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At least 595 records · Page 33

Opportunities for enhancing MLCommons efforts while leveraging insights from educational MLCommons earthquake benchmarks efforts

MLCommons is an effort to develop and improve the artificial intelligence (AI) ecosystem through benchmarks, public data sets, and research. It consists of members from start-ups, leading companies, academics, and non-profits from around the world. The goal is to make machine learning better for everyone. In order to increase participation by others, educational institutions provide valuable opportunities for engagement. In this article, we identify numerous insights obtained from different viewpoints as part of efforts to utilize high-performance computing (HPC) big data systems in existing education while developing and conducting science benchmarks for earthquake prediction. As this activity was conducted across multiple educational efforts, we project if and how it is possible to make such efforts available on a wider scale. This includes the integration of sophisticated benchmarks into courses and research activities at universities, exposing the students and researchers to topics that are otherwise typically not sufficiently covered in current course curricula as we witnessed from our practical experience across multiple organizations. As such, we have outlined the many lessons we learned throughout these efforts, culminating in the need for benchmark carpentry for scientists using advanced computational resources. The article also presents the analysis of an earthquake prediction code benchmark while focusing on the accuracy of the results and not only on the runtime; notedly, this benchmark was created as a result of our lessons learned. Energy traces were produced throughout these benchmarks, which are vital to analyzing the power expenditure within HPC environments. Additionally, one of the insights is that in the short time of the project with limited student availability, the activity was only possible by utilizing a benchmark runtime pipeline while developing and using software to generate jobs from the permutation of hyperparameters automatically. It integrates a templated job management framework for executing tasks and experiments based on hyperparameters while leveraging hybrid compute resources available at different institutions. The software is part of a collection called cloudmesh with its newly developed components, cloudmesh-ee (experiment executor) and cloudmesh-cc (compute coordinator).

58 GEOSCIENCES↗

Static Subspace Approximation for Random Phase Approximation Correlation Energies: Implementation and Performance

Developing theoretical understanding of complex reactions and processes at interfaces requires using methods that go beyond semilocal density functional theory to accurately describe the interactions between solvent, reactants and substrates. Methods based on many-body perturbation theory, such as the random phase approximation (RPA), have previously been limited due to their computational complexity. However, this is now a surmountable barrier due to the advances in computational power available, in particular through modern GPU-based supercomputers. In this work, we describe the implementation of RPA calculations within BerkeleyGW and show its favorable computational performance on large complex systems relevant for catalysis and electrochemistry applications. Our implementation builds off of the static subspace approximation which, by employing a compressed representation of the frequency dependent polarizability, enables the evaluation of the RPA correlation energy with significant acceleration and systematically controllable accuracy. We find that the computational cost of calculating the RPA correlation energy scales only linearly with system size for systems containing up to 50 thousand bands, and is expected to scale quadratically thereafter. We also show excellent strong scaling results across several supercomputers, demonstrating the performance and portability of this implementation.

algorithmic development↗

Computation-guided optimization of split protein systems

Splitting bioactive proteins into conditionally reconstituting fragments is a powerful strategy for building tools to study and control biological systems. However, split proteins often exhibit a high propensity to reconstitute, even without the conditional trigger, limiting their utility. Current approaches for tuning reconstitution propensity are laborious, context-specific or often ineffective. Here, we report a computational design strategy grounded in fundamental protein biophysics to guide experimental evaluation of a sparse set of mutants to identify an optimal functional window. We hypothesized that testing a limited set of mutants would direct subsequent mutagenesis efforts by predicting desirable mutant combinations from a vast mutational landscape. This strategy varies the degree of interfacial destabilization while preserving stability and catalytic activity. We validate our method by solving two distinct split protein design challenges, generating both design and mechanistic insights. Furthermore, this new technology will streamline the generation and use of split protein systems for diverse applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Center Master Plan For NASA Glenn Research Center

