16th International Conference on Nuclear Structure: NS2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galindo-Uribarri, Alfredo

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

16th International Conference on Nuclear Structure: NS2016

DOE PAGES

Galindo-Uribarri, Alfredo

2016-10-28

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

PubMed

Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

2010-12-08

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

Computer Security for Commercial Nuclear Power Plants - Literature Review for Korea Hydro Nuclear Power Central Research Institute

DOE Office of Scientific and Technical Information (OSTI.GOV)

Duran, Felicia Angelica; Waymire, Russell L.

2013-10-01

Sandia National Laboratories (SNL) is providing training and consultation activities on security planning and design for the Korea Hydro and Nuclear Power Central Research Institute (KHNPCRI). As part of this effort, SNL performed a literature review on computer security requirements, guidance and best practices that are applicable to an advanced nuclear power plant. This report documents the review of reports generated by SNL and other organizations [U.S. Nuclear Regulatory Commission, Nuclear Energy Institute, and International Atomic Energy Agency] related to protection of information technology resources, primarily digital controls and computer resources and their data networks. Copies of the key documentsmore » have also been provided to KHNP-CRI.« less

New Features in the Computational Infrastructure for Nuclear Astrophysics

NASA Astrophysics Data System (ADS)

Smith, M. S.; Lingerfelt, E. J.; Scott, J. P.; Hix, W. R.; Nesaraja, C. D.; Koura, H.; Roberts, L. F.

2006-04-01

The Computational Infrastructure for Nuclear Astrophysics is a suite of computer codes online at nucastrodata.org that streamlines the incorporation of recent nuclear physics results into astrophysical simulations. The freely-available, cross- platform suite enables users to upload cross sections and s-factors, convert them into reaction rates, parameterize the rates, store the rates in customizable libraries, setup and run custom post-processing element synthesis calculations, and visualize the results. New features include the ability for users to comment on rates or libraries using an email-type interface, a nuclear mass model evaluator, enhanced techniques for rate parameterization, better treatment of rate inverses, and creation and exporting of custom animations of simulation results. We also have online animations of r- process, rp-process, and neutrino-p process element synthesis occurring in stellar explosions.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Infinite possibilities: Computational structures technology

NASA Astrophysics Data System (ADS)

Beam, Sherilee F.

1994-12-01

Computational Fluid Dynamics (or CFD) methods are very familiar to the research community. Even the general public has had some exposure to CFD images, primarily through the news media. However, very little attention has been paid to CST--Computational Structures Technology. Yet, no important design can be completed without it. During the first half of this century, researchers only dreamed of designing and building structures on a computer. Today their dreams have become practical realities as computational methods are used in all phases of design, fabrication and testing of engineering systems. Increasingly complex structures can now be built in even shorter periods of time. Over the past four decades, computer technology has been developing, and early finite element methods have grown from small in-house programs to numerous commercial software programs. When coupled with advanced computing systems, they help engineers make dramatic leaps in designing and testing concepts. The goals of CST include: predicting how a structure will behave under actual operating conditions; designing and complementing other experiments conducted on a structure; investigating microstructural damage or chaotic, unpredictable behavior; helping material developers in improving material systems; and being a useful tool in design systems optimization and sensitivity techniques. Applying CST to a structure problem requires five steps: (1) observe the specific problem; (2) develop a computational model for numerical simulation; (3) develop and assemble software and hardware for running the codes; (4) post-process and interpret the results; and (5) use the model to analyze and design the actual structure. Researchers in both industry and academia continue to make significant contributions to advance this technology with improvements in software, collaborative computing environments and supercomputing systems. As these environments and systems evolve, computational structures technology will

Infinite possibilities: Computational structures technology

NASA Technical Reports Server (NTRS)

Beam, Sherilee F.

1994-01-01

Computational Fluid Dynamics (or CFD) methods are very familiar to the research community. Even the general public has had some exposure to CFD images, primarily through the news media. However, very little attention has been paid to CST--Computational Structures Technology. Yet, no important design can be completed without it. During the first half of this century, researchers only dreamed of designing and building structures on a computer. Today their dreams have become practical realities as computational methods are used in all phases of design, fabrication and testing of engineering systems. Increasingly complex structures can now be built in even shorter periods of time. Over the past four decades, computer technology has been developing, and early finite element methods have grown from small in-house programs to numerous commercial software programs. When coupled with advanced computing systems, they help engineers make dramatic leaps in designing and testing concepts. The goals of CST include: predicting how a structure will behave under actual operating conditions; designing and complementing other experiments conducted on a structure; investigating microstructural damage or chaotic, unpredictable behavior; helping material developers in improving material systems; and being a useful tool in design systems optimization and sensitivity techniques. Applying CST to a structure problem requires five steps: (1) observe the specific problem; (2) develop a computational model for numerical simulation; (3) develop and assemble software and hardware for running the codes; (4) post-process and interpret the results; and (5) use the model to analyze and design the actual structure. Researchers in both industry and academia continue to make significant contributions to advance this technology with improvements in software, collaborative computing environments and supercomputing systems. As these environments and systems evolve, computational structures technology will

Advances and trends in computational structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1986-01-01

Recent developments in computational structural mechanics are reviewed with reference to computational needs for future structures technology, advances in computational models for material behavior, discrete element technology, assessment and control of numerical simulations of structural response, hybrid analysis, and techniques for large-scale optimization. Research areas in computational structural mechanics which have high potential for meeting future technological needs are identified. These include prediction and analysis of the failure of structural components made of new materials, development of computational strategies and solution methodologies for large-scale structural calculations, and assessment of reliability and adaptive improvement of response predictions.

Generalized Nuclear Data: A New Structure (with Supporting Infrastructure) for Handling Nuclear Data

NASA Astrophysics Data System (ADS)

Mattoon, C. M.; Beck, B. R.; Patel, N. R.; Summers, N. C.; Hedstrom, G. W.; Brown, D. A.

2012-12-01

The Evaluated Nuclear Data File (ENDF) format was designed in the 1960s to accommodate neutron reaction data to support nuclear engineering applications in power, national security and criticality safety. Over the years, the scope of the format has been extended to handle many other kinds of data including charged particle, decay, atomic, photo-nuclear and thermal neutron scattering. Although ENDF has wide acceptance and support for many data types, its limited support for correlated particle emission, limited numeric precision, and general lack of extensibility mean that the nuclear data community cannot take advantage of many emerging opportunities. More generally, the ENDF format provides an unfriendly environment that makes it difficult for new data evaluators and users to create and access nuclear data. The Cross Section Evaluation Working Group (CSEWG) has begun the design of a new Generalized Nuclear Data (or 'GND') structure, meant to replace older formats with a hierarchy that mirrors the underlying physics, and is aligned with modern coding and database practices. In support of this new structure, Lawrence Livermore National Laboratory (LLNL) has updated its nuclear data/reactions management package Fudge to handle GND structured nuclear data. Fudge provides tools for converting both the latest ENDF format (ENDF-6) and the LLNL Evaluated Nuclear Data Library (ENDL) format to and from GND, as well as for visualizing, modifying and processing (i.e., converting evaluated nuclear data into a form more suitable to transport codes) GND structured nuclear data. GND defines the structure needed for storing nuclear data evaluations and the type of data that needs to be stored. But unlike ENDF and ENDL, GND does not define how the data are to be stored in a file. Currently, Fudge writes the structured GND data to a file using the eXtensible Markup Language (XML), as it is ASCII based and can be viewed with any text editor. XML is a meta-language, meaning that it

Computational Aspects of Heat Transfer in Structures

NASA Technical Reports Server (NTRS)

Adelman, H. M. (Compiler)

1982-01-01

Techniques for the computation of heat transfer and associated phenomena in complex structures are examined with an emphasis on reentry flight vehicle structures. Analysis methods, computer programs, thermal analysis of large space structures and high speed vehicles, and the impact of computer systems are addressed.

Nuclear Structure of 186Re

DTIC Science & Technology

2016-12-24

D population-depopulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 AME Atomic Mass Evaluation...this mass region are important for validating models of nuclear structure and reactions. The ENSDF feeds a specific data library relevant to nuclear...spherically asymmetric. Spherical asymmetry is common for nuclei between shell closures, such as those in the mid-shell 150  A  190 mass range of interest

Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques.

PubMed

Singh, Gurpreet; Mohanty, B P; Saini, G S S

2016-02-15

Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide. Copyright © 2015 Elsevier B.V. All rights reserved.

Nuclear Pore-Like Structures in a Compartmentalized Bacterium

PubMed Central

Sagulenko, Evgeny; Green, Kathryn; Yee, Benjamin; Morgan, Garry; Leis, Andrew; Lee, Kuo-Chang; Butler, Margaret K.; Chia, Nicholas; Pham, Uyen Thi Phuong; Lindgreen, Stinus; Catchpole, Ryan; Poole, Anthony M.; Fuerst, John A.

2017-01-01

Planctomycetes are distinguished from other Bacteria by compartmentalization of cells via internal membranes, interpretation of which has been subject to recent debate regarding potential relations to Gram-negative cell structure. In our interpretation of the available data, the planctomycete Gemmata obscuriglobus contains a nuclear body compartment, and thus possesses a type of cell organization with parallels to the eukaryote nucleus. Here we show that pore-like structures occur in internal membranes of G.obscuriglobus and that they have elements structurally similar to eukaryote nuclear pores, including a basket, ring-spoke structure, and eight-fold rotational symmetry. Bioinformatic analysis of proteomic data reveals that some of the G. obscuriglobus proteins associated with pore-containing membranes possess structural domains found in eukaryote nuclear pore complexes. Moreover, immunogold labelling demonstrates localization of one such protein, containing a β-propeller domain, specifically to the G. obscuriglobus pore-like structures. Finding bacterial pores within internal cell membranes and with structural similarities to eukaryote nuclear pore complexes raises the dual possibilities of either hitherto undetected homology or stunning evolutionary convergence. PMID:28146565

Nuclear Structure Research at TRIUMF

NASA Astrophysics Data System (ADS)

Garrett, P. E.; Andreyev, A.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Becker, J. A.; Boston, A. J.; Chakrawarthy, R. S.; Cline, D.; Cooper, R. J.; Churchman, R.; Cross, D.; Dashdorj, D.; Demand, G. A.; Dimmock, M. R.; Drake, T. E.; Finlay, P.; Gagon-Miosan, F.; Gallant, A. T.; Green, K. L.; Grint, A. N.; Grinyer, G. F.; Hackman, G.; Harkness, L. J.; Hayes, A. B.; Kanungo, R.; Kulp, W. D.; Leach, K. G.; Lee, G.; Leslie, J. R.; Martin, J.-P.; Mattoon, C.; Mills, W. J.; Morton, A. C.; Mythili, S.; Nelson, L.; Newman, O.; Nolan, P. J.; Padilla-Rodal, E.; Pearson, C. J.; Phillips, A. A.; Porter-Peden, M.; Ressler, J. J.; Roy, R.; Ruiz, C.; Savajols, H.; Sarazin, F.; Schumaker, M. A.; Scraggs, D. P.; Scraggs, H. C.; Strange, M. D.; Svensson, C. E.; Waddington, J. C.; Wan, J. M.; Whitbeck, A.; Williams, S. J.; Wong, J.; Wood, J. L.; Wu, C. Y.; Zganjar, E. F.

2007-04-01

The radioactive beam laboratory at TRIUMF is currently the highest power ISOL facility in the world. Taking advantage of the high-intensity beams, major programs in nuclear astrophysics, nuclear structure, and weak interaction studies have begun. The low-energy area, ISAC-I, is capable of delivering beams up to mass 30 at approx 1.7 MeV/u or 60 keV up to the mass of the primary target, whereas ISAC-II will ultimately provide beams up to mass 150 and approx 6.5 MeV/u. Major gamma -ray spectrometers for nuclear structure research consist of the 8pi spectrometer at ISAC-I, and the TIGRESS spectrometer now being constructed for ISAC-II. Results from recent experiments investigating the beta -decay of nuclei near N=90 and Coulomb excitation of 20,21Na are presented that highlight the capabilities of the spectrometers.

The non-independence discussion about cycle structure in the computer language: the final simplification of computer language in the structural design

NASA Astrophysics Data System (ADS)

Yang, Peilu

2013-03-01

In the first place, the article discusses the theory, content, development, and questions about structured programming design. The further extension on this basement provides the cycle structure in computer language is the sequence structure, branch structure, and the cycle structure with independence. Through the deeply research by the writer, we find the non-independence and reach the final simplification about the computer language design. In the first, the writer provides the language structure of linear structure (I structure) and curvilinear structure (Y structure). This makes the computer language has high proficiency with simplification during the program exploration. The research in this article is corresponding with the widely used dualistic structure in the computer field. Moreover, it is greatly promote the evolution of computer language.

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume II-program data (basic structural elements). Final report, 1 June 1977-30 September 1979

DOE Office of Scientific and Technical Information (OSTI.GOV)

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

A computer program for calculation of approximate embryo/fetus radiation dose in nuclear medicine applications.

PubMed

Bayram, Tuncay; Sönmez, Bircan

2012-04-01

In this study, we aimed to make a computer program that calculates approximate radiation dose received by embryo/fetus in nuclear medicine applications. Radiation dose values per MBq-1 received by embryo/fetus in nuclear medicine applications were gathered from literature for various stages of pregnancy. These values were embedded in the computer code, which was written in Fortran 90 program language. The computer program called nmfdose covers almost all radiopharmaceuticals used in nuclear medicine applications. Approximate radiation dose received by embryo/fetus can be calculated easily at a few steps using this computer program. Although there are some constraints on using the program for some special cases, nmfdose is useful and it provides practical solution for calculation of approximate dose to embryo/fetus in nuclear medicine applications. None declared.

Perturbation approach for nuclear magnetic resonance solid-state quantum computation

DOE PAGES

Berman, G. P.; Kamenev, D. I.; Tsifrinovich, V. I.

2003-01-01

A dynmore » amics of a nuclear-spin quantum computer with a large number ( L = 1000 ) of qubits is considered using a perturbation approach. Small parameters are introduced and used to compute the error in an implementation of an entanglement between remote qubits, using a sequence of radio-frequency pulses. The error is computed up to the different orders of the perturbation theory and tested using exact numerical solution.« less

Supporting the future nuclear workforce with computer-based procedures

DOE PAGES

Oxstrand, Johanna; Le Blanc, Katya

2016-05-01

Here we see that computer-based tools have dramatically increased ease and efficiency of everyday tasks. Gone are the days of paging through a paper catalog, transcribing product numbers, and calculating totals. Today, a consumer can find a product online with a simple search engine, and then purchase it in a matter of a few clicks. Paper catalogs have their place, but it is hard to imagine life without on-line shopping sites. All tasks conducted in a nuclear power plant are guided by procedures, which helps ensure safe and reliable operation of the plants. One prominent goal of the nuclear industrymore » is to minimize the risk of human errors. To achieve this goal one has to ensure tasks are correctly and consistently executed. This is partly achieved by training and by a structured approach to task execution, which is provided by procedures and work instructions. Procedures are used in the nuclear industry to direct workers' actions in a proper sequence. The governing idea is to minimize the reliance on memory and choices made in the field. However, the procedure document may not contain sufficient information to successfully complete the task. Therefore, the worker might have to carry additional documents such as turnover sheets, operation experience, drawings, and other procedures to the work site. The nuclear industry is operated with paper procedures like paper catalogs of the past. A field worker may carry a large stack of documents needed to complete a task to the field. Even though the paper process has helped keep the industry safe for decades, there are limitations to using paper. Paper procedures are static (i.e., the content does not change after the document is printed), difficult to search, and rely heavily on the field worker’s situational awareness and ability to consistently meet the high expectation of human performance excellence. With computer-based procedures (CBPs) that stack of papers may be reduced to the size of a small tablet or even

Supporting the future nuclear workforce with computer-based procedures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oxstrand, Johanna; Le Blanc, Katya

Here we see that computer-based tools have dramatically increased ease and efficiency of everyday tasks. Gone are the days of paging through a paper catalog, transcribing product numbers, and calculating totals. Today, a consumer can find a product online with a simple search engine, and then purchase it in a matter of a few clicks. Paper catalogs have their place, but it is hard to imagine life without on-line shopping sites. All tasks conducted in a nuclear power plant are guided by procedures, which helps ensure safe and reliable operation of the plants. One prominent goal of the nuclear industrymore » is to minimize the risk of human errors. To achieve this goal one has to ensure tasks are correctly and consistently executed. This is partly achieved by training and by a structured approach to task execution, which is provided by procedures and work instructions. Procedures are used in the nuclear industry to direct workers' actions in a proper sequence. The governing idea is to minimize the reliance on memory and choices made in the field. However, the procedure document may not contain sufficient information to successfully complete the task. Therefore, the worker might have to carry additional documents such as turnover sheets, operation experience, drawings, and other procedures to the work site. The nuclear industry is operated with paper procedures like paper catalogs of the past. A field worker may carry a large stack of documents needed to complete a task to the field. Even though the paper process has helped keep the industry safe for decades, there are limitations to using paper. Paper procedures are static (i.e., the content does not change after the document is printed), difficult to search, and rely heavily on the field worker’s situational awareness and ability to consistently meet the high expectation of human performance excellence. With computer-based procedures (CBPs) that stack of papers may be reduced to the size of a small tablet or even

Computation of Thermodynamic Equilibria Pertinent to Nuclear Materials in Multi-Physics Codes

NASA Astrophysics Data System (ADS)

Piro, Markus Hans Alexander

Nuclear energy plays a vital role in supporting electrical needs and fulfilling commitments to reduce greenhouse gas emissions. Research is a continuing necessity to improve the predictive capabilities of fuel behaviour in order to reduce costs and to meet increasingly stringent safety requirements by the regulator. Moreover, a renewed interest in nuclear energy has given rise to a "nuclear renaissance" and the necessity to design the next generation of reactors. In support of this goal, significant research efforts have been dedicated to the advancement of numerical modelling and computational tools in simulating various physical and chemical phenomena associated with nuclear fuel behaviour. This undertaking in effect is collecting the experience and observations of a past generation of nuclear engineers and scientists in a meaningful way for future design purposes. There is an increasing desire to integrate thermodynamic computations directly into multi-physics nuclear fuel performance and safety codes. A new equilibrium thermodynamic solver is being developed with this matter as a primary objective. This solver is intended to provide thermodynamic material properties and boundary conditions for continuum transport calculations. There are several concerns with the use of existing commercial thermodynamic codes: computational performance; limited capabilities in handling large multi-component systems of interest to the nuclear industry; convenient incorporation into other codes with quality assurance considerations; and, licensing entanglements associated with code distribution. The development of this software in this research is aimed at addressing all of these concerns. The approach taken in this work exploits fundamental principles of equilibrium thermodynamics to simplify the numerical optimization equations. In brief, the chemical potentials of all species and phases in the system are constrained by estimates of the chemical potentials of the system

Molecular Dynamics-based Simulations of Bulk/Interfacial Structures and Diffusion Behaviors in Nuclear Waste Glasses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Du, Jincheng; Rimsza, Jessica; Deng, Lu

This NEUP Project aimed to generate accurate atomic structural models of nuclear waste glasses by using large-scale molecular dynamics-based computer simulations and to use these models to investigate self-diffusion behaviors, interfacial structures, and hydrated gel structures formed during dissolution of these glasses. The goal was to obtain realistic and accurate short and medium range structures of these complex oxide glasses, to provide a mechanistic understanding of the dissolution behaviors, and to generate reliable information with predictive power in designing nuclear waste glasses for long-term geological storage. Looking back of the research accomplishments of this project, most of the scientific goalsmore » initially proposed have been achieved through intensive research in the three and a half year period of the project. This project has also generated a wealth of scientific data and vibrant discussions with various groups through collaborations within and outside of this project. Throughout the project one book chapter and 14 peer reviewed journal publications have been generated (including one under review) and 16 presentations (including 8 invited talks) have been made to disseminate the results of this project in national and international conference. Furthermore, this project has trained several outstanding graduate students and young researchers for future workforce in nuclear related field, especially on nuclear waste immobilization. One postdoc and four PhD students have been fully or partially supported through the project with intensive training in the field material science and engineering with expertise on glass science and nuclear waste disposal« less

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume I-program description and results (basic structural elements). Final report, 1 June 1977-30 September 1979

DOE Office of Scientific and Technical Information (OSTI.GOV)

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

Physical and Mechanical Metallurgy of Zirconium Alloys for Nuclear Applications: A Multi-Scale Computational Study

NASA Astrophysics Data System (ADS)

Glazoff, Michael Vasily

In the post-Fukushima world, thermal and structural stability of materials under extreme conditions is an important issue for the safety of nuclear reactors. Because the nuclear industry will continue using zirconium (Zr) cladding for the foreseeable future, it becomes critical to gain a fundamental understanding of several interconnected problems. First, what are the thermodynamic and kinetic factors affecting oxidation and hydrogen pick-up by these materials at normal, off-normal conditions, and in long-term storage? Secondly, what protective coatings could be used in order to gain valuable time at off-normal conditions (temperature exceeds ~1200°C (2200°F)? Thirdly, the kinetics of the coating's oxidation must be understood. Lastly, one needs automated inspection algorithms allowing identifying cladding's defects. This work attempts to explore the problem from a computational perspective, utilizing first principles atomistic simulations, computational thermodynamics, plasticity theory, and morphological algorithms of image processing for defect identification. It consists of the four parts dealing with these four problem areas preceded by the introduction. In the 1st part, computational thermodynamics and ab initio calculations were used to shed light upon the different stages of zircaloy oxidation and hydrogen pickup, and microstructure optimization to increase thermal stability. The 2 nd part describes the kinetic theory of oxidation of the several materials considered to be perspective coatings for Zr alloys: SiC and ZrSiO4. The 3rd part deals with understanding the respective roles of the two different plasticity mechanisms in Zr nuclear alloys: twinning (at low T) and crystallographic slip (higher T's). For that goal, an advanced plasticity model was proposed. In the 4th part projectional algorithms for defect identification in zircaloy coatings are described. Conclusions and recommendations are presented in the 5th part. This integrative approach's value

Introduction to the computational structural mechanics testbed

NASA Technical Reports Server (NTRS)

Lotts, C. G.; Greene, W. H.; Mccleary, S. L.; Knight, N. F., Jr.; Paulson, S. S.; Gillian, R. E.

1987-01-01

The Computational Structural Mechanics (CSM) testbed software system based on the SPAR finite element code and the NICE system is described. This software is denoted NICE/SPAR. NICE was developed at Lockheed Palo Alto Research Laboratory and contains data management utilities, a command language interpreter, and a command language definition for integrating engineering computational modules. SPAR is a system of programs used for finite element structural analysis developed for NASA by Lockheed and Engineering Information Systems, Inc. It includes many complementary structural analysis, thermal analysis, utility functions which communicate through a common database. The work on NICE/SPAR was motivated by requirements for a highly modular and flexible structural analysis system to use as a tool in carrying out research in computational methods and exploring computer hardware. Analysis examples are presented which demonstrate the benefits gained from a combination of the NICE command language with a SPAR computational modules.

Strategic disruption of nuclear pores structure, integrity and barrier for nuclear apoptosis.

PubMed

Shahin, Victor

2017-08-01

Apoptosis is a programmed cell death playing key roles in physiology and pathophysiology of multi cellular organisms. Its nuclear manifestation requires transmission of the death signals across the nuclear pore complexes (NPCs). In strategic sequential steps apoptotic factors disrupt NPCs structure, integrity and barrier ultimately leading to nuclear breakdown. The present review reflects on these steps. Copyright © 2017 Elsevier Ltd. All rights reserved.

New computing systems, future computing environment, and their implications on structural analysis and design

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Housner, Jerrold M.

1993-01-01

Recent advances in computer technology that are likely to impact structural analysis and design of flight vehicles are reviewed. A brief summary is given of the advances in microelectronics, networking technologies, and in the user-interface hardware and software. The major features of new and projected computing systems, including high performance computers, parallel processing machines, and small systems, are described. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed. The impact of the advances in computer technology on structural analysis and the design of flight vehicles is described. A scenario for future computing paradigms is presented, and the near-term needs in the computational structures area are outlined.

NVR-BIP: Nuclear Vector Replacement using Binary Integer Programming for NMR Structure-Based Assignments.

PubMed

Apaydin, Mehmet Serkan; Çatay, Bülent; Patrick, Nicholas; Donald, Bruce R

2011-05-01

Nuclear magnetic resonance (NMR) spectroscopy is an important experimental technique that allows one to study protein structure and dynamics in solution. An important bottleneck in NMR protein structure determination is the assignment of NMR peaks to the corresponding nuclei. Structure-based assignment (SBA) aims to solve this problem with the help of a template protein which is homologous to the target and has applications in the study of structure-activity relationship, protein-protein and protein-ligand interactions. We formulate SBA as a linear assignment problem with additional nuclear overhauser effect constraints, which can be solved within nuclear vector replacement's (NVR) framework (Langmead, C., Yan, A., Lilien, R., Wang, L. and Donald, B. (2003) A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments. Proc. the 7th Annual Int. Conf. Research in Computational Molecular Biology (RECOMB) , Berlin, Germany, April 10-13, pp. 176-187. ACM Press, New York, NY. J. Comp. Bio. , (2004), 11, pp. 277-298; Langmead, C. and Donald, B. (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J. Biomol. NMR , 29, 111-138). Our approach uses NVR's scoring function and data types and also gives the option of using CH and NH residual dipolar coupling (RDCs), instead of NH RDCs which NVR requires. We test our technique on NVR's data set as well as on four new proteins. Our results are comparable to NVR's assignment accuracy on NVR's test set, but higher on novel proteins. Our approach allows partial assignments. It is also complete and can return the optimum as well as near-optimum assignments. Furthermore, it allows us to analyze the information content of each data type and is easily extendable to accept new forms of input data, such as additional RDCs.

A computer-aided diagnosis system of nuclear cataract.

PubMed

Li, Huiqi; Lim, Joo Hwee; Liu, Jiang; Mitchell, Paul; Tan, Ava Grace; Wang, Jie Jin; Wong, Tien Yin

2010-07-01

Cataracts are the leading cause of blindness worldwide, and nuclear cataract is the most common form of cataract. An algorithm for automatic diagnosis of nuclear cataract is investigated in this paper. Nuclear cataract is graded according to the severity of opacity using slit lamp lens images. Anatomical structure in the lens image is detected using a modified active shape model. On the basis of the anatomical landmark, local features are extracted according to clinical grading protocol. Support vector machine regression is employed for grade prediction. This is the first time that the nucleus region can be detected automatically in slit lamp images. The system is validated using clinical images and clinical ground truth on >5000 images. The success rate of structure detection is 95% and the average grading difference is 0.36 on a 5.0 scale. The automatic diagnosis system can improve the grading objectivity and potentially be used in clinics and population studies to save the workload of ophthalmologists.

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

Computational composite mechanics for aerospace propulsion structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1986-01-01

Specialty methods are presented for the computational simulation of specific composite behavior. These methods encompass all aspects of composite mechanics, impact, progressive fracture and component specific simulation. Some of these methods are structured to computationally simulate, in parallel, the composite behavior and history from the initial fabrication through several missions and even to fracture. Select methods and typical results obtained from such simulations are described in detail in order to demonstrate the effectiveness of computationally simulating (1) complex composite structural behavior in general and (2) specific aerospace propulsion structural components in particular.

Computational composite mechanics for aerospace propulsion structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1987-01-01

Specialty methods are presented for the computational simulation of specific composite behavior. These methods encompass all aspects of composite mechanics, impact, progressive fracture and component specific simulation. Some of these methods are structured to computationally simulate, in parallel, the composite behavior and history from the initial frabrication through several missions and even to fracture. Select methods and typical results obtained from such simulations are described in detail in order to demonstrate the effectiveness of computationally simulating: (1) complex composite structural behavior in general, and (2) specific aerospace propulsion structural components in particular.

Situation awareness and trust in computer-based procedures in nuclear power plant operations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Throneburg, E. B.; Jones, J. M.

2006-07-01

Situation awareness and trust are two issues that need to be addressed in the design of computer-based procedures for nuclear power plants. Situation awareness, in relation to computer-based procedures, concerns the operators' knowledge of the plant's state while following the procedures. Trust concerns the amount of faith that the operators put into the automated procedures, which can affect situation awareness. This paper first discusses the advantages and disadvantages of computer-based procedures. It then discusses the known aspects of situation awareness and trust as applied to computer-based procedures in nuclear power plants. An outline of a proposed experiment is then presentedmore » that includes methods of measuring situation awareness and trust so that these aspects can be analyzed for further study. (authors)« less

Belief Structures of Students For and Against the Nuclear Freeze.

ERIC Educational Resources Information Center

Tankard, James W., Jr.

An investigation of college students' belief structures underlying their support or non-support of a nuclear freeze revealed a three-dimensional structure for beliefs in the areas of nuclear weapons and national defense. A questionnaire containing 25 belief statements concerning national defense and nuclear weapons and 4 media use questions was…

[Computational chemistry in structure-based drug design].

PubMed

Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

2013-07-01

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

Parallel computations and control of adaptive structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Alvin, Kenneth F.; Belvin, W. Keith; Chong, K. P. (Editor); Liu, S. C. (Editor); Li, J. C. (Editor)

1991-01-01

The equations of motion for structures with adaptive elements for vibration control are presented for parallel computations to be used as a software package for real-time control of flexible space structures. A brief introduction of the state-of-the-art parallel computational capability is also presented. Time marching strategies are developed for an effective use of massive parallel mapping, partitioning, and the necessary arithmetic operations. An example is offered for the simulation of control-structure interaction on a parallel computer and the impact of the approach presented for applications in other disciplines than aerospace industry is assessed.

Computer-aided design of antenna structures and components

NASA Technical Reports Server (NTRS)

Levy, R.

1976-01-01

This paper discusses computer-aided design procedures for antenna reflector structures and related components. The primary design aid is a computer program that establishes cross sectional sizes of the structural members by an optimality criterion. Alternative types of deflection-dependent objectives can be selected for designs subject to constraints on structure weight. The computer program has a special-purpose formulation to design structures of the type frequently used for antenna construction. These structures, in common with many in other areas of application, are represented by analytical models that employ only the three translational degrees of freedom at each node. The special-purpose construction of the program, however, permits coding and data management simplifications that provide advantages in problem size and execution speed. Size and speed are essentially governed by the requirements of structural analysis and are relatively unaffected by the added requirements of design. Computation times to execute several design/analysis cycles are comparable to the times required by general-purpose programs for a single analysis cycle. Examples in the paper illustrate effective design improvement for structures with several thousand degrees of freedom and within reasonable computing times.

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Two-level convolution formula for nuclear structure function

NASA Astrophysics Data System (ADS)

Ma, Boqiang

1990-05-01

A two-level convolution formula for the nuclear structure function is derived in considering the nucleus as a composite system of baryon-mesons which are also composite systems of quark-gluons again. The results show that the European Muon Colaboration effect can not be explained by the nuclear effects as nucleon Fermi motion and nuclear binding contributions.

Computer program for afterheat temperature distribution for mobile nuclear power plant

NASA Technical Reports Server (NTRS)

Parker, W. G.; Vanbibber, L. E.

1972-01-01

ESATA computer program was developed to analyze thermal safety aspects of post-impacted mobile nuclear power plants. Program is written in FORTRAN 4 and designed for IBM 7094/7044 direct coupled system.

Impact of computational structure-based methods on drug discovery.

PubMed

Reynolds, Charles H

2014-01-01

Structure-based drug design has become an indispensible tool in drug discovery. The emergence of structure-based design is due to gains in structural biology that have provided exponential growth in the number of protein crystal structures, new computational algorithms and approaches for modeling protein-ligand interactions, and the tremendous growth of raw computer power in the last 30 years. Computer modeling and simulation have made major contributions to the discovery of many groundbreaking drugs in recent years. Examples are presented that highlight the evolution of computational structure-based design methodology, and the impact of that methodology on drug discovery.

BigData and computing challenges in high energy and nuclear physics

NASA Astrophysics Data System (ADS)

Klimentov, A.; Grigorieva, M.; Kiryanov, A.; Zarochentsev, A.

2017-06-01

In this contribution we discuss the various aspects of the computing resource needs experiments in High Energy and Nuclear Physics, in particular at the Large Hadron Collider. This will evolve in the future when moving from LHC to HL-LHC in ten years from now, when the already exascale levels of data we are processing could increase by a further order of magnitude. The distributed computing environment has been a great success and the inclusion of new super-computing facilities, cloud computing and volunteering computing for the future is a big challenge, which we are successfully mastering with a considerable contribution from many super-computing centres around the world, academic and commercial cloud providers. We also discuss R&D computing projects started recently in National Research Center ``Kurchatov Institute''

The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

PubMed

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Structural Health Monitoring of Nuclear Spent Fuel Storage Facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Lingyu

Interim storage of spent nuclear fuel from reactor sites has gained additional importance and urgency for resolving waste-management-related technical issues. To ensure that nuclear power remains clean energy, monitoring has been identified by DOE as a high priority cross-cutting need, necessary to determine and predict the degradation state of the systems, structures, and components (SSCs) important to safety (ITS). Therefore, nondestructive structural condition monitoring becomes a need to be installed on existing or to be integrated into future storage system to quantify the state of health or to guarantee the safe operation of nuclear power plants (NPPs) during their extendedmore » life span. In this project, the lead university and the collaborating national laboratory teamed to develop a nuclear structural health monitoring (n-SHM) system based on in-situ piezoelectric sensing technologies that can monitor structural degradation and aging for nuclear spent fuel DCSS and similar structures. We also aimed to identify and quantify possible influences of nuclear spent fuel environment (temperature and radiation) to the piezoelectric sensor system and come up with adequate solutions and guidelines therefore. We have therefore developed analytical model for piezoelectric based n-SHM methods, with considerations of temperature and irradiation influence on the model of sensing and algorithms in acoustic emission (AE), guided ultrasonic waves (GUW), and electromechanical impedance spectroscopy (EMIS). On the other side, experimentally the temperature and irradiation influence on the piezoelectric sensors and sensing capabilities were investigated. Both short-term and long-term irradiation investigation with our collaborating national laboratory were performed. Moreover, we developed multi-modal sensing, validated in laboratory setup, and conducted the testing on the We performed multi-modal sensing development, verification and validation tests on very complex

Computational predictions of zinc oxide hollow structures

NASA Astrophysics Data System (ADS)

Tuoc, Vu Ngoc; Huan, Tran Doan; Thao, Nguyen Thi

2018-03-01

Nanoporous materials are emerging as potential candidates for a wide range of technological applications in environment, electronic, and optoelectronics, to name just a few. Within this active research area, experimental works are predominant while theoretical/computational prediction and study of these materials face some intrinsic challenges, one of them is how to predict porous structures. We propose a computationally and technically feasible approach for predicting zinc oxide structures with hollows at the nano scale. The designed zinc oxide hollow structures are studied with computations using the density functional tight binding and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications.

Computational Nuclear Physics and Post Hartree-Fock Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lietz, Justin; Sam, Novario; Hjorth-Jensen, M.

We present a computational approach to infinite nuclear matter employing Hartree-Fock theory, many-body perturbation theory and coupled cluster theory. These lectures are closely linked with those of chapters 9, 10 and 11 and serve as input for the correlation functions employed in Monte Carlo calculations in chapter 9, the in-medium similarity renormalization group theory of dense fermionic systems of chapter 10 and the Green's function approach in chapter 11. We provide extensive code examples and benchmark calculations, allowing thereby an eventual reader to start writing her/his own codes. We start with an object-oriented serial code and end with discussions onmore » strategies for porting the code to present and planned high-performance computing facilities.« less

A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA

PubMed Central

2010-01-01

Background The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Methods Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Results Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA.

PubMed

D'Onofrio, David J; An, Gary

2010-01-21

The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures. Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves. Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological systems do not have an

The development of regulatory expectations for computer-based safety systems for the UK nuclear programme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, P. J.; Westwood, R.N; Mark, R. T.

2006-07-01

The Nuclear Installations Inspectorate (NII) of the UK's Health and Safety Executive (HSE) has completed a review of their Safety Assessment Principles (SAPs) for Nuclear Installations recently. During the period of the SAPs review in 2004-2005 the designers of future UK naval reactor plant were optioneering the control and protection systems that might be implemented. Because there was insufficient regulatory guidance available in the naval sector to support this activity the Defence Nuclear Safety Regulator (DNSR) invited the NII to collaborate with the production of a guidance document that provides clarity of regulatory expectations for the production of safety casesmore » for computer based safety systems. A key part of producing regulatory expectations was identifying the relevant extant standards and sector guidance that reflect good practice. The three principal sources of such good practice were: IAEA Safety Guide NS-G-1.1 (Software for Computer Based Systems Important to Safety in Nuclear Power Plants), European Commission consensus document (Common Position of European Nuclear Regulators for the Licensing of Safety Critical Software for Nuclear Reactors) and IEC nuclear sector standards such as IEC60880. A common understanding has been achieved between the NII and DNSR and regulatory guidance developed which will be used by both NII and DNSR in the assessment of computer-based safety systems and in the further development of more detailed joint technical assessment guidance for both regulatory organisations. (authors)« less

Structural biology computing: Lessons for the biomedical research sciences.

PubMed

Morin, Andrew; Sliz, Piotr

2013-11-01

The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. Copyright © 2013 Wiley Periodicals, Inc.

NASA Workshop on Computational Structural Mechanics 1987, part 3

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Computational Structural Mechanics (CSM) topics are explored. Algorithms and software for nonlinear structural dynamics, concurrent algorithms for transient finite element analysis, computational methods and software systems for dynamics and control of large space structures, and the use of multi-grid for structural analysis are discussed.

Linear static structural and vibration analysis on high-performance computers

NASA Technical Reports Server (NTRS)

Baddourah, M. A.; Storaasli, O. O.; Bostic, S. W.

1993-01-01

Parallel computers offer the oppurtunity to significantly reduce the computation time necessary to analyze large-scale aerospace structures. This paper presents algorithms developed for and implemented on massively-parallel computers hereafter referred to as Scalable High-Performance Computers (SHPC), for the most computationally intensive tasks involved in structural analysis, namely, generation and assembly of system matrices, solution of systems of equations and calculation of the eigenvalues and eigenvectors. Results on SHPC are presented for large-scale structural problems (i.e. models for High-Speed Civil Transport). The goal of this research is to develop a new, efficient technique which extends structural analysis to SHPC and makes large-scale structural analyses tractable.

