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.

Evaluation of 3D airway imaging of obstructive sleep apnea with cone-beam computed tomography.

PubMed

Ogawa, Takumi; Enciso, Reyes; Memon, Ahmed; Mah, James K; Clark, Glenn T

2005-01-01

This study evaluates the use of cone-beam Computer Tomography (CT) for imaging the upper airway structure of Obstructive Sleep Apnea (OSA) patients. The total airway volume and the anteroposterior dimension of oropharyngeal airway showed significant group differences between OSA and gender-matched controls, so if we increase sample size these measurements may distinguish the two groups. We demonstrate the utility of diagnosis of anatomy with the 3D airway imaging with cone-beam Computed Tomography.

Automated analysis in generic groups

NASA Astrophysics Data System (ADS)

Fagerholm, Edvard

This thesis studies automated methods for analyzing hardness assumptions in generic group models, following ideas of symbolic cryptography. We define a broad class of generic and symbolic group models for different settings---symmetric or asymmetric (leveled) k-linear groups --- and prove ''computational soundness'' theorems for the symbolic models. Based on this result, we formulate a master theorem that relates the hardness of an assumption to solving problems in polynomial algebra. We systematically analyze these problems identifying different classes of assumptions and obtain decidability and undecidability results. Then, we develop automated procedures for verifying the conditions of our master theorems, and thus the validity of hardness assumptions in generic group models. The concrete outcome is an automated tool, the Generic Group Analyzer, which takes as input the statement of an assumption, and outputs either a proof of its generic hardness or shows an algebraic attack against the assumption. Structure-preserving signatures are signature schemes defined over bilinear groups in which messages, public keys and signatures are group elements, and the verification algorithm consists of evaluating ''pairing-product equations''. Recent work on structure-preserving signatures studies optimality of these schemes in terms of the number of group elements needed in the verification key and the signature, and the number of pairing-product equations in the verification algorithm. While the size of keys and signatures is crucial for many applications, another aspect of performance is the time it takes to verify a signature. The most expensive operation during verification is the computation of pairings. However, the concrete number of pairings is not captured by the number of pairing-product equations considered in earlier work. We consider the question of what is the minimal number of pairing computations needed to verify structure-preserving signatures. We build an automated tool to search for structure-preserving signatures matching a template. Through exhaustive search we conjecture lower bounds for the number of pairings required in the Type~II setting and prove our conjecture to be true. Finally, our tool exhibits examples of structure-preserving signatures matching the lower bounds, which proves tightness of our bounds, as well as improves on previously known structure-preserving signature schemes.

Sonic and Supersonic Jet Plumes

NASA Technical Reports Server (NTRS)

Venkatapathy, E.; Naughton, J. W.; Flethcher, D. G.; Edwards, Thomas A. (Technical Monitor)

1994-01-01

Study of sonic and supersonic jet plumes are relevant to understanding such phenomenon as jet-noise, plume signatures, and rocket base-heating and radiation. Jet plumes are simple to simulate and yet, have complex flow structures such as Mach disks, triple points, shear-layers, barrel shocks, shock- shear- layer interaction, etc. Experimental and computational simulation of sonic and supersonic jet plumes have been performed for under- and over-expanded, axisymmetric plume conditions. The computational simulation compare very well with the experimental observations of schlieren pictures. Experimental data such as temperature measurements with hot-wire probes are yet to be measured and will be compared with computed values. Extensive analysis of the computational simulations presents a clear picture of how the complex flow structure develops and the conditions under which self-similar flow structures evolve. From the computations, the plume structure can be further classified into many sub-groups. In the proposed paper, detail results from the experimental and computational simulations for single, axisymmetric, under- and over-expanded, sonic and supersonic plumes will be compared and the fluid dynamic aspects of flow structures will be discussed.

Introducing Managers to Expert Systems.

ERIC Educational Resources Information Center

Finlay, Paul N.; And Others

1991-01-01

Describes a short course to expose managers to expert systems, consisting of (1) introductory lecture; (2) supervised computer tutorial; (3) lecture and discussion about knowledge structuring and modeling; and (4) small group work on a case study using computers. (SK)

The Effects of Computer-Assisted Instruction Based on Top-Level Structure Method in English Reading and Writing Abilities of Thai EFL Students

ERIC Educational Resources Information Center

Jinajai, Nattapong; Rattanavich, Saowalak

2015-01-01

This research aims to study the development of ninth grade students' reading and writing abilities and interests in learning English taught through computer-assisted instruction (CAI) based on the top-level structure (TLS) method. An experimental group time series design was used, and the data was analyzed by multivariate analysis of variance…

An Informal Overview of the Unitary Group Approach

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

Sonnad, V.; Escher, J.; Kruse, M.

The Unitary Groups Approach (UGA) is an elegant and conceptually unified approach to quantum structure calculations. It has been widely used in molecular structure calculations, and holds the promise of a single computational approach to structure calculations in a variety of different fields. We explore the possibility of extending the UGA to computations in atomic and nuclear structure as a simpler alternative to traditional Racah algebra-based approaches. We provide a simple introduction to the basic UGA and consider some of the issues in using the UGA with spin-dependent, multi-body Hamiltonians requiring multi-shell bases adapted to additional symmetries. While the UGAmore » is perfectly capable of dealing with such problems, it is seen that the complexity rises dramatically, and the UGA is not at this time, a simpler alternative to Racah algebra-based approaches.« less

Intraclass Correlation Values for Planning Group-Randomized Trials in Education

ERIC Educational Resources Information Center

Hedges, Larry V.; Hedberg, E. C.

2007-01-01

Experiments that assign intact groups to treatment conditions are increasingly common in social research. In educational research, the groups assigned are often schools. The design of group-randomized experiments requires knowledge of the intraclass correlation structure to compute statistical power and sample sizes required to achieve adequate…

Computer codes developed and under development at Lewis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1992-01-01

The objective of this summary is to provide a brief description of: (1) codes developed or under development at LeRC; and (2) the development status of IPACS with some typical early results. The computer codes that have been developed and/or are under development at LeRC are listed in the accompanying charts. This list includes: (1) the code acronym; (2) select physics descriptors; (3) current enhancements; and (4) present (9/91) code status with respect to its availability and documentation. The computer codes list is grouped by related functions such as: (1) composite mechanics; (2) composite structures; (3) integrated and 3-D analysis; (4) structural tailoring; and (5) probabilistic structural analysis. These codes provide a broad computational simulation infrastructure (technology base-readiness) for assessing the structural integrity/durability/reliability of propulsion systems. These codes serve two other very important functions: they provide an effective means of technology transfer; and they constitute a depository of corporate memory.

Direct Simulations of Coupled Transport and Reaction on Nano-Scale X-Ray Computed Tomography Images of Platinum Group Metal-Free Catalyst Cathodes

DOE PAGES

Ogawa, S.; Komini Babu, S.; Chung, H. T.; ...

2016-08-22

The nano/micro-scale geometry of polymer electrolyte fuel cell (PEFC) catalyst layers critically affects cell performance. The small length scales and complex structure of these composite layers make it challenging to analyze cell performance and physics at the particle scale by experiment. We present a computational method to simulate transport and chemical reaction phenomena at the pore/particle-scale and apply it to a PEFC cathode with platinum group metal free (PGM-free) catalyst. Here, we numerically solve the governing equations for the physics with heterogeneous oxygen diffusion coefficient and proton conductivity evaluated using the actual electrode structure and ionomer distribution obtained using nano-scalemore » resolution X-ray computed tomography (nano-CT). Using this approach, the oxygen concentration and electrolyte potential distributions imposed by the oxygen reduction reaction are solved and the impact of the catalyst layer structure on performance is evaluated.« less

Direct Simulations of Coupled Transport and Reaction on Nano-Scale X-Ray Computed Tomography Images of Platinum Group Metal-Free Catalyst Cathodes

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

Ogawa, S.; Komini Babu, S.; Chung, H. T.

The nano/micro-scale geometry of polymer electrolyte fuel cell (PEFC) catalyst layers critically affects cell performance. The small length scales and complex structure of these composite layers make it challenging to analyze cell performance and physics at the particle scale by experiment. We present a computational method to simulate transport and chemical reaction phenomena at the pore/particle-scale and apply it to a PEFC cathode with platinum group metal free (PGM-free) catalyst. Here, we numerically solve the governing equations for the physics with heterogeneous oxygen diffusion coefficient and proton conductivity evaluated using the actual electrode structure and ionomer distribution obtained using nano-scalemore » resolution X-ray computed tomography (nano-CT). Using this approach, the oxygen concentration and electrolyte potential distributions imposed by the oxygen reduction reaction are solved and the impact of the catalyst layer structure on performance is evaluated.« less

T-RMSD: a web server for automated fine-grained protein structural classification.

PubMed

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-07-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd.

T-RMSD: a web server for automated fine-grained protein structural classification

PubMed Central

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

2013-01-01

This article introduces the T-RMSD web server (tree-based on root-mean-square deviation), a service allowing the online computation of structure-based protein classification. It has been developed to address the relation between structural and functional similarity in proteins, and it allows a fine-grained structural clustering of a given protein family or group of structurally related proteins using distance RMSD (dRMSD) variations. These distances are computed between all pairs of equivalent residues, as defined by the ungapped columns within a given multiple sequence alignment. Using these generated distance matrices (one per equivalent position), T-RMSD produces a structural tree with support values for each cluster node, reminiscent of bootstrap values. These values, associated with the tree topology, allow a quantitative estimate of structural distances between proteins or group of proteins defined by the tree topology. The clusters thus defined have been shown to be structurally and functionally informative. The T-RMSD web server is a free website open to all users and available at http://tcoffee.crg.cat/apps/tcoffee/do:trmsd. PMID:23716642

First Principles Study of Chemically Functionalized Graphene

NASA Astrophysics Data System (ADS)

Jha, Sanjiv; Vasiliev, Igor

2015-03-01

The electronic, structural and vibrational properties of carbon nanomaterials can be affected by chemical functionalization. We applied ab initio computational methods based on density functional theory to study the covalent functionalization of graphene with benzyne, carboxyl groups and tetracyanoethylene oxide (TCNEO). Our calculations were carried out using the SIESTA and Quantum-ESPRESSO electronic structure codes combined with the local density and generalized gradient approximations for the exchange correlation functional and norm-conserving Troullier-Martins pseudopotentials. The simulated Raman and infrared spectra of graphene functionalized with carboxyl groups and TCNEO were consistent with the available experimental results. The computed vibrational spectra of graphene functionalized with carboxyl groups showed that the presence of point defects near the functionalization site affects the Raman and infrared spectroscopic signatures of functionalized graphene. Supported by NSF CHE-1112388.

Society for College Science Teachers: High Technology.

