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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Proximity Portability and in Transit , M-to-N Data Partitioning and Movement in SENSEI [Book Chapter]

In high-performance parallel in situ processing, the term in transit processing refers to those configurations where data must move from a producer to a consumer that runs on separate resources. In the context of parallel and distributed computing on an HPC platform one of the central challenges is to determine a mapping of data from producer ranks to consumer ranks. This problem is complicated by the heterogeneity that arises in producer-consumer pairs, such as when producer and consumer codes have different levels of concurrency, different scaling characteristics, or different data models. The resulting mapping and movement of data from M producer to N consumer ranks can have a significant impact on aggregate application performance, particularly when the data consumer requires only a subset of the overall data for its task. This chapter focuses on the design considerations that underlie SENSEI’s implementation to this challenging problem. These design considerations extend the core SENSEI architecture and include ideas like the need to accommodate flexibility in the choice of different partitioning methods, the ability for a data consumer to request and receive only the subset of data needed for its particular operation, and the ability to leverage any of several different data transport tools. The idea of proximity portability, being able to use different data transport methods as part of an in transit workflow, is illustrated through the use of three different transport layers where switching from one transport tool to another is accomplished with only a configuration file change. Here, the chapter also includes a performance analysis summary showing the performance gains that are possible in terms of multiple metrics, such as memory footprint, time to solution, and amount of data moved, when using optimized partitioners in an in transit setting, gains that are made possible by the implementation shaped by specific design considerations.

Bethel, E. Wes↗
DOE OSTI2018

Movement, competition and pattern formation in a two prey–one predator food chain model

The complexity of interactions among species remains a captivating phenomenon in the ecology. In this paper, a food chain model characterized by two prey and one predator is analyzed. Unlike previous approaches, our analysis incorporates the velocity of the animals movement into the system, as well as rivalries between prey. We establish a condition for the coexistence of all populations which underscores the importance of the animals’ velocities. Indeed, failing to consider the velocities increases the margin of error in the prediction process. We illustrate various patterns caused by the phenomenon of transport-driven instability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Deep subsurface drip irrigation using coal-bed sodic water: Part I. Water and solute movement

Water co-produced with coal-bed methane (CBM) in the semi-arid Powder River Basin of Wyoming and Montana commonly has relatively low salinity and high sodium adsorption ratios that can degrade soil permeability where used for irrigation. Nevertheless, a desire to derive beneficial use from the water and a need to dispose of large volumes of it have motivated the design of a deep subsurface drip irrigation (SDI) system capable of utilizing that water. Drip tubing is buried 92 cm deep and irrigates at a relatively constant rate year-round, while evapotranspiration by the alfalfa and grass crops grown is seasonal. We use field data from two sites and computer simulations of unsaturated flow to understand water and solute movements in the SDI fields. Combined irrigation and precipitation exceed potential evapotranspiration by 300–480 mm annually. Initially, excess water contributes to increased storage in the unsaturated zone, and then drainage causes cyclical rises in the water table beneath the fields. Native chloride and nitrate below 200 cm depth are leached by the drainage. Some CBM water moves upward from the drip tubing, drawn by drier conditions above. Chloride from CBM water accumulates there as root uptake removes the water. Year over year accumulations indicated by computer simulations illustrate that infiltration of precipitation water from the surface only partially leaches such accumulations away. Field data show that 7% and 27% of added chloride has accumulated above the drip tubing in an alfalfa and grass field, respectively, following 6 years of irrigation. Maximum chloride concentrations in the alfalfa field are around 45 cm depth but reach the surface in parts of the grass field, illustrating differences driven by crop physiology. Deep SDI offers a means of utilizing marginal quality irrigation waters and managing the accumulation of their associated solutes in the crop rooting zone.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

Vertical movement of soluble carbon and nutrients from biocrusts to subsurface mineral soils

