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At least 1,009 records · Page 56

Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Trajectory prediction dimensionality reduction for low-cost connected automated vehicle systems

Here, to facilitate low-cost connected automated vehicle (CAV) system development, this study proposes two interpretable dimensionality reduction techniques in vehicle trajectory prediction, i.e., the piecewise Taylor series approximation (PTA) and the piecewise Fourier series approximation (PFA), to lower computation complexity, reduce device investment, and decrease computation energy consumption. Two benchmarks are developed, the long short-term memory (LSTM)-based model without dimensionality reduction and the LSTM-based model with encoder-decoder (a widely used dimensionality reduction technique). Results show that the four predictions have similar accuracy, and the training time (proportional to computation energy consumption) of models with dimensionality reduction techniques is greatly reduced. The reduction is even more significant when PTA/PFA is used. Sensitivity analysis advises PFA/PTA parameter selections to reduce computation complexity without significant loss of prediction accuracy. Further, the robustness of the LSTM PTA/PFA is proven by the investigation of data noises.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Numerical study of variable density turbulence interaction with a normal shock wave

Accurate numerical simulations of shock–turbulence interaction (STI) are conducted with a hybrid monotonicity-preserving–compact-finite-difference scheme for a detailed study of STI in variable density flows. Theoretical and numerical assessments of data confirm that all turbulence scales as well as the STI are well captured by the computational method. Linear interaction approximation (LIA) convergence tests conducted with the shock-capturing simulations exhibit a similar trend of converging to LIA predictions to shock-resolving direct numerical simulations (DNS). The effects of density variations on STI are studied by comparing the results corresponding to an upstream multi-fluid mixture with the single-fluid case. Here the results show that for the current parameter ranges, the turbulence amplification by the normal shock wave is much higher and the reduction in turbulence length scales is more significant when strong density variations exist. Turbulent mixing enhancement by the shock is also increased and stronger mixing asymmetry in the postshock region is observed when there is significant density variation. The turbulence structure is strongly modified by the shock wave, with a differential distribution of turbulent statistics in regions having different densities. The dominant mechanisms behind the variable density STI are identified by analysing the transport equations for the Reynolds stresses, vorticity, normalized mass flux and density specific volume covariance.

42 ENGINEERING↗

How Accurate Are Approximate Density Functionals for Noncovalent Interaction of Very Large Molecular Systems?

Noncovalent intermolecular interactions are very important in many research areas. Therefore, it is vital to understand the extent to which approximate density functionals give a proper description of noncovalent interactions. Previous research has demonstrated that some approximate density functionals can predict usefully accurate interaction energies for many noncovalent systems; however, most of that work is limited to small and moderate-sized molecules. Very recently though, accurate benchmarks have become available for some very large molecules. Here, the present work applies 21 approximate density functionals to compute the binding energies of seven large molecular systems that have a number of atoms ranging from 200 to 910. The results are judged by comparison to the recently published CIM-DLPNO-CCSD(T) results, which are assumed to provide a reliable benchmark. The five most accurate methods among those tested are found to be PW6B95-D4, PW6B95-D3(BJ), revM11, M06-L, and MN15.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

SchrödingerNet: A Universal Neural Network Solver for the Schrödinger Equation

Recent advances in machine learning have facilitated numerically accurate solution of the electronic Schrödinger equation (SE) by integrating various neural network (NN)-based wave function ansatzes with variational Monte Carlo methods. Nevertheless, such NN-based methods are all based on the Born–Oppenheimer approximation (BOA) and require computationally expensive training for each nuclear configuration. In this work, we propose a novel NN architecture, SchrödingerNet, to solve the full electronic-nuclear SE by defining a loss function designed to equalize local energies across the system. This approach is based on a translationally, rotationally and permutationally symmetry-adapted total wave function ansatz that includes both nuclear and electronic coordinates. Furthermore, this strategy not only allows for an efficient and accurate generation of a continuous potential energy surface at any geometry within the well-sampled nuclear configuration space, but also incorporates non-BOA corrections, through a single training process. Comparison with benchmarks of atomic and small molecular systems demonstrates its accuracy and efficiency.

