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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 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Modeling protein structures from predicted contacts with modern molecular dynamics potentials: accuracy, sensitivity, and refinement

Protein structure prediction has become increasingly popular and successful in recent years. An essential step for fragment-free, template-free methods is the generation of a final three-dimensional protein model from a set of predicted amino acid contacts that are often described by interresidue pairwise atomic distances. Here we explore the use of modern, open-source molecular dynamics (MD) engines, which have been continually developed over the last three decades with all-atom Hamiltonians to model biomolecular structure and dynamics, to generate accurate protein structures starting from a set of inferred pairwise distances. Additionally, the ability of MD empirical physical potentials to correct inaccuracies in the predicted geometries is tested. We rigorously characterize the effect of modeling parameters on results, the effect of different amounts of error in the predicted distances on the final structures, and test the ability of post-processing analysis to sort the best models out of a set of statistical replicas. We find that with exact distances and with noisy distances, the method can produce excellent structural models, and that the molecular dynamics force field seems to help correct errors in distance predictions, resisting the effects of applied noise.

Davidson, Russ↗
DOE OSTI2011

High‐Resolution Numerical Simulation and Analysis of Mach ReflectionStructures in Detonation Waves in Low‐Pressure H 2 –O 2 –Ar Mixtures: A Summary of Results Obtained with the Adaptive Mesh Refinement Framework AMROC

Numerical simulation can be key to the understanding of the multidimensional nature of transient detonation waves. However, the accurate approximation of realistic detonations is demanding as a wide range of scales needs to be resolved. This paper describes a successful solution strategy that utilizes logically rectangular dynamically adaptive meshes. The hydrodynamic transport scheme and the treatment of the nonequilibrium reaction terms are sketched. A ghost fluid approach is integrated into the method to allow for embedded geometrically complex boundaries. Large‐scale parallel simulations of unstable detonation structures of Chapman‐Jouguet detonations in low‐pressure hydrogen‐oxygen‐argon mixtures demonstrate the efficiency of the described techniques in practice. In particular, computations of regular cellular structures in two and three space dimensions and their development under transient conditions, that is, under diffraction and for propagation through bends are presented. Some of the observed patterns are classified by shock polar analysis, and a diagram of the transition boundaries between possible Mach reflection structures is constructed.

Deiterding, Ralf↗
DOE OSTI2019

Refined Lithostratigraphy of Upper and Middle Devonian Shales in West Virginia

The evolution of the formal lithostratigraphy for the Middle and Upper Devonian strata in the central Appalachian Basin has been complex. The original terminology (Chemung, Portage, Marcellus, Catskill, and others) was assigned in the latter 19th century. However, by the 1930s, the realization that these units changed in nature dramatically when traced laterally resulted in a crisis in stratigraphy that forced the differentiation of chronostratigraphy from lithostratigraphy. Further, the sheer size of the basin creates challenges, as stratigraphic terminology defined by examination along the outcrop belts at the basin margins is difficult to extend into the subsurface due to the distances involved, the different nature of outcrop and subsurface data, the different perspective of workers attempting to extend units either from the north and west or from the east, and the complex facies changes within the strata. As a result, the facies architecture and associated lithostratigraphic nomenclature for many Middle and Upper Devonian units remained unsettled, particularly in the basin center.

Boswell, Ray↗
DOE OSTI2012

Continuous Dynamic Grid Adaptation In A Global Atmospheric Model: Application And Refinement (Scientific Final Report)

This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the 'physics' of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer-reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2012

Collaborative Research: Continuous Dynamic Grid Adaptation in a Global Atmospheric Model: Application and Refinement [Scientific Final Report]

This project had goals of advancing the performance capabilities of the numerical general circulation model EULAG and using it to produce a fully operational atmospheric global climate model (AGCM) that can employ either static or dynamic grid stretching for targeted phenomena. The resulting AGCM combined EULAG's advanced dynamics core with the physics of the NCAR Community Atmospheric Model (CAM). Effort discussed below shows how we improved model performance and tested both EULAG and the coupled CAM-EULAG in several ways to demonstrate the grid stretching and ability to simulate very well a wide range of scales, that is, multi-scale capability. We leveraged our effort through interaction with an international EULAG community that has collectively developed new features and applications of EULAG, which we exploited for our own work summarized here. Overall, the work contributed to over 40 peer- reviewed publications and over 70 conference/workshop/seminar presentations, many of them invited.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

Streamlining and Refining FEDS Loads Models (Final Report)

The Facility Energy Decision System (FEDS) software is a powerful buildings energy analysis tool developed by Battelle at the Pacific Northwest National Laboratory with support from numerous organizations including several within the U.S. Department of Energy (DOE) and U.S. Department of Defense (DoD). FEDS is used extensively throughout the federal sector to examine building energy efficiency potential and recommend energy saving retrofit projects. The focus of this CRADA was to update the foundation of the FEDS loads models, to improve the core functionality and calculation methods and position the building efficiency analysis software for continued growth. The broader intent was to increase FEDS utility and user satisfaction via improving modeling accuracy, facilitating development and making possible a wide range of new and desired capability enhancements. This report provides an summary of the various tasks performed under the CRADA.

Dahowski, Robert T.↗
DOE OSTI2011

Nanostructure Determination by Co-Refining Models to Multiple Datasets

The results of the work are contained in the publications resulting from the grant (which are listed below). Here I summarize the main findings from the last period of the award, 2006-2007: • Published a paper in Science with Igor Levin outlining the “Nanostructure Problem”, our inability to solve structure at the nanoscale. • Published a paper in Nature demonstrating the first ever ab-initio structure determination of a nanoparticle from atomic pair distribution function (PDF) data. • Published one book and 3 overview articles on PDF methods and the nanostructure problem. • Completed a project that sought to find a structural response to the presence of the so-called “intermediate phase” in network glasses which appears close to the rigidity percolation threshold in these systems. The main result was that we did not see convincing evidence for this, which drew into doubt the idea that Ge x Se 1-x glasses were a model system exhibiting rigidity percolation.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Chemical composition analysis and product consistency tests supporting refinement of the Nepheline model for the high aluminum Hanford Glass composition region

In this report, SRNL provides chemical analyses and Product Consistency Test (PCT) results for a series of simulated HLW glasses fabricated by Pacific Northwest National Laboratory (PNNL) as part of an ongoing nepheline crystallization study. The results of these analyses will be used to improve the ability to predict crystallization of nepheline as a function of composition and heat treatment for glasses formulated at high alumina concentrations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2016

Chemical composition analysis and product consistency tests supporting refinement of the Nepheline Model for the high aluminum Hanford glass composition region

In this report, Savannah River National Laboratory provides chemical analyses and Product Consistency Test (PCT) results for a series of simulated high level waste (HLW) glasses fabricated by Pacific Northwest National Laboratory (PNNL) as part of an ongoing nepheline crystallization study. The results of these analyses will be used to improve the ability to predict crystallization of nepheline as a function of composition and heat treatment for glasses formulated at high alumina concentrations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