Nuclear data and related services

NASA Astrophysics Data System (ADS)

Tuli, J. K.

1985-10-01

National Nuclear Data Center (NNDC) maintains a number of data bases containing bibliographic information and evaluated as well as experimental nuclear properties. An evaluated computer file maintained by the NNDC, called the Evaluated Nuclear Structure Data File (ENSDF), contains nuclear structure information for all known nuclides. The ENSDF is the source for the journal Nuclear Data Sheets which is produced and edited by NNDC. The Evaluated Nuclear Data File (ENDF), on the other hand is designed for storage and retrieval of such evaluated nuclear data as are used in neutronic, photonic, and decay heat calculations in a large variety of applications. Some of the publications from these data bases are the Nuclear Wallet Cards, Radioactivity Handbook, and books on neutron cross sections and resonance parameters. In addition, the NNDC maintains three bibliographic files: NSR - for nuclear structure and decay data related references, CINDA - a bibliographic file for neutron induced reactions, and CPBIB for charged particle reactions. Selected retrievals from evaluated data and bibliographic files are possible on-line or on request from NNDC.

78 FR 47014 - Configuration Management Plans for Digital Computer Software Used in Safety Systems of Nuclear...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... Software Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear Regulatory Commission. ACTION... Computer Software Used in Safety Systems of Nuclear Power Plants.'' This RG endorses, with clarifications... Electrical and Electronic Engineers (IEEE) Standard 828-2005, ``IEEE Standard for Software Configuration...

Nuclear Cartography: Patterns in Binding Energies and Subatomic Structure

ERIC Educational Resources Information Center

Simpson, E. C.; Shelley, M.

2017-01-01

Nuclear masses and binding energies are some of the first nuclear properties met in high school physics, and can be used to introduce radioactive decays, fusion, and fission. With relatively little extension, they can also illustrate fundamental concepts in nuclear physics, such as shell structure and pairing, and to discuss how the elements…

Computational methods for structural load and resistance modeling

NASA Technical Reports Server (NTRS)

Thacker, B. H.; Millwater, H. R.; Harren, S. V.

1991-01-01

An automated capability for computing structural reliability considering uncertainties in both load and resistance variables is presented. The computations are carried out using an automated Advanced Mean Value iteration algorithm (AMV +) with performance functions involving load and resistance variables obtained by both explicit and implicit methods. A complete description of the procedures used is given as well as several illustrative examples, verified by Monte Carlo Analysis. In particular, the computational methods described in the paper are shown to be quite accurate and efficient for a material nonlinear structure considering material damage as a function of several primitive random variables. The results show clearly the effectiveness of the algorithms for computing the reliability of large-scale structural systems with a maximum number of resolutions.

RNA secondary structure prediction using soft computing.

PubMed

Ray, Shubhra Sankar; Pal, Sankar K

2013-01-01

Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

PubMed

Patel, Trushar R; Chojnowski, Grzegorz; Astha; Koul, Amit; McKenna, Sean A; Bujnicki, Janusz M

2017-04-15

The diverse functional cellular roles played by ribonucleic acids (RNA) have emphasized the need to develop rapid and accurate methodologies to elucidate the relationship between the structure and function of RNA. Structural biology tools such as X-ray crystallography and Nuclear Magnetic Resonance are highly useful methods to obtain atomic-level resolution models of macromolecules. However, both methods have sample, time, and technical limitations that prevent their application to a number of macromolecules of interest. An emerging alternative to high-resolution structural techniques is to employ a hybrid approach that combines low-resolution shape information about macromolecules and their complexes from experimental hydrodynamic (e.g. analytical ultracentrifugation) and solution scattering measurements (e.g., solution X-ray or neutron scattering), with computational modeling to obtain atomic-level models. While promising, scattering methods rely on aggregation-free, monodispersed preparations and therefore the careful development of a quality control pipeline is fundamental to an unbiased and reliable structural determination. This review article describes hydrodynamic techniques that are highly valuable for homogeneity studies, scattering techniques useful to study the low-resolution shape, and strategies for computational modeling to obtain high-resolution 3D structural models of RNAs, proteins, and RNA-protein complexes. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Computational structural mechanics methods research using an evolving framework

NASA Technical Reports Server (NTRS)

Knight, N. F., Jr.; Lotts, C. G.; Gillian, R. E.

1990-01-01

Advanced structural analysis and computational methods that exploit high-performance computers are being developed in a computational structural mechanics research activity sponsored by the NASA Langley Research Center. These new methods are developed in an evolving framework and applied to representative complex structural analysis problems from the aerospace industry. An overview of the methods development environment is presented, and methods research areas are described. Selected application studies are also summarized.

Nuclear matrix - structure, function and pathogenesis.

PubMed

Wasąg, Piotr; Lenartowski, Robert

2016-12-20

The nuclear matrix (NM), or nuclear skeleton, is the non-chromatin, ribonucleoproteinaceous framework that is resistant to high ionic strength buffers, nonionic detergents, and nucleolytic enzymes. The NM fulfills a structural role in eukaryotic cells and is responsible for maintaining the shape of the nucleus and the spatial organization of chromatin. Moreover, the NM participates in several cellular processes, such as DNA replication/repair, gene expression, RNA transport, cell signaling and differentiation, cell cycle regulation, apoptosis and carcinogenesis. Short nucleotide sequences called scaffold/matrix attachment regions (S/MAR) anchor the chromatin loops to the NM proteins (NMP). The NMP composition is dynamic and depends on the cell type and differentiation stage or metabolic activity. Alterations in the NMP composition affect anchoring of the S/MARs and thus alter gene expression. This review aims to systematize information about the skeletal structure of the nucleus, with particular emphasis on the organization of the NM and its role in selected cellular processes. We also discuss several diseases that are caused by aberrant NM structure or dysfunction of individual NM elements.

77 FR 50722 - Software Unit Testing for Digital Computer Software Used in Safety Systems of Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0195] Software Unit Testing for Digital Computer Software...) is issuing for public comment draft regulatory guide (DG), DG-1208, ``Software Unit Testing for Digital Computer Software used in Safety Systems of Nuclear Power Plants.'' The DG-1208 is proposed...

78 FR 47011 - Software Unit Testing for Digital Computer Software Used in Safety Systems of Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-02

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0195] Software Unit Testing for Digital Computer Software... revised regulatory guide (RG), revision 1 of RG 1.171, ``Software Unit Testing for Digital Computer Software Used in Safety Systems of Nuclear Power Plants.'' This RG endorses American National Standards...

Numerical Nuclear Second Derivatives on a Computing Grid: Enabling and Accelerating Frequency Calculations on Complex Molecular Systems.

PubMed

Yang, Tzuhsiung; Berry, John F

2018-06-04

The computation of nuclear second derivatives of energy, or the nuclear Hessian, is an essential routine in quantum chemical investigations of ground and transition states, thermodynamic calculations, and molecular vibrations. Analytic nuclear Hessian computations require the resolution of costly coupled-perturbed self-consistent field (CP-SCF) equations, while numerical differentiation of analytic first derivatives has an unfavorable 6 N ( N = number of atoms) prefactor. Herein, we present a new method in which grid computing is used to accelerate and/or enable the evaluation of the nuclear Hessian via numerical differentiation: NUMFREQ@Grid. Nuclear Hessians were successfully evaluated by NUMFREQ@Grid at the DFT level as well as using RIJCOSX-ZORA-MP2 or RIJCOSX-ZORA-B2PLYP for a set of linear polyacenes with systematically increasing size. For the larger members of this group, NUMFREQ@Grid was found to outperform the wall clock time of analytic Hessian evaluation; at the MP2 or B2LYP levels, these Hessians cannot even be evaluated analytically. We also evaluated a 156-atom catalytically relevant open-shell transition metal complex and found that NUMFREQ@Grid is faster (7.7 times shorter wall clock time) and less demanding (4.4 times less memory requirement) than an analytic Hessian. Capitalizing on the capabilities of parallel grid computing, NUMFREQ@Grid can outperform analytic methods in terms of wall time, memory requirements, and treatable system size. The NUMFREQ@Grid method presented herein demonstrates how grid computing can be used to facilitate embarrassingly parallel computational procedures and is a pioneer for future implementations.

Nuclear ``pasta'' structures in low-density nuclear matter and properties of the neutron-star crust

NASA Astrophysics Data System (ADS)

Okamoto, Minoru; Maruyama, Toshiki; Yabana, Kazuhiro; Tatsumi, Toshitaka

2013-08-01

In the neutron-star crust, nonuniform structure of nuclear matter—called the “pasta” structure—is expected. From recent studies of giant flares in magnetars, these structures might be related to some observables and physical quantities of the neutron-star crust. To investigate the above quantities, we numerically explore the pasta structure with a fully three-dimensional geometry and study the properties of low-density nuclear matter, based on the relativistic mean-field model and the Thomas-Fermi approximation. We observe typical pasta structures for fixed proton number fraction and two of them for cold catalyzed matter. We also discuss the crystalline configuration of “pasta.”

Nuclear transmutation in steels

NASA Astrophysics Data System (ADS)

Belozerova, A. R.; Shimanskii, G. A.; Belozerov, S. V.

2009-05-01

The investigations of the effects of nuclear transmutation in steels that are widely used in nuclear power and research reactors and in steels that are planned for the application in thermonuclear fusion plants, which are employed under the conditions of a prolonged action of neutron irradiation with different spectra, made it possible to study the effects of changes in the isotopic and chemical composition on the tendency of changes in the structural stability of these steels. For the computations of nuclear transmutation in steels, we used a program complex we have previously developed on the basis of algorithms for constructing branched block-type diagrams of nuclide transformations and for locally and globally optimizing these diagrams with the purpose of minimizing systematic errors in the calculation of nuclear transmutation. The dependences obtained were applied onto a Schaeffler diagram for steels used for structural elements of reactors. For the irradiation in fission reactors, we observed only a weak influence of the effects of nuclear transmutation in steels on their structural stability. On the contrary, in the case of irradiation with fusion neutrons, a strong influence of the effects of nuclear transmutation in steels on their structural stability has been noted.

Clustering Aspects in Nuclear Structure and Collisions

NASA Astrophysics Data System (ADS)

Horiuchi, H.

Four topics on nuclear clustering are discussed. The first subject is about the cluster formation in dilute matter which we think is now observed in heavy ion collisions at hundreds MeV/nucleon. The second subject is about our new proposal of the existense of alpha condensed states in light nuclei. Two other subjects are both about the clustering in neutron-rich nuclei. One is the cluster structures in neutron-rich Be and B isotopes. In these isotopes, the clustering prevails as fundamental characters of nuclear structure. The other is the report of our recent study about the possible relation of the clustering with the breaking of the neutron magic number N=20 in 32Mg and 30Ne.

Nuclear Structure in China 2010

NASA Astrophysics Data System (ADS)

Bai, Hong-Bo; Meng, Jie; Zhao, En-Guang; Zhou, Shan-Gui

2011-08-01

Personal view on nuclear physics research / Jie Meng -- High-spin level structures in [symbol]Zr / X. P. Cao ... [et al.] -- Constraining the symmetry energy from the neutron skin thickness of tin isotopes / Lie-Wen Chen ... [et al.] -- Wobbling rotation in atomic nuclei / Y. S. Chen and Zao-Chun Gao -- The mixing of scalar mesons and the possible nonstrange dibaryons / L. R. Dai ... [et al.] -- Net baryon productions and gluon saturation in the SPS, RHIC and LHC energy regions / Sheng-Qin Feng -- Production of heavy isotopes with collisions between two actinide nuclides / Z. Q. Feng ... [et al.] -- The projected configuration interaction method / Zao-Chun Gao and Yong-Shou Chen -- Applications of Nilsson mean-field plus extended pairing model to rare-earth nuclei / Xin Guan ... [et al.] -- Complex scaling method and the resonant states / Jian-You Guo ... [et al.] -- Probing the equation of state by deep sub-barrier fusion reactions / Hong-Jun Hao and Jun-Long Tian -- Doublet structure study in A[symbol]105 mass region / C. Y. He ... [et al.] -- Rotational bands in transfermium nuclei / X. T. He -- Shape coexistence and shape evolution [symbol]Yb / H. Hua ... [et al.] -- Multistep shell model method in the complex energy plane / R. J. Liotta -- The evolution of protoneutron stars with kaon condensate / Ang Li -- High spin structures in the [symbol]Lu nucleus / Li Cong-Bo ... [et al.] -- Nuclear stopping and equation of state / QingFeng Li and Ying Yuan -- Covariant description of the low-lying states in neutron-deficient Kr isotopes / Z. X. Li ... [et al.] -- Isospin corrections for superallowed [symbol] transitions / HaoZhao Liang ... [et al.] -- The positive-parity band structures in [symbol]Ag / C. Liu ... [et al.] -- New band structures in odd-odd [symbol]I and [symbol]I / Liu GongYe ... [et al.] -- The sd-pair shell model and interacting boson model / Yan-An Luo ... [et al.] -- Cross-section distributions of fragments in the calcium isotopes projectile

Computational challenges of structure-based approaches applied to HIV.

PubMed

Forli, Stefano; Olson, Arthur J

2015-01-01

Here, we review some of the opportunities and challenges that we face in computational modeling of HIV therapeutic targets and structural biology, both in terms of methodology development and structure-based drug design (SBDD). Computational methods have provided fundamental support to HIV research since the initial structural studies, helping to unravel details of HIV biology. Computational models have proved to be a powerful tool to analyze and understand the impact of mutations and to overcome their structural and functional influence in drug resistance. With the availability of structural data, in silico experiments have been instrumental in exploiting and improving interactions between drugs and viral targets, such as HIV protease, reverse transcriptase, and integrase. Issues such as viral target dynamics and mutational variability, as well as the role of water and estimates of binding free energy in characterizing ligand interactions, are areas of active computational research. Ever-increasing computational resources and theoretical and algorithmic advances have played a significant role in progress to date, and we envision a continually expanding role for computational methods in our understanding of HIV biology and SBDD in the future.

NASA Workshop on Computational Structural Mechanics 1987, part 1

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Topics in Computational Structural Mechanics (CSM) are reviewed. CSM parallel structural methods, a transputer finite element solver, architectures for multiprocessor computers, and parallel eigenvalue extraction are among the topics discussed.

Nuclear structure and dynamics with density functional theory

NASA Astrophysics Data System (ADS)

Stetcu, Ionel

2015-10-01

Even in the absence of ab initio methods capable of tackling heavy nuclei without restrictions, one can obtain an ab initio description of ground-state properties by means of the density functional theory (DFT), and its extension to superfluid systems in its local variant, the superfluid local density approximation (SLDA). Information about the properties of excited states can be obtained in the same framework by using an extension to the time-dependent (TD) phenomena. Unlike other approaches in which the nuclear structure information is used as a separate input into reaction models, the TD approach treats on the same footing the nuclear structure and dynamics, and is well suited to provide more reliable description for a large number of processes involving heavy nuclei, from the nuclear response to electroweak probes, to nuclear reactions, such as neutron-induced reactions, or nuclear fusion and fission. Such processes, sometimes part of integrated nuclear systems, have important applications in astrophysics, energy production, global security, etc. In this talk, I will present the simulation of a simple reaction, that is the Coulomb excitation of a 238U nucleus, and discuss the application of the TD-DFT formalism to the description of induced fission. I gratefully acknowledge partial support of the U.S. Department of Energy through an Early Career Award of the LANL/LDRD Program.

Assessment of Titanium Aluminide Alloys for High-Temperature Nuclear Structural Applications

NASA Astrophysics Data System (ADS)

Zhu, Hanliang; Wei, Tao; Carr, David; Harrison, Robert; Edwards, Lyndon; Hoffelner, Wolfgang; Seo, Dongyi; Maruyama, Kouichi

2012-12-01

Titanium aluminide (TiAl) alloys exhibit high specific strength, low density, good oxidation, corrosion, and creep resistance at elevated temperatures, making them good candidate materials for aerospace and automotive applications. TiAl alloys also show excellent radiation resistance and low neutron activation, and they can be developed to have various microstructures, allowing different combinations of properties for various extreme environments. Hence, TiAl alloys may be used in advanced nuclear systems as high-temperature structural materials. Moreover, TiAl alloys are good materials to be used for fundamental studies on microstructural effects on irradiation behavior of advanced nuclear structural materials. This article reviews the microstructure, creep, radiation, and oxidation properties of TiAl alloys in comparison with other nuclear structural materials to assess the potential of TiAl alloys as candidate structural materials for future nuclear applications.

Live CLEM imaging to analyze nuclear structures at high resolution.

PubMed

Haraguchi, Tokuko; Osakada, Hiroko; Koujin, Takako

2015-01-01

Fluorescence microscopy (FM) and electron microscopy (EM) are powerful tools for observing molecular components in cells. FM can provide temporal information about cellular proteins and structures in living cells. EM provides nanometer resolution images of cellular structures in fixed cells. We have combined FM and EM to develop a new method of correlative light and electron microscopy (CLEM), called "Live CLEM." In this method, the dynamic behavior of specific molecules of interest is first observed in living cells using fluorescence microscopy (FM) and then cellular structures in the same cell are observed using electron microscopy (EM). Following image acquisition, FM and EM images are compared to enable the fluorescent images to be correlated with the high-resolution images of cellular structures obtained using EM. As this method enables analysis of dynamic events involving specific molecules of interest in the context of specific cellular structures at high resolution, it is useful for the study of nuclear structures including nuclear bodies. Here we describe Live CLEM that can be applied to the study of nuclear structures in mammalian cells.

Nuclear Physics Laboratory 1979 annual report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adelberger, E.G.

1979-07-01

Research progress is reported in the following areas: astrophysics and cosmology, fundamental symmetries, nuclear structure, radiative capture, medium energy physics, heavy ion reactions, research by users and visitors, accelerator and ion source development, instrumentation and experimental techniques, and computers and computing. Publications are listed. (WHK)

PREFACE: Open Problems in Nuclear Structure Theory: Introduction Open Problems in Nuclear Structure Theory: Introduction

NASA Astrophysics Data System (ADS)

Dobaczewski, Jacek

2010-06-01

Nuclear structure theory is a domain of physics faced at present with great challenges and opportunities. A larger and larger body of high-precision experimental data has been and continues to be accumulated. Experiments on very exotic short-lived isotopes are the backbone of activity at numerous large-scale facilities. Over the years, tremendous progress has been made in understanding the basic features of nuclei. However, the theoretical description of nuclear systems is still far from being complete and is often not very precise. Many questions, both basic and practical, remain unanswered. The goal of publishing this special focus issue of Journal of Physics G: Nuclear and Particle Physics on Open Problems in Nuclear Structure Theory (OPeNST) is to construct a fundamental inventory thereof, so that the tasks and available options become more clearly exposed and that this will help to stimulate a boost in theoretical activity, commensurate with the experimental progress. The requested format and scope of the articles on OPeNST was quite flexible. The journal simply offered the possibility to provide a forum for the material, which is very often discussed at conferences during the coffee breaks but does not normally have sufficient substance to form regular publications. Nonetheless, very often formulating a problem provides a major step towards its solution, and it may constitute a scientific achievement on its own. Prospective authors were therefore invited to find their own balance between the two extremes of very general problems on the one hand (for example, to solve exactly the many-body equations for a hundred particles) and very specific problems on the other hand (for example, those that one could put in one's own grant proposal). The authors were also asked not to cover results already obtained, nor to limit their presentations to giving a review of the subject, although some elements of those could be included to properly introduce the subject matter

Structuring Cooperative Nuclear RIsk Reduction Initiatives with China.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandt, Larry; Reinhardt, Jason Christian; Hecker, Siegfried

The Stanford Center for International Security and Cooperation engaged several Chinese nuclear organizations in cooperative research that focused on responses to radiological and nuclear terrorism. The objective was to identify joint research initiatives to reduce the global dangers of such threats and to pursue initial technical collaborations in several high priority areas. Initiatives were identified in three primary research areas: 1) detection and interdiction of smuggled nuclear materials; 2) nuclear forensics; and 3) radiological (“dirty bomb”) threats and countermeasures. Initial work emphasized the application of systems and risk analysis tools, which proved effective in structuring the collaborations. The extensive engagementsmore » between national security nuclear experts in China and the U.S. during the research strengthened professional relationships between these important communities.« less

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

EVALUATED NUCLEAR STRUCTURE DATA FILE AND RELATED PRODUCTS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

TULI,J.K.

The Evaluated Nuclear Structure Data File (ENSDF) is a leading resource for the experimental nuclear data. It is maintained and distributed by the National Nuclear Data Center, Brookhaven National Laboratory. The file is mainly contributed to by an international network of evaluators under the auspice of the International Atomic Energy Agency. The ENSDF is updated, generally by mass number, i.e., evaluating together all isobars for a given mass number. If, however, experimental activity in an isobaric chain is limited to a particular nuclide then only that nuclide is updated. The evaluations are published in the journal Nuclear Data Sheets, Academicmore » Press, a division of Elsevier.« less

Scoring nuclear pleomorphism using a visual BoF modulated by a graph structure

NASA Astrophysics Data System (ADS)

Moncayo-Martínez, Ricardo; Romo-Bucheli, David; Arias, Viviana; Romero, Eduardo

2017-11-01

Nuclear pleomorphism has been recognized as a key histological criterium in breast cancer grading systems (such as Bloom Richardson and Nothingham grading systems). However, the nuclear pleomorphism assessment is subjective and presents high inter-reader variability. Automatic algorithms might facilitate quantitative estimation of nuclear variations in shape and size. Nevertheless, the automatic segmentation of the nuclei is difficult and still and open research problem. This paper presents a method using a bag of multi-scale visual features, modulated by a graph structure, to grade nuclei in breast cancer microscopical fields. This strategy constructs hematoxylin-eosin image patches, each containing a nucleus that is represented by a set of visual words in the BoF. The contribution of each visual word is computed by examining the visual words in an associated graph built when projecting the multi-dimensional BoF to a bi-dimensional plane where local relationships are conserved. The methodology was evaluated using 14 breast cancer cases of the Cancer Genome Atlas database. From these cases, a set of 134 microscopical fields was extracted, and under a leave-one-out validation scheme, an average F-score of 0.68 was obtained.

On-line computer system for use with low- energy nuclear physics experiments is reported

NASA Technical Reports Server (NTRS)

Gemmell, D. S.

1969-01-01

Computer program handles data from low-energy nuclear physics experiments which utilize the ND-160 pulse-height analyzer and the PHYLIS computing system. The program allows experimenters to choose from about 50 different basic data-handling functions and to prescribe the order in which these functions will be performed.

PREFACE: International Conference on Computing in High Energy and Nuclear Physics (CHEP'07)

NASA Astrophysics Data System (ADS)

Sobie, Randall; Tafirout, Reda; Thomson, Jana

2007-07-01

The 2007 International Conference on Computing in High Energy and Nuclear Physics (CHEP) was held on 2-7 September 2007 in Victoria, British Columbia, Canada. CHEP is a major series of international conferences for physicists and computing professionals from the High Energy and Nuclear Physics community, Computer Science and Information Technology. The CHEP conference provides an international forum to exchange information on computing experience and needs for the community, and to review recent, ongoing, and future activities. The CHEP'07 conference had close to 500 attendees with a program that included plenary sessions of invited oral presentations, a number of parallel sessions comprising oral and poster presentations, and an industrial exhibition. Conference tracks covered topics in Online Computing, Event Processing, Software Components, Tools and Databases, Software Tools and Information Systems, Computing Facilities, Production Grids and Networking, Grid Middleware and Tools, Distributed Data Analysis and Information Management and Collaborative Tools. The conference included a successful whale-watching excursion involving over 200 participants and a banquet at the Royal British Columbia Museum. The next CHEP conference will be held in Prague in March 2009. We would like thank the sponsors of the conference and the staff at the TRIUMF Laboratory and the University of Victoria who made the CHEP'07 a success. Randall Sobie and Reda Tafirout CHEP'07 Conference Chairs

Aeroelastic Model Structure Computation for Envelope Expansion

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.

2007-01-01

Structure detection is a procedure for selecting a subset of candidate terms, from a full model description, that best describes the observed output. This is a necessary procedure to compute an efficient system description which may afford greater insight into the functionality of the system or a simpler controller design. Structure computation as a tool for black-box modelling may be of critical importance in the development of robust, parsimonious models for the flight-test community. Moreover, this approach may lead to efficient strategies for rapid envelope expansion which may save significant development time and costs. In this study, a least absolute shrinkage and selection operator (LASSO) technique is investigated for computing efficient model descriptions of nonlinear aeroelastic systems. The LASSO minimises the residual sum of squares by the addition of an l(sub 1) penalty term on the parameter vector of the traditional 2 minimisation problem. Its use for structure detection is a natural extension of this constrained minimisation approach to pseudolinear regression problems which produces some model parameters that are exactly zero and, therefore, yields a parsimonious system description. Applicability of this technique for model structure computation for the F/A-18 Active Aeroelastic Wing using flight test data is shown for several flight conditions (Mach numbers) by identifying a parsimonious system description with a high percent fit for cross-validated data.

On the crystal structure of the vaterite polymorph of CaCO3: a calcium-43 solid-state NMR and computational assessment.

PubMed

Burgess, Kevin M N; Bryce, David L

2015-02-01

The vaterite polymorph of CaCO3 has puzzled crystallographers for decades in part due to difficulties in obtaining single crystals. The multiple proposed structures for the vaterite polymorph of CaCO3 are assessed using a combined (43)Ca solid-state nuclear magnetic resonance (SSNMR) spectroscopic and computational approach. A combination of improved experimental and computational methods, along with a calibrated chemical shift scale and (43)Ca nuclear quadrupole moment, allow for improved insights relative to our earlier work (Bryce et al., J. Am. Chem. Soc. 2008, 130, 9282). Here, we synthesize a (43)Ca isotopically-enriched sample of vaterite and perform high-resolution quadrupolar SSNMR experiments including magic-angle spinning (MAS), double-rotation (DOR), and multiple-quantum (MQ) MAS experiments at magnetic field strengths of 9.4 and 21.1T. We identify one crystallographically unique Ca(2+) site in vaterite with a slight distribution in both chemical shifts and quadrupolar parameters. Both the experimental (43)Ca electric field gradient tensor and the isotropic chemical shift for vaterite are compared to those calculated with the gauge-including projector-augmented-wave (GIPAW) DFT method in an attempt to identify the model that best represents the crystal structure of vaterite. Simulations of (43)Ca DOR and MAS NMR spectra based on the NMR parameters computed for a total of 18 structural models for vaterite allow us to distinguish between these models. Among these 18, the P3221 and C2 structures provide simulated spectra and diffractograms in best agreement with all experimental data. Copyright © 2014 Elsevier Inc. All rights reserved.

Computational structures technology and UVA Center for CST

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1992-01-01

Rapid advances in computer hardware have had a profound effect on various engineering and mechanics disciplines, including the materials, structures, and dynamics disciplines. A new technology, computational structures technology (CST), has recently emerged as an insightful blend between material modeling, structural and dynamic analysis and synthesis on the one hand, and other disciplines such as computer science, numerical analysis, and approximation theory, on the other hand. CST is an outgrowth of finite element methods developed over the last three decades. The focus of this presentation is on some aspects of CST which can impact future airframes and propulsion systems, as well as on the newly established University of Virginia (UVA) Center for CST. The background and goals for CST are described along with the motivations for developing CST, and a brief discussion is made on computational material modeling. We look at the future in terms of technical needs, computing environment, and research directions. The newly established UVA Center for CST is described. One of the research projects of the Center is described, and a brief summary of the presentation is given.

78 FR 47805 - Test Documentation for Digital Computer Software Used in Safety Systems of Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-06

... Documents Access and Management System (ADAMS): You may access publicly available documents online in the... Management Plans for Digital Computer Software used in Safety Systems of Nuclear Power Plants,'' issued for... Used in Safety Systems of Nuclear Power Plants AGENCY: Nuclear Regulatory Commission. ACTION: Revision...

Overview of computational structural methods for modern military aircraft

NASA Technical Reports Server (NTRS)

Kudva, J. N.

1992-01-01

Computational structural methods are essential for designing modern military aircraft. This briefing deals with computational structural methods (CSM) currently used. First a brief summary of modern day aircraft structural design procedures is presented. Following this, several ongoing CSM related projects at Northrop are discussed. Finally, shortcomings in this area, future requirements, and summary remarks are given.

A computer system to analyze showers in nuclear emulsions: Center Director's discretionary fund report

NASA Technical Reports Server (NTRS)

Meegan, C. A.; Fountain, W. F.; Berry, F. A., Jr.

1987-01-01

A system to rapidly digitize data from showers in nuclear emulsions is described. A TV camera views the emulsions though a microscope. The TV output is superimposed on the monitor of a minicomputer. The operator uses the computer's graphics capability to mark the positions of particle tracks. The coordinates of each track are stored on a disk. The computer then predicts the coordinates of each track through successive layers of emulsion. The operator, guided by the predictions, thus tracks and stores the development of the shower. The system provides a significant improvement over purely manual methods of recording shower development in nuclear emulsion stacks.

Pavement-Transportation Computer Assisted Structural Engineering (PCASE) Implementation of the Modified Berggren (ModBerg) Equation for Computing the Frost Penetration Depth within Pavement Structures

DTIC Science & Technology

2012-04-01

ER D C/ G SL T R -1 2 -1 5 Pavement -Transportation Computer Assisted Structural Engineering (PCASE) Implementation of the Modified...Berggren (ModBerg) Equation for Computing the Frost Penetration Depth within Pavement Structures G eo te ch n ic al a n d S tr u ct u re s La b or at...April 2012 Pavement -Transportation Computer Assisted Structural Engineering (PCASE) Implementation of the Modified Berggren (ModBerg) Equation for

SINGER: A Computer Code for General Analysis of Two-Dimensional Reinforced Concrete Structures. Volume 1. Solution Process

DTIC Science & Technology

1975-05-01

Conference on Earthquake Engineering, Santiago de Chile, 13-18 January 1969, Vol. I , Session B2, Chilean Association oil Seismology and Earth- quake...Nuclear Agency May 1975 DISTRIBUTED BY: KJ National Technical Information Service U. S. DEPARTMENT OF COMMERCE ^804J AFWL-TR-74-228, Vol. I ...CM o / i ’•fu.r ) V V AFWL-TR- 74-228 Vol. I SINGER: A COMPUTER CODE FOR GENERAL ANALYSIS OF TWO-DIMENSIONAL CONCRETE STRUCTURES Volum« I

BOLD VENTURE COMPUTATION SYSTEM for nuclear reactor core analysis, Version III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vondy, D.R.; Fowler, T.B.; Cunningham, G.W. III.

1981-06-01

This report is a condensed documentation for VERSION III of the BOLD VENTURE COMPUTATION SYSTEM for nuclear reactor core analysis. An experienced analyst should be able to use this system routinely for solving problems by referring to this document. Individual reports must be referenced for details. This report covers basic input instructions and describes recent extensions to the modules as well as to the interface data file specifications. Some application considerations are discussed and an elaborate sample problem is used as an instruction aid. Instructions for creating the system on IBM computers are also given.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

NASA Astrophysics Data System (ADS)

Zerkin, V. V.; Pritychenko, B.

2018-04-01

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ∼22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. It is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.

Computing the cross sections of nuclear reactions with nuclear clusters emission for proton energies between 30 MeV and 2.6 GeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Korovin, Yu. A.; Maksimushkina, A. V., E-mail: AVMaksimushkina@mephi.ru; Frolova, T. A.

2016-12-15

The cross sections of nuclear reactions involving emission of clusters of light nuclei in proton collisions with a heavy-metal target are computed for incident-proton energies between 30 MeV and 2.6 GeV. The calculation relies on the ALICE/ASH and CASCADE/INPE computer codes. The parameters determining the pre-equilibrium cluster emission are varied in the computation.

An introduction to using the FORTRAN programs provided with Computational Nuclear Physics 1 Nuclear Structure

NASA Technical Reports Server (NTRS)

Boytos, Matthew A.; Norbury, John W.

1992-01-01

The authors of this paper have provided a set of ready-to-run FORTRAN programs that should be useful in the field of theoretical nuclear physics. The purpose of this document is to provide a simple synopsis of the programs and their use. A separate section is devoted to each program set and includes: abstract; files; compiling, linking, and running; obtaining results; and a tutorial.

Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus.

PubMed

Razin, S V; Borunova, V V; Iarovaia, O V; Vassetzky, Y S

2014-07-01

Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.

Maria Goeppert Mayer, the Nuclear Shell Structure, and Magic Numbers

Science.gov Websites

dropdown arrow Site Map A-Z Index Menu Synopsis Maria Goeppert-Mayer, the Nuclear Shell Model, and Magic explanation of how neutrons and protons within atomic nuclei are structured. Called the "nuclear shell American husband, chemical physicist Joseph Mayer. At Argonne, Goeppert-Mayer learned most of her nuclear

Aeroelastic Model Structure Computation for Envelope Expansion

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.

2007-01-01

Structure detection is a procedure for selecting a subset of candidate terms, from a full model description, that best describes the observed output. This is a necessary procedure to compute an efficient system description which may afford greater insight into the functionality of the system or a simpler controller design. Structure computation as a tool for black-box modeling may be of critical importance in the development of robust, parsimonious models for the flight-test community. Moreover, this approach may lead to efficient strategies for rapid envelope expansion that may save significant development time and costs. In this study, a least absolute shrinkage and selection operator (LASSO) technique is investigated for computing efficient model descriptions of non-linear aeroelastic systems. The LASSO minimises the residual sum of squares with the addition of an l(Sub 1) penalty term on the parameter vector of the traditional l(sub 2) minimisation problem. Its use for structure detection is a natural extension of this constrained minimisation approach to pseudo-linear regression problems which produces some model parameters that are exactly zero and, therefore, yields a parsimonious system description. Applicability of this technique for model structure computation for the F/A-18 (McDonnell Douglas, now The Boeing Company, Chicago, Illinois) Active Aeroelastic Wing project using flight test data is shown for several flight conditions (Mach numbers) by identifying a parsimonious system description with a high percent fit for cross-validated data.

Computational predictions of the new Gallium nitride nanoporous structures

NASA Astrophysics Data System (ADS)

Lien, Le Thi Hong; Tuoc, Vu Ngoc; Duong, Do Thi; Thu Huyen, Nguyen

2018-05-01

Nanoporous structural prediction is emerging area of research because of their advantages for a wide range of materials science and technology applications in opto-electronics, environment, sensors, shape-selective and bio-catalysis, to name just a few. We propose a computationally and technically feasible approach for predicting Gallium nitride nanoporous structures with hollows at the nano scale. The designed porous structures are studied with computations using the density functional tight binding (DFTB) and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with their parent’s bulk stable phase. The electronic band structures of these nanoporous structures are finally examined in detail.

Structural considerations for underground nuclear power plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarne, Y.

The advantages and disadvantages of underground nuclear power plants are briefly reviewed. The impact of underground contruction on plant layout and structural design are discussed. Schedules and costs for construction are compared with those for conventional plants.

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE PAGES

Zerkin, V. V.; Pritychenko, B.

2018-02-04

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

The experimental nuclear reaction data (EXFOR): Extended computer database and Web retrieval system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zerkin, V. V.; Pritychenko, B.

The EXchange FORmat (EXFOR) experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource is based on numerical data sets and bibliographical information of ~22,000 experiments since the beginning of nuclear science. The principles of the computer database organization, its extended contents and Web applications development are described. New capabilities for the data sets uploads, renormalization, covariance matrix, and inverse reaction calculations are presented in this paper. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development, and research activities. Finally,more » it is publicly available at the websites of the International Atomic Energy Agency Nuclear Data Section, http://www-nds.iaea.org/exfor, the U.S. National Nuclear Data Center, http://www.nndc.bnl.gov/exfor, and the mirror sites in China, India and Russian Federation.« less

Studying the Effects of Nuclear Weapons Using a Slide-Rule Computer

ERIC Educational Resources Information Center

Shastri, Ananda

2007-01-01

This paper describes the construction of a slide-rule computer that allows one to quickly determine magnitudes of several effects that result from the detonation of a nuclear device. Suggestions for exercises are also included that allow high school and college-level physics students to explore scenarios involving these effects. It is hoped that…

Nuclear cartography: patterns in binding energies and subatomic structure

NASA Astrophysics Data System (ADS)

Simpson, E. C.; Shelley, M.

2017-11-01

Nuclear masses and binding energies are some of the first nuclear properties met in high school physics, and can be used to introduce radioactive decays, fusion, and fission. With relatively little extension, they can also illustrate fundamental concepts in nuclear physics, such as shell structure and pairing, and to discuss how the elements around us were formed in stars. One way of visualising these nuclear properties is through the nuclide chart, which maps all nuclides as a function of their proton and neutron numbers. Here we use the nuclide chart to illustrate various aspects of nuclear physics, and present 3D visualisations of it produced as part of the binding blocks project.

Computational Simulation of Composite Structural Fatigue

NASA Technical Reports Server (NTRS)

Minnetyan, Levon; Chamis, Christos C. (Technical Monitor)

2005-01-01

Progressive damage and fracture of composite structures subjected to monotonically increasing static, tension-tension cyclic, pressurization, and flexural cyclic loading are evaluated via computational simulation. Constituent material properties, stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for composites. Damage initiation, growth, accumulation, and propagation to fracture due to monotonically increasing static and cyclic loads are included in the simulations. Results show the number of cycles to failure at different temperatures and the damage progression sequence during different degradation stages. A procedure is outlined for use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of results with insight for design decisions.

Computational Simulation of Composite Structural Fatigue

NASA Technical Reports Server (NTRS)

Minnetyan, Levon

2004-01-01

Progressive damage and fracture of composite structures subjected to monotonically increasing static, tension-tension cyclic, pressurization, and flexural cyclic loading are evaluated via computational simulation. Constituent material properties, stress and strain limits are scaled up to the structure level to evaluate the overall damage and fracture propagation for composites. Damage initiation, growth, accumulation, and propagation to fracture due to monotonically increasing static and cyclic loads are included in the simulations. Results show the number of cycles to failure at different temperatures and the damage progression sequence during different degradation stages. A procedure is outlined for use of computational simulation data in the assessment of damage tolerance, determination of sensitive parameters affecting fracture, and interpretation of results with insight for design decisions.

