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NASA NTRS1996

Analysis of the access patterns at GSFC distributed active archive center

The Goddard Space Flight Center (GSFC) Distributed Active Archive Center (DAAC) has been operational for more than two years. Its mission is to support existing and pre Earth Observing System (EOS) Earth science datasets, facilitate the scientific research, and test Earth Observing System Data and Information System (EOSDIS) concepts. Over 550,000 files and documents have been archived, and more than six Terabytes have been distributed to the scientific community. Information about user request and file access patterns, and their impact on system loading, is needed to optimize current operations and to plan for future archives. To facilitate the management of daily activities, the GSFC DAAC has developed a data base system to track correspondence, requests, ingestion and distribution. In addition, several log files which record transactions on Unitree are maintained and periodically examined. This study identifies some of the users' requests and file access patterns at the GSFC DAAC during 1995. The analysis is limited to the subset of orders for which the data files are under the control of the Hierarchical Storage Management (HSM) Unitree. The results show that most of the data volume ordered was for two data products. The volume was also mostly made up of level 3 and 4 data and most of the volume was distributed on 8 mm and 4 mm tapes. In addition, most of the volume ordered was for deliveries in North America although there was a significant world-wide use. There was a wide range of request sizes in terms of volume and number of files ordered. On an average 78.6 files were ordered per request. Using the data managed by Unitree, several caching algorithms have been evaluated for both hit rate and the overhead ('cost') associated with the movement of data from near-line devices to disks. The algorithm called LRU/2 bin was found to be the best for this workload, but the STbin algorithm also worked well.

Johnson, Theodore↗

DOE OSTI2020

Structural and functional characterization of the dominant negative P-loop lysine mutation in the dy

Explore the source record for details and available documents.

Tornabene, Bryan A.↗

DOE OSTI2023

Model validation and selection in metabolic flux analysis and flux balance analysis

13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both methods use metabolic reaction network models of metabolism operating at steady state so that reaction rates (fluxes) and the levels of metabolic intermediates are constrained to be invariant. They provide estimated (MFA) or predicted (FBA) values of the fluxes through the network in vivo, which cannot be measured directly. These fluxes can shed light on basic biology and have been successfully used to inform metabolic engineering strategies. Several approaches have been taken to test the reliability of estimates and predictions from constraint-based methods and to compare alternative model architectures. Despite advances in other areas of the statistical evaluation of metabolic models, such as the quantification of flux estimate uncertainty, validation and model selection methods have been underappreciated and underexplored. We review the history and state-of-the-art in constraint-based metabolic model validation and model selection. Applications and limitations of the χ 2 -test of goodness-of-fit, the most widely used quantitative validation and selection approach in 13C-MFA, are discussed, and complementary and alternative forms of validation and selection are proposed. A combined model validation and selection framework for 13C-MFA incorporating metabolite pool size information that leverages new developments in the field is presented and advocated for. Finally, we discuss how adopting robust validation and selection procedures can enhance confidence in constraint-based modeling as a whole and ultimately facilitate more widespread use of FBA in biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Optimal Estimation Retrievals and Their Uncertainties: What Every Atmospheric Scientist Should Know

Remote sensing instruments are heavily used to provide observations for both the operational and research communities. These sensors do not provide direct observations of the desired atmospheric variables, but instead, retrieval algorithms are necessary to convert the indirect observations into the variable of interest. It is critical to be aware of the underlying assumptions made by many retrieval algorithms, including that the retrieval problem is often ill posed and that there are various sources of uncertainty that need to be treated properly. In short, the retrieval challenge is to invert a set of noisy observations to obtain estimates of atmospheric quantities. The problem is often complicated by imperfect forward models, by imperfect prior knowledge, and by the existence of nonunique solutions. Optimal estimation (OE) is a widely used physical retrieval method that combines measurements, prior information, and the corresponding uncertainties based on Bayes’s theorem to find an optimal solution for the atmospheric state. Furthermore, OE also allows the relative contributions of the different sources of error to the uncertainty in the final retrieved atmospheric state to be understood. Here, we provide a novel Python library to illustrate the use of OE for inverse problems in the atmospheric sciences. We introduce two example problems: how to retrieve drop size distribution parameters from radar observations and how to retrieve the temperature profile from ground-based microwave sensors. Using these examples, we discuss common pitfalls, how the various error sources impact the retrieval, and how the quality of the retrieval results can be quantified.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Gasoline Compression Ignition on a Light-Duty Multi-Cylinder Engine Using a Wide Range of Fuel Reactivities and Heavy Fuel Stratification