ERIC Educational Resources Information Center

Menefee, Robert

1983-01-01

Presents findings of a study group on high technology charged with determining a definition, assessing current educational response, and examining implications for the future. Topics addressed include: super-techs; computer-aided design/computer-aided manufacture (CAD/CAM); structural unemployment; a two-plus-two curriculum; and educational…

Computational Characterization of Electromagnetic Field Propagation in Complex Structures

DTIC Science & Technology

1998-04-10

34Computational characterization of electromagnetic field propagation in complex structures", DAAH01-91-D-ROOS D.O. 59. Dr. Michael Scalora performed the...Development, and Engineering Center, Bldg. 7804, Room 242 Redstone Arsenal, Alabama 35898-5248 USA Dr. Michael Scalora Quantum Optics Group Tel:(205...scheduled to appear. They are: (1) M. Scalora , J.P. Dowling, A.S. Manka, CM. Bowden, and J.W. Haus, Pulse Propagation Near Highly Reflective

A Selective Review of Group Selection in High-Dimensional Models

PubMed Central

Huang, Jian; Breheny, Patrick; Ma, Shuangge

2013-01-01

Grouping structures arise naturally in many statistical modeling problems. Several methods have been proposed for variable selection that respect grouping structure in variables. Examples include the group LASSO and several concave group selection methods. In this article, we give a selective review of group selection concerning methodological developments, theoretical properties and computational algorithms. We pay particular attention to group selection methods involving concave penalties. We address both group selection and bi-level selection methods. We describe several applications of these methods in nonparametric additive models, semiparametric regression, seemingly unrelated regressions, genomic data analysis and genome wide association studies. We also highlight some issues that require further study. PMID:24174707

Survey of Computer-Based Message Systems; COM/PortaCOM Conference System: Design Goals and Principles; Computer Conferencing Is More Than Electronic Mail; Effects of the COM Computer Conference System.

ERIC Educational Resources Information Center

Palme, Jacob

The four papers contained in this document provide: (1) a survey of computer based mail and conference systems; (2) an evaluation of systems for both individually addressed mail and group addressing through conferences and distribution lists; (3) a discussion of various methods of structuring the text data in existing systems; and (4) a…

Comparing Productive Online Dialogue in Two Group Styles: Cooperative and Collaborative

ERIC Educational Resources Information Center

Rose, Mary Annette

2004-01-01

This study examined the influence of group structures upon six groups of distributed graduate students as they pursued a six-week problem-based learning activity by communicating in an asynchronous computer conference. Henri and Rigault's (1996) content analysis framework and Howell-Richardson and Mellar's (1996) guidelines for interconnectedness…

Computer-Based Learning: Graphical Integration of Whole and Sectional Neuroanatomy Improves Long-Term Retention

PubMed Central

Naaz, Farah; Chariker, Julia H.; Pani, John R.

2013-01-01

A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as MRI images). Neuroanatomy was taught to two groups of participants using computer graphical models of the human brain. Both groups learned whole anatomy first with a three-dimensional model of the brain. One group then learned sectional anatomy using two-dimensional sectional representations, with the expectation that there would be transfer of learning from whole to sectional anatomy. The second group learned sectional anatomy by moving a virtual cutting plane through the three-dimensional model. In tests of long-term retention of sectional neuroanatomy, the group with graphically integrated representation recognized more neural structures that were known to be challenging to learn. This study demonstrates the use of graphical representation to facilitate a more elaborated (deeper) understanding of complex spatial relations. PMID:24563579

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

PubMed Central

2017-01-01

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal–organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groups into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure–energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy–structure–function maps. PMID:28776015

A Combination of Hand-held Models and Computer Imaging Programs Helps Students Answer Oral Questions about Molecular Structure and Function: A Controlled Investigation of Student Learning

PubMed Central

Peck, Ronald F.; Colton, Shannon; Morris, Jennifer; Chaibub Neto, Elias; Kallio, Julie

2009-01-01

We conducted a controlled investigation to examine whether a combination of computer imagery and tactile tools helps introductory cell biology laboratory undergraduate students better learn about protein structure/function relationships as compared with computer imagery alone. In all five laboratory sections, students used the molecular imaging program, Protein Explorer (PE). In the three experimental sections, three-dimensional physical models were made available to the students, in addition to PE. Student learning was assessed via oral and written research summaries and videotaped interviews. Differences between the experimental and control group students were not found in our typical course assessments such as research papers, but rather were revealed during one-on-one interviews with students at the end of the semester. A subset of students in the experimental group produced superior answers to some higher-order interview questions as compared with students in the control group. During the interview, students in both groups preferred to use either the hand-held models alone or in combination with the PE imaging program. Students typically did not use any tools when answering knowledge (lower-level thinking) questions, but when challenged with higher-level thinking questions, students in both the control and experimental groups elected to use the models. PMID:19255134

Quake Final Video

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

None

Critical infrastructures of the world are at constant risks for earthquakes. Most of these critical structures are designed using archaic, seismic, simulation methods that were built from early digital computers from the 1970s. Idaho National Laboratory’s Seismic Research Group are working to modernize the simulation methods through computational research and large-scale laboratory experiments.

Physicist's simple access to protein structures: the computer program WHAT IF

NASA Astrophysics Data System (ADS)

Altenberg-Greulich, Brigitte; Zech, Stephan G.; Stehlik, Dietmar; Vriend, Gert

2001-06-01

We describe the computer program WHAT IF and its application to two physical examples. For the DNA binding protein, OCT-1 (pou domain) the location of amino acids with a sidechain amino group is shown. Such knowledge is required when staining this molecule with a fluorescence dye, which binds chemically to the amino terminus as well as amino groups in sidechains. The program shows that most sidechain amino groups are protected when DNA is bound to OCT-1, allowing selective staining of the amino terminal NH2 group. A protein stained this way can be used in fluorescence spectroscopic studies on function aspects of OCT-1.

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.

Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures

PubMed Central

Vila, Jorge A.; Scheraga, Harold A.

2008-01-01

Interest centers here on the analysis of two different, but related, phenomena that affect side-chain conformations and consequently 13Cα chemical shifts and their applications to determine, refine, and validate protein structures. The first is whether 13Cα chemical shifts, computed at the DFT level of approximation with charged residues is a better approximation of observed 13Cα chemical shifts than those computed with neutral residues for proteins in solution. Accurate computation of 13Cα chemical shifts requires a proper representation of the charges, which might not take on integral values. For this analysis, the charges for 139 conformations of the protein ubiquitin were determined by explicit consideration of protein binding equilibria, at a given pH, that is, by exploring the 2ξ possible ionization states of the whole molecule, with ξ being the number of ionizable groups. The results of this analysis, as revealed by the shielding/deshield-ing of the 13Cα nucleus, indicated that: (i) there is a significant difference in the computed 13Cα chemical shifts, between basic and acidic groups, as a function of the degree of charge of the side chain; (ii) this difference is attributed to the distance between the ionizable groups and the 13Cα nucleus, which is shorter for the acidic Asp and Glu groups as compared with that for the basic Lys and Arg groups; and (iii) the use of neutral, rather than charged, basic and acidic groups is a better approximation of the observed 13Cα chemical shifts of a protein in solution. The second is how side-chain flexibility influences computed 13Cα chemical shifts in an additional set of ubiquitin conformations, in which the side chains are generated from an NMR-derived structure with the backbone conformation assumed to be fixed. The 13Cα chemical shift of a given amino acid residue in a protein is determined, mainly, by its own backbone and side-chain torsional angles, independent of the neighboring residues; the conformation of a given residue itself, however, depends on the environment of this residue and, hence, on the whole protein structure. As a consequence, this analysis reveals the role and impact of an accurate side-chain computation in the determination and refinement of protein conformation. The results of this analysis are: (i) a lower error between computed and observed 13Cα chemical shifts (by up to 3.7 ppm), was found for ~68% and ~63% of all ionizable residues and all non-Ala/Pro/Gly residues, respectively, in the additional set of conformations, compared with results for the model from which the set was derived; and (ii) all the additional conformations exhibit a lower root-mean-square-deviation (1.97 ppm ≤ rmsd ≤ 2.13 ppm), between computed and observed 13Cα chemical shifts, than the rmsd (2.32 ppm) computed for the starting conformation from which this additional set was derived. As a validation test, an analysis of the additional set of ubiquitin conformations, comparing computed and observed values of both 13Cα chemical shifts and χ1 torsional angles (given by the vicinal coupling constants, 3JN–Cγ and 3JC′–Cγ, is discussed. PMID:17975838

Innovative architectures for dense multi-microprocessor computers

NASA Technical Reports Server (NTRS)

Larson, Robert E.

1989-01-01

The purpose is to summarize a Phase 1 SBIR project performed for the NASA/Langley Computational Structural Mechanics Group. The project was performed from February to August 1987. The main objectives of the project were to: (1) expand upon previous research into the application of chordal ring architectures to the general problem of designing multi-microcomputer architectures, (2) attempt to identify a family of chordal rings such that each chordal ring can be simply expanded to produce the next member of the family, (3) perform a preliminary, high-level design of an expandable multi-microprocessor computer based upon chordal rings, (4) analyze the potential use of chordal ring based multi-microprocessors for sparse matrix problems and other applications arising in computational structural mechanics.

Hodge Numbers from Picard-Fuchs Equations

NASA Astrophysics Data System (ADS)

Doran, Charles F.; Harder, Andrew; Thompson, Alan

2017-06-01

Given a variation of Hodge structure over P^1 with Hodge numbers (1,1,\\dots,1), we show how to compute the degrees of the Deligne extension of its Hodge bundles, following Eskin-Kontsevich-Möller-Zorich, by using the local exponents of the corresponding Picard-Fuchs equation. This allows us to compute the Hodge numbers of Zucker's Hodge structure on the corresponding parabolic cohomology groups. We also apply this to families of elliptic curves, K3 surfaces and Calabi-Yau threefolds.

A computer-aided design system geared toward conceptual design in a research environment. [for hypersonic vehicles

NASA Technical Reports Server (NTRS)

STACK S. H.

1981-01-01

A computer-aided design system has recently been developed specifically for the small research group environment. The system is implemented on a Prime 400 minicomputer linked with a CDC 6600 computer. The goal was to assign the minicomputer specific tasks, such as data input and graphics, thereby reserving the large mainframe computer for time-consuming analysis codes. The basic structure of the design system consists of GEMPAK, a computer code that generates detailed configuration geometry from a minimum of input; interface programs that reformat GEMPAK geometry for input to the analysis codes; and utility programs that simplify computer access and data interpretation. The working system has had a large positive impact on the quantity and quality of research performed by the originating group. This paper describes the system, the major factors that contributed to its particular form, and presents examples of its application.

Invariance of an Extended Technology Acceptance Model Across Gender and Age Group

ERIC Educational Resources Information Center

Ahmad, Tunku Badariah Tunku; Madarsha, Kamal Basha; Zainuddin, Ahmad Marzuki; Ismail, Nik Ahmad Hisham; Khairani, Ahmad Zamri; Nordin, Mohamad Sahari

2011-01-01

In this study, we examined the likelihood of a TAME (extended technology acceptance model), in which the interrelationships among computer self-efficacy, perceived usefulness, intention to use and self-reported use of computer-mediated technology were tested. In addition, the gender- and age-invariant of its causal structure were evaluated. The…

Female Students' Experiences of Computer Technology in Single- versus Mixed-Gender School Settings

ERIC Educational Resources Information Center

Burke, Lee-Ann; Murphy, Elizabeth

2006-01-01

This study explores how female students compare learning computer technology in a single- versus a mixed- gender school setting. Twelve females participated, all of whom were enrolled in a grade 12 course in Communications' Technology. Data collection included a questionnaire, a semi-structured interview and focus groups. Participants described…

Organizational Communication: Theoretical Implications of Communication Technology Applications.

ERIC Educational Resources Information Center

Danowski, James A.

