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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Algebraic discrete quantum harmonic oscillator with dynamic resolution scaling

We develop an algebraic formulation for the discrete quantum harmonic oscillator (DQHO) from the Hamiltonian for two, coupled QHOs and provide a physical picture for the Kravchuk function eigenstates of the oscillator. The familiar $\mathfrak{su}(2)$ structure of the coupled QHO Hamiltonian divides its spectrum into sets corresponding to the DQHO at different resolutions. In addition to energy ladder operators, the formulation allows for the introduction of resolution ladder operators connecting all DQHOs with different resolutions, thus enabling the dynamic scaling of the resolution of finite degree-of-freedom quantum simulations. The coherent state of the DQHO is constructed, and its expected position is proven to oscillate as a classical harmonic oscillator. The DQHO coherent state recovers that of the quantum harmonic oscillator at large resolution.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Characterization of the ATLAS Liquid Argon Front-End ASIC ALFE2 for the HL-LHC upgrade

In this study, ALFE2 is an ATLAS Liquid Argon Calorimeter (LAr) Front-End ASIC designed for the HL-LHC upgrade. ALFE2 comprises four channels of pre-amplifiers and CR-(RC) 2 shapers with adjustable input impedance. ALFE2 features two separate gain outputs to provide 16-bit dynamic-range coverage and an optimum resolution. ALFE2 is characterized using a Front-End Test Board (FETB) based on a Zynq UltraScale+ MPSoC and two octal-channel 16-bit high-speed ADCs. The test results indicate that ALFE2 fulfills or greatly exceeds all specifications on gain, noise, linearity, uniformity, and radiation tolerance.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Hourly dynamic line ratings for existing transmission across the contiguous United States (preliminary results) [Slides]

The thermal rating of a transmission line depends on the rate at which heat generated by current flow through the line can be dissipated into the environment by convective and radiative cooling, keeping the conductor below a maximum operating temperature. Static or seasonal line ratings assume nearly-worst-case weather conditions (high ambient air temperature, high solar irradiance, and low wind speed), resulting in a low risk of "overrating" a line (i.e., allowing more current to flow than the line is designed for) but a high fraction of time when the line is "underrated" (i.e., able to flow more current while staying below the maximum temperature). Dynamic transmission line ratings (DLR) use real-time measurements of weather conditions, line sag, or line temperature to determine the thermal rating of transmission lines at hourly or higher time resolution, allowing for increased ratings during some (cold, windy, and/or dark) periods and correcting for overrating during other (hot, calm, and/or sunny) periods. Many studies have explored the benefits of DLR, but typically for small collections of transmission lines under a limited sample of weather conditions, leaving open the question of how widely applicable the benefits of DLR might be over diverse geographies and weather conditions. Here, we combine geospatial data on tens of thousands of transmission line routes across the contiguous United States with high-resolution hourly historical weather data for 2007-2013 to estimate the impact of DLR and other weather-adjusted rating systems. We compare static and dynamic line ratings to intermediate ratings adjusted by ambient temperature, day/night irradiance, clear-sky irradiance, and/or measured irradiance, illustrating the benefits of incorporating progressively more detailed weather data into the calculated line ratings. Moving from nighttime-adjusted ratings to clear-sky-adjusted ratings provides more benefit than moving from clear-sky-adjusted ratings to measured-irradiance-adjusted ratings. Depending on the assumed static windspeed for irradiance-adjusted-ratings, DLR either corrects for overrated hours or provides substantially increased ratings in the majority of hours on the majority of lines.

