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At least 1,459 records · Page 81

The Structure of Liquid and Amorphous Hafnia

Understanding the atomic structure of amorphous solids is important in predicting and tuning their macroscopic behavior. Here, we use a combination of high-energy X-ray diffraction, neutron diffraction, and molecular dynamics simulations to benchmark the atomic interactions in the high temperature stable liquid and low-density amorphous solid states of hafnia. The diffraction results reveal an average Hf–O coordination number of ~7 exists in both the liquid and amorphous nanoparticle forms studied. The measured pair distribution functions are compared to those generated from several simulation models in the literature. We have also performed ab initio and classical molecular dynamics simulations that show density has a strong effect on the polyhedral connectivity. The liquid shows a broad distribution of Hf–Hf interactions, while the formation of low-density amorphous nanoclusters can reproduce the sharp split peak in the Hf–Hf partial pair distribution function observed in experiment. The agglomeration of amorphous nanoparticles condensed from the gas phase is associated with the formation of both edge-sharing and corner-sharing HfO6,7 polyhedra resembling that observed in the monoclinic phase.

36 MATERIALS SCIENCE↗

Molecular Dynamics Investigation of the Relaxation Mechanism of Entangled Polymers after a Large Step Deformation

The chain retraction hypothesis of the tube model for nonlinear polymer rheology has been challenged by the recent small-angle neutron scattering (SANS) experiment. In this study, we further examine the microscopic relaxation mechanism of entangled polymer melts after a large step uniaxial extension by using large-scale molecular dynamics simulation. We show that the unique structural features associated with the chain retraction mechanism of the tube model are absent in our simulations, in agreement with the previous experimental results. In contrast to SANS experiments, molecular dynamics simulations allow us to accurately and unambiguously determine the evolution of the radius of gyration tensor of a long polymer chain after a large step deformation. Contrary to the prediction of the tube model, our simulations reveal that the radius of gyration in the perpendicular direction to stretching increases monotonically toward its equilibrium value throughout the stress relaxation. These results provide a critical step in improving our understanding of nonlinear rheology of entangled polymers.

36 MATERIALS SCIENCE↗

Sr-induced dipole scatter in Ba x Sr 1– x TiO 3 : Insights from a transferable-bond valence-based interatomic potential

In order to design next-generation ferroelectrics, a microscopic understanding of their macroscopic properties is critical. One means to achieve an atomistic description of ferroelectric and dielectric phenomena is classical molecular dynamics simulations. Previously, we have shown that interatomic potentials based on the bond valence molecular dynamics method can be used to study structural phase transitions, ferroelectric domain nucleation, and domain wall migration in several perovskite oxides and fixed-composition binary and ternary alloys. Most modern devices, however, use variable-composition perovskite oxide alloys such as Ba x Sr 1– x TiO 3 (BST). Here, we extend our bond valence approach to BST solid solutions and, in so doing, show that the potential parameters for each element are transferable between materials with different x . Using this potential, we perform bond valence molecular dynamics simulations investigating the temperature and composition dependence of the lattice constants, Ti displacements, and ferroelectric polarization of BST and find that our predictions match experiments and first-principles theory. Additionally, based on a detailed analysis of local dipole distributions in rhombohedral BST, we demonstrate that substitution of Sr for Ba scrambles dipoles, reduces global polarization, and enhances the order-disorder character of the ferroelectric-paraelectric phase transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Systematic coarse-graining in nucleation theory

In this work, we show that the standard method to obtain nucleation rate-predictions with the aid of atomistic Monte Carlo simulations leads to nucleation rate predictions that deviate 3 − 5 orders of magnitude from the recent brute-force molecular dynamics simulations [Diemand et al., J. Chem. Phys. 139, 074309 (2013)] conducted in the experimental accessible supersaturation regime for Lennard-Jones argon. We argue that this is due to the truncated state space the literature mostly relies on, where the number of atoms in a nucleus is considered the only relevant order parameter. We here formulate the nonequilibrium statistical mechanics of nucleation in an extended state space, where the internal energy and momentum of the nuclei are additionally incorporated. We show that the extended model explains the lack in agreement between the molecular dynamics simulations by Diemand et al. and the truncated state space. We demonstrate additional benefits of using the extended state space; in particular, the definition of a nucleus temperature arises very naturally and can be shown without further approximation to obey the fluctuation law of McGraw and LaViolette. In addition, we illustrate that our theory conveniently allows to extend existing theories to richer sets of order parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A generalized transport-velocity formulation for smoothed particle hydrodynamics