Communication technology (CT), which involves the use of computers in private and group communication, has had a major impact on theory and research in organizational communication over the past 30 years. From the 1950s to the early 1970s, mainframe computers were seen as managerial tools in creating more centralized organizational structures.…

System, method and computer-readable medium for locating physical phenomena

DOEpatents

Weseman, Matthew T [Idaho Falls, ID; Rohrbaugh, David T [Idaho Falls, ID; Richardson, John G [Idaho Falls, ID

2008-02-26

A method, system and computer product for detecting the location of a deformation of a structure includes baselining a defined energy transmitting characteristic for each of the plurality of laterally adjacent conductors attached to the structure. Each of the plurality of conductors includes a plurality of segments coupled in series and having an associated unit value representative of the defined energy transmitting characteristic. The plurality of laterally adjacent conductors includes a plurality of identity groups with each identity group including at least one of the plurality of segments from each of the plurality of conductors. Each of the plurality of conductors are monitored for a difference in the defined energy transmitting characteristic when compared with a baseline energy transmitting characteristic for each of the plurality of conductors. When the difference exceeds a threshold value, a location of the deformation along the structure is calculated.

Synergies and Distinctions between Computational Disciplines in Biomedical Research: Perspective from the Clinical and Translational Science Award Programs

PubMed Central

Bernstam, Elmer V.; Hersh, William R.; Johnson, Stephen B.; Chute, Christopher G.; Nguyen, Hien; Sim, Ida; Nahm, Meredith; Weiner, Mark; Miller, Perry; DiLaura, Robert P.; Overcash, Marc; Lehmann, Harold P.; Eichmann, David; Athey, Brian D.; Scheuermann, Richard H.; Anderson, Nick; Starren, Justin B.; Harris, Paul A.; Smith, Jack W.; Barbour, Ed; Silverstein, Jonathan C.; Krusch, David A.; Nagarajan, Rakesh; Becich, Michael J.

2010-01-01

Clinical and translational research increasingly requires computation. Projects may involve multiple computationally-oriented groups including information technology (IT) professionals, computer scientists and biomedical informaticians. However, many biomedical researchers are not aware of the distinctions among these complementary groups, leading to confusion, delays and sub-optimal results. Although written from the perspective of clinical and translational science award (CTSA) programs within academic medical centers, the paper addresses issues that extend beyond clinical and translational research. The authors describe the complementary but distinct roles of operational IT, research IT, computer science and biomedical informatics using a clinical data warehouse as a running example. In general, IT professionals focus on technology. The authors distinguish between two types of IT groups within academic medical centers: central or administrative IT (supporting the administrative computing needs of large organizations) and research IT (supporting the computing needs of researchers). Computer scientists focus on general issues of computation such as designing faster computers or more efficient algorithms, rather than specific applications. In contrast, informaticians are concerned with data, information and knowledge. Biomedical informaticians draw on a variety of tools, including but not limited to computers, to solve information problems in health care and biomedicine. The paper concludes with recommendations regarding administrative structures that can help to maximize the benefit of computation to biomedical research within academic health centers. PMID:19550198

Comparison of computer-assisted instruction (CAI) versus traditional textbook methods for training in abdominal examination (Japanese experience).

PubMed

Qayumi, A K; Kurihara, Y; Imai, M; Pachev, G; Seo, H; Hoshino, Y; Cheifetz, R; Matsuura, K; Momoi, M; Saleem, M; Lara-Guerra, H; Miki, Y; Kariya, Y

2004-10-01

This study aimed to compare the effects of computer-assisted, text-based and computer-and-text learning conditions on the performances of 3 groups of medical students in the pre-clinical years of their programme, taking into account their academic achievement to date. A fourth group of students served as a control (no-study) group. Participants were recruited from the pre-clinical years of the training programmes in 2 medical schools in Japan, Jichi Medical School near Tokyo and Kochi Medical School near Osaka. Participants were randomly assigned to 4 learning conditions and tested before and after the study on their knowledge of and skill in performing an abdominal examination, in a multiple-choice test and an objective structured clinical examination (OSCE), respectively. Information about performance in the programme was collected from school records and students were classified as average, good or excellent. Student and faculty evaluations of their experience in the study were explored by means of a short evaluation survey. Compared to the control group, all 3 study groups exhibited significant gains in performance on knowledge and performance measures. For the knowledge measure, the gains of the computer-assisted and computer-assisted plus text-based learning groups were significantly greater than the gains of the text-based learning group. The performances of the 3 groups did not differ on the OSCE measure. Analyses of gains by performance level revealed that high achieving students' learning was independent of study method. Lower achieving students performed better after using computer-based learning methods. The results suggest that computer-assisted learning methods will be of greater help to students who do not find the traditional methods effective. Explorations of the factors behind this are a matter for future research.

Establishing a group of endpoints in a parallel computer

DOEpatents

Archer, Charles J.; Blocksome, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanhong

2016-02-02

A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

Generalized zeta function representation of groups and 2-dimensional topological Yang-Mills theory: The example of GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q})

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

Roche, Ph., E-mail: philippe.roche@univ-montp2.fr

We recall the relation between zeta function representation of groups and two-dimensional topological Yang-Mills theory through Mednikh formula. We prove various generalisations of Mednikh formulas and define generalization of zeta function representations of groups. We compute some of these functions in the case of the finite group GL(2, #Mathematical Double-Struck Capital F#{sub q}) and PGL(2, #Mathematical Double-Struck Capital F#{sub q}). We recall the table characters of these groups for any q, compute the Frobenius-Schur indicator of their irreducible representations, and give the explicit structure of their fusion rings.

Discovering Network Structure Beyond Communities

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2011-11-01

To understand the formation, evolution, and function of complex systems, it is crucial to understand the internal organization of their interaction networks. Partly due to the impossibility of visualizing large complex networks, resolving network structure remains a challenging problem. Here we overcome this difficulty by combining the visual pattern recognition ability of humans with the high processing speed of computers to develop an exploratory method for discovering groups of nodes characterized by common network properties, including but not limited to communities of densely connected nodes. Without any prior information about the nature of the groups, the method simultaneously identifies the number of groups, the group assignment, and the properties that define these groups. The results of applying our method to real networks suggest the possibility that most group structures lurk undiscovered in the fast-growing inventory of social, biological, and technological networks of scientific interest.

Divide and conquer approach to quantum Hamiltonian simulation

NASA Astrophysics Data System (ADS)

Hadfield, Stuart; Papageorgiou, Anargyros

2018-04-01

We show a divide and conquer approach for simulating quantum mechanical systems on quantum computers. We can obtain fast simulation algorithms using Hamiltonian structure. Considering a sum of Hamiltonians we split them into groups, simulate each group separately, and combine the partial results. Simulation is customized to take advantage of the properties of each group, and hence yield refined bounds to the overall simulation cost. We illustrate our results using the electronic structure problem of quantum chemistry, where we obtain significantly improved cost estimates under very mild assumptions.

Knowledge-based computational intelligence development for predicting protein secondary structures from sequences.

PubMed

Shen, Hong-Bin; Yi, Dong-Liang; Yao, Li-Xiu; Yang, Jie; Chou, Kuo-Chen

2008-10-01

In the postgenomic age, with the avalanche of protein sequences generated and relatively slow progress in determining their structures by experiments, it is important to develop automated methods to predict the structure of a protein from its sequence. The membrane proteins are a special group in the protein family that accounts for approximately 30% of all proteins; however, solved membrane protein structures only represent less than 1% of known protein structures to date. Although a great success has been achieved for developing computational intelligence techniques to predict secondary structures in both globular and membrane proteins, there is still much challenging work in this regard. In this review article, we firstly summarize the recent progress of automation methodology development in predicting protein secondary structures, especially in membrane proteins; we will then give some future directions in this research field.

Health workers’ knowledge of and attitudes towards computer applications in rural African health facilities

PubMed Central

Sukums, Felix; Mensah, Nathan; Mpembeni, Rose; Kaltschmidt, Jens; Haefeli, Walter E.; Blank, Antje

2014-01-01

Background The QUALMAT (Quality of Maternal and Prenatal Care: Bridging the Know-do Gap) project has introduced an electronic clinical decision support system (CDSS) for pre-natal and maternal care services in rural primary health facilities in Burkina Faso, Ghana, and Tanzania. Objective To report an assessment of health providers’ computer knowledge, experience, and attitudes prior to the implementation of the QUALMAT electronic CDSS. Design A cross-sectional study was conducted with providers in 24 QUALMAT project sites. Information was collected using structured questionnaires. Chi-squared tests and one-way ANOVA describe the association between computer knowledge, attitudes, and other factors. Semi-structured interviews and focus groups were conducted to gain further insights. Results A total of 108 providers responded, 63% were from Tanzania and 37% from Ghana. The mean age was 37.6 years, and 79% were female. Only 40% had ever used computers, and 29% had prior computer training. About 80% were computer illiterate or beginners. Educational level, age, and years of work experience were significantly associated with computer knowledge (p<0.01). Most (95.3%) had positive attitudes towards computers – average score (±SD) of 37.2 (±4.9). Females had significantly lower scores than males. Interviews and group discussions showed that although most were lacking computer knowledge and experience, they were optimistic about overcoming challenges associated with the introduction of computers in their workplace. Conclusions Given the low levels of computer knowledge among rural health workers in Africa, it is important to provide adequate training and support to ensure the successful uptake of electronic CDSSs in these settings. The positive attitudes to computers found in this study underscore that also rural care providers are ready to use such technology. PMID:25361721

Health workers' knowledge of and attitudes towards computer applications in rural African health facilities.

PubMed

Sukums, Felix; Mensah, Nathan; Mpembeni, Rose; Kaltschmidt, Jens; Haefeli, Walter E; Blank, Antje

2014-01-01

The QUALMAT (Quality of Maternal and Prenatal Care: Bridging the Know-do Gap) project has introduced an electronic clinical decision support system (CDSS) for pre-natal and maternal care services in rural primary health facilities in Burkina Faso, Ghana, and Tanzania. To report an assessment of health providers' computer knowledge, experience, and attitudes prior to the implementation of the QUALMAT electronic CDSS. A cross-sectional study was conducted with providers in 24 QUALMAT project sites. Information was collected using structured questionnaires. Chi-squared tests and one-way ANOVA describe the association between computer knowledge, attitudes, and other factors. Semi-structured interviews and focus groups were conducted to gain further insights. A total of 108 providers responded, 63% were from Tanzania and 37% from Ghana. The mean age was 37.6 years, and 79% were female. Only 40% had ever used computers, and 29% had prior computer training. About 80% were computer illiterate or beginners. Educational level, age, and years of work experience were significantly associated with computer knowledge (p<0.01). Most (95.3%) had positive attitudes towards computers - average score (±SD) of 37.2 (±4.9). Females had significantly lower scores than males. Interviews and group discussions showed that although most were lacking computer knowledge and experience, they were optimistic about overcoming challenges associated with the introduction of computers in their workplace. Given the low levels of computer knowledge among rural health workers in Africa, it is important to provide adequate training and support to ensure the successful uptake of electronic CDSSs in these settings. The positive attitudes to computers found in this study underscore that also rural care providers are ready to use such technology.

