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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 OSTI2015

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we focus on protein-vectors that can be utilized in a wide array of bioinformatics investigations such as family classification, protein visualization, structure prediction, disordered protein identification, and protein-protein interaction prediction. In this method, we adopt artificial neural network approaches and represent a protein sequence with a single dense n-dimensional vector. To evaluate this method, we apply it in classification of 324,018 protein sequences obtained from Swiss-Prot belonging to 7,027 protein families, where an average family classification accuracy of 93%±0.06% is obtained, outperforming existing family classification methods. In addition, we use ProtVec representation to predict disordered proteins from structured proteins. Two databases of disordered sequences are used: the DisProt database as well as a database featuring the disordered regions of nucleoporins rich with phenylalanine-glycine repeats (FG-Nups). Using support vector machine classifiers, FG-Nup sequences are distinguished from structured protein sequences found in Protein Data Bank (PDB) with a 99.8% accuracy, and unstructured DisProt sequences are differentiated from structured DisProt sequences with 100.0% accuracy. These results indicate that by only providing sequence data for various proteins into this model, accurate information about protein structure can be determined. Importantly, this model needs to be trained only once and can then be applied to extract a comprehensive set of information regarding proteins of interest. Moreover, this representation can be considered as pre-training for various applications of deep learning in bioinformatics.

Science & Technology - Other Topics↗
DOE OSTI2022

X-ray crystal structure of the Escherichia coli RadD DNA repair protein bound to ADP reveals a novel zinc ribbon domain

Genome maintenance is an essential process in all cells. In prokaryotes, the RadD protein is important for survival under conditions that include DNA-damaging radiation. Precisely how RadD participates in genome maintenance remains unclear. Here we present a high-resolution X-ray crystal structure of ADP-bound Escherichia coli RadD, revealing a zinc-ribbon element that was not modelled in a previous RadD crystal structure. Insights into the mode of nucleotide binding and additional structure refinement afforded by the new RadD model will help to drive investigations into the activity of RadD as a genome stability and repair factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cost Analysis of Annual and Monthly Net Zero Energy Performance for Multifamily Buildings in the United States

As the United States continues its progress toward sustainable construction, net zero building design is becoming an increasingly important and popular topic. Two definitions of net zero energy performance, monthly and annual, provide different levels of energy autonomy and efficiency within a building. This article analyzes the viability and incremental cost for two-, three-, and four-story multifamily apartment buildings to reach both annual and monthly net zero energy performance throughout four climate zones in the United States using baseline reference buildings that represent current construction practices. Building size plays a large role in determining the capability for a building model to reach annual or monthly net zero. Two-story buildings are capable of reaching annual net zero with an increase in construction cost of about 4.4–5.6%. Three-story buildings in warmer climates can achieve annual net zero with an increase of about 5.1%, but models in colder climates cannot reach annual net zero performance. Four-story buildings cannot achieve net zero, owing to insufficient building area for solar arrays to produce electricity. Monthly net zero energy performance was significantly harder to achieve, with the only case reaching this goal being the two-story Houston based model, at an added cost of 8.2%. Generally speaking, only small buildings in warm climates will be able to achieve monthly net zero without vastly oversizing photovoltaic systems and increasing costs without adequate payback.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2014

Radiation from mixed multi-planar wire arrays

The study of radiation from different wire materials in wire array Z-pinch plasma is a very challenging topic because it is almost impossible to separate different plasmas at the stagnation. A new approach is suggested based on planar wire array (PWA) loads to assess this problem. Multi-planar wire arrays are implemented that consist of few planes, each with the same number of wires and masses but from different wire materials, arranged in parallel rows. In particular, the experimental results obtained with triple PWAs (TPWAs) on the UNR Zebra generator are analyzed with Wire Ablation Dynamics Model, non-local thermodynamic equilibrium kinetic model, and 2D radiation magneto-hydrodynamic to illustrate this new approach. In TPWAs, two wire planes were from mid-atomic-number wire material and another plane was from alloyed Al, placed either in the middle or at the edge of the TPWA. Spatial and temporal properties of K-shell Al and L-shell Cu radiations were analyzed and compared from these two configurations of TPWAs. Advantages of the new approach are demonstrated and future work is discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Reimagining Codesign for Advanced Scientific Computing: Report for the ASCR Workshop on Reimagining Codesign