Nuclear structure and decay data evaluation in Europe

NASA Astrophysics Data System (ADS)

Negret, Alexandru; Balabanski, Dimiter; Dimitriou, Paraskevi; Elekes, Zoltan; Mertzimekis, Theo J.; Pascu, Sorin; Timar, Janos

2017-09-01

Nuclear Structure and Decay Data (NSDD) activities in Europe include mass-chain and individual nuclei evaluations as well as horizontal evaluations and compilations, data dissemination and educational activities. As such they are essential for a large range of applications from energy, environmental, and medical to basic research in nuclear structure and reactions, all of which are intensively pursued in Europe. Although the NSDD evaluation groups in Europe form part of the international network of NSDD evaluators, which is coordinated by the International Atomic Energy Agency, they are faced with some very distinct challenges. We shortly present the NSDD Data Centre at IFIN-HH, Bucharest and discuss possible actions to improve the situation for the entire European NSDD evaluation effort.

Nuclear reactor fuel containment safety structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosewell, M.P.

A nuclear reactor fuel containment safety structure is disclosed and is shown to include an atomic reactor fuel shield with a fuel containment chamber and exhaust passage means, and a deactivating containment base attached beneath the fuel reactor shield and having exhaust passages, manifold, and fluxing and control material and vessels. 1 claim, 8 figures.

Nuclear structure studies with gamma-ray beams

DOE PAGES

Tonchev, Anton; Bhatia, Chitra; Kelley, John; ...

2015-05-28

In stable and weakly bound neutron-rich nuclei, a resonance-like concentration of dipole states has been observed for excitation energies below the neutron-separation energy. This clustering of strong dipole states has been named the Pygmy Dipole Resonance (PDR) in contrast to the Giant Dipole Resonance (GDR) that dominates the E1 response. Understanding the PDR is presently of great interest in nuclear structure and nuclear astrophysics. High-sensitivity studies of E1 and M1 transitions in closed-shell nuclei using monoenergetic and 100% linearly-polarized photon beams are presented.

Nuclear Structure Studies with Gamma-Ray Beams

NASA Astrophysics Data System (ADS)

Tonchev, Anton; Bhatia, Chitra; Kelley, John; Raut, Rajarshi; Rusev, Gencho; Tornow, Werner; Tsoneva, Nadia

2015-05-01

In stable and weakly bound neutron-rich nuclei, a resonance-like concentration of dipole states has been observed for excitation energies below the neutron-separation energy. This clustering of strong dipole states has been named the Pygmy Dipole Resonance (PDR) in contrast to the Giant Dipole Resonance (GDR) that dominates the E1 response. Understanding the PDR is presently of great interest in nuclear structure and nuclear astrophysics. High-sensitivity studies of E1 and M1 transitions in closed-shell nuclei using monoenergetic and 100% linearly-polarized photon beams are presented.

Designing a new structure for storing nuclear data: Progress of the Working Party for Evaluation Cooperation subgroup #38

DOE PAGES

Mattoon, C. M.; Beck, B. R.

2015-12-24

An international effort is underway to design a new structure for storing and using nuclear reaction data, with the goal of eventually replacing the current standard, ENDF-6. This effort, organized by the Working Party for Evaluation Cooperation, was initiated in 2012 and has resulted in a list of requirements and specifications for how the proposed new structure shall perform. The new structure will take advantage of new developments in computational tools, using a nested hierarchy to store data. Here, the structure can be stored in text form (such as an XML file) for human readability and data sharing, or itmore » can be stored in binary to optimize data access. In this paper, we present the progress towards completing the requirements, specifications and implementation of the new structure.« less

Designing a new structure for storing nuclear data: Progress of the Working Party for Evaluation Cooperation subgroup #38

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mattoon, C. M.; Beck, B. R.

An international effort is underway to design a new structure for storing and using nuclear reaction data, with the goal of eventually replacing the current standard, ENDF-6. This effort, organized by the Working Party for Evaluation Cooperation, was initiated in 2012 and has resulted in a list of requirements and specifications for how the proposed new structure shall perform. The new structure will take advantage of new developments in computational tools, using a nested hierarchy to store data. Here, the structure can be stored in text form (such as an XML file) for human readability and data sharing, or itmore » can be stored in binary to optimize data access. In this paper, we present the progress towards completing the requirements, specifications and implementation of the new structure.« less

A personal computer-based nuclear magnetic resonance spectrometer

NASA Astrophysics Data System (ADS)

Job, Constantin; Pearson, Robert M.; Brown, Michael F.

1994-11-01

Nuclear magnetic resonance (NMR) spectroscopy using personal computer-based hardware has the potential of enabling the application of NMR methods to fields where conventional state of the art equipment is either impractical or too costly. With such a strategy for data acquisition and processing, disciplines including civil engineering, agriculture, geology, archaeology, and others have the possibility of utilizing magnetic resonance techniques within the laboratory or conducting applications directly in the field. Another aspect is the possibility of utilizing existing NMR magnets which may be in good condition but unused because of outdated or nonrepairable electronics. Moreover, NMR applications based on personal computer technology may open up teaching possibilities at the college or even secondary school level. The goal of developing such a personal computer (PC)-based NMR standard is facilitated by existing technologies including logic cell arrays, direct digital frequency synthesis, use of PC-based electrical engineering software tools to fabricate electronic circuits, and the use of permanent magnets based on neodymium-iron-boron alloy. Utilizing such an approach, we have been able to place essentially an entire NMR spectrometer console on two printed circuit boards, with the exception of the receiver and radio frequency power amplifier. Future upgrades to include the deuterium lock and the decoupler unit are readily envisioned. The continued development of such PC-based NMR spectrometers is expected to benefit from the fast growing, practical, and low cost personal computer market.

Inspection of Nuclear Power Plant Containment Structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graves, H.L.; Naus, D.J.; Norris, W.E.

1998-12-01

Safety-related nuclear power plant (NPP) structures are designed to withstand loadings from a number of low-probability external and interval events, such as earthquakes, tornadoes, and loss-of-coolant accidents. Loadings incurred during normal plant operation therefore generally are not significant enough to cause appreciable degradation. However, these structures are susceptible to aging by various processes depending on the operating environment and service conditions. The effects of these processes may accumulate within these structures over time to cause failure under design conditions, or lead to costly repair. In the late 1980s and early 1990s several occurrences of degradation of NPP structures were discoveredmore » at various facilities (e.g., corrosion of pressure boundary components, freeze- thaw damage of concrete, and larger than anticipated loss of prestressing force). Despite these degradation occurrences and a trend for an increasing rate of occurrence, in-service inspection of the safety-related structures continued to be performed in a somewhat cursory manner. Starting in 1991, the U.S. Nuclear Regulatory Commission (USNRC) published the first of several new requirements to help ensure that adequate in-service inspection of these structures is performed. Current regulatory in-service inspection requirements are reviewed and a summary of degradation experience presented. Nondestructive examination techniques commonly used to inspect the NPP steel and concrete structures to identify and quantify the amount of damage present are reviewed. Finally, areas where nondestructive evaluation techniques require development (i.e., inaccessible portions of the containment pressure boundary, and thick heavily reinforced concrete sections are discussed.« less

Computer programs of information processing of nuclear physical methods as a demonstration material in studying nuclear physics and numerical methods

NASA Astrophysics Data System (ADS)

Bateev, A. B.; Filippov, V. P.

2017-01-01

The principle possibility of using computer program Univem MS for Mössbauer spectra fitting as a demonstration material at studying such disciplines as atomic and nuclear physics and numerical methods by students is shown in the article. This program is associated with nuclear-physical parameters such as isomer (or chemical) shift of nuclear energy level, interaction of nuclear quadrupole moment with electric field and of magnetic moment with surrounded magnetic field. The basic processing algorithm in such programs is the Least Square Method. The deviation of values of experimental points on spectra from the value of theoretical dependence is defined on concrete examples. This value is characterized in numerical methods as mean square deviation. The shape of theoretical lines in the program is defined by Gaussian and Lorentzian distributions. The visualization of the studied material on atomic and nuclear physics can be improved by similar programs of the Mössbauer spectroscopy, X-ray Fluorescence Analyzer or X-ray diffraction analysis.

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

NASA Astrophysics Data System (ADS)

Subramaniam, Karthigeyan

2016-08-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and processes in social settings like classrooms thereby providing glimpses into the complex dynamics of teacher-students interactions, configurations, and conventions during collective meaning making and knowledge creation. Data included observations, interviews, and focus group interviews. Analysis revealed that the dominant participation structure evident within participants' instruction with computer technology was ( Teacher) initiation-( Student and Teacher) response sequences-( Teacher) evaluate participation structure. Three key events characterized the how participants organized this participation structure in their classrooms: setting the stage for interactive instruction, the joint activity, and maintaining accountability. Implications include the following: (1) teacher educators need to tap into the knowledge base that underscores science teachers' learning to teach philosophies when computer technology is used in instruction. (2) Teacher educators need to emphasize the essential idea that learning and cognition is not situated within the computer technology but within the pedagogical practices, specifically the participation structures. (3) The pedagogical practices developed with the integration or with the use of computer technology underscored by the teachers' own knowledge of classroom contexts and curriculum needs to be the focus for how students learn science content with computer technology instead of just focusing on how computer technology solely supports students learning of science content.

Structural basis for the regulation of nuclear import of Epstein-Barr virus nuclear antigen 1 (EBNA1) by phosphorylation of the nuclear localization signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakada, Ryohei; Hirano, Hidemi; Structural Biology Research Center, Graduate School of Science, Nagoya University

Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) is expressed in every EBV-positive tumor and is essential for the maintenance, replication, and transcription of the EBV genome in the nucleus of host cells. EBNA1 is a serine phosphoprotein, and it has been shown that phosphorylation of S385 in the nuclear localization signal (NLS) of EBNA1 increases the binding affinity to the nuclear import adaptor importin-α1 as well as importin-α5, and stimulates nuclear import of EBNA1. To gain insights into how phosphorylation of the EBNA1 NLS regulates nuclear import, we have determined the crystal structures of two peptide complexes of importin-α1: onemore » with S385-phosphorylated EBNA1 NLS peptide, determined at 2.0 Å resolution, and one with non-phosphorylated EBNA1 NLS peptide, determined at 2.2 Å resolution. The structures show that EBNA1 NLS binds to the major and minor NLS-binding sites of importin-α1, and indicate that the binding affinity of the EBNA1 NLS to the minor NLS-binding site could be enhanced by phosphorylation of S385 through electrostatic interaction between the phosphate group of phospho-S385 and K392 of importin-α1 (corresponding to R395 of importin-α5) on armadillo repeat 8. - Highlights: • Nuclear import of EBNA1 can be regulated by phosphorylation of NLS. • Crystal structures of importin-α1 bound to the NLS peptides of EBNA1 are solved. • Structures provide insights into how phosphorylation can regulate nuclear import.« less

Military engine computational structures technology

NASA Technical Reports Server (NTRS)

Thomson, Daniel E.

1992-01-01

Integrated High Performance Turbine Engine Technology Initiative (IHPTET) goals require a strong analytical base. Effective analysis of composite materials is critical to life analysis and structural optimization. Accurate life prediction for all material systems is critical. User friendly systems are also desirable. Post processing of results is very important. The IHPTET goal is to double turbine engine propulsion capability by the year 2003. Fifty percent of the goal will come from advanced materials and structures, the other 50 percent will come from increasing performance. Computer programs are listed.

Vorinostat differentially alters 3D nuclear structure of cancer and non-cancerous esophageal cells.

PubMed

Nandakumar, Vivek; Hansen, Nanna; Glenn, Honor L; Han, Jessica H; Helland, Stephanie; Hernandez, Kathryn; Senechal, Patti; Johnson, Roger H; Bussey, Kimberly J; Meldrum, Deirdre R

2016-08-09

The histone deacetylase (HDAC) inhibitor vorinostat has received significant attention in recent years as an 'epigenetic' drug used to treat solid tumors. However, its mechanisms of action are not entirely understood, particularly with regard to its interaction with the aberrations in 3D nuclear structure that accompany neoplastic progression. We investigated the impact of vorinostat on human esophageal epithelial cell lines derived from normal, metaplastic (pre-cancerous), and malignant tissue. Using a combination of novel optical computed tomography (CT)-based quantitative 3D absorption microscopy and conventional confocal fluorescence microscopy, we show that subjecting malignant cells to vorinostat preferentially alters their 3D nuclear architecture relative to non-cancerous cells. Optical CT (cell CT) imaging of fixed single cells showed that drug-treated cancer cells exhibit significant alterations in nuclear morphometry. Confocal microscopy revealed that vorinostat caused changes in the distribution of H3K9ac-marked euchromatin and H3K9me3-marked constitutive heterochromatin. Additionally, 3D immuno-FISH showed that drug-induced expression of the DNA repair gene MGMT was accompanied by spatial relocation toward the center of the nucleus in the nuclei of metaplastic but not in non-neoplastic cells. Our data suggest that vorinostat's differential modulation of 3D nuclear architecture in normal and abnormal cells could play a functional role in its anti-cancer action.

Probabilistic structural mechanics research for parallel processing computers

NASA Technical Reports Server (NTRS)

Sues, Robert H.; Chen, Heh-Chyun; Twisdale, Lawrence A.; Martin, William R.

1991-01-01

Aerospace structures and spacecraft are a complex assemblage of structural components that are subjected to a variety of complex, cyclic, and transient loading conditions. Significant modeling uncertainties are present in these structures, in addition to the inherent randomness of material properties and loads. To properly account for these uncertainties in evaluating and assessing the reliability of these components and structures, probabilistic structural mechanics (PSM) procedures must be used. Much research has focused on basic theory development and the development of approximate analytic solution methods in random vibrations and structural reliability. Practical application of PSM methods was hampered by their computationally intense nature. Solution of PSM problems requires repeated analyses of structures that are often large, and exhibit nonlinear and/or dynamic response behavior. These methods are all inherently parallel and ideally suited to implementation on parallel processing computers. New hardware architectures and innovative control software and solution methodologies are needed to make solution of large scale PSM problems practical.

Synthesis of Efficient Structures for Concurrent Computation.

DTIC Science & Technology

1983-10-01

formal presentation of these techniques, called virtualisation and aggregation, can be found n [King-83$. 113.2 Census Functions Trees perform broadcast... Functions .. .. .. .. ... .... ... ... .... ... ... ....... 6 4 User-Assisted Aggregation .. .. .. .. ... ... ... .... ... .. .......... 6 5 Parallel...6. Simple Parallel Structure for Broadcasting .. .. .. .. .. . ... .. . .. . .... 4 Figure 7. Internal Structure of a Prefix Computation Network

COMPUTATIONAL METHODOLOGIES for REAL-SPACE STRUCTURAL REFINEMENT of LARGE MACROMOLECULAR COMPLEXES

PubMed Central

Goh, Boon Chong; Hadden, Jodi A.; Bernardi, Rafael C.; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C. Keith; Schulten, Klaus

2017-01-01

The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

Membrane proteins structures: A review on computational modeling tools.

PubMed

Almeida, Jose G; Preto, Antonio J; Koukos, Panagiotis I; Bonvin, Alexandre M J J; Moreira, Irina S

2017-10-01

Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Tungsten - Yttrium Based Nuclear Structural Materials

NASA Astrophysics Data System (ADS)

Ramana, Chintalapalle; Chessa, Jack; Martinenz, Gustavo

2013-04-01

The challenging problem currently facing the nuclear science community in this 21st century is design and development of novel structural materials, which will have an impact on the next-generation nuclear reactors. The materials available at present include reduced activation ferritic/martensitic steels, dispersion strengthened reduced activation ferritic steels, and vanadium- or tungsten-based alloys. These materials exhibit one or more specific problems, which are either intrinsic or caused by reactors. This work is focussed towards tungsten-yttrium (W-Y) based alloys and oxide ceramics, which can be utilized in nuclear applications. The goal is to derive a fundamental scientific understanding of W-Y-based materials. In collaboration with University of Califonia -- Davis, the project is designated to demonstrate the W-Y based alloys, ceramics and composites with enhanced physical, mechanical, thermo-chemical properties and higher radiation resistance. Efforts are focussed on understanding the microstructure, manipulating materials behavior under charged-particle and neutron irradiation, and create a knowledge database of defects, elemental diffusion/segregation, and defect trapping along grain boundaries and interfaces. Preliminary results will be discussed.

Promyelocytic Leukemia (Pml) Nuclear Bodies Are Protein Structures That Do Not Accumulate RNA

PubMed Central

Boisvert, François-Michel; Hendzel, Michael J.; Bazett-Jones, David P.

2000-01-01

The promyelocytic leukemia (PML) nuclear body (also referred to as ND10, POD, and Kr body) is involved in oncogenesis and viral infection. This subnuclear domain has been reported to be rich in RNA and a site of nascent RNA synthesis, implicating its direct involvement in the regulation of gene expression. We used an analytical transmission electron microscopic method to determine the structure and composition of PML nuclear bodies and the surrounding nucleoplasm. Electron spectroscopic imaging (ESI) demonstrates that the core of the PML nuclear body is a dense, protein-based structure, 250 nm in diameter, which does not contain detectable nucleic acid. Although PML nuclear bodies contain neither chromatin nor nascent RNA, newly synthesized RNA is associated with the periphery of the PML nuclear body, and is found within the chromatin-depleted region of the nucleoplasm immediately surrounding the core of the PML nuclear body. We further show that the RNA does not accumulate in the protein core of the structure. Our results dismiss the hypothesis that the PML nuclear body is a site of transcription, but support the model in which the PML nuclear body may contribute to the formation of a favorable nuclear environment for the expression of specific genes. PMID:10648561

Collective network for computer structures

DOEpatents

Blumrich, Matthias A [Ridgefield, CT; Coteus, Paul W [Yorktown Heights, NY; Chen, Dong [Croton On Hudson, NY; Gara, Alan [Mount Kisco, NY; Giampapa, Mark E [Irvington, NY; Heidelberger, Philip [Cortlandt Manor, NY; Hoenicke, Dirk [Ossining, NY; Takken, Todd E [Brewster, NY; Steinmacher-Burow, Burkhard D [Wernau, DE; Vranas, Pavlos M [Bedford Hills, NY

2011-08-16

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices ate included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network and class structures. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to needs of a processing algorithm.

Low Energy Nuclear Structure Modeling: Can It Be Improved?

NASA Astrophysics Data System (ADS)

Stone, Jirina R.

Since the discovery of the atomic nucleus in 1911 generations of physicists have devoted enormous effort to understand low energy nuclear structure. Properties of nuclei in their ground state, including mass, binding energy and shape, provide vital input to many areas of sub-atomic physics as well as astrophysics and cosmology. Low energy excited states are equally important for understanding nuclear dynamics. Yet, no consensus exists as to what is the best path to a theory which would not only consistently reproduce a wide variety of experimental data but also have enough predictive power to yield credible predictions in areas where data are still missing. In this contribution some of the main obstacles preventing building such a theory are discussed. These include modification of the free nucleon-nucleon force in the nuclear environment and effects of the sub-nucleon (quark) structure of the nucleon. Selected classes of nuclear models, mean-field, shell and ab-initio models are briefly outlined. Finally, suggestions are made for, at least partial, progress that can be achieved with the quark-meson coupling model, as reported in recent publication [1].

Novel computer-aided diagnosis of mesothelioma using nuclear structure of mesothelial cells in effusion cytology specimens

NASA Astrophysics Data System (ADS)

Tosun, Akif Burak; Yergiyev, Oleksandr; Kolouri, Soheil; Silverman, Jan F.; Rohde, Gustavo K.

2014-03-01

diagnostic standard is a pleural biopsy with subsequent histologic examination of the tissue demonstrating invasion by the tumor. The diagnostic tissue is obtained through thoracoscopy or open thoracotomy, both being highly invasive procedures. Thoracocenthesis, or removal of effusion fluid from the pleural space, is a far less invasive procedure that can provide material for cytological examination. However, it is insufficient to definitively confirm or exclude the diagnosis of malignant mesothelioma, since tissue invasion cannot be determined. In this study, we present a computerized method to detect and classify malignant mesothelioma based on the nuclear chromatin distribution from digital images of mesothelial cells in effusion cytology specimens. Our method aims at determining whether a set of nuclei belonging to a patient, obtained from effusion fluid images using image segmentation, is benign or malignant, and has a potential to eliminate the need for tissue biopsy. This method is performed by quantifying chromatin morphology of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the modified Fisher discriminant analysis, a k-nearest neighborhood classification, and a simple voting strategy. Our results show that we can classify the data of 10 different human cases with 100% accuracy after blind cross validation. We conclude that nuclear structure alone contains enough information to classify the malignant mesothelioma. We also conclude that the distribution of chromatin seems to be a discriminating feature between nuclei of benign and malignant mesothelioma cells.

Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.

PubMed

Kawaguchi, Risa; Kiryu, Hisanori

2016-05-06

RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Our novel software, "ParasoR", is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre

NASA Workshop on Computational Structural Mechanics 1987, part 2

NASA Technical Reports Server (NTRS)

Sykes, Nancy P. (Editor)

1989-01-01

Advanced methods and testbed/simulator development topics are discussed. Computational Structural Mechanics (CSM) testbed architecture, engine structures simulation, applications to laminate structures, and a generic element processor are among the topics covered.

Development and applications of two computational procedures for determining the vibration modes of structural systems. [aircraft structures - aerospaceplanes

NASA Technical Reports Server (NTRS)

Kvaternik, R. G.

1975-01-01

Two computational procedures for analyzing complex structural systems for their natural modes and frequencies of vibration are presented. Both procedures are based on a substructures methodology and both employ the finite-element stiffness method to model the constituent substructures. The first procedure is a direct method based on solving the eigenvalue problem associated with a finite-element representation of the complete structure. The second procedure is a component-mode synthesis scheme in which the vibration modes of the complete structure are synthesized from modes of substructures into which the structure is divided. The analytical basis of the methods contains a combination of features which enhance the generality of the procedures. The computational procedures exhibit a unique utilitarian character with respect to the versatility, computational convenience, and ease of computer implementation. The computational procedures were implemented in two special-purpose computer programs. The results of the application of these programs to several structural configurations are shown and comparisons are made with experiment.

Space-Time Fluid-Structure Interaction Computation of Flapping-Wing Aerodynamics

DTIC Science & Technology

2013-12-01

SST-VMST." The structural mechanics computations are based on the Kirchhoff -Love shell model. We use a sequential coupling technique, which is...mechanics computations are based on the Kirchhoff -Love shell model. We use a sequential coupling technique, which is ap- plicable to some classes of FSI...we use the ST-VMS method in combination with the ST-SUPS method. The structural mechanics computations are mostly based on the Kirchhoff –Love shell

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Fluid/Structure Interaction Studies of Aircraft Using High Fidelity Equations on Parallel Computers

NASA Technical Reports Server (NTRS)

Guruswamy, Guru; VanDalsem, William (Technical Monitor)

1994-01-01

Abstract Aeroelasticity which involves strong coupling of fluids, structures and controls is an important element in designing an aircraft. Computational aeroelasticity using low fidelity methods such as the linear aerodynamic flow equations coupled with the modal structural equations are well advanced. Though these low fidelity approaches are computationally less intensive, they are not adequate for the analysis of modern aircraft such as High Speed Civil Transport (HSCT) and Advanced Subsonic Transport (AST) which can experience complex flow/structure interactions. HSCT can experience vortex induced aeroelastic oscillations whereas AST can experience transonic buffet associated structural oscillations. Both aircraft may experience a dip in the flutter speed at the transonic regime. For accurate aeroelastic computations at these complex fluid/structure interaction situations, high fidelity equations such as the Navier-Stokes for fluids and the finite-elements for structures are needed. Computations using these high fidelity equations require large computational resources both in memory and speed. Current conventional super computers have reached their limitations both in memory and speed. As a result, parallel computers have evolved to overcome the limitations of conventional computers. This paper will address the transition that is taking place in computational aeroelasticity from conventional computers to parallel computers. The paper will address special techniques needed to take advantage of the architecture of new parallel computers. Results will be illustrated from computations made on iPSC/860 and IBM SP2 computer by using ENSAERO code that directly couples the Euler/Navier-Stokes flow equations with high resolution finite-element structural equations.

Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.

PubMed

Eddy, Sean R

2014-01-01

Transcriptomics experiments and computational predictions both enable systematic discovery of new functional RNAs. However, many putative noncoding transcripts arise instead from artifacts and biological noise, and current computational prediction methods have high false positive rates. I discuss prospects for improving computational methods for analyzing and identifying functional RNAs, with a focus on detecting signatures of conserved RNA secondary structure. An interesting new front is the application of chemical and enzymatic experiments that probe RNA structure on a transcriptome-wide scale. I review several proposed approaches for incorporating structure probing data into the computational prediction of RNA secondary structure. Using probabilistic inference formalisms, I show how all these approaches can be unified in a well-principled framework, which in turn allows RNA probing data to be easily integrated into a wide range of analyses that depend on RNA secondary structure inference. Such analyses include homology search and genome-wide detection of new structural RNAs.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Embedded random matrix ensembles from nuclear structure and their recent applications

NASA Astrophysics Data System (ADS)

Kota, V. K. B.; Chavda, N. D.

Embedded random matrix ensembles generated by random interactions (of low body rank and usually two-body) in the presence of a one-body mean field, introduced in nuclear structure physics, are now established to be indispensable in describing statistical properties of a large number of isolated finite quantum many-particle systems. Lie algebra symmetries of the interactions, as identified from nuclear shell model and the interacting boson model, led to the introduction of a variety of embedded ensembles (EEs). These ensembles with a mean field and chaos generating two-body interaction generate in three different stages, delocalization of wave functions in the Fock space of the mean-field basis states. The last stage corresponds to what one may call thermalization and complex nuclei, as seen from many shell model calculations, lie in this region. Besides briefly describing them, their recent applications to nuclear structure are presented and they are (i) nuclear level densities with interactions; (ii) orbit occupancies; (iii) neutrinoless double beta decay nuclear transition matrix elements as transition strengths. In addition, their applications are also presented briefly that go beyond nuclear structure and they are (i) fidelity, decoherence, entanglement and thermalization in isolated finite quantum systems with interactions; (ii) quantum transport in disordered networks connected by many-body interactions with centrosymmetry; (iii) semicircle to Gaussian transition in eigenvalue densities with k-body random interactions and its relation to the Sachdev-Ye-Kitaev (SYK) model for majorana fermions.

Modeling Human-Computer Decision Making with Covariance Structure Analysis.

ERIC Educational Resources Information Center

Coovert, Michael D.; And Others

Arguing that sufficient theory exists about the interplay between human information processing, computer systems, and the demands of various tasks to construct useful theories of human-computer interaction, this study presents a structural model of human-computer interaction and reports the results of various statistical analyses of this model.…

Computing Properties of Hadrons, Nuclei and Nuclear Matter from Quantum Chromodynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savage, Martin J.

This project was part of a coordinated software development effort which the nuclear physics lattice QCD community pursues in order to ensure that lattice calculations can make optimal use of present, and forthcoming leadership-class and dedicated hardware, including those of the national laboratories, and prepares for the exploitation of future computational resources in the exascale era. The UW team improved and extended software libraries used in lattice QCD calculations related to multi-nucleon systems, enhanced production running codes related to load balancing multi-nucleon production on large-scale computing platforms, and developed SQLite (addressable database) interfaces to efficiently archive and analyze multi-nucleon datamore » and developed a Mathematica interface for the SQLite databases.« less

Soil structure characterized using computed tomographic images

Treesearch

Zhanqi Cheng; Stephen H. Anderson; Clark J. Gantzer; J. W. Van Sambeek

2003-01-01

Fractal analysis of soil structure is a relatively new method for quantifying the effects of management systems on soil properties and quality. The objective of this work was to explore several methods of studying images to describe and quantify structure of soils under forest management. This research uses computed tomography and a topological method called Multiple...

Giga-voxel computational morphogenesis for structural design

NASA Astrophysics Data System (ADS)

Aage, Niels; Andreassen, Erik; Lazarov, Boyan S.; Sigmund, Ole

2017-10-01

In the design of industrial products ranging from hearing aids to automobiles and aeroplanes, material is distributed so as to maximize the performance and minimize the cost. Historically, human intuition and insight have driven the evolution of mechanical design, recently assisted by computer-aided design approaches. The computer-aided approach known as topology optimization enables unrestricted design freedom and shows great promise with regard to weight savings, but its applicability has so far been limited to the design of single components or simple structures, owing to the resolution limits of current optimization methods. Here we report a computational morphogenesis tool, implemented on a supercomputer, that produces designs with giga-voxel resolution—more than two orders of magnitude higher than previously reported. Such resolution provides insights into the optimal distribution of material within a structure that were hitherto unachievable owing to the challenges of scaling up existing modelling and optimization frameworks. As an example, we apply the tool to the design of the internal structure of a full-scale aeroplane wing. The optimized full-wing design has unprecedented structural detail at length scales ranging from tens of metres to millimetres and, intriguingly, shows remarkable similarity to naturally occurring bone structures in, for example, bird beaks. We estimate that our optimized design corresponds to a reduction in mass of 2-5 per cent compared to currently used aeroplane wing designs, which translates into a reduction in fuel consumption of about 40-200 tonnes per year per aeroplane. Our morphogenesis process is generally applicable, not only to mechanical design, but also to flow systems, antennas, nano-optics and micro-systems.

Giga-voxel computational morphogenesis for structural design.

PubMed

Aage, Niels; Andreassen, Erik; Lazarov, Boyan S; Sigmund, Ole

2017-10-04

In the design of industrial products ranging from hearing aids to automobiles and aeroplanes, material is distributed so as to maximize the performance and minimize the cost. Historically, human intuition and insight have driven the evolution of mechanical design, recently assisted by computer-aided design approaches. The computer-aided approach known as topology optimization enables unrestricted design freedom and shows great promise with regard to weight savings, but its applicability has so far been limited to the design of single components or simple structures, owing to the resolution limits of current optimization methods. Here we report a computational morphogenesis tool, implemented on a supercomputer, that produces designs with giga-voxel resolution-more than two orders of magnitude higher than previously reported. Such resolution provides insights into the optimal distribution of material within a structure that were hitherto unachievable owing to the challenges of scaling up existing modelling and optimization frameworks. As an example, we apply the tool to the design of the internal structure of a full-scale aeroplane wing. The optimized full-wing design has unprecedented structural detail at length scales ranging from tens of metres to millimetres and, intriguingly, shows remarkable similarity to naturally occurring bone structures in, for example, bird beaks. We estimate that our optimized design corresponds to a reduction in mass of 2-5 per cent compared to currently used aeroplane wing designs, which translates into a reduction in fuel consumption of about 40-200 tonnes per year per aeroplane. Our morphogenesis process is generally applicable, not only to mechanical design, but also to flow systems, antennas, nano-optics and micro-systems.

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

PubMed Central

O’Sullivan, Justin M.; Pai, Dave A.; Cridge, Andrew G.; Engelke, David R.; Ganley, Austen R. D.

2016-01-01

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfil the cellular demand for rRNA, the ribosomal RNA genes (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization. PMID:25436580

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

PubMed

O'Sullivan, Justin M; Pai, Dave A; Cridge, Andrew G; Engelke, David R; Ganley, Austen R D

2013-06-01

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribosomal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review, we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization.

77 FR 50720 - Test Documentation for Digital Computer Software Used in Safety Systems of Nuclear Power Plants

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0195] Test Documentation for Digital Computer Software...) is issuing for public comment draft regulatory guide (DG), DG-1207, ``Test Documentation for Digital... practices for test documentation for software and computer systems as described in the Institute of...

Applications of a global nuclear-structure model to studies of the heaviest elements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moeller, P.; Nix, J.R.

1993-10-01

We present some new results on heavy-element nuclear-structure properties calculated on the basis of the finite-range droplet model and folded-Yukawa single-particle potential. Specifically, we discuss calculations of nuclear ground-state masses and microscopic corrections, {alpha}-decay properties, {beta}-decay properties, fission potential-energy surfaces, and spontaneous-fission half-lives. These results, obtained in a global nuclear-structure approach, are particularly reliable for describing the stability properties of the heaviest elements.

Computational Chemistry Using Modern Electronic Structure Methods

ERIC Educational Resources Information Center

Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

2007-01-01

Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

Nuclear structure functions at a future electron-ion collider

DOE PAGES

Aschenauer, E. C.; Fazio, S.; Lamont, M. A. C.; ...

2017-12-07

The quantitative knowledge of heavy nuclei's partonic structure is currently limited to rather large values of momentum fraction x { robust experimental constraints below x ~ 10 -2 at low resolution scale Q 2 are particularly scarce. This is in sharp contrast to the free proton's structure which has been probed in deep inelastic scattering (DIS) measurements down to x ~ 10 -5 at perturbative resolution scales. The construction of an Electron-Ion Collider (EIC) with a possibility to operate with a wide variety of nuclei, will allow one to explore the low-x region in much greater detail. In the presentmore » paper we simulate the extraction of the nuclear structure functions from measurements of inclusive and charm reduced cross sections at an EIC. The potential constraints are studied by analyzing simulated data directly in a next-to-leading order global fit of nuclear parton distribution functions based on the recent EPPS16 analysis. A special emphasis is placed on studying the impact an EIC would have on extracting the nuclear gluon PDF, the partonic component most prone to non-linear e ects at low Q 2. In comparison to the current knowledge, we find that the gluon PDF can be measured at an EIC with significantly reduced uncertainties.« less

Nuclear structure functions at a future electron-ion collider

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aschenauer, E. C.; Fazio, S.; Lamont, M. A. C.

The quantitative knowledge of heavy nuclei's partonic structure is currently limited to rather large values of momentum fraction x { robust experimental constraints below x ~ 10 -2 at low resolution scale Q 2 are particularly scarce. This is in sharp contrast to the free proton's structure which has been probed in deep inelastic scattering (DIS) measurements down to x ~ 10 -5 at perturbative resolution scales. The construction of an Electron-Ion Collider (EIC) with a possibility to operate with a wide variety of nuclei, will allow one to explore the low-x region in much greater detail. In the presentmore » paper we simulate the extraction of the nuclear structure functions from measurements of inclusive and charm reduced cross sections at an EIC. The potential constraints are studied by analyzing simulated data directly in a next-to-leading order global fit of nuclear parton distribution functions based on the recent EPPS16 analysis. A special emphasis is placed on studying the impact an EIC would have on extracting the nuclear gluon PDF, the partonic component most prone to non-linear e ects at low Q 2. In comparison to the current knowledge, we find that the gluon PDF can be measured at an EIC with significantly reduced uncertainties.« less

Proceedings of the 2013 International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering - M and C 2013

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2013-07-01

The Mathematics and Computation Division of the American Nuclear (ANS) and the Idaho Section of the ANS hosted the 2013 International Conference on Mathematics and Computational Methods Applied to Nuclear Science and Engineering (M and C 2013). This proceedings contains over 250 full papers with topics ranging from reactor physics; radiation transport; materials science; nuclear fuels; core performance and optimization; reactor systems and safety; fluid dynamics; medical applications; analytical and numerical methods; algorithms for advanced architectures; and validation verification, and uncertainty quantification.

Crystal structure of importin-α3 bound to the nuclear localization signal of Ran-binding protein 3.

PubMed

Koyama, Masako; Matsuura, Yoshiyuki

2017-09-23

Ran-binding protein 3 (RanBP3) is a primarily nuclear Ran-binding protein that functions as an accessory factor in the Ran GTPase system. RanBP3 associates with Ran-specific nucleotide exchange factor RCC1 and enhances its catalytic activity towards Ran. RanBP3 also promotes CRM1-mediated nuclear export as well as CRM1-independent nuclear export of β-catenin, Smad2, and Smad3. Nuclear import of RanBP3 is dependent on the nuclear import adaptor protein importin-α and, RanBP3 is imported more efficiently by importin-α3 than by other members of the importin-α family. Protein kinase signaling pathways control nucleocytoplasmic transport through phosphorylation of RanBP3 at Ser58, immediately C-terminal to the nuclear localization signal (NLS) in the N-terminal region of RanBP3. Here we report the crystal structure of human importin-α3 bound to an N-terminal fragment of human RanBP3 containing the NLS sequence that is necessary and sufficient for nuclear import. The structure reveals that RanBP3 binds to importin-α3 residues that are strictly conserved in all seven isoforms of human importin-α at the major NLS-binding site, indicating that the region of importin-α outside the NLS-binding site, possibly the autoinhibotory importin-β1-binding domain, may be the key determinant for the preferential binding of RanBP3 to importin-α3. Computational docking simulation indicates that phosphorylation of RanBP3 at Ser58 could potentially stabilize the association of RanBP3 with importin-α through interactions between the phosphate moiety of phospho-Ser58 of RanBP3 and a cluster of basic residues (Arg96 and Lys97 in importin-α3) on armadillo repeat 1 of importin-α. Copyright © 2017 Elsevier Inc. All rights reserved.

Computer-Aided Design of RNA Origami Structures.

PubMed

Sparvath, Steffen L; Geary, Cody W; Andersen, Ebbe S

2017-01-01

RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets. The rich library of RNA structural and functional elements combined with the possibility to attach proteins through aptamer-based binding creates virtually limitless possibilities for constructing advanced RNA-based nanodevices.In this chapter we provide a detailed protocol for the single-stranded RNA origami design method using a simple 2-helix tall structure as an example. The first step involves 3D modeling of a double-crossover between two RNA double helices, followed by decoration with tertiary motifs. The second step deals with the construction of a 2D blueprint describing the secondary structure and sequence constraints that serves as the input for computer programs. In the third step, computer programs are used to design RNA sequences that are compatible with the structure, and the resulting outputs are evaluated and converted into DNA sequences to order.

An Adaptive Evaluation Structure for Computer-Based Instruction.

ERIC Educational Resources Information Center

Welsh, William A.

Adaptive Evaluation Structure (AES) is a set of linked computer programs designed to increase the effectiveness of interactive computer-assisted instruction at the college level. The package has four major features, the first of which is based on a prior cognitive inventory and on the accuracy and pace of student responses. AES adjusts materials…

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

PubMed Central

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10–20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease. PMID:26526043

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens.