Chemical calculations↗

Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium

In heterogeneous catalysis, free energy profiles of reactions govern the mechanisms, rates, and equilibria. Energetics are conventionally computed using the harmonic approximation (HA), which requires determination of critical states a priori. Here, we use neural networks to efficiently sample and directly calculate the free energy surface (FES) of a prototypical heterogeneous catalysis reaction—the dissociation of molecular nitrogen on ruthenium—at density-functional-theory-level accuracy. We find that the vibrational entropy of surface atoms, often neglected in HA for transition metal catalysts, contributes significantly to the reaction barrier. The minimum free energy path for dissociation reveals an “on-top” adsorbed molecular state prior to the transition state. While a previously reported flat-lying molecular metastable state can be identified in the potential energy surface, it is absent in the FES at relevant reaction temperatures. Finally, these findings demonstrate the importance of identifying critical points self-consistently on the FES for reactions that involve considerable entropic effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Compositionally Tuning Electron Transfer from Photoexcited Core/Shell Quantum Dots via Cation Exchange

It is critical to find methods to control the thermodynamic driving force for photoexcited charge transfer from quantum dots (QDs) and explore how this affects charge transfer rates, since the efficiency of QD-based photovoltaic and photocatalysis technologies depends on both this rate and the associated energetic losses. In this work, we introduce a single-pot shell growth and Cu-catalyzed cation exchange method to synthesize Cd x Zn 1-x Se/Cd y Zn 1-y S QDs with tunable driving forces for electron transfer. Functionalizing them with two molecular electron acceptors—naphthalenediimide (NDI) and anthraquinone (AQ)—allowed us to probe nearly 1 eV of driving forces. For AQ, at lower driving forces, we find that higher Zn content results in a 130-fold increase of electron transfer rate constants. However, at higher driving forces electron transfer dynamics are unaltered. Here, the data are understood using an Auger-assisted electron transfer model and analyzed with computational work to determine approximate binding geometries of these electron acceptors. Our work provides a method to tune QD reducing power and produces useful metrics for optimizing QD charge transfer systems that maximize rates of electron transfer while minimizing energetic losses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for “flip-flop” conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Electronic density-of-states of amorphous vanadium pentoxide films: Electrochemical data and density functional theory calculations

Thin films of V{sub 2}O{sub 5} were prepared by sputter deposition onto transparent and electrically conducting substrates and were found to be X-ray amorphous. Their electrochemical density of states was determined by chronopotentiometry and displayed a pronounced low-energy peak followed by an almost featureless contribution at higher energies. These results were compared with density functional theory calculations for amorphous V{sub 2}O{sub 5}. Significant similarities were found between measured data and computations; specifically, the experimental low-energy peak corresponds to a split-off part of the conduction band apparent in the computations. Furthermore, the calculations approximately reproduce the experimental band gap observed in optical measurements.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Communication: HK propagator uniformized along a one-dimensional manifold in weakly anharmonic systems

A simplification of the Heller-Herman-Kluk-Kay (HK) propagator is presented that does not suffer from the need for an increasing number of trajectories with dimensions of the system under study. This is accomplished by replacing HK’s uniformizing integral over all of phase space by a one-dimensional curve that is appropriately selected to lie along the fastest growing manifold of a defining trajectory. It is shown that this modification leads to eigenspectra of quantum states in weakly anharmonic systems that can outperform the comparatively computationally cheap thawed Gaussian approximation method and frequently approach the accuracy of spectra obtained with the full HK propagator.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Electronic structure and photovoltaic application of BiI{sub 3}

Rapid recent improvement in photovoltaic efficiency in hybrid lead halide perovskite materials has provided the impetus for understanding other, related main-group halide systems. Here, we show that the closely related but less toxic bismuth iodide BiI{sub 3} can show promising optoelectronic properties. Layered binary BiI{sub 3} is used here as the active layer in planar solar cell architectures (efficiency approximately 0.3%). Experimental and computational studies of absolute band positions of BiI{sub 3} are also presented, to help in the rational design of device architectures that would allow efficient charge transfer at the interfaces.

14 SOLAR ENERGY↗

Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Derivation of instanton rate theory from first principles

Instanton rate theory is used to study tunneling events in a wide range of systems including low-temperature chemical reactions. Despite many successful applications, the method has never been obtained from first principles, relying instead on the “Im F” premise. In this paper, the same expression for the rate of barrier penetration at finite temperature is rederived from quantum scattering theory [W. H. Miller, S. D. Schwartz, and J. W. Tromp, J. Chem. Phys. 79, 4889 (1983)] using a semiclassical Green’s function formalism. This justifies the instanton approach and provides a route to deriving the rate of other processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Explosive attractor solutions to a universal cubic delay equation

