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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Genomes to Structure and Function Workshop Report 2022

The goal of the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Program is to achieve a predictive understanding of complex biological, earth, and environmental systems with the aim of advancing the nation’s energy and infrastructure security. (https://www.energy.gov/science/ ber/biological-and-environmental-research). To pursue this goal, collaborations among experts in diverse research areas that lead to multidisciplinary projects are indispensable. The roles of DOE’s User Facilities, which offer unique and powerful resources for such research projects, are evolving, and expectations for the facilities are increasing. To respond to Users’ needs, the Joint Genome Institute (JGI) and Environmental Molecular Sciences Laboratory (EMSL) initiated the Facilities Integrating Collaborations for User Science (FICUS) program in 2014. This collaboration has grown into a popular and successful program, advancing more than 100 multidisciplinary projects to date. Similarly, the new interFacility collaborations among the JGI, EMSL, and User resources for BER structural biology and imaging at the Basic Energy Science (BES) Program’s synchrotron and neutron facilities are becoming essential for cutting-edge transdisciplinary science. To further explore the need for the BER research community to combine genomic, functional, and structural approaches to advance their research, an organizing committee was formed to develop and jointly host a 3-part workshop. The committee’s members represented seven DOE National Laboratory User Facilities (Appendix 1 lists the members). The “Genomes to Structure and Function” virtual workshop (see Appendices 2–5) was composed of three sessions. The first session, titled “Molecular Structures” (October 27– 28, 2021), highlighted diverse integrative experimental and computational approaches correlating structural data with sequencing and functional information, as well as predicting protein structures to model complex biological systems. The second session, “Intracellular Organization, and Material Synthesis and Decomposition” (December 15–16, 2021), covered imaging methods for observing, quantifying, and manipulating biosystems. The third session, “Imaging the Rhizosphere and Cellular Organization” (January 26–27, 2022) emphasized advanced and non-invasive imaging techniques applied to plant root-microbe-soil interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1984

RAMIS DBMS Update

Highlights of a round table discussion of end-user computing, IBM strategies, fourth generation languages, and directions for software innovation are presented as well as observations from an in-depth study of 271 organizations. The RAMIS data base management system is evaluated according to 10 defining criteria for a fourth-generation language: result-oriented programming; common language/demand level adaptability; application extension; user/machine insulation; work station environment; comprehensive software toolkit; integrating perspective on computing and data resources; end user data base capability; accessible dictionaries; and user assistance/facility coordination.

Head, J.↗
DOE OSTI2021

A review of machine learning in building load prediction

The surge of machine learning in recent years has been empowering engineer modeling in various fields. The decreasing hardware cost, increasing data accessibility, and advances of building automation system (BAS) allow the collection and storage of a significant amount of building operation data. The two facts provide great opportunities of applying machine learning to building energy systems modeling and analysis. There are a great number of research papers on this topic but there lacks a comprehensive and general review to summarize the current development, limitations, gaps and future trend. In this review paper series, machine learning techniques in building energy system modeling and analysis are reviewed under the organization and logic of the machine learning definition by Tom M. Mitchell: a computer program is said to learn from experience E with respect to some class of tasks T and performance measure P if its performance at tasks in T, as measured by P, improves with experience E. This paper is the first part of the review paper series, which focuses on building load prediction. First, the applications of building load prediction model (task T) are reviewed. Then, the modeling algorithms improving machine learning performance and accuracy (performance P) are reviewed. At the same time, the literature on the data perspective for modeling (experience E), including data engineering from sensors level to data level, pre-processing, feature extraction and selection, is reviewed. Finally, what is well-studied and what is lacking but with great potential are concluded; the gaps between present and future utilization of machine learning techniques are identified; the future trend and development are also predicted. The target readers of this paper are not only researchers from the building side who can get exposed to cutting edge machine learning tools, but also those from machine learning side who can understand the potential and challenge to apply machine learning in buildings.