PubMed

Liljeroos, Lassi; Malito, Enrico; Ferlenghi, Ilaria; Bottomley, Matthew James

2015-01-01

Vaccination is historically one of the most important medical interventions for the prevention of infectious disease. Previously, vaccines were typically made of rather crude mixtures of inactivated or attenuated causative agents. However, over the last 10-20 years, several important technological and computational advances have enabled major progress in the discovery and design of potently immunogenic recombinant protein vaccine antigens. Here we discuss three key breakthrough approaches that have potentiated structural and computational vaccine design. Firstly, genomic sciences gave birth to the field of reverse vaccinology, which has enabled the rapid computational identification of potential vaccine antigens. Secondly, major advances in structural biology, experimental epitope mapping, and computational epitope prediction have yielded molecular insights into the immunogenic determinants defining protective antigens, enabling their rational optimization. Thirdly, and most recently, computational approaches have been used to convert this wealth of structural and immunological information into the design of improved vaccine antigens. This review aims to illustrate the growing power of combining sequencing, structural and computational approaches, and we discuss how this may drive the design of novel immunogens suitable for future vaccines urgently needed to increase the global prevention of infectious disease.

Computational simulation of acoustic fatigue for hot composite structures

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Murthy, Pappu L. N.; Chamis, Christos C.; Nagpal, Vinod K.; Sutjahjo, Edhi

1991-01-01

Predictive methods/computer codes for the computational simulation of acoustic fatigue resistance of hot composite structures subjected to acoustic excitation emanating from an adjacent vibrating component are discussed. Select codes developed over the past two decades at the NASA Lewis Research Center are used. The codes include computation of acoustic noise generated from a vibrating component, degradation in material properties of a composite laminate at use temperature, dynamic response of acoustically excited hot multilayered composite structure, degradation in the first ply strength of the excited structure due to acoustic loading, and acoustic fatigue resistance of the excited structure, including the propulsion environment. Effects of the laminate lay-up and environment on the acoustic fatigue life are evaluated. The results show that, by keeping the angled plies on the outer surface of the laminate, a substantial increase in the acoustic fatigue life is obtained. The effect of environment (temperature and moisture) is to relieve the residual stresses leading to an increase in the acoustic fatigue life of the excited panel.

Computational Infrastructure for Engine Structural Performance Simulation

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1997-01-01

Select computer codes developed over the years to simulate specific aspects of engine structures are described. These codes include blade impact integrated multidisciplinary analysis and optimization, progressive structural fracture, quantification of uncertainties for structural reliability and risk, benefits estimation of new technology insertion and hierarchical simulation of engine structures made from metal matrix and ceramic matrix composites. Collectively these codes constitute a unique infrastructure readiness to credibly evaluate new and future engine structural concepts throughout the development cycle from initial concept, to design and fabrication, to service performance and maintenance and repairs, and to retirement for cause and even to possible recycling. Stated differently, they provide 'virtual' concurrent engineering for engine structures total-life-cycle-cost.

New computing systems and their impact on structural analysis and design

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.

1989-01-01

A review is given of the recent advances in computer technology that are likely to impact structural analysis and design. The computational needs for future structures technology are described. The characteristics of new and projected computing systems are summarized. Advances in programming environments, numerical algorithms, and computational strategies for new computing systems are reviewed, and a novel partitioning strategy is outlined for maximizing the degree of parallelism. The strategy is designed for computers with a shared memory and a small number of powerful processors (or a small number of clusters of medium-range processors). It is based on approximating the response of the structure by a combination of symmetric and antisymmetric response vectors, each obtained using a fraction of the degrees of freedom of the original finite element model. The strategy was implemented on the CRAY X-MP/4 and the Alliant FX/8 computers. For nonlinear dynamic problems on the CRAY X-MP with four CPUs, it resulted in an order of magnitude reduction in total analysis time, compared with the direct analysis on a single-CPU CRAY X-MP machine.

Increased reliability of nuclear magnetic resonance protein structures by consensus structure bundles.

PubMed

Buchner, Lena; Güntert, Peter

2015-02-03

Nuclear magnetic resonance (NMR) structures are represented by bundles of conformers calculated from different randomized initial structures using identical experimental input data. The spread among these conformers indicates the precision of the atomic coordinates. However, there is as yet no reliable measure of structural accuracy, i.e., how close NMR conformers are to the "true" structure. Instead, the precision of structure bundles is widely (mis)interpreted as a measure of structural quality. Attempts to increase precision often overestimate accuracy by tight bundles of high precision but much lower accuracy. To overcome this problem, we introduce a protocol for NMR structure determination with the software package CYANA, which produces, like the traditional method, bundles of conformers in agreement with a common set of conformational restraints but with a realistic precision that is, throughout a variety of proteins and NMR data sets, a much better estimate of structural accuracy than the precision of conventional structure bundles. Copyright © 2015 Elsevier Ltd. All rights reserved.

Parallel computation of three-dimensional aeroelastic fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sadeghi, Mani

This dissertation presents a numerical method for the parallel computation of aeroelasticity (ParCAE). A flow solver is coupled to a structural solver by use of a fluid-structure interface method. The integration of the three-dimensional unsteady Navier-Stokes equations is performed in the time domain, simultaneously to the integration of a modal three-dimensional structural model. The flow solution is accelerated by using a multigrid method and a parallel multiblock approach. Fluid-structure coupling is achieved by subiteration. A grid-deformation algorithm is developed to interpolate the deformation of the structural boundaries onto the flow grid. The code is formulated to allow application to general, three-dimensional, complex configurations with multiple independent structures. Computational results are presented for various configurations, such as turbomachinery blade rows and aircraft wings. Investigations are performed on vortex-induced vibrations, effects of cascade mistuning on flutter, and cases of nonlinear cascade and wing flutter.

A Dataset and a Technique for Generalized Nuclear Segmentation for Computational Pathology.

PubMed

Kumar, Neeraj; Verma, Ruchika; Sharma, Sanuj; Bhargava, Surabhi; Vahadane, Abhishek; Sethi, Amit

2017-07-01

Nuclear segmentation in digital microscopic tissue images can enable extraction of high-quality features for nuclear morphometrics and other analysis in computational pathology. Conventional image processing techniques, such as Otsu thresholding and watershed segmentation, do not work effectively on challenging cases, such as chromatin-sparse and crowded nuclei. In contrast, machine learning-based segmentation can generalize across various nuclear appearances. However, training machine learning algorithms requires data sets of images, in which a vast number of nuclei have been annotated. Publicly accessible and annotated data sets, along with widely agreed upon metrics to compare techniques, have catalyzed tremendous innovation and progress on other image classification problems, particularly in object recognition. Inspired by their success, we introduce a large publicly accessible data set of hematoxylin and eosin (H&E)-stained tissue images with more than 21000 painstakingly annotated nuclear boundaries, whose quality was validated by a medical doctor. Because our data set is taken from multiple hospitals and includes a diversity of nuclear appearances from several patients, disease states, and organs, techniques trained on it are likely to generalize well and work right out-of-the-box on other H&E-stained images. We also propose a new metric to evaluate nuclear segmentation results that penalizes object- and pixel-level errors in a unified manner, unlike previous metrics that penalize only one type of error. We also propose a segmentation technique based on deep learning that lays a special emphasis on identifying the nuclear boundaries, including those between the touching or overlapping nuclei, and works well on a diverse set of test images.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Beta delayed neutrons for nuclear structure and astrophysics

NASA Astrophysics Data System (ADS)

Grzywacz, Robert

2014-09-01

Beta-delayed neutron emission (β xn) is a significant or even dominant decay channel for the majority of very neutron-rich nuclei, especially for those on the r-process path. The recent theoretical models predicts that it may play more significant role then previously expected for astrophysics and this realization instigated a renewed experimental interest in this topic as a part of a larger scope of research on beta-decay strength distribution. Because studies of the decay strength directly probe relevant physics on the microscopic level, energy-resolved measurements of the beta-decay strength distribution is a better test of nuclear models than traditionally used experimental observables like half-lives and neutron branching ratios. A new detector system called the Versatile Array of Neutron Detectors at Low Energy (VANDLE) was constructed to directly address this issue. In its first experimental campaign at the Holifield Radioactive Ion Beam Facility neutron energy spectra in key regions of the nuclear chart were measured: near the shell closures at 78Ni and 132Sn, and for the deformed nuclei near 100Rb. In several cases, unexpectedly intense and concentrated, resonant-like, high-energy neutron structures were observed. These results were interpreted within shell model framework which clearly indicated that these neutron emission is driven by nuclear structure effects and are due to large Gamow-Teller type transition matrix elements. This research was sponsored in part by the National Nuclear Security Administration under the Stewardship Science Academic Alliances program through DOE Cooperative Agreement No. DE-FG52-08NA28552.

The Nuclear Energy Advanced Modeling and Simulation Enabling Computational Technologies FY09 Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Diachin, L F; Garaizar, F X; Henson, V E

2009-10-12

In this document we report on the status of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Enabling Computational Technologies (ECT) effort. In particular, we provide the context for ECT In the broader NEAMS program and describe the three pillars of the ECT effort, namely, (1) tools and libraries, (2) software quality assurance, and (3) computational facility (computers, storage, etc) needs. We report on our FY09 deliverables to determine the needs of the integrated performance and safety codes (IPSCs) in these three areas and lay out the general plan for software quality assurance to meet the requirements of DOE andmore » the DOE Advanced Fuel Cycle Initiative (AFCI). We conclude with a brief description of our interactions with the Idaho National Laboratory computer center to determine what is needed to expand their role as a NEAMS user facility.« less

Collective network for computer structures

DOEpatents

Blumrich, Matthias A; Coteus, Paul W; Chen, Dong; Gara, Alan; Giampapa, Mark E; Heidelberger, Philip; Hoenicke, Dirk; Takken, Todd E; Steinmacher-Burow, Burkhard D; Vranas, Pavlos M

2014-01-07

A system and method for enabling high-speed, low-latency global collective communications among interconnected processing nodes. The global collective network optimally enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the network via links to facilitate performance of low-latency global processing operations at nodes of the virtual network. The global collective network may be configured to provide global barrier and interrupt functionality in asynchronous or synchronized manner. When implemented in a massively-parallel supercomputing structure, the global collective network is physically and logically partitionable according to the needs of a processing algorithm.

Mathematical analysis of compressive/tensile molecular and nuclear structures

NASA Astrophysics Data System (ADS)

Wang, Dayu

Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

Recent advances in computational actinoid chemistry.

PubMed

Wang, Dongqi; van Gunsteren, Wilfred F; Chai, Zhifang

2012-09-07

We briefly review advances in computational actinoid (An) chemistry during the past ten years in regard to two issues: the geometrical and electronic structures, and reactions. The former addresses the An-O, An-C, and M-An (M is a metal atom including An) bonds in the actinoid molecular systems, including actinoid oxo and oxide species, actinoid-carbenoid, dinuclear and diatomic systems, and the latter the hydration and ligand exchange, the disproportionation, the oxidation, the reduction of uranyl, hydroamination, and the photolysis of uranium azide. Concerning their relevance to the electronic structures and reactions of actinoids and their importance in the development of an advanced nuclear fuel cycle, we also mentioned the work on actinoid carbides and nitrides, which have been proposed to be candidates of the next generation of nuclear fuel, and the oxidation of PuO(x), which is important to understand the speciation of actinoids in the environment, followed by a brief discussion on the urgent need for a heavier involvement of computational actinoid chemistry in developing advanced reprocessing protocols of spent nuclear fuel. The paper is concluded with an outlook.

Remote sensing of vegetation structure using computer vision

NASA Astrophysics Data System (ADS)

Dandois, Jonathan P.

High-spatial resolution measurements of vegetation structure are needed for improving understanding of ecosystem carbon, water and nutrient dynamics, the response of ecosystems to a changing climate, and for biodiversity mapping and conservation, among many research areas. Our ability to make such measurements has been greatly enhanced by continuing developments in remote sensing technology---allowing researchers the ability to measure numerous forest traits at varying spatial and temporal scales and over large spatial extents with minimal to no field work, which is costly for large spatial areas or logistically difficult in some locations. Despite these advances, there remain several research challenges related to the methods by which three-dimensional (3D) and spectral datasets are joined (remote sensing fusion) and the availability and portability of systems for frequent data collections at small scale sampling locations. Recent advances in the areas of computer vision structure from motion (SFM) and consumer unmanned aerial systems (UAS) offer the potential to address these challenges by enabling repeatable measurements of vegetation structural and spectral traits at the scale of individual trees. However, the potential advances offered by computer vision remote sensing also present unique challenges and questions that need to be addressed before this approach can be used to improve understanding of forest ecosystems. For computer vision remote sensing to be a valuable tool for studying forests, bounding information about the characteristics of the data produced by the system will help researchers understand and interpret results in the context of the forest being studied and of other remote sensing techniques. This research advances understanding of how forest canopy and tree 3D structure and color are accurately measured by a relatively low-cost and portable computer vision personal remote sensing system: 'Ecosynth'. Recommendations are made for optimal

Unified ab initio approaches to nuclear structure and reactions

DOE PAGES

Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

2016-04-13

The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

PREFACE: 11th International Spring Seminar on Nuclear Physics: Shell Model and Nuclear Structure - achievements of the past two decades

NASA Astrophysics Data System (ADS)

2015-02-01

The 11th International Seminar on Nuclear Physics was held in Ischia from May 12 to May 16, 2014. This Seminar was dedicated to Aldo Covello, who has been the promoter of this series of meetings, which started in Sorrento in 1986 and continued with meetings held every two or three years in the Naples area. Aldo's idea was to offer to a group of researchers, actively working in selected fields of Nuclear Physics, the opportunity to confront their points of view in a lively and informal way. The choice for the period of the year, Spring, as well as the sites chosen reflected this intent. The first meeting was of a purely theoretical nature, but it was immediately clear that the scope of these conferences needed to be enlarged calling into play the experimental community. Then, starting from the second meeting, all the following ones have been characterized by fruitful discussion between theoretical and experimental researchers on current achievements and future developments of nuclear structure. This may be read, in fact, as one of the motivating factors for Aldo's election as Fellow of the American Physical Society in 2008 "... for his outstanding contributions to the international nuclear physics community by providing, for over two decades, a venue for theorists and experimentalists to share their latest ideas." The present meeting, organized by Aldo's former students and with the benefit of his suggestions, has maintained this tradition. The title "Shell model and nuclear structure: achievements of the past two decades" recalls that of the 2nd International Spring Seminar "Shell Model and Nuclear Structure: where do we stand?". The main aim of this 11th Seminar was, in fact, to discuss the changes of the past two decades on our view of nuclei in terms of shell structure as well as the perspectives of the shell model, which has been one of the key points in Aldo's research. This point is well accounted by the Opening Speech of Igal Talmi, one of the fathers of the

Methods for Computationally Efficient Structured CFD Simulations of Complex Turbomachinery Flows

NASA Technical Reports Server (NTRS)

Herrick, Gregory P.; Chen, Jen-Ping

2012-01-01

This research presents more efficient computational methods by which to perform multi-block structured Computational Fluid Dynamics (CFD) simulations of turbomachinery, thus facilitating higher-fidelity solutions of complicated geometries and their associated flows. This computational framework offers flexibility in allocating resources to balance process count and wall-clock computation time, while facilitating research interests of simulating axial compressor stall inception with more complete gridding of the flow passages and rotor tip clearance regions than is typically practiced with structured codes. The paradigm presented herein facilitates CFD simulation of previously impractical geometries and flows. These methods are validated and demonstrate improved computational efficiency when applied to complicated geometries and flows.

Recent developments of the NESSUS probabilistic structural analysis computer program

NASA Technical Reports Server (NTRS)

Millwater, H.; Wu, Y.-T.; Torng, T.; Thacker, B.; Riha, D.; Leung, C. P.

1992-01-01

The NESSUS probabilistic structural analysis computer program combines state-of-the-art probabilistic algorithms with general purpose structural analysis methods to compute the probabilistic response and the reliability of engineering structures. Uncertainty in loading, material properties, geometry, boundary conditions and initial conditions can be simulated. The structural analysis methods include nonlinear finite element and boundary element methods. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. The scope of the code has recently been expanded to include probabilistic life and fatigue prediction of structures in terms of component and system reliability and risk analysis of structures considering cost of failure. The code is currently being extended to structural reliability considering progressive crack propagation. Several examples are presented to demonstrate the new capabilities.

The computational structural mechanics testbed procedures manual

NASA Technical Reports Server (NTRS)

Stewart, Caroline B. (Compiler)

1991-01-01

The purpose of this manual is to document the standard high level command language procedures of the Computational Structural Mechanics (CSM) Testbed software system. A description of each procedure including its function, commands, data interface, and use is presented. This manual is designed to assist users in defining and using command procedures to perform structural analysis in the CSM Testbed User's Manual and the CSM Testbed Data Library Description.

Field-Programmable Gate Array Computer in Structural Analysis: An Initial Exploration

NASA Technical Reports Server (NTRS)

Singleterry, Robert C., Jr.; Sobieszczanski-Sobieski, Jaroslaw; Brown, Samuel

2002-01-01

This paper reports on an initial assessment of using a Field-Programmable Gate Array (FPGA) computational device as a new tool for solving structural mechanics problems. A FPGA is an assemblage of binary gates arranged in logical blocks that are interconnected via software in a manner dependent on the algorithm being implemented and can be reprogrammed thousands of times per second. In effect, this creates a computer specialized for the problem that automatically exploits all the potential for parallel computing intrinsic in an algorithm. This inherent parallelism is the most important feature of the FPGA computational environment. It is therefore important that if a problem offers a choice of different solution algorithms, an algorithm of a higher degree of inherent parallelism should be selected. It is found that in structural analysis, an 'analog computer' style of programming, which solves problems by direct simulation of the terms in the governing differential equations, yields a more favorable solution algorithm than current solution methods. This style of programming is facilitated by a 'drag-and-drop' graphic programming language that is supplied with the particular type of FPGA computer reported in this paper. Simple examples in structural dynamics and statics illustrate the solution approach used. The FPGA system also allows linear scalability in computing capability. As the problem grows, the number of FPGA chips can be increased with no loss of computing efficiency due to data flow or algorithmic latency that occurs when a single problem is distributed among many conventional processors that operate in parallel. This initial assessment finds the FPGA hardware and software to be in their infancy in regard to the user conveniences; however, they have enormous potential for shrinking the elapsed time of structural analysis solutions if programmed with algorithms that exhibit inherent parallelism and linear scalability. This potential warrants further

Investigations of Nuclear Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarantites, Demetrios; Reviol, W.

The proposal addresses studies of nuclear structure at low-energies and development of instrumentation for that purpose. The structure studies deal with features of neutron-rich nuclei with unexplored shapes (football- or pear-shaped nuclei). The regions of interest are: neutron rich nuclei like 132-138Sn, or 48-54Ca, and the Zr, Mo, and Ru isotopes. The tools used can be grouped as follows: either Gammasphere or Gretina multi-gamma detector arrays and auxiliary detectors (Microball, Neutron Shell, and the newly completed Phoswich Wall).The neutron-rich nuclei are accessed by radioactive-beam binary reactions or by 252Cf spontaneous fission. The experiments with heavy radioactive beams aim at excitingmore » the beam nuclei by pick-up or transfer a neutron or a proton from a light target like 13C, 9Be, 11B or 14N .For these binary-reaction studies the Phoswich Wall detector system is essential. It is based on four multi-anode photomultiplier tubes on which CsI and thin fast-timing plastic scintillators are attached. Their signals are digitized with a high density microchip system.« less

Impact of new computing systems on computational mechanics and flight-vehicle structures technology

NASA Technical Reports Server (NTRS)

Noor, A. K.; Storaasli, O. O.; Fulton, R. E.

1984-01-01

Advances in computer technology which may have an impact on computational mechanics and flight vehicle structures technology were reviewed. The characteristics of supersystems, highly parallel systems, and small systems are summarized. The interrelations of numerical algorithms and software with parallel architectures are discussed. A scenario for future hardware/software environment and engineering analysis systems is presented. Research areas with potential for improving the effectiveness of analysis methods in the new environment are identified.

ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers

PubMed Central

Besnier, Francois; Glover, Kevin A.

2013-01-01

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/. PMID:23923012

Linking Nuclear Reactions and Nuclear Structure on the Way to the Drip Line

NASA Astrophysics Data System (ADS)

Dickhoff, Willem

2012-10-01

The present understanding of the role of short- and long-range physics in determining proton properties near the Fermi energy for stable closed-shell nuclei has relied on data from the (e,e'p) reaction. Hadronic tools to extract such spectroscopic information have been hampered by the lack of a consistent reaction description that provides unambiguous and undisputed results. The dispersive optical model (DOM), originally conceived by Claude Mahaux, provides a unified description of both elastic nucleon scattering and structure information related to single-particle properties below the Fermi energy. The DOM provides the starting point to provide a framework in which nuclear reactions and structure data can be analyzed consistently to provide unambiguous spectroscopic information including its asymmetry dependence. Recent extensions of this approach include the treatment of non-locality to describe experimental data like the nuclear charge density based on information of the spectral density below the Fermi energy, the application of the DOM ingredients to the description of transfer reactions, a comparison of the microscopic content of the nucleon self-energy based on Faddeev-RPA calculations emphasizing long-range correlations with DOM potentials, and a study of the relation between a self-energy which includes the effect of short-range correlations with DOM potentials. The most recent Dom implementation currently in progress abandons the constraint of local potentials completely to allow an accurate description of various properties of the nuclear ground state.

Structure of cold nuclear matter at subnuclear densities by quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Watanabe, Gentaro; Sato, Katsuhiko; Yasuoka, Kenji; Ebisuzaki, Toshikazu

2003-09-01

Structure of cold nuclear matter at subnuclear densities for the proton fraction x=0.5, 0.3, and 0.1 is investigated by quantum molecular dynamics (QMD) simulations. We demonstrate that the phases with slablike and rodlike nuclei, etc. can be formed dynamically from hot uniform nuclear matter without any assumptions on nuclear shape, and also systematically analyze the structure of cold matter using two-point correlation functions and Minkowski functionals. In our simulations, we also observe intermediate phases, which have complicated nuclear shapes. It has been found out that these phases can be characterized as those with negative Euler characteristic. Our result implies the existence of these kinds of phases in addition to the simple “pasta” phases in neutron star crusts and supernova inner cores. In addition, we investigate the properties of the effective QMD interaction used in the present work to examine the validity of our results. The resultant energy per nucleon ɛn of the pure neutron matter, the proton chemical μ(0)p in pure neutron matter and the nuclear surface tension Esurf are generally reasonable in comparison with other nuclear interactions.

Molecular and Structural Traits of Insulin Receptor Substrate 1/LC3 Nuclear Structures and Their Role in Autophagy Control and Tumor Cell Survival.

PubMed

Lassak, Adam; Dean, Mathew; Wyczechowska, Dorota; Wilk, Anna; Marrero, Luis; Trillo-Tinoco, Jimena; Boulares, A Hamid; Sarkaria, Jann N; Del Valle, Luis; Peruzzi, Francesca; Ochoa, Augusto; Reiss, Krzysztof

2018-05-15

Insulin receptor substrate 1 (IRS-1) is a common cytosolic adaptor molecule involved in signal transduction from insulin and insulin-like growth factor I (IGF-I) receptors. IRS-1 can also be found in the nucleus. We report here a new finding of unique IRS-1 nuclear structures, which we observed initially in glioblastoma biopsy specimens and glioblastoma xenografts. These nuclear structures can be reproduced in vitro by the ectopic expression of IRS-1 cDNA cloned in frame with the nuclear localization signal (NLS-IRS-1). In these structures, IRS-1 localizes at the periphery, while the center harbors a key autophagy protein, LC3. These new nuclear structures are highly dynamic, rapidly exchange IRS-1 molecules with the surrounding nucleoplasm, disassemble during mitosis, and require a growth stimulus for their reassembly and maintenance. In tumor cells engineered to express NLS-IRS-1, the IRS-1/LC3 nuclear structures repress autophagy induced by either amino acid starvation or rapamycin treatment. In this process, IRS-1 nuclear structures sequester LC3 inside the nucleus, possibly preventing its cytosolic translocation and the formation of new autophagosomes. This novel mechanism provides a quick and reversible way of inhibiting autophagy, which could counteract autophagy-induced cancer cell death under severe stress, including anticancer therapies. Copyright © 2018 American Society for Microbiology.

Nuclear Quadrupole Moments and Nuclear Shell Structure

DOE R&D Accomplishments Database

Townes, C. H.; Foley, H. M.; Low, W.

1950-06-23

Describes a simple model, based on nuclear shell considerations, which leads to the proper behavior of known nuclear quadrupole moments, although predictions of the magnitudes of some quadrupole moments are seriously in error.

Online Monitoring of Concrete Structures in Nuclear Power Plants: Interim Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahadevan, Sankaran; Cai, Guowei; Agarwal, Vivek

The existing fleet of nuclear power plants in the United States have initial operating licenses of 40 years, and many of these plants have applied for and received license extensions. As plant structures, systems, and components age, their useful life—considering both structural integrity and performance—is reduced as a result of deterioration of the materials. Assessment and management of aging concrete structures in nuclear plants require a more systematic approach than simple reliance on existing code-based design margins of safety. Structural health monitoring is required to produce actionable information regarding structural integrity that supports operational and maintenance decisions. The online monitoringmore » of concrete structures project conducted under the Advanced Instrumentation, Information, and Control Technologies Pathway of the Light Water Reactor Sustainability program at Idaho National Laboratory is seeking to develop and demonstrate capabilities for concrete structures health monitoring. Through this research project, several national laboratories and Vanderbilt University propose to develop a framework of research activities for the health monitoring of nuclear power plant concrete structures that includes the integration of four elements—damage modeling, monitoring, data analytics, and uncertainty quantification. This report briefly discusses activities in this project during October-December, 2014. The most significant activity during this period was the organizing of a two-day workshop on research needs in online monitoring of concrete structures, hosted by Vanderbilt University in November 2014. Thirty invitees from academia, industry and government participated in the workshop. The presentations and discussions at the workshop surveyed current activities related to concrete structures deterioration modeling and monitoring, and identified the challenges, knowledge gaps, and opportunities for advancing the state of the art; these

A computer vision-based approach for structural displacement measurement

NASA Astrophysics Data System (ADS)

Ji, Yunfeng

2010-04-01

Along with the incessant advancement in optics, electronics and computer technologies during the last three decades, commercial digital video cameras have experienced a remarkable evolution, and can now be employed to measure complex motions of objects with sufficient accuracy, which render great assistance to structural displacement measurement in civil engineering. This paper proposes a computer vision-based approach for dynamic measurement of structures. One digital camera is used to capture image sequences of planar targets mounted on vibrating structures. The mathematical relationship between image plane and real space is established based on computer vision theory. Then, the structural dynamic displacement at the target locations can be quantified using point reconstruction rules. Compared with other tradition displacement measurement methods using sensors, such as accelerometers, linear-variable-differential-transducers (LVDTs) and global position system (GPS), the proposed approach gives the main advantages of great flexibility, a non-contact working mode and ease of increasing measurement points. To validate, four tests of sinusoidal motion of a point, free vibration of a cantilever beam, wind tunnel test of a cross-section bridge model, and field test of bridge displacement measurement, are performed. Results show that the proposed approach can attain excellent accuracy compared with the analytical ones or the measurements using conventional transducers, and proves to deliver an innovative and low cost solution to structural displacement measurement.

PREFACE: New nuclear structure phenomena in the vicinity of closed shells

NASA Astrophysics Data System (ADS)

Johnson, A.; Wyss, R.

1995-01-01

The proceedings of the international symposium on "New Nuclear Structure Phenomena in the Vicinity of Closed Shells - SELMA 94", held in Stockholm, Uppsala and on the Baltic Sea from Aug. 30 - Sep. 3 are collected in this volume. Since almost 40% of the session time was kept open for discussions, it is difficult to give full justice to the character of the meeting in a written report. However, since also many posters are presented in this volume, we hope that some of the flavour of this lively symposium will pass onto the reader. We have chosen to group related contributions in order to facilitate the reading. Several articles, though, may fit into several categories. With the event of large detector arrays there has been a tremendous development in the field of nuclear spectroscopy. The discovery of super-deformation has been followed by detailed spectroscopy in the second well. Hence, the concept of shell closure is reinterpreted in general terms, involving shapes different from spherical. Close to the drip lines, we expect new shells and new structure effects to emerge. Loosely bound neutrons may form a new state of nuclear matter. The regions of the nuclear chart far from the line of stability can be explored in the future by means of radioactive ion beams. New structure effects, that one might encounter far from the line of stability was one of the themes of this conference. The strong impact of the nuclear shell model is also evident in other branches of physics, like the structure of metal-clusters. Special attention was paid to the Sn-isotopes. In the Sn-isotopic chain, spectroscopic measurements are extending beyond the doubly-magic nucleus 132Sn. Large efforts have recently been made to study nuclei in the vicinity of the doubly-magic nucleus 100Sn, the other extreme end of the chain. Spectroscopic data on 100Sn would open the entire shell for nuclear structure studies, ranging over a number of 32 neutrons. During the organization of this meeting, the

Spatial epigenetics: linking nuclear structure and function in higher eukaryotes.

PubMed

Jackson, Dean A

2010-09-20

Eukaryotic cells are defined by the genetic information that is stored in their DNA. To function, this genetic information must be decoded. In doing this, the information encoded in DNA is copied first into RNA, during RNA transcription. Primary RNA transcripts are generated within transcription factories, where they are also processed into mature mRNAs, which then pass to the cytoplasm. In the cytoplasm these mRNAs can finally be translated into protein in order to express the genetic information as a functional product. With only rare exceptions, the cells of an individual multicellular eukaryote contain identical genetic information. However, as different genes must be expressed in different cell types to define the structure and function of individual tissues, it is clear that mechanisms must have evolved to regulate gene expression. In higher eukaryotes, mechanisms that regulate the interaction of DNA with the sites where nuclear functions are performed provide one such layer of regulation. In this chapter, I evaluate how a detailed understanding of nuclear structure and chromatin dynamics are beginning to reveal how spatial mechanisms link chromatin structure and function. As these mechanisms operate to modulate the genetic information in DNA, the regulation of chromatin function by nuclear architecture defines the concept of 'spatial epigenetics'.

A new taxonomy for distributed computer systems based upon operating system structure

NASA Technical Reports Server (NTRS)

Foudriat, E. C.

1985-01-01

Characteristics of the resource structure found in the operating system are considered as a mechanism for classifying distributed computer systems. Since the operating system resources, themselves, are too diversified to provide a consistent classification, the structure upon which resources are built and shared are examined. The location and control character of this indivisibility provides the taxonomy for separating uniprocessors, computer networks, network computers (fully distributed processing systems or decentralized computers) and algorithm and/or data control multiprocessors. The taxonomy is important because it divides machines into a classification that is relevant or important to the client and not the hardware architect. It also defines the character of the kernel O/S structure needed for future computer systems. What constitutes an operating system for a fully distributed processor is discussed in detail.

DOE EPSCoR Initiative in Structural and computational Biology/Bioinformatics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallace, Susan S.

2008-02-21

The overall goal of the DOE EPSCoR Initiative in Structural and Computational Biology was to enhance the competiveness of Vermont research in these scientific areas. To develop self-sustaining infrastructure, we increased the critical mass of faculty, developed shared resources that made junior researchers more competitive for federal research grants, implemented programs to train graduate and undergraduate students who participated in these research areas and provided seed money for research projects. During the time period funded by this DOE initiative: (1) four new faculty were recruited to the University of Vermont using DOE resources, three in Computational Biology and one inmore » Structural Biology; (2) technical support was provided for the Computational and Structural Biology facilities; (3) twenty-two graduate students were directly funded by fellowships; (4) fifteen undergraduate students were supported during the summer; and (5) twenty-eight pilot projects were supported. Taken together these dollars resulted in a plethora of published papers, many in high profile journals in the fields and directly impacted competitive extramural funding based on structural or computational biology resulting in 49 million dollars awarded in grants (Appendix I), a 600% return on investment by DOE, the State and University.« less

Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket.

PubMed

Krull, Sandra; Thyberg, Johan; Björkroth, Birgitta; Rackwitz, Hans-Richard; Cordes, Volker C

2004-09-01

The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.

Bifocal computational near eye light field displays and Structure parameters determination scheme for bifocal computational display.

PubMed

Liu, Mali; Lu, Chihao; Li, Haifeng; Liu, Xu

2018-02-19

We propose a bifocal computational near eye light field display (bifocal computational display) and structure parameters determination scheme (SPDS) for bifocal computational display that achieves greater depth of field (DOF), high resolution, accommodation and compact form factor. Using a liquid varifocal lens, two single-focal computational light fields are superimposed to reconstruct a virtual object's light field by time multiplex and avoid the limitation on high refresh rate. By minimizing the deviation between reconstructed light field and original light field, we propose a determination framework to determine the structure parameters of bifocal computational light field display. When applied to different objective to SPDS, it can achieve high average resolution or uniform resolution display over scene depth range. To analyze the advantages and limitation of our proposed method, we have conducted simulations and constructed a simple prototype which comprises a liquid varifocal lens, dual-layer LCDs and a uniform backlight. The results of simulation and experiments with our method show that the proposed system can achieve expected performance well. Owing to the excellent performance of our system, we motivate bifocal computational display and SPDS to contribute to a daily-use and commercial virtual reality display.

Computational modeling of RNA 3D structures, with the aid of experimental restraints

PubMed Central

Magnus, Marcin; Matelska, Dorota; Łach, Grzegorz; Chojnowski, Grzegorz; Boniecki, Michal J; Purta, Elzbieta; Dawson, Wayne; Dunin-Horkawicz, Stanislaw; Bujnicki, Janusz M

2014-01-01

In addition to mRNAs whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of RNAs depends on their structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that simulate either the physical process of RNA structure formation (“Greek science” approach) or utilize information derived from known structures of other RNA molecules (“Babylonian science” approach). All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases, the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other. In this work, we review computational approaches for RNA structure prediction, with emphasis on implementations (particular programs) that can utilize restraints derived from experimental analyses. We also list experimental approaches, whose results can be relatively easily used by computational methods. Finally, we describe case studies where computational and experimental analyses were successfully combined to determine RNA structures that would remain out of reach for each of these approaches applied separately. PMID:24785264

Theoretical, Experimental, and Computational Evaluation of Several Vane-Type Slow-Wave Structures

NASA Technical Reports Server (NTRS)

Wallett, Thomas M.; Qureshi, A. Haq

1994-01-01

Several types of periodic vane slow-wave structures were fabricated. The dispersion characteristics were found by theoretical analysis, experimental testing, and computer simulation using the MAFIA code. Computer-generated characteristics agreed to approximately within 2 percent of the experimental characteristics for all structures. The theoretical characteristics, however, deviated increasingly as the width to height ratio became smaller. Interaction impedances were also computed based on the experimental and computer-generated resonance frequency shifts due to the introduction of a perturbing dielectric rod.

Computational structures for robotic computations

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Chang, P. R.

1987-01-01

The computational problem of inverse kinematics and inverse dynamics of robot manipulators by taking advantage of parallelism and pipelining architectures is discussed. For the computation of inverse kinematic position solution, a maximum pipelined CORDIC architecture has been designed based on a functional decomposition of the closed-form joint equations. For the inverse dynamics computation, an efficient p-fold parallel algorithm to overcome the recurrence problem of the Newton-Euler equations of motion to achieve the time lower bound of O(log sub 2 n) has also been developed.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

Conflicts of interest improve collective computation of adaptive social structures

PubMed Central

Brush, Eleanor R.; Krakauer, David C.; Flack, Jessica C.

2018-01-01

In many biological systems, the functional behavior of a group is collectively computed by the system’s individual components. An example is the brain’s ability to make decisions via the activity of billions of neurons. A long-standing puzzle is how the components’ decisions combine to produce beneficial group-level outputs, despite conflicts of interest and imperfect information. We derive a theoretical model of collective computation from mechanistic first principles, using results from previous work on the computation of power structure in a primate model system. Collective computation has two phases: an information accumulation phase, in which (in this study) pairs of individuals gather information about their fighting abilities and make decisions about their dominance relationships, and an information aggregation phase, in which these decisions are combined to produce a collective computation. To model information accumulation, we extend a stochastic decision-making model—the leaky integrator model used to study neural decision-making—to a multiagent game-theoretic framework. We then test alternative algorithms for aggregating information—in this study, decisions about dominance resulting from the stochastic model—and measure the mutual information between the resultant power structure and the “true” fighting abilities. We find that conflicts of interest can improve accuracy to the benefit of all agents. We also find that the computation can be tuned to produce different power structures by changing the cost of waiting for a decision. The successful application of a similar stochastic decision-making model in neural and social contexts suggests general principles of collective computation across substrates and scales. PMID:29376116

High Performance Computing and Storage Requirements for Nuclear Physics: Target 2017

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerber, Richard; Wasserman, Harvey

2014-04-30

In April 2014, NERSC, ASCR, and the DOE Office of Nuclear Physics (NP) held a review to characterize high performance computing (HPC) and storage requirements for NP research through 2017. This review is the 12th in a series of reviews held by NERSC and Office of Science program offices that began in 2009. It is the second for NP, and the final in the second round of reviews that covered the six Office of Science program offices. This report is the result of that review

Identifying local structural states in atomic imaging by computer vision

DOE Office of Scientific and Technical Information (OSTI.GOV)

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

Identifying local structural states in atomic imaging by computer vision

DOE PAGES

Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; ...

2016-11-02

The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

The computational structural mechanics testbed data library description

NASA Technical Reports Server (NTRS)

Stewart, Caroline B. (Compiler)

1988-01-01

The datasets created and used by the Computational Structural Mechanics Testbed software system are documented by this manual. A description of each dataset including its form, contents, and organization is presented.

The computational structural mechanics testbed data library description

NASA Technical Reports Server (NTRS)

Stewart, Caroline B. (Compiler)

1988-01-01

The datasets created and used by the Computational Structural Mechanics Testbed software system is documented by this manual. A description of each dataset including its form, contents, and organization is presented.

Comprehensive analysis of the dynamic structure of nuclear localization signals.

PubMed

Yamagishi, Ryosuke; Okuyama, Takahide; Oba, Shuntaro; Shimada, Jiro; Chaen, Shigeru; Kaneko, Hiroki

2015-12-01

Most transcription and epigenetic factors in eukaryotic cells have nuclear localization signals (NLSs) and are transported to the nucleus by nuclear transport proteins. Understanding the features of NLSs and the mechanisms of nuclear transport might help understand gene expression regulation, somatic cell reprogramming, thus leading to the treatment of diseases associated with abnormal gene expression. Although many studies analyzed the amino acid sequence of NLSs, few studies investigated their three-dimensional structure. Therefore, we conducted a statistical investigation of the dynamic structure of NLSs by extracting the conformation of these sequences from proteins examined by X-ray crystallography and using a quantity defined as conformational determination rate (a ratio between the number of amino acids determining the conformation and the number of all amino acids included in a certain region). We found that determining the conformation of NLSs is more difficult than determining the conformation of other regions and that NLSs may tend to form more heteropolymers than monomers. Therefore, these findings strongly suggest that NLSs are intrinsically disordered regions.

