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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 OSTI2015

Human γ-glutamyl transpeptidase 1: Structures of the free enzyme, inhibitor-bound tetrahedral transition states, and glutamate-bound enzyme reveal novel movement within the active site during catalysis [Human gamma-glutamyl transpeptidase: Inhibitor binding and movement within the active site]

γ-Glutamyl transpeptidase 1 (GGT1) is a cell surface, N-terminal nucleophile hydrolase that cleaves glutathione and other γ-glutamyl compounds. GGT1 expression is essential in cysteine homeostasis, and its induction has been implicated in the pathology of asthma, reperfusion injury, and cancer. In this study, we report four new crystal structures of human GGT1 (hGGT1) that show conformational changes within the active site as the enzyme progresses from the free enzyme to inhibitor-bound tetrahedral transition states and finally to the glutamate-bound structure prior to the release of this final product of the reaction. The structure of the apoenzyme shows flexibility within the active site. The serine-borate-bound hGGT1 crystal structure demonstrates that serine-borate occupies the active site of the enzyme, resulting in an enzyme-inhibitor complex that replicates the enzyme's tetrahedral intermediate/transition state. The structure of GGsTop-bound hGGT1 reveals its interactions with the enzyme and why neutral phosphonate diesters are more potent inhibitors than monoanionic phosphonates. These structures are the first structures for any eukaryotic GGT that include a molecule in the active site covalently bound to the catalytic Thr-381. The glutamate-bound structure shows the conformation of the enzyme prior to release of the final product and reveals novel information regarding the displacement of the main chain atoms that form the oxyanion hole and movement of the lid loop region when the active site is occupied. Lastly,tThese data provide new insights into the mechanism of hGGT1-catalyzed reactions and will be invaluable in the development of new classes of hGGT1 inhibitors for therapeutic use.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Nanoscale movements of cellulose microfibrils in primary cell walls

The growing plant cell wall is commonly considered to be a fibre-reinforced structure whose strength, extensibility and anisotropy depend on the orientation of crystalline cellulose microfibrils, their bonding to the polysaccharide matrix and matrix viscoelasticity. Structural reinforcement of the wall by stiff cellulose microfibrils is central to contemporary models of plant growth, mechanics and meristem dynamics. Although passive microfibril reorientation during wall extension has been inferred from theory and from bulk measurements, nanometre-scale movements of individual microfibrils have not been directly observed. For this, we combined nanometre-scale imaging of wet cell walls by atomic force microscopy (AFM) with a stretching device and endoglucanase treatment that induces wall stress relaxation and creep, mimicking wall behaviours during cell growth. Microfibril movements during forced mechanical extensions differ from those during creep of the enzymatically loosened wall. In addition to passive angular reorientation, we observed a diverse repertoire of microfibril movements that reveal the spatial scale of molecular connections between microfibrils. Our results show that wall loosening alters microfibril connectivity, enabling microfibril dynamics not seen during mechanical stretch. These insights into microfibril movements and connectivities need to be incorporated into refined models of plant cell wall structure, growth and morphogenesis.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

A novel approach for estimating densities of secretive species from road-survey and spatial-movement data

Accurate estimates of population density are a critical component of effective wildlife conservation and management. However, many snake species are so secretive that their density cannot be determined using traditional methods such as capture–mark–recapture. Thus, the status of most terrestrial snake populations remains completely unknown. We developed a novel simulation-based technique for estimating density of secretive snakes that combined behavioural observations of snake road-crossing behaviour (crossing speed), effort-corrected road-survey data, and simulations of spatial movement patterns derived from radio-telemetry, without relying on mark–recapture. Here, we used radio-telemetry data to parameterise individual-based movement models that estimate the frequency with which individual snakes cross roads and used information on survey vehicle speed and snake crossing speed to determine the probability of detecting a snake, given that it crosses the road transect during a survey. Snake encounter frequencies during systematic road surveys were then interpreted in light of detection probabilities and simulation model results to estimate snake densities and to assess various factors likely to affect abundance estimates. We demonstrated the broad applicability of this approach through a case study of the imperiled southern hognose snake (Heterodon simus) in the North Carolina (USA) Sandhills. We estimated that H. simus occurs at average densities of 0.17 ha –1 in the North Carolina Sandhills and explored the sensitivity of this estimate to assumptions and variation in model parameters. Our novel method allowed us to generate the first abundance estimates for H. simus. We found that H. simus exists at low densities relative to congeners and other mid-sized snake species, raising concern that this species may not only have declined in geographic range, but may also occur at low densities or be declining in their strongholds, such as the North Carolina Sandhills. We present a framework for estimating density of species that have traditionally been considered too secretive to study at the population level. This method will greatly enhance our ability to study and manage a wide variety of snake species and could be applied to other secretive wildlife species that are most frequently encountered during road surveys.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Following the movement of Cu ions in a SSZ-13 zeolite during dehydration, reduction and adsorption: a combined in situ TP-XRD, XANES/DRIFTS study

