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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Identification of a key water molecule involved in the macrophage migration inhibitory factor‐catalyzed tautomerization of para ‐hydroxyphenylpyruvate using neutron crystallography

Abstract Neutron crystallography was used to determine a 2.5‐Å resolution all‐atom structure of macrophage migration inhibitory factor (MIF) interacting with 3‐(4‐hydroxyphenyl)‐pyruvate (HPP). MIF is a pro‐inflammatory, pro‐tumorigenic protein that may be an attractive therapeutic target. MIF catalyzes the interconversion of the keto and enol forms of HPP by a tautomerase reaction. Although HPP is evidently not a physiological substrate of MIF, many compounds that inhibit this activity in enzymatic assays have been found also to inhibit physiological activities of MIF. Therefore, the MIF‐catalyzed HPP tautomerization reaction is used in initial screening of compounds in the search for inhibitors of MIF physiological activity. The neutron diffraction‐derived crystal structure reveals the position of a water molecule involved in the tautomerization reaction, and also confirms the charged state of lysine‐32 in the active site. The structure confirms the previously proposed catalytic mechanism of MIF, with the N‐terminal Pro‐1 abstracting a proton to generate an HPP enolate intermediate which is subsequently protonated. The structure reported herein reveals that this proton is supplied by a neighboring water molecule. Along with the neutron structure, a room‐temperature synchrotron x‐ray crystal structure reveals a covalent adduct between HPP and MIF. While this adduct is a result of radiation‐induced chemistry, its formation confirms the catalytic role of the active site residue because a covalent complex could only form if the reactive carbon of the substrate is correctly positioned by the enzyme.

Schröder, Gabriela C. [Department of Molecular and↗
DOE OSTI2020

Accuracy of XAS theory for unraveling structural changes of adsorbates: CO on Ni(100)

Studying surface reactions using ultrafast optical pump and X-ray probe experiments relies on accurate calculations of X-ray spectra of adsorbates for correct identification of the spectral signatures and their dynamical evolution. We show that experimental XAS can be well reproduced for the different binding sites in a static prototype system CO/Ni(100) at a standard DFT (GGA) level of theory, using a plane-wave basis and pseudopotentials. This validates its utility in analyzing ultrafast X-ray probe experiments. The accuracy of computed relative core level binding energies is about 0.2 eV, representing a lower limit for which spectral features can be resolved with this method. We also show that the commonly used Z +1 approximation gives very good core binding energy shifts overall. However, we find a discrepancy for CO adsorbed in the hollow site, which we assign to the significantly stronger hybridization in hollow bonding than in on-top.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

A deep generative model enables automated structure elucidation of novel psychoactive substances

Over the past decade, the illicit drug market has been reshaped by the proliferation of clandestinely produced designer drugs. These agents, referred to as new psychoactive substances (NPSs), are designed to mimic the physiological actions of better-known drugs of abuse while skirting drug control laws. The public health burden of NPS abuse obliges toxicological, police and customs laboratories to screen for them in law enforcement seizures and biological samples. However, the identification of emerging NPSs is challenging due to the chemical diversity of these substances and the fleeting nature of their appearance on the illicit market. Here, in this study, we present DarkNPS, a deep learning-enabled approach to automatically elucidate the structures of unidentified designer drugs using only mass spectrometric data. Our method employs a deep generative model to learn a statistical probability distribution over unobserved structures, which we term the structural prior. We show that the structural prior allows DarkNPS to elucidate the exact chemical structure of an unidentified NPS with an accuracy of 51% and a top-10 accuracy of 86%. Our generative approach has the potential to enable de novo structure elucidation for other types of small molecules that are routinely analysed by mass spectrometry.

Cheminformatics↗
NASA NTRS1973

Iron-absorption band analysis for the discrimination of iron-rich zones

The author has identified the following significant results. Study has concentrated on the two primary aspects of the project, structural analysis through evaluation of lineaments and circular features and spectral analyses through digital computer-processing techniques. Several previously unrecognized lineaments are mapped which may be the surface manifestations of major fault or fracture zones. Two of these, the Walker Lane and the Midas Trench lineament system, transect the predominantly NNE-NNW-trending moutain ranges for more than 500 km. Correlation of major lineaments with productive mining districts implies a genetic relationship, the 50 circular or elliptical features delineated suggest a related role for Tertiary volcanism. Color-ratio composites have been used to identify limonitic zones and to discriminate mafic and felsic rock by combing diazo color transparencies of three different ratios. EROS Data Center scene identification number for color composite in this report is ER 1 CC 500. Refinement of enhancement procedures for the ratio images is progressing. Fieldwork in coordination with both spectral and structural analyses is underway.