The Center Master Plan for NASA Glenn Research Center is a comprehensive survey of NASA Glenn's current facility assets and a vision of how we see the facilities will change over the next 20 years in order to support the changing NASA Mission. This Center Master Plan is a vital management tool used by all organizations for making near term decisions and in future planning. During the summer of 2004, I worked with Joseph Morris, the Chief Architect in the Facilities Division, on beginning this Center Master Planning Process. The previous Master Plan was completed by the Center in 1985 and contained general information on the background of the facility as well as maps detailing environmental and historic records, land use, utilities, etc. The new Master Plan is required for the Center by NASA headquarters and will include similar types of information as used in the past. The new study will provide additional features including showing how individual buildings are linked to the programs and missions that they serve. The Master Plan will show practical future options for the facility s assets with a twenty year look ahead. The Plan will be electronically retrievable so that it becomes a communications tool for Center personnel. A Center Master Plan, although required, is very beneficial to NASA Glenn Research Center in aiding management with the future direction of the campus. Keeping up-to-date information and future plans readily available to all of NASA Glenn will insure that future real property development efficiently and effectively supports the missions camed out and supported by the Center. A Center Master Plan will also facilitate coordination with Center supported programs, stakeholders, and customers. In addition, it will provide a basis for cooperative planning with local and other governmental organizations and ultimately ensure that future budgets include the Center program needs described in the plan. This will ensure that development plans are safe, practical, and cost effective. To properly formulate any future plans, background information and research are required. Before bringing in a consultant to tackle the three year process anticipated to prepare a Center Master Plan, my job was to gather information on different organizations contributions to the NASA mission, their facility needs, consistent trends they observe, etc. I conducted numerous interviews with personnel such as Directorate Representatives, Division Chiefs, Branch Chiefs, System Managers and Building Managers. I documented the information I received from them for future use. I used the information to create various color-coded maps layering the different data. This was done with the ending objective being to collect the information and place it in a database that will be linked with Aperture (a computer program that generates color-coded map layers from database information) and made electronically retrievable to the Planning Consultant, NASA personnel, program stakeholders, and other governmental agencies. My goal this summer was to gather information and ideas appropriate for use in NASA Glenn Research Center s Master Plan and organize them for future application by the Planning Consultant. By the end of the summer, after completion of my goal, I will utilize my knowledge and create an array of preliminary future plans for the facility that can be passed along as a guidance tool.

Bigach, Kristin M.↗

Institute for Catalysis in Energy Processes (ICEP) (Final Report)

The Institute for Catalysis in Energy Processes (ICEP) was a multi-PI program located at the Northwestern University Center for Catalysis and Surface Science from 2006-2024. Over several renewal cycles and several organizing themes, ICEP addressed fundamental questions in catalysis science. In turn, the scientific questions addressed were directly relevant to the efficient use of the nation’s resources to produce fuels and commodity chemicals, harness alternate energy sources for chemical reactions such as light or electricity, reduce emissions and waste, and minimize the impact of our use of plastics. Selective oxidation, (oxidative) dehydrogenation, deNOx, CO 2 reduction, hydrogen release, polymer decomposition / depolymerization, and many other reactions of intense interest to the US Department of Energy were studied in the center. Major ICEP strengths were in catalyst synthesis, in measurements that elucidated catalyst properties, in reaction mechanisms and kinetics, and in predictive theory and modeling. ICEP researchers were often the inventors or developers of materials and methods that were brought to bear on the Institute’s catalytic systems. Key characterization tools advanced through this project included resonance Raman and related techniques, sum frequency generation, and X-ray standing wave spectroscopy. Center members relied extensively on computational tools such as density functional theory and microkinetic modeling to fully investigate catalyst structures and catalytic mechanisms. ICEP researchers were early developers of atomic layer deposition (ALD) for catalyst synthesis and were early pioneers of metal organic frameworks for catalysis. ICEP innovations are found in areas of intense research such as single-atom catalysts, catalytic deconstruction of plastics, and catalytic MOFs, to name a few. Research areas initiated by ICEP indirectly led to DOE EFRCs, startup companies, and other achievements. Over its 18 years of existence, ICEP involved two different PIs (Stair and Notestein) and 24 senior investigators across several academic disciplines at Northwestern University. There were tight collaborations with Argonne National Laboratory, including specialized equipment and experiments permanently located there. The center supported ~400 person-years of effort by graduate students and postdocs, either directly through DOE support or indirectly by leveraging independent support provided to the trainees, e.g. through the NSF GRFP or internal fellowships. The project resulted in 328 manuscripts and numerous conference presentations.