Many research studies have focused on utilizing gasoline in modern compression ignition engines to reduce emissions and improve efficiency. Collectively, this combustion mode has become kn+own as gasoline compression ignition (GCI). One of the biggest challenges with GCI operation is maintaining control over the combustion process through the fuel injection strategy, such that the engine can be controlled on a cycle-by-cycle basis. Research studies have investigated a wide variety of GCI injection strategies (i.e., fuel stratification levels) to maintain control over the heat release rate while achieving low-temperature combustion (LTC). This work shows that at loads relevant to light-duty engines, partial fuel stratification (PFS) with gasoline provides very little controllability over the timing of combustion. On the contrary, heavy fuel stratification (HFS) provides very linear and pronounced control over the timing of combustion. However, the HFS strategy has challenges achieving LTC operation due to the air handling burdens associated with the high exhaust gas recirculation (EGR) rates that are required to reduce NOx emissions to near zero levels. In this work, a wide variety of gasoline fuel reactivities (octane numbers ranging from <40 to 87) were investigated to understand the engine performance and emissions of HFS-GCI operation on a multi-cylinder light-duty engine. Overall, the results indicate that over an EGR sweep at 4 bar brake mean effective pressure (BMEP), the gasoline fuels can achieve LTC operation with ultra-low NO x and soot emissions, while conventional diesel combustion (CDC) is unable to simultaneously achieve low NO x and soot. At 10 bar BMEP, all the gasoline fuels were compared to diesel, but using mixing controlled combustion and not LTC.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2024

Benchmarking Variables for Checkpointing in HPC Applications

Checkpoint/Restart (C/R) is a widely used fault tolerance mechanism in converged systems of cloud, edge, and HPC. However, users often rely on their experience to determine which variables to checkpoint, as there is currently no benchmark that can provide a reference. This can result in checkpointing redundant or even incorrect variables. To address this issue, we propose a benchmark suite that includes critical variables for checkpointing, which have been manually identified, and a method for identifying those critical variables, with 20 representative HPC applications. Our method involves analyzing data dependency between variables to identify critical variables analytically. We verify the identified variables' correctness with a widely used C/R library FTI by an ablation study. With our benchmark suite and data dependency analysis, HPC practitioners now have a reference for identifying checkpointing variables and better knowledge of what kind of variables to checkpoint.

Fu, Xiang↗

NASA NTRS1993

Establishment of computerized numerical databases on thermophysical and other properties of molten as well as solid materials and data evaluation and validation for generating recommended reliable reference data

