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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

When in-memory computing meets spiking neural networks—A perspective on device-circuit-system-and-algorithm co-design

This review explores the intersection of bio-plausible artificial intelligence in the form of spiking neural networks (SNNs) with the analog in-memory computing (IMC) domain, highlighting their collective potential for low-power edge computing environments. Through detailed investigation at the device, circuit, and system levels, we highlight the pivotal synergies between SNNs and IMC architectures. Additionally, we emphasize the critical need for comprehensive system-level analyses, considering the inter-dependencies among algorithms, devices, circuit, and system parameters, crucial for optimal performance. An in-depth analysis leads to the identification of key system-level bottlenecks arising from device limitations, which can be addressed using SNN-specific algorithm–hardware co-design techniques. This review underscores the imperative for holistic device to system design-space co-exploration, highlighting the critical aspects of hardware and algorithm research endeavors for low-power neuromorphic solutions.

Physics↗
DOE OSTI2025

Computational toolkit for predicting thickness of 2D materials using machine learning and autogenerated dataset by large language model

The thickness of 2D materials not only plays a crucial role in determining the performance of nanoelectronic and optoelectronic devices but also introduces complexities in predicting volume-dependent properties, such as energy storage capacity, due to the intrinsic vacuum within these materials. Although a plethora of experimental techniques, including but not limited to optical contrast, Raman spectroscopy, nonlinear optical spectroscopy, near-field optical imaging, and hyperspectral imaging, facilitate the measurement of 2D material thickness, comprehensive data for many materials remain elusive. Over the past decade, the exponential proliferation of 2D materials and their heterostructures has outstripped the capabilities of conventional experimental and computational approaches. In this evolving landscape, machine learning (ML) has emerged as an indispensable tool, offering a scalable approach to augment these traditional methodologies. Addressing the critical gap, we introduce THICK2D—Thickness Hierarchy Inference and Calculation Kit for 2D Materials. This Python-based computational framework harnesses an autogenerated thickness database, developed using large language models, and advanced ML algorithms to facilitate the rapid and scalable estimation of material thickness, relying solely on crystallographic data. To demonstrate the utility and robustness of THICK2D, we successfully used the toolkit to predict the thickness of more than 8000 2D-based materials, sourced from two extensive 2D materials databases. THICK2D is disseminated as an open-source utility, accessible on GitHub at https://github.com/gmp007/THICK2D, and archived on Zenodo at https://10.5281/zenodo.11216648.

Ekuma, Chinedu E. (ORCID:0000000258527556)↗
DOE OSTI2022

Massively parallel, computationally guided design of a proenzyme

Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Interleukin-2 superkines by computational design

Significance While computational engineering of therapeutic proteins is a desirable goal, in practice the optimization of protein–protein interactions requires substantial experimental intervention. We present here a computational approach that focuses on stabilizing core protein structures rather than engineering the protein–protein interface. Using this approach, we designed thermostabilized interleukin-2 (IL-2) variants that bind tightly to their receptor without experimental optimization, mimicking the properties of the yeast-display engineered IL-2 variant “super-2.” Our results suggest that structure-guided stabilization may be a general method for in silico affinity maturation of protein–protein interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2

The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small-molecule inhibitors of Mac1 have great therapeutic potential, at the outset of the COVID-19 pandemic, there were no well-validated inhibitors for this protein nor, indeed, the macrodomain enzyme family, making this target a pharmacological orphan. Here, we report the structure-based discovery and development of several different chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high-resolution protein crystallography, and binding evaluation. Potent scaffolds were designed with in silico fragment linkage and by ultra-large library docking of over 450 million molecules. Both techniques leverage the computational exploration of tangible chemical space and are applicable to other pharmacological orphans. Overall, 160 ligands in 119 different scaffolds were discovered, and 153 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. Our analyses discovered selective and cell-permeable molecules, unexpected ligand-mediated conformational changes within the active site, and key inhibitor motifs that will template future drug development against Mac1.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Chaotic neural dynamics facilitate probabilistic computations through sampling

Cortical neurons exhibit highly variable responses over trials and time. Theoretical works posit that this variability arises potentially from chaotic network dynamics of recurrently connected neurons. Here, we demonstrate that chaotic neural dynamics, formed through synaptic learning, allow networks to perform sensory cue integration in a sampling-based implementation. We show that the emergent chaotic dynamics provide neural substrates for generating samples not only of a static variable but also of a dynamical trajectory, where generic recurrent networks acquire these abilities with a biologically plausible learning rule through trial and error. Furthermore, the networks generalize their experience in the stimulus-evoked samples to the inference without partial or all sensory information, which suggests a computational role of spontaneous activity as a representation of the priors as well as a tractable biological computation for marginal distributions. These findings suggest that chaotic neural dynamics may serve for the brain function as a Bayesian generative model.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Development of HELIOS/BIPR/PARCS/MCNP6 Computation Route for WWER RPV Neutron Fluence Analysis and Validation Against Ex-Vessel Detector Measurement Data