Cu-SSZ-13 has been shown to possess high activity and superior N2 formation selectivity in the selective catalytic reduction of NOx under oxygen rich conditions. Here, a combination of synchrotron-based (XRD and XANES) and vibrational (DRIFTS) spectroscopy tools have been used to follow the changes in the location and coordination environment of copper ions in a Cu-SSZ-13 zeolite during calcinations, reduction with CO, and adsorption of CO and H2O. XANES spectra collected during these procedures provides critical information not only on the variation in the oxidation state of the copper species in the zeolite structure, but also on the changes in the coordination environment around these ions as they interact with the framework, and with different adsorbates (H2O and CO). Time-resolved XRD data indicate the movement of copper ions and the consequent variation of the unit cell parameters during dehydration. DRIFT spectra provide information about the adsorbed species present in the zeolite, as well as the oxidation states of and coordination environment around the copper ions. A careful analysis of the asymmetric T-O-T vibrations of the CHA framework perturbed by copper ions in different coordination environments proved to be especially informative. The results of this study will aid the identification of the location, coordination and oxidation states of copper ions obtained during in operando catalytic studies. Financial support was provided by the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy, Vehicle Technologies Program. Part of this work (sample preparation) was performed in the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). The EMSL is a national scientific user facility supported by the US DOE, Office of Biological and Environmental Research. PNNL is a multi-program national laboratory operated for the US DOE by Battelle. All of the spectroscopy work reported here was carried out at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL). NSLS is a national scientific user facility supported by the US DOE.

cation coordination↗
DOE OSTI2017

Quantifying drivers of wild pig movement across multiple spatial and temporal scales

The movement behavior of an animal is determined by extrinsic and intrinsic factors that operate at multiple spatio-temporal scales, yet much of our knowledge of animal movement comes from studies that examine only one or two scales concurrently. Understanding the drivers of animal movement across multiple scales is crucial for understanding the fundamentals of movement ecology, predicting changes in distribution, describing disease dynamics, and identifying efficient methods of wildlife conservation and management. We obtained over 400,000 GPS locations of wild pigs from 13 different studies spanning six states in southern U.S.A., and quantified movement rates and home range size within a single analytical framework. We used a generalized additive mixed model framework to quantify the effects of five broad predictor categories on movement: individual-level attributes, geographic factors, landscape attributes, meteorological conditions, and temporal variables. We examined effects of predictors across three temporal scales: daily, monthly, and using all data during the study period. We considered both local environmental factors such as daily weather data and distance to various resources on the landscape, as well as factors acting at a broader spatial scale such as ecoregion and season. We found meteorological variables (temperature and pressure), landscape features (distance to water sources), a broad-scale geographic factor (ecoregion), and individual-level characteristics (sex-age class), drove wild pig movement across all scales, but both the magnitude and shape of covariate relationships to movement differed across temporal scales. The analytical framework we present can be used to assess movement patterns arising from multiple data sources for a range of species while accounting for spatio-temporal correlations. Our analyses show the magnitude by which reaction norms can change based on the temporal scale of response data, illustrating the importance of appropriately defining temporal scales of both the movement response and covariates depending on the intended implications of research (e.g., predicting effects of movement due to climate change versus planning local-scale management). We argue that consideration of multiple spatial scales within the same framework (rather than comparing across separate studies post-hoc) gives a more accurate quantification of cross-scale spatial effects by appropriately accounting for error correlation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

