Engineering topics

Edwards, Robert

Publications and source records attributed to Edwards, Robert.

At least 19 records

DOE OSTI2024

Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families

Broadly reactive antibodies that target sequence-diverse antigens are of interest for vaccine design and monoclonal antibody therapeutic development because they can protect against multiple strains of a virus and provide a barrier to evolution of escape mutants. Using LIBRA-seq (linking B cell receptor to antigen specificity through sequencing) data for the B cell repertoire of an individual chronically infected with human immunodeficiency virus type 1 (HIV-1), we identified a lineage of IgG3 antibodies predicted to bind to HIV-1 Envelope (Env) and influenza A Hemagglutinin (HA). Two lineage members, antibodies 2526 and 546, were confirmed to bind to a large panel of diverse antigens, including several strains of HIV-1 Env, influenza HA, coronavirus (CoV) spike, hepatitis C virus (HCV) E protein, Nipah virus (NiV) F protein, and Langya virus (LayV) F protein. We found that both antibodies bind to complex glycans on the antigenic surfaces. Antibody 2526 targets the stem region of influenza HA and the N-terminal domain (NTD) region of SARS-CoV-2 spike. A crystal structure of 2526 Fab bound to mannose revealed the presence of a glycan-binding pocket on the light chain. Antibody 2526 cross-reacted with antigens from multiple pathogens and displayed no signs of autoreactivity. These features distinguish antibody 2526 from previously described glycan-reactive antibodies. Further study of this antibody class may aid in the selection and engineering of broadly reactive antibody therapeutics and can inform the development of effective vaccines with exceptional breadth of pathogen coverage.

Microbiology↗

DOE OSTI2023

Graph Contractions for Calculating Correlation Functions in Lattice QCD

Computing correlation functions for many-particle systems in Lattice QCD is vital to extract nuclear physics observables like the energy spectrum of hadrons such as protons. However, this type of calculation has long been considered to be very challenging and computing-resource intensive because of the complex nature of a hadron composed of quarks with many degrees of freedom. In particular, a correlation function can be calculated through a sum of all possible pairs of quark contractions, each of which is a batched tensor contraction, dictated by Wick's theorem. Because the number of terms of this sum can be very large for any hadronic system of interest, fast evaluation of the sum faces several challenges: an extremely large number of contractions, a huge memory footprint at runtime, and the speed of tensor contractions. In this paper, we present a Lattice QCD analysis software suite, Redstar, which addresses these challenges by utilizing novel algorithmic and software engineering methods targeting modern computing platforms such as many-core CPUs and GPUs. In particular, Redstar represents every term in the sum of a correlation function by a graph, applies efficient graph algorithms to reduce the number of contractions to lower the cost of computations, and minimizes the total memory footprint. Moreover, Redstar carries out the contractions on either CPUs or GPUs utilizing an internal and highly efficient Hadron contraction library. Specifically, we illustrate some important algorithmic optimizations of Redstar, show various key design features of Hadron library, and present the speedup values due to the optimizations along with performance figures for calculating six correlations functions on four computing platforms.

Chen, Jie↗

DOE OSTI2023

The case for an EIC Theory Alliance: Theoretical Challenges of the EIC

We outline the physics opportunities provided by the Electron Ion Collider (EIC). These include the study of the parton structure of the nucleon and nuclei, the onset of gluon saturation, the production of jets and heavy flavor, hadron spectroscopy and tests of fundamental symmetries. We review the present status and future challenges in EIC theory that have to be addressed in order to realize this ambitious and impactful physics program, including how to engage a diverse and inclusive workforce. In order to address these many-fold challenges, we propose a coordinated effort involving theory groups with differing expertise is needed. We discuss the scientific goals and scope of such an EIC Theory Alliance.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

The EIC on a Table Top (Final Report)

A research collaboration between JLab and the Atomic and Molecular Optics group of Olivier Pfister at UVA was established to adapt and enhance their optics-based Quantum Computing (QC) system for the calculation of Doubly-Deeply Virtual Compton Scattering amplitudes relevant for JLab12 and the EIC program. The formalism and simulation infrastructure for computing matrix elements of such Compton amplitudes was established. In partnership with UVA, JLab has provided the technical expertise to enhance the current system, and explored significantly scaling it to become a unique and powerful resource.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