A Novel Computer-Based Set-Up to Study Movement Coordination in Human Ensembles

PubMed Central

Alderisio, Francesco; Lombardi, Maria; Fiore, Gianfranco; di Bernardo, Mario

2017-01-01

Existing experimental works on movement coordination in human ensembles mostly investigate situations where each subject is connected to all the others through direct visual and auditory coupling, so that unavoidable social interaction affects their coordination level. Here, we present a novel computer-based set-up to study movement coordination in human groups so as to minimize the influence of social interaction among participants and implement different visual pairings between them. In so doing, players can only take into consideration the motion of a designated subset of the others. This allows the evaluation of the exclusive effects on coordination of the structure of interconnections among the players in the group and their own dynamics. In addition, our set-up enables the deployment of virtual computer players to investigate dyadic interaction between a human and a virtual agent, as well as group synchronization in mixed teams of human and virtual agents. We show how this novel set-up can be employed to study coordination both in dyads and in groups over different structures of interconnections, in the presence as well as in the absence of virtual agents acting as followers or leaders. Finally, in order to illustrate the capabilities of the architecture, we describe some preliminary results. The platform is available to any researcher who wishes to unfold the mechanisms underlying group synchronization in human ensembles and shed light on its socio-psychological aspects. PMID:28649217

The effects of computer simulation versus hands-on dissection and the placement of computer simulation within the learning cycle on student achievement and attitude

NASA Astrophysics Data System (ADS)

Hopkins, Kathryn Susan

The value of dissection as an instructional strategy has been debated, but not evidenced in research literature. The purpose of this study was to examine the efficacy of using computer simulated frog dissection as a substitute for traditional hands-on frog dissection and to examine the possible enhancement of achievement by combining the two strategies in a specific sequence. In this study, 134 biology students at two Central Texas schools were divided into the five following treatment groups: computer simulation of frog dissection, computer simulation before dissection, traditional hands-on frog dissection, dissection before computer simulation, and textual worksheet materials. The effects on achievement were evaluated by labeling 10 structures on three diagrams, identifying 11 pinned structures on a prosected frog, and answering 9 multiple-choice questions over the dissection process. Attitude was evaluated using a thirty item survey with a five-point Likert scale. The quasi-experimental design was pretest/post-test/post-test nonequivalent group for both control and experimental groups, a 2 x 2 x 5 completely randomized factorial design (gender, school, five treatments). The pretest/post-test design was incorporated to control for prior knowledge using analysis of covariance. The dissection only group evidenced a significantly higher performance than all other treatments except dissection-then-computer on the post-test segment requiring students to label pinned anatomical parts on a prosected frog. Interactions between treatment and school in addition to interaction between treatment and gender were found to be significant. The diagram and attitude post-tests evidenced no significant difference. Results on the nine multiple-choice questions about dissection procedures indicated a significant difference between schools. The interaction between treatment and school was also found to be significant. On a delayed post-test, a significant difference in gender was found on the diagram labeling segment of the post-test. Males were reported to have the higher score. Since existing research conflicts with this study's results, additional research using authentic assessment is recommended. Instruction should be aligned with dissection content and process objectives for each treatment group, and the teacher variable should be controlled.

Novel functionalized pyridine-containing DTPA-like ligand. Synthesis, computational studies and characterization of the corresponding Gd(III) complex.

PubMed

Artali, Roberto; Botta, Mauro; Cavallotti, Camilla; Giovenzana, Giovanni B; Palmisano, Giovanni; Sisti, Massimo

2007-08-07

A novel pyridine-containing DTPA-like ligand, carrying additional hydroxymethyl groups on the pyridine side-arms, was synthesized in 5 steps. The corresponding Gd(III) complex, potentially useful as an MRI contrast agent, was prepared and characterized in detail by relaxometric methods and its structure modeled by computational methods.

The Effect on Retention of Computer Assisted Instruction in Science Education

ERIC Educational Resources Information Center

Kara, Izzet

2008-01-01

The aim of this research is to determine the retention effect of Computer Assisted Instruction (CAI) on students' academic achievement for teaching the Physics topics. The research includes the Force and Pressure units of 7th grade Science Lesson. In this research, 132 students were structured as both control and experiment groups. Traditional…

High Performance Descriptive Semantic Analysis of Semantic Graph Databases

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

Joslyn, Cliff A.; Adolf, Robert D.; al-Saffar, Sinan

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to understand their inherent semantic structure, whether codified in explicit ontologies or not. Our group is researching novel methods for what we call descriptive semantic analysis of RDF triplestores, to serve purposes of analysis, interpretation, visualization, and optimization. But data size and computational complexity makes it increasingly necessary to bring high performance computational resources to bear on this task. Our research group built a novel high performance hybrid system comprisingmore » computational capability for semantic graph database processing utilizing the large multi-threaded architecture of the Cray XMT platform, conventional servers, and large data stores. In this paper we describe that architecture and our methods, and present the results of our analyses of basic properties, connected components, namespace interaction, and typed paths such for the Billion Triple Challenge 2010 dataset.« less

An integral-factorized implementation of the driven similarity renormalization group second-order multireference perturbation theory

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

Hannon, Kevin P.; Li, Chenyang; Evangelista, Francesco A., E-mail: francesco.evangelista@emory.edu

2016-05-28

We report an efficient implementation of a second-order multireference perturbation theory based on the driven similarity renormalization group (DSRG-MRPT2) [C. Li and F. A. Evangelista, J. Chem. Theory Comput. 11, 2097 (2015)]. Our implementation employs factorized two-electron integrals to avoid storage of large four-index intermediates. It also exploits the block structure of the reference density matrices to reduce the computational cost to that of second-order Møller–Plesset perturbation theory. Our new DSRG-MRPT2 implementation is benchmarked on ten naphthyne isomers using basis sets up to quintuple-ζ quality. We find that the singlet-triplet splittings (Δ{sub ST}) of the naphthyne isomers strongly depend onmore » the equilibrium structures. For a consistent set of geometries, the Δ{sub ST} values predicted by the DSRG-MRPT2 are in good agreements with those computed by the reduced multireference coupled cluster theory with singles, doubles, and perturbative triples.« less

Prediction of brain-computer interface aptitude from individual brain structure.

PubMed

Halder, S; Varkuti, B; Bogdan, M; Kübler, A; Rosenstiel, W; Sitaram, R; Birbaumer, N

2013-01-01

Brain-computer interface (BCI) provide a non-muscular communication channel for patients with impairments of the motor system. A significant number of BCI users is unable to obtain voluntary control of a BCI-system in proper time. This makes methods that can be used to determine the aptitude of a user necessary. We hypothesized that integrity and connectivity of involved white matter connections may serve as a predictor of individual BCI-performance. Therefore, we analyzed structural data from anatomical scans and DTI of motor imagery BCI-users differentiated into high and low BCI-aptitude groups based on their overall performance. Using a machine learning classification method we identified discriminating structural brain trait features and correlated the best features with a continuous measure of individual BCI-performance. Prediction of the aptitude group of each participant was possible with near perfect accuracy (one error). Tissue volumetric analysis yielded only poor classification results. In contrast, the structural integrity and myelination quality of deep white matter structures such as the Corpus Callosum, Cingulum, and Superior Fronto-Occipital Fascicle were positively correlated with individual BCI-performance. This confirms that structural brain traits contribute to individual performance in BCI use.

Prediction of brain-computer interface aptitude from individual brain structure

PubMed Central

Halder, S.; Varkuti, B.; Bogdan, M.; Kübler, A.; Rosenstiel, W.; Sitaram, R.; Birbaumer, N.

2013-01-01

Objective: Brain-computer interface (BCI) provide a non-muscular communication channel for patients with impairments of the motor system. A significant number of BCI users is unable to obtain voluntary control of a BCI-system in proper time. This makes methods that can be used to determine the aptitude of a user necessary. Methods: We hypothesized that integrity and connectivity of involved white matter connections may serve as a predictor of individual BCI-performance. Therefore, we analyzed structural data from anatomical scans and DTI of motor imagery BCI-users differentiated into high and low BCI-aptitude groups based on their overall performance. Results: Using a machine learning classification method we identified discriminating structural brain trait features and correlated the best features with a continuous measure of individual BCI-performance. Prediction of the aptitude group of each participant was possible with near perfect accuracy (one error). Conclusions: Tissue volumetric analysis yielded only poor classification results. In contrast, the structural integrity and myelination quality of deep white matter structures such as the Corpus Callosum, Cingulum, and Superior Fronto-Occipital Fascicle were positively correlated with individual BCI-performance. Significance: This confirms that structural brain traits contribute to individual performance in BCI use. PMID:23565083

Nitroxoline Molecule: Planar or Not? A Story of Battle between π-π Conjugation and Interatomic Repulsion.

PubMed

Tikhonov, Denis S; Sharapa, Dmitry I; Otlyotov, Arseniy A; Solyankin, Peter M; Rykov, Anatolii N; Shkurinov, Alexander P; Grikina, Olga E; Khaikin, Leonid S

2018-02-15

The conformational properties of the nitro group in nitroxoline (8-hydroxy-5-nitroquinoline, NXN) were investigated in the gas phase by means of gas electron diffraction (GED) and quantum chemical calculations, and also with solid-state analysis performed using terahertz time-domain spectroscopy (THz-TDS). The results of the GED refinement show that in the equilibrium structure the NO 2 group is twisted by angle ϕ = 8 ± 3° with respect to the 8-hydroxyoquinoline plane. This is the result of interatomic repulsion of oxygen in the NO 2 group from the closest hydrogen, which overcomes the energy gain from the π-π conjugation of the nitro group and aromatic system of 8-hydroxyoquinoline. The computation of equilibrium geometry using MP2/cc-pVXZ (X = T, Q) shows a large overestimation of the ϕ value, while DFT with the cc-pVTZ basis set performs reasonably well. On the other hand, DFT computations with double-ζ basis sets yield a planar structure of NXN. The refined potential energy surface of the torsion vibration the of nitro group in the condensed phase derived from the THz-TDS data indicates the NXN molecule to be planar. This result stays in good agreement with the previous X-ray structure determination. The strength of the π-system conjugation for the NO 2 group and 8-hydroxyoquinoline is discussed using NBO analysis, being further supported by comparison of the refined semiexperimental gas-phase structure of NXN from GED with other nitrocompounds.

Non-polynomial closed string field theory: loops and conformal maps

NASA Astrophysics Data System (ADS)

Hua, Long; Kaku, Michio

1990-11-01

Recently, we proposed the complete classical action for the non-polynomial closed string field theory, which succesfully reproduced all closed string tree amplitudes. (The action was simultaneously proposed by the Kyoto group). In this paper, we analyze the structure of the theory. We (a) compute the explicit conformal map for all g-loop, p-puncture diagrams, (b) compute all one-loop, two-puncture maps in terms of hyper-elliptic functions, and (c) analyze their modular structure. We analyze, but do not resolve, the question of modular invariance.

Computer based interpretation of infrared spectra-structure of the knowledge-base, automatic rule generation and interpretation

NASA Astrophysics Data System (ADS)

Ehrentreich, F.; Dietze, U.; Meyer, U.; Abbas, S.; Schulz, H.

1995-04-01

It is a main task within the SpecInfo-Project to develop interpretation tools that can handle a great deal more of the complicated, more specific spectrum-structure-correlations. In the first step the empirical knowledge about the assignment of structural groups and their characteristic IR-bands has been collected from literature and represented in a computer readable well-structured form. Vague, verbal rules are managed by introduction of linguistic variables. The next step was the development of automatic rule generating procedures. We had combined and enlarged the IDIOTS algorithm with the algorithm by Blaffert relying on set theory. The procedures were successfully applied to the SpecInfo database. The realization of the preceding items is a prerequisite for the improvement of the computerized structure elucidation procedure.