In March 2021, the U.S. Department of Energy’s Advanced Scientific Computing Research program convened the Workshop on Reimagining Codesign. The workshop, also known as ReCoDe, was organized around discussions on eight topic areas: (1) codesign for traditional high-performance computing workloads; (2) codesign of memory/storage systems; (3) codesign of machine learning, neuromorphic, quantum, and other non-von Neumann accelerators; (4) codesign for edge computing and processing at experimental instruments; (5) codesign for security and privacy; (6) hardware design tools and open-source hardware for high-productivity codesign; (7) tools, software stack, and programming languages for high-productivity codesign; and (8) quantitative tools and data collection for modeling and simulation for codesign. The panels identified four Priority Research Directions from these deliberations: (1) breakthrough computing capabilities with targeted heterogeneity and rapid design; (2) software and applications that embrace radical architecture diversity; (3) engineered security and integrity, from transistors to applications; and (4) design with data-rich processes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

44th Annual Anomalous Absorption Conference

Conference Grant Report July 14, 2015 Submitted to the U. S. Department of Energy Attn: Dr. Sean Finnegan By the University of California, San Diego 9500 Gilman Drive La Jolla, California 92093 On behalf of the 44th Annual Anomalous Absorption Conference 8-13 June 2014, in Estes Park, Colorado Support Requested: $10,100 Amount expended: $3,216.14 Performance Period: 1 March 20 14 to 28 February 20 15 Principal Investigator Dr. Farhat Beg Center for Energy Research University of California, San Diego 9500 Gilman Drive La Jolla, California 92093-0417 858-822-1266 (telephone) 858-534-4543 (fax) fbeg@ucsd.edu Administrative Point of Contact: Brandi Pate, 858-534-0851, blpate®ucsd.edu I. Background The forty-fourth Anomalous Absorption Conference was held in Estes Park, Colorado from June 5-8, 2014 (aac2014.ucsd.edu). The first Anomalous Absorption Conference was held in 1971 to assemble experts in the poorly understood area of laser-plasma absorption. The goal of that conference was to address the anomalously large laser absorption seen in plasma experiments with respect to the laser absorption predicted by linear plasma theory. Great progress in this research area has been made in the decades since that first meeting, due in part to the scientific interactions that have occurred annually at this conference. Specifically, this includes the development of nonlinear laser-plasma theory and the simulation of laser interactions with plasmas. Each summer since that first meeting, this week-long conference has been held at unique locations in North America as a scientific forum for intense scientific exchanges relevant to the interaction of laser radiation with plasmas. Responsibility for organizing the conference has traditional rotated each year between the major Inertial Confinement Fusion (ICF) laboratories and universities including LANL, LLNL, LLE, UCLA UC Davis and NRL. As the conference has matured over the past four decades, its technical footprint has expanded beyond ICF-related laser-plasma interactions to encompass closely related technical areas including laser particle acceleration, high-intensity laser effects, short­ pulse laser interactions, PIC and Vlasov/rad-hydro modeling, inertial and magnetic fusion plasmas, advanced plasma diagnostics, alternate ignition schemes, EOS/transport/opacity, and this year, x­ ray free-electron lasers and their applications. The conference continues to be a showcase for the presentation and discussion of the latest developments in these areas. II. Meeting Report The conference was extremely successful with more than one hundred participants. There were ninety-nine (99) abstracts submitted. There were forty-four (44) presentations including eleven (11) invited talks. The following topics were covered: a) Radiation Hydrodynamics b) Implosion Plasma Kinetic Effects c) Alternate Ignition Schemes d) Astrophysical Phenomena e) Opacity/Transport/EOS f) High Power Lasers and Facilities g) High-Intensity Laser-Matter Interactions h) Hydrodynamics and Hydro-instabilities i) Hot Dense Plasma Atomic Processes j) High Energy Density Physics k) Laser Particle Acceleration Physics l) Advanced Plasma Diagnostics m) Advanced light sources and applications Despite significant advertising, there were two students who applied for the travel grants: Charlie Jarrott and Joohwan Kim. The total funds expended were $3,216.14.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Timing Is everything: quantifying regulatory and market readiness levels for technology transition policy analysis

