable, agreement with more complicated current state-of-the-art two-body potentials.
Publisher: Elsevier BV
Date: 1986
Publisher: Informa UK Limited
Date: 11-1996
Publisher: Elsevier BV
Date: 15-08-1996
Publisher: AIP Publishing
Date: 15-07-2005
DOI: 10.1063/1.1946749
Abstract: 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.
Publisher: Elsevier BV
Date: 2016
Publisher: Elsevier BV
Date: 09-2003
Publisher: American Physical Society (APS)
Date: 17-07-2015
Publisher: AIP Publishing
Date: 02-11-2009
DOI: 10.1063/1.3253686
Abstract: Molecular dynamics simulations are reported for the solid-liquid coexistence properties of n-6 Lennard-Jones fluids, where n=12, 11, 10, 9, 8, and 7. The complete phase behavior for these systems has been obtained by combining these data with vapor-liquid simulations. The influence of n on the solid-liquid coexistence region is compared using relative density difference and miscibility gap calculations. Analytical expressions for the coexistence pressure, liquid, and solid densities as a function of temperature have been determined, which accurately reproduce the molecular simulation data. The triple point temperature, pressure, and liquid and solid densities are estimated. The triple point temperature and pressure scale with respect to 1/n, resulting in simple linear relationships that can be used to determine the pressure and temperature for the limiting ∞-6 Lennard-Jones potential. The simulation data are used to obtain parameters for the Raveché, Mountain, and Streett and Lindemann melting rules, which indicate that they are obeyed by the n-6 Lennard Jones potentials. In contrast, it is demonstrated that the Hansen–Verlet freezing rule is not valid for n-6 Lennard-Jones potentials.
Publisher: Wiley
Date: 08-1994
Publisher: IEEE
Date: 06-2006
Publisher: AIP Publishing
Date: 14-12-2010
DOI: 10.1063/1.3512996
Publisher: American Chemical Society (ACS)
Date: 04-1989
DOI: 10.1021/IE00088A016
Publisher: American Physical Society (APS)
Date: 16-05-2022
Publisher: AIP Publishing
Date: 25-02-2015
DOI: 10.1063/1.4908530
Abstract: General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.
Publisher: American Chemical Society (ACS)
Date: 04-1992
DOI: 10.1021/J100188A052
Publisher: AIP Publishing
Date: 15-08-2006
DOI: 10.1063/1.2275309
Abstract: 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.
Publisher: Elsevier BV
Date: 1988
Publisher: AIP Publishing
Date: 28-01-2006
DOI: 10.1063/1.2155482
Abstract: 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.
Publisher: AIP Publishing
Date: 28-11-2022
DOI: 10.1063/5.0125809
Abstract: We report the accurate determination of solid-liquid equilibria using a novel molecular simulation method that can be used for solid-liquid equilibria from low to high pressures. A re-evaluation is reported of the solid-liquid equilibria of the noble gases interacting via ab initio two-body potentials combined with three-body interactions and quantum corrections and the results are compared with both existing simulation data and experimental values. The new simulation method yields results that are generally in closer agreement with the experiment than exiting methods, highlighting the important role of the method in fully understanding the interatomic interactions responsible for solid-liquid equilibria. The quality of the comparison of simulation results with the experiment indicates that the solid-liquid equilibria of the noble gases can be now predicted with exceptional accuracy over a large range of pressures.
Publisher: American Physical Society (APS)
Date: 12-2009
Publisher: Informa UK Limited
Date: 10-04-1996
Publisher: AIP Publishing
Date: 15-08-2012
DOI: 10.1063/1.4739308
Abstract: The conformational ersity of ATP/Mg:ATP in motor proteins was investigated using molecular dynamics and data mining. Adenosine triphosphate (ATP) conformations were found to be constrained mostly by inter cavity motifs in the motor proteins. It is demonstrated that ATP favors extended conformations in the tight pockets of motor proteins such as F1-ATPase and actin whereas compact structures are favored in motor proteins such as RNA polymerase and DNA helicase. The incorporation of Mg2+ leads to increased flexibility of ATP molecules. The differences in the conformational dynamics of ATP/Mg:ATP in various motor proteins was quantified by the radius of gyration. The relationship between the simulation results and those obtained by data mining of motor proteins available in the protein data bank is analyzed. The data mining analysis of motor proteins supports the conformational ersity of the phosphate group of ATP obtained computationally.