Application of desktop computers in nuclear engineering education

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graves, H.W. Jr.

1990-01-01

Utilization of desktop computers in the academic environment is based on the same objectives as in the industrial environment - increased quality and efficiency. Desktop computers can be extremely useful teaching tools in two general areas: classroom demonstrations and homework assignments. Although differences in emphasis exist, tutorial programs share many characteristics with interactive software developed for the industrial environment. In the Reactor Design and Fuel Management course at the University of Maryland, several interactive tutorial programs provided by Energy analysis Software Service have been utilized. These programs have been designed to be sufficiently structured to permit an orderly, disciplined solutionmore » to the problem being solved, and yet be flexible enough to accommodate most problem solution options.« less

On the unification of nuclear-structure theory: A response to Bortignon and Broglia

NASA Astrophysics Data System (ADS)

Cook, Norman D.

2016-09-01

Nuclear-structure theory is unusual among the diverse fields of quantum physics. Although it provides a coherent description of all known isotopes on the basis of a quantum-mechanical understanding of nucleon states, nevertheless, in the absence of a fundamental theory of the nuclear force acting between nucleons, the prediction of all ground-state and excited-state nuclear binding energies is inherently semi-empirical. I suggest that progress can be made by returning to the foundational work of Eugene Wigner from 1937, where the mathematical symmetries of nucleon states were first defined. Those symmetries were later successfully exploited in the development of the independent-particle model ( IPM ˜ shell model , but the geometrical implications noted by Wigner were neglected. Here I review how the quantum-mechanical, but remarkably easy-to-understand geometrical interpretation of the IPM provides constraints on the parametrization of the nuclear force. The proposed "geometrical IPM" indicates a way forward toward the unification of nuclear-structure theory that Bortignon and Broglia have called for.

Computational Methods for Structural Mechanics and Dynamics

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

Topics addressed include: transient dynamics; transient finite element method; transient analysis in impact and crash dynamic studies; multibody computer codes; dynamic analysis of space structures; multibody mechanics and manipulators; spatial and coplanar linkage systems; flexible body simulation; multibody dynamics; dynamical systems; and nonlinear characteristics of joints.

Multiphysics Computational Analysis of a Solid-Core Nuclear Thermal Engine Thrust Chamber

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Canabal, Francisco; Cheng, Gary; Chen, Yen-Sen

2007-01-01

The objective of this effort is to develop an efficient and accurate computational heat transfer methodology to predict thermal, fluid, and hydrogen environments for a hypothetical solid-core, nuclear thermal engine - the Small Engine. In addition, the effects of power profile and hydrogen conversion on heat transfer efficiency and thrust performance were also investigated. The computational methodology is based on an unstructured-grid, pressure-based, all speeds, chemically reacting, computational fluid dynamics platform, while formulations of conjugate heat transfer were implemented to describe the heat transfer from solid to hydrogen inside the solid-core reactor. The computational domain covers the entire thrust chamber so that the afore-mentioned heat transfer effects impact the thrust performance directly. The result shows that the computed core-exit gas temperature, specific impulse, and core pressure drop agree well with those of design data for the Small Engine. Finite-rate chemistry is very important in predicting the proper energy balance as naturally occurring hydrogen decomposition is endothermic. Locally strong hydrogen conversion associated with centralized power profile gives poor heat transfer efficiency and lower thrust performance. On the other hand, uniform hydrogen conversion associated with a more uniform radial power profile achieves higher heat transfer efficiency, and higher thrust performance.

Cloud Quantum Computing of an Atomic Nucleus

NASA Astrophysics Data System (ADS)

Dumitrescu, E. F.; McCaskey, A. J.; Hagen, G.; Jansen, G. R.; Morris, T. D.; Papenbrock, T.; Pooser, R. C.; Dean, D. J.; Lougovski, P.

2018-05-01

We report a quantum simulation of the deuteron binding energy on quantum processors accessed via cloud servers. We use a Hamiltonian from pionless effective field theory at leading order. We design a low-depth version of the unitary coupled-cluster ansatz, use the variational quantum eigensolver algorithm, and compute the binding energy to within a few percent. Our work is the first step towards scalable nuclear structure computations on a quantum processor via the cloud, and it sheds light on how to map scientific computing applications onto nascent quantum devices.

Cloud Quantum Computing of an Atomic Nucleus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dumitrescu, Eugene F.; McCaskey, Alex J.; Hagen, Gaute

Here, we report a quantum simulation of the deuteron binding energy on quantum processors accessed via cloud servers. We use a Hamiltonian from pionless effective field theory at leading order. We design a low-depth version of the unitary coupled-cluster ansatz, use the variational quantum eigensolver algorithm, and compute the binding energy to within a few percent. Our work is the first step towards scalable nuclear structure computations on a quantum processor via the cloud, and it sheds light on how to map scientific computing applications onto nascent quantum devices.

Cloud Quantum Computing of an Atomic Nucleus.

PubMed

Dumitrescu, E F; McCaskey, A J; Hagen, G; Jansen, G R; Morris, T D; Papenbrock, T; Pooser, R C; Dean, D J; Lougovski, P

2018-05-25

We report a quantum simulation of the deuteron binding energy on quantum processors accessed via cloud servers. We use a Hamiltonian from pionless effective field theory at leading order. We design a low-depth version of the unitary coupled-cluster ansatz, use the variational quantum eigensolver algorithm, and compute the binding energy to within a few percent. Our work is the first step towards scalable nuclear structure computations on a quantum processor via the cloud, and it sheds light on how to map scientific computing applications onto nascent quantum devices.

Cloud Quantum Computing of an Atomic Nucleus

DOE PAGES

Dumitrescu, Eugene F.; McCaskey, Alex J.; Hagen, Gaute; ...

2018-05-23

Here, we report a quantum simulation of the deuteron binding energy on quantum processors accessed via cloud servers. We use a Hamiltonian from pionless effective field theory at leading order. We design a low-depth version of the unitary coupled-cluster ansatz, use the variational quantum eigensolver algorithm, and compute the binding energy to within a few percent. Our work is the first step towards scalable nuclear structure computations on a quantum processor via the cloud, and it sheds light on how to map scientific computing applications onto nascent quantum devices.

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

PubMed Central

Lorenz, William A.; Clote, Peter

2011-01-01

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must involve energetically unfavorable folding steps. Here, we present a novel, efficient algorithm to compute the partition function over all locally optimal secondary structures of a given RNA sequence. Our software, RNAlocopt runs in time and space. Additionally, RNAlocopt samples a user-specified number of structures from the Boltzmann subensemble of all locally optimal structures. We apply RNAlocopt to show that (1) the number of locally optimal structures is far fewer than the total number of structures – indeed, the number of locally optimal structures approximately equal to the square root of the number of all structures, (2) the structural diversity of this subensemble may be either similar to or quite different from the structural diversity of the entire Boltzmann ensemble, a situation that depends on the type of input RNA, (3) the (modified) maximum expected accuracy structure, computed by taking into account base pairing frequencies of locally optimal structures, is a more accurate prediction of the native structure than other current thermodynamics-based methods. The software RNAlocopt constitutes a technical breakthrough in our study of the folding landscape for RNA secondary structures. For the first time, locally optimal structures (kinetic traps in the Turner energy model) can be rapidly generated for long RNA sequences, previously impossible with methods that involved exhaustive enumeration. Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy. Web server

Nuclear Physics Exascale Requirements Review: An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Nuclear Physics, June 15 - 17, 2016, Gaithersburg, Maryland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlson, Joseph; Savage, Martin J.; Gerber, Richard

Imagine being able to predict — with unprecedented accuracy and precision — the structure of the proton and neutron, and the forces between them, directly from the dynamics of quarks and gluons, and then using this information in calculations of the structure and reactions of atomic nuclei and of the properties of dense neutron stars (NSs). Also imagine discovering new and exotic states of matter, and new laws of nature, by being able to collect more experimental data than we dream possible today, analyzing it in real time to feed back into an experiment, and curating the data with fullmore » tracking capabilities and with fully distributed data mining capabilities. Making this vision a reality would improve basic scientific understanding, enabling us to precisely calculate, for example, the spectrum of gravity waves emitted during NS coalescence, and would have important societal applications in nuclear energy research, stockpile stewardship, and other areas. This review presents the components and characteristics of the exascale computing ecosystems necessary to realize this vision.« less

Passive cooling system for nuclear reactor containment structure

DOEpatents

Gou, Perng-Fei; Wade, Gentry E.

1989-01-01

A passive cooling system for the contaminant structure of a nuclear reactor plant providing protection against overpressure within the containment attributable to inadvertent leakage or rupture of the system components. The cooling system utilizes natural convection for transferring heat imbalances and enables the discharge of irradiation free thermal energy to the atmosphere for heat disposal from the system.

Center for Computational Structures Technology

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Perry, Ferman W.

1995-01-01

The Center for Computational Structures Technology (CST) is intended to serve as a focal point for the diverse CST research activities. The CST activities include the use of numerical simulation and artificial intelligence methods in modeling, analysis, sensitivity studies, and optimization of flight-vehicle structures. The Center is located at NASA Langley and is an integral part of the School of Engineering and Applied Science of the University of Virginia. The key elements of the Center are: (1) conducting innovative research on advanced topics of CST; (2) acting as pathfinder by demonstrating to the research community what can be done (high-potential, high-risk research); (3) strong collaboration with NASA scientists and researchers from universities and other government laboratories; and (4) rapid dissemination of CST to industry, through integration of industrial personnel into the ongoing research efforts.

Right Size Determining the Staff Necessary to Sustain Simulation and Computing Capabilities for Nuclear Security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikkel, Daniel J.; Meisner, Robert

The Advanced Simulation and Computing Campaign, herein referred to as the ASC Program, is a core element of the science-based Stockpile Stewardship Program (SSP), which enables assessment, certification, and maintenance of the safety, security, and reliability of the U.S. nuclear stockpile without the need to resume nuclear testing. The use of advanced parallel computing has transitioned from proof-of-principle to become a critical element for assessing and certifying the stockpile. As the initiative phase of the ASC Program came to an end in the mid-2000s, the National Nuclear Security Administration redirected resources to other urgent priorities, and resulting staff reductions inmore » ASC occurred without the benefit of analysis of the impact on modern stockpile stewardship that is dependent on these new simulation capabilities. Consequently, in mid-2008 the ASC Program management commissioned a study to estimate the essential size and balance needed to sustain advanced simulation as a core component of stockpile stewardship. The ASC Program requires a minimum base staff size of 930 (which includes the number of staff necessary to maintain critical technical disciplines as well as to execute required programmatic tasks) to sustain its essential ongoing role in stockpile stewardship.« less

NASA CST aids U.S. industry. [computational structures technology

NASA Technical Reports Server (NTRS)

Housner, Jerry M.; Pinson, Larry D.

1993-01-01

The effect of NASA's computational structures Technology (CST) research on aerospace vehicle design and operation is discussed. The application of this research to proposed version of a high-speed civil transport, to composite structures in aerospace, to the study of crack growth, and to resolving field problems is addressed.

Nuclear Reactor Physics

NASA Astrophysics Data System (ADS)

Stacey, Weston M.

2001-02-01

An authoritative textbook and up-to-date professional's guide to basic and advanced principles and practices Nuclear reactors now account for a significant portion of the electrical power generated worldwide. At the same time, the past few decades have seen an ever-increasing number of industrial, medical, military, and research applications for nuclear reactors. Nuclear reactor physics is the core discipline of nuclear engineering, and as the first comprehensive textbook and reference on basic and advanced nuclear reactor physics to appear in a quarter century, this book fills a large gap in the professional literature. Nuclear Reactor Physics is a textbook for students new to the subject, for others who need a basic understanding of how nuclear reactors work, as well as for those who are, or wish to become, specialists in nuclear reactor physics and reactor physics computations. It is also a valuable resource for engineers responsible for the operation of nuclear reactors. Dr. Weston Stacey begins with clear presentations of the basic physical principles, nuclear data, and computational methodology needed to understand both the static and dynamic behaviors of nuclear reactors. This is followed by in-depth discussions of advanced concepts, including extensive treatment of neutron transport computational methods. As an aid to comprehension and quick mastery of computational skills, he provides numerous examples illustrating step-by-step procedures for performing the calculations described and chapter-end problems. Nuclear Reactor Physics is a useful textbook and working reference. It is an excellent self-teaching guide for research scientists, engineers, and technicians involved in industrial, research, and military applications of nuclear reactors, as well as government regulators who wish to increase their understanding of nuclear reactors.

Unveiling saturation effects from nuclear structure function measurements at the EIC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marquet, Cyrille; Moldes, Manoel R.; Zurita, Pia

Here, we analyze the possibility of extracting a clear signal of non-linear parton saturation effects from future measurements of nuclear structure functions at the Electron–Ion Collider (EIC), in the small-x region. Our approach consists in generating pseudodata for electron-gold collisions, using the running-coupling Balitsky–Kovchegov evolution equation, and in assessing the compatibility of these saturated pseudodata with existing sets of nuclear parton distribution functions (nPDFs), extrapolated if necessary. The level of disagreement between the two is quantified by applying a Bayesian reweighting technique. This allows to infer the parton distributions needed in order to describe the pseudodata, which we find quitemore » different from the actual distributions, especially for sea quarks and gluons. This tension suggests that, should saturation effects impact the future nuclear structure function data as predicted, a successful refitting of the nPDFs may not be achievable, which would unambiguously signal the presence of non-linear effects.« less

Unveiling saturation effects from nuclear structure function measurements at the EIC

DOE PAGES

Marquet, Cyrille; Moldes, Manoel R.; Zurita, Pia

2017-07-21

Here, we analyze the possibility of extracting a clear signal of non-linear parton saturation effects from future measurements of nuclear structure functions at the Electron–Ion Collider (EIC), in the small-x region. Our approach consists in generating pseudodata for electron-gold collisions, using the running-coupling Balitsky–Kovchegov evolution equation, and in assessing the compatibility of these saturated pseudodata with existing sets of nuclear parton distribution functions (nPDFs), extrapolated if necessary. The level of disagreement between the two is quantified by applying a Bayesian reweighting technique. This allows to infer the parton distributions needed in order to describe the pseudodata, which we find quitemore » different from the actual distributions, especially for sea quarks and gluons. This tension suggests that, should saturation effects impact the future nuclear structure function data as predicted, a successful refitting of the nPDFs may not be achievable, which would unambiguously signal the presence of non-linear effects.« less

Detailed requirements for a next generation nuclear data structure.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, D.

2016-07-05

This document attempts to compile the requirements for the top-levels of a hierarchical arrangement of nuclear data such as found in the ENDF format. This set of requirements will be used to guide the development of a new data structure to replace the legacy ENDF format.

The nuclear membrane-associated honeycomb structure of the unicellular organism Amoeba proteus: on the search for homologies with the nuclear lamina of metazoa.

PubMed

Schmidt, M; Grossmann, U; Krohne, G

1995-07-01

In the protozoon Amoeba proteus, a complex and highly organized structure with the morphology of a honeycomb is associated with the nucleoplasmic surface of the nuclear membrane. We have tested whether this structure exhibits similarity to the nuclear lamina of metazoic organisms. First, we have shown that the honeycomb layer is composed of 3 to 5 nm thick protein fibrils resistant to treatment with detergent, high salt, and digestion with nucleases, thus possessing properties typical for karyoskeletal elements. However, in contrast to the meshwork of lamin filaments in somatic cells of metazoic organisms, the honeycomb layer is not tightly anchored to the nucleoplasmic side of pore complexes, or to the inner nuclear membrane. Second, in microinjection experiments we investigated whether fluorescently labeled lamins of Xenopus laevis (lamins A and LI) and Drosophila melanogaster (lamin Dmo) were able to associate in vivo with the Amoeba proteus honeycomb structure. In microinjected amoeba these three lamins were efficiently transported into the nucleus, but did not associate with the nuclear envelope. Our results suggest that the Amoeba proteus nuclear envelope, including the honeycomb layer, does not contain proteins exhibiting high homologies to lamins of metazoan species thus preventing the localized assembly of microinjected lamins along the nuclear periphery.

Computational strategies to address chromatin structure problems

NASA Astrophysics Data System (ADS)

Perišić, Ognjen; Schlick, Tamar

2016-06-01

While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin’s dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber’s structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure.

Structural and functional adaptations of the mammalian nuclear envelope to meet the meiotic requirements.

PubMed

Link, Jana; Jahn, Daniel; Alsheimer, Manfred

2015-01-01

Numerous studies in the past years provided definite evidence that the nuclear envelope is much more than just a simple barrier. It rather constitutes a multifunctional platform combining structural and dynamic features to fulfill many fundamental functions such as chromatin organization, regulation of transcription, signaling, but also structural duties like maintaining general nuclear architecture and shape. One additional and, without doubt, highly impressive aspect is the recently identified key function of selected nuclear envelope components in driving meiotic chromosome dynamics, which in turn is essential for accurate recombination and segregation of the homologous chromosomes. Here, we summarize the recent work identifying new key players in meiotic telomere attachment and movement and discuss the latest advances in our understanding of the actual function of the meiotic nuclear envelope.

Structure-Based Low-Rank Model With Graph Nuclear Norm Regularization for Noise Removal.

PubMed

Ge, Qi; Jing, Xiao-Yuan; Wu, Fei; Wei, Zhi-Hui; Xiao, Liang; Shao, Wen-Ze; Yue, Dong; Li, Hai-Bo

2017-07-01

Nonlocal image representation methods, including group-based sparse coding and block-matching 3-D filtering, have shown their great performance in application to low-level tasks. The nonlocal prior is extracted from each group consisting of patches with similar intensities. Grouping patches based on intensity similarity, however, gives rise to disturbance and inaccuracy in estimation of the true images. To address this problem, we propose a structure-based low-rank model with graph nuclear norm regularization. We exploit the local manifold structure inside a patch and group the patches by the distance metric of manifold structure. With the manifold structure information, a graph nuclear norm regularization is established and incorporated into a low-rank approximation model. We then prove that the graph-based regularization is equivalent to a weighted nuclear norm and the proposed model can be solved by a weighted singular-value thresholding algorithm. Extensive experiments on additive white Gaussian noise removal and mixed noise removal demonstrate that the proposed method achieves a better performance than several state-of-the-art algorithms.

Changing Nuclear Landscape and Unique PML Structures During Early Epigenetic Transitions of Human Embryonic Stem Cells

PubMed Central

Butler, John T.; Hall, Lisa L.; Smith, Kelly P.; Lawrence, Jeanne B.

2010-01-01

The complex nuclear structure of somatic cells is important to epigenomic regulation, yet little is known about nuclear organization of human embryonic stem cells (hESC). Here we surveyed several nuclear structures in pluripotent and transitioning hESC. Observations of centromeres, telomeres, SC35 speckles, Cajal Bodies, lamin A/C and emerin, nuclear shape and size demonstrate a very different “nuclear landscape” in hESC. This landscape is remodeled during a brief transitional window, concomitant with or just prior to differentiation onset. Notably, hESC initially contain abundant signal for spliceosome assembly factor, SC35, but lack discrete SC35 domains; these form as cells begin to specialize, likely reflecting cell-type specific genomic organization. Concomitantly, nuclear size increases and shape changes as lamin A/C and emerin incorporate into the lamina. During this brief window, hESC exhibit dramatically different PML-defined structures, which in somatic cells are linked to gene regulation and cancer. Unlike the numerous, spherical somatic PML bodies, hES cells often display ~1–3 large PML structures of two morphological types: long linear “rods” or elaborate “rosettes”, which lack substantial SUMO-1, Daxx, and Sp100.These occur primarily between Day 0–2 of differentiation and become rare thereafter. PML rods may be “taut” between other structures, such as centromeres, but clearly show some relationship with the lamina, where PML often abuts or fills a “gap” in early lamin A/C staining. Findings demonstrate that pluripotent hES cells have a markedly different overall nuclear architecture, remodeling of which is linked to early epigenomic programming and involves formation of unique PML-defined structures. PMID:19449340

Selectivity in Ligand Binding to Uranyl Compounds: A Synthetic, Structural, Thermodynamic and Computational Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnold, John

The uranyl cation (UO 2 2+) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due tomore » the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. We believe that the goal of developing a practical system for uranium separation from seawater will not be attained without new insights into our existing fundamental knowledge of actinide chemistry. We posit that detailed studies of the kinetic and thermodynamic factors that influence interactions between f-elements and ligands with a range of donor atoms is essential to any major advance in this important area. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. We anticipate that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials.« less

EPRI Guide to Managing Nuclear Utility Protective Clothing Programs. PCEVAL User`s Manual, A computer code for evaluating the economics of nuclear plant protective clothing programs: Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, J.J.; Kelly, D.M.

1993-10-01

The Electric Power Research Institute (EPRI) commissioned a radioactive waste related project (RP2414-34) in 1989 to produce a guide for developing and managing nuclear plant protective clothing programs. Every nuclear facility must coordinate some type of protective clothing program for its radiation workers to ensure proper and safe protection for the wearer and to maintain control over the spread of contamination. Yet, every nuclear facility has developed its own unique program for managing such clothing. Accordingly, a need existed for a reference guide to assist with standardizing protective clothing programs and in controlling the potentially escalating economics of such programs.more » The initial Guide to Managing Nuclear Utility Protective Clothing Programs, NP-7309, was published in May 1991. Since that time, a number of utilities have reviewed and/or used the report to enhance their protective clothing programs. Some of these utilities requested that a computer program be developed to assist utilities in evaluating the economics of protective clothing programs consistent with the guidance in NP-7309. The PCEVAL computer code responds to that industry need. This report, the PCEVAL User`s Manual, provides detailed instruction on use of the software.« less

Parallel structures in human and computer memory

NASA Astrophysics Data System (ADS)

Kanerva, Pentti

1986-08-01

If we think of our experiences as being recorded continuously on film, then human memory can be compared to a film library that is indexed by the contents of the film strips stored in it. Moreover, approximate retrieval cues suffice to retrieve information stored in this library: We recognize a familiar person in a fuzzy photograph or a familiar tune played on a strange instrument. This paper is about how to construct a computer memory that would allow a computer to recognize patterns and to recall sequences the way humans do. Such a memory is remarkably similar in structure to a conventional computer memory and also to the neural circuits in the cortex of the cerebellum of the human brain. The paper concludes that the frame problem of artificial intelligence could be solved by the use of such a memory if we were able to encode information about the world properly.

Parallel structures in human and computer memory

NASA Technical Reports Server (NTRS)

Kanerva, P.

1986-01-01

If one thinks of our experiences as being recorded continuously on film, then human memory can be compared to a film library that is indexed by the contents of the film strips stored in it. Moreover, approximate retrieval cues suffice to retrieve information stored in this library. One recognizes a familiar person in a fuzzy photograph or a familiar tune played on a strange instrument. A computer memory that would allow a computer to recognize patterns and to recall sequences the way humans do is constructed. Such a memory is remarkably similiar in structure to a conventional computer memory and also to the neural circuits in the cortex of the cerebellum of the human brain. It is concluded that the frame problem of artificial intelligence could be solved by the use of such a memory if one were able to encode information about the world properly.

Exploitation of realistic computational anthropomorphic phantoms for the optimization of nuclear imaging acquisition and processing protocols.

PubMed

Loudos, George K; Papadimitroulas, Panagiotis G; Kagadis, George C

2014-01-01

Monte Carlo (MC) simulations play a crucial role in nuclear medical imaging since they can provide the ground truth for clinical acquisitions, by integrating and quantifing all physical parameters that affect image quality. The last decade a number of realistic computational anthropomorphic models have been developed to serve imaging, as well as other biomedical engineering applications. The combination of MC techniques with realistic computational phantoms can provide a powerful tool for pre and post processing in imaging, data analysis and dosimetry. This work aims to create a global database for simulated Single Photon Emission Computed Tomography (SPECT) and Positron Emission Tomography (PET) exams and the methodology, as well as the first elements are presented. Simulations are performed using the well validated GATE opensource toolkit, standard anthropomorphic phantoms and activity distribution of various radiopharmaceuticals, derived from literature. The resulting images, projections and sinograms of each study are provided in the database and can be further exploited to evaluate processing and reconstruction algorithms. Patient studies using different characteristics are included in the database and different computational phantoms were tested for the same acquisitions. These include the XCAT, Zubal and the Virtual Family, which some of which are used for the first time in nuclear imaging. The created database will be freely available and our current work is towards its extension by simulating additional clinical pathologies.

ENGINEERING AND CONSTRUCTING THE HALLAM NUCLEAR POWER FACILITY REACTOR STRUCTURE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahlmeister, J E; Haberer, W V; Casey, D F

1960-12-15

The Hallam Nuclear Power Facility reactor structure, including the cavity liner, is described, and the design philosophy and special design requirements which were developed during the preliminary and final engineering phases of the project are explained. The structure was designed for 600 deg F inlet and 1000 deg F outlet operating sodium temperatures and fabricated of austenitic and ferritic stainless steels. Support for the reactor core components and adequate containment for biological safeguards were readily provided even though quite conservative design philosophy was used. The calculated operating characteristics, including heat generation, temperature distributions and stress levels for full-power operation, aremore » summarized. Ship fabrication and field installation experiences are also briefly related. Results of this project have established that the sodium graphite reactor permits practical and economical fabrication and field erection procedures; considerably higher operating design temperatures are believed possible without radical design changes. Also, larger reactor structures can be similarly constructed for higher capacity (300 to 1000 Mwe) nuclear power plants. (auth)« less

Teachers' Organization of Participation Structures for Teaching Science with Computer Technology

ERIC Educational Resources Information Center

Subramaniam, Karthigeyan

2016-01-01

This paper describes a qualitative study that investigated the nature of the participation structures and how the participation structures were organized by four science teachers when they constructed and communicated science content in their classrooms with computer technology. Participation structures focus on the activity structures and…

Computational simulation of acoustic fatigue for hot composite structures

NASA Technical Reports Server (NTRS)

Singhal, S. N.; Nagpal, V. K.; Murthy, P. L. N.; Chamis, C. C.

1991-01-01

This paper presents predictive methods/codes for computational simulation of acoustic fatigue resistance of hot composite structures subjected to acoustic excitation emanating from an adjacent vibrating component. Select codes developed over the past two decades at the NASA Lewis Research Center are used. The codes include computation of (1) acoustic noise generated from a vibrating component, (2) degradation in material properties of the composite laminate at use temperature, (3) dynamic response of acoustically excited hot multilayered composite structure, (4) degradation in the first-ply strength of the excited structure due to acoustic loading, and (5) acoustic fatigue resistance of the excited structure, including propulsion environment. Effects of the laminate lay-up and environment on the acoustic fatigue life are evaluated. The results show that, by keeping the angled plies on the outer surface of the laminate, a substantial increase in the acoustic fatigue life is obtained. The effect of environment (temperature and moisure) is to relieve the residual stresses leading to an increase in the acoustic fatigue life of the excited panel.

Computation of Flow Through Water-Control Structures Using Program DAMFLO.2

USGS Publications Warehouse

Sanders, Curtis L.; Feaster, Toby D.

2004-01-01

As part of its mission to collect, analyze, and store streamflow data, the U.S. Geological Survey computes flow through several dam structures throughout the country. Flows are computed using hydraulic equations that describe flow through sluice and Tainter gates, crest gates, lock gates, spillways, locks, pumps, and siphons, which are calibrated using flow measurements. The program DAMFLO.2 was written to compute, tabulate, and plot flow through dam structures using data that describe the physical properties of dams and various hydraulic parameters and ratings that use time-varying data, such as lake elevations or gate openings. The program uses electronic computer files of time-varying data, such as lake elevation or gate openings, retrieved from the U.S. Geological Survey Automated Data Processing System. Computed time-varying flow data from DAMFLO.2 are output in flat files, which can be entered into the Automated Data Processing System database. All computations are made in units of feet and seconds. DAMFLO.2 uses the procedures and language developed by the SAS Institute Inc.

Structural basis for nuclear import complex dissociation by RanGTP.

PubMed

Lee, Soo Jae; Matsuura, Yoshiyuki; Liu, Sai Man; Stewart, Murray

2005-06-02

Nuclear protein import is mediated mainly by the transport factor importin-beta that binds cytoplasmic cargo, most often via the importin-alpha adaptor, and then transports it through nuclear pore complexes. This active transport is driven by disassembly of the import complex by nuclear RanGTP. The switch I and II loops of Ran change conformation with nucleotide state, and regulate its interactions with nuclear trafficking components. Importin-beta consists of 19 HEAT repeats that are based on a pair of antiparallel alpha-helices (referred to as the A- and B-helices). The HEAT repeats stack to yield two C-shaped arches, linked together to form a helicoidal molecule that has considerable conformational flexibility. Here we present the structure of full-length yeast importin-beta (Kap95p or karyopherin-beta) complexed with RanGTP, which provides a basis for understanding the crucial cargo-release step of nuclear import. We identify a key interaction site where the RanGTP switch I loop binds to the carboxy-terminal arch of Kap95p. This interaction produces a change in helicoidal pitch that locks Kap95p in a conformation that cannot bind importin-alpha or cargo. We suggest an allosteric mechanism for nuclear import complex disassembly by RanGTP.

Response analysis of a nuclear containment structure with nonlinear soil-structure interaction under bi-directional ground motion

NASA Astrophysics Data System (ADS)

Kumar, Santosh; Raychowdhury, Prishati; Gundlapalli, Prabhakar

2015-06-01

Design of critical facilities such as nuclear power plant requires an accurate and precise evaluation of seismic demands, as any failure of these facilities poses immense threat to the community. Design complexity of these structures reinforces the necessity of a robust 3D modeling and analysis of the structure and the soil-foundation interface. Moreover, it is important to consider the multiple components of ground motion during time history analysis for a realistic simulation. Present study is focused on investigating the seismic response of a nuclear containment structure considering nonlinear Winkler-based approach to model the soil-foundation interface using a distributed array of inelastic springs, dashpots and gap elements. It is observed from this study that the natural period of the structure increases about 10 %, whereas the force demands decreases up to 24 % by considering the soil-structure interaction. Further, it is observed that foundation deformations, such as rotation and sliding are affected by the embedment ratio, indicating an increase of up to 56 % in these responses for a reduction of embedment from 0.5 to 0.05× the width of the footing.

Multiscale Space-Time Computational Methods for Fluid-Structure Interactions

DTIC Science & Technology

2015-09-13

prescribed fully or partially, is from an actual locust, extracted from high-speed, multi-camera video recordings of the locust in a wind tunnel . We use...With creative methods for coupling the fluid and structure, we can increase the scope and efficiency of the FSI modeling . Multiscale methods, which now...play an important role in computational mathematics, can also increase the accuracy and efficiency of the computer modeling techniques. The main

Distributed computer taxonomy based on O/S structure

NASA Technical Reports Server (NTRS)

Foudriat, Edwin C.

1985-01-01

The taxonomy considers the resource structure at the operating system level. It compares a communication based taxonomy with the new taxonomy to illustrate how the latter does a better job when related to the client's view of the distributed computer. The results illustrate the fundamental features and what is required to construct fully distributed processing systems. The problem of using network computers on the space station is addressed. A detailed discussion of the taxonomy is not given here. Information is given in the form of charts and diagrams that were used to illustrate a talk.

NASTRAN Analysis Comparison to Shock Tube Tests Used to Simulate Nuclear Overpressures

NASA Technical Reports Server (NTRS)

Wheless, T. K.

1985-01-01

This report presents a study of the effectiveness of the NASTRAN computer code for predicting structural response to nuclear blast overpressures. NASTRAN's effectiveness is determined by comparing results against shock tube tests used to simulate nuclear overpressures. Seven panels of various configurations are compared in this study. Panel deflections are the criteria used to measure NASTRAN's effectiveness. This study is a result of needed improvements in the survivability/vulnerability analyses subjected to nuclear blast.

Control mechanism of double-rotator-structure ternary optical computer

NASA Astrophysics Data System (ADS)

Kai, SONG; Liping, YAN

2017-03-01

Double-rotator-structure ternary optical processor (DRSTOP) has two characteristics, namely, giant data-bits parallel computing and reconfigurable processor, which can handle thousands of data bits in parallel, and can run much faster than computers and other optical computer systems so far. In order to put DRSTOP into practical application, this paper established a series of methods, namely, task classification method, data-bits allocation method, control information generation method, control information formatting and sending method, and decoded results obtaining method and so on. These methods form the control mechanism of DRSTOP. This control mechanism makes DRSTOP become an automated computing platform. Compared with the traditional calculation tools, DRSTOP computing platform can ease the contradiction between high energy consumption and big data computing due to greatly reducing the cost of communications and I/O. Finally, the paper designed a set of experiments for DRSTOP control mechanism to verify its feasibility and correctness. Experimental results showed that the control mechanism is correct, feasible and efficient.

JPL control/structure interaction test bed real-time control computer architecture

NASA Technical Reports Server (NTRS)

Briggs, Hugh C.

1989-01-01

The Control/Structure Interaction Program is a technology development program for spacecraft that exhibit interactions between the control system and structural dynamics. The program objectives include development and verification of new design concepts - such as active structure - and new tools - such as combined structure and control optimization algorithm - and their verification in ground and possibly flight test. A focus mission spacecraft was designed based upon a space interferometer and is the basis for design of the ground test article. The ground test bed objectives include verification of the spacecraft design concepts, the active structure elements and certain design tools such as the new combined structures and controls optimization tool. In anticipation of CSI technology flight experiments, the test bed control electronics must emulate the computation capacity and control architectures of space qualifiable systems as well as the command and control networks that will be used to connect investigators with the flight experiment hardware. The Test Bed facility electronics were functionally partitioned into three units: a laboratory data acquisition system for structural parameter identification and performance verification; an experiment supervisory computer to oversee the experiment, monitor the environmental parameters and perform data logging; and a multilevel real-time control computing system. The design of the Test Bed electronics is presented along with hardware and software component descriptions. The system should break new ground in experimental control electronics and is of interest to anyone working in the verification of control concepts for large structures.

Structure elucidation of organic compounds aided by the computer program system SCANNET

NASA Astrophysics Data System (ADS)

Guzowska-Swider, B.; Hippe, Z. S.

1992-12-01

Recognition of chemical structure is a very important problem currently solved by molecular spectroscopy, particularly IR, UV, NMR and Raman spectroscopy, and mass spectrometry. Nowadays, solution of the problem is frequently aided by the computer. SCANNET is a computer program system for structure elucidation of organic compounds, developed by our group. The structure recognition of an unknown substance is made by comparing its spectrum with successive reference spectra of standard compounds, i.e. chemical compounds of known chemical structure, stored in a spectral database. The computer program system SCANNET consists of six different spectral databases for following the analytical methods: IR, UV, 13C-NMR, 1H-NMR and Raman spectroscopy, and mass spectrometry. A chemist, to elucidate a structure, can use one of these spectral methods or a combination of them and search the appropriate databases. As the result of searching each spectral database, the user obtains a list of chemical substances whose spectra are identical and/or similar to the spectrum input into the computer. The final information obtained from searching the spectral databases is in the form of a list of chemical substances having all the examined spectra, for each type of spectroscopy, identical or simlar to those of the unknown compound.

A Comparative Study of Multi-material Data Structures for Computational Physics Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garimella, Rao Veerabhadra; Robey, Robert W.

The data structures used to represent the multi-material state of a computational physics application can have a drastic impact on the performance of the application. We look at efficient data structures for sparse applications where there may be many materials, but only one or few in most computational cells. We develop simple performance models for use in selecting possible data structures and programming patterns. We verify the analytic models of performance through a small test program of the representative cases.

SSME structural computer program development. Volume 2: BOPACE users manual

NASA Technical Reports Server (NTRS)

Vos, R. G.

1973-01-01

A computer program for use with a thermal-elastic-plastic-creep structural analyzer is presented. The following functions of the computer program are discussed: (1) analysis of very high temperature and large plastic-creep effects, (2) treatment of cyclic thermal and mechanical loads, (3) development of constitutive theory which closely follows actual behavior under variable temperature conditions, (4) stable numerical solution approach which avoids cumulative errors, and (5) capability of handling up to 1000 degrees of freedom. The computer program is written in FORTRAN IV and has been run on the IBM 360 and UNIVAC 1108 computer systems.

Computation of records of streamflow at control structures

USGS Publications Warehouse

Collins, Dannie L.

1977-01-01

Traditional methods of computing streamflow records on large, low-gradient streams require a continuous record of water-surface slope over a natural channel reach. This slope must be of sufficient magnitude to be accuratly measured with available stage measuring devices. On highly regulated streams, this slope approaches zero during periods of low flow and accurate measurement is difficult. Methods are described to calibrate multipurpose regulating control structures to more accurately compute streamflow records on highly-regulated streams. Hydraulic theory, assuming steady, uniform flow during a computational interval, is described for five different types of flow control. The controls are: Tainter gates, hydraulic turbines, fixed spillways, navigation locks, and crest gates. Detailed calibration procedures are described for the five different controls as well as for several flow regimes for some of the controls. The instrumentation package and computer programs necessary to collect and process the field data are discussed. Two typical calibration procedures and measurement data are presented to illustrate the accuracy of the methods. (Woodard-USGS)

Co-ordination of the International Network of Nuclear Structure and Decay Data Evaluators; Summary Report of an IAEA Technical Meeting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abriola, D.; Tuli, J.

The IAEA Nuclear Data Section convened the 18th meeting of the International Network of Nuclear Structure and Decay Data Evaluators at the IAEA Headquarters, Vienna, 23 to 27 March 2009. This meeting was attended by 22 scientists from 14 Member States, plus IAEA staff, concerned with the compilation, evaluation and dissemination of nuclear structure and decay data. A summary of the meeting, recommendations/conclusions, data centre reports, and various proposals considered, modified and agreed by the participants are contained within this document. The International Network of Nuclear Structure and Decay Data (NSDD) Evaluators holds biennial meetings under the auspices of themore » IAEA, and consists of evaluation groups and data service centres in several countries. This network has the objective of providing up-to-date nuclear structure and decay data for all known nuclides by evaluating all existing experimental data. Data resulting from this international evaluation collaboration is included in the Evaluated Nuclear Structure Data File (ENSDF) and published in the journals Nuclear Physics A and Nuclear Data Sheets (NDS).« less

Adiabatic quantum computing with spin qubits hosted by molecules.