Liang, Zhang↗
DOE OSTI2020

Robust, Accurate, and Efficient: Quantum Embedding Using the Huzinaga Level-Shift Projection Operator for Complex Systems

Using wave function (WF) in density functional theory (DFT) embedding methods provides a framework for performing localized, high-accuracy WF calculations on a system, while not incurring the full computational cost of the WF calculation on the full system. To effectively partition a system into localized WF and DFT subsystems, we utilize the Huzinaga level-shift projection operator within an absolutely localized basis. In this work, we study the ability of the absolutely localized Huzinaga level-shift projection operator method to study complex WF and DFT partitions, including partitions between multiple covalent bonds, a double bond, and transition-metal–ligand bonds. We find that our methodology can accurately describe all of these complex partitions. Additionally, we study the robustness of this method with respect to the WF method, specifically where the embedded systems were described using a multiconfigurational WF method. We found that the method is systematically improvable with respect to both the number of atoms in the WF region and the size of the basis set used, with energy errors less than 1 kcal/mol. Additionally, we calculated the adsorption energy of H2 to a model of an iron metal–organic framework (Fe-MOF-74) to within 1 kcal/mol compared to CASPT2 calculations performed on the full model while incurring only a small fraction of the full computational cost. In conclusion, this work demonstrates that the absolutely localized Huzinaga level-shift projection operator method is applicable to very complex systems with difficult electronic structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1973

Feasibility study of an Integrated Program for Aerospace-vehicle Design (IPAD) system. Volume 6: Implementation schedule, development costs, operational costs, benefit assessment, impact on company organization, spin-off assessment, phase 1, tasks 3 to 8

A baseline implementation plan, including alternative implementation approaches for critical software elements and variants to the plan, was developed. The basic philosophy was aimed at: (1) a progressive release of capability for three major computing systems, (2) an end product that was a working tool, (3) giving participation to industry, government agencies, and universities, and (4) emphasizing the development of critical elements of the IPAD framework software. The results of these tasks indicate an IPAD first release capability 45 months after go-ahead, a five year total implementation schedule, and a total developmental cost of 2027 man-months and 1074 computer hours. Several areas of operational cost increases were identified mainly due to the impact of additional equipment needed and additional computer overhead. The benefits of an IPAD system were related mainly to potential savings in engineering man-hours, reduction of design-cycle calendar time, and indirect upgrading of product quality and performance.

Garrocq, C. A.↗
DOE OSTI2022

Activated relaxation in supercooled monodisperse atomic and polymeric WCA fluids: Simulation and ECNLE theory

Here, we combine simulation and Elastically Collective Nonlinear Langevin Equation (ECNLE) theory to study the activated relaxation in monodisperse atomic and polymeric Weeks–Chandler–Andersen (WCA) liquids over a wide range of temperatures and densities in the supercooled regime under isochoric conditions. By employing novel crystal-avoiding simulations, metastable equilibrium dynamics is probed in the absence of complications associated with size polydispersity. Based on a highly accurate structural input from integral equation theory, ECNLE theory is found to describe well the simulated density and temperature dependences of the alpha relaxation time of atomic fluids using a single system-specific parameter, a c , that reflects the nonuniversal relative importance of local cage and collective elastic barriers. For polymer fluids, the explicit dynamical effect of local chain connectivity is modeled at the fundamental dynamic free energy trajectory level based on a different parameter, N c , that quantifies the degree of intramolecular correlation of bonded segment activated barrier hopping. For the flexible chain model studied, a physically intuitive value of N c ≈ 2 results in good agreement between simulation and theory. A direct comparison between atomic and polymeric systems reveals that chain connectivity can speed up activated segmental relaxation due to weakening of equilibrium packing correlations but can slow down relaxation due to local bonding constraints. The empirical thermodynamic scaling idea for the alpha time is found to work well at high densities or temperatures but fails when both density and temperature are low. The rich and subtle behaviors revealed from simulation for atomic and polymeric WCA fluids are all well captured by ECNLE theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Science-Driven Data Management for Multi-Tiered Storage (Final Report)