Publisher: AIP Publishing
Date: 20-04-2004
DOI: 10.1063/1.1697383
Abstract: The assertion by Sadus [J. Chem. Phys. 115, 1460 (2001) 116, 5913(E) (2002)] that the Dieterici–Carnahan–Starling (DCS) equation of state he has proposed yields more accurate predictions of the phase coexistence of fluids than the traditional additive approach used to develop equations of state is challenged. The main point invoked concerns the behavior of mean-field equations of state in the neighborhood of the critical point. It is concluded that, whereas the DCS equation of state may be a useful addition, it is not more accurate over the whole of the phase coexistence of fluids than existing, additive, equations of state.
Publisher: Royal Society of Chemistry (RSC)
Date: 1999
DOI: 10.1039/A902834J
Publisher: AIP Publishing
Date: 10-11-2003
DOI: 10.1063/1.1623476
Abstract: The solid–liquid equilibrium phase transition of a one-component Lennard-Jones system is determined by equilibrium and nonequilibrium molecular dynamics simulation methods. One method uses the observation that the scaling exponent of the pressure or energy of a shearing Lennard-Jones liquid is approximately 1 at the solid phase. This enables us to locate the density of the coexisting solid phase. The coexisting liquid phase density is then obtained by constructing a tie line between the coexisting solid phase point and the liquid phase curve. Alternatively, the coexisting liquid phase density can be efficiently obtained by observing the change in pressure as a function of strain rate and density. The coexisting solid phase density can be then obtained from a tie line from the liquid curve to the solid curve. These calculations are the first reported use of combined equilibrium and nonequilibrium molecular dynamics methods for phase coexistence at equilibrium. Our results are in very good agreement with those obtained by alternative simulation methods for phase equilibria.
Publisher: Elsevier BV
Date: 11-2003
Publisher: Elsevier BV
Date: 06-1993
Publisher: Elsevier BV
Date: 02-1993
Publisher: AIP Publishing
Date: 10-01-2019
DOI: 10.1063/1.5080308
Abstract: A method is reported that enables second virial coefficient properties to be used to obtain relatively simple two-body intermolecular potentials. Generic n-m Lennard-Jones/Mie potentials are transformed into two-body potentials for neon, argon, krypton, and xenon. Comparison with results from highly accurate ab initio potentials indicates good agreement. A complete potential for real fluids is obtained by combining the two-body potentials with a density-dependent term for three-body interactions. Vapor-liquid equilibria molecular simulation data for the new potentials are compared with the experiment, which demonstrates the effectiveness of the two- and three-body contributions. The combination of the two-body 10-8 Lennard-Jones/Mie potential and three-body term is a good overall choice for the noble gases.
Publisher: AIP Publishing
Date: 17-03-2011
DOI: 10.1063/1.3559678
Abstract: The thermodynamic properties of pressure, energy, isothermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule–Thomson coefficient, and speed of sound are considered in a classical molecular dynamics ensemble. These properties were obtained using the treatment of Lustig [J. Chem. Phys. 100, 3048 (1994)] and Meier and Kabelac [J. Chem. Phys. 124, 064104 (2006)], whereby thermodynamic state variables are expressible in terms of phase-space functions determined directly from molecular dynamics simulations. The complete thermodynamic information about an equilibrium system can be obtained from this general formalism. We apply this method to the Gaussian core model fluid because the complex phase behavior of this simple model provides a severe test for this treatment. Waterlike and other anomalies are observed for some of the thermodynamic properties of the Gaussian core model fluid.
Publisher: American Physical Society (APS)
Date: 25-08-2006
Publisher: AIP Publishing
Date: 15-05-2023
DOI: 10.1063/5.0148248
Abstract: An intermolecular potential is reported for molecular hydrogen that combines two-body interactions from ab initio data with three-body interactions. The accuracy of the two-body potential is validated by comparison with experimental second virial coefficient data. Experimental pressure–density–temperature data are used to validate the addition of three-body interactions, often yielding very accurate predictions. Classical Monte Carlo simulations that neglect quantum effects are reported for the vapor–liquid equilibria (VLE), critical properties, and the triple point. A comparison with experimental data indicates that the effect of quantum interactions is to narrow the VLE phase envelope and to lower the critical temperature. The three-body interactions have a considerable influence on the phase behavior, resulting in good agreement with the experimental density. The critical properties of the two-body + three-body potential for hydrogen provide an alternative set of input parameters to improve the accuracy of theoretical predictions at temperatures above 100 K. In the vicinity of the critical point, the coexistence densities do not obey the law of rectilinear diameters, which is a feature that has largely been overlooked in both experimental data and reference equations of state.