PubMed

Yamamoto, Satoru; Nakazawa, Shigeaki; Sugisaki, Kenji; Sato, Kazunobu; Toyota, Kazuo; Shiomi, Daisuke; Takui, Takeji

2015-01-28

A molecular spin quantum computer (MSQC) requires electron spin qubits, which pulse-based electron spin/magnetic resonance (ESR/MR) techniques can afford to manipulate for implementing quantum gate operations in open shell molecular entities. Importantly, nuclear spins, which are topologically connected, particularly in organic molecular spin systems, are client qubits, while electron spins play a role of bus qubits. Here, we introduce the implementation for an adiabatic quantum algorithm, suggesting the possible utilization of molecular spins with optimized spin structures for MSQCs. We exemplify the utilization of an adiabatic factorization problem of 21, compared with the corresponding nuclear magnetic resonance (NMR) case. Two molecular spins are selected: one is a molecular spin composed of three exchange-coupled electrons as electron-only qubits and the other an electron-bus qubit with two client nuclear spin qubits. Their electronic spin structures are well characterized in terms of the quantum mechanical behaviour in the spin Hamiltonian. The implementation of adiabatic quantum computing/computation (AQC) has, for the first time, been achieved by establishing ESR/MR pulse sequences for effective spin Hamiltonians in a fully controlled manner of spin manipulation. The conquered pulse sequences have been compared with the NMR experiments and shown much faster CPU times corresponding to the interaction strength between the spins. Significant differences are shown in rotational operations and pulse intervals for ESR/MR operations. As a result, we suggest the advantages and possible utilization of the time-evolution based AQC approach for molecular spin quantum computers and molecular spin quantum simulators underlain by sophisticated ESR/MR pulsed spin technology.

A brief overview of computational structures technology related activities at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.

1992-01-01

The presentation gives a partial overview of research and development underway in the Structures Division of LeRC, which collectively is referred to as the Computational Structures Technology Program. The activities in the program are diverse and encompass four major categories: (1) composite materials and structures; (2) probabilistic analysis and reliability; (3) design optimization and expert systems; and (4) computational methods and simulation. The approach of the program is comprehensive and entails exploration of fundamental theories of structural mechanics to accurately represent the complex physics governing engine structural performance, formulation, and implementation of computational techniques and integrated simulation strategies to provide accurate and efficient solutions of the governing theoretical models by exploiting the emerging advances in computer technology, and validation and verification through numerical and experimental tests to establish confidence and define the qualities and limitations of the resulting theoretical models and computational solutions. The program comprises both in-house and sponsored research activities. The remainder of the presentation provides a sample of activities to illustrate the breadth and depth of the program and to demonstrate the accomplishments and benefits that have resulted.

Thai Language Sentence Similarity Computation Based on Syntactic Structure and Semantic Vector

NASA Astrophysics Data System (ADS)

Wang, Hongbin; Feng, Yinhan; Cheng, Liang

2018-03-01

Sentence similarity computation plays an increasingly important role in text mining, Web page retrieval, machine translation, speech recognition and question answering systems. Thai language as a kind of resources scarce language, it is not like Chinese language with HowNet and CiLin resources. So the Thai sentence similarity research faces some challenges. In order to solve this problem of the Thai language sentence similarity computation. This paper proposes a novel method to compute the similarity of Thai language sentence based on syntactic structure and semantic vector. This method firstly uses the Part-of-Speech (POS) dependency to calculate two sentences syntactic structure similarity, and then through the word vector to calculate two sentences semantic similarity. Finally, we combine the two methods to calculate two Thai language sentences similarity. The proposed method not only considers semantic, but also considers the sentence syntactic structure. The experiment result shows that this method in Thai language sentence similarity computation is feasible.

Computing elastic anisotropy to discover gum-metal-like structural alloys

NASA Astrophysics Data System (ADS)

Winter, I. S.; de Jong, M.; Asta, M.; Chrzan, D. C.

2017-08-01

The computer aided discovery of structural alloys is a burgeoning but still challenging area of research. A primary challenge in the field is to identify computable screening parameters that embody key structural alloy properties. Here, an elastic anisotropy parameter that captures a material's susceptibility to solute solution strengthening is identified. The parameter has many applications in the discovery and optimization of structural materials. As a first example, the parameter is used to identify alloys that might display the super elasticity, super strength, and high ductility of the class of TiNb alloys known as gum metals. In addition, it is noted that the parameter can be used to screen candidate alloys for shape memory response, and potentially aid in the optimization of the mechanical properties of high-entropy alloys.

Neuroanatomy of cranial computed tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kretschmann, H.J.; Weinrich, W.

1985-01-01

Based on the fundamental structures visualized by means of computed tomography, the authors present the functional systems which are relevant in neurology by means of axial cross-sections. All drawings were prepared from original preparations by means of a new technique which is similar to the grey values of X-ray CT and nuclear magnetic resonance tomography. A detailed description is given of the topics of neurofunctional lesions.

Ran-dependent nuclear export mediators: a structural perspective

PubMed Central

Güttler, Thomas; Görlich, Dirk

2011-01-01

Nuclear export is an essential eukaryotic activity. It proceeds through nuclear pore complexes (NPCs) and is mediated by soluble receptors that shuttle between nucleus and cytoplasm. RanGTPase-dependent export mediators (exportins) constitute the largest class of these carriers and are functionally highly versatile. All of these exportins load their substrates in response to RanGTP binding in the nucleus and traverse NPCs as ternary RanGTP–exportin–cargo complexes to the cytoplasm, where GTP hydrolysis leads to export complex disassembly. The different exportins vary greatly in their substrate range. Recent structural studies of both protein- and RNA-specific exporters have illuminated how exportins bind their cargoes, how Ran triggers cargo loading and how export complexes are disassembled in the cytoplasm. Here, we review the current state of knowledge and highlight emerging principles as well as prevailing questions. PMID:21878989

Computer program simplifies selection of structural steel columns

NASA Technical Reports Server (NTRS)

Vissing, G. S.

1966-01-01

Computer program rapidly selects appropriate size steel columns and base plates for construction of multistory structures. The program produces a printed record containing the size of a section required at a particular elevation, the stress produced by the loads, and the allowable stresses for that section.

GPU-accelerated computing for Lagrangian coherent structures of multi-body gravitational regimes

NASA Astrophysics Data System (ADS)

Lin, Mingpei; Xu, Ming; Fu, Xiaoyu

2017-04-01

Based on a well-established theoretical foundation, Lagrangian Coherent Structures (LCSs) have elicited widespread research on the intrinsic structures of dynamical systems in many fields, including the field of astrodynamics. Although the application of LCSs in dynamical problems seems straightforward theoretically, its associated computational cost is prohibitive. We propose a block decomposition algorithm developed on Compute Unified Device Architecture (CUDA) platform for the computation of the LCSs of multi-body gravitational regimes. In order to take advantage of GPU's outstanding computing properties, such as Shared Memory, Constant Memory, and Zero-Copy, the algorithm utilizes a block decomposition strategy to facilitate computation of finite-time Lyapunov exponent (FTLE) fields of arbitrary size and timespan. Simulation results demonstrate that this GPU-based algorithm can satisfy double-precision accuracy requirements and greatly decrease the time needed to calculate final results, increasing speed by approximately 13 times. Additionally, this algorithm can be generalized to various large-scale computing problems, such as particle filters, constellation design, and Monte-Carlo simulation.

Alterations in nuclear structure promote lupus autoimmunity in a mouse model

PubMed Central

Singh, Namrata; Johnstone, Duncan B.; Martin, Kayla A.; Tempera, Italo; Kaplan, Mariana J.

2016-01-01

ABSTRACT Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by the development of autoantibodies that recognize components of the cell nucleus. The vast majority of lupus research has focused on either the contributions of immune cell dysfunction or the genetics of the disease. Because granulocytes isolated from human SLE patients had alterations in neutrophil nuclear morphology that resembled the Pelger–Huet anomaly, and had prominent mis-splicing of mRNA encoding the nuclear membrane protein lamin B receptor (LBR), consistent with their Pelger–Huet-like nuclear morphology, we used a novel mouse model system to test the hypothesis that a disruption in the structure of the nucleus itself also contributes to the development of lupus autoimmunity. The lupus-prone mouse strain New Zealand White (NZW) was crossed with c57Bl/6 mice harboring a heterozygous autosomal dominant mutation in Lbr (B6.Lbric/+), and the (NZW×B6.Lbric)F1 offspring were evaluated for induction of lupus autoimmunity. Only female (NZW×B6.Lbric)F1 mice developed lupus autoimmunity, which included splenomegaly, kidney damage and autoantibodies. Kidney damage was accompanied by immune complex deposition, and perivascular and tubule infiltration of mononuclear cells. The titers of anti-chromatin antibodies exceeded those of aged female MRL-Faslpr mice, and were predominantly of the IgG2 subclasses. The anti-nuclear antibody staining profile of female (NZW×B6.Lbric)F1 sera was complex, and consisted of an anti-nuclear membrane reactivity that colocalized with the A-type lamina, in combination with a homogeneous pattern that was related to the recognition of histones with covalent modifications that are associated with gene activation. An anti-neutrophil IgM recognizing calreticulin, but not myeloperoxidase (MPO) or proteinase 3 (PR3), was also identified. Thus, alterations in nuclear structure contribute to lupus autoimmunity when expressed in the context of a lupus

Possible 6-qubit NMR quantum computer device material; simulator of the NMR line width

NASA Astrophysics Data System (ADS)

Hashi, K.; Kitazawa, H.; Shimizu, T.; Goto, A.; Eguchi, S.; Ohki, S.

2002-12-01

For an NMR quantum computer, splitting of an NMR spectrum must be larger than a line width. In order to find a best device material for a solid-state NMR quantum computer, we have made a simulation program to calculate the NMR line width due to the nuclear dipole field by the 2nd moment method. The program utilizes the lattice information prepared by commercial software to draw a crystal structure. By applying this program, we can estimate the NMR line width due to the nuclear dipole field without measurements and find a candidate material for a 6-qubit solid-state NMR quantum computer device.

Computing Properties of Hadrons, Nuclei and Nuclear Matter from Quantum Chromodynamics (LQCD)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Negele, John W.

Building on the success of two preceding generations of Scientific Discovery through Advanced Computing (SciDAC) projects, this grant supported the MIT component (P.I. John Negele) of a multi-institutional SciDAC-3 project that also included Brookhaven National Laboratory, the lead laboratory with P. I. Frithjof Karsch serving as Project Director, Thomas Jefferson National Accelerator Facility with P. I. David Richards serving as Co-director, University of Washington with P. I. Martin Savage, University of North Carolina with P. I. Rob Fowler, and College of William and Mary with P. I. Andreas Stathopoulos. Nationally, this multi-institutional project coordinated the software development effort that themore » nuclear physics lattice QCD community needs to ensure that lattice calculations can make optimal use of forthcoming leadership-class and dedicated hardware, including that at the national laboratories, and to exploit future computational resources in the Exascale era.« less

Quantum computation with indefinite causal structures

NASA Astrophysics Data System (ADS)

Araújo, Mateus; Guérin, Philippe Allard; Baumeler, ńmin

2017-11-01

One way to study the physical plausibility of closed timelike curves (CTCs) is to examine their computational power. This has been done for Deutschian CTCs (D-CTCs) and postselection CTCs (P-CTCs), with the result that they allow for the efficient solution of problems in PSPACE and PP, respectively. Since these are extremely powerful complexity classes, which are not expected to be solvable in reality, this can be taken as evidence that these models for CTCs are pathological. This problem is closely related to the nonlinearity of this models, which also allows, for example, cloning quantum states, in the case of D-CTCs, or distinguishing nonorthogonal quantum states, in the case of P-CTCs. In contrast, the process matrix formalism allows one to model indefinite causal structures in a linear way, getting rid of these effects and raising the possibility that its computational power is rather tame. In this paper, we show that process matrices correspond to a linear particular case of P-CTCs, and therefore that its computational power is upperbounded by that of PP. We show, furthermore, a family of processes that can violate causal inequalities but nevertheless can be simulated by a causally ordered quantum circuit with only a constant overhead, showing that indefinite causality is not necessarily hard to simulate.

Solving subsurface structural problems using a computer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Witte, D.M.

1987-02-01

Until recently, the solution of subsurface structural problems has required a combination of graphical construction, trigonometry, time, and patience. Recent advances in software available for both mainframe and microcomputers now reduce the time and potential error of these calculations by an order of magnitude. Software for analysis of deviated wells, three point problems, apparent dip, apparent thickness, and the intersection of two planes, as well as the plotting and interpretation of these data can be used to allow timely and accurate exploration or operational decisions. The available computer software provides a set of utilities, or tools, rather than a comprehensive,more » intelligent system. The burden for selection of appropriate techniques, computation methods, and interpretations still lies with the explorationist user.« less

A systematic and feasible method for computing nuclear contributions to electrical properties of polyatomic molecules

NASA Astrophysics Data System (ADS)

Luis, Josep M.; Duran, Miquel; Andrés, José L.

1997-08-01

An analytic method to evaluate nuclear contributions to electrical properties of polyatomic molecules is presented. Such contributions control changes induced by an electric field on equilibrium geometry (nuclear relaxation contribution) and vibrational motion (vibrational contribution) of a molecular system. Expressions to compute the nuclear contributions have been derived from a power series expansion of the potential energy. These contributions to the electrical properties are given in terms of energy derivatives with respect to normal coordinates, electric field intensity or both. Only one calculation of such derivatives at the field-free equilibrium geometry is required. To show the useful efficiency of the analytical evaluation of electrical properties (the so-called AEEP method), results for calculations on water and pyridine at the SCF/TZ2P and the MP2/TZ2P levels of theory are reported. The results obtained are compared with previous theoretical calculations and with experimental values.

Free energy minimization to predict RNA secondary structures and computational RNA design.

PubMed

Churkin, Alexander; Weinbrand, Lina; Barash, Danny

2015-01-01

Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

An extended view of nuclear lamin structure, function, and dynamics.

PubMed

Paddy, M R; Agard, D A; Sedat, J W

1992-08-01

Molecularly-based studies of nuclear lamins have progressed at a rapid rate in the last decade. However, we still have no answer to the most important question: what are the functions of lamins? In this review we describe recent experiments which challenge traditional views of lamin function and structure. These surprising results indicate that much lamin functionality remains to be discovered, and that more global approaches to lamin structure and function are especially appropriate at this time.

Nonobservable nature of the nuclear shell structure: Meaning, illustrations, and consequences

NASA Astrophysics Data System (ADS)

Duguet, T.; Hergert, H.; Holt, J. D.; Somà, V.

2015-09-01

Background: The concept of single-nucleon shells constitutes a basic pillar of our understanding of nuclear structure. Effective single-particle energies (ESPEs) introduced by French [Proceedings of the International School of Physics "Enrico Fermi," Course XXXVI, Varenna 1965, edited by C. Bloch (Academic Press, New York, 1966)] and Baranger [Nucl. Phys. A 149, 225 (1970), 10.1016/0375-9474(70)90692-5] represent the most appropriate tool to relate many-body observables to a single-nucleon shell structure. As briefly discussed in Duguet and Hagen [Phys. Rev. C 85, 034330 (2012), 10.1103/PhysRevC.85.034330], the dependence of ESPEs on one-nucleon transfer probability matrices makes them purely theoretical quantities that "run" with the nonobservable resolution scale λ employed in the calculation. Purpose: Given that ESPEs provide a way to interpret the many-body problem in terms of simpler theoretical ingredients, the goal is to specify the terms, i.e., the exact sense and conditions, in which this interpretation can be conducted meaningfully. Methods: While the nuclear shell structure is both scale and scheme dependent, the present study focuses on the former. A detailed discussion is provided to illustrate the scale (in)dependence of observables and nonobservables and the reasons why ESPEs, i.e., the shell structure, belong to the latter category. State-of-the-art multireference in-medium similarity renormalization group and self-consistent Gorkov Green's function many-body calculations are employed to corroborate the formal analysis. This is done by comparing the behavior of several observables and of nonobservable ESPEs (and spectroscopic factors) under (quasi) unitary similarity renormalization group transformations of the Hamiltonian parametrized by the resolution scale λ . Results: The formal proofs are confirmed by the results of ab initio many-body calculations in their current stage of implementation. In practice, the unitarity of the similarity

Chromatin insulator bodies are nuclear structures that form in response to osmotic stress and cell death

PubMed Central

Schoborg, Todd; Rickels, Ryan; Barrios, Josh

2013-01-01

Chromatin insulators assist in the formation of higher-order chromatin structures by mediating long-range contacts between distant genomic sites. It has been suggested that insulators accomplish this task by forming dense nuclear foci termed insulator bodies that result from the coalescence of multiple protein-bound insulators. However, these structures remain poorly understood, particularly the mechanisms triggering body formation and their role in nuclear function. In this paper, we show that insulator proteins undergo a dramatic and dynamic spatial reorganization into insulator bodies during osmostress and cell death in a high osmolarity glycerol–p38 mitogen-activated protein kinase–independent manner, leading to a large reduction in DNA-bound insulator proteins that rapidly repopulate chromatin as the bodies disassemble upon return to isotonicity. These bodies occupy distinct nuclear territories and contain a defined structural arrangement of insulator proteins. Our findings suggest insulator bodies are novel nuclear stress foci that can be used as a proxy to monitor the chromatin-bound state of insulator proteins and provide new insights into the effects of osmostress on nuclear and genome organization. PMID:23878275

Analysis of the transient response of nuclear spins in GaAs with/without nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Rasly, Mahmoud; Lin, Zhichao; Yamamoto, Masafumi; Uemura, Tetsuya

2016-05-01

As an alternative to studying the steady-state responses of nuclear spins in solid state systems, working within a transient-state framework can reveal interesting phenomena. The response of nuclear spins in GaAs to a changing magnetic field was analyzed based on the time evolution of nuclear spin temperature. Simulation results well reproduced our experimental results for the transient oblique Hanle signals observed in an all-electrical spin injection device. The analysis showed that the so called dynamic nuclear polarization can be treated as a cooling tool for the nuclear spins: It works as a provider to exchange spin angular momentum between polarized electron spins and nuclear spins through the hyperfine interaction, leading to an increase in the nuclear polarization. In addition, a time-delay of the nuclear spin temperature with a fast sweep of the external magnetic field produces a possible transient state for the nuclear spin polarization. On the other hand, the nuclear magnetic resonance acts as a heating tool for a nuclear spin system. This causes the nuclear spin temperature to jump to infinity: i.e., the average nuclear spins along with the nuclear field vanish at resonant fields of 75As, 69Ga and 71Ga, showing an interesting step-dip structure in the oblique Hanle signals. These analyses provide a quantitative understanding of nuclear spin dynamics in semiconductors for application in future computation processing.

Computational Approaches for Revealing the Structure of Membrane Transporters: Case Study on Bilitranslocase.

PubMed

Venko, Katja; Roy Choudhury, A; Novič, Marjana

2017-01-01

The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap. If combined with experimental data the computational information enables rapid, low cost and successful predictions of the molecular structure of unsolved proteins. The reliability of the predictions depends on the availability and accuracy of experimental data associated with structural information. In this review, the following methods are proposed for in silico structure elucidation: sequence-dependent predictions of transmembrane regions, predictions of transmembrane helix-helix interactions, helix arrangements in membrane models, and testing their stability with molecular dynamics simulations. We also demonstrate the usage of the computational methods listed above by proposing a model for the molecular structure of the transmembrane protein bilitranslocase. Bilitranslocase is bilirubin membrane transporter, which shares similar tissue distribution and functional properties with some of the members of the Organic Anion Transporter family and is the only member classified in the Bilirubin Transporter Family. Regarding its unique properties, bilitranslocase is a potentially interesting drug target.

Computer-generated formulas for three-center nuclear-attraction integrals (electrostatic potential) for Slater-type orbitals

NASA Technical Reports Server (NTRS)

Jones, H. W.

1984-01-01

The computer-assisted C-matrix, Loewdin-alpha-function, single-center expansion method in spherical harmonics has been applied to the three-center nuclear-attraction integral (potential due to the product of separated Slater-type orbitals). Exact formulas are produced for 13 terms of an infinite series that permits evaluation to ten decimal digits of an example using 1s orbitals.

Alternative Goal Structures for Computer Game-Based Learning

ERIC Educational Resources Information Center

Ke, Fengfeng

2008-01-01

This field study investigated the application of cooperative, competitive, and individualistic goal structures in classroom use of computer math games and its impact on students' math performance and math learning attitudes. One hundred and sixty 5th-grade students were recruited and randomly assigned to Teams-Games-Tournament cooperative gaming,…

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Solution-state structure and affinities of cyclodextrin: Fentanyl complexes by nuclear magnetic resonance spectroscopy and molecular dynamics simulation

DOE PAGES

Mayer, Brian P.; Kennedy, Daniel J.; Lau, Edmond Y.; ...

2016-02-04

Cyclodextrins (CDs) are investigated for their ability to form inclusion complexes with the analgesic fentanyl and three similar molecules: acetylfentanyl, thiofentanyl, and acetylthiofentanyl. Stoichiometry, binding strength, and complex structure are revealed through nuclear magnetic resonance (NMR) techniques and discussed in terms of molecular dynamics (MD) simulations. It was found that β-cyclodextrin is generally capable of forming the strongest complexes with the fentanyl panel. Two-dimensional NMR data and computational chemical calculations are used to derive solution-state structures of the complexes. Binding of the fentanyls to the CDs occurs at the amide phenyl ring, leaving the majority of the molecule solvated bymore » water, an observation common to all four fentanyls. This finding suggests a universal binding behavior, as the vast majority of previously synthesized fentanyl analogues contain this structural moiety. Furthermore, this baseline study serves as the most complete work on CD:fentanyl complexes to date and provides the insights into strategies for producing future generations of designer cyclodextrins capable of stronger and more selective complexation of fentanyl and its analogues.« less

Computation material science of structural-phase transformation in casting aluminium alloys

NASA Astrophysics Data System (ADS)

Golod, V. M.; Dobosh, L. Yu

2017-04-01

Successive stages of computer simulation the formation of the casting microstructure under non-equilibrium conditions of crystallization of multicomponent aluminum alloys are presented. On the basis of computer thermodynamics and heat transfer during solidification of macroscale shaped castings are specified the boundary conditions of local heat exchange at mesoscale modeling of non-equilibrium formation the solid phase and of the component redistribution between phases during coalescence of secondary dendrite branches. Computer analysis of structural - phase transitions based on the principle of additive physico-chemical effect of the alloy components in the process of diffusional - capillary morphological evolution of the dendrite structure and the o of local dendrite heterogeneity which stochastic nature and extent are revealed under metallographic study and modeling by the Monte Carlo method. The integrated computational materials science tools at researches of alloys are focused and implemented on analysis the multiple-factor system of casting processes and prediction of casting microstructure.

Parallel-vector computation for structural analysis and nonlinear unconstrained optimization problems

NASA Technical Reports Server (NTRS)

Nguyen, Duc T.

1990-01-01

Practical engineering application can often be formulated in the form of a constrained optimization problem. There are several solution algorithms for solving a constrained optimization problem. One approach is to convert a constrained problem into a series of unconstrained problems. Furthermore, unconstrained solution algorithms can be used as part of the constrained solution algorithms. Structural optimization is an iterative process where one starts with an initial design, a finite element structure analysis is then performed to calculate the response of the system (such as displacements, stresses, eigenvalues, etc.). Based upon the sensitivity information on the objective and constraint functions, an optimizer such as ADS or IDESIGN, can be used to find the new, improved design. For the structural analysis phase, the equation solver for the system of simultaneous, linear equations plays a key role since it is needed for either static, or eigenvalue, or dynamic analysis. For practical, large-scale structural analysis-synthesis applications, computational time can be excessively large. Thus, it is necessary to have a new structural analysis-synthesis code which employs new solution algorithms to exploit both parallel and vector capabilities offered by modern, high performance computers such as the Convex, Cray-2 and Cray-YMP computers. The objective of this research project is, therefore, to incorporate the latest development in the parallel-vector equation solver, PVSOLVE into the widely popular finite-element production code, such as the SAP-4. Furthermore, several nonlinear unconstrained optimization subroutines have also been developed and tested under a parallel computer environment. The unconstrained optimization subroutines are not only useful in their own right, but they can also be incorporated into a more popular constrained optimization code, such as ADS.

Cloud4Psi: cloud computing for 3D protein structure similarity searching.

PubMed

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-10-01

Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. © The Author 2014. Published by Oxford University Press.

Cloud4Psi: cloud computing for 3D protein structure similarity searching

PubMed Central

Mrozek, Dariusz; Małysiak-Mrozek, Bożena; Kłapciński, Artur

2014-01-01

Summary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units. Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/. For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm. Contact: dariusz.mrozek@polsl.pl PMID:24930141

Structural Reproduction of Social Networks in Computer-Mediated Communication Forums

ERIC Educational Resources Information Center

Stefanone, M. A.; Gay, G.

2008-01-01

This study explores the relationship between the structure of an existing social network and the structure of an emergent discussion-board network in an undergraduate university class. Thirty-one students were issued with laptop computers that remained in their possession for the duration of the semester. While using these machines, participants'…

Computationally efficient algorithm for Gaussian Process regression in case of structured samples

NASA Astrophysics Data System (ADS)

Belyaev, M.; Burnaev, E.; Kapushev, Y.

2016-04-01

Surrogate modeling is widely used in many engineering problems. Data sets often have Cartesian product structure (for instance factorial design of experiments with missing points). In such case the size of the data set can be very large. Therefore, one of the most popular algorithms for approximation-Gaussian Process regression-can be hardly applied due to its computational complexity. In this paper a computationally efficient approach for constructing Gaussian Process regression in case of data sets with Cartesian product structure is presented. Efficiency is achieved by using a special structure of the data set and operations with tensors. Proposed algorithm has low computational as well as memory complexity compared to existing algorithms. In this work we also introduce a regularization procedure allowing to take into account anisotropy of the data set and avoid degeneracy of regression model.

Structure, function, and behaviour of computational models in systems biology

PubMed Central

2013-01-01

Background Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such “bio-models” necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. Results We present a conceptual framework – the meaning facets – which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model’s components (structure), the meaning of the model’s intended use (function), and the meaning of the model’s dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. Conclusions The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research

The hyperfine structure in the rotational spectra of D{sub 2}{sup 17}O and HD{sup 17}O: Confirmation of the absolute nuclear magnetic shielding scale for oxygen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Puzzarini, Cristina, E-mail: cristina.puzzarini@unibo.it; Cazzoli, Gabriele; Harding, Michael E.

2015-03-28

Guided by theoretical predictions, the hyperfine structures of the rotational spectra of mono- and bideuterated-water containing {sup 17}O have been experimentally investigated. To reach sub-Doppler resolution, required to resolve the hyperfine structure due to deuterium quadrupole coupling as well as to spin-rotation (SR) and dipolar spin-spin couplings, the Lamb-dip technique has been employed. The experimental investigation and in particular, the spectral analysis have been supported by high-level quantum-chemical computations employing coupled-cluster techniques and, for the first time, a complete experimental determination of the hyperfine parameters involved was possible. The experimentally determined {sup 17}O spin-rotation constants of D{sub 2}{sup 17}O andmore » HD{sup 17}O were used to derive the paramagnetic part of the corresponding nuclear magnetic shielding constants. Together with the computed diamagnetic contributions as well as the vibrational and temperature corrections, the latter constants have been employed to confirm the oxygen nuclear magnetic shielding scale, recently established on the basis of spin-rotation data for H{sub 2}{sup 17}O [Puzzarini et al., J. Chem. Phys. 131, 234304 (2009)].« less

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Structural determinants of nuclear export signal orientation in binding to exportin CRM1

DOE PAGES

Fung, Ho Yee Joyce; Fu, Szu -Chin; Brautigam, Chad A.; ...

2015-09-08

The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). A comparison of minus and plus NESs identified structural and sequencemore » determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.« less

Topology optimization aided structural design: Interpretation, computational aspects and 3D printing.

PubMed

Kazakis, Georgios; Kanellopoulos, Ioannis; Sotiropoulos, Stefanos; Lagaros, Nikos D

2017-10-01

Construction industry has a major impact on the environment that we spend most of our life. Therefore, it is important that the outcome of architectural intuition performs well and complies with the design requirements. Architects usually describe as "optimal design" their choice among a rather limited set of design alternatives, dictated by their experience and intuition. However, modern design of structures requires accounting for a great number of criteria derived from multiple disciplines, often of conflicting nature. Such criteria derived from structural engineering, eco-design, bioclimatic and acoustic performance. The resulting vast number of alternatives enhances the need for computer-aided architecture in order to increase the possibility of arriving at a more preferable solution. Therefore, the incorporation of smart, automatic tools in the design process, able to further guide designer's intuition becomes even more indispensable. The principal aim of this study is to present possibilities to integrate automatic computational techniques related to topology optimization in the phase of intuition of civil structures as part of computer aided architectural design. In this direction, different aspects of a new computer aided architectural era related to the interpretation of the optimized designs, difficulties resulted from the increased computational effort and 3D printing capabilities are covered here in.

Structural computational modeling of RNA aptamers.

PubMed

Xu, Xiaojun; Dickey, David D; Chen, Shi-Jie; Giangrande, Paloma H

2016-07-01

RNA aptamers represent an emerging class of biologics that can be easily adapted for personalized and precision medicine. Several therapeutic aptamers with desirable binding and functional properties have been developed and evaluated in preclinical studies over the past 25years. However, for the majority of these aptamers, their clinical potential has yet to be realized. A significant hurdle to the clinical adoption of this novel class of biologicals is the limited information on their secondary and tertiary structure. Knowledge of the RNA's structure would greatly facilitate and expedite the post-selection optimization steps required for translation, including truncation (to reduce costs of manufacturing), chemical modification (to enhance stability and improve safety) and chemical conjugation (to improve drug properties for combinatorial therapy). Here we describe a structural computational modeling methodology that when coupled to a standard functional assay, can be used to determine key sequence and structural motifs of an RNA aptamer. We applied this methodology to enable the truncation of an aptamer to prostate specific membrane antigen (PSMA) with great potential for targeted therapy that had failed previous truncation attempts. This methodology can be easily applied to optimize other aptamers with therapeutic potential. Copyright © 2016. Published by Elsevier Inc.

Orbital transfer of large space structures with nuclear electric rockets

NASA Technical Reports Server (NTRS)

Silva, T. H.; Byers, D. C.

1980-01-01

This paper discusses the potential application of electric propulsion for orbit transfer of a large spacecraft structure from low earth orbit to geosynchronous altitude in a deployed configuration. The electric power was provided by the spacecraft nuclear reactor space power system on a shared basis during transfer operations. Factors considered with respect to system effectiveness included nuclear power source sizing, electric propulsion thruster concept, spacecraft deployment constraints, and orbital operations and safety. It is shown that the favorable total impulse capability inherent in electric propulsion provides a potential economic advantage over chemical propulsion orbit transfer vehicles by reducing the number of Space Shuttle flights in ground-to-orbit transportation requirements.

Evaluation of prompt gamma-ray data and nuclear structure of niobium-94 with statistical model calculations

NASA Astrophysics Data System (ADS)

Turkoglu, Danyal

Precise knowledge of prompt gamma-ray intensities following neutron capture is critical for elemental and isotopic analyses, homeland security, modeling nuclear reactors, etc. A recently-developed database of prompt gamma-ray production cross sections and nuclear structure information in the form of a decay scheme, called the Evaluated Gamma-ray Activation File (EGAF), is under revision. Statistical model calculations are useful for checking the consistency of the decay scheme, providing insight on its completeness and accuracy. Furthermore, these statistical model calculations are necessary to estimate the contribution of continuum gamma-rays, which cannot be experimentally resolved due to the high density of excited states in medium- and heavy-mass nuclei. Decay-scheme improvements in EGAF lead to improvements to other databases (Evaluated Nuclear Structure Data File, Reference Input Parameter Library) that are ultimately used in nuclear-reaction models to generate the Evaluated Nuclear Data File (ENDF). Gamma-ray transitions following neutron capture in 93Nb have been studied at the cold-neutron beam facility at the Budapest Research Reactor. Measurements have been performed using a coaxial HPGe detector with Compton suppression. Partial gamma-ray production capture cross sections at a neutron velocity of 2200 m/s have been deduced relative to that of the 255.9-keV transition after cold-neutron capture by 93Nb. With the measurement of a niobium chloride target, this partial cross section was internally standardized to the cross section for the 1951-keV transition after cold-neutron capture by 35Cl. The resulting (0.1377 +/- 0.0018) barn (b) partial cross section produced a calibration factor that was 23% lower than previously measured for the EGAF database. The thermal-neutron cross sections were deduced for the 93Nb(n,gamma ) 94mNb and 93Nb(n,gamma) 94gNb reactions by summing the experimentally-measured partial gamma-ray production cross sections associated

Nuclear-relaxed elastic and piezoelectric constants of materials: Computational aspects of two quantum-mechanical approaches.

PubMed

Erba, Alessandro; Caglioti, Dominique; Zicovich-Wilson, Claudio Marcelo; Dovesi, Roberto

2017-02-15

Two alternative approaches for the quantum-mechanical calculation of the nuclear-relaxation term of elastic and piezoelectric tensors of crystalline materials are illustrated and their computational aspects discussed: (i) a numerical approach based on the geometry optimization of atomic positions at strained lattice configurations and (ii) a quasi-analytical approach based on the evaluation of the force- and displacement-response internal-strain tensors as combined with the interatomic force-constant matrix. The two schemes are compared both as regards their computational accuracy and performance. The latter approach, not being affected by the many numerical parameters and procedures of a typical quasi-Newton geometry optimizer, constitutes a more reliable and robust mean to the evaluation of such properties, at a reduced computational cost for most crystalline systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Exploration of structure and function in biomolecules through solid-state NMR and computational methods

NASA Astrophysics Data System (ADS)

Heider, Elizabeth M.

Solid-State Nuclear Magnetic Resonance (SSNMR) spectroscopy and quantum mechanical calculations are powerful analysis tools. Leveraged independently, each method yields important nuclear and molecular information. Used in concert, SSNMR and computational techniques provide complementary data about the structure of solids. These methods are particularly useful in characterizing the structures of microcrystalline organic compounds and revealing mechanisms of biological activity. Such applications may possess special relevance in analysis of pharmaceutical products; 90% of all pharmaceuticals are marketed as solids and bioactivity is strongly linked with molecular conformation. Accordingly, this dissertation employs both SSNMR and quantum mechanical computation to study three bioactive molecules: citrinin, two forms of Atrasentan (Abt-627), and paclitaxel (Taxol RTM). First, a computational study is utilized to determine the mechanism for unusual antioxidant activity in citrinin. Here, molecular geometries and bond dissociation enthalpies (BDE) of the citrinin O--H groups are calculated from first principles (ab initio). The total molecular Hamiltonian is determined by approximating the individual contributors to energy including electronic energy and contributions from modes of molecular vibration. This study of citrinin clearly identifies specific reaction sites in the active form, establishing the central role of intramolecular hydrogen bonding in this activity. Notably, it is discovered that citrinin itself is not the active species. Instead, a pair of hydrated Michael addition products of citrinin act as radical scavengers via O--H bond dissociation. Next, two separate compounds of the anticancer drug Abt-627 (form I and form II) are examined via SSNMR. The three principal values of the 13C diagonalized chemical shift tensor are acquired through the high resolution 2D experiment, FIREMAT. Isotropic chemical shift assignments are made utilizing both dipolar

Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes.

PubMed

Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V; Ford, Ian J; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W

2015-01-01

The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

PubMed Central

Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

2014-01-01

The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ~5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC1. Whilst the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized2-5, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins5,6, and is therefore not well understood. Here, we show that stiffness topography7 with sharp atomic force microscopy tips can generate nanoscale cross sections of the NPC. The cross sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy2-5. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport, and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel. PMID:25420031

Nanoscale stiffness topography reveals structure and mechanics of the transport barrier in intact nuclear pore complexes

NASA Astrophysics Data System (ADS)

Bestembayeva, Aizhan; Kramer, Armin; Labokha, Aksana A.; Osmanović, Dino; Liashkovich, Ivan; Orlova, Elena V.; Ford, Ian J.; Charras, Guillaume; Fassati, Ariberto; Hoogenboom, Bart W.

2015-01-01

The nuclear pore complex (NPC) is the gate for transport between the cell nucleus and the cytoplasm. Small molecules cross the NPC by passive diffusion, but molecules larger than ∼5 nm must bind to nuclear transport receptors to overcome a selective barrier within the NPC. Although the structure and shape of the cytoplasmic ring of the NPC are relatively well characterized, the selective barrier is situated deep within the central channel of the NPC and depends critically on unstructured nuclear pore proteins, and is therefore not well understood. Here, we show that stiffness topography with sharp atomic force microscopy tips can generate nanoscale cross-sections of the NPC. The cross-sections reveal two distinct structures, a cytoplasmic ring and a central plug structure, which are consistent with the three-dimensional NPC structure derived from electron microscopy. The central plug persists after reactivation of the transport cycle and resultant cargo release, indicating that the plug is an intrinsic part of the NPC barrier. Added nuclear transport receptors accumulate on the intact transport barrier and lead to a homogenization of the barrier stiffness. The observed nanomechanical properties in the NPC indicate the presence of a cohesive barrier to transport and are quantitatively consistent with the presence of a central condensate of nuclear pore proteins in the NPC channel.

Is nuclear matter a quantum crystal?

NASA Technical Reports Server (NTRS)

Canuto, V.; Chitre, S. M.

1973-01-01

A possible alternative to the ordinary gas-like computation for nuclear matter is investigated under the assumption that the nucleons are arranged in a lattice. BCC, FCC and HCP structures are investigated. Only HCP shows a minimum in the energy vs. density curve with a modest binding energy of -1.5 MeV. The very low density limit is investigated and sensible results are obtained only if the tensor force decreases with the density. A study of the elastic properties indicates that the previous structures are mechanically unstable against shearing stresses.