Scientific discovery at the exascale will not be possible without significant new research in the management, storage and retrieval over the long lifespan of the extreme amounts of data that will be produced. Our thesis is that adding application level knowledge about data to guide the actions of the storage system provides substantial benefits to the organization, storage, and access to extreme scale data, resulting in improved productivity for computational science. In this project we will demonstrate novel techniques to facilitate efficient mapping of data objects, even partitioning individual variables, from the user space onto multiple storage tiers, and enable application-guided data reductions and transformations to address capacity and bandwidth bottlenecks. Our goal is to address the associated Input/ Output (I/O) and storage challenges in the context of current and emerging storage landscapes, and expedite insights into mission critical scientific processes.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Position Papers for the ASCR Workshop on Reimagining Codesign

On behalf of the Advanced Scientific Computing Research (ASCR) program in the US Department of Energy (DOE) Office of Science, we are organizing a Workshop on Reimagining Codesign (ReCoDe). Codesign is the process of jointly designing interoperating components of a computing system—in particular: applications, algorithms, system software, programming models, and the hardware on which they run. The goal is to maximize the overall performance, efficiency, and other desirable qualities of the system as a whole. Codesign is a standard methodology in the embedded-systems community, where space, power, and cost constraints are commonly pitted against execution speed for a tightly constrained feature set. Over the last decade, the DOE has invested in codesign efforts to foster the development of exascale computing systems for broad classes of scientific and engineering applications. The ReCoDe workshop hopes to explore how scientific applications of interest to the DOE can be accelerated through close interactions with hardware designers and software-stack developers, in which all components adapt to each other’s requirements and constraints. We want to answer the question of what are the key tools and methodologies for accomplishing codesign in today’s computing landscape, and what will be the highest impact targets for meeting DOE’s emerging mission requirements. This workshop aims to bring together DOE, industry, and academia to identify opportunities to build on past codesign successes and identify new areas that are either emerging or that may need reimagining for the future. We want to continue to find opportunities that can be pursued as a joint effort and continue to break down the traditional customer/vendor dichotomy with true partnerships. From this work, DOE will benefit from increased application performance relative to what stock hardware or existing general-purpose roadmaps can provide, and vendors will benefit from expanding their hardware’s capabilities to address needs they might have not otherwise anticipated and thereby create more widespread interest in their products. The workshop will be structured around a set of breakout sessions, with every attendee expected to participate actively in the discussions. Afterward, workshop attendees—from DOE, industry, and academia—will produce a report for ASCR that summarizes the findings made during the workshop.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1983

General approaches for achieving high speed computations

The basic organizational approach to achieve high speed computations has been to execute several instructions concurrently. Various algorithmic structures and related computer organizations have been identified and used for this purpose. Each of them is better suited for some classes of applications, provides a potential speed-up with respect to the sequential computer, and suffers from degradation factors that reduce the effective speed-up obtained. The basic algorithmic structures are presented, the corresponding computer organizations described and the potential degradation factors identified. Also included are considerations related to the cost of the system and to the corresponding programming methodology.

Lang, T.↗
NASA NTRS1989

Intelligent Network Management and Functional Cerebellum Synthesis

Transdisciplinary modeling of the cerebellum across histology, physiology, and network engineering provides preliminary results at three organization levels: input/output links to central nervous system networks; links between the six neuron populations in the cerebellum; and computation among the neurons of the populations. Older models probably underestimated the importance and role of climbing fiber input which seems to supply write as well as read signals, not just to Purkinje but also to basket and stellate neurons. The well-known mossy fiber-granule cell-Golgi cell system should also respond to inputs originating from climbing fibers. Corticonuclear microcomplexing might be aided by stellate and basket computation and associate processing. Technological and scientific implications of the proposed cerebellum model are discussed.

Loebner, Egon E.↗
DOE OSTI2021

High Throughput Mapping of Single Molecules’ Redox Potentials on Electrode

By synchronizing electrochemical potential scanning with a single-molecule localization super-resolution fluorescence microscope, kinetic fluorescence changes of hundreds of single molecular redox events were tracked simultaneously with high throughput, and subsequent cross-correlation function analysis mapped single molecules’ redox potentials (times) out on the imaging area from site to site in unprecedented detail by extracting electrochemically induced fluorescence change from apparently random fluorescence on/off blinking. This work paves the way toward mapping redox states at single-molecule levels in high throughput in chemical and biological systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Density Functional Tight-Binding Models for Band Structures of Transition-Metal Alloys and Surfaces across the d -Block