The Center for Information and Numerical Data Analysis and Synthesis, (CINDAS), measures and maintains databases on thermophysical, thermoradiative, mechanical, optical, electronic, ablation, and physical properties of materials. Emphasis is on aerospace structural materials especially composites and on infrared detector/sensor materials. Within CINDAS, the Department of Defense sponsors at Purdue several centers: the High Temperature Material Information Analysis Center (HTMIAC), the Ceramics Information Analysis Center (CIAC) and the Metals Information Analysis Center (MIAC). The responsibilities of CINDAS are extremely broad encompassing basic and applied research, measurement of the properties of thin wires and thin foils as well as bulk materials, acquisition and search of world-wide literature, critical evaluation of data, generation of estimated values to fill data voids, investigation of constitutive, structural, processing, environmental, and rapid heating and loading effects, and dissemination of data. Liquids, gases, molten materials and solids are all considered. The responsibility of maintaining widely used databases includes data evaluation, analysis, correlation, and synthesis. Material property data recorded on the literature are often conflicting, diverging, and subject to large uncertainties. It is admittedly difficult to accurately measure materials properties. Systematic and random errors both enter. Some errors result from lack of characterization of the material itself (impurity effects). In some cases assumed boundary conditions corresponding to a theoretical model are not obtained in the experiments. Stray heat flows and losses must be accounted for. Some experimental methods are inappropriate and in other cases appropriate methods are carried out with poor technique. Conflicts in data may be resolved by curve fitting of the data to theoretical or empirical models or correlation in terms of various affecting parameters. Reasons (e.g. phase transitions) must be found for unusual dependence or any anomaly. Such critical evaluation involves knowledge of theory, experience in measurement, familiarity with metallurgy (microstructural behavior) and not inconsiderable judgment. An examination of typical data compiled and analyzed by CINDAS shows that the thermal conductivity of a material reported in the literature may vary by a factor of two of more; the range of reported values increases as temperature increases reflecting the difficulty of high temperature measurements. Often only estimates of melt behavior are available, despite the importance of melt properties in modeling, welding, or other solidification processes. There may be only a few measurements available for properties such as kinematic viscosity, even for widely used materials such as stainless steel. In the face of such a paucity of existing data and in a national environment where too few new data are being generated it is nonetheless the responsibility of CINDAS to select and disseminate recommended values of a wide variety of thermophysical properties.

Ho, C. Y.↗

DOE OSTI2025

Synthesis of nanodiamonds encapsulated by zeolitic imidazole framework-8 for quantum sensing applications

Nitrogen vacancy (NV)-containing nanodiamonds are widely used in quantum sensing applications due to their high sensitivity to magnetic fields, relatively low cost, and ability to be initialized, manipulated, and read out at room temperature. Quantum sensing techniques such as optically detected magnetic resonance (ODMR) and spin relaxometry have exploited the sensitivity of the NV nanodiamonds to magnetic fields to detect a range of analytes, such as pH, metal ions, and biomolecules. However, diversifying the sensing targets accessible by NV diamond quantum sensors typically requires careful engineering of the diamond surface chemistry with stimuli-responsive functional groups. Here, a simple protocol for coating NV nanodiamonds with the zeolitic imidazole framework 8 (ZIF-8), a widely used metal-organic framework, is presented. ZIF-8 is a highly porous material that has been used as a selective sensor for gasses, metal ions, and other analytes. The material is well-characterized by x-ray diffraction, transmission electron microscopy, scanning electron microscopy, x-ray photoelectron spectroscopy, and luminescence spectroscopy. Encapsulation of NV nanodiamonds with a porous scaffold such as ZIF-8 provides a promising method for improving the selectivity for the quantum sensing of various analytes. Importantly, the ZIF-8 coating does not impact the luminescence properties of the NV diamond, which is a key readout in ODMR and spin relaxometry sensing approaches. Indeed, the ODMR spectra with and without the ZIF-8 shell is nearly identical. Moreover, the ZIF-8 coating increases the longitudinal spin relaxation time of the NV nanodiamond by a factor of 4 relative to aggregated diamond, a desirable outcome for spin relaxation-based quantum sensing. Metal-organic framework composites with nanodiamonds thus are an exciting strategy for enhancing NV nanodiamond performance in applications such as quantum sensing and quantum-enhanced nuclear magnetic resonance spectroscopy.

nitrogen vacancy nanodiamond↗

DOE OSTI2023

Ion concentration ratio measurements of ion beams generated by a commercial microwave electron cyclotron resonance plasma source

