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At least 1,063 records · Page 59

Perspective on Integrative Simulations of Bioenergetic Domains

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

59 BASIC BIOLOGICAL SCIENCES↗

Simple and efficient algorithms for training machine learning potentials to force data

Machine learning models, trained on data from ab initio quantum simulations, are yielding molecular dynamics potentials with unprecedented accuracy. One limiting factor is the quantity of available training data, which can be expensive to obtain. A quantum simulation often provides all atomic forces, in addition to the total energy of the system. These forces provide much more information than the energy alone. It may appear that training a model to this large quantity of force data would introduce significant computational costs. Actually, training to all available force data should only be a few times more expensive than training to energies alone. Here, we present a new algorithm for efficient force training, and benchmark its accuracy by training to forces from real-world datasets for organic chemistry and bulk aluminum.

74 ATOMIC AND MOLECULAR PHYSICS↗

Quantum hardware accelerators for real-world applications (CRADA FP00007654 Final Report)

The research Bleximo Corp. conducted at Cyclotron Road was focused on developing application-specific superconducting quantum processors for high-value problems in quantum chemistry, in particular, calculating chemical binding energy in biomolecular systems, such as protein-ligand complexes, with chemical precision. Several candidate architectures were identified through simulations, which included experimentally-proven quantum bit architectures and realistic noise and cross-talk models in multi-qubit superconducting quantum processors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Variational Quantum Algorithms for Semidefinite Programming

A semidefinite program (SDP) is a particular kind of convex optimization problem with applications in operations research, combinatorial optimization, quantum information science, and beyond. In this work, we propose variational quantum algorithms for approximately solving SDPs. For one class of SDPs, we provide a rigorous analysis of their convergence to approximate locally optimal solutions, under the assumption that they are weakly constrained (i.e., N " M, where N is the dimension of the input matrices and M is the number of constraints). We also provide algorithms for a more general class of SDPs that requires fewer assumptions. Finally, we numerically simulate our quantum algorithms for applications such as MaxCut, and the results of these simulations provide evidence that convergence still occurs in noisy settings.

97 MATHEMATICS AND COMPUTING↗

Finding Electronic Structure Machine Learning Surrogates without Training

A myriad of phenomena in materials science and chemistry rely on quantum-level simulations of the electronic structure in matter. While moving to larger length and time scales has been a pressing issue for decades, such large-scale electronic structure calculations are still challenging despite modern software approaches and advances in high-performance computing. The silver lining in this regard is the use of machine learning to accelerate electronic structure calculations – this line of research has recently gained growing attention. The grand challenge therein is finding a suitable machine-learning model during a process called hyperparameter optimization. This, however, causes a massive computational overhead in addition to that of data generation. We accelerate the construction of machine-learning surrogate models by roughly two orders of magnitude by circumventing excessive training during the hyperparameter optimization phase. We demonstrate our workflow for Kohn-Sham density functional theory, the most popular computational method in materials science and chemistry.

36 MATERIALS SCIENCE↗

CFD Analysis of RLUOB Zone 1 HEPA Filter Plenum and Testing Manifolds

The purpose of this computational fluid dynamics (CFD) analysis is to ensure that Camfil Farr’s upstream and downstream injection and sampling manifolds can meet or exceed the requirements outlined in the ASME AG-1 1997 a(2000) Code on Nuclear Air and Gas Treatment for the testing of HEPA and adsorbent filters. This paper will present a numerical simulation of airflow in the Radiological Laboratory Utility Office Building (RLUOB) zone 1 HEPA filter plenum and testing manifolds using the commercial CFD software ANSYS FLUENT 2020R1. The CFD analysis focuses on the investigation of the air flow distribution and air-aerosol mixing uniformity. The evaluation was done for all steps of the modeling process: grid generation, physics setup, simulation, and post-processing. The mass flow rate in each section of the zone 1 injection and sampling manifolds is also reported.