WE-A-17A-11: Implanted Brachytherapy Seed Movement Due to Transrectal Ultrasound Probe-Induced Prostate Deformation

Purpose: To characterize the movement of implanted brachytherapy seeds due to transrectal ultrasound probe-induced prostate deformation and to estimate the effects on prostate dosimetry. Methods: Implanted probe-in and probe-removed seed distributions were reconstructed for 10 patients using C-arm fluoroscopy imaging. The prostate was delineated on ultrasound and registered to the fluoroscopy seeds using a visible subset of seeds and residual needle tracks. A linear tensor and shearing model correlated the seed movement with position. The seed movement model was used to infer the underlying prostate deformation and to simulate the prostate contour without probe compression. Changes in prostate and surrogate urethra dosimetry were calculated. Results: Seed movement patterns reflecting elastic decompression, lateral shearing, and rectal bending were observed. Elastic decompression was characterized by anterior-posterior expansion and superior-inferior and lateral contractions. For lateral shearing, anterior movement up to 6 mm was observed for extraprostatic seeds in the lateral peripheral region. The average intra-prostatic seed movement was 1.3 mm, and the residual after linear modeling was 0.6 mm. Prostate D90 increased by 4 Gy on average (8 Gy max) and was correlated with elastic decompression. For selected patients, lateral shearing resulted in differential change in D90 of 7 Gy between anterior and posterior quadrants, and increase in whole prostate D90 of 4 Gy. Urethra D10 increased by 4 Gy. Conclusion: Seed movement upon probe removal was characterized. The proposed model captured the linear correlation between seed movement and position. Whole prostate dose coverage increased slightly, due to the small but systematic seed movement associated with elastic decompression. Lateral shearing movement increased dose coverage in the anterior-lateral region, at the expense of the posterior-lateral region. The effect on whole prostate D90 was smaller due to the subset of peripheral seeds involved, but lateral shearing movement can have greater consequences for local dose coverage.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Deep reinforcement learning of cell movement in the early stage of C.elegans embryogenesis

Motivation: Cell movement in the early phase of Caenorhabditis elegans development is regulated by a highly complex process in which a set of rules and connections are formulated at distinct scales. Previous efforts have demonstrated that agent-based, multi-scale modeling systems can integrate physical and biological rules and provide new avenues to study developmental systems. However, the application of these systems to model cell movement is still challenging and requires a comprehensive understanding of regulatory networks at the right scales. Recent developments in deep learning and reinforcement learning provide an unprecedented opportunity to explore cell movement using 3D time-lapse microscopy images. Results: We present a deep reinforcement learning approach within an agent-based modeling system to characterize cell movement in the embryonic development of C.elegans. Our modeling system captures the complexity of cell movement patterns in the embryo and overcomes the local optimization problem encountered by traditional rule-based, agent-based modeling that uses greedy algorithms. Here, we tested our model with two real developmental processes: the anterior movement of the Cpaaa cell via intercalation and the rearrangement of the superficial left-right asymmetry. In the first case, the model results suggested that Cpaaa’s intercalation is an active directional cell movement caused by the continuous effects from a longer distance (farther than the length of two adjacent cells), as opposed to a passive movement caused by neighbor cell movements. In the second case, a leader-follower mechanism well explained the collective cell movement pattern in the asymmetry rearrangement. These results showed that our approach to introduce deep reinforcement learning into agent-based modeling can test regulatory mechanisms by exploring cell migration paths in a reverse engineering perspective. Lastly, this model opens new doors to explore the large datasets generated by live imaging. Availability and implementation: Source code is available at https://github.com/zwang84/drl4cellmovement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SU-E-J-17: Intra-Fractional Prostate Movement Correction During Treatment Delivery Period for Prostate Cancer Using the Intra-Fractional Orthogonal KV-MV Image Pairs

