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At least 217 records · Page 12

The LLNL nuclear data infrastructure for the GNDS data format

The next generation of nuclear data infrastructure tools at the Livermore National Laboratory (LLNL) consists of pipeline of codes that read and process nuclear data from evaluated files saved in the new GNDS (Generalised Nuclear Data Structure) nuclear data format. The processing code FUDGE (For Updating Data and Generating Evaluations) is at the front-end of this pipeline as it reads and process the evaluated data for use in downstream transport codes. FUDGE is Python based with C and C++ extensions for computationally intensive tasks. As is the case for the evaluated data, the processed output is also saved in the GNDS format and the GIDI+ API is provided as the interface between the processed data and the transport codes. GIDI+ is a C++ based suite of codes and it includes GIDI (General Interaction Data Interface), a library for reading and writing GNDS data, and MCGIDI which is the cross section lookup, and reaction and product distribution sampling interface between Monte Carlo transport codes and the GNDS data. GIDI provides methods for easy access to the multi-group processed GNDS data and this is demonstrated through its implementation in ARDRA, the LLNL deterministic transport code. The evaluation and sampling methods in MCGIDI are available as both CPU and GPU methods which facilitates the use of MCGIDI in both traditional CPU-based as well as the next generation mixed model computational architectures. This is demonstrated through the GIDI+ implementation in MERCURY, the LLNL Monte Carlo transport code. (authors)

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗

Design of Unstructured Adaptive (UA) NAS Parallel Benchmark Featuring Irregular, Dynamic Memory Accesses

We describe the design of a new method for the measurement of the performance of modern computer systems when solving scientific problems featuring irregular, dynamic memory accesses. The method involves the solution of a stylized heat transfer problem on an unstructured, adaptive grid. A Spectral Element Method (SEM) with an adaptive, nonconforming mesh is selected to discretize the transport equation. The relatively high order of the SEM lowers the fraction of wall clock time spent on inter-processor communication, which eases the load balancing task and allows us to concentrate on the memory accesses. The benchmark is designed to be three-dimensional. Parallelization and load balance issues of a reference implementation will be described in detail in future reports.

Feng, Hui-Yu↗

Containerless Processing in Reduced Gravity Using the TEMPUS Facility

Containerless processing provides a high purity environment for the study of high-temperature, very reactive materials. It is an important method which provides access to the metastable state of an undercooled melt. In the absence of container walls, the nucleation rate is greatly reduced and undercooling up to (Tm-Tn)/Tm approx. 0.2 can be obtained, where Tm and Tn are the melting and nucleation temperatures, respectively. Electromagnetic levitation represents a method particularly well-suited for the study of metallic melts. The TEMPUS facility is a research instrument designed to perform electromagnetic levitation studies in reduced gravity. It provides temperatures up to 2600 C, levitation of several grams of material and access to the undercooled state for an extended period of time (up to hours).

Roger, Jan R.↗

Attacking the information access problem with expert systems

The results of applications research directed at finding an improved method of storing and accessing information are presented. Twelve microcomputer-based expert systems shells and five laser-optical formats have been studied, and the general and specific methods of interfacing these technologies are being tested in prototype systems. Shell features and interfacing capabilities are discussed, and results from the study of five laser-optical formats are recounted including the video laser, compact, and WORM disks, and laser cards and film. Interfacing, including laser disk device driver interfacing, is discussed and it is pointed out that in order to control the laser device from within the expert systems application, the expert systems shell must be able to access the device driver software. Potential integrated applications are investigated and an initial list is provided including consumer services, travel, law enforcement, human resources, marketing, and education and training.

Ragusa, James M.↗

Case-Based Capture and Reuse of Aerospace Design Rationale

The goal of this project was to apply artificial intelligence techniques to facilitate capture and reuse of aerospace design rationale. The project combined case-based reasoning (CBR) and concept maps (CMaps) to develop methods for capturing, organizing, and interactively accessing records of experiences encapsulating the methods and rationale underlying expert aerospace design, in order to bring the captured knowledge to bear to support future reasoning. The project's results contribute both principles and methods for effective design-aiding systems that aid capture and access of useful design knowledge. The project has been guided by the tenets that design-aiding systems must: (1) Leverage a designer's knowledge, rather than attempting to replace it; (2) Be able to reflect different designers' differing conceptualizations of the design task, and to clarify those conceptualizations to others; (3) Include capabilities to capture information both by interactive knowledge modeling and during normal use; and (4) Integrate into normal designer tasks as naturally and unobtrusive as possible.