New explosive attractor solutions have been found in a universal cubic delay equation that has been studied in both the plasma and the fluid mechanics literature. Through computational simulations and analytic approximations, it is found that the oscillatory component of the explosive mode amplitude solutions are described through multi-frequency Fourier expansions with respect to a pseudo-time variable. The spectral dependence of these solutions as a function of a system parameter, ϕ, is studied. The mode amplitude that is described in the explosive regime has two main features: a well-known envelope (t0−t)−5/2, with t0 the blow-up time of the amplitude, and a spectrum of discrete oscillations with ever-increasing frequencies, which may give experimental information about the properties of a system's equilibrium.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cluster perturbation theory X: A parallel implementation of Lagrangian perturbation series for the coupled cluster singles and doubles ground-state energy through fifth order

We describe an efficient implementation of cluster perturbation and Møller-Plesset Lagrangian energy series through fifth order that target the coupled cluster singles and doubles energy utilizing the resolution of the identity approximation. We illustrate the computational performance of the implementation by performing ground state energy calculations on systems with up to 1200 basis functions using a single node and by comparison to conventional CCSD calculations. We further show that our hybrid MPI/OMP parallel implementation that also utilizes graphical processing units can be used to obtain fifth order energies on systems with almost 1200 basis functions with a 90 minute "time to solution" running on Frontier at Oak Ridge National Laboratory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Statistical model of exotic rotational correlations in emergent space-time

A statistical model is formulated to compute exotic rotational correlations that arise as inertial frames and causal structure emerge on large scales from entangled Planck scale quantum systems. Noncommutative quantum dynamics are represented by random transverse displacements that respect causal symmetry. Entanglement is represented by covariance of these displacements in Planck scale intervals defined by future null cones of events on an observer's world line. Light that propagates in a nonradial direction inherits a projected component of the exotic rotational correlation that accumulates as a random walk in phase. A calculation of the projection and accumulation leads to exact predictions for statistical properties of exotic Planck scale correlations in an interferometer of any configuration. The cross-covariance for two nearly co-located interferometers is shown to depart only slightly from the autocovariance. Specific examples are computed for configurations that approximate realistic experiments, and show that the model can be rigorously tested.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Developing an Evolutionary Baseline Model for Humans: Jointly Inferring Purifying Selection with Population History

Building evolutionarily appropriate baseline models for natural populations is not only important for answering fundamental questions in population genetics—including quantifying the relative contributions of adaptive versus nonadaptive processes—but also essential for identifying candidate loci experiencing relatively rare and episodic forms of selection (e.g., positive or balancing selection). Here, a baseline model was developed for a human population of West African ancestry, the Yoruba, comprising processes constantly operating on the genome (i.e., purifying and background selection, population size changes, recombination rate heterogeneity, and gene conversion). Specifically, to perform joint inference of selective effects with demography, an approximate Bayesian approach was employed that utilizes the decay of background selection effects around functional elements, taking into account genomic architecture. This approach inferred a recent 6-fold population growth together with a distribution of fitness effects that is skewed towards effectively neutral mutations. Importantly, these results further suggest that, although strong and/or frequent recurrent positive selection is inconsistent with observed data, weak to moderate positive selection is consistent but unidentifiable if rare.

59 BASIC BIOLOGICAL SCIENCES↗

Semi-inclusive deep-inelastic scattering on a polarized spin-1 target. II. Deuteron and spectator nucleon tagging

We develop the theoretical framework for semi-inclusive deep-inelastic scattering on a polarized spin-1 target and apply it to scattering on the polarized deuteron with spectator nucleon tagging. In Part I (previous article), we present the general form of the semi-inclusive cross section and polarization observables for the spin-1 target. In Part II (this article), we consider deep-inelastic scattering on the polarized deuteron with spectator nucleon tagging as a special case of target fragmentation. Methods of light-front quantization are employed to separate nuclear and hadronic structure in the high-energy process and achieve a composite description. The light-front wave function of the polarized deuteron is obtained from a rotationally covariant three-dimensional wave function in the center-of-mass frame of the proton-neutron system. The tagged structure functions are computed in the impulse approximation. The momentum and spin distribution of the active nucleon are controlled by the deuteron polarization and the detected spectator momentum (𝐷/𝑆 wave ratio). The cross section and spin asymmetries are evaluated for general deuteron polarization (vector and tensor, longitudinal and transverse) as functions of the spectator momentum. Tensor-polarized spin asymmetries of order unity are achieved for spectator momenta of approximately 300 MeV, which select configurations with a large 𝐷 wave. Sum rules for the tagged spin structure functions are derived. The results can be used for simulations of spectator tagging in future polarized fixed-target experiments (Jefferson Lab) or at the Electron-Ion Collider.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