36 MATERIALS SCIENCE↗

Reaction Mechanism Generator v3.0: Advances in Automatic Mechanism Generation

In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters. Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. Most notably, RMG can now generate heterogeneous catalysis models in addition to the previously available gas- and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release includes parallelization for faster model generation and a new molecule isomorphism approach to improve computational performance. RMG has also been updated to use Python 3, ensuring compatibility with the latest cheminformatics and machine learning packages. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System

Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. Here this study describes a quantum simulation method that explores the influence of light polarization on electron transfer between two molecules. By implementing precise and coherent control among the quantum states of trapped atomic ions, we can induce quantum dynamics that mimic the electron-transfer dynamics in molecules. We use three-level systems (qutrits), rather than traditional two-level systems (qubits), to enhance the simulation efficiency and realize high-fidelity simulations of electron-transfer dynamics. We treat the quantum interference between the electron coupling pathways from a donor with two degenerate excited states to an acceptor and analyze the transfer efficiency. We also examine the potential error sources that enter the quantum simulations. The trapped-ion systems have favorable scalings with system size compared to those of classical computers, promising access to richer electron-transfer simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Dynamics of photosynthetic light harvesting systems interacting with N-photon Fock states

Here, we develop a method to simulate the excitonic dynamics of realistic photosynthetic light harvesting systems, including non-Markovian coupling to phonon degrees of freedom, under excitation by N-photon Fock state pulses. This method combines the input–output and the hierarchical equations of motion formalisms into a double hierarchy of density matrix equations. We show analytically that under weak field excitation relevant to natural photosynthesis conditions, an N-photon Fock state input and a corresponding coherent state input give rise to equal density matrices in the excited manifold. However, an N-photon Fock state input induces no off-diagonal coherence between the ground and excited subspaces, in contrast with the coherences created by a coherent state input. We derive expressions for the probability to absorb a single Fock state photon with or without the influence of phonons. For short pulses (or, equivalently, wide bandwidth pulses), we show that the absorption probability has a universal behavior that depends only upon a system-dependent effective energy spread parameter Δ and an exciton–light coupling constant Γ. This holds for a broad range of chromophore systems and for a variety of pulse shapes. We also analyze the absorption probability in the opposite long pulse (narrow bandwidth) regime. We then derive an expression for the long time emission rate in the presence of phonons and use it to study the difference between collective vs independent emission. Finally, we present a numerical simulation for the LHCII monomer (14-mer) system under single photon excitation that illustrates the use of the double hierarchy equations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing the Potential Energy Profile of the I + (H 2 O) 3 → HI + (H 2 O) 2 OH Forward and Reverse Reactions: High Level CCSD(T) Studies with Spin-Orbit Coupling Included