Muscle tension line concept in nasolabial muscle complex--based on 3-dimensional reconstruction of nasolabial muscle fibers.

PubMed

Yin, Ningbei; Wu, Jiajun; Chen, Bo; Song, Tao; Ma, Hengyuan; Zhao, Zhenmin; Wang, Yongqian; Li, Haidong; Wu, Di

2015-03-01

Plastic surgeons have attempted various ways to rebuild the aesthetic subunits of the upper lip in patients with cleft lip with less than perfect results in most cases. We propose that repairing the 3 muscle tension line groups in the nasolabial complex will have improved aesthetic results. Micro-computed tomographic scans were performed on the nasolabial tissues of 5 normal aborted fetuses and used to construct a 3-dimensional model to study the nasolabial muscle complex structure. The micro-computed tomographic (CT) scans showed the close relationship and interaction between the muscle fibers of nasalis, pars peripheralis, levator labii superioris, and pars marginalis. Based on the 2-dimensional images obtained from the micro-computed tomographic scans, we suggest the concept of nasolabial muscle complex and muscle tension line group theory: there is a close relationship among the alar part of the nasalis, depressor septi muscle, orbicularis oris muscle, and levator labii superioris alaeque nasi. The tension line groups are 3 tension line structures in the nasolabial muscle complex that interlock with each other at the intersections and maintain the specific shape and aesthetics of the lip and nose.

The process group approach to reliable distributed computing

NASA Technical Reports Server (NTRS)

Birman, Kenneth P.

1991-01-01

The difficulty of developing reliable distributed software is an impediment to applying distributed computing technology in many settings. Experience with the ISIS system suggests that a structured approach based on virtually synchronous process groups yields systems which are substantially easier to develop, fault-tolerance, and self-managing. Six years of research on ISIS are reviewed, describing the model, the types of applications to which ISIS was applied, and some of the reasoning that underlies a recent effort to redesign and reimplement ISIS as a much smaller, lightweight system.

"MONSTROUS MOONSHINE" and Physics

NASA Astrophysics Data System (ADS)

Pushkin, A. V.

The report presents some results obtained by the author on the quantum gravitation theory. Algebraic structure of this theory proves to be related to the commutative nonassociative Griess algebra. The theory symmetry is the automorphism group of Griess algebra: "Monster" simple group. Knowledge of the theory symmetry allows to compute observed physical values in the `zero' approximation. The report presents such computed results for values {m_{p}}/{m_{c}} and α, for the latter the `zero' approximation accuracy, controlled by the theory, being one order of magnitude higher than the accuracy of modern measurements.

Focus on Methodology: Beyond paper and pencil: Conducting computer-assisted data collection with adolescents in group settings.

PubMed

Raffaelli, Marcela; Armstrong, Jessica; Tran, Steve P; Griffith, Aisha N; Walker, Kathrin; Gutierrez, Vanessa

2016-06-01

Computer-assisted data collection offers advantages over traditional paper and pencil measures; however, little guidance is available regarding the logistics of conducting computer-assisted data collection with adolescents in group settings. To address this gap, we draw on our experiences conducting a multi-site longitudinal study of adolescent development. Structured questionnaires programmed on laptop computers using Audio Computer Assisted Self-Interviewing (ACASI) were administered to groups of adolescents in community-based and afterschool programs. Although implementing ACASI required additional work before entering the field, we benefited from reduced data processing time, high data quality, and high levels of youth motivation. Preliminary findings from an ethnically diverse sample of 265 youth indicate favorable perceptions of using ACASI. Using our experiences as a case study, we provide recommendations on selecting an appropriate data collection device (including hardware and software), preparing and testing the ACASI, conducting data collection in the field, and managing data. Copyright © 2016 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

Reassessment of the Unique Mode of Binding between Angiotensin II Type 1 Receptor and Their Blockers

PubMed Central

Matsuo, Yoshino; Saku, Keijiro; Karnik, Sadashiva S.

2013-01-01

While the molecular structures of angiotensin II (Ang II) type 1 (AT1) receptor blockers (ARBs) are very similar, they are also slightly different. Although each ARB has been shown to exhibit a unique mode of binding to AT1 receptor, different positions of the AT1 receptor have been analyzed and computational modeling has been performed using different crystal structures for the receptor as a template and different kinds of software. Therefore, we systematically analyzed the critical positions of the AT1 receptor, Tyr113, Tyr184, Lys199, His256 and Gln257 using a mutagenesis study, and subsequently performed computational modeling of the binding of ARBs to AT1 receptor using CXCR4 receptor as a new template and a single version of software. The interactions between Tyr113 in the AT1 receptor and the hydroxyl group of olmesartan, between Lys199 and carboxyl or tetrazole groups, and between His256 or Gln257 and the tetrazole group were studied. The common structure, a tetrazole group, of most ARBs similarly bind to Lys199, His256 and Gln257 of AT1 receptor. Lys199 in the AT1 receptor binds to the carboxyl group of EXP3174, candesartan and azilsartan, whereas oxygen in the amidecarbonyl group of valsartan may bind to Lys199. The benzimidazole portion of telmisartan may bind to a lipophilic pocket that includes Tyr113. On the other hand, the n-butyl group of irbesartan may bind to Tyr113. In conclusion, we confirmed that the slightly different structures of ARBs may be critical for binding to AT1 receptor and for the formation of unique modes of binding. PMID:24260317

Statistics, Computation, and Modeling in Cosmology

NASA Astrophysics Data System (ADS)

Jewell, Jeff; Guiness, Joe; SAMSI 2016 Working Group in Cosmology

2017-01-01

Current and future ground and space based missions are designed to not only detect, but map out with increasing precision, details of the universe in its infancy to the present-day. As a result we are faced with the challenge of analyzing and interpreting observations from a wide variety of instruments to form a coherent view of the universe. Finding solutions to a broad range of challenging inference problems in cosmology is one of the goals of the “Statistics, Computation, and Modeling in Cosmology” workings groups, formed as part of the year long program on ‘Statistical, Mathematical, and Computational Methods for Astronomy’, hosted by the Statistical and Applied Mathematical Sciences Institute (SAMSI), a National Science Foundation funded institute. Two application areas have emerged for focused development in the cosmology working group involving advanced algorithmic implementations of exact Bayesian inference for the Cosmic Microwave Background, and statistical modeling of galaxy formation. The former includes study and development of advanced Markov Chain Monte Carlo algorithms designed to confront challenging inference problems including inference for spatial Gaussian random fields in the presence of sources of galactic emission (an example of a source separation problem). Extending these methods to future redshift survey data probing the nonlinear regime of large scale structure formation is also included in the working group activities. In addition, the working group is also focused on the study of ‘Galacticus’, a galaxy formation model applied to dark matter-only cosmological N-body simulations operating on time-dependent halo merger trees. The working group is interested in calibrating the Galacticus model to match statistics of galaxy survey observations; specifically stellar mass functions, luminosity functions, and color-color diagrams. The group will use subsampling approaches and fractional factorial designs to statistically and computationally efficiently explore the Galacticus parameter space. The group will also use the Galacticus simulations to study the relationship between the topological and physical structure of the halo merger trees and the properties of the resulting galaxies.

Individual Functional ROI Optimization via Maximization of Group-wise Consistency of Structural and Functional Profiles

PubMed Central

Li, Kaiming; Guo, Lei; Zhu, Dajiang; Hu, Xintao; Han, Junwei; Liu, Tianming

2013-01-01

Studying connectivities among functional brain regions and the functional dynamics on brain networks has drawn increasing interest. A fundamental issue that affects functional connectivity and dynamics studies is how to determine the best possible functional brain regions or ROIs (regions of interest) for a group of individuals, since the connectivity measurements are heavily dependent on ROI locations. Essentially, identification of accurate, reliable and consistent corresponding ROIs is challenging due to the unclear boundaries between brain regions, variability across individuals, and nonlinearity of the ROIs. In response to these challenges, this paper presents a novel methodology to computationally optimize ROIs locations derived from task-based fMRI data for individuals so that the optimized ROIs are more consistent, reproducible and predictable across brains. Our computational strategy is to formulate the individual ROI location optimization as a group variance minimization problem, in which group-wise consistencies in functional/structural connectivity patterns and anatomic profiles are defined as optimization constraints. Our experimental results from multimodal fMRI and DTI data show that the optimized ROIs have significantly improved consistency in structural and functional profiles across individuals. These improved functional ROIs with better consistency could contribute to further study of functional interaction and dynamics in the human brain. PMID:22281931

Implant Supported Distal Extension over Denture Retained by Two Types of Attachments. A Comparative Radiographic Study by Cone Beam Computed Tomography

PubMed Central

Mahrous, Ahmed I; Aldawash, Hussien A; Soliman, Tarek A; Banasr, Fahad H; Abdelwahed, Ahmed

2015-01-01

Background: This study was conducted to compare and evaluate the effect of two different attachments (locator attachment and ball and socket [B&S] attachment) on implants and natural abutments supporting structures, in cases of limited inter-arch spaces in mandibular Kennedy Class I implant supported removable partial over dentures by measuring the bone height changes through the cone beam radiographic technology. Materials and Methods: Two implants were positioned in the first or second molar area following the two-stage surgical protocol. Two equal groups were divided ten for each: Group I: Sides were the placed implants restored by the locator attachment. Group II: The other sides, implants were restored by B&S attachment. Evaluation of the implants and main abutments supporting structures of each group was done at the time of removable partial over denture insertion, 6, 12 and 18 months by measuring the bone height changes using cone beam computed tomography. Results: Implants with locator attachment showed marginal bone height better effects on implants and main abutments supporting structures. Conclusion: Implants restored by locator attachment shows better effects on bone of both main natural abutments and implant than those restored with ball and socket. PMID:26028894

Automatic identification of abstract online groups

DOEpatents

Engel, David W; Gregory, Michelle L; Bell, Eric B; Cowell, Andrew J; Piatt, Andrew W

2014-04-15

Online abstract groups, in which members aren't explicitly connected, can be automatically identified by computer-implemented methods. The methods involve harvesting records from social media and extracting content-based and structure-based features from each record. Each record includes a social-media posting and is associated with one or more entities. Each feature is stored on a data storage device and includes a computer-readable representation of an attribute of one or more records. The methods further involve grouping records into record groups according to the features of each record. Further still the methods involve calculating an n-dimensional surface representing each record group and defining an outlier as a record having feature-based distances measured from every n-dimensional surface that exceed a threshold value. Each of the n-dimensional surfaces is described by a footprint that characterizes the respective record group as an online abstract group.

Structural Biology of Tumor Necrosis Factor Demonstrated for Undergraduates Instruction by Computer Simulation

ERIC Educational Resources Information Center

Roy, Urmi

2016-01-01

This work presents a three-dimensional (3D) modeling exercise for undergraduate students in chemistry and health sciences disciplines, focusing on a protein-group linked to immune system regulation. Specifically, the exercise involves molecular modeling and structural analysis of tumor necrosis factor (TNF) proteins, both wild type and mutant. The…

Structures and transitions in tungsten grain boundaries

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

Frolov, T.; Zhu, Q.; Marian, J.

