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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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DOE OSTI2025

Machine learning prediction of enzyme optimum pH

The relationship between pH and enzyme catalytic activity, especially the optimal pH (pH opt ) at which enzymes function, is critical for biotechnological applications. Hence, computational methods to predict pH opt will enhance enzyme discovery and design by facilitating accurate identification of enzymes that function optimally at specific pH levels, and by elucidating sequence-function relationships. Here, in this study, we proposed and evaluated various machine learning methods for predicting pH opt , conducting extensive hyperparameter optimization and training over 11,000 model instances. Our results demonstrate that models utilizing language model embeddings markedly outperform other methods in predicting pHopt. We present EpHod, the best-performing model, to predict pHopt, making it publicly available to researchers. From sequence data, EpHod directly learns structural and biophysical features that relate to pH opt , including proximity of residues to the catalytic centre and the accessibility of solvent molecules. Overall, EpHod presents a promising advancement in pH opt prediction and will potentially speed up the development of enzyme technologies.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Exploring cryo-electron microscopy with molecular dynamics

Single particle analysis cryo-electron microscopy (EM) and molecular dynamics (MD) have been complimentary methods since cryo-EM was first applied to the field of structural biology. The relationship started by biasing structural models to fit low-resolution cryo-EM maps of large macromolecular complexes not amenable to crystallization. The connection between cryo-EM and MD evolved as cryo-EM maps improved in resolution, allowing advanced sampling algorithms to simultaneously refine backbone and sidechains. Moving beyond a single static snapshot, modern inferencing approaches integrate cryo-EM and MD to generate structural ensembles from cryo-EM map data or directly from the particle images themselves. We summarize the recent history of MD innovations in the area of cryo-EM modeling. The merits for the myriad of MD based cryo-EM modeling methods are discussed, as well as, the discoveries that were made possible by the integration of molecular modeling with cryo-EM. Lastly, current challenges and potential opportunities are reviewed.

Biochemistry & Molecular Biology↗

DOE OSTI2022

Absolute colors and phase coefficients of asteroids

Context: We use the phase curves of small bodies to measure absolute magnitudes and, together with complementary theoretical and laboratory results, to understand the micro- and macroscopic properties of their surfaces. Although we can observe asteroids up to phase angles of about 30 deg, the range of phase angles covered by outer Solar System objects usually does not go further than 7-10 deg for centaurs and 2 deg for trans-Neptunian objects, and a linear relation between magnitude and phase angle may be assumed. Aims: We aim to directly compare data taken for objects in the inner Solar System (inside the orbit of Jupiter) with data for centaurs and trans-Neptunian objects. Methods: We use the SLOAN Moving Objects Catalog (MOC) data to construct phase curves restricted to phase angles of less than or equal to 7.5 deg, which is compatible with the angles observed for the trans-Neptunian and Centaur population. We assume a linear model for the photometric behavior to obtain absolute magnitudes and phase coefficients in the ugirz, V, and R filters. Results: We obtain absolute magnitudes in seven filters for over 4000 objects. Our comparison with outer Solar System objects suggests the surfaces have a common property: intrinsically redder objects become blue with increasing phase angle, while the opposite happens for intrinsically bluer objects.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

Thermal-fluctuation effects on small-scale statistics in turbulent gas flow

Kolmogorov's theory of turbulence assumes that the small-scale turbulent structures in the energy cascade are universal and are determined by the energy dissipation rate and the kinematic viscosity alone. However, thermal fluctuations, absent from the continuum description, terminate the energy cascade near the Kolmogorov length scale. Here, we propose a simple superposition model to account for the effects of thermal fluctuations on small-scale turbulence statistics. Furthermore, for compressible Taylor–Green vortex flow, we demonstrate that the superposition model in conjunction with data from direct numerical simulation of the Navier–Stokes equations yields spectra and structure functions that agree with the corresponding quantities computed from the direct simulation Monte Carlo method of molecular gas dynamics, verifying the importance of thermal fluctuations in the dissipation range.

42 ENGINEERING↗

DOE OSTI2024

Extended dynamic mode decomposition for model reduction in fluid dynamics simulations

High computational cost and storage/memory requirements of fluid dynamics simulations constrain their usefulness as a predictive tool. Reduced-order models (ROMs) provide a viable solution to this challenge by extracting the key underlying dynamics of a complex system directly from data. We investigate the efficacy and robustness of an extended dynamic mode decomposition (xDMD) algorithm in constructing ROMs of three-dimensional cardiovascular computations. Focusing on the ROMs' accuracy in representation and interpolation, we relate these metrics to the truncation rank of singular value decomposition, which underpins xDMD and other approaches to ROM construction. Our key innovation is to relate the truncation rank to the singular values of the original flow problem. This result establishes a priori guidelines for the xDMD deployment and its likely success as a means of data compression and reconstruction of the system's dynamics from dominant spatiotemporal structures present in the data.