People save for retirement throughout their career because it is virtually impossible to save all you’ll need in retirement the year before you retire. Similarly, without installing incremental amounts of clean fossil, renewable or transformative energy technologies throughout the coming decades, a radical and immediate change will be near impossible the year before a policy goal is set to be in place. This notion of steady installation growth over acute installations of technology to meet policy goals is the core topic of discussion for this research. This research operationalizes this notion by developing the theoretical underpinnings of regulatory and market acceptance delays by building upon the common Technology Readiness Level (TRL) framework and offers two new additions to the research community. The new and novel Regulatory Readiness Level (RRL) and Market Readiness Level (MRL) frameworks were developed. These components, collectively called the Technology, Regulatory and Market (TRM) readiness level framework allow one to build new constraints into existing Integrated Assessment Models (IAMs) to address research questions such as, ‘To meet our desired technical and policy goals, what are the factors that affect the rate we must install technology to achieve these goals in the coming decades?’

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Analysis of tumor-immune functional responses in a mathematical model of neoantigen cancer vaccines

Cancer neoantigen vaccines have emerged as a promising approach to stimulating the immune system to fight cancer. We propose a simple model including key elements of cancer-immune interactions and conduct a phase plane analysis to understand the immunological mechanisms of cancer neoantigen vaccines. Analytical results are obtained for two widely used functional forms that represent the killing rate of tumor cells by immune cells: the law of mass action (LMA) and the dePillis-Radunskaya Law (LPR). Using the LMA, our results reveal that a slowly growing tumor can escape the immune surveillance and that there is a unique periodic solution. The LPR offers richer dynamics, in which tumor elimination and uncontrolled tumor growth are both present. We show that tumor elimination requires sufficient number of initial activated T cells in relationship to the malignant cells, which lends support to using the neoantigen cancer vaccine as an adjuvant therapy after the primary tumor is surgically removed or treated using radiotherapy. We also derive a sufficient condition for uncontrolled tumor growth under the assumption of the LPR. Here, the juxtaposition of analyses with these two different choices for the killing rate function highlights their importance on model behavior and biological implications, by which we hope to spur further theoretical and experimental work to understand mechanisms underlying different functional forms for the killing rate.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Genome expansion by a CRISPR trimmer-integrase

CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR–Cas systems lack Cas4. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Aerosol optical, microphysical, chemical and radiative properties of high aerosol load cases over the Arctic based on AERONET measurements

Columnar mass concentrations of aerosol components over the Arctic are estimated using microphysical parameters derived from direct sun extinction and sky radiance measurements of Aerosol Robotic Network. Aerosol optical, microphysical, chemical and radiative properties show that Arctic aerosols are dominated by fine mode particles, especially for high aerosol load cases. The average aerosol optical depth (AOD) of the selected Arctic sites in the sampling period is approximately 0.08, with 75% composed of fine mode particles. The fine mode fraction mostly exceeds 0.9 when AOD greater than 0.4. The ammonium sulfate-like component (AS) contributes about 68% of total dry aerosol mass for high-AOD events. The estimated compositions and back trajectories show that the transported aerosol particles from biomass burning events have large amounts of black carbon (BC) and brown carbon, while those from pollution events are characterised by large AS fractions. The instantaneous radiative forcing at the top-of-atmosphere is higher for the more absorbing components, and varies greatly with surface albedo and solar zenith angle. A regression model of columnar composition and radiative forcing within the atmosphere (RFATM) for Arctic aerosol is established, showing that BC dominates a positive RFATM with a high warming efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

The non-random walk of chiral magnetic charge carriers in artificial spin ice

The flow of magnetic charge carriers (dubbed magnetic monopoles) through frustrated spin ice lattices, governed simply by Coulombic forces, represents a new direction in electromagnetism. Artificial spin ice nanoarrays realise this effect at room temperature, where the magnetic charge is carried by domain walls. Control of domain wall path is one important element of utilizing this new medium. By imaging the transit of domain walls across different connected 2D honeycomb structures we contribute an important aspect which will enable that control to be realized. Although apparently equivalent paths are presented to a domain wall as it approaches a Y-shaped vertex from a bar parallel to the field, we observe a stark non-random path distribution, which we attribute to the chirality of the magnetic charges. These observations are supported by detailed statistical modelling and micromagnetic simulations. The identification of chiral control to magnetic charge path selectivity invites analogy with spintronics.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Unexpected host dependency of Antarctic Nanohaloarchaeota