42 ENGINEERING↗

Mean force emission theory for classical bremsstrahlung in strongly coupled plasmas

This work presents mean force emission theory, which extends the classical theory of bremsstrahlung emission to strongly coupled plasmas. In the high-frequency limit, the theory reduces to solving for the electron trajectory during a binary collision, but where the electron–ion interactions occur through the potential of mean force. In the low-frequency limit, it uses an autocorrelation formalism that captures effects of multiple collisions and strongly correlated motion. The predictions are benchmarked by comparison with first-principles classical molecular dynamics simulations of a fully ionized hydrogen plasma in which all interactions are repulsive. The comparison shows good agreement up to Coulomb coupling strengths of Γ∼30. The theory improves upon traditional models by including strong coupling effects and systematically including the effect of multiple collisions. Furthermore, mean force emission theory provides evidence that the Drude correction factor commonly used in quantum calculations of optical quantities may not be adequate at strong coupling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Adaptive Variational Quantum Computing Approaches for Green’s Functions and Nonlinear Susceptibilities

Here, we present and benchmark quantum computing approaches for calculating real-time single-particle Green’s functions and nonlinear susceptibilities of Hamiltonian systems. The approaches leverage adaptive variational quantum algorithms for state preparation and propagation. Using automatically generated compact circuits, the dynamical evolution is performed over sufficiently long times to achieve adequate frequency resolution of the response functions. We showcase accurate Green’s function calculations using a statevector simulator on classical hardware for Fermi-Hubbard chains of 4 and 6 sites, with maximal ansatz circuit depths of 65 and 424 layers, respectively, and for the molecule LiH with a maximal ansatz circuit depth of 81 layers. Additionally, we consider an antiferromagnetic quantum spin-1 model that incorporates the Dzyaloshinskii-Moriya interaction to illustrate calculations of the third-order nonlinear susceptibilities, which can be measured in two-dimensional coherent spectroscopy experiments. These results demonstrate that real-time approaches using adaptive parametrized circuits to evaluate linear and nonlinear response functions can be feasible with near-term quantum processors.

97 MATHEMATICS AND COMPUTING↗

Unleashed from constrained optimization: quantum computing for quantum chemistry employing generator coordinate inspired method

Hybrid quantum-classical approaches offer potential solutions to quantum chemistry problems, yet they often manifest as constrained optimization problems. Here, we explore the interconnection between constrained optimization and generalized eigenvalue problems through the Unitary Coupled Cluster (UCC) excitation generators. Inspired by the generator coordinate method, we employ these UCC excitation generators to construct non-orthogonal, overcomplete many-body bases, projecting the system Hamiltonian into an effective Hamiltonian, which bypasses issues such as barren plateaus that heuristic numerical minimizers often encountered in standard variational quantum eigensolver (VQE). Diverging from conventional quantum subspace expansion methods, we introduce an adaptive scheme that robustly constructs the many-body basis sets from a pool of the UCC excitation generators. This scheme supports the development of a hierarchical ADAPT quantum-classical strategy, enabling a balanced interplay between subspace expansion and ansatz optimization to address complex, strongly correlated quantum chemical systems cost-effectively, setting the stage for more advanced quantum simulations in chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

First Principles Simulations of Electrified Interfaces in Electrochemistry

This chapter discusses some of the recent advances made in the first principles modeling of electrochemical catalysts. It also discusses the key development, namely the ability to explicitly treat the effects of surface electrification due to electrochemical processes and applied voltages in a computationally efficient manner. The chapter introduces the thermodynamics and statistical mechanics of electrified metal-solution interfaces. It then discusses the structure of the electrode-electrolyte interface and the effects of applied voltages, followed by an overview of the first-principles model and a motivating example. The chapter also provides a brief summary of classical thermodynamics and describes the basics of thermodynamic detour. It considers the thermodynamics of macroscopic systems and introduces several useful fundamental relations. Here, the chapter also considers a system to exist in a certain macrostate, which is a particular thermodynamic state specified by a set of fixed properties such as constant particle number, constant volume, and constant temperature.