The standard smoothed particle hydrodynamics (SPH) method suffers from tensile instability. In fluid-dynamics simulations this instability leads to particle clumping and void regions when negative pressure occurs. In solid-dynamics simulations, it results in unphysical structure fragmentation. In this work the transport-velocity formulation of Adami et al. (2013) is generalized for providing a solution of this long-standing problem. Other than imposing a global background pressure, a variable background pressure is used to modify the particle transport velocity and eliminate the tensile instability completely. Furthermore, such a modification is localized by defining a shortened smoothing length. The generalized formulation is suitable for fluid and solid materials with and without free surfaces. The results of extensive numerical tests on both fluid and solid dynamics problems indicate that the new method provides a unified approach for multi-physics SPH simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Transformation-induced plasticity in bulk metallic glass composites evidenced by in-situ neutron diffraction

Transformation-induced plasticity in a strain-softening amorphous matrix consisting of austenite B2 phase was studied by in-situ neutron diffraction, coupled with molecular dynamic simulation. It was found that the martensitic transformation from B2 to B19' upon loading commenced at the macroscopic yielding which increased with the decrease of the fraction of the parent austenite B2 phase, and the threshold lattice strain for the martensitic transformation is almost the same in different samples, suggesting that the martensitic transformation in the current glassy matrix is strain-controlled. Analysis of load partition and strain accommodation unveiled that B2 has elastic anisotropy, and the desirable elastic match between B2 and the amorphous matrix ensures a good cooperative deformation. Additionally, molecular dynamic simulation revealed that atoms at the interface between B2 and the amorphous matrix deviated from the standard B2 lattices and acted as nucleation site for the martensitic transformation, eventually giving rise to the strain-controlled martensitic transformation. Our findings provide new insights into the mechanism of phase transformation-mediated plasticity at the microscopic level, and have useful implications for developing novel, high-performance bulk metallic glass composites.

36 MATERIALS SCIENCE↗

FACETS Dynamical Downscaling Simulations over North America by the CAM-MPAS Variable-Resolution Model

Comprehensive assessment of climate datasets created by statistical or dynamical models is important for effectively communicating model projection and associated uncertainty to stakeholders and decision-makers. The Department of Energy FACETS project aims to foster such communication through development of metrics and their demonstration on a hierarchy of downscaled climate datasets to quantify aspects of climate change projections that are credible, particularly for supporting decisions related to the energy-water-land nexus. As a part of this effort, we have produced a regional climate dataset using the Model for Prediction Across Scales coupled to the Community Atmosphere Model (CAM-MPAS). This global modeling framework is configured with variable-resolution meshes featuring higher resolutions over North America, as well as quasi-uniform resolution meshes across the globe. The variable-resolution configurations allow fine-scale features to be better resolved inside the refinement and interact with global-scale circulations. The dataset includes multiple uniform- (240km and 120km) and variable-resolution (200-50km, 100-25km, and 46-12km) simulations that are designed to be compatible with other regional climate simulations that contribute to the hierarchy of downscaled climate datasets of the project. Furthermore, the dataset consists of simulations for both the present-day (1989-2010) and future (2079-2100) climate and post-processing of the model output has been coordinated across the project for consistency to facilitate common analysis across the hierarchy of datasets. Altogether, this CAM-MPAS model dataset provides a unique opportunity to assess the influence of resolutions and modeling framework on model credibility and climate change projection.

Sakaguchi, Koichi↗

Computational Enzymology and Organophosphorus Degrading Enzymes: Promising Approaches Toward Remediation Technologies of Warfare Agents and Pesticides

The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.The re-emergence of chemical weapons as a global threat in hands of terrorist groups, together with an increasing number of pesticides intoxications and environmental contaminations worldwide, has called the attention of the scientific community for the need of improvement in the technologies for detoxification of organophosphorus (OP) compounds. A compelling strategy is the use of bioremediation by enzymes that are able to hydrolyze these molecules to harmless chemical species. Several enzymes have been studied and engineered for this purpose. However, their mechanisms of action are not well understood. Theoretical investigations may help elucidate important aspects of these mechanisms and help in the development of more efficient bio-remediators. In this review, we point out the major contributions of computational methodologies applied to enzyme based detoxification of OPs. Furthermore, we highlight the use of PTE, PON, DFP, and BuChE as enzymes used in OP detoxification process and how computational tools such as molecular docking, molecular dynamics simulations and combined quantum mechanical/molecular mechanics have and will continue to contribute to this very important area of research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coupling Chemical Energy with Protein Conformational Changes to Translocate Small Molecules Across Membranes