Publisher: Elsevier BV
Date: 04-1994
Publisher: AIP Publishing
Date: 22-12-2020
DOI: 10.1063/5.0031517
Abstract: Molecular simulations are performed for the (m + 1, m) potential to systematically investigate the effect of changing the range of particle cohesion on both vapor–liquid equilibria and thermodynamic properties of fluids. The results are reported for m = 4–11, which represent a progressive narrowing of the potential energy well. The conventional Lennard-Jones potential is used as a reference point for normal fluid behavior. Small values of m result in a broadening of the phase envelope compared with the Lennard-Jones potential, whereas a contraction is observed in other cases. The critical properties are reported, and a relationship between the critical temperature and the Boyle temperature is determined. The low values of the critical compressibility factor when m & 6 reflect the behavior observed for real fluids such as n-alkanes. The results for supercritical thermodynamic properties are much more varied. Properties such as pressure, potential energy, isochoric thermal pressure coefficient, and thermal expansion coefficient vary consistently with m, whereas other properties such as the Joule–Thomson coefficient exhibit much more nuanced behavior. Maximum and minimum values are reported for both the isochoric heat capacity and isothermal compressibility. A minimum in the speed of sound is also observed.
Publisher: AIP Publishing
Date: 19-07-2019
DOI: 10.1063/1.5109052
Abstract: Fully a priori predictions are reported for the vapor-liquid equilibria (VLE) properties of Ar, Kr, and Xe using molecular simulation techniques and recently developed ab initio two-body interatomic potentials. Simulation data are reported at temperatures from near the triple point to close to the critical point. The two-body ab initio potentials exaggerate the size of the experimental VLE temperature-density envelope, overestimating the critical temperature and underestimating the vapor pressure. These deficiencies can be partially rectified by the addition of a density-dependent three-body term. At many temperatures, the ab initio + three-body simulations for Kr and Xe predict the vapor pressure to an accuracy that is close to experimental uncertainty. The predicted VLE coexisting densities for Xe almost match experimental data. The improvement with experiment is also reflected in more accurate enthalpies of vaporization. The fully a priori predictions for all of the VLE properties of either Kr or Xe are noticeably superior to simulations using the Lennard-Jones potential.
Publisher: AIP Publishing
Date: 21-02-2019
DOI: 10.1063/1.5091046
Publisher: AIP Publishing
Date: 14-05-2003
DOI: 10.1063/1.1568083
Abstract: F 1 - ATPase hydrolyzes ATP into ADP and Pi and converts chemical energy into mechanical rotation with exceptionally high efficiency. This energy-transducing molecular motor increasingly attracts interest for its unique cellular functions and promising application in nanobiotechnology. To better understand the chemomechanics of rotation and loading dynamics of F1-ATPase, we propose a computational model based on enzyme kinetics and Langevin dynamics. We show that the torsional energy and stepwise rotation can be regulated by a series of near-equilibrium reactions when nucleotides bind or unbind, as well as characterized by an effective “ratchet” drag coefficient and a fitting chemomechanic coefficient. For the case of driving an actin filament, the theoretical load-rotation profile is analyzed and comparison with experimental data indicates reasonable agreement. The chemomechanics described in this work is of fundamental importance to all ATP-fueled motor proteins.
Publisher: AIP Publishing
Date: 10-10-2006
DOI: 10.1063/1.2353117
Abstract: 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.