36 MATERIALS SCIENCE↗

INSPIRED: Inelastic neutron scattering prediction for instantaneous results and experimental design

Inelastic neutron scattering (INS) has unique advantages in probing how atoms vibrate and how the vibrations propagate and interact. Such dynamic information is crucial in understanding various material properties, from heat capacity, thermal conductivity, phase transitions, and chemical reactions to more exotic quantum behavior. The analysis and interpretation of the INS spectra often start from a model structure of the sample, followed by a series of calculations to obtain the simulated spectra to compare with experiments. The conventional way to perform such calculations usually requires significant time, computing resources, and specialized expertise. Here, we present a new program named INSPIRED (Inelastic Neutron Scattering Prediction for Instantaneous Results and Experimental Design), which enables users to perform rapid INS simulations in several different ways on their personal computers in just a few clicks, with the crystal structure as the only input file. Specifically, the users can choose a pre-trained symmetry-aware neural network (coupled with an autoencoder) to predict the phonon density of states (DOS), 1D S(E) and 2D S(|Q|,E) spectra for any given structure. One can also choose an existing density functional theory (DFT) calculation from a database (containing over 12,000 crystals), and quickly obtain the simulated INS spectra for single crystals and powders. It is also possible to use pre-trained universal machine learning force fields to relax a given crystal structure, calculate the phonon dispersion and DOS, and, subsequently, the INS spectra. All these functions are implemented with a PyQt graphic user interface. Finally, we expect these new tools will benefit broad user communities and significantly improve the efficiency of experiment design, execution, and data analysis for INS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Electric-field-induced crossover of polarization reversal mechanisms in Al 1–x Sc x N ferroelectrics

Scandium-doped aluminum nitride, Al 1–x Sc x N, represents a new class of displacive ferroelectric materials with high polarization and sharp hysteresis along with high-temperature resilience, facile synthesizability and compatibility with standard CMOS fabrication techniques. The fundamental physics behind the transformation of unswitchable piezoelectric AlN into switchable Al–Sc–N ferroelectrics depends upon important atomic properties such as local structure, dopant distributions and the presence of competing mechanism of polarization switching in the presence of an applied electric-field that have not been understood. We computationally synthesize Al 1–x Sc x N to quantify the inhomogeneity of Sc distribution and phase segregation, and characterize its crystal and electronic structure as a function of Sc-doping. Nudged elastic band calculations of the potential energy surface and quantum molecular dynamics simulations of direct electric-field-driven ferroelectric switching reveal a crossover between two polarization reversal mechanisms—inhomogeneous nucleation-and-growth mechanism originating near Sc-rich regions in the limit of low applied fields and nucleation-limited-switching in the high-field regime. Finally, understanding polarization reversal pathways for these two mechanisms as well as the role of local Sc concentration on activation barriers provides design rules to identify other combinations of dopant elements, such as Zr, Mg etc. to synthesize superior AlN-based ferroelectric materials.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

State preparation of lattice field theories using quantum optimal control

Here, we explore the application of quantum optimal control (QOC) techniques to state preparation of lattice field theories on quantum computers. As a first example, we focus on the Schwinger model, quantum electrodynamics in 1+1 dimensions. We demonstrate that QOC can significantly speed up the ground state preparation compared to gate-based methods, even for models with long-range interactions. Using classical simulations, we explore the dependence on the interqubit coupling strength and the device connectivity, and we study the optimization in the presence of noise. While our simulations indicate potential speedups, the results strongly depend on the device specifications. In addition, we perform exploratory studies on the preparation of thermal states. Our results motivate further studies of QOC techniques in the context of quantum simulations for fundamental physics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Feasibility of the LAMMPS SPH Package for Simulating Bubble Motion in Vibrating Containers

The Smoothed Particle Hydrodynamics (SPH) package within LAMMPS is explored as a possible tool for simulating the motion of bubbles in a vibrating liquid-filled container. As an initial test case, the unphysical but computationally less intense situation of a two-dimensional single bubble rising in a quiescent liquid under the influence of gravity is considered herein. Although physically plausible behavior was obtained under certain conditions, this behavior depends strongly on the system parameters. Moreover, the large density ratio between the liquid and bubble requires extremely small timesteps, which make the simulations undesirably computationally expensive. Ultimately, it was determined that this method is not feasible for providing quantitatively accurate results for the desired application.