2017-02-07

The objective of this study is to develop a computational methodology to predict structure, energies of tungsten grain boundaries as a function of misorientation and inclination. The energies and the mobilities are the necessary input for thermomechanical model of recrystallization of tungsten for magnetic fusion applications being developed by the Marian Group at UCLA.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps

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

Chojnowski, Grzegorz, E-mail: gchojnowski@genesilico.pl; Waleń, Tomasz; University of Warsaw, Banacha 2, 02-097 Warsaw

2015-03-01

A computer program that builds crystal structure models of nucleic acid molecules is presented. Brickworx is a computer program that builds crystal structure models of nucleic acid molecules using recurrent motifs including double-stranded helices. In a first step, the program searches for electron-density peaks that may correspond to phosphate groups; it may also take into account phosphate-group positions provided by the user. Subsequently, comparing the three-dimensional patterns of the P atoms with a database of nucleic acid fragments, it finds the matching positions of the double-stranded helical motifs (A-RNA or B-DNA) in the unit cell. If the target structure ismore » RNA, the helical fragments are further extended with recurrent RNA motifs from a fragment library that contains single-stranded segments. Finally, the matched motifs are merged and refined in real space to find the most likely conformations, including a fit of the sequence to the electron-density map. The Brickworx program is available for download and as a web server at http://iimcb.genesilico.pl/brickworx.« less

76 FR 1442 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-10

... Group; Macromolecular Structure and Function D Study Section. Date: February 8-9, 2011. Time: 8 a.m. to...; Biomedical Computing and Health Informatics Study Section. Date: February 8, 2011. Time: 8 a.m. to 5 p.m... Skin Sciences Integrated Review Group; Skeletal Muscle and Exercise Physiology Study Section. Date...

The relative effectiveness of computer-based and traditional resources for education in anatomy.

PubMed

Khot, Zaid; Quinlan, Kaitlyn; Norman, Geoffrey R; Wainman, Bruce

2013-01-01

There is increasing use of computer-based resources to teach anatomy, although no study has compared computer-based learning to traditional. In this study, we examine the effectiveness of three formats of anatomy learning: (1) a virtual reality (VR) computer-based module, (2) a static computer-based module providing Key Views (KV), (3) a plastic model. We conducted a controlled trial in which 60 undergraduate students had ten minutes to study the names of 20 different pelvic structures. The outcome measure was a 25 item short answer test consisting of 15 nominal and 10 functional questions, based on a cadaveric pelvis. All subjects also took a brief mental rotations test (MRT) as a measure of spatial ability, used as a covariate in the analysis. Data were analyzed with repeated measures ANOVA. The group learning from the model performed significantly better than the other two groups on the nominal questions (Model 67%; KV 40%; VR 41%, Effect size 1.19 and 1.29, respectively). There was no difference between the KV and VR groups. There was no difference between the groups on the functional questions (Model 28%; KV, 23%, VR 25%). Computer-based learning resources appear to have significant disadvantages compared to traditional specimens in learning nominal anatomy. Consistent with previous research, virtual reality shows no advantage over static presentation of key views. © 2013 American Association of Anatomists.

CPU timing routines for a CONVEX C220 computer system

NASA Technical Reports Server (NTRS)

Bynum, Mary Ann

1989-01-01

The timing routines available on the CONVEX C220 computer system in the Structural Mechanics Division (SMD) at NASA Langley Research Center are examined. The function of the timing routines, the use of the timing routines in sequential, parallel, and vector code, and the interpretation of the results from the timing routines with respect to the CONVEX model of computing are described. The timing routines available on the SMD CONVEX fall into two groups. The first group includes standard timing routines generally available with UNIX 4.3 BSD operating systems, while the second group includes routines unique to the SMD CONVEX. The standard timing routines described in this report are /bin/csh time,/bin/time, etime, and ctime. The routines unique to the SMD CONVEX are getinfo, second, cputime, toc, and a parallel profiling package made up of palprof, palinit, and palsum.

Computer simulations in the high school: students' cognitive stages, science process skills and academic achievement in microbiology

NASA Astrophysics Data System (ADS)

Huppert, J.; Michal Lomask, S.; Lazarowitz, R.

2002-08-01

Computer-assisted learning, including simulated experiments, has great potential to address the problem solving process which is a complex activity. It requires a highly structured approach in order to understand the use of simulations as an instructional device. This study is based on a computer simulation program, 'The Growth Curve of Microorganisms', which required tenth grade biology students to use problem solving skills whilst simultaneously manipulating three independent variables in one simulated experiment. The aims were to investigate the computer simulation's impact on students' academic achievement and on their mastery of science process skills in relation to their cognitive stages. The results indicate that the concrete and transition operational students in the experimental group achieved significantly higher academic achievement than their counterparts in the control group. The higher the cognitive operational stage, the higher students' achievement was, except in the control group where students in the concrete and transition operational stages did not differ. Girls achieved equally with the boys in the experimental group. Students' academic achievement may indicate the potential impact a computer simulation program can have, enabling students with low reasoning abilities to cope successfully with learning concepts and principles in science which require high cognitive skills.

Does exposure to computers affect the routine parameters of semen quality?

PubMed

Sun, Yue-Lian; Zhou, Wei-Jin; Wu, Jun-Qing; Gao, Er-Sheng

2005-09-01

To assess whether exposure to computers harms the semen quality of healthy young men. A total of 178 subjects were recruited from two maternity and children healthcare centers in Shanghai, 91 with a history of exposure to computers (i.e., exposure for 20 h or more per week in the last 2 years) and 87 persons to act as control (no or little exposure to computers). Data on the history of exposure to computers and other characteristics were obtained by means of a structured questionnaire interview. Semen samples were collected by masturbation in the place where the semen samples were analyzed. No differences in the distribution of the semen parameters (semen volume, sperm density, percentage of progressive sperm, sperm viability and percentage of normal form sperm) were found between the exposed group and the control group. Exposure to computers was not found to be a risk factor for inferior semen quality after adjusting for potential confounders, including abstinence days, testicle size, occupation, history of exposure to toxic substances. The present study did not find that healthy men exposed to computers had inferior semen quality.

A randomized, controlled, single-blind trial of teaching provided by a computer-based multimedia package versus lecture.

PubMed

Williams, C; Aubin, S; Harkin, P; Cottrell, D

2001-09-01

Computer-based teaching may allow effective teaching of important psychiatric knowledge and skills. To investigate the effectiveness and acceptability of computer-based teaching. A single-blind, randomized, controlled study of 166 undergraduate medical students at the University of Leeds, involving an educational intervention of either a structured lecture or a computer-based teaching package (both of equal duration). There was no difference in knowledge between the groups at baseline or immediately after teaching. Both groups made significant gains in knowledge after teaching. Students who attended the lecture rated their subjective knowledge and skills at a statistically significantly higher level than students who had used the computers. Students who had used the computer package scored higher on an objective measure of assessment skills. Students did not perceive the computer package to be as useful as the traditional lecture format, despite finding it easy to use and recommending its use to other students. Medical students rate themselves subjectively as learning less from computer-based as compared with lecture-based teaching. Objective measures suggest equivalence in knowledge acquisition and significantly greater skills acquisition for computer-based teaching.

On the representation matrices of the spin permutation group. [for atomic and molecular electronic structures

NASA Technical Reports Server (NTRS)

Wilson, S.

1977-01-01

A method is presented for the determination of the representation matrices of the spin permutation group (symmetric group), a detailed knowledge of these matrices being required in the study of the electronic structure of atoms and molecules. The method is characterized by the use of two different coupling schemes. Unlike the Yamanouchi spin algebraic scheme, the method is not recursive. The matrices for the fundamental transpositions can be written down directly in one of the two bases. The method results in a computationally significant reduction in the number of matrix elements that have to be stored when compared with, say, the standard Young tableaux group theoretical approach.

Parallel Structures of Computer-Assisted Signature Pedagogy: The Case of Integrated Spreadsheets

ERIC Educational Resources Information Center

Abramovich, Sergei; Easton, Jonathan; Hayes, Victoria O.

2012-01-01

This article was motivated by the authors' work on a project with a group of 2nd-grade students in a computer lab of a rural school in upstate New York. From this project, one goal of which was to provide a capstone experience for a teacher candidate in teaching application-oriented mathematics with technology, the ideas about parallel structures…

Optimal design of structures with multiple design variables per group and multiple loading conditions on the personal computer

NASA Technical Reports Server (NTRS)

Nguyen, D. T.; Rogers, J. L., Jr.

1986-01-01

A finite element based programming system for minimum weight design of a truss-type structure subjected to displacement, stress, and lower and upper bounds on design variables is presented. The programming system consists of a number of independent processors, each performing a specific task. These processors, however, are interfaced through a well-organized data base, thus making the tasks of modifying, updating, or expanding the programming system much easier in a friendly environment provided by many inexpensive personal computers. The proposed software can be viewed as an important step in achieving a 'dummy' finite element for optimization. The programming system has been implemented on both large and small computers (such as VAX, CYBER, IBM-PC, and APPLE) although the focus is on the latter. Examples are presented to demonstrate the capabilities of the code. The present programming system can be used stand-alone or as part of the multilevel decomposition procedure to obtain optimum design for very large scale structural systems. Furthermore, other related research areas such as developing optimization algorithms (or in the larger level: a structural synthesis program) for future trends in using parallel computers may also benefit from this study.

To bend or not to bend: experimental and computational studies of structural preference in Ln(Tp(iPr)2)2 (Ln = Sm, Tm).

PubMed

Momin, Aurélien; Carter, Lee; Yang, Yi; McDonald, Robert; Essafi Labouille, Stéphanie; Nief, François; Del Rosal, Iker; Sella, Andrea; Maron, Laurent; Takats, Josef

2014-11-17

The synthesis and characterization of Ln(Tp(iPr2))2 (Ln = Sm, 3Sm; Tm, 3Tm) are reported. While the simple (1)H NMR spectra of the compounds indicate a symmetrical solution structure, with equivalent pyrazolyl groups, the solid-state structure revealed an unexpected, "bent sandwich-like" geometry. By contrast, the structure of the less sterically congested Tm(Tp(Me2,4Et))2 (4) adopts the expected symmetrical structure with a linear B-Tm-B arrangement. Computational studies to investigate the origin of the unexpected bent structure of the former compounds indicate that steric repulsion between the isopropyl groups forces the Tp ligands apart and permits the development of unusual interligand C-H···N hydrogen-bonding interactions that help stabilize the structure. These results find support in the similar geometry of the Tm(III) analogue [Tm(Tp(iPr2))2]I, 3Tm(+), and confirm that the low symmetry is not the result of a metal-ligand interaction. The relevance of these results to the general question of the coordination geometry of MX2 and M(C5R5)2 (M = heavy alkaline earth and Ln(II), X = halide, and C5R5 = bulky persubstituted cyclopentadienyl) complexes and the importance of secondary H-bonding and nonbonding interactions on the structure are highlighted.

Process for predicting structural performance of mechanical systems

DOEpatents

Gardner, David R.; Hendrickson, Bruce A.; Plimpton, Steven J.; Attaway, Stephen W.; Heinstein, Martin W.; Vaughan, Courtenay T.

1998-01-01

A process for predicting the structural performance of a mechanical system represents the mechanical system by a plurality of surface elements. The surface elements are grouped according to their location in the volume occupied by the mechanical system so that contacts between surface elements can be efficiently located. The process is well suited for efficient practice on multiprocessor computers.

Multivariate statistics of the Jacobian matrices in tensor based morphometry and their application to HIV/AIDS.