Publisher: Elsevier BV
Date: 10-1994
Publisher: Elsevier BV
Date: 07-2001
Publisher: AIP Publishing
Date: 21-02-2019
DOI: 10.1063/1.5091043
Publisher: Springer International Publishing
Date: 2016
Publisher: Elsevier BV
Date: 1988
Publisher: Royal Society of Chemistry (RSC)
Date: 13-02-2002
DOI: 10.1039/B108822J
Publisher: American Chemical Society (ACS)
Date: 21-07-2021
Publisher: Informa UK Limited
Date: 10-06-2000
Publisher: Royal Society of Chemistry (RSC)
Date: 2000
DOI: 10.1039/B004198J
Publisher: AIP Publishing
Date: 15-10-2013
DOI: 10.1063/1.4824626
Abstract: Molecular dynamics simulations are reported for the thermodynamic properties of n-m Lennard-Jones fluids, where n = 10 and 12, and m = 5 and 6. Results are reported for the thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound at supercritical conditions covering a wide range of fluid densities. The thermodynamic criteria for maxima/minima in the isochoric and isobaric heat capacities are identified and the simulation results are also compared with calculations from Lennard-Jones equations of state. The Johnson et al. [Mol. Phys. 78, 591 (1993)] equation of state can be used to reproduce all heat capacity phenomena reported [T. M. Yigzawe and R. J. Sadus, J. Chem. Phys. 138, 194502 (2013)] from molecular dynamics simulations for the 12-6 Lennard-Jones potential. Significantly, these calculations and molecular dynamics results for other n-m Lennard-Jones potentials support the existence of Cp minima at supercritical conditions. The values of n and m also have a significant influence on many other thermodynamic properties.
Publisher: Mary Ann Liebert Inc
Date: 08-2020
Publisher: IEEE
Date: 09-2013
Publisher: Springer Science and Business Media LLC
Date: 11-1994
DOI: 10.1007/BF01458828
Publisher: AIP Publishing
Date: 16-05-2013
DOI: 10.1063/1.4803855
Abstract: The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.
Publisher: Elsevier BV
Date: 06-2020
Publisher: Elsevier BV
Date: 09-2005
DOI: 10.1016/J.BBAPAP.2005.06.013
Abstract: 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.
Publisher: AIP Publishing
Date: 28-12-2013
DOI: 10.1063/1.4855655
Publisher: Elsevier BV
Date: 1995
Publisher: Informa UK Limited
Date: 20-07-2003
Publisher: AIP Publishing
Date: 28-11-2020
DOI: 10.1063/5.0029552
Abstract: The role of cohesive r−4 interactions on the existence of a vapor phase and the formation of vapor–liquid equilibria is investigated by performing molecular simulations for the n-4 potential. The cohesive r−4 interactions delay the emergence of a vapor phase until very high temperatures. The critical temperature is up to 5 times higher than normal fluids, as represented by the Lennard-Jones potential. The greatest overall influence on vapor–liquid equilibria is observed for the 5–4 potential, which is the lowest repulsive limit of the potential. Increasing n initially mitigates the influence of r−4 interactions, but the moderating influence declines for n & 12. A relationship is reported between the critical temperature and the Boyle temperature, which allows the critical temperature to be determined for a given n value. The n-4 potential could provide valuable insight into the behavior of non-conventional materials with both very low vapor pressures at elevated temperatures and highly dipolar interactions.
Publisher: AIP Publishing
Date: 11-03-2014
DOI: 10.1063/1.4867282
Abstract: Thermodynamic and diffusion properties of water + methane mixtures in a single liquid phase are studied using NVT molecular dynamics. An extensive comparison is reported for the thermal pressure coefficient, compressibilities, expansion coefficients, heat capacities, Joule-Thomson coefficient, zero frequency speed of sound, and diffusion coefficient at methane concentrations up to 15% in the temperature range of 298–650 K. The simulations reveal a complex concentration dependence of the thermodynamic properties of water + methane mixtures. The compressibilities, heat capacities, and diffusion coefficients decrease with increasing methane concentration, whereas values of the thermal expansion coefficients and speed of sound increase. Increasing methane concentration considerably retards the self-diffusion of both water and methane in the mixture. These effects are caused by changes in hydrogen bond network, solvation shell structure, and dynamics of water molecules induced by the solvation of methane at constant volume conditions.
Publisher: Public Library of Science (PLoS)
Date: 06-11-2018
Publisher: Elsevier BV
Date: 12-1985
Publisher: AIP Publishing
Date: 30-11-2004
DOI: 10.1063/1.1818678
Abstract: 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.
