Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session X19: Classical and Quantum Molecular Dynamics |
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Sponsoring Units: DCOMP Chair: Isaac Tamblyn, Lawrence Berkeley National Laboratory Room: D170 |
Thursday, March 24, 2011 2:30PM - 2:42PM |
X19.00001: Structure and Dynamics of Shock-Induced Nanobubble Collapse in Water Mohammad Vedadi, Amit Choubey, Ken-ichi Nomura, Rajiv Kalia, Aiichiro Nakano, Priya Vashishta, Adri van Duin Structure of water under shock and shock-induced collapse of nanobubbles in water are investigated with molecular dynamics simulations based on a reactive force field. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. In the presence of a nanobubble, we observe a focused nanojet at the onset of nanobubble shrinkage and a secondary shock wave upon nanobubble collapse. The secondary shock wave propagates spherically backwards and induces high pressure as it propagates. Both the propagation velocity and the induced pressure are larger than those of the primary shock. We explored effects of nanobubble radius and shock amplitude on nanojet formation. The nanojet size increases by increasing particle velocity but the effect of increasing radius is more significant. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock-induced collapse of a nanobubble in the vicinity of a cell membrane creates a transient nanopore when the nanojet impacts the membrane. Transient cell poration has potential applications in drug delivery. [Preview Abstract] |
Thursday, March 24, 2011 2:42PM - 2:54PM |
X19.00002: Thermal conductivity of ultra high temperature ceramics (UHTC) $ZrB_2$ and $HfB_2$ from atomistic simulations John Lawson, Murray Daw, Charles Bauschlicher Ultra high temperature ceramics (UHTC) including $ZrB_2$ and $HfB_2$ are characterized by high melting point, good strength, and reasonable oxidation resistance. These materials are of interest for use as sharp leading edges for hypersonic vehicles among other applications. Progress in computational modeling of UHTCs has been limited in part due to the absence of suitable interatomic potentials. Recently, we developed Tersoff style parametrizations of such potentials for both $ZrB_2$ and $HfB_2$ appropriate for atomistic simulations. As an application, Green-Kubo molecular dynamics simulations were performed to evaluate the lattice thermal conductivity for single crystals of $ZrB_2$ and $HfB_2$. The atomic mass difference in these binary compounds leads to oscilations in the time correlation function of the heat current, in contrast to the more typical monotonic decay seen in monoatomic materials. Results at room temperature and at elevated temperatures will be reported. [Preview Abstract] |
Thursday, March 24, 2011 2:54PM - 3:06PM |
X19.00003: A robust and monotonically convergent iterative algorithm for solving the Kohn-Sham equations in metallic systems Jean-Luc Fattebert We propose a new iterative algorithm to efficiently calculate the electronic structure in Density Functional Theory calculations of metallic systems and warm dense matter with high electronic temperature. This parameter-free algorithm directly searches for a set of wave functions and a compatible single particle density that minimizes the Mermin finite temperature functional. It is particularly useful for simulating physical systems considered difficult to converge, such as large systems with variable occupancies and presenting charge sloshing. We demonstrate the effectiveness of the proposed algorithm and its implementation by applying it to challenging large scale problem in First-Principles Molecular Dynamics simulations. [Preview Abstract] |
Thursday, March 24, 2011 3:06PM - 3:18PM |
X19.00004: Molecular Dynamics with Quantum Fluctuations Ionut Georgescu, Jason Deckman, Vladimir Mandelshtam A new Quantum Dynamics approach, called Gaussian Molecular Dynamics (GMD), is introduced. As in the Centroid Molecular Dynamics (CMD), the N-body quantum system is mapped to an N-body classical system with an effective Hamiltonian arising within the Variational Gaussian Wave-packet approximation. The approach is exact for the harmonic oscillator and for the high-temperature limit, accurate in the short time limit and is computationally very efficient. GMD is furthermore used to estimate the diffusion constant and the spectrum of the velocity auto-correlation function of low pressure para-hydrogen at 14K and respectively 25K. The results are consistent with known experimental and theoretical results, such as CMD and RPMD. [Preview Abstract] |
Thursday, March 24, 2011 3:18PM - 3:30PM |