PubMed

Lepore, Natasha; Brun, Caroline A; Chiang, Ming-Chang; Chou, Yi-Yu; Dutton, Rebecca A; Hayashi, Kiralee M; Lopez, Oscar L; Aizenstein, Howard J; Toga, Arthur W; Becker, James T; Thompson, Paul M

2006-01-01

Tensor-based morphometry (TBM) is widely used in computational anatomy as a means to understand shape variation between structural brain images. A 3D nonlinear registration technique is typically used to align all brain images to a common neuroanatomical template, and the deformation fields are analyzed statistically to identify group differences in anatomy. However, the differences are usually computed solely from the determinants of the Jacobian matrices that are associated with the deformation fields computed by the registration procedure. Thus, much of the information contained within those matrices gets thrown out in the process. Only the magnitude of the expansions or contractions is examined, while the anisotropy and directional components of the changes are ignored. Here we remedy this problem by computing multivariate shape change statistics using the strain matrices. As the latter do not form a vector space, means and covariances are computed on the manifold of positive-definite matrices to which they belong. We study the brain morphology of 26 HIV/AIDS patients and 14 matched healthy control subjects using our method. The images are registered using a high-dimensional 3D fluid registration algorithm, which optimizes the Jensen-Rényi divergence, an information-theoretic measure of image correspondence. The anisotropy of the deformation is then computed. We apply a manifold version of Hotelling's T2 test to the strain matrices. Our results complement those found from the determinants of the Jacobians alone and provide greater power in detecting group differences in brain structure.

Group implicit concurrent algorithms in nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Ortiz, M.; Sotelino, E. D.

1989-01-01

During the 70's and 80's, considerable effort was devoted to developing efficient and reliable time stepping procedures for transient structural analysis. Mathematically, the equations governing this type of problems are generally stiff, i.e., they exhibit a wide spectrum in the linear range. The algorithms best suited to this type of applications are those which accurately integrate the low frequency content of the response without necessitating the resolution of the high frequency modes. This means that the algorithms must be unconditionally stable, which in turn rules out explicit integration. The most exciting possibility in the algorithms development area in recent years has been the advent of parallel computers with multiprocessing capabilities. So, this work is mainly concerned with the development of parallel algorithms in the area of structural dynamics. A primary objective is to devise unconditionally stable and accurate time stepping procedures which lend themselves to an efficient implementation in concurrent machines. Some features of the new computer architecture are summarized. A brief survey of current efforts in the area is presented. A new class of concurrent procedures, or Group Implicit algorithms is introduced and analyzed. The numerical simulation shows that GI algorithms hold considerable promise for application in coarse grain as well as medium grain parallel computers.

The pKa Cooperative: A Collaborative Effort to Advance Structure-Based Calculations of pKa values and Electrostatic Effects in Proteins

PubMed Central

Nielsen, Jens E.; Gunner, M. R.; Bertrand García-Moreno, E.

2012-01-01

The pKa Cooperative http://www.pkacoop.org was organized to advance development of accurate and useful computational methods for structure-based calculation of pKa values and electrostatic energy in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational and experimental studies of protein electrostatics. To improve structure-based energy calculations it is necessary to better understand the physical character and molecular determinants of electrostatic effects. The Cooperative thus intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pKa values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pKa values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pKa values in water. Many computational methods were tested in this 1st Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to assess objectively the performance of many computational methods tested on this one extensive dataset. This volume of PROTEINS: Structure, Function, and Bioinformatics introduces the pKa Cooperative, presents reports submitted by participants in the blind prediction challenge, and highlights some of the problems in structure-based calculations identified during this exercise. PMID:22002877

Batch Computed Tomography Analysis of Projectiles

DTIC Science & Technology

2016-05-01

error calculation. Projectiles are then grouped together according to the similarity of their components. Also discussed is graphical- cluster analysis...ballistic, armor, grouping, clustering 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF...Fig. 10 Graphical structure of 15 clusters of the jacket/core radii profiles with plots of the profiles contained within each cluster . The size of

Computing Power of Tests of the Variance of Treatment Effects in Designs with Two Levels of Nesting

ERIC Educational Resources Information Center

Konstantopoulos, Spyros

2008-01-01

Experiments that involve nested structures may assign treatment conditions either to entire groups (such as classrooms or schools) or individuals within groups (such as students). Although typically the interest in field experiments is in determining the significance of the overall treatment effect, it is equally important to examine the…

Sensitivities to Early Exchange in Synchronous Computer-Supported Collaborative Learning (CSCL) Groups

ERIC Educational Resources Information Center

Kapur, Manu; Voiklis, John; Kinzer, Charles K.

2008-01-01

This study reports the impact of high sensitivity to early exchange in 11th-grade, CSCL triads solving well- and ill-structured problems in Newtonian Kinematics. A mixed-method analysis of the evolution of participation inequity (PI) in group discussions suggested that participation levels tended to get locked-in relatively early on in the…

SAR matrices: automated extraction of information-rich SAR tables from large compound data sets.

PubMed

Wassermann, Anne Mai; Haebel, Peter; Weskamp, Nils; Bajorath, Jürgen

2012-07-23

We introduce the SAR matrix data structure that is designed to elucidate SAR patterns produced by groups of structurally related active compounds, which are extracted from large data sets. SAR matrices are systematically generated and sorted on the basis of SAR information content. Matrix generation is computationally efficient and enables processing of large compound sets. The matrix format is reminiscent of SAR tables, and SAR patterns revealed by different categories of matrices are easily interpretable. The structural organization underlying matrix formation is more flexible than standard R-group decomposition schemes. Hence, the resulting matrices capture SAR information in a comprehensive manner.

Deducing 2D crystal structure at the liquid/solid interface with atomic resolution: a combined STM and SFG study.

PubMed

McClelland, Arthur A; Ahn, Seokhoon; Matzger, Adam J; Chen, Zhan

2009-11-17

Sum frequency generation vibrational spectroscopy (SFG) has been applied to study two-dimensional (2D) crystals formed by an isophthalic acid diester on the surface of highly oriented pyrolytic graphite, providing complementary measurements to scanning tunneling microscopy (STM) and computational modeling. SFG results indicate that both aromatic and C=O groups in the 2D crystal tilt from the surface. This study demonstrates that a combination of SFG and STM techniques can be used to gain a more complete picture of 2D crystal structure, and it is necessary to consider solvent-2D crystal interactions and dynamics in the computer models to achieve an accurate representation of interfacial structure.

Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

PubMed

Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

2018-06-11

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

TGA, Hirshfeld, Raman spectroscopy and computational studies of diethylammonium hexachloroplumbate [(C2H5)2NH2]2PbCl6

NASA Astrophysics Data System (ADS)

Ouasri, A.; El-Adel, L.; Zouihri, H.; Rhandour, A.; Jalbout, A. F.

2018-04-01

Diethylammonium hexachloroplumbate [(C2H5)2NH2]2PbCl6 was found to be monoclinic with P21/n (Z = 2) as space group at room temperature. The TGA analysis shows that this compound is slightly hygroscopic and presents moisture in itself. The Raman spectrum (50-4000 cm-1) of this compound recorded at room temperature was discussed on the basis of the factor group analysis using the structural data obtained recently [5]. The experimental frequencies are compared to those obtained by Density Functional Theory (DFT) by using the B3LYP functional and the 6-31G(d) (SDD) basis set. The thermodynamic properties and geometries of this compound have been determinated and characterized. The significant intermolecular interactions in the crystal structure are identified and analyzed using the Hirshfeld surface and fingerprint plots computational methods.

Network Support for Group Coordination

DTIC Science & Technology

2000-01-01

telecommuting and ubiquitous computing [40], the advent of networked multimedia, and less expensive technology have shifted telecollaboration into...of Computer Engineering,Santa Cruz,CA,95064 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/ MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10...participants A and B, the payoff structure for choosing two actions i and j is P = Aij + Bij . If P = 0, then the interaction is called a zero -sum game, and

Insights into Hydrate Formation and Stability of Morphinanes from a Combination of Experimental and Computational Approaches

PubMed Central

2014-01-01

Morphine, codeine, and ethylmorphine are important drug compounds whose free bases and hydrochloride salts form stable hydrates. These compounds were used to systematically investigate the influence of the type of functional groups, the role of water molecules, and the Cl– counterion on molecular aggregation and solid state properties. Five new crystal structures have been determined. Additionally, structure models for anhydrous ethylmorphine and morphine hydrochloride dihydrate, two phases existing only in a very limited humidity range, are proposed on the basis of computational dehydration modeling. These match the experimental powder X-ray diffraction patterns and the structural information derived from infrared spectroscopy. All 12 structurally characterized morphinane forms (including structures from the Cambridge Structural Database) crystallize in the orthorhombic space group P212121. Hydrate formation results in higher dimensional hydrogen bond networks. The salt structures of the different compounds exhibit only little structural variation. Anhydrous polymorphs were detected for all compounds except ethylmorphine (one anhydrate) and its hydrochloride salt (no anhydrate). Morphine HCl forms a trihydrate and dihydrate. Differential scanning and isothermal calorimetry were employed to estimate the heat of the hydrate ↔ anhydrate phase transformations, indicating an enthalpic stabilization of the respective hydrate of 5.7 to 25.6 kJ mol–1 relative to the most stable anhydrate. These results are in qualitative agreement with static 0 K lattice energy calculations for all systems except morphine hydrochloride, showing the need for further improvements in quantitative thermodynamic prediction of hydrates having water···water interactions. Thus, the combination of a variety of experimental techniques, covering temperature- and moisture-dependent stability, and computational modeling allowed us to generate sufficient kinetic, thermodynamic and structural information to understand the principles of hydrate formation of the model compounds. This approach also led to the detection of several new crystal forms of the investigated morphinanes. PMID:25036525

APINetworks: A general API for the treatment of complex networks in arbitrary computational environments

NASA Astrophysics Data System (ADS)

Niño, Alfonso; Muñoz-Caro, Camelia; Reyes, Sebastián

2015-11-01

The last decade witnessed a great development of the structural and dynamic study of complex systems described as a network of elements. Therefore, systems can be described as a set of, possibly, heterogeneous entities or agents (the network nodes) interacting in, possibly, different ways (defining the network edges). In this context, it is of practical interest to model and handle not only static and homogeneous networks but also dynamic, heterogeneous ones. Depending on the size and type of the problem, these networks may require different computational approaches involving sequential, parallel or distributed systems with or without the use of disk-based data structures. In this work, we develop an Application Programming Interface (APINetworks) for the modeling and treatment of general networks in arbitrary computational environments. To minimize dependency between components, we decouple the network structure from its function using different packages for grouping sets of related tasks. The structural package, the one in charge of building and handling the network structure, is the core element of the system. In this work, we focus in this API structural component. We apply an object-oriented approach that makes use of inheritance and polymorphism. In this way, we can model static and dynamic networks with heterogeneous elements in the nodes and heterogeneous interactions in the edges. In addition, this approach permits a unified treatment of different computational environments. Tests performed on a C++11 version of the structural package show that, on current standard computers, the system can handle, in main memory, directed and undirected linear networks formed by tens of millions of nodes and edges. Our results compare favorably to those of existing tools.

Process for predicting structural performance of mechanical systems

DOEpatents

Gardner, D.R.; Hendrickson, B.A.; Plimpton, S.J.; Attaway, S.W.; Heinstein, M.W.; Vaughan, C.T.

1998-05-19

A process for predicting the structural performance of a mechanical system represents the mechanical system by a plurality of surface elements. The surface elements are grouped according to their location in the volume occupied by the mechanical system so that contacts between surface elements can be efficiently located. The process is well suited for efficient practice on multiprocessor computers. 12 figs.