EmrE is a small, homodimeric membrane transporter that exploits the established pH gradient across the E. coli inner membrane to export polyaromatic cations that might otherwise inhibit cellular growth. While herculean efforts through experimental studies have established many fundamental facts about the specificity and rate of substrate transport in EmrE, the low resolution of the available structures have hampered efforts to tie those findings to the EmrE coupling mechanism between proton and small molecule substrates. Here we present a full three-dimensional structure of EmrE optimized against available cyro-EM data to delineate the critical interactions by which EmrE regulates its conformation. We use the generated structural model to conduct equilibrium and nonequilibrium molecular dynamics simulations to probe EmrE dynamics under different substrate loading states, representing different states in the transport cycle. The model is stable under extended simulation, and reveals that water dynamics within the EmrE lumen change substantially with the loading state. The water dynamics cause hydrogen bonding networks to shift radically when the protonation states change for a pair of solvent-exposed glutamate residues (E14) within the lumen of the transporter, which are proposed to act as proton binding sites during the transport cycle. One specific hydrogen bond from a tyrosine (Y60) of one monomer to a glutamate (E14) on the opposite monomer is especially critical, as it locks the protein conformation when the glutamate is deprotonated. Furthermore, the hydrogen bond provided by Y60 lowers the pK a of the interacting glutamate relative to its partner on the opposite monomer such that it will protonate second, establishing the need for both glutamates to be protonated for the hydrogen bond to break and a substrate-free transition to take place.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamic Rupture Simulations of Caldera Collapse Earthquakes: Effects of Wave Radiation, Magma Viscosity, and Evidence of Complex Nucleation at Kilauea 2018

All instrumented basaltic caldera collapses have generated M w > 5 very long period earthquakes. However, previous studies of source dynamics have been limited to lumped models treating the caldera block as rigid, leaving open questions related to how ruptures initiate and propagate around the ring fault, and the seismic expressions of those dynamics. Here, we present the first 3D numerical model capturing the nucleation and propagation of ring fault rupture, the mechanical coupling to the underlying viscoelastic magma, and the associated seismic wavefield. We demonstrate that seismic radiation, neglected in previous models, acts as a damping mechanism reducing coseismic slip by up to half, with effects most pronounced for large magma chamber volume/ring fault radius or highly compliant crust/compressible magma. Viscosity of basaltic magma has negligible effect on collapse dynamics. In contrast, viscosity of silicic magma significantly reduces ring fault slip. We use the model to simulate the 2018 Kilauea caldera collapse. Three stages of collapse, characterized by ring fault rupture initiation and propagation, deceleration of the downward-moving caldera block and magma column, and post-collapse resonant oscillations, in addition to chamber pressurization, are identified in simulated and observed (unfiltered) near-field seismograms. A detailed comparison of simulated and observed displacement waveforms corresponding to collapse earthquakes with hypocenters at various azimuths of the ring fault reveals a complex nucleation phase for earthquakes initiated on the northwest. Our numerical simulation framework will enhance future efforts to reconcile seismic and geodetic observations of caldera collapse with conceptual models of ring fault and magma chamber dynamics.

58 GEOSCIENCES↗

Machine Learning Enabled Atomistic Study of the Micro-Cold Spray Process [Poster]

Micro-cold spray is typically conducted by impacting 200-2000 nm particles at velocities of ~500 m/s. Molecular dynamics simulations have been used to study micro cold spray, but the particles that can be simulated using conventional potentials are much smaller than those used experimentally. The viewgraphs taken from molecular dynamics simulations and shown below are cross-sections of a 50 nm Ta particle with a 3 nm oxide layer impacting at 500 m/s using a machine learning enabled DeePMD potential. Using more expensive reactive interatomic potentials, the previous largest particle size for a metal/oxide impact simulation was 12 nm.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Numerical Simulation of Rolling-Airframes Using a Multi-Level Cartesian Method

A supersonic rolling missile with two synchronous canard control surfaces is analyzed using an automated, inviscid, Cartesian method. Sequential-static and time-dependent dynamic simulations of the complete motion are computed for canard dither schedules for level flight, pitch, and yaw maneuver. The dynamic simulations are compared directly against both high-resolution viscous simulations and relevant experimental data, and are also utilized to compute dynamic stability derivatives. The results show that both the body roll rate and canard dither motion influence the roll-averaged forces and moments on the body. At the relatively, low roll rates analyzed in the current work these dynamic effects are modest, however the dynamic computations are effective in predicting the dynamic stability derivatives which can be significant for highly-maneuverable missiles.