14 SOLAR ENERGY↗
DOE OSTI2023

A 4 x 4 SiPM Sensor Array with Fast Preamplified Output Engineered for the PWO Detectors of the EIC EEEMCAL

The PbWO4 scintillation detectors for the Electron-Ion Collider Electron Endcap Electromagnetic Calorimeter (EEEMCAL) cannot use vacuum photomultipler tubes due to the high magnetic field environment. We are presenting a readout solution with a 4 x 4 SiPM array directly coupled to a preamplification and summing stage. A second amplification stage with variable gain and offset adjustments is also included in the compact electronics module. The integrated power supply feeds the signal processing chain and the adjustable bias control. The parameter settings are saved locally on a EEPROM and are adjustable via the integrated communication interface through USB or RS485. The design was optimized to maximize signal collection energy resolution, for fast timing and wide dynamic range while keeping a small footprint with low power consumption and heat dissipation. The output response is fast enough to meet the 100 ? 200 ns digitization gate requirements for the detector. The electronics assembly requires no active cooling and includes a temperature sensor and a gain compensation of thermal variations which are important features for stable operation in large scale detector structures. A detector prototype was constructed with 20 mm x 20 mm x 200 mm PWO crystals affixed with individual SiPM array readouts and arranged in a 3 x 3 array. This detector was tested at the Thomas Jefferson National Accelerator Facility with 5GeV positrons. We will present the results of these detector characterization measurements.

Philip, O.↗
DOE OSTI2024

Photon number resolving detection with a single-photon detector and adaptive storage loop

Abstract Photon number resolving (PNR) measurements are beneficial or even necessary for many applications in quantum optics. Unfortunately, PNR detectors are usually large, slow, expensive, and difficult to operate. However, if the input signal is multiplexed, photon ‘click’ detectors, that lack an intrinsic PNR capability, can still be used to realize photon number resolution. Here, we investigate the operation of a single click detector, together with a storage line with tunable outcoupling. Using adaptive feedback to adjust the storage outcoupling rate, the dynamic range of the detector can in certain situations be extended by up to an order of magnitude relative to a purely passive setup. An adaptive approach can thus allow for photon number variance below the quantum shot noise limit under a wider range of conditions than using a passive multiplexing approach. This can enable applications in quantum enhanced metrology and quantum computing.

Sullivan, Nicholas M. (ORCID:0000000248447296)↗
DOE OSTI2024

helios: An R package to process heating and cooling degrees for GCAM

helios is an open-source R package that estimates population-weighted heating and cooling degree-hours (HDH and CDH) and degree-days (HDD and CDD) at various temporal (e.g., energy dispatch segments, monthly, yearly) and spatial scales (e.g., U.S. states, global political regions, countries). The degree hour and degree day outputs from helios are used to inform electricity demand load in the Global Change Analysis Model (GCAM) as well as in GCAM-USA (which is the version of GCAM with U.S. state-level details). helios uses a workflow with four steps: processing raw data; calculating heating and cooling degrees; visualizing performance diagnostics; and outputing results in various formats. There are two sources of widely-used climate data compatible with helios: (1) hourly climate data with 12-km resolution that are dynamically downscaled with the Weather Research and Forecasting (WRF) model and projected using a thermal global warming (TGW) approach; and (2) daily climate data with 0.5-degree resolution from the Coupled Model Intercomparison Project (CMIP) that is bias-adjusted and statistical downscaled by the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP). In summary, helios is a model that standardizes methodology of heating and cooling degrees-hours and degree-days using publicly available data and advance the understanding of the impact of spatial and temporal temperature variability on building energy services.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

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

High-resolution (30-m) urban land cover projections for Los Angeles California Urban Area: 2010 to 2100 under SSP5

These data represent simulations of future land use and land cover (LULCC) for Los Angeles urban area (U.S. Census Bureau defined area) as raster tiff images at a 30-m pixel resolution and at decadal time steps from 2010 to 2100. LULCC classes in this product follow the National Land Cover Dataset (NLCD) classification. NLCD 21-24 correspond to open developed, low developed, medium developed, and high developed urban land classes, respectively. Only urban land cover classes (NLCD class 21, 22, 23, and 24) are dynamic over time; however, all NLCD classes are included in the final product. Therefore, NLCD classes that do not convert to an urban class will be similar to year 2000. The products were developed using a hybridized statistical and cellular automata approach. Linear mixed models (LMMs) were used to estimate future urban land budgets based on 1-km urban land fraction projections from Gao and Pesaresi (2021), whereas separate generalized linear mixed models (GLMMs) were used to estimate shifts in urban land intensities based on retrospective shifts in NLCD urban class intensities over a 20- year period. Based on urban land allocations from the statistical models, a cellular-automata and downscaling routine was used to simulate dynamic urban land expansion at a 30-m resolution based on suitability criteria. Scenarios of future urban landcover change projections include variant solutions for the Shared Socioeconomic Pathway 5 (SSP5) based on different population assumptions, different land use intensification assumptions, variable land zoning constraints, and iterative adjustments to correct for over allocation of urban expansion across decadal time periods from 2010 to 2100. This results in 320 raster products.