X19.00005: Biased Monte Carlo technique to accelerate Molecular Dynamics simulations of rare events Pratyush Tiwary, Axel van de Walle We propose a hybrid Monte Carlo (MC) -Molecular Dynamics (MD) technique to study temporally rare event dynamics. By using biased MC sampling (Metropolis-Hastings), we avoid actually visiting low energy states in the MD and instead carry out a quick estimate of the mean escape time to be added to the computer clock. The method does not assume anything about the nature of the transition surfaces separating basins in the energy surface. We then apply the method to the case of dislocation kink movement in BCC metals at low temperatures. [Preview Abstract] |
Thursday, March 24, 2011 3:30PM - 3:42PM |
X19.00006: Ab initio molecular dynamics simulations using a Chebyshev-filtered subspace iteration technique for modeling amorphous silicon dioxide Minjung Kim, Khoonghong Khoo, James Chelikowsky Ab initio molecular dynamics simulations are a powerful tool for examining liquids and amorphous materials; however, such simulations are often computationally intensive. We present a molecular dynamics method that dramatically reduces the computational load using a new algorithm based on Chebyshev-filtered subspace iteration. We apply this method to amorphous silicon dioxide. Amorphous silicon dioxide has been intensively studied owing to its broad applications to electronic devices and photonics. We perform ab initio molecular dynamics simulations to obtain the amorphous structure of silicon dioxide. We employ implement several new procedures to investigate the effect of quenching rates and system sizes. The calculated structure factor for our amorphous structure is in good agreement with experimental data. We performed structural relaxations to calculate the hyperfine splitting constants. Our calculated hyperfine splitting constants of $E^\prime_\gamma$ oxygen defect centers show excellent agreement with electron paramagnetic resonance experiments. We will also discuss statistical results of oxygen-related defect centers. [Preview Abstract] |
Thursday, March 24, 2011 3:42PM - 3:54PM |
X19.00007: Molecular Dynamics simulations of Carbon-Oxygen mixtures in the Core of White Dwarf Stars Andre da Silva Schneider, Joe Hughto, Charles Horowitz, Don Berry A White Dwarf will be the final evolutionary state of most of the stars in our galaxy. The core of these faint and compact stars is a mixture of ions immersed in a degenerate electron gas. The latent heat of fusion of this mixture is important for White Dwarf cooling from which the age of stellar systems can be inferred. Assuming Carbon and Oxygen to be the most abundant elements we studied the phase diagram of the mixture using large classical molecular dynamics simulations. The ion interactions were modeled by a screened Coulomb potential and the system was kept in a half-solid half-liquid state. Understanding the chemical separation that takes place helps estimate the central abundance of these elements and is important for observations of White Dwarfs in globular star clusters [1]. \\[4pt] [1] C.J. Horowitz, A.S. Schneider, and D.K. Berry, Physical Review Letters 104, 231101 (2010) [Preview Abstract] |
Thursday, March 24, 2011 3:54PM - 4:06PM |
X19.00008: Diffusion in Yukawa Crystals in White Dwarfs and Neutron Stars Joseph Hughto, Charles Horowitz, Andre Schneider Compact stars, white dwarfs and neutron stars, contain strongly interacting liquid and solid systems that we model using screened Yukawa interactions. Diffusion of impurities can release significant gravitational energy. We calculate diffusion constants using Molecular Dynamics (MD) simulations for both multicomponent liquid and single component solid systems. Diffusion in the solid depends strongly on the number and nature of crystal defects. We are not aware of previous direct calculations of diffusion in Yukawa crystals. [Preview Abstract] |
Thursday, March 24, 2011 4:06PM - 4:18PM |
X19.00009: MD Simulations of the Breaking Strain of Coulomb Crystals in Neutron Stars: Star mountains and gravitational waves Charles Horowitz, Joe Hughto, Andre Schneider, Don Berry Neutron stars --- collapses stars half again as massive as the sun but with a 10-kilometer radius --- have solid crusts made of dense coulomb crystals. We perform large-scale molecular dynamic simulations of the breaking strain (strength) of this crust including the effects of impurities, defects, and grain boundaries. We find neutron star crust to be the strongest material known, with a breaking stress 10 billion times stronger than steel [1]. This is because of the high density, high pressure, and the long-range nature of the coulomb interactions where each ion interacts with thousands of its neighbors. The crust can support massive mountains that, on a rapidly rotating neutron star, can radiate detectable gravitational waves. These oscillations of space and time, predicted by Einstein almost 100 years ago, should be detected in the next few years. \\[4pt] [1] C. J. Horowitz and Kai Kadau, Phys. Rev. Letters 102, 191102 (2009). [Preview Abstract] |