Nuclear spin noise in the central spin model

NASA Astrophysics Data System (ADS)

Fröhling, Nina; Anders, Frithjof B.; Glazov, Mikhail

2018-05-01

We study theoretically the fluctuations of the nuclear spins in quantum dots employing the central spin model which accounts for the hyperfine interaction of the nuclei with the electron spin. These fluctuations are calculated both with an analytical approach using homogeneous hyperfine couplings (box model) and with a numerical simulation using a distribution of hyperfine coupling constants. The approaches are in good agreement. The box model serves as a benchmark with low computational cost that explains the basic features of the nuclear spin noise well. We also demonstrate that the nuclear spin noise spectra comprise a two-peak structure centered at the nuclear Zeeman frequency in high magnetic fields with the shape of the spectrum controlled by the distribution of the hyperfine constants. This allows for direct access to this distribution function through nuclear spin noise spectroscopy.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

Two key areas of crucial importance to the computer-based simulation of large space structures are discussed. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area involves massively parallel computers.

Computational methods and software systems for dynamics and control of large space structures

NASA Technical Reports Server (NTRS)

Park, K. C.; Felippa, C. A.; Farhat, C.; Pramono, E.

1990-01-01

This final report on computational methods and software systems for dynamics and control of large space structures covers progress to date, projected developments in the final months of the grant, and conclusions. Pertinent reports and papers that have not appeared in scientific journals (or have not yet appeared in final form) are enclosed. The grant has supported research in two key areas of crucial importance to the computer-based simulation of large space structure. The first area involves multibody dynamics (MBD) of flexible space structures, with applications directed to deployment, construction, and maneuvering. The second area deals with advanced software systems, with emphasis on parallel processing. The latest research thrust in the second area, as reported here, involves massively parallel computers.

Achievements and challenges in structural bioinformatics and computational biophysics.

PubMed

Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

2015-01-01

The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

Achievements and challenges in structural bioinformatics and computational biophysics

PubMed Central

Samish, Ilan; Bourne, Philip E.; Najmanovich, Rafael J.

2015-01-01

Motivation: The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. Results: An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. Conclusion: The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. Contact: Rafael.Najmanovich@USherbrooke.ca PMID:25488929

Fermi liquid, clustering, and structure factor in dilute warm nuclear matter

NASA Astrophysics Data System (ADS)

Röpke, G.; Voskresensky, D. N.; Kryukov, I. A.; Blaschke, D.

2018-02-01

Properties of nuclear systems at subsaturation densities can be obtained from different approaches. We demonstrate the use of the density autocorrelation function which is related to the isothermal compressibility and, after integration, to the equation of state. This way we connect the Landau Fermi liquid theory well elaborated in nuclear physics with the approaches to dilute nuclear matter describing cluster formation. A quantum statistical approach is presented, based on the cluster decomposition of the polarization function. The fundamental quantity to be calculated is the dynamic structure factor. Comparing with the Landau Fermi liquid theory which is reproduced in lowest approximation, the account of bound state formation and continuum correlations gives the correct low-density result as described by the second virial coefficient and by the mass action law (nuclear statistical equilibrium). Going to higher densities, the inclusion of medium effects is more involved compared with other quantum statistical approaches, but the relation to the Landau Fermi liquid theory gives a promising approach to describe not only thermodynamic but also collective excitations and non-equilibrium properties of nuclear systems in a wide region of the phase diagram.

Two-Year-Olds Compute Syntactic Structure On-Line

ERIC Educational Resources Information Center

Bernal, Savita; Dehaene-Lambertz, Ghislaine; Millotte, Severine; Christophe, Anne

2010-01-01

Syntax allows human beings to build an infinite number of new sentences from a finite stock of words. Because toddlers typically utter only one or two words at a time, they have been thought to have no syntax. Using event-related potentials (ERPs), we demonstrated that 2-year-olds do compute syntactic structure when listening to spoken sentences.…

National Nuclear Data Center

Science.gov Websites

reaction data Sigma Retrieval & Plotting Nuclear structure & decay Data Nuclear Science References Experimental Unevaluated Nuclear Data List Evaluated Nuclear Structure Data File NNDC databases Ground and isomeric states properties Nuclear structure & decay data journal Nuclear reaction model code Tools and

STARS: An integrated general-purpose finite element structural, aeroelastic, and aeroservoelastic analysis computer program

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.

1991-01-01

The details of an integrated general-purpose finite element structural analysis computer program which is also capable of solving complex multidisciplinary problems is presented. Thus, the SOLIDS module of the program possesses an extensive finite element library suitable for modeling most practical problems and is capable of solving statics, vibration, buckling, and dynamic response problems of complex structures, including spinning ones. The aerodynamic module, AERO, enables computation of unsteady aerodynamic forces for both subsonic and supersonic flow for subsequent flutter and divergence analysis of the structure. The associated aeroservoelastic analysis module, ASE, effects aero-structural-control stability analysis yielding frequency responses as well as damping characteristics of the structure. The program is written in standard FORTRAN to run on a wide variety of computers. Extensive graphics, preprocessing, and postprocessing routines are also available pertaining to a number of terminals.

The Structure and Properties of Silica Glass Nanostructures using Novel Computational Systems

NASA Astrophysics Data System (ADS)

Doblack, Benjamin N.

The structure and properties of silica glass nanostructures are examined using computational methods in this work. Standard synthesis methods of silica and its associated material properties are first discussed in brief. A review of prior experiments on this amorphous material is also presented. Background and methodology for the simulation of mechanical tests on amorphous bulk silica and nanostructures are later presented. A new computational system for the accurate and fast simulation of silica glass is also presented, using an appropriate interatomic potential for this material within the open-source molecular dynamics computer program LAMMPS. This alternative computational method uses modern graphics processors, Nvidia CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model select materials, this enhancement allows the addition of accelerated molecular dynamics simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal of this project is to investigate the structure and size dependent mechanical properties of silica glass nanohelical structures under tensile MD conditions using the innovative computational system. Specifically, silica nanoribbons and nanosprings are evaluated which revealed unique size dependent elastic moduli when compared to the bulk material. For the nanoribbons, the tensile behavior differed widely between the models simulated, with distinct characteristic extended elastic regions. In the case of the nanosprings simulated, more clear trends are observed. In particular, larger nanospring wire cross-sectional radii (r) lead to larger Young's moduli, while larger helical diameters (2R) resulted in smaller Young's moduli. Structural transformations and theoretical models are also analyzed to identify

Computational Modeling in Structural Materials Processing

NASA Technical Reports Server (NTRS)

Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

High temperature materials such as silicon carbide, a variety of nitrides, and ceramic matrix composites find use in aerospace, automotive, machine tool industries and in high speed civil transport applications. Chemical vapor deposition (CVD) is widely used in processing such structural materials. Variations of CVD include deposition on substrates, coating of fibers, inside cavities and on complex objects, and infiltration within preforms called chemical vapor infiltration (CVI). Our current knowledge of the process mechanisms, ability to optimize processes, and scale-up for large scale manufacturing is limited. In this regard, computational modeling of the processes is valuable since a validated model can be used as a design tool. The effort is similar to traditional chemically reacting flow modeling with emphasis on multicomponent diffusion, thermal diffusion, large sets of homogeneous reactions, and surface chemistry. In the case of CVI, models for pore infiltration are needed. In the present talk, examples of SiC nitride, and Boron deposition from the author's past work will be used to illustrate the utility of computational process modeling.

Perceptual organization in computer vision - A review and a proposal for a classificatory structure

NASA Technical Reports Server (NTRS)

Sarkar, Sudeep; Boyer, Kim L.

1993-01-01

The evolution of perceptual organization in biological vision, and its necessity in advanced computer vision systems, arises from the characteristic that perception, the extraction of meaning from sensory input, is an intelligent process. This is particularly so for high order organisms and, analogically, for more sophisticated computational models. The role of perceptual organization in computer vision systems is explored. This is done from four vantage points. First, a brief history of perceptual organization research in both humans and computer vision is offered. Next, a classificatory structure in which to cast perceptual organization research to clarify both the nomenclature and the relationships among the many contributions is proposed. Thirdly, the perceptual organization work in computer vision in the context of this classificatory structure is reviewed. Finally, the array of computational techniques applied to perceptual organization problems in computer vision is surveyed.

Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

ERIC Educational Resources Information Center

Likic, Vladimir A.

2006-01-01

This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

Computer program for determining mass properties of a rigid structure

NASA Technical Reports Server (NTRS)

Hull, R. A.; Gilbert, J. L.; Klich, P. J.

1978-01-01

A computer program was developed for the rapid computation of the mass properties of complex structural systems. The program uses rigid body analyses and permits differences in structural material throughout the total system. It is based on the premise that complex systems can be adequately described by a combination of basic elemental shapes. Simple geometric data describing size and location of each element and the respective material density or weight of each element were the only required input data. From this minimum input, the program yields system weight, center of gravity, moments of inertia and products of inertia with respect to mutually perpendicular axes through the system center of gravity. The program also yields mass properties of the individual shapes relative to component axes.

Analysis of the transient response of nuclear spins in GaAs with/without nuclear magnetic resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rasly, Mahmoud; Lin, Zhichao; Yamamoto, Masafumi

As an alternative to studying the steady-state responses of nuclear spins in solid state systems, working within a transient-state framework can reveal interesting phenomena. The response of nuclear spins in GaAs to a changing magnetic field was analyzed based on the time evolution of nuclear spin temperature. Simulation results well reproduced our experimental results for the transient oblique Hanle signals observed in an all-electrical spin injection device. The analysis showed that the so called dynamic nuclear polarization can be treated as a cooling tool for the nuclear spins: It works as a provider to exchange spin angular momentum between polarizedmore » electron spins and nuclear spins through the hyperfine interaction, leading to an increase in the nuclear polarization. In addition, a time-delay of the nuclear spin temperature with a fast sweep of the external magnetic field produces a possible transient state for the nuclear spin polarization. On the other hand, the nuclear magnetic resonance acts as a heating tool for a nuclear spin system. This causes the nuclear spin temperature to jump to infinity: i.e., the average nuclear spins along with the nuclear field vanish at resonant fields of {sup 75}As, {sup 69}Ga and {sup 71}Ga, showing an interesting step-dip structure in the oblique Hanle signals. These analyses provide a quantitative understanding of nuclear spin dynamics in semiconductors for application in future computation processing.« less

The Legnaro National Laboratories and the SPES facility: nuclear structure and reactions today and tomorrow

NASA Astrophysics Data System (ADS)

de Angelis, Giacomo; Fiorentini, Gianni

2016-11-01

There is a very long tradition of studying nuclear structure and reactions at the Legnaro National Laboratories (LNL) of the Istituto Nazionale di Fisica Nucleare (Italian Institute of Nuclear Physics). The wide expertise acquired in building and running large germanium arrays has made the laboratories one of the most advanced research centers in γ-ray spectroscopy. The ’gamma group’ has been deeply involved in all the national and international developments of the last 20 years and is currently one of the major contributors to the AGATA project, the first (together with its American counterpart GRETINA) γ-detector array based on γ-ray tracking. This line of research is expected to be strongly boosted by the coming into operation of the SPES radioactive ion beam project, currently under construction at LNL. In this report, written on the occasion of the 40th anniversary of the Nobel prize awarded to Aage Bohr, Ben R Mottelson and Leo Rainwater and particularly focused on the physics of nuclear structure, we intend to summarize the different lines of research that have guided nuclear structure and reaction research at LNL in the last decades. The results achieved have paved the way for the present SPES facility, a new laboratories infrastructure producing and accelerating radioactive ion beams of fission fragments and other isotopes.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Proposal for grid computing for nuclear applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Idris, Faridah Mohamad; Ismail, Saaidi; Haris, Mohd Fauzi B.

2014-02-12

The use of computer clusters for computational sciences including computational physics is vital as it provides computing power to crunch big numbers at a faster rate. In compute intensive applications that requires high resolution such as Monte Carlo simulation, the use of computer clusters in a grid form that supplies computational power to any nodes within the grid that needs computing power, has now become a necessity. In this paper, we described how the clusters running on a specific application could use resources within the grid, to run the applications to speed up the computing process.

The NASA NASTRAN structural analysis computer program - New content

NASA Technical Reports Server (NTRS)

Weidman, D. J.

1978-01-01

Capabilities of a NASA-developed structural analysis computer program, NASTRAN, are evaluated with reference to finite-element modelling. Applications include the automotive industry as well as aerospace. It is noted that the range of sub-programs within NASTRAN has expanded, while keeping user cost low.

Data Structures in Natural Computing: Databases as Weak or Strong Anticipatory Systems

NASA Astrophysics Data System (ADS)

Rossiter, B. N.; Heather, M. A.

2004-08-01

Information systems anticipate the real world. Classical databases store, organise and search collections of data of that real world but only as weak anticipatory information systems. This is because of the reductionism and normalisation needed to map the structuralism of natural data on to idealised machines with von Neumann architectures consisting of fixed instructions. Category theory developed as a formalism to explore the theoretical concept of naturality shows that methods like sketches arising from graph theory as only non-natural models of naturality cannot capture real-world structures for strong anticipatory information systems. Databases need a schema of the natural world. Natural computing databases need the schema itself to be also natural. Natural computing methods including neural computers, evolutionary automata, molecular and nanocomputing and quantum computation have the potential to be strong. At present they are mainly at the stage of weak anticipatory systems.

Nuclear Data Networks

Science.gov Websites

calibrations. NSDD The international network of Nuclear Structure and Decay Data evaluators Group of and updating of nuclear structure data contained in Evaluated Nuclear Structure Data File (ENSDF

Physics with gamma-beams and charged particle detectors: I) Nuclear structure II) Nuclear astrophysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gai, Moshe

The Charged Particle Working Group (CPWG) is proposing to construct large area Silicon Strip Detector (SSD), a gas Time Projection Chamber detector read by an electronic readout system (eTPC) and a Bubble Chamber (BC) containing superheated high purity water to be used in measurements utilizing intense gamma-ray beams from the newly constructed ELI-NP facility at Magurele, Bucharest in Romania. We intend to use the SSD and eTPC detectors to address essential problems in nuclear structure physics, such as clustering and the many alpha-decay of light nuclei such as {sup 12}C and {sup 16}O. All three detectors (SSD, eTPC and BC)more » will be used to address central problems in nuclear astrophysics such as the astrophysical cross section factor of the {sup 12}C(α,γ) reaction and other processes central to stellar evolution. The CPWG intends to submit to the ELI-NP facility a Technical Design Report (TDR) for the proposed detectors.« less

10. Photocopy of drawing, February 1958, NUCLEAR REACTOR FACILITY, STRUCTURAL ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

10. Photocopy of drawing, February 1958, NUCLEAR REACTOR FACILITY, STRUCTURAL CROSS SECTION. Giffals & Vallet, Inc., L. Rosetti, Associated Architects and Engineers, Detroit, Michigan; and U.S. Army Engineer Division, New England Corps of Engineers, Boston, Massachusetts. Drawing Number 35-84-04. (Original: AMTL Engineering Division, Watertown). - Watertown Arsenal, Building No. 100, Wooley Avenue, Watertown, Middlesex County, MA

Natural circulating passive cooling system for nuclear reactor containment structure

DOEpatents

Gou, Perng-Fei; Wade, Gentry E.

1990-01-01

A passive cooling system for the contaminant structure of a nuclear reactor plant providing protection against overpressure within the containment attributable to inadvertent leakage or rupture of the system components. The cooling system utilizes natural convection for transferring heat imbalances and enables the discharge of irradiation free thermal energy to the atmosphere for heat disposal from the system.

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible

Computational Structures Technology for Airframes and Propulsion Systems

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Compiler); Housner, Jerrold M. (Compiler); Starnes, James H., Jr. (Compiler); Hopkins, Dale A. (Compiler); Chamis, Christos C. (Compiler)

1992-01-01

This conference publication contains the presentations and discussions from the joint University of Virginia (UVA)/NASA Workshops. The presentations included NASA Headquarters perspectives on High Speed Civil Transport (HSCT), goals and objectives of the UVA Center for Computational Structures Technology (CST), NASA and Air Force CST activities, CST activities for airframes and propulsion systems in industry, and CST activities at Sandia National Laboratory.

THE AIMS AND ACTIVITIES OF THE INTERNATIONAL NETWORK OF NUCLEAR STRUCTURE AND DECAY DATA EVALUATORS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

NICHOLS,A.L.; TULI, J.K.

International Network of Nuclear Structure and Decay Data (NSDD) Evaluators consists of a number of evaluation groups and data service centers in several countries that appreciate the merits of working together to maintain and ensure the quality and comprehensive content of the ENSDF database (Evaluated Nuclear Structure Data File). Biennial meetings of the network are held under the auspices of the International Atomic Energy Agency (IAEA) to assign evaluation responsibilities, monitor progress, discuss improvements and emerging difficulties, and agree on actions to be undertaken by individual members. The evaluated data and bibliographic details are made available to users via variousmore » media, such as the journals ''Nuclear Physics A'' and ''Nuclear Data Sheets'', the World Wide Web, on CD-ROM, wall charts of the nuclides and ''Nuclear Wallet Cards''. While the ENSDF master database is maintained by the US National Nuclear Data Center at the Brookhaven National Laboratory, these data are also available from other nuclear data centers including the IAEA Nuclear Data Section. The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy, in cooperation with the IAEA, organizes workshops on NSDD at regular intervals. The primary aims of these particular workshops are to provide hands-on training in the data evaluation processes, and to encourage new evaluators to participate in NSDD activities. The technical contents of these NSDD workshops are described, along with the rationale for the inclusion of various topics.« less

Interactive computer graphics system for structural sizing and analysis of aircraft structures

NASA Technical Reports Server (NTRS)

Bendavid, D.; Pipano, A.; Raibstein, A.; Somekh, E.

1975-01-01

A computerized system for preliminary sizing and analysis of aircraft wing and fuselage structures was described. The system is based upon repeated application of analytical program modules, which are interactively interfaced and sequence-controlled during the iterative design process with the aid of design-oriented graphics software modules. The entire process is initiated and controlled via low-cost interactive graphics terminals driven by a remote computer in a time-sharing mode.

Nuclear matrix and hnRNP share a common structural constituent associated with premessenger RNA.

PubMed Central

Gallinaro, H; Puvion, E; Kister, L; Jacob, M

1983-01-01

Nuclear matrix and heterogeneous nuclear ribonucleoprotein (hnRNP) were compared to establish whether premessenger RNA (premRNA) was associated with a same constituent in both structures. The isolation of nuclear matrix included the removal of chromatin and of 0.4 M KCl-soluble material. HnRNP, isolated by a standard method was also treated by 0.4 M KCl. Both isolation procedures caused the removal of DNA, histones, a fraction of small nuclear RNA and of nonhistone proteins including the hnRNP proteins in the 30 000-40 000 mol. wt. range. High resolution autoradiography showed that hnRNA remained associated with the residual fibrils in both structures. They both contained the same premRNA and maturation products as shown by the analysis of the transcripts of the early region 3 of adenovirus 2. In addition, the small nuclear RNA and protein of the salt-resistant complexes were also present in the matrix. The results are compatible with the idea that the salt-resistant complexes from hnRNP constitute the fibrils associated with premRNA in the nucleoplasmic matrix. The fibrils may be the basic unit of splicing and their organization in matrix might provide the spatial configuration necessary for regulation. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 7. PMID:6557026

Computed tomography: Will the slices reveal the truth

PubMed Central

Haridas, Harish; Mohan, Abarajithan; Papisetti, Sravanthi; Ealla, Kranti K. R.

2016-01-01

With the advances in the field of imaging sciences, new methods have been developed in dental radiology. These include digital radiography, density analyzing methods, cone beam computed tomography (CBCT), magnetic resonance imaging, ultrasound, and nuclear imaging techniques, which provide high-resolution detailed images of oral structures. The current review aims to critically elaborate the use of CBCT in endodontics. PMID:27652253

Theoretical interpretation of the nuclear structure of 88Se within the ACM and the QPM models.

NASA Astrophysics Data System (ADS)

Gratchev, I. N.; Thiamova, G.; Alexa, P.; Simpson, G. S.; Ramdhane, M.

2018-02-01

The four-parameter algebraic collective model (ACM) Hamiltonian is used to describe the nuclear structure of 88Se. It is shown that the ACM is capable of providing a reasonable description of the excitation energies and relative positions of the ground-state band and γ band. The most probable interpretation of the nuclear structure of 88Se is that of a transitional nucleus. The Quasiparticle-plus-Phonon Model (QPM) was also applied to describe the nuclear motion in 88Se. Preliminarily calculations show that the collectivity of second excited state {2}2+ is weak and that this state contains a strong two-quasiparticle component.

Computational Analysis of Mine Blast on a Commercial Vehicle Structure

DTIC Science & Technology

2007-01-01

ANALYSIS OF MINE BLAST ON A COMMERCIAL VEHICLE STRUCTURE M. Grujicic 1∗ , B. Pandurangan 1 , I. Haque 1 , B. A. Cheeseman 2 , W. N. Roy 2 and R. R. Skaggs...buried in (either dry or saturated sand) underneath the vehicle’s front right wheel is analyzed computationally. The computational analysis included the...A frequency analysis of the pressure versus time signals and visual observation clearly show the differences in the blast loads resulting from the

Nuclear physics: quantitative single-cell approaches to nuclear organization and gene expression.

PubMed

Lionnet, T; Wu, B; Grünwald, D; Singer, R H; Larson, D R

2010-01-01

The internal workings of the nucleus remain a mystery. A list of component parts exists, and in many cases their functional roles are known for events such as transcription, RNA processing, or nuclear export. Some of these components exhibit structural features in the nucleus, regions of concentration or bodies that have given rise to the concept of functional compartmentalization--that there are underlying organizational principles to be described. In contrast, a picture is emerging in which transcription appears to drive the assembly of the functional components required for gene expression, drawing from pools of excess factors. Unifying this seemingly dual nature requires a more rigorous approach, one in which components are tracked in time and space and correlated with onset of specific nuclear functions. In this chapter, we anticipate tools that will address these questions and provide the missing kinetics of nuclear function. These tools are based on analyzing the fluctuations inherent in the weak signals of endogenous nuclear processes and determining values for them. In this way, it will be possible eventually to provide a computational model describing the functional relationships of essential components.

Evaluation of the Retrieval of Nuclear Science Document References Using the Universal Decimal Classification as the Indexing Language for a Computer-Based System

ERIC Educational Resources Information Center

Atherton, Pauline; And Others

A single issue of Nuclear Science Abstracts, containing about 2,300 abstracts, was indexed by Universal Decimal Classification (UDC) using the Special Subject Edition of UDC for Nuclear Science and Technology. The descriptive cataloging and UDC-indexing records formed a computer-stored data base. A systematic random sample of 500 additional…

PREFACE: 21st International Conference on Computing in High Energy and Nuclear Physics (CHEP2015)

NASA Astrophysics Data System (ADS)

Sakamoto, H.; Bonacorsi, D.; Ueda, I.; Lyon, A.

2015-12-01

The International Conference on Computing in High Energy and Nuclear Physics (CHEP) is a major series of international conferences intended to attract physicists and computing professionals to discuss on recent developments and trends in software and computing for their research communities. Experts from the high energy and nuclear physics, computer science, and information technology communities attend CHEP events. This conference series provides an international forum to exchange experiences and the needs of a wide community, and to present and discuss recent, ongoing, and future activities. At the beginning of the successful series of CHEP conferences in 1985, the latest developments in embedded systems, networking, vector and parallel processing were presented in Amsterdam. The software and computing ecosystem massively evolved since then, and along this path each CHEP event has marked a step further. A vibrant community of experts on a wide range of different high-energy and nuclear physics experiments, as well as technology explorer and industry contacts, attend and discuss the present and future challenges, and shape the future of an entire community. In such a rapidly evolving area, aiming to capture the state-of-the-art on software and computing through a collection of proceedings papers on a journal is a big challenge. Due to the large attendance, the final papers appear on the journal a few months after the conference is over. Additionally, the contributions often report about studies at very heterogeneous statuses, namely studies that are completed, or are just started, or yet to be done. It is not uncommon that by the time a specific paper appears on the journal some of the work is over a year old, or the investigation actually happened in different directions and with different methodologies than originally presented at the conference just a few months before. And by the time the proceedings appear in journal form, new ideas and explorations have

The importance of structural anisotropy in computational models of traumatic brain injury.

PubMed

Carlsen, Rika W; Daphalapurkar, Nitin P

2015-01-01

Understanding the mechanisms of injury might prove useful in assisting the development of methods for the management and mitigation of traumatic brain injury (TBI). Computational head models can provide valuable insight into the multi-length-scale complexity associated with the primary nature of diffuse axonal injury. It involves understanding how the trauma to the head (at the centimeter length scale) translates to the white-matter tissue (at the millimeter length scale), and even further down to the axonal-length scale, where physical injury to axons (e.g., axon separation) may occur. However, to accurately represent the development of TBI, the biofidelity of these computational models is of utmost importance. There has been a focused effort to improve the biofidelity of computational models by including more sophisticated material definitions and implementing physiologically relevant measures of injury. This paper summarizes recent computational studies that have incorporated structural anisotropy in both the material definition of the white matter and the injury criterion as a means to improve the predictive capabilities of computational models for TBI. We discuss the role of structural anisotropy on both the mechanical response of the brain tissue and on the development of injury. We also outline future directions in the computational modeling of TBI.

Protein Structure Determination by Assembling Super-Secondary Structure Motifs Using Pseudocontact Shifts.

PubMed

Pilla, Kala Bharath; Otting, Gottfried; Huber, Thomas

2017-03-07

Computational and nuclear magnetic resonance hybrid approaches provide efficient tools for 3D structure determination of small proteins, but currently available algorithms struggle to perform with larger proteins. Here we demonstrate a new computational algorithm that assembles the 3D structure of a protein from its constituent super-secondary structural motifs (Smotifs) with the help of pseudocontact shift (PCS) restraints for backbone amide protons, where the PCSs are produced from different metal centers. The algorithm, DINGO-PCS (3D assembly of Individual Smotifs to Near-native Geometry as Orchestrated by PCSs), employs the PCSs to recognize, orient, and assemble the constituent Smotifs of the target protein without any other experimental data or computational force fields. Using a universal Smotif database, the DINGO-PCS algorithm exhaustively enumerates any given Smotif. We benchmarked the program against ten different protein targets ranging from 100 to 220 residues with different topologies. For nine of these targets, the method was able to identify near-native Smotifs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nuclear Shell Structure and Beta Decay I. Odd A Nuclei II. Even A Nuclei

DOE R&D Accomplishments Database

Mayer, M.G.; Moszkowski, S.A.; Nordheim, L.W.

1951-05-01

In Part I a systematics is given of all transitions for odd A nuclei for which sufficiently reliable data are available. The allowed or forbidden characters of the transitions are correlated with the positions of the initial and final odd nucleon groups in the nuclear shell scheme. The nuclear shells show definite characteristics with respect to parity of the ground states. The latter is the same as the one obtained from known spins and magnetic moments in a one-particle interpretation. In Part II a systematics of the beta transitions of even-A nuclei is given. An interpretation of the character of the transitions in terms of nuclear shell structure is achieved on the hypothesis that the odd nucleon groups have the same structure as in odd-A nuclei, together with a simple coupling rule between the neutron and proton groups in odd-odd nuclei.

Large-Scale Computation of Nuclear Magnetic Resonance Shifts for Paramagnetic Solids Using CP2K.

PubMed

Mondal, Arobendo; Gaultois, Michael W; Pell, Andrew J; Iannuzzi, Marcella; Grey, Clare P; Hutter, Jürg; Kaupp, Martin

2018-01-09

Large-scale computations of nuclear magnetic resonance (NMR) shifts for extended paramagnetic solids (pNMR) are reported using the highly efficient Gaussian-augmented plane-wave implementation of the CP2K code. Combining hyperfine couplings obtained with hybrid functionals with g-tensors and orbital shieldings computed using gradient-corrected functionals, contact, pseudocontact, and orbital-shift contributions to pNMR shifts are accessible. Due to the efficient and highly parallel performance of CP2K, a wide variety of materials with large unit cells can be studied with extended Gaussian basis sets. Validation of various approaches for the different contributions to pNMR shifts is done first for molecules in a large supercell in comparison with typical quantum-chemical codes. This is then extended to a detailed study of g-tensors for extended solid transition-metal fluorides and for a series of complex lithium vanadium phosphates. Finally, lithium pNMR shifts are computed for Li 3 V 2 (PO 4 ) 3 , for which detailed experimental data are available. This has allowed an in-depth study of different approaches (e.g., full periodic versus incremental cluster computations of g-tensors and different functionals and basis sets for hyperfine computations) as well as a thorough analysis of the different contributions to the pNMR shifts. This study paves the way for a more-widespread computational treatment of NMR shifts for paramagnetic materials.

229Thorium-doped calcium fluoride for nuclear laser spectroscopy.

PubMed

Dessovic, P; Mohn, P; Jackson, R A; Winkler, G; Schreitl, M; Kazakov, G; Schumm, T

2014-03-12

The (229)thorium isotope presents an extremely low-energy isomer state of the nucleus which is expected around 7.8 eV, in the vacuum ultraviolet (VUV) regime. This unique system may bridge between atomic and nuclear physics, enabling coherent manipulation and precision spectroscopy of nuclear quantum states using laser light. It has been proposed to implant (229)thorium into VUV transparent crystal matrices to facilitate laser spectroscopy and possibly realize a solid-state nuclear clock. In this work, we validate the feasibility of this approach by computer modelling of thorium doping into calcium fluoride single crystals. Using atomistic modelling and full electronic structure calculations, we find a persistent large band gap and no additional electronic levels emerging in the middle of the gap due to the presence of the dopant, which should allow direct optical interrogation of the nuclear transition.Based on the electronic structure, we estimate the thorium nuclear quantum levels within the solid-state environment. Precision laser spectroscopy of these levels will allow the study of a broad range of crystal field effects, transferring Mössbauer spectroscopy into the optical regime.

Toward high-resolution computational design of helical membrane protein structure and function

PubMed Central

Barth, Patrick; Senes, Alessandro

2016-01-01

The computational design of α-helical membrane proteins is still in its infancy but has made important progress. De novo design has produced stable, specific and active minimalistic oligomeric systems. Computational re-engineering can improve stability and modulate the function of natural membrane proteins. Currently, the major hurdle for the field is not computational, but the experimental characterization of the designs. The emergence of new structural methods for membrane proteins will accelerate progress PMID:27273630

Scalable quantum computation scheme based on quantum-actuated nuclear-spin decoherence-free qubits

NASA Astrophysics Data System (ADS)

Dong, Lihong; Rong, Xing; Geng, Jianpei; Shi, Fazhan; Li, Zhaokai; Duan, Changkui; Du, Jiangfeng

2017-11-01

We propose a novel theoretical scheme of quantum computation. Nuclear spin pairs are utilized to encode decoherence-free (DF) qubits. A nitrogen-vacancy center serves as a quantum actuator to initialize, readout, and quantum control the DF qubits. The realization of CNOT gates between two DF qubits are also presented. Numerical simulations show high fidelities of all these processes. Additionally, we discuss the potential of scalability. Our scheme reduces the challenge of classical interfaces from controlling and observing complex quantum systems down to a simple quantum actuator. It also provides a novel way to handle complex quantum systems.

Structural mode significance using INCA. [Interactive Controls Analysis computer program

NASA Technical Reports Server (NTRS)

Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

1990-01-01

Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

Computational simulation of composite structures with and without damage. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Wilt, Thomas F.

1994-01-01

A methodology is described which uses finite element analysis of various laminates to computationally simulate the effects of delamination damage initiation and growth on the structural behavior of laminated composite structures. The delamination area is expanded according to a set pattern. As the delamination area increases, how the structural response of the laminate changes with respect to buckling and strain energy release rate are investigated. Rules are presented for laminates of different configurations, materials and thickness. These results demonstrate that computational simulation methods can provide alternate methods to investigate the complex delamination damage mechanisms found in composite structures.

Integrating structure-based and ligand-based approaches for computational drug design.

PubMed

Wilson, Gregory L; Lill, Markus A

2011-04-01

Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the structure of the protein or on the biological and physicochemical properties of bound ligands, respectively. In recent years there has been a trend towards integrating these two methods in order to enhance the reliability and efficiency of computer-aided drug-design approaches by combining information from both the ligand and the protein. This trend resulted in a variety of methods that include: pseudoreceptor methods, pharmacophore methods, fingerprint methods and approaches integrating docking with similarity-based methods. In this article, we will describe the concepts behind each method and selected applications.

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales.

PubMed

Palumbi, S R; Baker, C S

1994-05-01

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.

The TRIUMF nuclear structure program and TIGRESS

NASA Astrophysics Data System (ADS)

Garrett, P. E.; Andreyev, A.; Austin, R. A. E.; Ball, G. C.; Bandyopadhyay, D.; Becker, J. A.; Boston, A. J.; Boston, H. C.; Chakrawarthy, R. S.; Churchman, R.; Cline, D.; Cooper, R. J.; Cross, D.; Dashdorj, D.; Demand, G. A.; Dimmock, M. R.; Drake, T.; Finlay, P.; Gagnon, K.; Gallant, A. T.; Green, K. L.; Grint, A. N.; Grinyer, G. F.; Hackman, G.; Harkness, L. J.; Hayes, A. B.; Kanungo, R.; Kulp, W. D.; Leach, K. G.; Lee, G.; Leslie, J. R.; Maharaj, R.; Martin, J.-P.; Mattoon, C.; Mills, W. J.; Morton, A. C.; Nelson, L.; Newman, O.; Nolan, P. J.; Padilla-Rodal, E.; Pearson, C. J.; Phillips, A. A.; Porter-Peden, M.; Ressler, J. J.; Ruiz, C.; Sarazin, F.; Schumaker, M. A.; Scraggs, D. P.; Strange, M. D.; Subramanian, M.; Svensson, C. E.; Waddington, J. C.; Wan, J.; Whitbeck, A.; Williams, S. J.; Wood, J. L.; Wong, J. C.; Wu, C. Y.; Zganjar, E. F.

2007-08-01

The isotope separator and accelerator (ISAC) facility located at the TRIUMF laboratory in Vancouver, Canada, is one of the world's most advanced isotope separator on-line-type radioactive ion beam facilities. An extensive γ-ray spectroscopy programme at ISAC is centred around two major research facilities: (i) the 8π γ-ray spectrometer for β-delayed γ-ray spectroscopy experiments with the low-energy beams from ISAC-I, and (ii) the next generation TRIUMF-ISAC gamma-ray escape suppressed spectrometer (TIGRESS) for in-beam experiments with the accelerated radioactive-ion beams. An overview of these facilities and recent results from the diverse programme of nuclear structure and fundamental interaction studies they support is presented.

Standardized Procedure Content And Data Structure Based On Human Factors Requirements For Computer-Based Procedures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bly, Aaron; Oxstrand, Johanna; Le Blanc, Katya L

2015-02-01

Most activities that involve human interaction with systems in a nuclear power plant are guided by procedures. Traditionally, the use of procedures has been a paper-based process that supports safe operation of the nuclear power industry. However, the nuclear industry is constantly trying to find ways to decrease the human error rate, especially the human errors associated with procedure use. Advances in digital technology make computer-based procedures (CBPs) a valid option that provides further enhancement of safety by improving human performance related to procedure use. The transition from paper-based procedures (PBPs) to CBPs creates a need for a computer-based proceduremore » system (CBPS). A CBPS needs to have the ability to perform logical operations in order to adjust to the inputs received from either users or real time data from plant status databases. Without the ability for logical operations the procedure is just an electronic copy of the paper-based procedure. In order to provide the CBPS with the information it needs to display the procedure steps to the user, special care is needed in the format used to deliver all data and instructions to create the steps. The procedure should be broken down into basic elements and formatted in a standard method for the CBPS. One way to build the underlying data architecture is to use an Extensible Markup Language (XML) schema, which utilizes basic elements to build each step in the smart procedure. The attributes of each step will determine the type of functionality that the system will generate for that step. The CBPS will provide the context for the step to deliver referential information, request a decision, or accept input from the user. The XML schema needs to provide all data necessary for the system to accurately perform each step without the need for the procedure writer to reprogram the CBPS. The research team at the Idaho National Laboratory has developed a prototype CBPS for field workers as well as

A versatile computer-controlled pulsed nuclear quadrupole resonance spectrometer

NASA Astrophysics Data System (ADS)

Fisher, Gregory; MacNamara, Ernesto; Santini, Robert E.; Raftery, Daniel

1999-12-01

A new, pulsed nuclear quadrupole resonance (NQR) spectrometer capable of performing a variety of pulsed and swept experiments is described. The spectrometer features phase locked, superheterodyne detection using a commercial spectrum analyzer and a fully automatic, computer-controlled tuning and matching network. The tuning and matching network employs stepper motors which turn high power air gap capacitors in a "moving grid" optimization strategy to minimize the reflected power from a directional coupler. In the duplexer circuit, digitally controlled relays are used to switch different lengths of coax cable appropriate for the different radio frequencies. A home-built pulse programmer card controls the timing of radio frequency pulses sent to the probe, while data acquisition and control software is written in Microsoft Quick Basic. Spin-echo acquisition experiments are typically used to acquire the data, although a variety of pulse sequences can be employed. Scan times range from one to several hours depending upon the step resolution and the spectral range required for each experiment. Pure NQR spectra of NaNO2 and 3-aminopyridine are discussed.

Midi-maxi computer interaction in the interpretation of nuclear medicine procedures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schlapper, G.A.

1977-01-01

A study of renal function with an Anger Gamma Camera coupled with a Digital Equipment Corporation Gamma-11 System and an IBM System 370 demonstrates the potential of quantitative determinations of physiological function through the application of midi-maxi computer interaction in the interpretation of nuclear medicine procedures. It is shown that radiotracers can provide an opportunity to assess physiological processes of renal function by noninvasively following the path of a tracer as a function of time. Time-activity relationships obtained over seven anatomically defined regions are related to parameters of a seven compartment model employed to describe the renal clearance process. Themore » values obtained for clinically significant parameters agree with known renal pathophysiology. Differentiation of failure of acute, chronic, and obstructive forms is indicated.« less

Automatic Estimation of the Radiological Inventory for the Dismantling of Nuclear Facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia-Bermejo, R.; Felipe, A.; Gutierrez, S.