Land↗
DOE OSTI2023

High-resolution (30-m) urban land cover projections for Los Angeles California Urban Area: 2010 to 2100 under SSP3 and SSP5 [Updated simulations based on population-driven urban intensity transitions]

These data (v3) are updated from previous versions (1 and 2) in that they include consider the effects of population on transitions in urban land intensity. This leads to more reasonable differences in urban land projections under variant SSPs. For the present dataset, both SSP3 and SSP5 are provided. These data represent simulations of future land use and land cover (LULCC) for Los Angeles urban area (U.S. Census Bureau defined area) as raster tiff images at a 30-m pixel resolution and at decadal time steps from 2010 to 2100. LULCC classes in this product follow the National Land Cover Dataset (NLCD) classification. NLCD 21-24 correspond to open developed, low developed, medium developed, and high developed urban land classes, respectively. Only urban land cover classes (NLCD class 21, 22, 23, and 24) are dynamic over time; however, all NLCD classes are included in the final product. Therefore, NLCD classes that do not convert to an urban class will be similar to year 2000. The products were developed using a hybridized statistical and cellular automata approach. Linear mixed models (LMMs) were used to estimate future urban land budgets based on 1-km urban land fraction projections from Gao and Pesaresi (2021), whereas separate generalized linear mixed models (GLMMs) were used to estimate shifts in urban land intensities based on retrospective shifts in NLCD urban class intensities over a 20- year period. Based on urban land allocations from the statistical models, a cellular-automata and downscaling routine was used to simulate dynamic urban land expansion at a 30-m resolution based on suitability criteria. Scenarios of future urban landcover change projections include variant solutions for the Shared Socioeconomic Pathway 5 (SSP5) and SSP 3 based on different population assumptions, different land use intensification assumptions, variable land zoning constraints, and iterative adjustments to correct for over allocation of urban expansion across decadal time periods from 2010 to 2100. This results in 320 raster products.

Land↗
DOE OSTI2024

FARM User Guidance and Instructions

The FARM (Feasible Actuator Range Modifier) module is a component of the RAVEN-based FORCE framework for the analysis of Integrated Energy Systems (IES). FARM aids HERON in the solution of the power dispatch problem by evaluating feasible set-point signals to be issued to the control systems of the different IES unit components. Set-points need to satisfy limits on both production variables (i.e., the variables to be optimized such as the electrical power, etc.) and process variables tied to the service life of equipment (e.g., steam flowrate, vessel pressure, turbine firing temperature, etc.). To enforce all these limits, a two-stage approach is adopted. First, the power dispatcher algorithm in HERON module estimates set-points that meet the constraints on the production variables, e.g., power levels and power ramp rate limits. These constraints are called explicit constraints. Then, if necessary, FARM adjusts these set-points to ensure the respect of the limits on the process variables of interest, given the knowledge of the system dynamics acquired through machine learning algorithms. These constraints are called implicit constraints. From this standpoint, FARM constitutes a bridge between the HERON power dispatcher that adopts a simplified description of the IES unit (low-resolution physics) and the HYBRID high-fidelity models (high-resolution physics). In this report, the general workflow and the software requirements of FARM module are summarized, and the detailed instructions for installing FARM software, running built-in example cases, deriving Linear Parameter-Varying (LPV) state-space models, and using FARM for user-defined power dispatch problems are provided.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

