Bulletin of the American Physical Society
APS March Meeting 2019
Volume 64, Number 2
Monday–Friday, March 4–8, 2019; Boston, Massachusetts
Session L21: Emerging Trends in Molecular Dynamics Simulations and Data Analytics IIFocus

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Sponsoring Units: DCOMP Chair: Duy Le, University of Central Florida Room: BCEC 157B 
Wednesday, March 6, 2019 11:15AM  11:51AM 
L21.00001: Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A PersistentEmbryo Approach Invited Speaker: Yang Sun The nucleation of a crystalline phase in liquid is a typical rare event and is usually inaccessible within the limited timescales of conventional molecular dynamics (MD) simulations under experimental conditions. In this talk, we present a “persistent embryo” method to facilitate crystal nucleation in MD simulations, in which a small crystal embryo is inserted into the liquid, with spring forces applied to keep the embryo from melting. The springs are gradually weakened as the embryo grows and are completed removed when the nucleus size remains significantly smaller than the critical size. In this way, one can observe the spontaneous fluctuations of a critical nucleus in an unbiased environment, without any assumptions on the shape of the critical nucleus. We applied this method to simulate crystal nucleation under realistic experimental conditions and obtained results that compare favorably with experiments and other simulation methods. We will show this accelerated dynamic approach provides ample statistics for the critical sampling of the nucleation. 
Wednesday, March 6, 2019 11:51AM  12:27PM 
L21.00002: TBD Invited Speaker: KlausRobert Müller tbd 
Wednesday, March 6, 2019 12:27PM  12:39PM 
L21.00003: Cavitation in Water Induced by a SnO_{2} Nanoparticle and a Strong Electric Field Shane Jackson, Aiichiro Nakano, Priya Vashishta, Rajiv Kalia Molecular dynamic simulations are performed to examine the effect of an electric field on a system consisting of a SnO_{2} nanoparticle embedded in water under ambient conditions. Cavitation is observed in the presence of uniform electric fields ranging from 0.042 to 0.25 V/Angstrom in both the SPCE and the HydrogenBonding Polarizable (HBP) force field models for water. Over at least one order of magnitude, the cavity onset time t is related to the electric field through the KohlrauschWilliamsWatts form E(t) =E_{0}exp((t/τ)^{β} , with b = d*/(d* + 2) = 3/7 where d* = d/2, d being the dimensionality of the system. The bubbles are found to rapidly collapse upon removal of the electric field. Results for the structure and dynamics of water along with the electric field distributions in the system will be presented. 
Wednesday, March 6, 2019 12:39PM  12:51PM 
L21.00004: Interaction Potential for Faceted Nanoparticles. Brian Lee, Gaurav Arya There is a growing interest in studying the assembly of faceted nanocrystals due to the potential of such anisotropic particles to yield unconventional structures with unique electrical, optical, and mechanical properties. While the van der Waals (vdW) interactions between spherical particles can be welldescribed by analytical functions, no such closedform expressions are available to describe the vdW interactions between faceted particles. This is especially problematic in molecular simulations of particle assembly, where exact descriptions of interparticle energies in terms of interatomic interactions become computationally prohibitive, requiring a polynomial time algorithm. In this work, we formulate analytical expressions for vdW interactions between faceted particle by taking advantage of available expressions for macroscopic body interactions and by converting the energy integration over the particles’ bodies to integration over the particles’ facets. We show that the expressions provide reasonably accurate descriptions of the position and orientation dependence of vdW interactions. Since this method is a constant time algorithm, O(1), it could improve the computational efficiency of simulating faceted particles by several orders of magnitude. 
Wednesday, March 6, 2019 12:51PM  1:03PM 
L21.00005: Atomic Structure of Supported Metal Nano Clusters on MoS_{2} Monolayer Using Deep Potentials Wissam Saidi, Yongliang Shi, Linfeng Zhang, Han Wang, Weinan E, Jin Zhao In nanometer clusters (NCs), the specific arrangement of metal atoms 
Wednesday, March 6, 2019 1:03PM  1:15PM 
L21.00006: LargeScale Atomistic Simulations of Materials using SNAP Potentials Aidan Thompson, Mitchell A Wood, Mary Alice Cusentino Molecular dynamics (MD) is a powerful materials simulation method whose accuracy is limited by the interatomic potential (IAP). SNAP is an automated quantum datadriven approach to IAP generation that balances accuracy and computational cost. The energy is formulated in terms of a very general set of geometric invariants that characterize the local neighborhood of each atom. The SNAP approach has been used to develop potentials for studying plasticity in tantalum, intrinsic defects in indium phosphide, and plasma surface interactions in tungsten and beryllium. In each case, large quantummechanical data sets of energy, force, and stress are accurately reproduced and crossvalidation on additional test data is performed. The resultant potentials enable highfidelity MD simulations with thousands to millions of atoms. The relatively large computational cost of SNAP is offset by the LAMMPS implementation, enabling the efficient use of large CPU and GPU clusters. 
