Bulletin of the American Physical Society
2008 APS March Meeting
Volume 53, Number 2
Monday–Friday, March 10–14, 2008; New Orleans, Louisiana
Session Y13: Classical Molecular Dynamics and Fluids |
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Sponsoring Units: DCOMP Chair: Brian Good, NASA GRC Room: Morial Convention Center 204 |
Friday, March 14, 2008 11:15AM - 11:27AM |
Y13.00001: Canonical sampling through velocity rescaling Giovanni Bussi, Davide Donadio, Michele Parrinello We present [1] a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties. [1] G. Bussi, D. Donadio and M. Parrinello, J. Chem. Phys. 126, 014101 (2007) [Preview Abstract] |
Friday, March 14, 2008 11:27AM - 11:39AM |
Y13.00002: Well-tempered metadynamics: a smoothly-converging and tunable free-energy method Alessandro Barducci, Giovanni Bussi, Michele Parrinello We present [1] a method for determining the free energy dependence on a selected number of order parameters using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevantregions of the order parameter space. The algorithm is tested on the reconstruction of alanine dipeptide free energy landscape. [1] A. Barducci, G. Bussi and M. Parrinello, Phys. Rev. Lett., accepted (2007). [Preview Abstract] |
Friday, March 14, 2008 11:39AM - 11:51AM |
Y13.00003: Hard-sphere variational CPMD approach Gerald Faussurier, Christophe Blancard, Pier Luigi Silvestrelli We present a variational method to determine the total free energy of the electron and ion system using the Gibbs-Bogolyubov inequality and a hard-sphere reference system applied to the quantum molecular dynamics code CPMD. Numerical results and comparisons with quantum molecular dynamics simulations and experiments are presented and discussed for dense and expanded aluminum. [Preview Abstract] |
Friday, March 14, 2008 11:51AM - 12:03PM |
Y13.00004: Classical Simulation {\it versus} Perturbation Theory of Anharmonicity in 2D Lennard-Jones Triangular Lattice Xiao Shen, Tao Sun, Julie Stern, Philip B. Allen Classical molecular dynamics simulation and perturbation theory are two methods that can treat the anharmonicity in solids. Classical molecular dynamics simulation can treat anharmonic effects to high order. Perturbation theory beyond lowest order is difficult, and has convergence issues. However, perturbation theory easily treats the thermodynamic limit, while simulation is necessarily done on a finite system. This raises interesting questions such as whether molecular dynamic simulation will give the correct decay rate when the phonon mean free path is larger than the simulation cell. We try to answer such questions, and explore the limits of both methods, by comparing their results. The system we studied is a two dimensional triangular lattice model with a Lennard-Jones potential. [Preview Abstract] |
Friday, March 14, 2008 12:03PM - 12:15PM |
Y13.00005: Dissipation in an electric field-driven synthetic rotary caltrop-based molecular motor Corina Barbu, Vincent Crespi A molecular caltrop has a three-legged base for attachment to a substrate and a vertical molecular shaft functionalized with a dipole-carrying molecular rotor at the upper end. The desired rotational motion of the rotor can generate dissipation when the motor is driven at frequencies which are close to the natural frequencies of soft vibrational modes in the structure or librational of the rotator about field direction. Classical molecular dynamics simulations elucidate the role of these resonances and investigate motor performance under external drive. [Preview Abstract] |
Friday, March 14, 2008 12:15PM - 12:27PM |
Y13.00006: Convergence Rates of a Dynamic Monte Carlo Rejection-Free Method for Interacting particles Marta Guerra, Mark Novotny, Hiroshi Watanabe, Nobuyasu Ito We calculated the efficiency of a Rejection-Free Monte Carlo method\footnote{H. Watanawe, S. Yukawa, M.A. Novotny and N. Ito, \textit{Efficiency of Rejection-free dynamic Monte Carlo methods for homogeneous spin models, hard disk systems, and hard sphere system}, Phys. Rew. E, \textbf{74}, 026707 (2006)} in the limit of low temperatures and/or high densities for $d$-dimensional particles interacting through a repulsive power-law $r^p$ as well as Lennard-Jones Interactions. Theoretically we find the algorithmic efficiency is proportional to $\rho^{\frac{p+2}{2}}T^{-\frac{d}{2}}$ where $\rho$ is the particle density and T the temperature. For different powers ($p$) in 1, 2 and 3 dimensions as a function of $T$ and $\rho$, we report results in agreement with our theoretical predictions [Preview Abstract] |