The estimation of the radiological inventory of Nuclear Facilities to be dismantled is a process that included information related with the physical inventory of all the plant and radiological survey. Estimation of the radiological inventory for all the components and civil structure of the plant could be obtained with mathematical models with statistical approach. A computer application has been developed in order to obtain the radiological inventory in an automatic way. Results: A computer application that is able to estimate the radiological inventory from the radiological measurements or the characterization program has been developed. In this computer applications has beenmore » included the statistical functions needed for the estimation of the central tendency and variability, e.g. mean, median, variance, confidence intervals, variance coefficients, etc. This computer application is a necessary tool in order to be able to estimate the radiological inventory of a nuclear facility and it is a powerful tool for decision taken in future sampling surveys.« less

Center for computation and visualization of geometric structures. Final report, 1992 - 1995

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-11-01

This report describes the overall goals and the accomplishments of the Geometry Center of the University of Minnesota, whose mission is to develop, support, and promote computational tools for visualizing geometric structures, for facilitating communication among mathematical and computer scientists and between these scientists and the public at large, and for stimulating research in geometry.

Nuclear medium effects in structure functions of nucleon at moderate Q2

NASA Astrophysics Data System (ADS)

Haider, H.; Zaidi, F.; Sajjad Athar, M.; Singh, S. K.; Ruiz Simo, I.

2015-11-01

Recent experiments performed on inclusive electron scattering from nuclear targets have measured the nucleon electromagnetic structure functions F1 (x ,Q2), F2 (x ,Q2) and FL (x ,Q2) in 12C, 27Al, 56Fe and 64Cu nuclei. The measurements have been done in the energy region of 1 GeV2 nuclear medium effects in these structure functions arising due to the Fermi motion, binding energy, nucleon correlations, mesonic contributions from pion and rho mesons and shadowing effects. The calculations are performed in a local density approximation using a relativistic nucleon spectral function which includes nucleon correlations. The numerical results are compared with the recent experimental data from JLab and also with some earlier experiments.

Structural materials for Gen-IV nuclear reactors: Challenges and opportunities

NASA Astrophysics Data System (ADS)

Murty, K. L.; Charit, I.

2008-12-01

Generation-IV reactor design concepts envisioned thus far cater toward a common goal of providing safer, longer lasting, proliferation-resistant and economically viable nuclear power plants. The foremost consideration in the successful development and deployment of Gen-IV reactor systems is the performance and reliability issues involving structural materials for both in-core and out-of-core applications. The structural materials need to endure much higher temperatures, higher neutron doses and extremely corrosive environment, which are beyond the experience of the current nuclear power plants. Materials under active consideration for use in different reactor components include various ferritic/martensitic steels, austenitic stainless steels, nickel-base superalloys, ceramics, composites, etc. This paper presents a summary of various Gen-IV reactor concepts, with emphasis on the structural materials issues depending on the specific application areas. This paper also discusses the challenges involved in using the existing materials under both service and off-normal conditions. Tasks become increasingly complex due to the operation of various fundamental phenomena like radiation-induced segregation, radiation-enhanced diffusion, precipitation, interactions between impurity elements and radiation-produced defects, swelling, helium generation and so forth. Further, high temperature capability (e.g. creep properties) of these materials is a critical, performance-limiting factor. It is demonstrated that novel alloy and microstructural design approaches coupled with new materials processing and fabrication techniques may mitigate the challenges, and the optimum system performance may be achieved under much demanding conditions.

Physical and mechanical metallurgy of zirconium alloys for nuclear applications: a multi-scale computational study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glazoff, Michael Vasily

2014-10-01

In the post-Fukushima world, the stability of materials under extreme conditions is an important issue for the safety of nuclear reactors. Because the nuclear industry is going to continue using advanced zirconium cladding materials in the foreseeable future, it become critical to gain fundamental understanding of the several interconnected problems. First, what are the thermodynamic and kinetic factors affecting the oxidation and hydrogen pick-up by these materials at normal, off-normal conditions, and in long-term storage? Secondly, what protective coatings (if any) could be used in order to gain extremely valuable time at off-normal conditions, e.g., when temperature exceeds the criticalmore » value of 2200°F? Thirdly, the kinetics of oxidation of such protective coating or braiding needs to be quantified. Lastly, even if some degree of success is achieved along this path, it is absolutely critical to have automated inspection algorithms allowing identifying defects of cladding as soon as possible. This work strives to explore these interconnected factors from the most advanced computational perspective, utilizing such modern techniques as first-principles atomistic simulations, computational thermodynamics of materials, diffusion modeling, and the morphological algorithms of image processing for defect identification. Consequently, it consists of the four parts dealing with these four problem areas preceded by the introduction and formulation of the studied problems. In the 1st part an effort was made to employ computational thermodynamics and ab initio calculations to shed light upon the different stages of oxidation of ziraloys (2 and 4), the role of microstructure optimization in increasing their thermal stability, and the process of hydrogen pick-up, both in normal working conditions and in long-term storage. The 2nd part deals with the need to understand the influence and respective roles of the two different plasticity mechanisms in Zr nuclear alloys

The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

PubMed

Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

2017-01-15

During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

Interactive computer graphics and its role in control system design of large space structures

NASA Technical Reports Server (NTRS)

Reddy, A. S. S. R.

1985-01-01

This paper attempts to show the relevance of interactive computer graphics in the design of control systems to maintain attitude and shape of large space structures to accomplish the required mission objectives. The typical phases of control system design, starting from the physical model such as modeling the dynamics, modal analysis, and control system design methodology are reviewed and the need of the interactive computer graphics is demonstrated. Typical constituent parts of large space structures such as free-free beams and free-free plates are used to demonstrate the complexity of the control system design and the effectiveness of the interactive computer graphics.

Operate a Nuclear Power Plant.

ERIC Educational Resources Information Center

Frimpter, Bonnie J.; And Others

1983-01-01

Describes classroom use of a computer program originally published in Creative Computing magazine. "The Nuclear Power Plant" (runs on Apple II with 48K memory) simulates the operating of a nuclear generating station, requiring students to make decisions as they assume the task of managing the plant. (JN)

Developing a structural health monitoring system for nuclear dry cask storage canister

NASA Astrophysics Data System (ADS)

Sun, Xiaoyi; Lin, Bin; Bao, Jingjing; Giurgiutiu, Victor; Knight, Travis; Lam, Poh-Sang; Yu, Lingyu

2015-03-01

Interim storage of spent nuclear fuel from reactor sites has gained additional importance and urgency for resolving waste-management-related technical issues. In total, there are over 1482 dry cask storage system (DCSS) in use at US plants, storing 57,807 fuel assemblies. Nondestructive material condition monitoring is in urgent need and must be integrated into the fuel cycle to quantify the "state of health", and more importantly, to guarantee the safe operation of radioactive waste storage systems (RWSS) during their extended usage period. A state-of-the-art nuclear structural health monitoring (N-SHM) system based on in-situ sensing technologies that monitor material degradation and aging for nuclear spent fuel DCSS and similar structures is being developed. The N-SHM technology uses permanently installed low-profile piezoelectric wafer sensors to perform long-term health monitoring by strategically using a combined impedance (EMIS), acoustic emission (AE), and guided ultrasonic wave (GUW) approach, called "multimode sensing", which is conducted by the same network of installed sensors activated in a variety of ways. The system will detect AE events resulting from crack (case for study in this project) and evaluate the damage evolution; when significant AE is detected, the sensor network will switch to the GUW mode to perform damage localization, and quantification as well as probe "hot spots" that are prone to damage for material degradation evaluation using EMIS approach. The N-SHM is expected to eventually provide a systematic methodology for assessing and monitoring nuclear waste storage systems without incurring human radiation exposure.

Computational Methods for Structural Mechanics and Dynamics, part 1

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling.

Study of Computational Structures for Multiobject Tracking Algorithms

DTIC Science & Technology

1986-12-01

MULTIOBJECT TRACKING ALGORITHMS 12. PERSONAL AUTHOR(S) i Allen, Thomas G .; Kurien, Thomas; Washburn, Robert B. Jr. 13a. TYPE OF REPORT 13b. TIME COVERED 14...mentioned possible restructurings of the tracking algorithm that increase the amount of available parallelism ’ g ~. are investigated. This step is extremely...sufficient for our needs here. In the following section we will examine the structure and computational requirements of the track- g , oriented approach

The determination of the in situ structure by nuclear spin contrast variation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stuhrmann, H.B.; Nierhaus, K.H.

1994-12-31

Polarized neutron scattering from polarized nuclear spins in hydrogenous substances opens a new way of contrast variation. The enhanced contrast due to proton spin polarization was used for the in situ structure determination of tRNA of the functional complex of the E.coli ribosome.

Computer Modeling of the Earliest Cellular Structures and Functions

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Chipot, Christophe; Schweighofer, Karl

2000-01-01

In the absence of extinct or extant record of protocells (the earliest ancestors of contemporary cells). the most direct way to test our understanding of the origin of cellular life is to construct laboratory models of protocells. Such efforts are currently underway in the NASA Astrobiology Program. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures and developing designs for molecules that perform proto-cellular functions. Many of these functions, such as import of nutrients, capture and storage of energy. and response to changes in the environment are carried out by proteins bound to membrane< We will discuss a series of large-scale, molecular-level computer simulations which demonstrate (a) how small proteins (peptides) organize themselves into ordered structures at water-membrane interfaces and insert into membranes, (b) how these peptides aggregate to form membrane-spanning structures (eg. channels), and (c) by what mechanisms such aggregates perform essential proto-cellular functions, such as proton transport of protons across cell walls, a key step in cellular bioenergetics. The simulations were performed using the molecular dynamics method, in which Newton's equations of motion for each item in the system are solved iteratively. The problems of interest required simulations on multi-nanosecond time scales, which corresponded to 10(exp 6)-10(exp 8) time steps.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

Nuclear quantum effects on structure and transport properties of dense liquid helium

NASA Astrophysics Data System (ADS)

Kang, Dongdong; Dai, Jiayu; Yuan, Jianmin

2015-11-01

Transport properties of dense liquid helium under the conditions of planet's core and cool atmosphere of white dwarfs are important for determining the structure and evolution of these astrophysical objects. We have investigated these properties of dense liquid helium by using the improved centroid path-integral simulations combined with density functional theory. The results show that with the inclusion of nuclear quantum effects (NQEs), the self-diffusion is largely higher while the shear viscosity is notably lower than the results of without the inclusion of NQEs due to the lower collision cross sections even when the NQEs have little effects on the static structures. The potential surface of helium atom along the simulation trajectory is quite different between MD and PIMD simulations. We have shown that the quantum nuclear character induces complex behaviors for ionic transport properties of dense liquid helium. NQEs bring more fluctuations of local electronic density of states than the classical treatment. Therefore, in order to construct more reasonable structure and evolution model for the planets and WDs, NQEs must be reconsidered when calculating the transport properties at certain temperature and density conditions.

Highly-Parallel, Highly-Compact Computing Structures Implemented in Nanotechnology

NASA Technical Reports Server (NTRS)

Crawley, D. G.; Duff, M. J. B.; Fountain, T. J.; Moffat, C. D.; Tomlinson, C. D.

1995-01-01

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

Serotype-specific differences in dengue virus non-structural protein 5 nuclear localization.

PubMed

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D

2013-08-02

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes.

Serotype-specific Differences in Dengue Virus Non-structural Protein 5 Nuclear Localization*

PubMed Central

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D.

2013-01-01

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes. PMID:23770669

Distinct structural and mechanical properties of the nuclear lamina in Hutchinson-Gilford progeria syndrome.

PubMed

Dahl, Kris Noel; Scaffidi, Paola; Islam, Mohammad F; Yodh, Arjun G; Wilson, Katherine L; Misteli, Tom

2006-07-05

The nuclear lamina is a network of structural filaments, the A and B type lamins, located at the nuclear envelope and throughout the nucleus. Lamin filaments provide the nucleus with mechanical stability and support many basic activities, including gene regulation. Mutations in LMNA, the gene encoding A type lamins, cause numerous human diseases, including the segmental premature aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here we show that structural and mechanical properties of the lamina are altered in HGPS cells. We demonstrate by live-cell imaging and biochemical analysis that lamins A and C become trapped at the nuclear periphery in HGPS patient cells. Using micropipette aspiration, we show that the lamina in HGPS cells has a significantly reduced ability to rearrange under mechanical stress. Based on polarization microscopy results, we suggest that the lamins are disordered in the healthy nuclei, whereas the lamins in HGPS nuclei form orientationally ordered microdomains. The reduced deformability of the HGPS nuclear lamina possibly could be due to the inability of these orientationally ordered microdomains to dissipate mechanical stress. Surprisingly, intact HGPS cells exhibited a degree of resistance to acute mechanical stress similar to that of cells from healthy individuals. Thus, in contrast to the nuclear fragility seen in lmna null cells, the lamina network in HGPS cells has unique mechanical properties that might contribute to disease phenotypes by affecting responses to mechanical force and misregulation of mechanosensitive gene expression.

Concealed nuclear material identification via combined fast-neutron/γ-ray computed tomography (FNGCT): a Monte Carlo study

NASA Astrophysics Data System (ADS)

Licata, M.; Joyce, M. J.

2018-02-01

The potential of a combined and simultaneous fast-neutron/γ-ray computed tomography technique using Monte Carlo simulations is described. This technique is applied on the basis of a hypothetical tomography system comprising an isotopic radiation source (americium-beryllium) and a number (13) of organic scintillation detectors for the production and detection of both fast neutrons and γ rays, respectively. Via a combination of γ-ray and fast neutron tomography the potential is demonstrated to discern nuclear materials, such as compounds comprising plutonium and uranium, from substances that are used widely for neutron moderation and shielding. This discrimination is achieved on the basis of the difference in the attenuation characteristics of these substances. Discrimination of a variety of nuclear material compounds from shielding/moderating substances (the latter comprising lead or polyethylene for example) is shown to be challenging when using either γ-ray or neutron tomography in isolation of one another. Much-improved contrast is obtained for a combination of these tomographic modalities. This method has potential applications for in-situ, non-destructive assessments in nuclear security, safeguards, waste management and related requirements in the nuclear industry.

An overview of computational simulation methods for composite structures failure and life analysis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1993-01-01

Three parallel computational simulation methods are being developed at the LeRC Structural Mechanics Branch (SMB) for composite structures failure and life analysis: progressive fracture CODSTRAN; hierarchical methods for high-temperature composites; and probabilistic evaluation. Results to date demonstrate that these methods are effective in simulating composite structures failure/life/reliability.

Systems and methods for dismantling a nuclear reactor

DOEpatents

Heim, Robert R; Adams, Scott Ryan; Cole, Matthew Denver; Kirby, William E; Linnebur, Paul Damon

2014-10-28

Systems and methods for dismantling a nuclear reactor are described. In one aspect the system includes a remotely controlled heavy manipulator ("manipulator") operatively coupled to a support structure, and a control station in a non-contaminated portion of a workspace. The support structure provides the manipulator with top down access into a bioshield of a nuclear reactor. At least one computing device in the control station provides remote control to perform operations including: (a) dismantling, using the manipulator, a graphite moderator, concrete walls, and a ceiling of the bioshield, the manipulator being provided with automated access to all internal portions of the bioshield; (b) loading, using the manipulator, contaminated graphite blocks from the graphite core and other components from the bioshield into one or more waste containers; and (c) dispersing, using the manipulator, dust suppression and contamination fixing spray to contaminated matter.

Atomic structure of the Y complex of the nuclear pore

DOE PAGES

Kelley, Kotaro; Knockenhauer, Kevin E.; Kabachinski, Greg; ...

2015-03-30

The nuclear pore complex (NPC) is the principal gateway for transport into and out of the nucleus. Selectivity is achieved through the hydrogel-like core of the NPC. The structural integrity of the NPC depends on ~15 architectural proteins, which are organized in distinct subcomplexes to form the >40-MDa ring-like structure. In this paper, we present the 4.1-Å crystal structure of a heterotetrameric core element ('hub') of the Y complex, the essential NPC building block, from Myceliophthora thermophila. Using the hub structure together with known Y-complex fragments, we built the entire ~0.5-MDa Y complex. Our data reveal that the conserved coremore » of the Y complex has six rather than seven members. Finally, evolutionarily distant Y-complex assemblies share a conserved core that is very similar in shape and dimension, thus suggesting that there are closely related architectural codes for constructing the NPC in all eukaryotes.« less

Computer simulations of structural transitions in large ferrofluid aggregates

NASA Astrophysics Data System (ADS)

Yoon, Mina; Tomanek, David

2003-03-01

We have developed a quaternion molecular dynamics formalism to study structural transitions in systems of ferrofluid particles in colloidal suspensions. Our approach takes advantage of the viscous damping provided by the surrounding liquid and enables us to study the time evolution of these systems over milli-second time periods as a function of the number of particles, initial geometry, and an externally applied magnetic field. Our computer simulations for aggregates containing tens to hundreds of ferrofluid particles suggest that these systems relax to the global optimum structure in a step-wise manner. During the relaxation process, the potential energy decreases by two mechanisms, which occur on different time scales. Short time periods associated with structural relaxations within a given morphology are followed by much slower processes that generally lead to a simpler morphology. We discuss possible applications of these externally driven structural transitions for targeted medication delivery.

The Next Frontier in Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarrao, John

2016-11-16

Exascale computing refers to computing systems capable of at least one exaflop or a billion calculations per second (1018). That is 50 times faster than the most powerful supercomputers being used today and represents a thousand-fold increase over the first petascale computer that came into operation in 2008. How we use these large-scale simulation resources is the key to solving some of today’s most pressing problems, including clean energy production, nuclear reactor lifetime extension and nuclear stockpile aging.

Methods and benefits of experimental seismic evaluation of nuclear power plants. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1979-07-01

This study reviews experimental techniques, instrumentation requirements, safety considerations, and benefits of performing vibration tests on nuclear power plant containments and internal components. The emphasis is on testing to improve seismic structural models. Techniques for identification of resonant frequencies, damping, and mode shapes, are discussed. The benefits of testing with regard to increased damping and more accurate computer models are oulined. A test plan, schedule and budget are presented for a typical PWR nuclear power plant.

Two-Dimensional Nuclear Magnetic Resonance Structure Determination Module for Introductory Biochemistry: Synthesis and Structural Characterization of Lyso-Glycerophospholipids

ERIC Educational Resources Information Center

Garrett, Teresa A.; Rose, Rebecca L.; Bell, Sidney M.

2013-01-01

In this laboratory module, introductory biochemistry students are exposed to two-dimensional [superscript 1]H-nuclear magnetic resonance of glycerophospholipids (GPLs). Working in groups of three, students enzymatically synthesized and purified a variety of 2-acyl lyso GPLs. The structure of the 2-acyl lyso GPL was verified using [superscript…

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Using NERSC High-Performance Computing (HPC) systems for high-energy nuclear physics applications with ALICE

NASA Astrophysics Data System (ADS)

Fasel, Markus

2016-10-01

High-Performance Computing Systems are powerful tools tailored to support large- scale applications that rely on low-latency inter-process communications to run efficiently. By design, these systems often impose constraints on application workflows, such as limited external network connectivity and whole node scheduling, that make more general-purpose computing tasks, such as those commonly found in high-energy nuclear physics applications, more difficult to carry out. In this work, we present a tool designed to simplify access to such complicated environments by handling the common tasks of job submission, software management, and local data management, in a framework that is easily adaptable to the specific requirements of various computing systems. The tool, initially constructed to process stand-alone ALICE simulations for detector and software development, was successfully deployed on the NERSC computing systems, Carver, Hopper and Edison, and is being configured to provide access to the next generation NERSC system, Cori. In this report, we describe the tool and discuss our experience running ALICE applications on NERSC HPC systems. The discussion will include our initial benchmarks of Cori compared to other systems and our attempts to leverage the new capabilities offered with Cori to support data-intensive applications, with a future goal of full integration of such systems into ALICE grid operations.

Expression of DNAJB12 or DNAJB14 Causes Coordinate Invasion of the Nucleus by Membranes Associated with a Novel Nuclear Pore Structure

PubMed Central

Goodwin, Edward C.; Motamedi, Nasim; Lipovsky, Alex; Fernández-Busnadiego, Rubén; DiMaio, Daniel

2014-01-01

DNAJB12 and DNAJB14 are transmembrane proteins in the endoplasmic reticulum (ER) that serve as co-chaperones for Hsc70/Hsp70 heat shock proteins. We demonstrate that over-expression of DNAJB12 or DNAJB14 causes the formation of elaborate membranous structures within cell nuclei, which we designate DJANGOS for DNAJ-associated nuclear globular structures. DJANGOS contain DNAJB12, DNAJB14, Hsc70 and markers of the ER lumen and ER and nuclear membranes. Strikingly, they are evenly distributed underneath the nuclear envelope and are of uniform size in any one nucleus. DJANGOS are composed primarily of single-walled membrane tubes and sheets that connect to the nuclear envelope via a unique configuration of membranes, in which the nuclear pore complex appears anchored exclusively to the outer nuclear membrane, allowing both the inner and outer nuclear membranes to flow past the circumference of the nuclear pore complex into the nucleus. DJANGOS break down rapidly during cell division and reform synchronously in the daughter cell nuclei, demonstrating that they are dynamic structures that undergo coordinate formation and dissolution. Genetic studies showed that the chaperone activity of DNAJ/Hsc70 is required for the formation of DJANGOS. Further analysis of these structures will provide insight into nuclear pore formation and function, activities of molecular chaperones, and mechanisms that maintain membrane identity. PMID:24732912

Marketing and commercialization of computational research services.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toevs, J. W.

Physical and computational scientists and mathematicians in Russia's nuclear cities are turning their work toward generating profits from Western markets. Successful ventures require an understanding of the marketing of contract research as well as Western expectations regarding contract execution, quality, and performance. This paper will address fundamentals in business structure, marketing, and contract performance for organizations engaging in the marketing and commercialization of research services. Considerable emphasis will be placed on developing adequate communication within the organization.

The Next Frontier in Computing

ScienceCinema

Sarrao, John

2018-06-13

Exascale computing refers to computing systems capable of at least one exaflop or a billion calculations per second (1018). That is 50 times faster than the most powerful supercomputers being used today and represents a thousand-fold increase over the first petascale computer that came into operation in 2008. How we use these large-scale simulation resources is the key to solving some of today’s most pressing problems, including clean energy production, nuclear reactor lifetime extension and nuclear stockpile aging.

Recent advances in computational structural reliability analysis methods

NASA Astrophysics Data System (ADS)

Thacker, Ben H.; Wu, Y.-T.; Millwater, Harry R.; Torng, Tony Y.; Riha, David S.

1993-10-01

The goal of structural reliability analysis is to determine the probability that the structure will adequately perform its intended function when operating under the given environmental conditions. Thus, the notion of reliability admits the possibility of failure. Given the fact that many different modes of failure are usually possible, achievement of this goal is a formidable task, especially for large, complex structural systems. The traditional (deterministic) design methodology attempts to assure reliability by the application of safety factors and conservative assumptions. However, the safety factor approach lacks a quantitative basis in that the level of reliability is never known and usually results in overly conservative designs because of compounding conservatisms. Furthermore, problem parameters that control the reliability are not identified, nor their importance evaluated. A summary of recent advances in computational structural reliability assessment is presented. A significant level of activity in the research and development community was seen recently, much of which was directed towards the prediction of failure probabilities for single mode failures. The focus is to present some early results and demonstrations of advanced reliability methods applied to structural system problems. This includes structures that can fail as a result of multiple component failures (e.g., a redundant truss), or structural components that may fail due to multiple interacting failure modes (e.g., excessive deflection, resonate vibration, or creep rupture). From these results, some observations and recommendations are made with regard to future research needs.

Recent advances in computational structural reliability analysis methods

NASA Technical Reports Server (NTRS)

Thacker, Ben H.; Wu, Y.-T.; Millwater, Harry R.; Torng, Tony Y.; Riha, David S.

1993-01-01

The goal of structural reliability analysis is to determine the probability that the structure will adequately perform its intended function when operating under the given environmental conditions. Thus, the notion of reliability admits the possibility of failure. Given the fact that many different modes of failure are usually possible, achievement of this goal is a formidable task, especially for large, complex structural systems. The traditional (deterministic) design methodology attempts to assure reliability by the application of safety factors and conservative assumptions. However, the safety factor approach lacks a quantitative basis in that the level of reliability is never known and usually results in overly conservative designs because of compounding conservatisms. Furthermore, problem parameters that control the reliability are not identified, nor their importance evaluated. A summary of recent advances in computational structural reliability assessment is presented. A significant level of activity in the research and development community was seen recently, much of which was directed towards the prediction of failure probabilities for single mode failures. The focus is to present some early results and demonstrations of advanced reliability methods applied to structural system problems. This includes structures that can fail as a result of multiple component failures (e.g., a redundant truss), or structural components that may fail due to multiple interacting failure modes (e.g., excessive deflection, resonate vibration, or creep rupture). From these results, some observations and recommendations are made with regard to future research needs.

A Flexible and Non-instrusive Approach for Computing Complex Structural Coverage Metrics

NASA Technical Reports Server (NTRS)

Whalen, Michael W.; Person, Suzette J.; Rungta, Neha; Staats, Matt; Grijincu, Daniela

2015-01-01

Software analysis tools and techniques often leverage structural code coverage information to reason about the dynamic behavior of software. Existing techniques instrument the code with the required structural obligations and then monitor the execution of the compiled code to report coverage. Instrumentation based approaches often incur considerable runtime overhead for complex structural coverage metrics such as Modified Condition/Decision (MC/DC). Code instrumentation, in general, has to be approached with great care to ensure it does not modify the behavior of the original code. Furthermore, instrumented code cannot be used in conjunction with other analyses that reason about the structure and semantics of the code under test. In this work, we introduce a non-intrusive preprocessing approach for computing structural coverage information. It uses a static partial evaluation of the decisions in the source code and a source-to-bytecode mapping to generate the information necessary to efficiently track structural coverage metrics during execution. Our technique is flexible; the results of the preprocessing can be used by a variety of coverage-driven software analysis tasks, including automated analyses that are not possible for instrumented code. Experimental results in the context of symbolic execution show the efficiency and flexibility of our nonintrusive approach for computing code coverage information

Phenomenological study of nuclear structure of neutron-rich 88Rb isotope

NASA Astrophysics Data System (ADS)

Gupta, Surbhi; Gupta, Anuradha; Bharti, Arun

2018-05-01

A theoretical study of the nuclear structure of odd-odd 88Rb nucleus in the A ˜100 mass region is carried out by using the angular-momentum-projection technique implemented in the Projected Shell Model (PSM). The influence of the high-j orbitals, h11/2 for neutrons and g9/2 for protons on the structure of 88Rb isotope is investigated in the present case by assuming an axial symmetry in the deformed basis. For this isotope, PSM calculations are performed to obtain the yrast line and also the description of the formation of the yrast level structure from multi-quasi-particle configurations. The back-bending in moment of inertia and transition energies have also been calculated and compared with the experimental data.

Computer assisted Objective structured clinical examination versus Objective structured clinical examination in assessment of Dermatology undergraduate students.

PubMed

Chaudhary, Richa; Grover, Chander; Bhattacharya, S N; Sharma, Arun

2017-01-01

The assessment of dermatology undergraduates is being done through computer assisted objective structured clinical examination at our institution for the last 4 years. We attempted to compare objective structured clinical examination (OSCE) and computer assisted objective structured clinical examination (CA-OSCE) as assessment tools. To assess the relative effectiveness of CA-OSCE and OSCE as assessment tools for undergraduate dermatology trainees. Students underwent CA-OSCE as well as OSCE-based evaluation of equal weightage as an end of posting assessment. The attendance as well as the marks in both the examination formats were meticulously recorded and statistically analyzed using SPSS version 20.0. Intercooled Stata V9.0 was used to assess the reliability and internal consistency of the examinations conducted. Feedback from both students and examiners was also recorded. The mean attendance for the study group was 77% ± 12.0%. The average score on CA- OSCE and OSCE was 47.4% ± 19.8% and 53.5% ± 18%, respectively. These scores showed a mutually positive correlation, with Spearman's coefficient being 0.593. Spearman's rank correlation coefficient between attendance scores and assessment score was 0.485 for OSCE and 0.451 for CA-OSCE. The Cronbach's alpha coefficient for all the tests ranged from 0.76 to 0.87 indicating high reliability. The comparison was based on a single batch of 139 students. Such an evaluation on more students in larger number of batches over successive years could help throw more light on the subject. Computer assisted objective structured clinical examination was found to be a valid, reliable and effective format for dermatology assessment, being rated as the preferred format by examiners.

A Diagnostic Study of Computer Application of Structural Communication Grid

ERIC Educational Resources Information Center

Bahar, Mehmet; Aydin, Fatih; Karakirik, Erol

2009-01-01

In this article, Structural communication grid (SCG), an alternative measurement and evaluation technique, has been firstly summarised and the design, development and implementation of a computer based SCG system have been introduced. The system is then tested on a sample of 154 participants consisting of candidate students, science teachers and…

Seismic risk management solution for nuclear power plants

DOE PAGES

Coleman, Justin; Sabharwall, Piyush

2014-12-01

Nuclear power plants should safely operate during normal operations and maintain core-cooling capabilities during off-normal events, including external hazards (such as flooding and earthquakes). Management of external hazards to expectable levels of risk is critical to maintaining nuclear facility and nuclear power plant safety. Seismic risk is determined by convolving the seismic hazard with seismic fragilities (capacity of systems, structures, and components). Seismic isolation (SI) is one protective measure showing promise to minimize seismic risk. Current SI designs (used in commercial industry) reduce horizontal earthquake loads and protect critical infrastructure from the potentially destructive effects of large earthquakes. The benefitmore » of SI application in the nuclear industry is being recognized and SI systems have been proposed in American Society of Civil Engineer Standard 4, ASCE-4, to be released in the winter of 2014, for light water reactors facilities using commercially available technology. The intent of ASCE-4 is to provide criteria for seismic analysis of safety related nuclear structures such that the responses to design basis seismic events, computed in accordance with this standard, will have a small likelihood of being exceeded. The U.S. nuclear industry has not implemented SI to date; a seismic isolation gap analysis meeting was convened on August 19, 2014, to determine progress on implementing SI in the U.S. nuclear industry. The meeting focused on the systems and components that could benefit from SI. As a result, this article highlights the gaps identified at this meeting.« less

Parvovirus Induced Alterations in Nuclear Architecture and Dynamics

PubMed Central

Ihalainen, Teemu O.; Niskanen, Einari A.; Jylhävä, Juulia; Paloheimo, Outi; Dross, Nicolas; Smolander, Hanna; Langowski, Jörg; Timonen, Jussi; Vihinen-Ranta, Maija

2009-01-01

The nucleus of interphase eukaryotic cell is a highly compartmentalized structure containing the three-dimensional network of chromatin and numerous proteinaceous subcompartments. DNA viruses induce profound changes in the intranuclear structures of their host cells. We are applying a combination of confocal imaging including photobleaching microscopy and computational methods to analyze the modifications of nuclear architecture and dynamics in parvovirus infected cells. Upon canine parvovirus infection, expansion of the viral replication compartment is accompanied by chromatin marginalization to the vicinity of the nuclear membrane. Dextran microinjection and fluorescence recovery after photobleaching (FRAP) studies revealed the homogeneity of this compartment. Markedly, in spite of increase in viral DNA content of the nucleus, a significant increase in the protein mobility was observed in infected compared to non-infected cells. Moreover, analyzis of the dynamics of photoactivable capsid protein demonstrated rapid intranuclear dynamics of viral capsids. Finally, quantitative FRAP and cellular modelling were used to determine the duration of viral genome replication. Altogether, our findings indicate that parvoviruses modify the nuclear structure and dynamics extensively. Intranuclear crowding of viral components leads to enlargement of the interchromosomal domain and to chromatin marginalization via depletion attraction. In conclusion, parvoviruses provide a useful model system for understanding the mechanisms of virus-induced intranuclear modifications. PMID:19536327

ROR nuclear receptors: structures, related diseases, and drug discovery

PubMed Central

Zhang, Yan; Luo, Xiao-yu; Wu, Dong-hai; Xu, Yong

2015-01-01

Nuclear receptors (NRs) are ligand-regulated transcription factors that regulate metabolism, development and immunity. The NR superfamily is one of the major classes of drug targets for human diseases. Retinoic acid receptor-related orphan receptor (ROR) α, β and γ belong to the NR superfamily, and these receptors are still considered as 'orphan' receptors because the identification of their endogenous ligands has been controversial. Recent studies have demonstrated that these receptors are regulated by synthetic ligands, thus emerge as important drug targets for the treatment of multiple sclerosis, rheumatoid arthritis, psoriasis, etc. Studying the structural basis and ligand development of RORs will pave the way for a better understanding of the roles of these receptors in human diseases. Here, we review the structural basis, disease relevance, strategies for ligand identification, and current status of development of therapeutic ligands for RORs. PMID:25500868

Structural determination of importin alpha in complex with beak and feather disease virus capsid nuclear localization signal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patterson, Edward I.; EH Graham Centre for Agricultural Innovation; Dombrovski, Andrew K.

2013-09-06

Highlights: •Circovirus capsid proteins contain large nuclear localization signals (NLS). •A method of nuclear import has not been elucidated. •Beak and feather disease virus (BFDV) capsid NLS was crystallized with importin α. •The structure showed BFDV NLS binding to the major site of importin α. •Result shows implications for mechanism of nuclear transport for all circoviruses. -- Abstract: Circoviruses represent a rapidly increasing genus of viruses that infect a variety of vertebrates. Replication requires shuttling viral molecules into the host cell nucleus, a process facilitated by capsid-associated protein (Cap). Whilst a nuclear localization signal (NLS) has been shown to mediatemore » nuclear translocation, the mode of nuclear transport remains to be elucidated. To better understand this process, beak and feather disease virus (BFDV) Cap NLS was crystallized with nuclear import receptor importin-α (Impα). Diffraction yielded structural data to 2.9 Å resolution, and the binding site on both Impα and BFDV Cap NLS were well resolved. The binding mechanism for the major site is likely conserved across circoviruses as supported by the similarity of NLSs in circovirus Caps. This finding illuminates a crucial step for infection of host cells by this viral family, and provides a platform for rational drug design against the binding interface.« less

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Millán, Judith; Basterretxea, Francisco; Fernández, José A; Castaño, Fernando

2011-04-28

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).

Fine-structural cytochemical and immunocytochemical observations on nuclear bodies in the bovine 2-cell embryo.

PubMed

Kopecný, V; Biggiogera, M; Pivko, J; Pavlok, A; Martin, T E; Kaufmann, S H; Shaper, J H; Fakan, S

2000-11-01

Nuclear bodies occurring during the 2-cell stage of bovine embryos (obtained either by in vitro fertilisation of in vitro matured ovarian oocytes, or collection after fertilisation and cleavage in vivo) were studied using ultrastructural cytochemistry and immunocytochemistry to determine whether their occurrence may be linked with the onset of embryonic transcription. In addition, the species-specific ultrastructural features of the interchromatin structures of the 2-cell bovine embryo were displayed. Three different types of nuclear bodies were distinguished: (i) nucleolus precursor bodies (NPBs), (ii) loose bodies (LBs) and (iii) dense bodies (DBs). In order to determine their possible functional significance, we considered parallels between these three nuclear entities and interchromatin compartments reported in other cells. As detected by their preferential ribonucleoprotein staining, all types of nuclear bodies contained ribonucleoproteins. In contrast to the other types of nuclear bodies studied, NPBs contained argyrophilic proteins but in no case they did show morphological features of functional nucleoli. Both compact and vacuolated forms of NPBs were seen in both in vivo and in vitro embryos, sometimes simultaneously in the same nucleus. LBs and DBs reacted with antibodies to Sm antigen, indicating the presence of a group of nucleoplasmic, non-nucleolar small nuclear ribonucleoproteins (snRNPs). The immunoreactivity for Sm antigen was more intense and homogeneous in DBs than in LBs. DBs were seen in both categories of embryo. A possible kinship of DBs with the sphere organelle known from oocytes of different animal species or the prominent spherical inclusions of the early mouse embryo nuclei is suggested. The last type of intranuclear body, the LBs, showed a composite structure. Their granular component, occurring in clusters and displaying immunoreactivity for Sm antigen, was similar to interchromatin granules and was therefore named IG-like granules

Analyzing Sliding Stability of Structures Using the Modified Computer Program GWALL. Revision,

DTIC Science & Technology

1983-11-01

R136 954 RNRLYZING SLIDING STRBILITY OF STRUCTURES USING THE i/i MODIFIED COMPUTER PRO..(U) ARMY ENGINEER WATERRYS EXPERIMENT STATION VICKSBURG MS...GWALL and/or the graphics software package, Graphics Compati- bility System (GCS). Input Features 4. GWALL is very easy to use because it allows the...Prepared Data File 9. Time-sharing computer systems do not always respond quickly to the userts commands, especially when there are many users

Extreme Scale Computing to Secure the Nation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, D L; McGraw, J R; Johnson, J R

2009-11-10

Since the dawn of modern electronic computing in the mid 1940's, U.S. national security programs have been dominant users of every new generation of high-performance computer. Indeed, the first general-purpose electronic computer, ENIAC (the Electronic Numerical Integrator and Computer), was used to calculate the expected explosive yield of early thermonuclear weapons designs. Even the U. S. numerical weather prediction program, another early application for high-performance computing, was initially funded jointly by sponsors that included the U.S. Air Force and Navy, agencies interested in accurate weather predictions to support U.S. military operations. For the decades of the cold war, national securitymore » requirements continued to drive the development of high performance computing (HPC), including advancement of the computing hardware and development of sophisticated simulation codes to support weapons and military aircraft design, numerical weather prediction as well as data-intensive applications such as cryptography and cybersecurity U.S. national security concerns continue to drive the development of high-performance computers and software in the U.S. and in fact, events following the end of the cold war have driven an increase in the growth rate of computer performance at the high-end of the market. This mainly derives from our nation's observance of a moratorium on underground nuclear testing beginning in 1992, followed by our voluntary adherence to the Comprehensive Test Ban Treaty (CTBT) beginning in 1995. The CTBT prohibits further underground nuclear tests, which in the past had been a key component of the nation's science-based program for assuring the reliability, performance and safety of U.S. nuclear weapons. In response to this change, the U.S. Department of Energy (DOE) initiated the Science-Based Stockpile Stewardship (SBSS) program in response to the Fiscal Year 1994 National Defense Authorization Act, which requires, 'in the absence of