FARM supervisory capabilities for thermal energy storage

The FARM (Feasible Actuator Range Modifier) module is a component of the RAVEN-based FORCE framework for the analysis of Integrated Energy Systems (IES). FARM aids HERON in the solution of the power dispatch problem by evaluating feasible set-point signals to be issued to the control systems of the different IES unit components. Set-points need to satisfy limits on both production variables (i.e., the variables to be optimized such as the electrical power, etc.) and process variables tied to the service life of equipment (e.g., steam flowrate, vessel pressure, turbine firing temperature, etc.). To enforce all these limits, a two-stage approach is adopted. First, the power dispatcher algorithm in HERON module estimates set-points that meet the constraints on the production variables, e.g., power levels and power ramp rate limits. These constraints are called explicit constraints. Then, if necessary, FARM adjusts these set-points to ensure the respect of the limits on the process variables of interest, given the knowledge of the system dynamics acquired through machine learning algorithms. These constraints are called implicit constraints. From this standpoint, FARM constitutes a bridge between the HERON power dispatcher that adopts a simplified description of the IES unit (low-resolution physics) and the HYBRID high-fidelity models (high-resolution physics). In this report, an overview of the major capabilities of the latest release of FARM is provided, along with a summary of the tool demonstration campaign conducted at the Dynamic Energy Technology and Integration Laboratory (DETAIL) facility. These results assess the performance of the control system architecture embedding FARM both as a Validator of the HERON power dispatcher and as a real time Supervisory control scheme. Additionally, the report outlines the areas that FARM might benefit from, along with proposed solutions.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Advanced Computational Modeling of High-Level Waste Vitrification at the Hanford Site

The U.S. Department of Energy (DOE) has selected vitrification for stabilizing legacy tank waste at the Hanford site, where radioactive waste from plutonium production was historically stored in underground tanks. This waste will be separated into low-activity waste (LAW) and high-level waste (HLW) fractions and processed at the Waste Treatment and Immobilization Plant (WTP). At WTP, glass melters are used for the vitrification of radioactive tank waste, transforming it into a stable borosilicate glass form for safe long-term storage. The melter vessel is constructed from highly durable and heat-resistant materials, where the vitrification process occurs. The main regions that are modeled are the melt pool, plenum, cold cap, riser/discharge chamber, and surrounding structure with insulation layers. Forced convection induced by air bubblers at the base of the melter ensure uniform temperature distribution and provide heat to the cold cap layer. The cold cap is a region of reacting batch feed that floats on top of the molten glass and is where the batch-to-glass reactions occur. Joule heating provided by electrodes mounted along the vertical walls of the melter and immersed directly in the glass, generates the necessary heat for the net endothermic conversion processes that occur in the cold cap. The high temperatures, radioactivity, and opaque nature of the glass prevent direct observation inside the melters. Therefore, computational models are essential for providing insight into factors that affect melter throughput. Thermocouples in the plenum provide operators with plenum temperature measurements. Operational adjustments include bubbling rate, voltage supplied to the electrodes, feed adjustments, and glass removal rate. Different computational fluid dynamics (CFD) models have been developed, each serving a specific purpose. There are CFD models of different scale melters, as well as models that capture the two-phase flow interfaces of rising bubbles in the molten glass or models with a simplified molten glass region so that the surrounding structure and plenum can be feasibly incorporated. Pilot-scale melter models have been developed to serve as validation of the methods employed in the simulation of the full-scale WTP melters. Models incorporating resolved bubbling are used to develop momentum source terms to implement into a single phase, multi-region, steady-state flow model that is being validated by measured process parameters such as glass production rate, voltage, input power, plenum temperatures, etc. The resolved bubbling model uses the multiphase volume of fluid approach to model the system with a high-resolution interface capturing scheme to maintain sharp interfaces between the molten glass and the air phase. The suite of CFD models is continually being improved to incorporate more realistic physics and achieve faster turnaround time. For example, an incremental controller is implemented to automatically adjust electrode voltage within the simulation to a molten glass set point temperature of 1150°C. Newer models feature improved meshes to ensure conformal meshes between regions and eliminate unnecessary mesh refinement in areas that are not of interest (such as boundary layers in offgas ports). Instead of explicitly modeling the structural, refractory, and insulation layers of the melter, a thermal resistance approach is used with published correlations used for boundary conditions. The development of robust and efficient CFD models will be instrumental in enabling the WTP to successfully fulfill its mission of safely stabilizing legacy nuclear waste.