Friday, March 14, 2008 12:27PM - 12:39PM |
Y13.00007: Introducing the Reduced Monte Carlo Scheme (RMCS) with Application for Hard Sphere Equation of State and First Order Phase Transition Uduzei Edgal, David Huber This is the first demonstration of a novel approach, the ``Reduced Monte Carlo Scheme'' (RMCS), developed for the investigation of the statistical thermodynamic properties of multi-scale material systems (classical and quantum) over the entire temperature and density range, with arbitrary inter-particle interactions. RMCS employs a new ensemble, the ``nearest neighbor ensemble'' involving the PDF for ``n'' nearest neighbor configurations. RMCS results for the equation of state of the hard sphere system from low densities to densities in the neighborhood of closest packing will be discussed. The power of RMCS as a materials investigative tool will be tested within the region of first order phase transition as well as for correct asymptotic behavior of the solid phase equation of state. Early results show that RMCS provides accurate results in the fluid phase employing ``small'' n values, thus suggesting that RMCS may provide a highly efficient computational scheme in contrast to traditional Monte Carlo methods which normally require ``large'' systems for computation. Also to be discussed briefly, is the outlook for the development of the quantum version of RMCS for quantum systems. [Preview Abstract] |
Friday, March 14, 2008 12:39PM - 12:51PM |
Y13.00008: ABSTRACT WITHDRAWN |
Friday, March 14, 2008 12:51PM - 1:03PM |
Y13.00009: Angular momentum form of Verlet algorithm for rigid molecules Miyabi Hiyama, Tomoyuki Kinjo, Shiaki Hyodo We seek to make an algorithm based on the Verlet method which could be applied to non-Hamiltonian and explicit time dependent Hamiltonian systems for rigid molecules. For the first step of this aim, we will propose an algorithm based on the Verlet method for rigid molecules and investigate the characteristics of this algorithm for simple system. In our algorithm, the equations of motion for rigid molecules are integrated by Verlet framework in the angular momentum form. This simple algorithm is named `the angular momentum Verlet algorithm'. We will show the results of MD simulations for 125 carbon tetrachloride molecules using the angular momentum Verlet algorithm. The relative total energy fluctuations are compared with those using the standard leap-frog and the Gear predictor-corrector algorithms. The energy drift using the angular momentum Verlet algorithm is smaller than that using the leap-frog or the Gear predictor-corrector algorithms, especially in the case of MD simulation with the large time interval. [Preview Abstract] |
Friday, March 14, 2008 1:03PM - 1:15PM |
Y13.00010: Absorbing boundary conditions for molecular dynamics and multiscale modeling S. Namilae, D.M. Nicholson, P.K.V.V. Nukala, C.Y. Gao, Y.N. Osetsky, D.J. Keffer We present an application of differential equation based local absorbing boundary conditions to molecular dynamics. The absorbing boundary conditions result in the absorbtion of the majority of waves incident perpendicular to the bounding surface. We demonstrate that boundary conditions developed for the wave equation can be applied to molecular dynamics. Comparisons with damping material boundary conditions are discussed. The concept is extended to the formulation of an atomistic-continuum multiscale scheme with handshaking between the regions based on absorbing boundary conditions. The multiscale model is effective in minimizing spurious reflections at the interface. [Preview Abstract] |
Friday, March 14, 2008 1:15PM - 1:27PM |
