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DOE OSTI2024

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↗

DOE OSTI2014

Geochemical Reaction Mechanism Discovery from Molecular Simulation

Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile, and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. We summarize some common methods that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and discuss their strengths and weaknesses. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The impact that molecular simulation has had on our understanding of geochemical reactivity are highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Search for New Phenomena Using W/Z + (b)-Jets Measurements Performed with the ATLAS Detector

The Project proposed to use data of the ATLAS experiment, obtained during the 2011 and 2012 data-taking campaigns, to pursue studies of the strong interaction (QCD) and to examine promising signatures for new physics. The Project also contains a service component dedicated to a detector development initiative. The objective of the strong interaction studies is to determine how various predictions from the main theory (QCD) compare to the data. Results of a set of measurements developed by the Tufts team indicate that the dominant factor of discrepancy between data and QCD predictions come from the mis-modeling of the low energy gluon radiation as described by algorithms called parton showers. The discrepancies introduced by parton showers on LHC predictions could even be larger than the effect due to completely new phenomena (dark matter, supersymmetry, etc.) and could thus block further discoveries at the LHC. Some of the results obtained in the course of this Project also specify how QCD predictions must be improved in order to open the possibility for the discovery of something completely new at the LHC during Run-II. This has been integrated in the Run-II ATLAS physics program. Another objective of Tufts studies of the strong interaction was to determine how the hypothesis about an intrinsic heavy-quark component of the proton (strange, charm or bottom quarks) could be tested at the LHC. This hypothesis has been proposed by theorists 30 years ago and is still controversial. The Tufts team demonstrated that intrinsic charms can be observed, or severely constrained, at the LHC, and determine how the measurement should be performed in order to maximize its sensitivity to such an intrinsic heavy-quark component of the proton. Tufts also embarked on performing the measurement that is in progress, but final results are not yet available. They should shade a light of understanding on the fundamental structure of the proton. Determining the nature of dark matter particles, composing about 25% of all the matter in the universe, is one of the most exciting research goals at the LHC. Within this Project, the Tufts team proposed a way to improve over the standard approach used to look for dark matter at the LHC in events involving jets and a large amount of unbalanced energy in the detector (jets+ETmiss). The Tufts team has developed a measurement to test these improvements on data available (ATLAS 2012 dataset), in order to be ready to apply them on the new Run-II data that will be available at the end of 2015. Preliminary results on the proposed measurement indicate that a very high precision can be obtained on results free of detector effects. That will allow for better constrains of dark matter theories and will spare the needs for huge computing resources in order to compare dark matter theories to data. Finally, the Tufts team played a leading role in the development and the organization of the 6Et trigger, the detector component needed to collect the data used in dark matter searches and in many other analyses. The team compared the performance of the various algorithms capable of reconstructing the value of the ETmiss on each LHC collision event, and developed a strategy to commission these algorithms online. Tufts also contributed in the development of the ETmiss trigger monitoring software. Finally, the PI of this Project acted as the co-coordinator of the group of researchers at CERN taking care of the development and the operation of this detector component. The ETmiss trigger is now taking data, opening the possibility for the discovery of otherwise undetectable particles at the LHC.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

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↗

DOE OSTI2019

Explore: An Advanced Computing Agenda for Competitiveness

Over the course of this three-year grant, the Council on Competitiveness (Council) hosted six meetings of its Advanced Computing Roundtable made up of experts from a broad cross section of advanced computing users and manufacturers, and four Advanced Computing for Competitiveness Regional Forums to explore issues related to advanced computing in regions, states and localities. More than two hundred experts, stakeholders and policymakers from the federal and state levels participated in this work and provided their time and expertise to help define the opportunity in advanced computing and the barriers to it reaching its full potential as a game-changing competitive advantage for the United States economy and national security. Building on the insights of the Council’s Advanced Computing Roundtable and findings and recommendations from the four U.S. Department of Energy-supported Forums, the Council has identified several broad policy objectives for the United States related to advanced computing leadership and implementation. The United States must: Compete at the high end of advanced computing. Continue investing to be a technology leader as the world moves toward exascale computing, including in hardware, software and applications. America also must lead in strategic areas like extending Moore’s Law and quantum computing. Improve the ability of HPC-using firms to leverage advanced computing. The Council recommends steps to improve computational skills, increase industry partnerships with laboratories and academia, and expand and strengthen software partnerships. Regulatory agencies also should accelerate efforts to use modeling and simulation within the regulatory process. Expand the number of HPC-using companies in America. Too few firms are able to leverage advanced computing to innovate and compete. Federal, state and local economic development efforts should be utilized to lower barriers and teach small and medium-sized firms, particularly manufacturers, to use advanced modeling, simulation and analytics. Coordinate federal action. Federal agencies should continue to act in a coordinated fashion on advanced computing challenges through the Joint Program Office for Strategic Computing. Leverage HPC to compete in strategic technologies and applications. Leadership in advanced computing is tightly linked to leadership in artificial intelligence, the Internet of Things, cybersecurity, additive manufacturing and other emerging technologies. Public and private sector leaders should collaborate on research and partnership efforts that ensure world-class computing environments for strategic technology leadership.