In hypersaline environments, Nanohaloarchaeota (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaeota [DPANN] superphylum) are thought to be free-living microorganisms. We report cultivation of 2 strains of Antarctic Nanohaloarchaeota and show that they require the haloarchaeon Halorubrum lacusprofundi for growth. By performing growth using enrichments and fluorescence-activated cell sorting, we demonstrated successful cultivation of Candidatus Nanohaloarchaeum antarcticus, purification of Ca. Nha. antarcticus away from other species, and growth and verification of Ca. Nha. antarcticus with Hrr. lacusprofundi ; these findings are analogous to those required for fulfilling Koch’s postulates. We use fluorescent in situ hybridization and transmission electron microscopy to assess cell structures and interactions; metagenomics to characterize enrichment taxa, generate metagenome assembled genomes, and interrogate Antarctic communities; and proteomics to assess metabolic pathways and speculate about the roles of certain proteins. Metagenome analysis indicates the presence of a single species, which is endemic to Antarctic hypersaline systems that support the growth of haloarchaea. The presence of unusually large proteins predicted to function in attachment and invasion of hosts plus the absence of key biosynthetic pathways (e.g., lipids) in metagenome assembled genomes of globally distributed Nanohaloarchaeota indicate that all members of the lineage have evolved as symbionts. Our work expands the range of archaeal symbiotic lifestyles and provides a genetically tractable model system for advancing understanding of the factors controlling microbial symbiotic relationships.

Science & Technology - Other Topics↗
DOE OSTI2024

DiffLense: a conditional diffusion model for super-resolution of gravitational lensing data

Abstract Gravitational lensing data is frequently collected at low resolution due to instrumental limitations and observing conditions. Machine learning-based super-resolution techniques offer a method to enhance the resolution of these images, enabling more precise measurements of lensing effects and a better understanding of the matter distribution in the lensing system. This enhancement can significantly improve our knowledge of the distribution of mass within the lensing galaxy and its environment, as well as the properties of the background source being lensed. Traditional super-resolution techniques typically learn a mapping function from lower-resolution to higher-resolution samples. However, these methods are often constrained by their dependence on optimizing a fixed distance function, which can result in the loss of intricate details crucial for astrophysical analysis. In this work, we introduce DiffLense , a novel super-resolution pipeline based on a conditional diffusion model specifically designed to enhance the resolution of gravitational lensing images obtained from the Hyper Suprime-Cam Subaru Strategic Program (HSC-SSP). Our approach adopts a generative model, leveraging the detailed structural information present in Hubble space telescope (HST) counterparts. The diffusion model, trained to generate HST data, is conditioned on HSC data pre-processed with denoising techniques and thresholding to significantly reduce noise and background interference. This process leads to a more distinct and less overlapping conditional distribution during the model’s training phase. We demonstrate that DiffLense outperforms existing state-of-the-art single-image super-resolution techniques, particularly in retaining the fine details necessary for astrophysical analyses.

Computer Science↗
DOE OSTI2014

Transient viscoelasticity study of tobacco mosaic virus/Ba2+ superlattice

Recently, we reported a new method to synthesize the rod-like tobacco mosaic virus (TMV) superlattice. To explore its potentials in nanolattice templating and tissue scaffolding, this work focused the viscoelasticity of the superlattice with a novel transient method via atomic force microscopy (AFM). For measuring viscoelasticity, in contrast to previous methods that assessed the oscillating response, the method proposed in this work enabled us to determine the transient response (creep or relaxation) of micro/nanobiomaterials. The mathematical model and numerical process were elaborated to extract the viscoelastic properties from the indentation data. The adhesion between the AFM tip and the sample was included in the indentation model. Through the functional equation method, the elastic solution for the indentation model was extended to the viscoelastic solution so that the time dependent force vs. displacement relation could be attained. To simplify the solving of the differential equation, a standard solid model was modified to obtain the elastic and viscoelastic components of the sample. The viscoelastic responses with different mechanical stimuli and the dynamic properties were also investigated.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Proceedings of the 2013 International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering - M and C 2013