Three different pathways for the atomic iodine plus water trimer reaction I + (H 2 O) 3 → HI + (H 2 O) 2 OH were preliminarily examined by the DFT-MPW1K method. Related to previous predictions for the F/Cl/Br + (H 2 O) 3 reactions, three pathways for the I + (H 2 O) 3 reaction are linked in terms of geometry and energetics. To legitimize the results, the “gold standard” CCSD(T) method was employed to investigate the lowest-lying pathway with the correlation-consistent polarized valence basis set up to cc-pVQZ(-PP). According to the CCSD(T)/cc-pVQZ(-PP)//CCSD(T)/cc-pVTZ(-PP) results, the I + (H 2 O) 3 → HI + (H 2 O) 2 OH reaction is predicted to be endothermic by 47.0 kcal mol -1 . The submerged transition state is predicted to lie 43.7 kcal mol -1 above the separated reactants. The I···(H 2 O) 3 entrance complex lies below the separated reactants by 4.1 kcal mol -1 , and spin-orbit coupling has a significant impact on this dissociation energy. The HI···(H 2 O) 2 OH exit complex is bound by 4.3 kcal mol -1 in relation to the separated products. Compared with simpler I + (H 2 O) 2 and I + H 2 O reactions, the I + (H 2 O) 3 reaction is energetically between them in general. It is speculated that the reaction between the iodine atom and the larger water clusters may be energetically analogous to the I + (H 2 O) 3 reaction. The iodine reaction I + (H 2 O) 3 is connected with the analogous valence isoelectronic bromine/chlorine reactions Br/Cl + (H 2 O) 3 but much different from the F + (H 2 O) 3 reaction. Significant difference with other halogen systems, especially for barrier heights, are seen for the iodine systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time propagation of electronic wavefunctions using nonorthogonal determinant expansions

The use of truncated configuration interaction in real-time time-dependent simulations of electron dynamics provides a balance of computational cost and accuracy, while avoiding some of the failures associated with real-time time-dependent density functional theory. However, low-order truncated configuration interaction also has limitations, such as overestimation of polarizability in configuration interaction singles, even when perturbative doubles are included. Increasing the size of the determinant expansion may not be computationally feasible, and so, in this work, we investigate the use of nonorthogonality in the determinant expansion to establish the extent to which higher-order substitutions can be recovered, providing an improved description of electron dynamics. Model systems are investigated to quantify the extent to which different methods accurately reproduce the (hyper)polarizability, including the high-harmonic generation spectrum of H 2 , water, and butadiene.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The organic surface of 5145 Pholus: Constraints set by scattering theory

No known body in the Solar System has a spectrum redder than that of object 5145 Pholus. We use Hapke scattering theory and optical constants measured in this laboratory to examine the ability of mixtures of a number of organic solids and ices to reproduce the observed spectrum and phase variation. The primary materials considered are poly-HCN, kerogen, Murchison organic extract, Titan tholin, ice tholin, and water ice. In a computer grid search of over 10 million models, we find an intraparticle mixture of 15% Titan tholin, 10% poly-HCN, and 75% water ice with 10-micrometers particles to provide an excellent fit. Replacing water ice with ammonia ice improves the fits significantly while using a pure hydrocarbon tholin, Tholin alpha, instead of Titan tholin makes only modest improvements. All acceptable fits require Titan tholin or some comparable material to provide the steep slope in the visible, and poly-HCN or some comparable material to provide strong absorption in the near-infrared. A pure Titan tholin surface with 16-micrometers particles, as well as all acceptable Pholus models, fit the present spectrophotometric data for the transplutonian object 1992 QB(sub 1). The feasibility of gas-phase chemistry to generate material like Titan tholin on such small objects is examined. An irradiated transient atmosphere arising from sublimating ices may generate at most a few centimeters of tholin over the lifetime of the Solar System, but this is insignificant compared to the expected lag deposit of primordial contaminants left behind by the sublimating ice. Irradiation of subsurface N2/CH4 or NH3/CH4 ice by cosmic rays may generate approximately 20 cm of tholin in the upper 10 m of regolith in the same time scale but the identity of this tholin to its gas-phase equivalent has not been demonstrated.