Mechanics↗

DOE OSTI2022

Disentangling the chemistry of Australian plant exudates from a unique historical collection

For thousands of years, the unique physicochemical properties of plant exudates have defined uses in material culture and practical applications. Native Australian plant exudates, including resins, kinos, and gums, have been used and continue to be used by Aboriginal Australians for numerous technical and cultural purposes. A historic collection of well-preserved native Australian plant exudates, assembled a century ago by plant naturalists, gives a rare window into the history and chemical composition of these materials. Here we report the full hierarchical characterization of four genera from this collection, Xanthorrhoea, Callitris, Eucalyptus, and Acacia, from the local elemental speciation, to functional groups and main molecular markers. We use high-resolution X-ray Raman spectroscopy (XRS) to achieve bulk-sensitive chemical speciation of these plant exudates, including insoluble, amorphous, and cross-linked fractions, without the limitation of invasive and/or surface specific methods. Combinatorial testing of the XRS data allows direct classification of these complex natural species as terpenoid, aromatic, phenolic, and polysaccharide materials. Differences in intragenera chemistry was evidenced by detailed interpretation of the XRS spectral features. We complement XRS with Fourier-transform infrared (FT-IR) spectroscopy, gas chromatography–mass spectrometry (GC-MS), and pyrolysis–GC-MS (Py-GC-MS). This multimodal approach provides a fundamental understanding of the chemistry of these natural materials long used by Aboriginal Australian peoples.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Lagrangian large eddy simulations via physics-informed machine learning

High-Reynolds number homogeneous isotropic turbulence (HIT) is fully described within the Navier–Stokes (NS) equations, which are notoriously difficult to solve numerically. Engineers, interested primarily in describing turbulence at a reduced range of resolved scales, have designed heuristics, known as large eddy simulation (LES). LES is described in terms of the temporally evolving Eulerian velocity field defined over a spatial grid with the mean-spacing correspondent to the resolved scale. This classic Eulerian LES depends on assumptions about effects of subgrid scales on the resolved scales. Here, we take an alternative approach and design LES heuristics stated in terms of Lagrangian particles moving with the flow. Our Lagrangian LES, thus L-LES, is described by equations generalizing the weakly compressible smoothed particle hydrodynamics formulation with extended parametric and functional freedom, which is then resolved via Machine Learning training on Lagrangian data from direct numerical simulations of the NS equations. The L-LES model includes physics-informed parameterization and functional form, by combining physics-based parameters and physics-inspired Neural Networks to describe the evolution of turbulence within the resolved range of scales. The subgrid-scale contributions are modeled separately with physical constraints to account for the effects from unresolved scales. We build the resulting model under the differentiable programming framework to facilitate efficient training. We experiment with loss functions of different types, including physics-informed ones accounting for statistics of Lagrangian particles. We show that our L-LES model is capable of reproducing Eulerian and unique Lagrangian turbulence structures and statistics over a range of turbulent Mach numbers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

High precision magnetic field measurement and mapping of the LEReC 180 degree bending magnet using very low field NMR with hall combined probe (140 - 350 gauss)

The Relativistic Heavy Ion Collider (RHIC) at BNL are using the Low Energy RHIC Electron Cooling (LEReC) to conduct experiments that search for the quantum chromodynamic (QCD) critical point. The first ever electron cooling based on the RF acceleration of electron beams was experimentally demonstrated on April 5, 2019 at LEReC at BNL. The first critical step in obtaining successful 3D non-magnetized cooling of the Au ion bunches in the RHIC cooling section was matching the electron beam energy with a relative error less than 5*10 -4 to the ion beam energy. Part of the LEReC beamline is a dipole magnet that bends the electron beam 180 degree. One of the most outstanding measurement challenges is that the dipole field is so low (≈200 G). Most of the existing NMR probes can only measure fields >400 G. Lower signal-to-noise ratio at low fields is requires the use of larger sample volumes. Working with CAYLAR, a NMR probe has been redesigned and optimized for these low field measurements with high resolution. We report the methods, challenges, and results for extensive magnetic field mappings of the 180 dipole magnet. A combination of NMR and Hall sensors has been successfully implemented to measure uniform field regimes inside the magnet center area and non-uniform field regimes at the magnet ends. Detailed measurement and mapping have been performed at five radii and five heights along the beam trajectory. Meanwhile a finite element magnetic modeling simulation of the magnet using Opera software has been performed. The calculated and measured data are compared, and the calculated data is good reference for measured data over long length mapping from magnet edge to center. The measured magnetic measurement data is directly useful for beam instrumentation, diagnostics and operation.