Y13.00011: Coupling atomistic molecular dynamics and fluctuating hydrodynamics: shear and sound Rafael Delgado-Buscalioni, Gianni de Fabritiis Bridging spatio-temporal scales is the main objective of multiscale modeling and one of the hot-topics in the simulation community. However, compared to gas and solid phase, hybrid schemes based on molecular-continuum domain decomposition of the liquid phase are relatively less developed. The present hybrid model (see PRL 97, 134501 and PRE 76, 036709) is the first to include several decisive features: the molecular domain is described with atomistic accuracy (chemical specificity), and it is embedded within a continuum fluid description based on the Landau-Lifshitz fluctuating hydrodynamics equations. The hybrid scheme is thermodynamically consistent (e.g. the MD domain is an open subsystem in agreement with the grand canonical ensemble) and fluctuations of mass, momentum and stress are seamlessly connected across the molecular-continuum interface. As the scheme is based on mass and momentum conservation, it enables to solve shear and sound waves traveling across both domains. Due to its relevance we consider water as working solvent. As a test case, we have studied the reflection of sound waves by a lipid monolayer (DMPC) immersed in aqueous solvent. [Preview Abstract] |
Friday, March 14, 2008 1:27PM - 1:39PM |
Y13.00012: Concurrent triple-scale simulation of molecular liquids Matej Praprotnik, Kurt Kremer, Rafael Delgado-Buscalioni We present a triple-scale simulation of a molecular liquid, in which the atomistic, coarse-grained and continuum descriptions of the liquid are concurrently coupled. The presented approach successfully sorts out the problem of large molecules insertion in the hybrid particle-continuum simulations and thus opens up the possibility to perform efficient grand-canonical molecular dynamics simulations of open molecular liquid systems. [Preview Abstract] |
Friday, March 14, 2008 1:39PM - 1:51PM |
Y13.00013: Averaged Equations for Species Interactions in Binary Particulate Systems Duan Zhang, Jin Liu Averaged equations for disperse two-phase flows are relatively well-studied compared to averaged equations for binary particulate systems. Disperse two-phase flows can be viewed as a limit of binary particulate system, in which the continuous phase consists of large amount of small particles, such as molecules, and the disperse phase consists of smaller number of large particles. Therefore averaged equations for disperse two-phase flows provide a guidance for the derivation of averaged equations for binary particulate systems. A correct system of averaged equations for binary particulate systems has to recover the averaged equations for disperse two-phase flows in this limit. In this talk it is shown that this can only be done by introducing an interspecies stress in a binary particulate system. Although the framework of deriving the averaged equations is applicable to general particulate systems, numerical simulations are performed for a granular system to study the behaviors of the species exchange force, intraspecies stresses and interspecies stress. [Preview Abstract] |
Friday, March 14, 2008 1:51PM - 2:03PM |
Y13.00014: The Scaling of Atomistic Fluid Dynamics Simulations John Barber, Kai Kadau, Timothy Germann, Berni Alder A series of large-scale atomistic simulations of the Rayleigh-Taylor instability was performed using up to 5.7 billion particles. The results of these simulations, which included a wide range of time and length scales, suggest that atomistic fluid dynamics simulations exhibit a scaling similar to that predicted for Navier-Stokes solvers. Furthermore, quantitative comparison to a macroscopic Rayleigh-Taylor experiment further suggests that the results of atomistic simulations - even for complex non-stationary flows - can be scaled up to describe larger systems. [Preview Abstract] |
Friday, March 14, 2008 2:03PM - 2:15PM |
Y13.00015: A numerical method for miscible two-fluid flow at a large density ratio Siina Haapanen A computational algorithm for direct numerical simulation of a binary system of miscible fluids at a large density ratio is described. The flow is three-dimensional, with two of the three spatial dimensions periodic. A pseudo-spectral discretization is used in the periodic directions, and an eigth order compact finite difference scheme is utilized in the non-periodic direction. The Mach number of the flow is small, and the equations of motion are integrated forward in time using a fractional step method. A constant coefficient elliptic equation (Poisson equation) is solved to determine the pressure. The method is applied to test problems including the Rayleigh-Taylor instability and a miscible two-fluid shear flow. The accuracy of the method, and its stability at a large density ratio of the fluids are discussed. [Preview Abstract] |
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