Murman, Scott M.↗

An Integrated Transmission-Distribution Co-Simulation for a Distribution System with High Renewable Penetration

Traditionally, transmission and distribution system dynamic simulations are performed independently. However, dynamic co-simulation of transmission-distribution systems can be beneficial in analyzing distribution systems with high penetration of distributed renewable resources. The authors describe a framework for conducting transmission-distribution dynamic co-simulation (TDDS). A model of a real network including detailed models of solar photovoltaic units in the distribution system is constructed. The initial operating point of the network is validated against field measurements. The TDDS tool is used to simulate a single line-to-ground fault on the distribution system, highlighting the need for conducting transmission-distribution co-simulations.

14 SOLAR ENERGY↗

Short-range order and dynamics of atoms in liquid gallium

The features of the microscopic structure, as well as one-particle and collective dynamics of liquid gallium in the temperature range from T = 313 to 1273 K, are studied on the p = 1.0 atm isobar. Detailed analysis of the data on diffraction of neutrons and X-rays, as well as the results of atomic dynamics simulation, lead to some conclusions about the structure. In particular, for preset conditions, gallium is in the equilibrium liquid phase showing no features of any stable local crystalline clusters. The pronounced asymmetry of the principle peak of the static structure factor and the characteristic “shoulder” in its right-hand part appearing at temperatures close to the melting point, which are clearly observed in the diffraction data, are due to the fact that the arrangement of the nearest neighbors of an arbitrary atom in the system is estimated statistically from the range of correlation length values and not by a single value as in the case of simple liquids. Compactly located dimers with a very short bond make a significant contribution to the statistics of nearest neighbors. The temperature dependence of the self-diffusion coefficient calculated from atomic dynamics simulation agrees well with the results obtained from experimental spectra of the incoherent scattering function. Interpolation of the temperature dependence of the self-diffusion coefficient on a logarithmic scale reveals two linear regions with a transition temperature of about 600 K. The spectra of the dynamic structure factor and spectral densities of the local current calculated by simulating the atomic dynamics indicate the existence of acoustic vibrations with longitudinal and transverse polarizations in liquid gallium, which is confirmed by experimental data on inelastic scattering of neutrons and X-rays. It is found that the vibrational density of states is completely reproduced by the generalized Debye model, which makes it possible to decompose the total vibrational motion into individual contributions associated with the formation of acoustic waves with longitudinal and transverse polarizations. Comparison of the heights of the low-frequency component and of the high-frequency peak in the spectral density of vibrational states also indicates a temperature of T ≈ 600 K, at which the diffusion type of one-particle dynamics changes to the vibrational type upon a decrease in temperature. It is demonstrated that the modified Einstein–Stokes relation can be derived using the generalized Debye model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor–acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states. However, due to the lack of polarization, which imparts subtle changes in the charge distribution on atoms, molecular simulations fail to produce accurate average dipole moments. We developed the first polarizable model for a molecular triad to investigate the structural and dynamic properties of a molecular triad in the ground state in an explicit organic solvent, tetrahydrofuran (THF). We performed first-principles electronic structure calculations of the individual components in the triad as well as THF and then fit the partial atomic charges to the electrostatic potential using the i-RESP methodology. We validated these force field parameters by comparing the thermodynamic and dynamic properties obtained from molecular dynamics simulations with those from experiments. We enhanced the sampling of the triad conformations with replica exchange molecular dynamics simulations. We characterized the effects of induced polarization on the structural stability of the triad by analyzing the free energy landscapes constructed with polarizable force fields. Furthermore, by using principal component analysis, we found that the molecular triad conformations adopted a small range of torsional angles with induced polarization. The triad conformation solvated in polar solvent with a polarizable force field qualitatively agrees with that obtained from nuclear magnetic resonance spectroscopy.

Starovoytov, Oleg N.↗