Wilson, Peter D.↗

Biological Electron Transfer and Catalysis EFRC

The focus of the Biological Electron Transfer and Catalysis (BETCy) EFRC research is elucidating mechanisms of conversion of electrochemical potential into chemical bond energy and is organized into two integrated Thrusts: Electron Bifurcation Catalysis and Electron Transfer Kinetics. We are developing a collective knowledge of metalloenzymes as models for redox reactions by applying physical science and computational tools to characterize biochemical reactions catalyzed by multi- subunit enzymes harboring arrays of iron-sulfur clusters and flavin cofactors. Understanding these mechanisms is central to overcoming the thermodynamic barriers that currently limit production of reduced products and fuels. Biological systems have elegant strategies for converting electrochemical potential energy into chemical bond energy (e.g., C-H, H-H, and N-H) stored in reduced compounds that can serve as advanced biofuels. One significant limitation for the production of highly reduced compounds is that their production in natural and industrial processes relies on low oxidation-reduction potential chemicals as feedstocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Co-op at Sandia National Laboratories (July - December 2019, Final Report)

This co-op was performed at Sandia National Laboratories (SNL) within the Weapon Surety Engineering 11 Department (9435), which is a customer-focused organization that provides engineering and system analysis expertise to ensure a safe deterrent throughout the entire weapon lifecycle. Engineers in 9435 develop a deep knowledge in both component and system function to support rigorous evaluation and mitigation of potential failure modes. They operate across multiple engineering disciplines (mechanical, electrical, computer, materials and systems engineering) with opportunities to develop crossdisciplinary capability. The team supports a variety of stockpile systems and is part of the product teams during development, design and production, as well as advanced concept and exploratory efforts. 9435 engineers use their extensive component and system knowledge, as well as experimental data and modeling, to ensure products function as intended with assured safety. Members of the department learn the function of multiple components, how those components integrate within the system and apply surety principles and processes to ensure a safe, secure, reliable, and effective U.S. nuclear deterrent.

42 ENGINEERING↗

CRCNS22 Learning Rules in the Hippocampus and their Mapping to Neuromorphic Systems (Final Technical Report)

Large scale biologically-realistic computational models are key to investigating the interplay between structure and function in nervous systems, thus paving the way to new clinical methods and neuro-inspired computing solutions. This project focuses on the hippocampus, in particular the CA3-CA1 regions, due to their role in associative learning and memory, pattern separation and completion, and spatial navigation. Investigations into the neuronal organization and learning rule(s) of this circuit can shed light into how declarative memories are formed, stored, recalled and forgotten and inform computational, experimental and clinical neuroscience work. Our project aims at developing a novel data-driven methodology supported by a broad heterogeneous base of neuroscience experimental knowledge and inspired from advances in computer science and engineering. Specifically, this work will benchmark existing and new learning rules within a full-scale spiking neural network simulation of the CA3-CA1 region. The model will be based on an open-source repository, called the Hippocampome, which contains neuronal morphologies, firing patterns, synapse probabilities, and most other required parameters for all known neuron types in the rodent hippocampal formation. The model will be first trained in a supervised fashion for associative memory tasks using backpropagation through time traditionally used in computer science, enhanced with a new technique called the surrogate gradient method. This optimization method will be used to obtain a global loss minimization, but it is not biologically inspired as it assumes the use of data not locally available to the synapses. However, we propose its use as a benchmarking tool, to compare the training performance of local biologically plausible and hardware-mappable learning rules at scale. New rules or combinations will be proposed and tested as needed, based on the obtained results. Progress in this area will also drive the development of novel hardware-mappable algorithms for continual lifelong learning and categorization of new events from few presented examples. This project goes beyond the existing state-of-the-art by looking at large scale realistic neuronal circuits as networks trainable via global optimization methods such as surrogate gradient descent. The objective function of the brain that supports learning is largely unknown, but it is likely that it operates through local learning rules. Studying network trajectories around local minima as proposed in this work represents a useful strategy for understanding whether a network is training by using a specific (set of) learning rule(s). Starting from a completely untrained network is a challenging test since it is difficult to determine how the learning rule affects the trajectory of the network. This interdisciplinary project will help understand what rule governs learning in these regions or if multiple learning rules are involved. The work will develop a robust methodology to measure if the network is converging to the target solution, oscillating around it, or diverging away.