Purpose: To evaluate the intra-fractional prostate movement range during the beam delivery and implement new IGRT method to correct the prostate movement during the hypofractionated prostate treatment delivery. Methods: To evaluate the prostate internal motion range during the beam delivery, 11 conventional treatments were utilized. Two-arc RapidArc plans were used for the treatment delivery. Orthogonal KV imaging is performed in the middle of the treatment to correct intra-fractional prostate movement. However, it takes gantry-mounted on-board imaging system relative long time to finish the orthogonal KV imaging because of gantry rotation. To avoid gantry movement and accelerate the IGRT processing time, orthogonal KV-MV image pair is tested using the OBI daily QA Cube phantom. Results: The average prostate movement between two orthogonal KV image pairs was 0.38cm (0.20cm ∼ 0.85cm). And the interval time between them was 6.71 min (4.64min ∼ 9.22 min). 2-arc beam delivery time is within 3 minutes for conventional RapidArc treatment delivery. Hypofractionated treatment or SBRT need 4 partial arc and possible non-coplanar technology, which need much longer beam delivery time. Therefore prostate movement might be larger. New orthogonal KV-MV image pair is a new method to correct the prostate movement in the middle of the beam delivery if real time tracking method is not available. Orthogonal KV-MV image pair doesn’t need gantry rotation. Images were acquired quickly which minimized possible new prostate movement. Therefore orthogonal KV-MV image pair is feasible for IGRT. Conclusion: Hypofractionated prostate treatment with less PTV margin always needs longer beam delivery time. Therefore prostate movement correction during the treatment delivery is critical. Orthogonal KV-MV imaging pair is efficient and accurate to correct the prostate movement during treatment beam delivery. Due to limited fraction number and high dose per fraction, the MV imaging dose is negligible.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

A three-dimensional model of terrain-induced updrafts for movement ecology studies

Abstract Background Spatially explicit simulation models of animal movements through the atmosphere necessarily require a representation of the spatial and temporal variation of atmospheric conditions. In particular, for movements of soaring birds that rely extensively on vertical updrafts to avoid flapping flight, accurate and reliable estimation of the vertical component of wind is critical. The interaction between wind and complex terrain shapes both the horizontal and vertical wind fields, highlighting the need to model the coupling between local terrain features and atmospheric conditions at scales relevant to animal movement. Methods In this work, we propose a new empirical model for estimating the orographic updraft field. The model is developed using computational fluid dynamics simulations of canonical atmospheric conditions over moderately complex terrain. To isolate buoyancy and thermal effects, and focus on terrain-induced effects, we use only simulations of a neutrally stratified atmosphere to develop the model. The model, which we name Engineering Vertical Velocity Estimator (EVVE), is simple to implement and is a function of the underlying terrain elevation map, the desired height above ground level (AGL), and wind conditions at a reference height (80 m). We validate the model with data from the Alaiz mountain (Spain) field campaign. Results Compared to observations, the proposed improved model estimates the updrafts at 120 m AGL with a mean error of 0.11 m/s ( $$\sigma =0.28$$ σ = 0.28 m/s), compared to 0.85 m/s ( $$\sigma =0.58$$ σ = 0.58 m/s) for its baseline. For typical land-based wind turbine hub heights of 80 m AGL, the proposed model has a mean error of 0.04 m/s ( $$\sigma =0.25$$ σ = 0.25 m/s), compared to baseline 0.54 m/s ( $$\sigma =0.45$$ σ = 0.45 m/s) estimations. We illustrate an application of the model in movement ecology by comparing simulated tracks and presence maps of golden eagles ( Aquila chrysaetos ) moving across two distinct landscapes. The tracks and presence maps are obtained using a simple heuristic-based movement model, with the updraft field given by the proposed model and a wind vector-based estimation approach that is currently in wide use in movement ecology studies of raptors and other soaring birds. Conclusions We highlight that movement model results can be sensitive to the underlying orographic updraft model, especially in studies of fine-scale movements in regions of complex topography. We suggest adopting the proposed model rather than the wind vector estimation method for studies of soaring bird movements.

17 WIND ENERGY↗