A commercially available electron cyclotron resonance (ECR) plasma source (GenII Plasma Source, tectra GmbH) is widely used for surface processing. This plasma source is compatible with ultrahigh vacuum systems, and its working pressure is relatively low, around 10 –6 –10 –4 Torr even without differential pumping. Here, we report ion flux concentration ratios for each ion species in an ion beam from this source, as measured by a mass/energy analyzer that is a combination of a quadrupole mass spectrometer, an electrostatic energy analyzer, and focusing ion optics. In this study, the examined beams were those arising from plasmas produced from feed gases of H 2 , D 2 , N 2 , O 2 , Ar, and dry air over a range of input power and working pressures. H 2 (D 2 ) plasmas are widely used for nuclear fusion applications and, hence, the ion concentration ratios of H + , H 2 + , and H 3 + reported here will be useful information for research that applies this plasma source to well-controlled plasma-material interaction studies. Ion energy distributions, stability of operation, and impurity concentrations were also assessed for each of the plasma species investigated.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Summary of Biomass Scale Cubical Triaxial Tester Results

09 BIOMASS FUELS↗

DOE OSTI2023

Finite element modeling of biomass hopper flow

Hoppers are widely used biomass handling devices that channel bulk biomass from storage to subsequent handling equipment. Jenike’s longstanding approach, based on the Mohr-Coulomb model, has been successfully used to design hoppers handling cohesionless granular materials such as grains and other agricultural produces. However, designing a hopper to ensure reliable biomass flow is found to be challenging due to cohesion, irregular particle shape, and bulk material elastoplasticity. This study aims to address the biomass handling engineering challenge with alternative constitutive material models concerning the flow behavior of bulk solids. Finite element modeling is an approach that allows for implementation of different material models, whose underlying constitutive theories assist in investigating the origin and manifestation of bulk mechanical behavior of granular materials. This study focuses on the incipient gravity hopper flow of two types of biomass feedstocks, i.e., ground corn stover and Douglas fir wood. Three widely used constitutive material models, i.e., Mohr-Coulomb model, modified Cam-Clay model, and Drucker-Prager/Cap model, are implemented. Using the flow pattern represented by the volume of biomass exhibiting more than 7% of axial strain (Kamath and Puri, 1999), the finite element model predicts that the bulk corn stover particulate material forms an arch, which represents a hampered transition from the static state to the dynamic flow-state out of the hopper, whereas bulk Douglas fir wood particulate material develops a reliable mass flow pattern. A laboratory scale hopper was used to experimentally determine the biomass flow conditions, which were subsequently compared with the predicted onset of flow by a finite element model (FEM). The developed FEM was found to correctly predict the initiation of mass flow for the milled Douglas fir wood, whereas corn stover was predicted to establish a strong core flow suggesting an unreliable handling characteristic. This observation aligns with the reported poor handling of milled corn stover.

09 BIOMASS FUELS↗

NASA NTRS2014

A Historical Analysis of Crane Mishaps at Kennedy Space Center

Cranes and hoists are widely used in many areas. Crane accidents and handling mishaps are responsible for injuries, costly equipment damage, and program delays. Most crane accidents are caused by preventable factors. Understanding these factors is critical when designing cranes and preparing lift plans. Analysis of previous accidents provides insight into current recommendations for crane safety. Cranes and hoists are used throughout Kennedy Space Center to lift everything from machine components to critical flight hardware. Unless they are trained crane operators, most NASA employees and contractors do not need to undergo specialized crane training and may not understand the safety issues surrounding the use of cranes and hoists. A single accident with a crane or hoist can injure or kill people, cause severe equipment damage, and delay or terminate a program. Handling mishaps can also have a significant impact on the program. Simple mistakes like bouncing or jarring a load, or moving the crane down when it should go up, can damage fragile flight hardware and cause major delays in processing. Hazardous commodities (high pressure gas, hypergolic propellants, and solid rocket motors) can cause life safety concerns for the workers performing the lifting operations. Most crane accidents are preventable with the correct training and understanding of potential hazards. Designing the crane with human factors taken into account can prevent many accidents. Engineers are also responsible for preparing lift plans where understanding the safety issues can prevent or mitigate potential accidents. Cranes are widely used across many areas of KSC. Failure of these cranes often leads to injury, high damage costs, and significant delays in program objectives. Following a basic set of principles and procedures during design, fabrication, testing, regular use, and maintenance can significantly minimize many of these failures. As the accident analysis shows, load drops are often caused or influenced by human factors. Therefore, proper training and understanding of crane safety throughout the workforce is critical. It is important that the engineers designing the cranes, lift planners preparing the lift plans, operators performing the lifts, and training officers conducting the operator training all understand the problems that can happen with cranes and how to ensure the safety of the workforce and equipment being lifted.

