Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session A13: Focus Session: Metropolis Thesis Prize and Multiscale Modeling |
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Sponsoring Units: DCOMP Chair: Jorge Jose, SUNY Buffalo Room: 309 |
Monday, March 16, 2009 8:00AM - 8:12AM |
A13.00001: Flexibility and Direction Reversal in Flapping Locomotion Saverio Spagnolie, Michael Shelley In order to better understand the role of flexibility in the flapping of wings and fins in Nature, experimentalists at NYU have studied a heaving foil with passive pitching. We analyze this system numerically, having constructed a high-order accurate numerical scheme to solve the full Navier-Stokes equations in two-dimensions to study the dynamics. We are able to reproduce qualitatively the results of the experiments: by increasing the flapping frequency, we find regions of improved performance when compared to a rigid wing, regions of under-performance, and a bi-stable regime where the flapping wing can move horizontally in either direction. The numerical simulations have led to predictions of other modes of flapping locomotion, which have subsequently been observed in experiments. We also find that a symmetry breaking transition to forward flapping flight, as observed in experiments of a heaving foil with no pitching, may be directed with only very slight flexibility. [Preview Abstract] |
Monday, March 16, 2009 8:12AM - 8:24AM |
A13.00002: Modeling the combined effect of surface roughness and shear rate on slip flow of simple fluids Anoosheh Niavarani, Nikolai Priezjev Molecular dynamics (MD) and continuum simulations are carried out to investigate the combined effect of shear rate and surface roughness on interfacial slip in simple fluids. For weak wall-fluid interaction energy, the nonlinear shear rate dependence of the slip length in a flow past atomically flat surfaces is obtained from MD simulations. Both the magnitude of the slip length and the slope of its rate-dependence are significantly reduced in the presence of periodic surface roughness. Continuum simulations are used to reproduce the behavior of the effective slip length in a flow over periodically corrugated surface at low shear rates. The continuum analysis includes the functional form of the slip length vs. local shear rate computed from MD simulations. The discrepancy between MD and continuum results at higher shear rates is explained by examination of the local velocity profiles and pressure distribution along the wavy surface. [Preview Abstract] |
Monday, March 16, 2009 8:24AM - 8:36AM |
A13.00003: KMC simulations in 3+1 dimensions and the effects of attachment probabilities and potential gradients on island morphologies Christopher Fleck, Judith Yang, Alan McGaughey, Jun Ren Thin film growth and nano-oxidation have received significant attention lately, especially given the interesting nature of Cu$_{2}$O growth. Our long-term vision is for a comprehensive, fundamental understanding of a gas-surface reaction via coordinated multi-scale theoretical and in situ experimental efforts. The link between the theoretical and experimental efforts is our kinetic Monte Carlo (kMC) code that simulates general behavior of the irreversible nucleation and growth of epitaxial islands. This simulation was originally a versatile 2+1 dimensional kMC code (Thin Film Oxidation or TFOx) that considered a wide range of elementary steps, including deposition, adsorption, dissociation of gas molecules, surface diffusion, aggregation, desorption, and substrate-mediated indirect interactions between static adatoms. Recently, TFOx has been extended to a 3+1 dimensional kMC code composed of a C++ console program and Python GUI, such that parameterized testing, parallel execution, and 3D growth capabilities are feasible. Emphasis has been placed on the affects of the potential gradient, multilayer nucleation and sticking parameter on the 3D island morphology. [Preview Abstract] |
Monday, March 16, 2009 8:36AM - 9:12AM |
A13.00004: Nicholas Metropolis Award for Outstanding Doctoral Thesis Work in Computational Physics Talk: Understanding Nano-scale Electronic Systems via Large-scale Computation Invited Speaker: Chao Cao Nano-scale physical phenomena and processes, especially those in electronics, have drawn great attention in the past decade. Experiments have shown that electronic and transport properties of functionalized carbon nanotubes are sensitive to adsorption of gas molecules such as H2, NO2, and NH3. Similar measurements have also been performed to study adsorption of proteins on other semiconductor nano-wires. These experiments suggest that nano-scale systems can be useful for making future chemical and biological sensors. Aiming to understand the physical mechanisms underlying and governing property changes at nano-scale, we start off by investigating, via first-principles method, the electronic structure of Pd-CNT before and after hydrogen adsorption, and continue with coherent electronic transport using non-equilibrium Greenâ€™s function techniques combined with density functional theory. Once our results are fully analyzed they can be used to interpret and understand experimental data, with a few difficult issues to be addressed. Finally, we discuss a newly developed multi-scale computing architecture, OPAL, that coordinates simultaneous execution of multiple codes. Inspired by the capabilities of this computing framework, we present a scenario of future modeling and simulation of multi-scale, multi-physical processes. [Preview Abstract] |