Rowan, L. C.↗
DOE OSTI2026

Small-molecule modulation of β-arrestins

β-Arrestins are multifunctional regulators of G-protein-coupled receptor (GPCR) signalling and orchestrate diverse downstream signalling events and physiological responses across the GPCR superfamily. Although GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GPCR kinases, direct chemical tools to modulate β-arrestin activities have remained conspicuously absent. Here we report the identification of small-molecule inhibitors that selectively target β-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical and structural analyses. These inhibitors disrupt β-arrestin engagement with agonist-activated GPCRs, impairing desensitization, internalization and β-arrestin-dependent physiological functions while sparing G protein–receptor coupling. Cryo-electron microscopy, molecular dynamics simulations and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a pocket within the central crest of β-arrestin1 formed by the middle, C and lariat loops, a critical receptor-binding interface, stabilizing a distinct conformation that is incompatible with full β-arrestin–receptor engagement. Together, these findings establish a mechanistic framework for β-arrestin modulation, reveal a novel allosteric site for structure-based drug design, and open new avenues for transducer-targeted, pathway-specific GPCR therapeutic agents.

Kahsai, Alem W. [Duke University, Durham, NC (Unit↗
DOE OSTI2021

Genome-wide discovery of G-quadruplexes in barley

G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5' untranslated region (5' UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Structure-function studies of Vibrio cholerae quorum-sensing receptor CqsR signal recognition

Ethanolamine signaling through the transmembrane quorum-sensing receptor CqsR influencesVibrio choleraeniche recognition and host colonization. In this study, we present a comprehensive structure-function analysis of CqsR. Specifically, we have determined X-ray crystal structures of the CqsR periplasmic domain bound to the signaling agonist ethanolamine and its analogs, serinol and L-alaninol, as well as the ligand-free (apo) form of CqsR. The periplasmic ligand-binding domain of CqsR is a Cache domain, the most prevalent extracellular sensory module in prokaryotes. Our findings provide a rare structural comparison of ligand-bound and unbound states of a Cache domain receptor. Coupled with thermodynamic binding assays and genetic analyses, these structures elucidate the molecular basis of CqsR ligand specificity. This study not only advances the understanding of Cache domain function but also informs the identification of ligands for orphan Cache receptors and the rational design of signaling agonists and antagonists. Lastly, we discuss ligand-induced conformational changes in the CqsR Cache domains and explore the potential for the existence of additional regulatory ligands.

Microbiology↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Trail Creek in Taylor River Watershed, Colorado 2024-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors near Trail Creek. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format TR-X-Y, where TR refers to Trail Creek, X is the treatment block identifier, and Y is the location identifier. Specifically, TR-ASCC1 is the control treatment block under the Adaptive Silviculture for Climate Change (ASCC) project, and TR-ASCC2 is the clear-cut treatment block. TR-ASCC-EHSn is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and TR-ASCC-ERTn (upslope n=1) are ecohydrology sites along the electrical resistivity tomography transects. The sample and location information can be found in metadata.csv, and the data from the soil sensors will be included in a future data version when the observation period becomes sufficiently long for data analysis. Sampling and Measurements Each sample falls into one of the two sampling methods – (1) intact cores or (2) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. The intact cores were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

EARTH SCIENCE > LAND SURFACE > SOILS↗
NASA NTRS1973

Applicability of ERTS-1 to lineament and photogeologic mapping in Montana: Preliminary report

A lineament map prepared from a mosaic of western Montana shows about 85 lines not represented on the state geologic map, including elements of a northeast-trending set through central western Montana which merit ground truth checking and consideration in regional structural analysis. Experimental fold annotation resulted in a significant local correction to the state geologic map. Photogeologic mapping studies produced only limited success in identification of rock types, but they did result in the precise delineation of a late Cretaceous or early Tertiary volcanic field (Adel Mountain field) and the mapping of a connection between two granitic bodies shown on the state map. Imagery was used successfully to map clay pans associated with bentonite beds in gently dipping Bearpaw Shale. It is already apparent that ERTS imagery should be used to facilitate preparation of a much needed statewide tectonic map and that satellite imagery mapping, aided by ground calibration, provides and economical means to discover and correct errors in the state geologic map.