The Case for an EIC Theory Alliance

This documents outlines the case for the creation of an EIC Theory Alliance. The EIC will be a unique and versatile facility that will enable the understanding of some of the most compelling questions in the physics of the strong nuclear force. To fully exploit the potential of the EIC, a focused theory effort will be required. The goal of the EIC Theory Alliance is to provide support and stewardship of the theory effort in EIC physics, broadly defined, over the lifetime of the facility. It will promote EIC theory and contribute to workforce development through: support of graduate students; EIC Theory Fellowships for postdocs; bridge positions at universities; and short and long term visitor programs to enhance collaboration between groups. In addition, the alliance will organize topical schools and workshops. The EIC Theory Alliance will be a decentralized organization, open to participation by anyone in the community who is interested in EIC physics, i.e., it will be a membership organization, where members elect an executive board which will effectively run the alliance. The executive board will determine the major scientific thrusts of the theory alliance, make decisions regarding at which universities bridge faculty positions will be created, and serve as a search committee for EIC-related positions. Furthermore, the executive board will coordinate the organization of workshops and schools related to the research activities of the alliance. In addition, the EIC theory alliance will seek out and nurture international cooperation to maximally leverage the available funding. The EIC theory alliance has a wider range of physics goals and longer lifetime, commensurate with that of the EIC research program, than individual nuclear theory topical collaborations. The structure of the EIC Theory Alliance will build on previous examples of successful alliances in nuclear theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Non-singlet quark helicity $\mathrm{PDF}$s of the nucleon from pseudo-distributions

The non-singlet helicity quark parton distribution functions (PDFs) of the nucleon are determined from lattice QCD, by jointly leveraging pseudo-distributions and the distillation spatial smearing paradigm. A Lorentz decomposition of appropriately isolated space-like matrix elements reveals pseudo-distributions that contain information on the leading-twist helicity PDFs, as well as an invariant amplitude that induces an additional z 2 contamination of the leading-twist signal. An analysis of the short-distance behavior of the space-like matrix elements using matching coefficients computed to next-to-leading order (NLO) exposes the desired PDF up to this additional z 2 contamination. Due to the non-conservation of the axial current, we elect to isolate the helicity PDFs normalized by the nucleon axial charge at the same scale μ 2 . The leading-twist helicity PDFs as well as several sources of systematic error, including higher-twist effects, discretization errors, and the aforementioned z 2 contaminating amplitude are jointly determined by characterizing the computed pseudo-distribution in a basis of Jacobi polynomials. The Akaike Information Criterion is exploited to effectively average over distinct model parameterizations and cuts on the pseudo-distribution. Encouraging agreement is observed with recent global analyses of each non-singlet quark helicity PDF, notably a rather small non-singlet anti-quark helicity PDF for all quark momentum fractions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2022

Nuclear Physics Exascale Requirements Review: An Office of Science Review sponsored jointly by Advanced Scientific Computing Research and Nuclear Physics, June 15 - 17, 2016, Gaithersburg, Maryland

Imagine being able to predict — with unprecedented accuracy and precision — the structure of the proton and neutron, and the forces between them, directly from the dynamics of quarks and gluons, and then using this information in calculations of the structure and reactions of atomic nuclei and of the properties of dense neutron stars (NSs). Also imagine discovering new and exotic states of matter, and new laws of nature, by being able to collect more experimental data than we dream possible today, analyzing it in real time to feed back into an experiment, and curating the data with full tracking capabilities and with fully distributed data mining capabilities. Making this vision a reality would improve basic scientific understanding, enabling us to precisely calculate, for example, the spectrum of gravity waves emitted during NS coalescence, and would have important societal applications in nuclear energy research, stockpile stewardship, and other areas. This review presents the components and characteristics of the exascale computing ecosystems necessary to realize this vision.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2022

Lattice QCD and the Computational Frontier

The search for new physics requires a joint experimental and theoretical effort. Lattice QCD is already an essential tool for obtaining precise model-free theoretical predictions of the hadronic processes underlying many key experimental searches, such as those involving heavy flavor physics, the anomalous magnetic moment of the muon, nucleon-neutrino scattering, and rare, second-order electroweak processes. As experimental measurements become more precise over the next decade, lattice QCD will play an increasing role in providing the needed matching theoretical precision. Achieving the needed precision requires simulations with lattices with substantially increased resolution. As we push to finer lattice spacing we encounter an array of new challenges. They include algorithmic and software-engineering challenges, challenges in computer technology and design, and challenges in maintaining the necessary human resources. In this white paper we describe those challenges and discuss ways they are being dealt with. Overcoming them is key to supporting the community effort required to deliver the needed theoretical support for experiments in the coming decade.