Leake, David B.↗

Thermophysical Property Measurement and Materials Research in the NASA/MSFC Electrostatic Levitator

Containerless processing is an important tool for thermophysical property measurements and materials research. The freedom from a crucible allows processing of liquid materials in a metastable undercooled state, as well as allowing processing of high temperature and highly reactive melts. Electrostatic levitation (ESL) is a containerless method which provides a number of unique advantages, including the decoupling of positioning force from sample heating, the ability to operate in ultra-high vacuum or at moderate gas pressure (approximately 3 atm), and the ability to process non-conducting materials. ESL also has the potential to reduce internal flow velocities below those possible with electromagnetic, acoustic, or aero-acoustic techniques. The ESL facility at NASA's Marshall Space Flight Center (MSFC) is in use for thermophysical property measurements and materials research by a number of different internal and external investigators. The methods for obtaining access to the facility, as well as a summary of current capabilities and some future directions will be discussed. In electrostatic levitation, the acceleration of gravity (or residual acceleration in reduced gravity) is opposed by the action of an applied electric field on a charged sample. This positioning method is applicable to any material which can be electrically charged, whether solid or liquid, conducting, or insulating. Because the position of the sample is unstable, a 3-dimensional active control loop rapidly adjusts the applied field to maintain levitation and minimize motion of the sample. Heating lasers melt the sample, and may be adjusted to maintain specified thermal profiles. Microgravity allows electrostatic levitation to work even more effectively. With the need to cancel less than 1 milli-g, the applied field required is reduced from approximately 10 MV/m to approximately 10 kV/m. Alternatively, a microgravity ESL can position larger samples than is possible on the ground, or it can position samples which maintain their charge poorly. Microgravity also reduces the effects of buoyant convection and sedimentation. In the MSFC ESL, many different classes of experiments and measurements have been demonstrated in collaboration with many investigators. These capabilities include heat capacity measurement, phase diagram determination, and nucleation and growth experiments including nucleation rate, TTT curves, and phase selection. We have demonstrated the capability of triggering recalescence of an undercooled liquid sample without loss of levitation. Currently under development are techniques for measuring the surface tension, viscosity, and density of levitated samples, as well as other thermophysical properties. Expanded levitation capabilities including various gas environments for sample processing, sample rotation control and management of thermal gradients are under development for the MSFC ESL. Containerless processing allows research on materials which may not be processed any other way. Electrostatic levitation extends the range of containerless processing to include many materials and classes of materials which cannot be processed by conventional electromagnetic, acoustic, or aerodynamic levitation techniques.

Rogers, Jan↗

Containerless Processing in Reduced Gravity Using the TEMPUS Facility during MSL-1 and MSL-1R

Containerless processing provides a high purity environment for the study of high-temperature, very reactive materials. It is an important method which provides access to the metastable state of an undercooled melt. In the absence of container walls, the nucleation rate is greatly reduced and undercooling up to (Tm-Tn)/Tm approx. equal to 0.2 can be obtained, where Tm and Tn are the melting and nucleation temperatures, respectively. Electromagnetic levitation represents a method particularly well-suited for the study of metallic melts. The TEMPUS (Tiegelfreies ElektroMagnetisches Prozessieren Unter Schwerelosgkeit) facility is a research instrument designed to perform electromagnetic levitation studies in reduced gravity. TEMPUS is a joint undertaking between DARA, the German Space Agency, and the Microgravity Science and Applications Division of NASA. The George C. Marshall Space Flight Center provides the leadership for scientific and management efforts which support the four US PI teams which performed experiments in the TEMPUS facility. The facility is sensitive to accelerations in the 1-10 Hz range. This became evident during the MSL-1 mission. Analysis of accelerometer and video data indicated that loss of sample control occurred during crew exercise periods which created disturbances in this frequency range. Prior to the MSL-1R flight the TEMPUS team, the accelerometer support groups and the mission operations team developed a strategy to provide for the operation of the facility without such disturbances. The successful implementation of this plan led to the highly successful operation of this facility during MSL-1R.

Rogers, Jan R.↗

LinkWinds: An Approach to Visual Data Analysis

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration and analysis system resulting from a NASA/JPL program of research into graphical methods for rapidly accessing, displaying and analyzing large multivariate multidisciplinary datasets. It is an integrated multi-application execution environment allowing the dynamic interconnection of multiple windows containing visual displays and/or controls through a data-linking paradigm. This paradigm, which results in a system much like a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but provides a highly intuitive, easy to learn user interface on top of the traditional graphical user interface.