Weidman, R. M.↗
NASA NTRS1975

General purpose simulation system of the data management system for space shuttle mission 18

The simulation program of the science and engineering data management system for the space shuttle is presented. The programming language used was General Purpose Simulation System V (OS). The data flow was modeled from its origin at the experiments or subsystems to transmission from the space shuttle. Mission 18 was the particular flight chosen for simulation. First, the general structure of the program is presented and the trade studies which were performed are identified. Inputs required to make runs are discussed followed by identification of the output statistics. Some areas for model modifications are pointed out. A detailed model configuration, program listing and results are included.

Bengtson, N. M.↗
NASA NTRS1975

Confirmation of interstellar N2H/+/

The proposed identification of the triplet of interstellar lines recently discovered at 93.174 GHz with the molecular ion N2H(+) is confirmed by resolving the predicted hyperfine structure of the inner nitrogen nucleus in the narrow-line molecular source OMC-2 in the Orion Nebula. The hyperfine constants of N2H(+) are derived from the observational data, and the rest center frequency of the J = 1-0 rotational transition is determined. It is noted that the full width at half-maximum of the weakest line (F sub 1 = 0-1) is only 230 kHz (0.74 km/sec in radial velocity), making it the narrowest molecular emission line (excluding maser point sources) thus far observed in the direction of a H II region or IR source.

Thaddeus, P.↗
NASA NTRS1988

Integrated Analysis Of Static Distributed Systems

Integrated approach encompasses modeling, identification of parameters, estimation of states, and control. Applies to models specified in part by possibly interconnected elliptic partial differential equations for deflections of structures under static loads. Appropriate for systems in which time-dependent effects negligibleand where control forces applied without exciting significiant dynamic behavior.

Rodriguez, Guillermo↗
NASA NTRS1987

A Programming Environment Evaluation Methodology for Object-Oriented Systems

The object-oriented design strategy as both a problem decomposition and system development paradigm has made impressive inroads into the various areas of the computing sciences. Substantial development productivity improvements have been demonstrated in areas ranging from artificial intelligence to user interface design. However, there has been very little progress in the formal characterization of these productivity improvements and in the identification of the underlying cognitive mechanisms. The development and validation of models and metrics of this sort require large amounts of systematically-gathered structural and productivity data. There has, however, been a notable lack of systematically-gathered information on these development environments. A large part of this problem is attributable to the lack of a systematic programming environment evaluation methodology that is appropriate to the evaluation of object-oriented systems.

Dominick, Wayne D.↗
NASA NTRS1988

A knowledge-based approach to identification and adaptation in dynamical systems control

Artificial intelligence techniques are applied to the problems of model form and parameter identification of large-scale dynamic systems. The object-oriented knowledge representation is discussed in the context of causal modeling and qualitative reasoning. Structured sets of rules are used for implementing qualitative component simulations, for catching qualitative discrepancies and quantitative bound violations, and for making reconfiguration and control decisions that affect the physical system. These decisions are executed by backward-chaining through a knowledge base of control action tasks. This approach was implemented for two examples: a triple quadrupole mass spectrometer and a two-phase thermal testbed. Results of tests with both of these systems demonstrate that the software replicates some or most of the functionality of a human operator, thereby reducing the need for a human-in-the-loop in the lower levels of control of these complex systems.

Glass, B. J.↗
NASA NTRS1992

X-ray and optical emission-line filaments in the cooling flow cluster 2A 0335 + 096

We present a new high-resolution X-ray image of the 2A 0335 + 096 cluster of galaxies obtained with the High Resolution Imager (HRI) aboard the ROSAT satellite. The presence of dense gas having a very short cooling time in the central regions confirms its earlier identification as a cooling flow. The X-ray emission from the central regions of the cooling flow shows a great deal of filamentary structure. Using the crude spectral resolution of the HRI, we show that these filaments are the result of excess emission, rather than foreground X-ray absorption. Although there are uncertainties in the pointing, many of the X-ray features in the cooling flow region correspond to features in H-alpha optical line emission. This suggests that the optical emission line gas has resulted directly from the cooling of X-ray-emitting gas. The filament material cannot be in hydrostatic equilibrium, and it is likely that other forces such as rotation, turbulence, and magnetic fields influence the dynamical state of the gas.