Wednesday, March 6, 2019 1:15PM  1:27PM 
L21.00007: A meanfield algorithm with decoherence and detailed balance for nonadiabatic molecular dynamics Jun Kang, LinWang Wang Decoherence and detailed balance are two major issues for mixed quantum/classic nonadiabatic molecular dynamics (NAMD) simulations. In this work we introduce a new meanfield dynamics approach with decoherence and detailed balance (MFDD) for NAMD. This method is able to explicitly treat the decoherence between different pairs of electronic states. Moreover, the energyincreasing and energydecreasing electronic transitions are distinguished by dividing the density matrix into two parts. The detailed balance correction is then included by a Boltzmann factor applied to the energyincreasing transitions. The MFDD is applied to study hothole cooling and transfer processes in Si quantum dot (QD) systems. The calculated hot carrier relaxation time is in consistent with experiments. In the QDpair systems, the cooling time shows weak dependence with the QD spacing. However, the charge transfer rate between QDs is found to decreases exponentially as the QD spacing increases, which is attributed to the decreased state anticrossing strength. When the QD spacing is smaller than 1.1 nm, the hotcarrier transfer between two QDs can be quite efficient. It is also shown that the explicit treatment of decoherence time is important. 
Wednesday, March 6, 2019 1:27PM  1:39PM 
L21.00008: MultiResolution Simulations using the Integral Equation CoarseGraining Method Mohammadhasan Dinpajooh, Marina Giuseppina Guenza We use the variablelevel coarsegrained (CG) description of polymer melts to obtain the effective CG potentials (ECGPs) for multiresolution simulations of pure polymer melts represented at various CG resolutions. Starting from the Integral Equation CoarseGraining approach, we obtain the numerical and analytical ECGPs in the multiresolution simulations that are different from the ECGPs in singleresolution simulations. Therefore, the composition, temperature, and density dependences of such ECGPs can be investigated. In particular, the ECGPs between the polymer melts, represented by n_{bα} blobs, decay slowly with a long tail characteristic scaling exponent of N_{bα}^{1/4}(φ_{α}+ (1φ_{α}) (n_{bα}/n_{bβ})^{3}))^{1/4}, where φ_{α} is the volume mole fraction of species α, N_{bα }is the number of monomers in a given blob of type α, and β shows the other species. The ECGPs allow one to avoid any hybrid region in multiresolution simulations while quantitatively producing the structural and thermodynamical properties of the related atomistic systems such as radial distribution function and pressure. 
Wednesday, March 6, 2019 1:39PM  1:51PM 
L21.00009: Development of a universal Electron Force Field Isidro Losada López, Michelle Fritz, Paula MoriSanchez, Marivi Fernandez Serra, Jose M Soler In many cases, the unavailability of an adequate classical force field is a major barrier for molecular dynamics simulations. In these cases, density functional theory (DFT) provides a universal but expensive option. We propose an intermediate approach based on an ‘electron force field’ (eFF) [Su and Goddard, PRL 99, 185003 (2007)]. Inspired by VSEPR theory, we expand the electron density as a sum of overlapping spherical electron ‘balls’ (eballs). The eballs interact through electrostatic forces, Pauli repulsion, and exchangecorrelation. The electronic total energy is calculated as a universal function of the eball positions and widths. As in DFT, it is independent of the nuclei, which interact only electrostatically. We parameterize this universal, manybody function by fitting to DFT calculations of a large number of molecules and solids at equilibrium, distorted, and reaction geometries. 
Wednesday, March 6, 2019 1:51PM  2:03PM 
L21.00010: Modeling of La^{3+} doping segregation in nanocrystalline yttriastabilized zirconia using a combintaion of atomistic MD, Monte Carlo and Nudged Elatic Band calculations Shenli Zhang, Roland Faller The effect of La3+ doping on the structure and ionic conductivity change in nanocrystalline yttriastabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics and Nudge Elastic Band simulations. Simulations of specific grain boundary configurations are developed. Systems with and withoout La doping are studied and equilibrated using a combintaion of techniques and eventually anaylzed using Voronoi tesselation analysis for the density of the dopants. 
Wednesday, March 6, 2019 2:03PM  2:15PM 
L21.00011: Ultrafast detonation of hydrazoic acid: a case study of the ChIMES model Huy Pham, Nir Goldman, Laurence Fried Understanding the chemical evolution and states of matter of an energetic material under detonation is challenging due to the short time scales of chemical reactions and risk of experimental work. Firstprinciple molecular dynamics simulations can provide valuable insights into such systems. However, the computational cost associated with those simulations limits their applicability to relatively small systems and short time scales. We have developed the Chebyshev Interaction Model for Efficient Simulation (ChIMES), a reactive force field, using force matching to trajectories from density functional theory (DFT). This force field has been shown to be capable of retaining the accuracy of DFT simulation while increasing orders of magnitude in computational efficiency. In this work, we use ChIMES to study hydrazoic acid, an azide energetic material that exhibits an ultrafast detonation during a shock wave. We find that our models are able to accurately reproduce the structural and dynamic properties computed from DFT at different thermodynamic states. The ability to describe charge transfer and chemical reactions is also discussed. 
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