Dryland ecosystems can be constrained by low soil fertility. Within drylands, the soil nutrient and organic carbon (C) cycling that does occur is often mediated by soil surface communities known as biological soil crusts (biocrusts), which cycle C and nutrients in the top ca. 0–2 cm of soil. However, the degree to which biocrusts are influencing soil fertility and biogeochemical cycling in deeper, subsurface mineral soils is unclear. The movement of dissolved resources from biocrusts to deeper soil layers in leachate may be one of the main mechanisms through which biocrust fertility is transferred downward towards deeper microbial communities and plant roots occurring within mineral soil. Here, in this study, we examined the role of biocrust leachate in contributing to subsurface nutrient and soluble C pools and subsurface microbial cycling. We collected biocrusts from three biocrust successional stages and explored resource pools in situ at multiple soil depths, while collecting leachate and measuring nutrient and organic C concentrations and metabolite composition from each successional stage in the laboratory. After four leachate collections, we conducted an incubation of mineral soil collected from below each biocrust successional stage to measure heterotrophic microbial CO 2 flux and biomass. Overall, our findings observed that the degree of nutrient and C connectivity between biocrusts and the sub-crust mineral soil depended on the biocrust successional stage and the element being considered, and the influence of biocrust successional stage on mineral soil CO 2 flux is likely related to long-term resource build up. Together, our results suggest that the influence of biocrust leachate on subsurface mineral soil is complex and context dependent, but, over longer time periods and at later successional stages, can have measurable effects on dryland soil biogeochemical cycling with feedbacks to resource availability and CO 2 flux.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

A downhole CO 2 sensor to monitor CO 2 movement in situ for geologic carbon storage

Here this paper describes how a downhole CO 2 chemical sensor was prepared for use in determining the concentration of CO 2 in water, particularly in harsh, high-pressure environments such as those found in geological formations considered for the geologic storage of CO 2 . The sensor consisted of a pair of Ir/IrO x and Ag/AgCl electrodes, a gas-permeable membrane, a bicarbonate-based internal electrolyte solution, and porous stainless steel as supporting material. The sensor was tested in the solution with different concentrations of CO 2 and displayed very good CO 2 sensing performance under pressures of 1000, 2000, and 3000 psi. A linear relationship between the sensor response potential and the logarithm of the CO 2 concentration was obtained for the sensor under different pressures. Reproducibility of the sensor was examined and the results indicated that the sensor displayed excellent reproducibility. CO 2 /brine core flooding tests were carried out to evaluate the performance of the CO 2 sensor in simulate CO 2 storage process. The results indicated that the sensor could detect CO 2 movement in the tests. Further studies showed that the sensor could be reused by brine flooding after CO 2 /brine flushed the core. The results of the core flooding tests demonstrated that the sensor had potential application for CO 2 monitoring in carbon storage.

25 ENERGY STORAGE↗
DOE OSTI2012

Robustness Against Interfraction Prostate Movement in Scanned Ion Beam Radiation Therapy

Purpose: To assess the robustness of scanned ion beam treatment plans against the interfraction internal target motion and evaluate the limits of validity of target-based isocenter realignment for prostate cancer radiation therapy. Methods and Materials: For 12 prostate patients, scanned beam carbon ion treatment plans were prepared using 2 lateral opposed beams and the raster scanning technique with different clinical target volume (CTV) to planning target volume (PTV) margins (2-10 mm). Internal target motion of 2-15 mm in anteroposterior (AP), superoinferior (SI), and left-to-right (LR) directions was simulated by displacing the CTV contours with respect to the computed tomography data. The plans were recalculated with and without target-based isocenter realignment and the CTV coverage was assessed. Results: For CTV shifts within the applied planning margin, the CI-98% is greater than 98.0%, both with and without isocenter realignment. Without realignment, because of the sharp lateral gradients, the CI-98% shows rapid fall as soon as the target shift exceeds the applied planning margin for all displacement directions. With isocenter realignment, the coverage improves notably for shifts in AP and SI directions and the CI-98% is restored to >95.0% for plans optimized with a 2-mm margin, >97% with a 3-mm margin, and >98% with larger margins. For large corrections, predominately in AP direction, cold spots in the CTV may occur. Their magnitude is dependent on the patients' individual anatomies. Conclusions: Within the physiological limits of internal prostate movement, target-based isocenter realignment results in improved CTV coverage for shifts in AP and SI directions exceeding the applied planning margin. Assuming optimal patient setup reproducibility (eg, immobilization, setup error correction, patient preparation protocols), hence negligible interfraction bone and soft-tissue variations, changes in traversed densities resulting from target-based realignment applied with a reduced planning margin do not induce significant dose deterioration in most of the cases.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Temporal coarse-graining method to simulate the movement of atoms