Materials Handling↗

NASA NTRSDate not supplied

Global Reference Atmospheric Model (GRAM) Advancements and Additions

Introduction:The Global Reference Atmospheric Model (GRAM) is one of the most widely used engineering models of the atmosphere. GRAM development and maintenance has been led by NASA Marshall Space Flight Center (MSFC). The NASA Science Mission Directorate (SMD) has provided funding support to upgrade the GRAMs since Fiscal Year 2018. NASA Langley Research Center has been working with MSFC on the upgrades.This presentation will provide details regarding the upgrades that have been made to the existing GRAMs, the development of new GRAMs, as well as the ongoing objectives, tasks, and milestones re-lated to the GRAM upgrades funded by NASA SMD. GRAM: The GRAMs are engineering-oriented atmospheric models that estimate mean values and statistical variations of the atmospheric properties for numerous planetary destinations.They provide mean values and variability for any point in the atmosphere as well as seasonal, geographic, and altitude variations. GRAM outputs include atmospheric density, temperature, pressure, winds, and chemical composition along a user-defined path.Theyhave been widely used by the engineering community because of their ability to create realistic dispersions. GRAMs have been integrated into high fidelity flight dynamic simulations of launch, entry, descent and landing (EDL), aerobraking and aerocapture. MSFC has been developing and updating GRAMs since 1974; GRAMs are currently available for Earth, Mars, Venus, Neptune, and Titan. GRAM Upgrade Status: Code Moderization.The planetary GRAMs are being rearchitected from Fortran to a common object-ori-entedC++ framework called the GRAM Suite. This new architecture creates a common GRAM library of data models and utilities. The first C++ releases of the existing planetary GRAMs (Mars, Venus, Neptune, and Titan-GRAM) in the GRAM Suite are straight conversions from the latest Fortran version. Model Upgrades.The focus of the model upgrade task is to improve the atmosphere models in the existing GRAMs and to establish a foundation for developing GRAMs for additional destinations. The GRAM ephemerishas been upgraded to the NASA Navigation and Ancillary Information Facility (NAIF) SPICE toolkit (version N0066). The calculation of the speed of sound has also been improved in the GRAMs. The GRAM team has received updated Mars General Circulation Model (MGCM) datasets from NASA Ames Research Center. Mars Global Ionosphere-Thermosphere Model (M-GITM) data is being obtained toreplace the Mars Thermospheric General Circulation Model (MTGCM) data in legacy Mars-GRAM. M-GITM and updated MGCM data will be incorporated into a future GRAM Suite release.Twoprojects that will improve the atmospheric model data in the GRAMs have been funded by the GRAM team since Fiscal Year 2020. Sanjay Limaye and Patrick Fry at the University of Wisconsin are reanalyzing the Venus Express radio occultation observations and analyzing the Akatsukiradio occultation observations.This will lead tothe calculation of number density, temperature, and pressure profiles for the 40-90 km altitude range. Kunio Sayanagi, Justin Garland, and Ryan McCabeat Hampton University are developing empirical global models for Venus,Jupiter, Saturn, Uranus, Neptune, and Titan that incorporates the latest data available for each of these planetary destinations. Upgraded GRAM Releases. GRAM Suite Version 1.0 was released in May 2020 and contains the rearchitected Neptune-GRAM, including the common GRAM framework and planet–specific code. GRAM Suite Version 1.1 was released in September 2020 and addedthe rearchitected Titan-GRAM to the GRAM Suite. A User Guide and Programmer’s Manualarereleased with all GRAMs. The rearchitected Mars and Venus-GRAMs will be released in upcomingversions of the GRAM Suite. New GRAM Releases. New GRAMs have been de-veloped for Uranus and Jupiter. Uranus-GRAM is based on an individual profile generated by Gary Allen (ARC) from Voyager 2 occultation data and will be released in GRAM Suite Version 1.2. Jupiter-GRAM is based on individual profile produced from Al Seiff’s Ju-piter model[1].Jupiter-GRAM will be released in GRAM Suite Version 1.3. Saturn-GRAM is currently under development and will be released in a future version of the GRAM Suite. Conclusions: GRAMs are vital and frequently used toolsets. Releases of the GRAM Suite, upgrades of the existing planetary GRAMs, and development of new planetary GRAMs are ongoing. NASA SMD funding has been essential to addressing current limitations and accomplishing GRAM developmental goals. Continua-tion ofSMD fundingwill ensure the development, up-grades, and maintenance of the GRAMs. References: [1] Seiff, A., et al. (1998) JGR, 103, 22,857-22,889. Acknowledgments: The authors gratefully acknowledge support from the NASA SMD