Publisher: American Physical Society (APS)
Date: 10-01-2018
Publisher: AIP Publishing
Date: 15-07-2001
DOI: 10.1063/1.1380711
Abstract: In 1873, van der Waals proposed a simple equation of state that qualitatively described the phase behavior of fluids. Since then, the principles behind the van der Waals equation have been used and refined countless times in the quest for an accurate equation of state. Despite the enormous amount of work reported, the goal of a simple and accurate equation of state for even relatively simple systems, such as monatomic or polyatomic gases, has proved elusive. Therefore, the analysis of phase equilibria with equations of state is more often than not an exercise in data fitting rather than genuine prediction. In this work, we revisit the early work of Dieterici. When coupled with modern developments in equations of state, this little used approach has the potential of generating useful equations of state. To illustrate the usefulness of the Dieterici formula, we use it to derive a simple equation of state based on the Carnahan–Starling hard-sphere term and van der Waals interactions. This simple approach yields more accurate predictions of the phase co-existence of fluids than the traditional additive approach used to develop equations of state.
Publisher: AIP Publishing
Date: 22-01-2007
DOI: 10.1063/1.2428302
Abstract: The authors performed Gibbs ensemble simulations on the vapor-liquid equilibrium of water to investigate the influence of incorporating intramolecular degrees of freedom in the simple point charge (SPC) water model. Results for vapor pressures, saturation densities, heats of vaporization, and the critical point for two different flexible models are compared with data for the corresponding rigid SPC and SPC/E models. They found that the introduction of internal vibrations, and also their parametrization, has an observable effect on the prediction of the vapor-liquid coexistence curve. The flexible SPC/Fw model, although optimized to describe bulk diffusion and dielectric constants at ambient conditions, gives the best prediction of saturation densities and the critical point of the examined models.
Publisher: Informa UK Limited
Date: 20-12-1999
Publisher: AIP Publishing
Date: 22-03-2001
DOI: 10.1063/1.1351855
Abstract: Liquid crystals exhibit orientation-dependent phases ranging from a disordered (isotropic) phase to a highly ordered crystalline phase. In between these extremes, increasing order can result in nematic and smectic phases. Typically, molecular simulation studies of liquid-crystal behavior use a nonspherical hard-body monomer. In this work, molecular simulation is used to study dimers of hard prolate ellipsoids. The results indicate that dimers of hard prolate ellipsoids exhibit a rich ersity of liquid-crystal behavior including smectic phases. In some cases, the dimer model may be a more realistic alternative to the conventional monomer model for liquid-crystal behavior.
Publisher: Elsevier BV
Date: 1988
Publisher: Wiley
Date: 15-04-2008
DOI: 10.1002/PROT.22056
Abstract: Receiver domains are key molecular switches in bacterial signaling. Structural studies have shown that the receiver domain of the nitrogen regulatory protein C (NtrC) exists in a conformational equilibrium encompassing both inactive and active states, with phosphorylation of Asp54 allosterically shifting the equilibrium towards the active state. To analyze dynamical fluctuations and correlations in NtrC as it undergoes activation, we have applied a coarse-grained dynamics algorithm using elastic network models. Normal mode analysis reveals possible dynamical pathways for the transition of NtrC from the inactive state to the active state. The diagonalized correlation between the inactive and the active (phosphorylated) state shows that most correlated motions occur around the active site of Asp54 and in the region Thr82 to Tyr101. This indicates a coupled correlation of dynamics in the "Thr82-Tyr101" motion. With phosphorylation inducing significant flexibility changes around the active site and alpha3 and alpha4 helices, we find that this activation makes the active-site region and the loops of alpha3/beta4 and alpha4/beta5 more stable. This means that phosphorylation entropically favors the receiver domain in its active state, and the induced conformational changes occur in an allosteric manner. Analyses of the local flexibility and long-range correlated motion also suggest a dynamics criterion for determining the allosteric cooperativity of NtrC, and may be applicable to other proteins.
Publisher: Wiley
Date: 10-2023
DOI: 10.1002/HSR2.1629
Publisher: AIP Publishing
Date: 19-03-2002
DOI: 10.1063/1.1455624
Publisher: American Chemical Society (ACS)
Date: 06-1992
DOI: 10.1021/J100192A001
Publisher: AIP Publishing
Date: 25-01-2013
DOI: 10.1063/1.4779295
Abstract: Molecular dynamics simulation results are reported for the pressure, isothermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient and speed of sound of liquid water using a polarizable potential [Li et al., J. Chem. Phys. 127, 154509 (2007)]. These properties were obtained for a wide range of temperatures and pressures at a common liquid density using the treatment of Lustig [J. Chem. Phys. 100, 3048 (1994)] and Meier and Kabelac [J. Chem. Phys. 124, 064104 (2006)], whereby thermodynamic state variables are expressible in terms of phase-space functions determined directly from molecular dynamics simulations. Comparison with experimental data indicates that the polarizable potential can be used to predict most thermodynamic properties with a very good degree of accuracy.