Monday, March 16, 2009 9:12AM - 9:24AM |
A13.00005: Role of Adatom Relaxations in Computing Lattice-gas Energies: Multisite Interactions Rajesh Sathiyanarayanan, T. L. Einstein In simple lattice-gas models, only nearest-neighbor pair interactions are used to model adatom interactions. However, multisite interactions, such as trios and quartos, are necessary to understand certain surface properties like the orientation dependence of step stiffness and the equilibrium shape of islands. Strong multisite interactions are found to be present on a variety of metallic surfaces. Unlike pair interactions, the relaxations of adatoms in a multisite interaction are not along bond directions. Hence, these adatoms can shift significantly from their high-symmetry positions, making multisite interactions more sensitive to relaxations. Using VASP calculations, we showed that trios are very sensitive to lateral adatom relaxations on Pt(111) and Cu(100)\footnote[2]{Rajesh Sathiyanarayanan \textit{et al.}, Surf. Sci. \textbf{602} (2008) 1243.}. Our recent calculations on Cu(110) indicate that in addition to trios, quartos also undergo a big change due to adatom relaxations. Such findings severely limit the effectiveness of lattice-gas models in characterizing surface interactions. We discuss alternate approaches to this problem. [Preview Abstract] |
Monday, March 16, 2009 9:24AM - 9:36AM |
A13.00006: Rapid and Accurate Estimates of Alloy Phase Diagrams for Design and Assessment Teck Tan, Duane Johnson Based on first-principles cluster expansion (CE), we obtain rapid but accurate assessments of alloy T vs c phase diagrams from a mean-field theory that conserves sum rules over pair correlations. Such conserving mean-field theories are less complicated than the popular cluster variation method, and better reproduce the Monte Carlo (MC) phase boundaries and T$_{c}$ for the nearest-neighbor Ising model [1]. The free-energy f(T,c) is a simple analytic expression and its value at fixed T or c is obtained by solving a set of n non-linear coupled equations, where n is determined by the number of sublattices in the groundstate structure and the range of pair correlations included. While MC is ``exact,'' conserving mean-field theories are 10 to 10$^{3}$ faster, allowing for rapid phase diagram construction, dramatically saving computation time. We have generalized the method to account for multibody interactions to enable phase diagram calculations via first-principles CE, and its accuracy is showed vis-\`a-vis exact MC for several alloy systems. The method is included in our Thermodynamic ToolKit (TTK), available for general use in 2009. [1] V. I. Tokar, Comput. Mater. Sci.\textbf{ 8} (1997), p.8 [Preview Abstract] |
Monday, March 16, 2009 9:36AM - 9:48AM |
A13.00007: Chemistry effects on dislocation mobility in refractory bcc metals Nicholas Kioussis, Zhengzheng Chen, Gang Lu, Nasr Ghoniem Using a novel concurrent multiscale approach we demonstrate that the \textit{local environment} of transition-metal solutes in refractory bcc metals has a large effect on the mobility and slip paths of dislocation. The results reveal that solid solutes or nano-clusters of different geometries may lead to solid-solution hardening (SSH) or softening (SSS), in agreement with experiment, including spontaneous dislocation glide and activation of new slip planes. The underlying electronic mechanism is also studied by the multiscale approach. Solutes nano-cluster can affect Peierls potential surface (PPS) dramatically. The results indicate that it is the change of the anisotropy of the lattice resistance induced by solutes that result in the different behavior of the dislocation according to the different geometries of solutes nano-clusters. [Preview Abstract] |
Monday, March 16, 2009 9:48AM - 10:00AM |
A13.00008: Computational studies of thermal evolutions of extended interstitial defects in silicon. Hyoungki Park, John W. Wilkins Annealing induces the nucleation of extended defect clusters in silicon and their evolution, where clusters grow by capturing or interchanging interstitials, and change their crystallographic structure in order to minimize the formation energy. Extensive molecular dynamics (MD) simulations and first-principle nudged elastic band (NEB) simulations explore the thermal transitions from one structure to another of three energetically competing extended interstitial defects: two rod-like defects $\{311\}$ and $\{111\}$, and Frank dislocation loop. MD simulations capture critical sequences of atomistic processes during transitions from $\{311\}$ and $\{111\}$ defects to Frank loops as their atomic configurations and habit planes change, and massively parallelized NEB simulations within the local density approximation reveal the energetics of reaction barriers. [Preview Abstract] |
Monday, March 16, 2009 10:00AM - 10:12AM |