Magnetic Field Measurement↗

DOE OSTI2024

Coastal bacteria and protists assimilate viral carbon and nitrogen

Abstract Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Deblending galaxies with variational autoencoders: A joint multiband, multi-instrument approach

ABSTRACT Blending of galaxies has a major contribution in the systematic error budget of weak-lensing studies, affecting photometric and shape measurements, particularly for ground-based, deep, photometric galaxy surveys, such as the Rubin Observatory Legacy Survey of Space and Time (LSST). Existing deblenders mostly rely on analytic modelling of galaxy profiles and suffer from the lack of flexible yet accurate models. We propose to use generative models based on deep neural networks, namely variational autoencoders (VAE), to learn probabilistic models directly from data. We train a VAE on images of centred, isolated galaxies, which we reuse, as a prior, in a second VAE-like neural network in charge of deblending galaxies. We train our networks on simulated images including six LSST bandpass filters and the visible and near-infrared bands of the Euclid satellite, as our method naturally generalizes to multiple bands and can incorporate data from multiple instruments. We obtain median reconstruction errors on ellipticities and r-band magnitude between ±0.01 and ±0.05, respectively, in most cases, and ellipticity multiplicative bias of 1.6 per cent for blended objects in the optimal configuration. We also study the impact of decentring and prove the method to be robust. This method only requires the approximate centre of each target galaxy, but no assumptions about the number of surrounding objects, pointing to an iterative detection/deblending procedure we leave for future work. Finally, we discuss future challenges about training on real data and obtain encouraging results when applying transfer learning.

Arcelin, Bastien↗

DOE OSTI2021

A massive open cluster hiding in full sight

ABSTRACT Obscuration and confusion conspire to limit our knowledge of the inner Milky Way. Even at moderate distances, the identification of stellar systems becomes compounded by the extremely high density of background sources. Here, we provide a very revealing example of these complications by unveiling a large, massive, young cluster in the Sagittarius arm that has escaped detection until now despite containing more than 30 stars brighter than G = 13. By combining Gaia DR2 astrometry, Gaia and 2MASS photometry, and optical spectroscopy, we find that the new cluster, which we name Valparaiso 1, located at $\sim 2.3\,$ kpc, is about 75 Ma old and includes a large complement of evolved stars, among which we highlight the 4 d classical Cepheid CM Sct and an M-type giant that probably represents the first detection of an asymptotic giant branch star in a Galactic young open cluster. Although strong differential reddening renders accurate parameter determination unfeasible with the current data set, direct comparison to clusters of similar age suggests that Valparaiso 1 was born as one of the most massive clusters in the solar neighbourhood, with an initial mass close to $10^{4}\, \mathrm{M}_{\odot }$.

Negueruela, I.↗

DOE OSTI2021

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗

DOE OSTI2023

Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics

SARS-CoV-2 depends on -1 programmed ribosomal frameshifting (-1 PRF) to express proteins essential for its replication. The RNA pseudoknot stimulating -1 PRF is thus an attractive drug target. However, the structural models of this pseudoknot obtained from cryo-EM and crystallography differ in some important features, leaving the pseudoknot structure unclear. We measured the solution structure of the pseudoknot using small-angle X-ray scattering (SAXS). The measured profile did not agree with profiles computed from the previously solved structures. Beginning with each of these solved structures, we used the SAXS data to direct all atom molecular dynamics (MD) simulations to improve the agreement in profiles. In all cases, this refinement resulted in a bent conformation that more closely resembled the cryo-EM structures than the crystal structure. Applying the same approach to a point mutant abolishing -1 PRF revealed a notably more bent structure with reoriented helices. This work clarifies the dynamic structures of the SARS-CoV-2 pseudoknot in solution.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

Quantum dynamics simulation of the advection-diffusion equation

The advection-diffusion equation is simulated via several quantum algorithms. Three formulations are considered: (1) Trotterization, (2) variational quantum time evolution (VarQTE), and (3) adaptive variational quantum dynamics simulation (AVQDS). These schemes were originally developed for the Hamiltonian simulation of many-body quantum systems. The finite-difference discretized operator of the transport equation is formulated as a Hamiltonian and solved without the need for ancillary qubits. Computations are conducted on a quantum simulator (IBM Qiskit Aer) and a superconducting quantum hardware (IBM Fez). The former emulates the latter without the noise. The actual hardware implementation experiences significant noise. The results of the quantum simulator are compared with data from direct numerical simulation (DNS) with infidelities of the order 10 −5 . In the quantum simulator, Trotterization is observed to have the lowest infidelity and is suitable for fault-tolerant computation. The AVQDS algorithm requires the lowest gate count and circuit depth. The VarQTE algorithm is the next best in terms of gate counts, but the number of its optimization variables is directly proportional to the number of qubits. Due to current hardware limitations, Trotterization cannot be implemented, as it has an overwhelmingly large number of operations. Meanwhile, AVQDS and VarQTE can be executed at the hardware level. These algorithms present a new paradigm for computational transport phenomena on quantum computers.