Boyle, Peter↗

DOE OSTI2021

Nucleon valence quark distribution functions from Lattice QCD

We present results on the nucleon valence quark distribution extracted from Lattice QCD simulations, using a gauge ensemble of Nf=2+1 Wilson-Clover fermions with a pion mass of m?=350 MeV and lattice spacing of a=0.091 fm. We obtain reduced Ioffe Time Distributions (rITDs) by computing appropriate matrix elements on the lattice, and elaborate on the extraction of the desired quark distributions from the rITDs following the pseudo-PDF approach. A set of techniques are considered in order to ensure ground state dominance. Theoretical and experimental implications of our calculation are discussed.

Kallidonis, Christos↗

DOE OSTI2021

MultiPhATE2: code for functional annotation and comparison of phage genomes

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Nuclear Physics Network Requirements Review: One-Year Update

A Nuclear Physics Network Requirements Review, conducted by ESnet in collaboration with the DOE SC, was held on May 8 and 9, 2019. A continuation of this process involves “checkup” procedures to be conducted after one and two years have passed. ESnet and the DOE SC, in collaboration with the previous participants, held a virtual meeting on September 2, 2020, to continue the review process. Topics of discussion included the following: Programmatic updates from the DOE SC ASCR. Programmatic updates from the DOE SC NP. Programmatic updates from ESnet. Brief updates from case study authors. A general discussion and Q&A on findings and actions from the review. This report outlines the areas of discussion, new findings and actions, and updates to the overall process of science for several key NP initiatives since 2019 and looking into 2021.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Reaching High Momenta using Distillation

We present a study of the use of a momentum-smeared variant of distillation for studying the structure of baryons at high momentum from lattice QCD. In particular, we focus on the dispersion relation and the nucleon currents and compare with results for the nucleon at rest.

Richards, David↗

DOE OSTI2020

Session 077 - Panel: Wednesday US DOE Featured Site: Lexington, KY Office (Portsmouth and Paducah Sites) (R1.14)

This panel featured the DoE's Portsmouth Paducah Project Office (PPPO), which is responsible for the management and cleanup of at the Portsmouth, Ohio and Paducah, Kentucky former Gaseous Diffusion Plant sites. Portsmouth is primed for the first major skyline change at the site the upcoming demolition of the X-326 process building and initial operations of the Onsite Waste Disposal Facility. The Paducah site is working on the C-400 city block initiative allowing DOE to tackle the main source of groundwater contamination at the site, in conjunction with deactivation and demolition of the C-400 Cleaning Building. PPPO's DUF6 conversion plants have 7 lines in continuous operation at both sites providing the opportunity to ramp up cylinder processing. Panelists with presentations: DOE PPO Update (Robert Edwards, Joel Bradburne); Portsmouth/Paducah Project Office (PPPO) (Joel Bradburne, Robert Edwards); PADUCAH (Jennifer Woodard, Myrna Espinosa Redfield); Depleted Uranium Hexafluoride Conversion Project (Reinhard Knerr, Zack Smith); Paducah Deactivation and Remediation Project (Myrna Espinosa Redfield); Mid-America Conversion Services - Seven Lines One Project (Zack Smith)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2019

Panel Session 120B: DOE Portsmouth Paducah Project Office (PPPO) Update

This panel focused on the Portsmouth/Paducah Project Office (PPPO) of the US DOE Office of Environmental Management, Lexington, Kentucky, the US DOE Featured Site for Thursday. It showcased recent progress, challenges and planned efforts in radioactive waste management, waste disposition, environmental remediation and D and D at the Portsmouth (Ohio) and Paducah (KY) Gaseous Diffusion Plant Sites, as well as the Depleted Uranium Hexafluoride (DUF6) Conversion Project with facilities at both sites Presentations proposed include: 1 - Portsmouth/Paducah Project Office (PPPO) (Joel Bradburne, US DOE Portsmouth/Paducah Project Office (USA)); 2 - Portsmouth (Jeff Bettinger, US DOE Portsmouth/Paducah Project Office (USA)); 3 - Paducah (Jennifer Woodard, US DOE Portsmouth/Paducah Project Office (USA)); 4 - Depleted Uranium Hexafluoride Conversion Project (Reinhard Knerr, US DOE Portsmouth/Paducah Project Office (USA)); 5 - Portsmouth Deactivation and Demolition Project (Bob Smith, Fluor-BWXT Portsmouth (USA)); 6 - Paducah Deactivation and Remediation Project (Jeff Bradford, Four Rivers Nuclear Partnership - FRNP (USA)); 7 - Seven Lines-One Project (Zack Smith, SNC Lavalin (USA))