A13.00009: Multiscale Modeling of Catalysis and its Application to Hydrogen Production through the Water Gas Shift Reaction on Nanoparticles Altaf Karim, James T. Muckerman We describe a density functional kinetic Monte Carlo approach enabling us to study and simulate the steady-state condition of the water gas shift (WGS) reaction on Cu and Au nano-particles supported on ZnO(0001) surfaces. We have adopted a multiscale modeling paradigm in which density functional theory can be used to determine the behavior of systems at much larger length and time scales by coupling it with kinetic Monte Carlo methods. In the first step, density functional theory is used to obtain the energetics of the relevant atomistic processes of the WGS reaction on Cu and Au nanoparticles. Subsequently, the kinetic Monte Carlo method is employed, which accounts for the spatial distribution, fluctuations, and evolution of chemical species under steady-state conditions. Our simulations show that, in agreement with experiments, the hydrogen production rate strongly depends on size and structure of the nanoparticles. [Preview Abstract] |
Monday, March 16, 2009 10:12AM - 10:24AM |
A13.00010: Preparation of nanoporous systems for the study of the mechanical properties of silica aerogels by Molecular Dynamics simulations John S. Rivas Murillo, Martina E. Bachlechner, Ever J. Barbero This presentation focuses on the application of the Molecular Dynamics technique to study the mechanical properties of silica aerogels through the simulation of a tension test. It covers multiple areas, including aspects related to the preparation of a well-relaxed nanoporous system from the expansion of an amorphous bulk sample and the influence of the initial configuration of the system on the final results of the simulated tension test. The results presented here will help to develop a more complete procedure to prepare a proper sample for the study of the mechanical properties of a nanoporous system by using Molecular Dynamics. Comparison of the simulation results and previously published experimental data is provided [Preview Abstract] |
Monday, March 16, 2009 10:24AM - 10:36AM |
A13.00011: A hierarchical DPD thermostat to avoid over and/or underdamping at long wavelengths in MD simulations Kevin Green, Colin Denniston, Martin Muser In this talk, we present a new approach to use dissipative particle dynamics as a thermostat in molecular dynamics simulations. The main idea is to have DPD act on groups of atoms so that damping can be tuned as a function of length scale. This allows one to achieve a quality factor of vibrations, which is barely wavelength dependent. The number of floating point operations per time step is orders of magnitude less for the new approach than for regular DPD or any other thermostat acting on individual particles. In addition, the method avoids both underdamping of natural and/or DPD dynamics at long wavelengths L and overdamping which is unavoidable at large L for Langevin or Nose-Hoover based thermostats. Thus correlation times for observables that live on long wavelengths L, are of order L, rather than of order L$^2$ as for conventional thermostats. [Preview Abstract] |
Monday, March 16, 2009 10:36AM - 10:48AM |
A13.00012: Determination of the ground state structures of binary alloys via global space group optimziation (GSGO) with no restrictions on composition:Al-Sc. Giancarlo Trimarchi, Arthur J. Freeman, Alex Zunger Here, we extend the GSGO evolutionary algorithm scheme to survey crystal structures of binary A-B systems {\em without} constraint on the A$_{p}$B$_{q}$ composition. At each generation of the randomly started evolutionary sequences, the formation energy convex hull for the actual population is determined. The search proceeds by replacing the structures farthest away from the convex hull with new ones produced via mating and mutation with no constraints on composition. As a test of this new procedure, we searched the ground state compounds of the Al-Sc alloy whose lattice types are not easily inferred from that of the Al and Sc constituents, respectively fcc and hcp solids. Repeated, independent evolutionary sequences with six and eight atoms in the supercell were performed yielding as ground states respectively B$8_{2}$, B2, and C$15$, and D$0_{19}$, B2, and L$1_{0}$, as known from experiment and previous {\em ab-initio} studies. This yields a synthesis of the final convex hull. [Preview Abstract] |
Monday, March 16, 2009 10:48AM - 11:00AM |
A13.00013: Non-crystalline state of silicon studied by multicanonical simulation combined with first-principles calculation Yoshihide Yoshimoto By combining multicanonical ensemble molecular dynamics and first-principles calculations, non-crystalline state of silicon is studied. This attempt contrast with quenching molecular dynamics simulations whose speed is usually by far quicker than that of experimental quenchings. To make the molecular dynamics simulation tractable, a model interatomic potential is used. The parameter, however, is determined by first-principles calculation so that the discrepancy between the first-principles interatomic potential and the model one is minimized on the typical configuration set of the multicanonical ensemble. Because multicanonical ensemble represents the whole thermodynamics of the system, the obtained model will conserve the thermodynamics to a maximum extent. (thermodynamic downfolding of an interatomic potential [1]) The transition between amorphous silicon and liquid silicon, and the density maximum of liquid silicon as a function of temperature will be discussed. (Silicon has similar structure to that of water) [1] Y. Yoshimoto, J. Chem. Phys., 125, 184103 (2006) [Preview Abstract] |
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