Here, a computational route was developed for precise calculation of fast neutron fluence on a WWER-type reactor pressure vessel (RPV). The method is based on the transfer of neutronics data from HELIOS-2 lattice calculations and nodal diffusion neutronics data (power, density, and temperature) from BIPR7.1 and PARCS 3.36/PATHS core calculations into a three-dimensional (pinwise axially distributed) fixed neutron source for modeling of transport of fast neutrons from the reactor core to the outer surface of the RPV using MCNP6.2. Validation of the proposed computational method was carried out based on comparative analysis of MCNP6.2-predicted and neutron dosimetry–measured reaction rates [ 54 Fe(n,p) 54 Мn, 93 Nb(n,n') 93 mNb, and 58 Ni(n,р) 58 Со] on the outer surface of the Armenian Nuclear Power Plant (ANPP) Unit 2 RPV. Validation revealed that the MCNP6.2-predicted fast neutron fluence results are very sensitive to the ENDF-B neutron data. Particularly, MCNP6.2 with ENDF/B-VIII.0 significantly underpredicts (20% to 30%) fast neutron fluence while using ENDF/B-VII.1 data overpredicts it. Adding revised beta-released evaluations of 54 Fe, 56 Fe, 57 Fe, and 16 O from the International Nuclear Data Evaluation Network (INDEN) to ENDF/B-VIII.0 allows one to obtain reasonable agreement with measurement results for all types of measured reaction rates.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

HPC-driven computational reproducibility in numerical relativity codes: a use case study with IllinoisGRMHD

Abstract Reproducibility of results is a cornerstone of the scientific method. Scientific computing encounters two challenges when aiming for this goal. Firstly, reproducibility should not depend on details of the runtime environment, such as the compiler version or computing environment, so results are verifiable by third-parties. Secondly, different versions of software code executed in the same runtime environment should produceconsistent numerical results for physical quantities. In this manuscript, we test the feasibility of reproducing scientific results obtained using theIllinoisGRMHDcode that is part of an open-source community software for simulation in relativistic astrophysics, theEinstein Toolkit. We verify that numerical results of simulating a single isolated neutron star withIllinoisGRMHDcan be reproduced, and compare them to results reported by the code authors in 2015. We use two different supercomputers: Expanse at SDSC, and Stampede2 at TACC. By compiling the source code archived along with the paper on both Expanse and Stampede2, we find thatIllinoisGRMHDreproduces results published in its announcement paper up to errors comparable to round-off level changes in initial data parameters. We also verify that a current version ofIllinoisGRMHDreproduces these results once we account for bug fixes which have occurred since the original publication.

Astronomy & Astrophysics↗
DOE OSTI2022

Toward full simulations for a liquid metal blanket: part 2. Computations of MHD flows with volumetric heating for a PbLi blanket prototype at Ha ~10 4 and Gr ~10 12

On the pathway toward full simulations for a liquid metal (LM) blanket, this part 2 extends a previous study of purely magnetohydrodynamic (MHD) flows in a DCLL blanket in reference Chen et al (2020 Nucl. Fusion 60 076003) to more general conditions when the MHD flow is coupled with heat transfer. The simulated prototypic blanket module includes all components of a real LM blanket system, such as supply ducts, inlet and outlet manifolds, multiple poloidal ducts and a U-turn zone. Volumetric heating generated by fusion neutrons is added to simulate thermal effects in the flowing lead–lithium (PbLi) breeder. The MHD flow equations and the energy equation are solved with a DNS-type finite-volume code ‘MHD-UCAS’ on a very fine mesh of 470 × 10 6 cells. The applied magnetic field is 5 T (Hartmann number Ha ~ 10 4 ), the PbLi velocity in the poloidal ducts is 10 cm s –1 (Reynolds number Re ~10 5 ), whereas the maximum volumetric heating is 30 MW m –3 (Grashof number Gr ~ 10 12 ). Four cases have been simulated, including forced- and mixed-convection flows, and either an electrically conducting or insulating blanket structure. Various comparisons are made between the four computed cases and also against the purely MHD flows computed earlier in reference Chen et al (2020 Nucl. Fusion 60 076003) with regards to the (1) MHD pressure drop, (2) flow balancing, (3) temperature field, (4) flows in particular blanket components, and (5) 3D and turbulent flow effects. The strongest buoyancy effects were found in the poloidal ducts. In the electrically non-conducting blanket, the buoyancy forces lead to significant modifications of the flow structure, such as formation of reverse flows, whereas their effect on the MHD pressure drop is relatively small. In the electrically conducting blanket case, the buoyancy effects on the flow and MHD pressure drop are almost negligible.