First-principles electronic structure simulations are an invaluable tool for understanding chemical bonding and reactions. While machine-learning models such as interatomic potentials significantly accelerate the exploration of potential energy surfaces, electronic structure information is generally lost. Particularly in the field of heterogeneous catalysis, simulated electron band structures provide fundamental insights into catalytic reactivity. This ab initio knowledge is preserved in semiempirical methods such as density functional tight binding (DFTB), which extend the accessible computational length and time scales beyond first-principles approaches. In this paper here we present Shell-Optimized Atomic Confinement (SOAC) DFTB electronic-part-only parametrizations for bulk and surface band structures of all d-block transition metals that enable efficient predictions of electronic descriptors for large structures or high-throughput studies on complex systems outside the computational reach of density functional theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1986

The force on the flex: Global parallelism and portability

A parallel programming methodology, called the force, supports the construction of programs to be executed in parallel by an unspecified, but potentially large, number of processes. The methodology was originally developed on a pipelined, shared memory multiprocessor, the Denelcor HEP, and embodies the primitive operations of the force in a set of macros which expand into multiprocessor Fortran code. A small set of primitives is sufficient to write large parallel programs, and the system has been used to produce 10,000 line programs in computational fluid dynamics. The level of complexity of the force primitives is intermediate. It is high enough to mask detailed architectural differences between multiprocessors but low enough to give the user control over performance. The system is being ported to a medium scale multiprocessor, the Flex/32, which is a 20 processor system with a mixture of shared and local memory. Memory organization and the type of processor synchronization supported by the hardware on the two machines lead to some differences in efficient implementations of the force primitives, but the user interface remains the same. An initial implementation was done by retargeting the macros to Flexible Computer Corporation's ConCurrent C language. Subsequently, the macros were caused to directly produce the system calls which form the basis for ConCurrent C. The implementation of the Fortran based system is in step with Flexible Computer Corporations's implementation of a Fortran system in the parallel environment.

Jordan, H. F.↗
DOE OSTI2021

Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks

Machine learning has emerged as a powerful approach in materials discovery. Its major challenge is selecting features that create interpretable representations of materials, useful across multiple prediction tasks. We introduce an end-to-end machine learning model that automatically generates descriptors that capture a complex representation of a material’s structure and chemistry. This approach builds on computational topology techniques (namely, persistent homology) and word embeddings from natural language processing. It automatically encapsulates geometric and chemical information directly from the material system. We demonstrate our approach on multiple nanoporous metal–organic framework datasets by predicting methane and carbon dioxide adsorption across different conditions. Our results show considerable improvement in both accuracy and transferability across targets compared to models constructed from the commonly-used, manually-curated features, consistently achieving an average 25–30% decrease in root-mean-squared-deviation and an average increase of 40–50% in R 2 scores. A key advantage of our approach is interpretability: Our model identifies the pores that correlate best to adsorption at different pressures, which contributes to understanding atomic-level structure–property relationships for materials design.

97 MATHEMATICS AND COMPUTING↗
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↗
NASA NTRS1974

Investigations in space-related molecular biology

Improved instrumentation and preparation techniques for high resolution, high voltage cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens are reported. Computer correlated ultrastructural and biochemical work on hydrated and dried cell membranes and related biological systems provided information on membrane organization, ice crystal formation and ordered water, RNA virus linked to cancer, lunar rock samples, and organometallic superconducting compounds. Apollo 11, 12, 14, and 15 specimens were analyzed

Fernandez-Moran, H.↗
NASA NTRS1986

Design component method for sensitivity analysis of built-up structures

A 'design component method' that provides a unified and systematic organization of design sensitivity analysis for built-up structures is developed and implemented. Both conventional design variables, such as thickness and cross-sectional area, and shape design variables of components of built-up structures are considered. It is shown that design of components of built-up structures can be characterized and system design sensitivity expressions obtained by simply adding contributions from each component. The method leads to a systematic organization of computations for design sensitivity analysis that is similar to the way in which computations are organized within a finite element code.

Choi, Kyung K.↗