advanced computing↗

DOE OSTI2020

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↗

DOE OSTI2014

Oxygen transport properties estimation by DSMC-CT simulations

Coupling DSMC simulations with classical trajectories calculations is emerging as a powerful tool to improve predictive capabilities of computational rarefied gas dynamics. The considerable increase of computational effort outlined in the early application of the method (Koura,1997) can be compensated by running simulations on massively parallel computers. In particular, GPU acceleration has been found quite effective in reducing computing time (Ferrigni,2012; Norman et al.,2013) of DSMC-CT simulations. The aim of the present work is to study rarefied Oxygen flows by modeling binary collisions through an accurate potential energy surface, obtained by molecular beams scattering (Aquilanti, et al.,1999). The accuracy of the method is assessed by calculating molecular Oxygen shear viscosity and heat conductivity following three different DSMC-CT simulation methods. In the first one, transport properties are obtained from DSMC-CT simulations of spontaneous fluctuation of an equilibrium state (Bruno et al, Phys. Fluids, 23, 093104, 2011). In the second method, the collision trajectory calculation is incorporated in a Monte Carlo integration procedure to evaluate the Taxman’s expressions for the transport properties of polyatomic gases (Taxman,1959). In the third, non-equilibrium zero and one-dimensional rarefied gas dynamic simulations are adopted and the transport properties are computed from the non-equilibrium fluxes of momentum and energy. The three methods provide close values of the transport properties, their estimated statistical error not exceeding 3%. The experimental values are slightly underestimated, the percentage deviation being, again, few percent.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2015

2–stage stochastic Runge–Kutta for stochastic delay differential equations

This paper proposes a newly developed one-step derivative-free method, that is 2-stage stochastic Runge-Kutta (SRK2) to approximate the solution of stochastic delay differential equations (SDDEs) with a constant time lag, r > 0. General formulation of stochastic Runge-Kutta for SDDEs is introduced and Stratonovich Taylor series expansion for numerical solution of SRK2 is presented. Local truncation error of SRK2 is measured by comparing the Stratonovich Taylor expansion of the exact solution with the computed solution. Numerical experiment is performed to assure the validity of the method in simulating the strong solution of SDDEs.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

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↗

DOE OSTI2018

Perspective: Ab initio force field methods derived from quantum mechanics

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2016

Stability and accuracy of 3D neutron transport simulations using the 2D/1D method in MPACT

A consistent “2D/1D” neutron transport method is derived from the 3D Boltzmann transport equation, to calculate fuel-pin-resolved neutron fluxes for realistic full-core Pressurized Water Reactor (PWR) problems. The 2D/1D method employs the Method of Characteristics to discretize the radial variables and a lower order transport solution to discretize the axial variable. This paper describes the theory of the 2D/1D method and its implementation in the MPACT code, which has become the whole-core deterministic neutron transport solver for the Consortium for Advanced Simulations of Light Water Reactors (CASL) core simulator VERA-CS. Several applications have been performed on both leadership-class and industry-class computing clusters. Results are presented for whole-core solutions of the Watts Bar Nuclear Power Station Unit 1 and compared to both continuous-energy Monte Carlo results and plant data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2016

Adaptive surrogate modeling by ANOVA and sparse polynomial dimensional decomposition for global sensitivity analysis in fluid simulation

The Polynomial Dimensional Decomposition (PDD) is employed in this work for the global sensitivity analysis and uncertainty quantification (UQ) of stochastic systems subject to a moderate to large number of input random variables. Due to the intimate connection between the PDD and the Analysis of Variance (ANOVA) approaches, PDD is able to provide a simpler and more direct evaluation of the Sobol' sensitivity indices, when compared to the Polynomial Chaos expansion (PC). Unfortunately, the number of PDD terms grows exponentially with respect to the size of the input random vector, which makes the computational cost of standard methods unaffordable for real engineering applications. In order to address the problem of the curse of dimensionality, this work proposes essentially variance-based adaptive strategies aiming to build a cheap meta-model (i.e. surrogate model) by employing the sparse PDD approach with its coefficients computed by regression. Three levels of adaptivity are carried out in this paper: 1) the truncated dimensionality for ANOVA component functions, 2) the active dimension technique especially for second- and higher-order parameter interactions, and 3) the stepwise regression approach designed to retain only the most influential polynomials in the PDD expansion. During this adaptive procedure featuring stepwise regressions, the surrogate model representation keeps containing few terms, so that the cost to resolve repeatedly the linear systems of the least-squares regression problem is negligible. The size of the finally obtained sparse PDD representation is much smaller than the one of the full expansion, since only significant terms are eventually retained. Consequently, a much smaller number of calls to the deterministic model is required to compute the final PDD coefficients.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2019