12 - MGMT OF RADIOACTIVE AND NON-RADIOACTIVE WASTE↗
DOE OSTI2024

Stochastic modal velocity field in rough-wall turbulence

Stochastically generated instantaneous velocity profiles are used to reproduce the outer region of rough-wall turbulent boundary layers in a range of Reynolds numbers extending from the wind tunnel to field conditions. Each profile consists in a sequence of steps, defined by the modal velocities and representing uniform momentum zones (UMZs), separated by velocity jumps representing the internal shear layers. Height-dependent UMZ is described by a minimal set of attributes: thickness, mid-height elevation, and streamwise (modal) and vertical velocities. These are informed by experimental observations and reproducing the statistical behaviour of rough-wall turbulence and attached eddy scaling, consistent with the corresponding experimental datasets. Sets of independently generated profiles are reorganized in the streamwise direction to form a spatially consistent modal velocity field, starting from any randomly selected profile. The operation allows one to stretch or compress the velocity field in space, increases the size of the domain and adjusts the size of the largest emerging structures to the Reynolds number of the simulated flow. By imposing the autocorrelation function of the modal velocity field to be anchored on the experimental measurements, we obtain a physically based spatial resolution, which is employed in the computation of the velocity spectrum, and second-order structure functions. The results reproduce the Kolmogorov inertial range extending from the UMZ and their attached-eddy vertical organization to the very-large-scale motions (VLSMs) introduced with the reordering process. The dynamic role of VLSM is confirmed in the –u'w' co-spectra and in their vertical derivative, representing a scale-dependent pressure gradient contribution.

42 ENGINEERING↗
DOE OSTI2024

Measurement of Photovoltaic Module Deformation Dynamics During Hail Impact Using Digital Image Correlation

Stereo high-speed video of photovoltaic modules undergoing laboratory hail tests was processed using digital image correlation to determine module surface deformation during and immediately following impact. The purpose of this work was to demonstrate a methodology for characterizing module impact response differences as a function of construction and incident hail parameters. Video capture and digital image analysis were able to capture out-of-plane module deformation to a resolution of ±0.1 mm at 11 kHz on an in-plane grid of 10 × 10 mm over the area of a 1 × 2 m commercial photovoltaic module. With lighting and optical adjustments, the technique was adaptable to arbitrary module designs, including size, backsheet color, and cell interconnection. Furthermore, impacts were observed to produce an initially localized dimple in the glass surface, with peak deflection proportional to the square root of incident energy. Subsequent deformation propagation and dissipation were also captured, along with behavior for instances when the module glass fractured. Natural frequencies of the module were identifiable by analyzing module oscillations postimpact. Limitations of the measurement technique were that the impacting ice ball obscured the data field immediately surrounding the point of contact, and both ice and glass fracture events occurred within 100 μs, which was not resolvable at the chosen frame rate. Increasing the frame rate and visualizing the back surface of the impact could be applied to avoid these issues. Applications for these data include validating computational models for hail impacts, identifying the natural frequencies of a module, and identifying damage initiation mechanisms.

14 SOLAR ENERGY↗
DOE OSTI2023

Novel Calibration Approach for Monitoring Aerosol Hydrogen Isotopes Using Laser-Induced Breakdown Spectroscopy for Molten Salt Reactor Off-Gas Streams