59 BASIC BIOLOGICAL SCIENCES↗

Human factors aspects of control room design

A plan for the design and analysis of a multistation control room is reviewed. It is found that acceptance of the computer based information system by the uses in the control room is mandatory for mission and system success. Criteria to improve computer/user interface include: match of system input/output with user; reliability, compatibility and maintainability; easy to learn and little training needed; self descriptive system; system under user control; transparent language, format and organization; corresponds to user expectations; adaptable to user experience level; fault tolerant; dialog capability user communications needs reflected in flexibility, complexity, power and information load; integrated system; and documentation.

Jenkins, J. P.↗

Annual report

The overall goal of the Tuskegee University Center for Food Production, Processing and Waste Management in Controlled Ecological Life Support Systems (CELSS) is to provide tested information and technologies applicable to bioregenerative food production systems for life support on long-term manned space mission. Specifically, the center is developing information, computer simulated models, methodologies and technology for sweetpotato and peanut biomass production and processing, inclusive of waste management and recycling of these crops selected by NASA for CELSS. The Center is organized into interdisciplinary teams of life scientists and engineers that work together on specific objectives and long-term goals. Integral to the goal of the Center is the development of both basic and applied research information and the training of young scientists and engineers, especially underrepresented minorities that will increase the professional pool in these disciplines and contribute to the advancement of space sciences and exploration.

Source record↗

Other Planetary Systems: The View From Our Neighborhood

The structure and contents of the Solar System offer an initial model for other planetary systems in this and other galaxies. Our knowledge of the bodies in the Solar System and their physical conditions has grown enormously in the three decades of planetary exploration. Parallel to the uncovering of new facts has been a great expansion of our understanding of just how these conditions came to be. Telescopic studies and missions to all the planets (except Pluto) have shown spectacular and unexpected diversity among those planets, their satellites, the asteroids, and the comets. Highlights include the organic-rich crust of comets, volcanic activity on planetary satellites, randomly oriented magnetic fields of the major planets, the existence of a huge population of planetesimals just beyond Neptune, dramatic combinations of exogenic and endogenic forces shaping the solid bodies throughout the Solar System, and much more. Simultaneously, computational, laboratory, and conceptual advances have shown that the Solar System is not fully evolved either dynamically or chemically. The discovery of clearly identified interstellar (presolar) material in the meteorites and comets connects us directly with the matter in the molecular cloud from which the Solar System originated. At the same time, an increased understanding of the chemistry of comets and the impact history of the planets has demonstrated the dependence of the origin and evolution of life on Earth on powerful exogenic factors. This presentation summarizes some of the new knowledge of the Solar System and proposes specific character ist ics that may be observed in (or used as criteria for identification of) extrasolar planetary systems.

Cruikshank, Dale P.↗

Effective Team Support: From Task and Cognitive Modeling to Software Agents for Time-Critical Complex Work Environments

The purpose of this research contract was to perform multidisciplinary research between CMU psychologists, computer scientists and NASA researchers to design a next generation collaborative system to support a team of human experts and intelligent agents. To achieve robust performance enhancement of such a system, we had proposed to perform task and cognitive modeling to thoroughly understand the impact technology makes on the organization and on key individual personnel. Guided by cognitively-inspired requirements, we would then develop software agents that support the human team in decision making, information filtering, information distribution and integration to enhance team situational awareness. During the period covered by this final report, we made substantial progress in completing a system for empirical data collection, cognitive modeling, and the building of software agents to support a team's tasks, and in running experiments for the collection of baseline data.

Remington, Roger W.↗