We propose a novel method to simulate the movement of atoms at finite temperature. The main idea of our method is to derive “renormalized,” or coarse-grained in time, dynamics from the Euler–Maruyama scheme, which is the standard method for solving the stochastic differential equations numerically. Based on this renormalization, we propose a new algorithm for solving overdamped Langevin equations. We test our renormalization scheme on two models and demonstrate that the results obtained by this method are consistent with those obtained by the standard method. Our algorithm performs better than the standard scheme, especially at low temperatures and with multiple processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

A large-scale, agent-based simulation of metropolitan freight movements with passenger and freight market interactions

This study summarizes the first stage in the implementation of an agent-based freight modeling system that has a global representation of agents and detailed modeling of a large-scale transportation network. The model is used to evaluate the transportation and energy impacts of goods movement across urban and national scales. The framework is implemented within POLARIS, a C++-based Planning and Operations Language for Agent-based Regional Integrated Simulation, which consists of an activity-based modeling (ABM) and dynamic traffic assignment (DTA) system that has robust features for passenger travel. This platform provides a tool to model interactions among consumers, producers, and the transportation system. The main objective of this initial implementation is to implement a freight model within POLARIS following an agent-based paradigm with behavioral and simulation methods. This paper presents the initial framework and illustrates the application of the model. Building upon earlier works, a parcel location assignment algorithm for business establishments in the population is documented, along with a method for estimating establishment production and consumption volumes. In addition to population generation, other features of the model include push-pull supply chains, multimodal path choice, choice of transportation logistics node, and dynamic traffic assignment. A module with e-commerce supply and demand was also developed to analyze the effects of e-commerce delivery on last-mile energy use and congestion.

agent-based freight↗
DOE OSTI2017

Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase

The key mevalonate pathway enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR) uses the cofactor NAD(P)H to reduce HMG-CoA to mevalonate in the production of countless metabolites and natural products. Although inhibition of HMGR by statin drugs is well-understood, several mechanistic details of HMGR catalysis remain unresolved, and the structural basis for the wide range of cofactor specificity for either NADH or NADPH among HMGRs from different organisms is also unknown. Here, we present crystal structures of HMGR from Streptococcus pneumoniae (SpHMGR) alongside kinetic data of the enzyme’s cofactor preferences. Furthermore, our structure of SpHMGR bound with its kinetically preferred NADPH cofactor suggests how NADPH-specific binding and recognition are achieved. In addition, our structure of HMG-CoA-bound SpHMGR reveals large, previously unknown conformational domain movements that may control HMGR substrate binding and enable cofactor exchange without intermediate release during the catalytic cycle. Taken together, this work provides critical new insights into both the HMGR reaction mechanism and the structural basis of cofactor specificity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement

Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Spontaneous pairing and cooperative movements of micro-particles in a two dimensional plasma crystal

In an argon plasma of 20 W rf discharge at a pressure of 1.38 Pa, a stable highly ordered monolayer of microparticles is suspended. We observe spontaneous particle pairing when suddenly reducing the gas pressure. Special types of dynamical activity, in particular, entanglement and cooperative movements of coupled particles have been registered. In the course of the experiment first appeared single vertical pairs of particles, in further they gradually accumulated causing melting of the entire crystal. To record pairing events, the particle suspension is side-view imaged using a vertically extended laser sheet. The long-lasting pre-melting phase assured the credible recording and identification of isolated particle pairs. The high monolayer charge density is crucial to explain the spontaneous pairing events observed in our experiments as the mutual repulsion between the particles comprising the monolayer make its vertical extend thicker.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2015

Exploring the stochastic dynamics of correlated movement of receptor proteins in plasma membranes in vivo