Online monitoring is a key challenge for the continued development of molten salt reactor (MSR) technology. Laser-induced breakdown spectroscopy (LIBS) has previously been demonstrated to be a viable tool for monitoring aerosolized species and noble gases in real time, but the ability to discern varying isotopes in these streams has not yet been investigated for MSR applications. Tritium will form in MSRs from ternary fission and from (n,α)-reactions occurring in lithium-containing salts. This study compares three spectrometers of varying resolutions and types for measuring hydrogen isotope shifts in LIBS spectra of wetted filter paper. For each spectrometer, multivariate models were built (i.e., principal component regression, partial least squares regression, and multivariate curve resolution) to quantify the isotope ratio. The top models were then modified and corrected to apply the models to aerosol samples with varying isotope ratios. This novel calibration strategy offers an 82% reduction in volume of the calibration samples needed and is a more viable pathway for calibrating deployable LIBS systems. Lastly, this calibration model was compared with an all-aerosol trained model for monitoring hydrogen isotopes during a real-time test where the protium/deuterium ratio, along with representative salt species (i.e., lithium, sodium, and potassium) were adjusted dynamically. Results of this test validated the predictive capabilities of the transferred model and highlighted the capabilities of LIBS for real-time monitoring of MSR effluent streams.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Performance of cross-flow turbines with varying blade materials and unsupported blade span

Cross-flow turbines could play a larger role in the diversification of the global energy supply if the impact of more cost-competitive design choices on performance and rotor dynamics was better understood. This study focuses on rotor performance and blade strain measurements while varying the following parameters: blade materials and blade free end length by changing strut support position. Towing tank experiments were performed with a modular 1-meter diameter cross-flow turbine consisting of three NACA 0018 blades with two support struts. One strut was fixed at the lower end of the turbine, while the second strut was adjustable, thereby changing the length of the free end. The blade materials tested were carbon, E-glass, and hollow E-glass fiber composites, in decreasing order of stiffness and cost. High-resolution distributed fiber optic sensors were embedded in two of the three rotor blades for each material and provided hundreds of strain measurements per blade. Turbine performance and blade strain were measured while varying tow speed and tip speed ratio. Performance tests were conducted at towing speeds sufficiently high for the performance to be independent of Reynolds number. E-glass blades and carbon blades performed similarly for the most rigid strut configurations. Higher strain was measured on the E-glass blades, and their performance was reduced for less rigid configurations compared to the carbon fiber blades. The performance of the highly deflective hollow E-glass blades was lower overall and became even more degraded for longer unsupported blade span. Furthermore, the results provide insight into the use of various blade materials in cross-flow turbines and guidance on allowable free end length for each material type.

16 TIDAL AND WAVE POWER↗
DOE OSTI2023

Coupled catalytic states and the role of metal coordination in Cas9

Controlling the activity of the CRISPR–Cas9 system is essential to its safe adoption for clinical and research applications. Although the conformational dynamics of Cas9 are known to control its enzymatic activity, details of how Cas9 influences the catalytic processes at both nuclease domains remain elusive. Here we report five cryo-electron microscopy structures of the active Acidothermus cellulolyticus Cas9 complex along the reaction path at 2.2–2.9 Å resolution. We observed that a large movement in one nuclease domain, triggered by the cognate DNA, results in noticeable changes in the active site of the other domain that is required for metal coordination and catalysis. Furthermore, the conformations synchronize the reaction intermediates, enabling coupled cutting of the two DNA strands. Consistent with the roles of conformations in organizing the active sites, adjustments to the metal-coordination residues lead to altered metal specificity of A. cellulolyticus Cas9 and commonly used Streptococcus pyogenes Cas9 in cells.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields

In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate chemical restraints and, therefore, accurate macromolecular structures. In particular, it is desirable to have accurate restraints for known and novel ligand entities. Quantum mechanics (QM) can minimize the energy of a ligand by adjusting its geometry, and these geometries can be used to generate restraints for macromolecular refinement. This article describes a library of approximately 37 000 small molecules extracted from the Chemical Component Dictionary in the Protein Data Bank and minimized by density-functional QM. The library includes restraint files for use in crystallography or cryo-EM refinement, along with files suitable for molecular-dynamics simulation. Because the geometries are validated using the Cambridge Structural Database, the restraints library provides users with both functional restraints and minimized geometries. This work also provides procedures for generating new and accurate restraints.

Amber↗