Jacobson, Allan S.↗

Link Winds: A visual data analysis system and its application to the atmospheric ozone depletion problem

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration system resulting from a NASA Jet Propulsion Laboratory (JPL) program of research into the application of graphical methods for rapidly accessing, displaying, and analyzing large multi variate multidisciplinary data sets. Running under UNIX it is an integrated multi-application executing environment using a data-linking paradigm to dynamically interconnect and control multiple windows containing a variety of displays and manipulators. This paradigm, resulting in a system similar to a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but leads to a highly intuitive, easy-to-learn user interface. It provides great flexibility in rapidly interacting with large masses of complex data to detect trends, correlations, and anomalies. The system, containing an expanding suite of non-domain-specific applications, provides for the ingestion of a variety of data base formats and hard -copy output of all displays. Remote networked workstations running LinkWinds may be interconnected, providing a multiuser science environment (MUSE) for collaborative data exploration by a distributed science team. The system is being developed in close collaboration with investigators in a variety of science disciplines using both archived and real-time data. It is currently being used to support the Microwave Limb Sounder (MLS) in orbit aboard the Upper Atmosphere Research Satellite (UARS). This paper describes the application of LinkWinds to this data to rapidly detect features, such as the ozone hole configuration, and to analyze correlations between chemical constituents of the atmosphere.

Jacobson, Allan S.↗

Calculating Charge Transport in Semiconductors

Method, called flux method, improvement over conventional methods, easy to use, and applies in operating regime not accessible to conventional macroscopic methods. Key concept of flux method follows behavior of particle flux rather than concentration of particles. Method not subject to limitations that follow from local or infinitesimal analysis.

Byvik, C. E.↗

Clean assembly and integration techniques for the Hubble Space Telescope High Fidelity Mechanical Simulator

A mechanical simulator of the Hubble Space Telescope (HST) Aft Shroud was built to perform verification testing of the Servicing Mission Scientific Instruments (SI's) and to provide a facility for astronaut training. All assembly, integration, and test activities occurred under the guidance of a contamination control plan, and all work was reviewed by a contamination engineer prior to implementation. An integrated approach was followed in which materials selection, manufacturing, assembly, subsystem integration, and end product use were considered and controlled to ensure that the use of the High Fidelity Mechanical Simulator (HFMS) as a verification tool would not contaminate mission critical hardware. Surfaces were cleaned throughout manufacturing, assembly, and integration, and reverification was performed following major activities. Direct surface sampling was the preferred method of verification, but access and material constraints led to the use of indirect methods as well. Although surface geometries and coatings often made contamination verification difficult, final contamination sampling and monitoring demonstrated the ability to maintain a class M5.5 environment with surface levels less than 400B inside the HFMS.

Hughes, David W.↗

An upper bound for codes in a two-access binary erasure channel

A method for determining an upper bound for the size of a code for a two-access binary erasure channel is presented. For uniquely decodable codes, this bound gives a combinatorial proof of a result by Liao. Examples of the bound are given for codes with minimum distance 4.

Van Tilborg, H. C. A.↗

A non‐intrusive domain‐decomposition model reduction method for linear steady‐state partial differential equations with random coefficients

Abstract Domain decomposition methods have been proved to be an effective strategy to reduce the dimension of parametric partial differential equations (PDEs). However, existing domain decomposition methods for parametric PDEs are usually intrusive, which means domain decomposition based solvers need to be implemented from scratch for each target parametric PDE. To address this issue, we develop a new non‐intrusive domain‐decomposition model reduction method for linear steady‐state PDEs with random‐field coefficients. As a variant of our previous work by Mu and Zhang, the new method only needs access to the final linear system, that is, the global stiffness matrix and the right hand side, of a deterministic PDE solver, in order to build a domain‐decomposition‐based reduced model without intrusive implementation from scratch. The key idea is to remove the interface condition between sub‐domains and rely on the correlation between columns of the linear system to couple the sub‐domains. The non‐intrusive feature enables the applicability of the proposed method to a broader class of uncertainty quantification problems, where many legacy codes/solvers can be fully reused by our method. Two numerical examples including diffusion equations with random diffusivity and convection‐dominated transport with random velocity, are provided to demonstrate the effectiveness and efficiency of our method.