Physics↗
DOE OSTI2023

Extending the distributed computing infrastructure of the CMS experiment with HPC resources

Particle accelerators are an important tool to study the fundamental properties of elementary particles. Currently the highest energy accelerator is the LHC at CERN, in Geneva, Switzerland. Each of its four major detectors, such as the CMS detector, produces dozens of Petabytes of data per year to be analyzed by a large international collaboration. The processing is carried out on the Worldwide LHC Computing Grid, that spans over more than 170 compute centers around the world and is used by a number of particle physics experiments. Recently the LHC experiments were encouraged to make increasing use of HPC resources. While Grid resources are homogeneous with respect to the used Grid middleware, HPC installations can be very different in their setup. In order to integrate HPC resources into the highly automatized processing setups of the CMS experiment a number of challenges need to be addressed. For processing, access to primary data and metadata as well as access to the software is required. At Grid sites all this is achieved via a number of services that are provided by each center. However at HPC sites many of these capabilities cannot be easily provided and have to be enabled in the user space or enabled by other means. At HPC centers there are often restrictions regarding network access to remote services, which is again a severe limitation. The paper discusses a number of solutions and recent experiences by the CMS experiment to include HPC resources in processing campaigns.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Computational approaches to Coherent Synchrotron Radiation in two and three dimensions

Coherent Synchrotron Radiation (CSR) is an important and often detrimental effect in particle accelerators. While one-dimensional models have been successfully used to design and explain the behavior of modern machines, questions remain about their domain of validity. In recent years, two- and three-dimensional models have been developed that are amenable to efficient numerical computation. This article gives an overview of CSR computation from its discovery through the present state of the art.

43 PARTICLE ACCELERATORS↗
DOE OSTI2021

Indexed improvements for real-time trotter evolution of a (1 + 1) field theory using NISQ quantum computers

Today's quantum computers offer the possibility of performing real-time calculations for quantum field theory scattering processes motivated by high energy physics. In order to follow the successful roadmap which has been established for the calculation of static properties at Euclidean time, it is crucial to develop new algorithmic methods to deal with the limitations of current noisy intermediate-scale quantum (NISQ) devices and to establish quantitative measures of the progress made with different devices. In this paper, we report recent progress in these directions. We show that nonlinear aspects of the trotter errors allow us to take much larger step then suggested by low-order analysis. This is crucial to reach physically relevant time scales with today's NISQ technology. We propose to use an index averaging absolute values of the difference between the accurately calculated trotter evolution of site occupations and their actual measurements on NISQ machines (G index) as a measure to compare results that have been obtained from different hardware platforms. Using the transverse Ising model in one spatial dimension with four sites we apply this metric across several hardware platforms. We study the results including readout mitigation and Richardson extrapolations and show that the mitigated measurements are very effective based on the analysis of the trotter step size modifications. Furthermore, we discuss how this advance in the trotter step size procedures can improve quantum computing physics scattering results and how this technical advance can be applied to other machines and noise mitigation methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Measurement of the work statistics of an open quantum system using a quantum computer

Abstract We report on the experimental measurement of the work statistics of a genuinely open quantum system using a quantum computer. Such measurement has remained elusive thus far due to the inherent difficulty in measuring the total energy change of a system-bath compound (which is the work) in the open quantum system scenario. We overcome this difficulty by applying the interferometric scheme, originally conceived for closed systems, to the open system case and implement it on a superconducting quantum computer, taking advantage of the relatively high levels of noise on current quantum hardware to realize an open quantum system. We demonstrate that the method can be used as a diagnostic tool to probe physical properties of the system-bath compound, such as its temperature and specific transition frequencies in its spectrum. Our experiments corroborate that the interferometric scheme is a promising tool to achieve the long-sought experimental validation of the Jarzynski equality for arbitrary open quantum systems.