Publisher: American Physical Society (APS)
Date: 19-07-2001
Publisher: American Physical Society (APS)
Date: 22-11-2019
Publisher: Informa UK Limited
Date: 03-2006
Publisher: AIP Publishing
Date: 20-08-2018
DOI: 10.1063/1.5041320
Abstract: The second virial coefficient (B), Boyle temperature (TB), and temperature maximum (Tmax) are determined for the n-m Lennard-Jones/Mie (LJ/M) potential. The full range of n, m behavior is investigated between the 5-4 LJ/M, hard sphere (n = ∞) + attractive (m ≥ 4) term (HSAm), and hard sphere potential limits. The (n = m + 1)-m LJ/M potential has an important role in characterising the overall behavior of second virial coefficient properties. Different TB, Tmax behavior is observed for n(constant)-m LJ/M and n-m(constant) LJ/M potentials. In the former case, there are two distinct linear (5 ≤ n ≤ 30) and non-linear regions (n & 30). In the latter case, there is a minimum in Tmax in two distinct non-linear regions (4 ≤ m ≤ 34 and 35 ≤ m ≤ 150) followed by a maximum TB region (m ≥ 151). Analytical relationships for some of the behavior are determined and numerical values of TB for a range of n and m values are reported. Molecular simulation data are used to determine simple relationships between TB and both the critical temperature and triple point temperature for the special case of the n-6 LJ/M potential.
Publisher: AIP Publishing
Date: 15-07-2005
DOI: 10.1063/1.1955530
Abstract: 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 β=0.39, which is identical to the value obtained from the analysis of the experimental saturation densities.
Publisher: AIP Publishing
Date: 22-07-1999
DOI: 10.1063/1.479412
Abstract: Gibbs ensemble Monte Carlo simulations are reported for the vapor–liquid phase coexistence of argon, krypton, and xenon. The calculations employ accurate two-body potentials in addition to contributions from three-body dispersion interactions resulting from third-order triple-dipole, dipole–dipole–quadrupole, dipole–quadrupole–quadrupole, quadrupole–quadrupole–quadrupole, and fourth-order triple-dipole terms. It is shown that vapor–liquid equilibria are affected substantially by three-body interactions. The addition of three-body interactions results in good overall agreement of theory with experimental data. In particular, the subcritical liquid-phase densities are predicted accurately.
Publisher: AIP Publishing
Date: 21-11-2013
DOI: 10.1063/1.4832381
Abstract: The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm3 for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.
Publisher: AIP Publishing
Date: 17-10-2007
DOI: 10.1063/1.2786449
Abstract: The role of nonadditive interactions on the structure and dielectric properties of water is investigated at different temperatures using molecular dynamics. A new intermolecular potential is developed which contains an ab initio description of two-body additive interactions plus nonadditive contributions from both three-body interactions and polarization. Polarization is the main nonadditive influence, resulting in improved agreement with experiment for the radial distribution function, dielectric constant, and dipole moment. A comparison is also made with other widely used intermolecular potentials. The new potential provides a superior prediction of the dielectric constant and dipole moment. It also predicts the relative contribution of hydrogen bonding better than the SPC/E potential [Berendsen et al., J. Phys. Chem. 91, 6269 (1987)].
Publisher: American Chemical Society (ACS)
Date: 21-02-2020
Publisher: Royal Society of Chemistry (RSC)
Date: 2001
DOI: 10.1039/B008061F
Publisher: AIP Publishing
Date: 08-2005
DOI: 10.1063/1.1992482
Abstract: 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.
Start Date: 2003
End Date: 12-2004
Amount: $135,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 2005
End Date: 12-2007
Amount: $258,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2019
End Date: 12-2024
Amount: $420,000.00
Funder: Australian Research Council
View Funded ActivityStart Date: 02-2012
End Date: 05-2015
Amount: $320,000.00
Funder: Australian Research Council
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