Zhang, Guannan↗

Advanced imaging of the macrostructure and microstructure of bone

Noninvasive and/or nondestructive techniques are capable of providing more macro- or microstructural information about bone than standard bone densitometry. Although the latter provides important information about osteoporotic fracture risk, numerous studies indicate that bone strength is only partially explained by bone mineral density. Quantitative assessment of macro- and microstructural features may improve our ability to estimate bone strength. The methods available for quantitatively assessing macrostructure include (besides conventional radiographs) quantitative computed tomography (QCT) and volumetric quantitative computed tomography (vQCT). Methods for assessing microstructure of trabecular bone noninvasively and/or nondestructively include high-resolution computed tomography (hrCT), micro-computed tomography (muCT), high-resolution magnetic resonance (hrMR), and micromagnetic resonance (muMR). vQCT, hrCT and hrMR are generally applicable in vivo; muCT and muMR are principally applicable in vitro. Although considerable progress has been made in the noninvasive and/or nondestructive imaging of the macro- and microstructure of bone, considerable challenges and dilemmas remain. From a technical perspective, the balance between spatial resolution versus sampling size, or between signal-to-noise versus radiation dose or acquisition time, needs further consideration, as do the trade-offs between the complexity and expense of equipment and the availability and accessibility of the methods. The relative merits of in vitro imaging and its ultrahigh resolution but invasiveness versus those of in vivo imaging and its modest resolution but noninvasiveness also deserve careful attention. From a clinical perspective, the challenges for bone imaging include balancing the relative advantages of simple bone densitometry against the more complex architectural features of bone or, similarly, the deeper research requirements against the broader clinical needs. The considerable potential biological differences between the peripheral appendicular skeleton and the central axial skeleton have to be addressed further. Finally, the relative merits of these sophisticated imaging techniques have to be weighed with respect to their applications as diagnostic procedures requiring high accuracy or reliability on one hand and their monitoring applications requiring high precision or reproducibility on the other. Copyright 2000 S. Karger AG, Basel.

NASA Discipline Musculoskeletal↗

Probabilistic Path Planning of Montgolfier Balloons in Strong, Uncertain Wind Fields

Lighter-than-air vehicles such as hot-air balloons have been proposed for exploring Saturn s moon Titan, as well as other bodies with significant atmospheres. For these vehicles to navigate effectively, it is critical to incorporate the effects of surrounding wind fields, especially as these winds will likely be strong relative to the control authority of the vehicle. Predictive models of these wind fields are available, and previous research has considered problems of planning paths subject to these predicted forces. However, such previous work has considered the wind fields as known a priori, whereas in practical applications, the actual wind vector field is not known exactly and may deviate significantly from the wind velocities estimated by the model. A probabilistic 3D path-planning algorithm was developed for balloons to use uncertain wind models to generate time-efficient paths. The nominal goal of the algorithm is to determine what altitude and what horizontal actuation, if any is available on the vehicle, to use to reach a particular goal location in the least expected time, utilizing advantageous winds. The solution also enables one to quickly evaluate the expected time-to-goal from any other location and to avoid regions of large uncertainty. This method is designed for balloons in wind fields but may be generalized for any buoyant vehicle operating in a vector field. To prepare the planning problem, the uncertainty in the wind field is modeled. Then, the problem of reaching a particular goal location is formulated as a Markov decision process (MDP) using a discretized space approach. Solving the MDP provides a policy of what actuation option (how much buoyancy change and, if applicable, horizontal actuation) should be selected at any given location to minimize the expected time-to-goal. The results provide expected time-to-goal values from any given location on the globe in addition to the action policy. This stochastic approach can also provide insights not accessible by deterministic methods; for example, one can evaluate variability and risk associated with different scenarios, rather than only viewing the expected outcome.

Wolf, Michael↗

Say where you sample: Increasing site selection transparency in urban ecology

Urban ecological studies have the potential to extend our understanding of socio-ecological systems beyond that of an individual city or region. Cross-comparative empirical work and synthesis are imperative to develop a general urban ecological theory. This can be achieved only if studies are replicable and generalizable. Transparency in methods reporting facilitates generalizability and replicability by documenting the decisions scientists make during the various steps of research design; this is particularly true for sampling design and selection because of their impact on both internal and external validity and the potential to unintentionally introduce bias. Three interdependent aspects of sample design are study sample selection (e.g., specific organisms, soils, or water), sample specification (measurement of specific variable of interest), and site selection (locations sampled). Of these, documentation of site selection—the where component of sample design—is underrepresented in the urban ecology literature. Using a stratified random sample of 158 papers from 12 major urban ecology journals, we investigated how researchers selected study sites in urban ecosystems and evaluated whether their site selection methods were transparent. We extracted data from these papers using a 50-question, theory-based questionnaire and a multiple-reviewer approach. Our sample represented almost 45 years of urban ecology research across 40 different countries. We found that more than 80% of the papers read were not transparent in their site selection methodology. We do not believe site selection methods are replicable for 70% of the papers read. Key weaknesses include incomplete descriptions of populations and sampling frames, urban gradients, sample selection methods, and property access. Low transparency in reporting the where methodology limits urban ecologists’ ability to assess the internal and external validity of studies’ findings and to replicate published studies; it also limits the generalizability of existing studies. The challenges of low transparency are particularly relevant in urban ecology, a field where standard protocols for site selection and delineation are still being developed. These limitations interfere with the fields’ ability to build theory and inform policy. We conclude by offering a set of recommendations to increase transparency, replicability, and generalizability.

54 ENVIRONMENTAL SCIENCES↗