Oftelie, Lindsay Bassman (ORCID:0000000335421553)↗
DOE OSTI2025

Intermediate-temperature topological Uhlmann phase on IBM quantum computers

A spin-1 system can exhibit an intermediate-temperature topological regime with a quantized Uhlmann phase sandwiched by topologically trivial low- and high-temperature regimes. We present a quantum circuit consisting of system and ancilla qubits plus a probe qubit which prepares an initial state corresponding to the purified state of a spin-1 system at finite temperature, evolves the system according to the Uhlmann process, and measures the Uhlmann phase via expectation values of the probe qubit. Although classical simulations suggest the quantized Uhlmann phase is observable on International Business Machines (IBM’s) noisy intermediate-scale quantum (NISQ) computers, an implementation of the circuit without any optimization exceeds the gate count for the error budget and results in unresolved signals. Through a series of optimization with Qiskit and BQSKit, the gate count can be substantially reduced, making the jumps of the Uhlmann phase more visible. A recent hardware upgrade of IBM quantum computers further improves the signals and leads to a clearer demonstration of interesting finite-temperature topological phenomena on NISQ hardware.

Mastandrea, Christopher [Univ. of California, Merc↗
DOE OSTI2022

Approximate Bayesian Computation applied to the Diffuse Gamma-Ray Sky

ABSTRACT Many sources contribute to the diffuse gamma-ray background (DGRB), including star forming galaxies, active galactic nuclei, and cosmic ray interactions in the Milky Way. Exotic sources, such as dark matter annihilation, may also make some contribution. The photon counts-in-pixels distribution is a powerful tool for analysing the DGRB and determining the relative contributions of different sources. However, including photon energy information in a likelihood analysis of the counts-in-pixels distribution quickly becomes computationally intractable as the number of source types and energy bins increase. Here, we apply the likelihood-free method of approximate Bayesian computation (ABC) to the problem. We consider a mock analysis that includes contributions from dark matter annihilation in Galactic subhaloes as well as astrophysical backgrounds. We show that our results using ABC are consistent with the exact likelihood when energy information is discarded, and that significantly tighter parameter constraints can be obtained with ABC when energy information is included. ABC presents a powerful tool for analysing the DGRB and understanding its varied origins.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Scattering phase shift in quantum mechanics on quantum computers

Here, we investigate the feasibility of extracting infinite volume scattering phase shift on quantum computers in a simple one-dimensional quantum mechanical model, using the formalism established in the work by Guo and Gasparian [Phys. Rev. D 108, 074504 (2023)] that relates the integrated correlation functions for a trapped system to the infinite volume scattering phase shifts through a weighted integral. The system is first discretized in a finite box with periodic boundary conditions, and the formalism in real time is verified by employing a contact interaction potential with exact solutions. Quantum circuits are then designed and constructed to implement the formalism on current quantum computing architectures. To overcome the fast oscillatory behavior of the integrated correlation functions in real-time simulation, different methods of postdata analysis are proposed and discussed. Test results on IBM hardware show that good agreement can be achieved with two qubits, but complete failure ensues with three qubits due to two-qubit gate operation errors and thermal relaxation errors.

Guo, Peng [Dakota State Univ., Madison, SD (United↗
DOE OSTI2025

Optimizing stochastic algorithms for hadron correlation function computations in lattice QCD using a localized distillation basis

Distillation is a quark-smearing method for the construction of a broad class of hadron operators useful in lattice QCD computations and defined via a projection operator into a vector space of smooth gauge-covariant fields. A new orthonormal basis for this space is constructed which builds in locality. This basis is useful for the construction of stochastic methods to estimate the correlation functions computed in Monte Carlo calculations relevant for hadronic physics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Bosonic field digitization for quantum computers

Quantum simulation of quantum field theory is a flagship application of quantum computers that promises to deliver capabilities beyond classical computing. The realization of quantum advantage will require methods that can accurately predict error scaling as a function of the resolution and parameters of the model and that can be implemented efficiently on quantum hardware. In this paper, we address the representation of lattice bosonic fields in a discretized field amplitude basis, develop methods to predict error scaling, and present efficient qubit implementation strategies. A low-energy subspace of the bosonic Hilbert space, defined by a boson occupation number cutoff, can be represented with exponentially good accuracy by a low-energy subspace of a finite-size Hilbert space. The finite representation construction and the associated errors are directly related to the accuracy of the Nyquist-Shannon sampling and the finite Fourier transforms of the boson number states in the field and the conjugate-field bases. We analyze the relation between the boson mass, the discretization parameters used for wave function sampling, and the finite representation size. Numerical simulations of small size Φ 4 problems demonstrate that the boson mass optimizing the sampling of the ground state wave function is a good approximation to the optimal boson mass yielding the minimum low-energy subspace size. However, we find that accurate sampling of general wave functions does not necessarily result in accurate representation. Finally, we develop methods for validating and adjusting the discretization parameters to achieve more accurate simulations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