The Mathematics and Computation Division of the American Nuclear (ANS) and the Idaho Section of the ANS hosted the 2013 International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (M and C 2013). This proceedings contains over 250 full papers with topics ranging from reactor physics; radiation transport; materials science; nuclear fuels; core performance and optimization; reactor systems and safety; fluid dynamics; medical applications; analytical and numerical methods; algorithms for advanced architectures; and validation verification, and uncertainty quantification.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2018

Student-Friendly Guide to Molecular Integrals

Preceding even the Hartree–Fock method, molecular integrals are the very foundation upon which quantum chemical molecular modeling depends. Discussions of molecular integrals are normally found only in advanced and technical texts or articles. The objective of the present article is to provide less experienced readers, or students in a physical/computational chemistry course, a thorough understanding of molecular integrals. Through a series of detailed Handouts, the student/reader can participate in the derivation of molecular integrals, and in turn implement them in computer code. Hartree–Fock theory is discussed in enough detail to motivate the molecular integrals and address such topics as the atomic orbital basis. An introduction to the programming language of choice, Python3, is provided, tailored toward developing the essential skills necessary for implementing molecular integrals. In conclusion, the article is intended to be useful not only to instructors of physical/computational chemistry, but also to any reader who has independently sought a primer on this elusive subject.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

The Forward Physics Facility at the High-Luminosity LHC

High energy collisions at the High-Luminosity Large Hadron Collider (LHC) produce a large number of particles along the beam collision axis, outside of the acceptance of existing LHC experiments. The proposed Forward Physics Facility (FPF), to be located several hundred meters from the ATLAS interaction point and shielded by concrete and rock, will host a suite of experiments to probe standard model (SM) processes and search for physics beyond the standard model (BSM). In this report, we review the status of the civil engineering plans and the experiments to explore the diverse physics signals that can be uniquely probed in the forward region. FPF experiments will be sensitive to a broad range of BSM physics through searches for new particle scattering or decay signatures and deviations from SM expectations in high statistics analyses with TeV neutrinos in this low-background environment. High statistics neutrino detection will also provide valuable data for fundamental topics in perturbative and non-perturbative QCD and in weak interactions. Experiments at the FPF will enable synergies between forward particle production at the LHC and astroparticle physics to be exploited. We report here on these physics topics, on infrastructure, detector, and simulation studies, and on future directions to realize the FPF’s physics potential.

47 OTHER INSTRUMENTATION↗
DOE OSTI2014

WE-D-BRE-01: A Sr-90 Irradiation Device for the Study of Cutaneous Radiation Injury

Purpose: To determine dosimetric character for a custom-built Sr-90 beta irradiator designed for the study of Cutaneous Radiation Injury (CRI) in a porcine animal model. In the event of a radiological accident or terrorist event, Sr-90, a fission by-product, will likely be produced. CRI is a main concern due to the low energy and superficial penetration in tissue of beta particles from Sr-90. Seven 100 mCi plaque Sr-90 radiation sources within a custom-built irradiation device create a 40 mm diameter region of radiation-induced skin injury as part of a larger project to study the efficacy of a topical keratin-based product in CRI healing. Methods: A custom-built mobile irradiation device was designed and implemented for in vivo irradiations. Gafchromic™ EBT3 radiochromic film and a PTW Markus chamber type 23343 were utilized for dosimetric characterization of the beta fluence at the surface produced by this device. Films were used to assess 2-dimensional dose distribution and percent depth dose characteristics of the radiation field. Ion chamber measurements provided dose rate data within the field. Results: The radiation field produced by the irradiation device is homogeneous with high uniformity (∼5%) and symmetry (∼3%) with a steep dose fall-off with depth from the surface. Dose rates were determined to be 3.8 Gy/min and 3.3 Gy/min for film and ion chamber measurements, respectively. A dose rate of 3.4 Gy/min was used to calculate irradiation times for in vivo irradiations. Conclusion: The custom-built irradiation device enables the use of seven Sr-90 beta sources in an array to deliver a 40 mm diameter area of homogeneous skin dose with a dose rate that is useful for research purposes and clinically relevant for the induction of CRI. Doses of 36 and 42 Gy successfully produce Grade III CRI and are used in the study of the efficacy of KeraStat™. This project has been funded in whole or in part with Federal funds from the Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, Office of the Secretary, Department of Health and Human Services, under Contract No. HHSO100201200007C.

07 ISOTOPE AND RADIATION SOURCES↗