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DOE OSTI2019

Hadron Spectroscopy

There has been substantial progress in determining the excited state spectrum of hadrons. Recent activity has focused on extracting the resonance behavior of states, revealing how the spectrum is manifested from the theory Quantum Chromodynamics. Some of this progress is reviewed, and future opportunities are discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2019

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates

To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE’s modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Energy Sciences Network (ESnet): Nuclear Physics Network Requirements Review Report

In May 2019, ESnet and the Office of Nuclear Physics (NP) of the DOE Office of Science organized an ESnet requirements review of NP-supported activities. Preparation for this event included identification of key stakeholders to the process: program and facility management, research groups, technology providers, and a number of external observers. These individuals were asked to prepare formal case study documents about their relationship to the NP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward. A series of pre-planning meetings better prepared case study authors for this task and facilitated a smooth transition to the in-person review.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2018

Panel reports session

This section brings together the reports of the 31 panel sessions listed below: - Avoiding the Human Capital Cliff in the DOE (PS22); - Implementing Technically-Based Cleanup; US DOE Balancing Regulatory and Fiscal Complexity (PS24); - United Kingdom - Remediation of Sellafield Legacy Ponds and Silos (PS25); - Aligning Decision-Making to Deliver Timely Results in Large Clean-up Programs (PS38); - Transition to Government Owned-Contractor Operated Site at Canadian Nuclear Laboratories (PS39); - Emerging Middle East Nuclear States' Status and Plans (PS40); - NPP Panel on Waste Management (PS41); - Robotics - International Innovations in Robotic Decommissioning Technology (PS43); - Fukushima Panel (1/2): Japan Fukushima Daiichi Decommissioning Update (PS54); - Fukushima Panel (2/2): Update on the Revitalization of Fukushima and the Surrounding Area (PS55); - US DOE LLW On-Site Disposal: LLW Disposal Facility Federal Review Group Review Process (PS56); - Challenges in DOE HLW Tank Management: Facility Start-up and Waste Disposition (PS57); - Waste Management Planning for Utility Small Modular Reactors (PS58); - US Nuclear Power Plant Waste Management - LLW Disposal Issues (PS59); - DOE-EM Robotics and Emerging Technologies Road-map (4/8) (PS60); - Graduating Students and New Scientists and Engineers - Wants and Needs - Are Companies Even Listening? (PS63); - U.S. Nuclear Robotics: Yesterday, Today, Tomorrow (5/8) (PS74); - US DOE Mixed Waste: Proposals for Dealing with Problematic Waste Streams and Policy Changes (PS76); - Current and Emerging US NRC LLW Regulatory Topics (PS77); - Agency Perspectives (US and International) on the Use of Risk and Dose Assessment Tools (PS80); - Progress on Deep Repository Programs Around the World (PS81); - US DOE Procurement and Contracting Opportunities (PS82); - Collaboration across Borders to Deliver Cleanup and Decommissioning Challenges (PS93a); - DOE Mission Success through Application of Practices and Solutions (PS94); - Challenges in Cask Certification - International Perspectives (PS96); - Robotics: Leveraging Innovations in Science and Technology to Benefit Safety Performance (PS98); - DOE Panel: DOE EM Featured Office - Portsmouth/Paducah Project Office (PS109); - Robotics: Lessons Learned from Industrial Robotics Deployment that can be Applied to the Nuclear Field (PS110a); - Roundtable: DOE Radioactive Management - Energy Facility Contractors Group - Waste Management Working Group (EFCOG WMWG) (PS118); - Thursday Topical Session 'Management of Used Nuclear Fuel: Will the United States Reengage and Align with International Efforts' (PS124); - Remotely Operated Vehicles for Emergency, Disaster, and Operational Upset Response (PS125)

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