Thursday, March 24, 2011 4:18PM - 4:30PM |
X19.00010: Tracer Diffusion for Rough Hard Spheres Olga Kravchenko, Mark Thachuk We present a study of tracer diffusion in a rough sphere fluid. In such fluid collisions between particles exchange rotational and translational energy and momentum. As tracer particles grow in size, their diffusion constant is described by the Stokes-Einstein hydrodynamic result. In this limit, smooth hard spheres are shown to adopt ``slip'' boundary conditions. The current results show that rough hard spheres adopt boundary conditions proportional to their degree of roughness, defined by the radius of gyration. Spheres with maximum roughness adopt ``stick'' boundary conditions while those with intermediate roughness adopt values between the ``slip'' and ``stick'' limits. This dependence is found to be almost linear. Changes in the diffusion constants as a function of roughness are also examined and it is found that the dependence is stronger than suggested by the low-density, Boltzmann result. Rough hard spheres model the effect of inelasticity of a real collision and show that even without the presence of attractive forces, the boundary conditions for large particles can deviate from ``slip'' and approach ``stick.'' [Preview Abstract] |
Thursday, March 24, 2011 4:30PM - 4:42PM |
X19.00011: Solvation and thermal effects on the optical properties of naturaldyes: a case study on the flavylium cyanin Arrigo Calzolari, Baris Malcioglu, Ralph Gebauer, Daniele Varsano, Stefano Baroni We present a first-principles study of the effects of both hydration and thermal dynamics on the optical properties of a natural anthocyanin dye, namely, \textit{cyanin} (Cya), in aqueous solution. We combine Car-Parrinello molecular dynamics and time-dependent density functional theory (TDDFT) [1] approaches to simulate the time evolution of UV-vis spectrum of the hydrated Cya molecule at room temperature [2,3]. The spectrum of the dye calculated in the gas phase [4] is characterized by two peaks in the red and in the blue, which would bring about a greenish hue incompatible with the dark purple coloration observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab-initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of molecular distortions, induced by thermal fluctuations. [1] \textit{turbo}-TDDFT, B. Walker, A. Saitta, R. Gebauer, S. Baroni, \textit{Phys. Rev. Lett. }\textbf{2006}, $96$, 113001. [2] A. Calzolari, et. al , \textit{J. Chem. Phys.} \textbf{132}, 114304 (2010). [3] O.B. Malcioglu, A. Calzolari, R. Ghebauer, D. Varsano, and S. Baroni, preprint (2010). [4] A. Calzolari, et al, \textit{J. Phys. Chem. A} \textbf{113} 8801 (2009). [Preview Abstract] |
Thursday, March 24, 2011 4:42PM - 4:54PM |
X19.00012: ABSTRACT WITHDRAWN |
Thursday, March 24, 2011 4:54PM - 5:06PM |
X19.00013: Model inter-atomic potential for Cu-Zr system generated using a multicanonical simulation combined with a first-principles calculation Yoshihide Yoshimoto We can obtain an accurate force field for a molecular dynamics simulation from a first principles calculation. However, the available physical time for a direct first-principles molecular dynamics simulation is often limited to $\sim 10$ ps because of its high computational cost. If we want to achieve much longer physical time, a possible approach is to build a model inter-atomic potential from a first-principles calculation. As a kind of this approach, Yoshimoto has proposed the ``thermodynamic downfolding'' method[1,2] which generates an inter-atomic potential based on a multicanonical simulation combined with a first-principles calculation. With this method, we can expect that the thermodynamics of the system is conserved to a maximum extent. In this presentation, application of the method to Cu-Zr system will be reported. This system is interesting because at an composition this system become a bulk metallic glass which has several technologically attracting properties. The melting properties of the system will be covered.\\[4pt] [1] Y. Yoshimoto, J. Chem. Phys., 125, 184103 (2006)\\[0pt] [2] Y. Yoshimoto, J. Phys. Soc. Jpn., 79, 034602 (2010). [Preview Abstract] |
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