Alipanah, Hirad [Univ. of Pittsburgh, PA (United S↗

DOE OSTI2022

Checking nonflow assumptions and results via PHENIX published correlations in p+p, p+Au, d+Au, and 3 He+Au at √ s NN=200 GeV

Recently the PHENIX Collaboration has made available two-particle correlation Fourier coefficients for multiple detector combinations in minimum bias p+p and 0–5% central p+Au, d+Au, and 3 He+Au collisions at √ s NN = 200 GeV [Phys. Rev. C 105, 024901 (2022)]. Using these coefficients for three sets of two-particle correlations, azimuthal anisotropy coefficients v 2 and v 3 are extracted for midrapidity charged hadrons as a function of transverse momentum. In this paper, we use the available coefficients to explore various nonflow hypotheses as well as to compare the results with theoretical model calculations. The nonflow methods fail basic closure tests with ampt and pythia/angantyr, particularly when including correlations with particles in the low multiplicity light-projectile going direction. In data, the nonflow adjusted v 2 results are modestly lower in p+Au and the adjusted v 3 results are more significantly higher in p+Au and d+Au. However, the resulting higher values for the ratio v 3 /v 2 in p+Au at RHIC compared to p+Pb at the LHC is additional evidence for a significant overcorrection. Incorporating these additional checks, the conclusion that these flow coefficients are dominated by initial geometry coupled with final-state interactions (e.g., hydrodynamic expansion of quark-gluon plasma) remains true, and explanations based solely on initial-state glasma are ruled out. The detailed balance between intrinsic and fluctuation-driven geometry and the exact role of weakly versus strongly coupled prehydrodynamic evolution remains an open question for triangular flow, requiring further theoretical and experimental investigation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2024

Probabilistic neural networks for improved analyses with phenomenological R -matrix

Here we present a method for measurement analyses based on probabilistic deep neural networks that provide several advantages over conventional analyses with phenomenological models. These include predicting physical quantities directly from data, the rapid generation of statistically robust uncertainties, and the ability to bypass some parameters that may induce ambiguities and complications in data analysis. As deep learning methods make predictions through “black boxes,” the uncertainty quantification is typically challenging. We use a probabilistic framework that provides thorough uncertainty quantification and is straightforward to follow in practice. With the network architecture based on the Transformer, we demonstrate the current method for predicting nuclear resonance parameters from scattering data using the phenomenological R-matrix model.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Search for strongly interacting massive particles generating trackless jets in proton–proton collisions at $\sqrt{s} = 13\,\text {TeV}$

A search for dark matter in the form of strongly interacting massive particles (SIMPs) using the CMS detector at the LHC is presented. The SIMPs would be produced in pairs that manifest themselves as pairs of jets without tracks. The energy fraction of jets carried by charged particles is used as a key discriminator to suppress efficiently the large multijet background, and the remaining background is estimated directly from data. The search is performed using proton–proton collision data corresponding to an integrated luminosity of 16.1 fb -1 , collected with the CMS detector in 2016. No significant excess of events is observed above the expected background. For the simplified dark matter model under consideration, SIMPs with masses up to 100 GeV are excluded and further sensitivity is explored towards higher masses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Design and analysis of CXL performance models for tightly-coupled heterogeneous computing

Truly heterogeneous systems enable partitioned workloads to be mapped to the hardware that nets the best performance. However, current practice requires that inter-device communication between different vendors' hardware use host memory as an intermediary step. To date, there are no widely adopted solutions that allow accelerators to directly transfer data. A new cache-coherent protocol, CXL, aims to facilitate easier, fine-grained sharing between accelerators. In this work we analyze existing methods for designing heterogeneous applications that target GPUs and FPGAs working collaboratively, followed by an exploration to show the benefits of a CXL-enabled system. Specifically, we develop a test application that utilizes both an NVIDIA P100 GPU and a Xilinx U250 FPGA to show current communication limitations. From this application, we capture overall execution time and throughput measurements on the FPGA and GPU. We use these measurements as inputs to novel CXL performance models to show that using CXL caching instead of host memory results in a 1.31X speedup, while a more tightly-coupled pipelined implementation using CXL-enabled hardware would result in a speedup of 1.45X.

Cabrera, Anthony↗