42 ENGINEERING↗

Shuttling Majorana zero modes in disordered and noisy topological superconductors

The braiding of Majorana zero modes (MZMs) forms the fundamental building block for topological quantum computation. Braiding protocols which involve the physical exchange of MZMs are typically envisioned on a network of topological superconducting wires. An important component of these protocols is the transport of MZMs, which can be performed by using electric gates to locally tune sections of the wire between topologically trivial and nontrivial phases. In this work, we numerically simulate this transport by tuning a single section of a superconducting wire which contains either disorder (uncorrelated and correlated) or noise. We focus on the impact of these additional effects on the diabatic error, which describes unwanted transitions between the ground state and excited states. We show that the behavior of the average diabatic error is predominantly controlled by the statistics of the minimum bulk energy gap which is suppressed in the presence of disorder. The increase in diabatic error can be several orders of magnitude and is most deleterious when the disorder correlation length is a finite fraction of the transport distance and negligible when these lengths are far apart. In the presence of noise, the diabatic error is significantly enhanced due to optical transitions which depend on the minimum bulk energy gap as well as the frequency modes present in the noise. The results presented here serve to further characterize the diabatic error in disordered and noisy settings, which are important considerations in practical implementations of physical braiding schemes.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electronic Structure of InAs and InSb Surfaces: Density Functional Theory and Angle-Resolved Photoemission Spectroscopy

The electronic structure of surfaces plays a key role in the properties of quantum devices. However, surfaces are also the most challenging to simulate and engineer. Here, in this work, the electronic structure of InAs(001), InAs(111), and InSb(110) surfaces is studied using a combination of density functional theory (DFT) and angle-resolved photoemission spectroscopy (ARPES). Large-scale first principles simulations are enabled by using DFT calculations with a machine-learned Hubbard U correction [npj Comput. Mater. 6, 180 (2020)]. To facilitate direct comparison with ARPES results, a “bulk unfolding” scheme is implemented by projecting the calculated band structure of a supercell surface slab model onto the bulk primitive cell. For all three surfaces, a good agreement is found between DFT calculations and ARPES. For InAs(001), the simulations clarify the effect of the surface reconstruction. Different reconstructions are found to produce distinctive surface states, which may be detected by ARPES with low photon energies. For InAs(111) and InSb(110), the simulations help elucidate the effect of oxidation. Owing to larger charge transfer from As to O than from Sb to O, oxidation of InAs(111) leads to significant band bending and produces an electron pocket, whereas oxidation of InSb(110) does not. The combined theoretical and experimental results may inform the design of quantum devices based on InAs and InSb semiconductors, for example, topological qubits utilizing the Majorana zero modes.

42 ENGINEERING↗

Potential Applications of Quantum Computing at Los Alamos National Laboratory, v0.3.0

Since the scientific revolution in the 16th and 17th centuries, the process of scientific discovery has followed an iterative feedback process of observation, hypothesis development and testing with physical experiments, which is widely referred to as the scientific method. This process remained largely unchanged until the middle of the 20th century, when the emergence of digital computers empowered scientist to build and inspect detailed simulations of physical phenomena. Over the last century, computational tools have transformed modern approaches to scientific discovery by enabling fast and affordable hypothesis testing before physical experiments are conducted, shown in Figure 1-1. Some notable examples include: global climate forecasts to understand how the environment may change over decades [130]; modeling the behavior of plasma to design fusion reactors [59]; and understanding the behavior of molecules in biological processes [161, 223].

36 MATERIALS SCIENCE↗