Ligand-induced receptor dimerization plays a crucial role in the signaling process of living cells. In this study, we developed a theoretical model and performed single-molecule tracking to explore the correlated diffusion processes of liganded epidermal growth factor receptors prior to dimer formation. We disclosed that both an attractive potential between liganded receptor proteins in proximity and correlated fluctuations in the local environments of the proteins play an important role to produce the observed correlated movement of the receptors. This result can serve as the foundation to shed light on the way in which receptor functions are regulated in plasma membranes in vivo.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Ion movement in thin Nafion films under an applied electric field

In this study, the electromechanical response of Nafion films with and without an ionic liquid (1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide) ([emim]Tf 2 N) additive were characterized under an applied electric field in situ using neutron reflectometry (NR) and voltage modulated atomic force microscopy (VM-AFM). NR showed that pure Nafion films exhibited no response under field strengths of ~0.18 V/μm, while VM-AFM measurements showed a minimal response at higher field strengths (~200 V/μm), which is ascribed to the residual water presence in the films. The addition of ionic liquid resulted in clear electroresponsiveness seen in both NR and VM-AFM. NR results indicated mass migration away from the cathodic interface driven by the [emim] + movement in the direction of the electric field. The lack of ionic liquid accumulation at the electrode interfaces contrasts the bulk electromechanical behavior of similar systems reported in the literature. VM-AFM measurements were able to resolve the relative contributions of the [emim] + cation and Tf 2 N - anion to film deformation by alternating the direction of the applied field and support the [emim] + dominant migration seen in the NR results. Lastly, the findings presented here emphasize the need for the nanoscale analysis of material properties of electroresponsive thin film systems and demonstrate the potential for probing electric field effects using in situ techniques.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Movement and collision of Lagrangian particles in hydro-turbine intakes: a case study

Studies of the stress/survival of migratory fish during downstream passage through operating hydro-turbines are normally conducted to determine the fish-friendliness of units. One field approach consisting of recording extreme hydraulics with autonomous sensors is largely sensitive to the conditions of sensor release and the initial trajectories at the turbine intake. This study applies a modelling strategy based on flow simulations using computational fluid dynamics and Lagrangian particle tracking to represent the travel of live fish and autonomous sensor devices through hydro-turbine intakes. For the flow field calculation, the simulations were conducted with both a time-averaging turbulence model and an eddy-resolving technique. For the particle tracking calculation, different modelling assumptions for turbulence forcing, mass formulation, buoyancy, and release condition were tested. The modelling assumptions are evaluated with respect to data sets collected using a laboratory physical model and an autonomous sensor device deployed at Ice Harbor Dam (Snake River, State of Washington, U.S.A.) at the same discharge and release point as in the present computer simulations. We found an acceptable agreement between the simulated results and observed data and discuss relevant features of Lagrangian particle movement that are critical in turbine design and in the experimental design of field studies.

CFD↗
DOE OSTI2019

Spatial changes in trace element and strontium isotope water chemistry in a temperate river system with application to sturgeon movement

Understanding patterns in trace element concentrations and water quality within river systems provides a foundation to evaluate retrospective movements and habitat use of fish. Because trace elements are incorporated into calcified structures of fishes relative to water concentrations, baseline maps have application for fisheries management, including for rare species such as sturgeons. Therefore, trace elements [strontium (Sr), barium (Ba), manganese (Mn), zinc (Zn), and magnesium (Mg)], strontium isotopes ( 87 Sr/ 86 Sr), dissolved oxygen and salinity were measured in the Pearl River and Lake Pontchartrain watersheds, within Mississippi and Louisiana, USA for application in assessing riverine use by Gulf Sturgeon Acipenser oxyrinchus desotoi. Water samples were collected during the summer-fall period when juvenile Gulf Sturgeon were anticipated to be present and analyzed by solution and multi-collector inductively coupled plasma mass spectrometry. Trace element to calcium (Ca) ratios in Sr, Ba, Zn, and Mg were distinguishable between the upper Pearl River and the Bogue Chitto River tributary, and the upper Pearl River and lower Pearl River. For most trace elements and 87 Sr/ 86 Sr, there was a gradual increase from upper river regions to lower river regions, and large differences between freshwater and saline areas. Lake Pontchartrain watershed rivers were not easily differentiated, but regions of low dissolved oxygen concentrations in the lower reaches suggest available Gulf Sturgeon habitat may be seasonally limited. Therefore, maps of water microchemistry in the Pearl River watershed allow for retrospective analyses of fish watershed use.