Stimulated X-ray Raman and Absorption Spectroscopy of Iron–Sulfur Dimers

Iron–sulfur complexes play an important role in biological processes such as metabolic electron transport. A detailed understanding of the mechanism of long-range electron transfer requires knowledge of the electronic structure of the complexes, which has traditionally been challenging to obtain, either by theory or by experiment, but the situation has begun to change with advances in quantum chemical methods and intense free electron laser light sources. We compute the spectra for stimulated X-ray Raman spectroscopy (SXRS) and absorption spectroscopy of homovalent and mixed-valence [2Fe–2S] complexes, using the ab initio density matrix renormalization group algorithm. The simulated spectra show clear signatures of the theoretically predicted dense low-lying excited states within the d–d manifold. Finally, the difference in spectral intensity between the absorption-active and Raman-active states provides a potential mechanism to selectively excite states by a proper tuning of the excitation pump, to access the electronic dynamics within this manifold.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

SU-C-207-05: A Comparative Study of Noise-Reduction Algorithms for Low-Dose Cone-Beam Computed Tomography

Purpose: To study different noise-reduction algorithms and to improve the image quality of low dose cone beam CT for patient positioning in radiation therapy. Methods: In low-dose cone-beam CT, the reconstructed image is contaminated with excessive quantum noise. In this study, three well-developed noise reduction algorithms namely, a) penalized weighted least square (PWLS) method, b) split-Bregman total variation (TV) method, and c) compressed sensing (CS) method were studied and applied to the images of a computer–simulated “Shepp-Logan” phantom and a physical CATPHAN phantom. Up to 20% additive Gaussian noise was added to the Shepp-Logan phantom. The CATPHAN phantom was scanned by a Varian OBI system with 100 kVp, 4 ms and 20 mA. For comparing the performance of these algorithms, peak signal-to-noise ratio (PSNR) of the denoised images was computed. Results: The algorithms were shown to have the potential in reducing the noise level for low-dose CBCT images. For Shepp-Logan phantom, an improvement of PSNR of 2 dB, 3.1 dB and 4 dB was observed using PWLS, TV and CS respectively, while for CATPHAN, the improvement was 1.2 dB, 1.8 dB and 2.1 dB, respectively. Conclusion: Penalized weighted least square, total variation and compressed sensing methods were studied and compared for reducing the noise on a simulated phantom and a physical phantom scanned by low-dose CBCT. The techniques have shown promising results for noise reduction in terms of PSNR improvement. However, reducing the noise without compromising the smoothness and resolution of the image needs more extensive research.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

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↗

DOE OSTI2016

WE-DE-BRA-05: Monte Carlo Simulation of a Novel Multi-Layer MV Imager

Purpose: To develop and validate a Monte Carlo (MC) model of a novel multi-layer imager (MLI) for megavolt (MV) energy beams. The MC model will enable performance optimization of the MLI design for clinical applications including patient setup verification, tumor tracking and MVCBCT. Methods: The MLI is composed of four layers of converter, scintillator and light detector, each layer similar to the current clinical AS1200 detector (Varian Medical Systems, Inc). The MLI model was constructed using the Geant4 Application for Tomographic Emission (GATE v7.1) and includes interactions for x-ray photons, charged particles and optical photons. Computational experiments were performed to assess Modulation Transfer Function (MTF), Detective Quantum Efficiency (DQE) and Noise Power Spectrum normalized by photon fluence and average detector signal (qNNPS). Results were compared with experimental measurements. The current work incorporates, in one model, the complete chain of events occurring in the imager; i.e. starting from x-ray interaction to charged particle transport and energy deposition to subsequent generation, interactions and detection of optical photons. Results: There is good agreement between measured and simulated MTF, qNNPS and DQE values. Normalized root mean squared error (NRMSE) between measured and simulated values over all four layers was 2.18%, 2.43% and 6.05% for MTF, qNNPS and DQE respectively. The relative difference between simulated and measured values for qNNPS(0) was 1.68% and 1.57% for DQE(0). Current results were obtained using a 6MV Varian Truebeam™ spectrum. Conclusion: A comprehensive Monte Carlo model of the MLI prototype was developed to allow optimization of detector components. The model was assessed in terms of imaging performance using standard metrics (i.e. MTF, qNNPS, DQE). Good agreement was found between simulated and measured values. The model will be used to assess alternative detector constructions to facilitate advanced clinical imaging applications including MV-CBCT and tumor tracking. The project was supported, partially, by a grant from Varian Medical Systems, Inc., and Award No. R01CA188446-01 from the National Cancer Institute. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Cancer Institute or the National Institutes of Health.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

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↗