Sarazin, Craig L.↗
NASA NTRS2007

NASA-STD 3001 and the Human Integration Design Handbook (HIDH): Evolution of NASA-STD-3000

The Habitability & Environmental Factors and Space Medicine Divisions have developed the Space Flight Human System Standard (SFHSS) (NASA-STD-3001) to replace NASA-STD-3000 as a new NASA standard for all human spaceflight programs. The SFHSS is composed of 2 volumes. Volume 1, Crew Health, contains medical levels of care, permissible exposure limits, and fitness for duty criteria, and permissible outcome limits as a means of defining successful operating criteria for the human system. Volume 2, Habitability and Environmental Health, contains environmental, habitability and human factors standards. Development of the Human Integration Design Handbook (HIDH), a companion to the standard, is currently under construction and entails the update and revision of NASA-STD-3000 data. This new handbook will, in the fashion of NASA STD-3000, assist engineers and designers in appropriately applying habitability, environmental and human factors principles to spacecraft design. Organized in a chapter-module-element structure, the HIDH will provide the guidance for the development of requirements, design considerations, lessons learned, example solutions, background research, and assist in the identification of gaps and research needs in the disciplines. Subject matter experts have been and continue to be solicited to participate in the update of the chapters. The purpose is to build the HIDH with the best and latest data, and provide a broad representation from experts in industry, academia, the military and the space program. The handbook and the two standards volumes work together in a unique way to achieve the required level of human-system interface. All new NASA programs will be required to meet Volumes 1 and 2. Volume 2 presents human interface goals in broad, non-verifiable standards. Volume 2 also requires that each new development program prepare a set of program-specific human factors requirements. These program-specific human and environmental factors requirements must be verifiable and tailored to assure the new system meets the Volume 2 standards. Programs will use the HIDH to write their verifiable program-specific requirements.

Pickett, Lynn↗
NASA NTRS2013

Advances in the Development of a WCl6 CVD System for Coating UO2 Powders with Tungsten

W-UO2 CERMET fuels are under development to enable Nuclear Thermal Propulsion (NTP) for deep space exploration. Research efforts with an emphasis on fuel fabrication, testing, and identification of potential risks is underway. One primary risk is fuel loss due to CTE mismatch between W and UO2 and the grain boundary structure of W particles resulting in higher thermal stresses. Mechanical failure can result in significant reduction of the UO2 by hot hydrogen. Fuel loss can be mitigated if the UO2 particles are coated with a layer of high density tungsten before the consolidation process. This paper discusses the work to date, results, and advances of a fluidized bed chemical vapor deposition (CVD) system that utilizes the H2-WCl6 reduction process. Keywords: Space, Nuclear, Thermal, Propulsion, Fuel, CERMET, CVD, Tungsten, Uranium

Mireles, Omar R.↗
NASA NTRS2013

An Indirect System Identification Technique for Stable Estimation of Continuous-Time Parameters of the Vestibulo-Ocular Reflex (VOR)

The vestibulo-ocular reflex (VOR) is a well-known dual mode bifurcating system that consists of slow and fast modes associated with nystagmus and saccade, respectively. Estimation of continuous-time parameters of nystagmus and saccade models are known to be sensitive to estimation methodology, noise and sampling rate. The stable and accurate estimation of these parameters are critical for accurate disease modelling, clinical diagnosis, robotic control strategies, mission planning for space exploration and pilot safety, etc. This paper presents a novel indirect system identification method for the estimation of continuous-time parameters of VOR employing standardised least-squares with dual sampling rates in a sparse structure. This approach permits the stable and simultaneous estimation of both nystagmus and saccade data. The efficacy of this approach is demonstrated via simulation of a continuous-time model of VOR with typical parameters found in clinical studies and in the presence of output additive noise.

Kukreja, Sunil L.↗