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

Cellulose synthase-like D movement in the plasma membrane requires enzymatic activity

Cellulose Synthase-Like D (CSLD) proteins, important for tip growth and cell division, are known to generate β-1,4-glucan. However, whether they are propelled in the membrane as the glucan chains they produce assemble into microfibrils is unknown. To address this, we endogenously tagged all eight CSLDs in Physcomitrium patens and discovered that they all localize to the apex of tip-growing cells and to the cell plate during cytokinesis. Actin is required to target CSLD to cell tips concomitant with cell expansion, but not to cell plates, which depend on actin and CSLD for structural support. Like Cellulose Synthase (CESA), CSLD requires catalytic activity to move in the plasma membrane. We discovered that CSLD moves significantly faster, with shorter duration and less linear trajectories than CESA. In contrast to CESA, CSLD movement was insensitive to the cellulose synthesis inhibitor isoxaben, suggesting that CSLD and CESA function within different complexes possibly producing structurally distinct cellulose microfibrils.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Virtual machine provisioning, code management, and data movement design for the Fermilab HEPCloud Facility

The Fermilab HEPCloud Facility Project has as its goal to extend the current Fermilab facility interface to provide transparent access to disparate resources including commercial and community clouds, grid federations, and HPC centers. This facility enables experiments to perform the full spectrum of computing tasks, including data-intensive simulation and reconstruction. We have evaluated the use of the commercial cloud to provide elasticity to respond to peaks of demand without overprovisioning local resources. Full scale data-intensive workflows have been successfully completed on Amazon Web Services for two High Energy Physics Experiments, CMS and NOνA, at the scale of 58000 simultaneous cores. This paper describes the significant improvements that were made to the virtual machine provisioning system, code caching system, and data movement system to accomplish this work. The virtual image provisioning and contextualization service was extended to multiple AWS regions, and to support experiment-specific data configurations. A prototype Decision Engine was written to determine the optimal availability zone and instance type to run on, minimizing cost and job interruptions. We have deployed a scalable on-demand caching service to deliver code and database information to jobs running on the commercial cloud. It uses the frontiersquid server and CERN VM File System (CVMFS) clients on EC2 instances and utilizes various services provided by AWS to build the infrastructure (stack). We discuss the architecture and load testing benchmarks on the squid servers. We also describe various approaches that were evaluated to transport experimental data to and from the cloud, and the optimal solutions that were used for the bulk of the data transport. Finally, we summarize lessons learned from this scale test, and our future plans to expand and improve the Fermilab HEP Cloud Facility.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5

Abstract Cells employ diverse strategies to repair double-strand breaks (DSBs), a dangerous form of DNA damage that threatens genome integrity. Eukaryotic nuclei consist of different chromatin environments, each displaying distinct molecular and biophysical properties that can significantly influence the DSB-repair process. DSBs arising in the compact and silenced heterochromatin domains have been found to move to the heterochromatin periphery in mouse and Drosophila to prevent aberrant recombination events. However, it is poorly understood how chromatin components, such as histone post-translational modifications, contribute to these DSB movements within heterochromatin. Using irradiation as well as locus-specific DSB induction in Drosophila tissues and cultured cells, we find enrichment of histone H3 lysine 9 acetylation (H3K9ac) at DSBs in heterochromatin but not euchromatin. We find this increase is mediated by the histone acetyltransferase dGcn5, which rapidly localizes to heterochromatic DSBs. Moreover, we demonstrate that in the absence of dGcn5, heterochromatic DSBs display impaired recruitment of the SUMO E3 ligase Nse2/Qjt and fail to relocate to the heterochromatin periphery to complete repair. In summary, our results reveal a previously unidentified role for dGcn5 and H3K9ac in heterochromatic DSB repair and underscore the importance of differential chromatin responses at heterochromatic and euchromatic DSBs to promote safe repair.

Biochemistry & Molecular Biology↗