atmospheric models↗

DOE OSTI2022

How Can Construction Process Simulation Modeling Aid the Integration of Lean Principles in the Factory-Built Housing Industry?

New and existing factories that produce and deliver factory-built housing can benefit from construction process simulation modeling to explore the integration of Lean principles in their operations. Construction process simulation modeling provides digital or virtual recreations of the real-world factory environments to visualize, quantify, analyze, and optimize their underlying behavior, including factory productivity, material flow, labor dynamics, bottlenecks, and work scope. One of the key benefits of process simulation modeling is the ability to create and compare "what-if" scenarios, including integrating Lean principles such as reducing waste (for example, transportation, waiting), line balancing, and just-in-time concepts. In general, three process simulation methods are widely used: discrete event simulation (DES), agentbased modeling (ABM), and system dynamics (SD). Myriad process simulation software also is available, but depending on the industry, complexity of the system, and purposes of the simulation, some software might be more appropriate. Similar to how computer-aided design (CAD) software such as AutoCAD and Rhinoceros enable building design of modular or factory-built housing, process simulation modeling software such as jStrobe, ProModel, and AnyLogic can enable factory design of new and existing factories to deliver modular affordable housing at scale, as opposed to traditional site-built construction. Software with DES capabilities can help generate a process model that is a logical representation of resources and activities in a factory. Software with CAD-DES integration can leverage product-process data integration to help spatially visualize a DES model of the factory in the CAD environment. Software with multimethod simulation capabilities, widely used in the manufacturing industry, brings together DES, ABM, and SD in a single platform that allows visualization, quantification, analyses, and optimization at varying data fidelities. Near-real-time data from an existing factory can be directly plugged into multimethod simulation software so that the construction process simulation model is a near-accurate representation of the real-world factory conditions. This report provides insights into the use of simulation as an aid to integrate Lean concepts in factories, including guidelines for selecting the appropriate process simulation modeling method and software. These insights have been developed as part of ongoing process simulation modeling research, development, and demonstration projects at the U.S. Department of Housing and Urban Development, the U.S. Department of Energy, and the National Renewable Energy Laboratory focused on how process simulation models can enable better integration of resilience, energy efficiency, and low-carbon design strategies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2023

Effects of error, chimera, bias, and GC content on the accuracy of amplicon sequencing

ABSTRACT Targeted amplicon sequencing is widely used in microbial ecology studies. However, sequencing artifacts and amplification biases are of great concern. To identify sources of these artifacts, a systematic analysis was performed using mock communities comprised of 16S rRNA genes from 33 bacterial strains. Our results indicated that while sequencing errors were generally isolated to low-abundance operational taxonomic units, chimeric sequences were a major source of artifacts. Singleton and doubleton sequences were primarily chimeras. Formation of chimeric sequences was significantly correlated with the GC content of the targeted sequences. Low-GC-content mock community members exhibited lower rates of chimeric sequence formation. GC content also had a large impact on sequence recovery. The quantitative capacity was notably limited, with substantial recovery variations and weak correlation between anticipated and observed strain abundances. The mock community strains with higher GC content had higher recovery rates than strains with lower GC content. Amplification bias was also observed due to the differences in primer affinity. A two-step PCR strategy reduced the number of chimeric sequences by half. In addition, comparative analyses based on the mock communities showed that several widely used sequence processing pipelines/methods, including DADA2, Deblur, UCLUST, UNOISE, and UPARSE, had different advantages and disadvantages in artifact removal and rare species detection. These results are important for improving sequencing quality and reliability and developing new algorithms to process targeted amplicon sequences. IMPORTANCE Amplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Reliable and Efficient Machine Learning (Final Technical Report)

Modern scientific experiments generate massive amounts of data at a pace much faster than humans can manually analyze. While machine learning has revolutionized commercial data analysis (such as recommending movies or recognizing faces), applying these tools to complex scientific discovery is challenging because scientific answers must be precise, interpretable, and adhere to physical laws. The research under this project aims to develop new mathematical tools and computer algorithms specifically designed for scientific applications. Major progress has been made in automatically cleaning and deconstructing messy experimental data, analyzing the visual information of physical phenomena, determining the underlying physical variables, and providing rig orous mathematical analysis of interesting algorithms and concepts widely used in machine learning. This project addressed the critical gap between our ability to generate massive scientific data and our ability to extract interpretable information from it. We established mathematical foundations for Scientific Machine Learning (SciML) aimed at effective data analytics and automated discovery. Our work focused on three core objectives: (1) developing reliable feature extraction methods for dynamic high-dimensional data, (2) establishing mathematical foundations for discovering dynamics via neural networks, and (3) creating rigorous optimization techniques for these models. Key outcomes come from two fronts. On the practical side, they include the development of algorithms that significantly enhance the extraction of signals from field data, as well as the capability to handle situations that exhibit smooth variations or physical stretching due to temperature changes. They also include the creation of an automated framework for discovering fundamental state variables from raw experimental data, demonstrating the ability to identify intrinsic physical dimensions without prior knowledge of the governing laws. On the theoretical front, the research results in theoretical advances in Optimal Transport, a widely used notion in SciML, specifically regarding functions with fixed-size nodal sets, provide sharp bounds relevant to uncertainty quantification. Meanwhile, the outcomes also include the establishment of convergence theories for nonlocal gradient descent methods, enabling robust optimization with noisy data in high-dimensional settings commonly encountered in scientific modeling. The project also helps creating opportunities to train the next generation of researchers, equipping them with the necessary technical skills for today’s workplace and preparing them for future advances.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Continuously tunable uniaxial strain control of van der Waals heterostructure devices

Uniaxial strain has been widely used as a powerful tool for investigating and controlling the properties of quantum materials. However, existing strain techniques have so far mostly been limited to use with bulk crystals. Although recent progress has been made in extending the application of strain to two-dimensional van der Waals (vdW) heterostructures, these techniques have been limited to optical characterization and extremely simple electrical device geometries. Here, we report a piezoelectric-based in situ uniaxial strain technique enabling simultaneous electrical transport and optical spectroscopy characterization of dual-gated vdW heterostructure devices. Critically, our technique remains compatible with vdW heterostructure devices of arbitrary complexity fabricated on conventional silicon/silicon dioxide wafer substrates. We demonstrate a large and continuously tunable strain of up to –0.15% at millikelvin temperatures, with larger strain values also likely achievable. We quantify the strain transmission from the silicon wafer to the vdW heterostructure, and further demonstrate the ability of strain to modify the electronic properties of twisted bilayer graphene. Our technique provides a highly versatile new method for exploring the effect of uniaxial strain on both the electrical and optical properties of vdW heterostructures and can be easily extended to include additional characterization techniques.

Electrical properties and parameters↗