Website on Protein Interaction and Protein Structure Related Work

NASA Technical Reports Server (NTRS)

Samanta, Manoj; Liang, Shoudan; Biegel, Bryan (Technical Monitor)

2003-01-01

In today's world, three seemingly diverse fields - computer information technology, nanotechnology and biotechnology are joining forces to enlarge our scientific knowledge and solve complex technological problems. Our group is dedicated to conduct theoretical research exploring the challenges in this area. The major areas of research include: 1) Yeast Protein Interactions; 2) Protein Structures; and 3) Current Transport through Small Molecules.

Structural and vibrational investigations of a neurotransmitter molecule: Serotonin (5-hydroxy tryptamine)

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, R. A.

2016-11-01

Structural and vibrational studies have been carried out for the most stable conformer of serotonin (5-HT) at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. In light of the computed vibrational parameters the observed IR and Raman frequencies have been analyzed. To help assign the vibrational fundamentals the GAR2PED software has been used to compute PEDs. Several of the fundamentals are drastically changed in going from indole to serotonin. The two NH bonds of the NH2 group are slightly different possibly due to bonding of the two H atoms of the NH2 group with different atoms. The rocking and wagging modes of the NH2 groups show mixing with the other modes while the remaining four modes are pure group modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO energy gap supports to pharmacological active property of the serotonin molecule. The HOMO and LUMO study suggests the existence of charge transfer within the molecule. The NBO analysis has been carried out to gather information regarding the proper and improper hydrogen bonds.

Computational Investigation of Amine–Oxygen Exciplex Formation

PubMed Central

Haupert, Levi M.; Simpson, Garth J.; Slipchenko, Lyudmila V.

2012-01-01

It has been suggested that fluorescence from amine-containing dendrimer compounds could be the result of a charge transfer between amine groups and molecular oxygen [Chu, C.-C.; Imae, T. Macromol. Rapid Commun. 2009, 30, 89.]. In this paper we employ equation-of-motion coupled cluster computational methods to study the electronic structure of an ammonia–oxygen model complex to examine this possibility. The results reveal several bound electronic states with charge transfer character with emission energies generally consistent with previous observations. However, further work involving confinement, solvent, and amine structure effects will be necessary for more rigorous examination of the charge transfer fluorescence hypothesis. PMID:21812447

"Group IV Nanomembranes, Nanoribbons, and Quantum Dots: Processing, Characterization, and Novel Devices"

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

liu, feng

This theoretical project has been carried out in close interaction with the experimental project at UW-Madison under the same title led by PI Max Lagally and co-PI Mark Eriksson. Extensive computational studies have been performed to address a broad range of topics from atomic structure, stability, mechanical property, to electronic structure, optoelectronic and transport properties of various nanoarchitectures in the context of Si and other solid nanomembranes. These have been done by using combinations of different theoretical and computational approaches, ranging from first-principles calculations and molecular dynamics (MD) simulations to finite-element (FE) analyses and continuum modeling.

Merging K-means with hierarchical clustering for identifying general-shaped groups.

PubMed

Peterson, Anna D; Ghosh, Arka P; Maitra, Ranjan

2018-01-01

Clustering partitions a dataset such that observations placed together in a group are similar but different from those in other groups. Hierarchical and K -means clustering are two approaches but have different strengths and weaknesses. For instance, hierarchical clustering identifies groups in a tree-like structure but suffers from computational complexity in large datasets while K -means clustering is efficient but designed to identify homogeneous spherically-shaped clusters. We present a hybrid non-parametric clustering approach that amalgamates the two methods to identify general-shaped clusters and that can be applied to larger datasets. Specifically, we first partition the dataset into spherical groups using K -means. We next merge these groups using hierarchical methods with a data-driven distance measure as a stopping criterion. Our proposal has the potential to reveal groups with general shapes and structure in a dataset. We demonstrate good performance on several simulated and real datasets.

Heterocyclic energetic materials: Synthesis, characterization and computational design

NASA Astrophysics Data System (ADS)

Tsyshevsky, Roman; Pagoria, Philip; Smirnov, Aleksander; Kuklja, Maija

2017-06-01

Achievement of the tailored properties (high performance, low sensitivity, etc.) in targeted new energetic materials (EM) remains a great challenge. Recently, attention of researchers has shifted from conventional nitroester-, nitramine-, and nitroaromatic-based explosives to new heterocyclic EM with oxygen- and nitrogenrich molecular structures. They have increased densities and formation enthalpies complemented by attractive performance and high stability to external stimuli. We will demonstrate that oxadiazol-containing heterocycles offer a convenient playground to probe specific chemical functional groups as building blocks for design of EM. We discuss a joint experimental and computational approach for design, characterization, synthesis, and modeling of novel heterocyclic EM. Combinatorically, we comprehensively analyzed how overall stability and performance of each material in the family (BNFF, LLM-172, LLM-175, LLM-191, LLM-192, LLM-200) depends upon their chemical composition and details of the molecular structure (such as a substitution of a nitro group by an amino group and 1,2,5-oxadiazole fragment by 1,2,3- or 1,2,4-oxadiazol ring). We will also discuss proposed new EM with predicted superior chemical and physical properties. P. Pagoria, R. Tsyshevsky, A. Smirnov.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol

NASA Astrophysics Data System (ADS)

Jha, Omkant; Yadav, T. K.; Yadav, R. A.

2018-01-01

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311 ++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH2 group the other four modes are pure group modes. The rocking and wagging modes of the NH2 group show mixing with the other modes. The two Osbnd H stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding.

Molecular structure activity on pharmaceutical applications of Phenacetin using spectroscopic investigation

NASA Astrophysics Data System (ADS)

Madanagopal, A.; Periandy, S.; Gayathri, P.; Ramalingam, S.; Xavier, S.

2017-01-01

The pharmaceutical compound; Phenacetin was investigated by analyzing FT-IR, FT-Raman and 1H &13C NMR spectra. The hybrid efficient computational calculations performed for computing physical and chemical parameters. The cause of pharmaceutical activity due to the substitutions; carboxylic, methyl and amine groups in appropriate positions on the pedestal compound was deeply investigated. Moreover, 13C NMR and 1H NMR chemical shifts correlated with TMS standard to explain the truth of compositional ratio of base and ligand groups. The bathochromic shift due to chromophores over the energy levels in UV-Visible region was strongly emphasized the Anti-inflammatory chemical properties. The chemical stability was pronounced by the strong kubo gap which showed the occurring of charge transformation within the molecule. The occurrence of the chemical reaction was feasibly interpreted by Gibbs free energy profile. The standard vibrational analysis stressed the active participation of composed ligand groups for the existence of the analgesic as well as antipyretic properties of the Phenacetin compound. The strong dipole interaction energy utilization for the transition among non-vanishing donor and acceptor for composition of the molecular structure was interpreted.

Computational Aerodynamics of Shuttle Orbiter Damage Scenarios in Support of the Columbia Accident Investigation

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Prabhu, Ramadas K.

2004-01-01

In support of the Columbia Accident Investigation, inviscid computations of the aerodynamic characteristics for various Shuttle Orbiter damage scenarios were performed using the FELISA unstructured CFD solver. Computed delta aerodynamics were compared with the reconstructed delta aerodynamics in order to postulate a progression of damage through the flight trajectory. By performing computations at hypervelocity flight and CF4 tunnel conditions, a bridge was provided between wind tunnel testing in Langley's 20-Inch CF4 facility and the flight environment experienced by Columbia during re-entry. The rapid modeling capability of the unstructured methodology allowed the computational effort to keep pace with the wind tunnel and, at times, guide the wind tunnel efforts. These computations provided a detailed view of the flowfield characteristics and the contribution of orbiter components (such as the vertical tail and wing) to aerodynamic forces and moments that were unavailable from wind tunnel testing. The damage scenarios are grouped into three categories. Initially, single and multiple missing full RCC panels were analyzed to determine the effect of damage location and magnitude on the aerodynamics. Next is a series of cases with progressive damage, increasing in severity, in the region of RCC panel 9. The final group is a set of wing leading edge and windward surface deformations that model possible structural deformation of the wing skin due to internal heating of the wing structure. By matching the aerodynamics from selected damage scenarios to the reconstructed flight aerodynamics, a progression of damage that is consistent with the flight data, debris forensics, and wind tunnel data is postulated.

Effect of geometry structure on critical properties

NASA Astrophysics Data System (ADS)

Jiang, Qing; Jiang, Xue-fan

1997-02-01

The effective-field renormalization group (EFRG) scheme is utilized to compute critical properties of the transverse Ising model (TIM) in a quantum-spin system. We distinguish differences between lattices of the same coordination number but of different structures and take effects of the first fluctuation correction into account. The improved results for the critical transverse field are obtained for several lattice structures even by considering the smallest possible cluster, which is in good agreement with series results.

The Effects of Cooperative, Competitive, and Individualistic Goal Structures on Computer-Assisted Instruction.

DTIC Science & Technology

1985-02-18

expected to double in each of the next five years. This growth of computer technology presents education with several challenges. One of the...provide some reassurence to educators who P worry that the group discussion will slow down the progress of students’ learning . The second issue examined...on learning from media. Review of Educational Research, 53, 445-459. Collins, A., Bruce, B., & Rubin, A. (1982). Microcomputer-based writing activities

Intramolecular cation-π interactions in protonated phenylalanine derivatives.

PubMed

Fu, Weiqiang; Carr, Patrick J J; Lecours, Michael J; Burt, Michael; Marta, Rick A; Steinmetz, Vincent; Fillion, Eric; McMahon, Terrance B; Hopkins, W Scott

2016-12-21

The structures and properties of a series of phenylalanine (Phe) derivatives have been investigated in a joint computational and experimental infrared multiple photon dissociation (IRMPD) study. IRMPD spectra in the 1000-2000 cm -1 region show that protonation is localized on the amine group in all cases. Intramolecular cation-π interactions between the ammonium group and the phenyl ring heavily influence molecular geometries and properties such as gas phase basicity and proton affinity. By varying substituents on the phenyl ring, one can sensitively tune the cation-π interaction and, therefore, the molecular structure and properties. Variations in molecular structures and properties as a function of phenyl ring substitution are shown to correlate with substituent Hammett parameters.

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

PubMed

Eirín-López, José M

2013-01-01

The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

A general probabilistic model for group independent component analysis and its estimation methods

PubMed Central

Guo, Ying

2012-01-01

SUMMARY Independent component analysis (ICA) has become an important tool for analyzing data from functional magnetic resonance imaging (fMRI) studies. ICA has been successfully applied to single-subject fMRI data. The extension of ICA to group inferences in neuroimaging studies, however, is challenging due to the unavailability of a pre-specified group design matrix and the uncertainty in between-subjects variability in fMRI data. We present a general probabilistic ICA (PICA) model that can accommodate varying group structures of multi-subject spatio-temporal processes. An advantage of the proposed model is that it can flexibly model various types of group structures in different underlying neural source signals and under different experimental conditions in fMRI studies. A maximum likelihood method is used for estimating this general group ICA model. We propose two EM algorithms to obtain the ML estimates. The first method is an exact EM algorithm which provides an exact E-step and an explicit noniterative M-step. The second method is an variational approximation EM algorithm which is computationally more efficient than the exact EM. In simulation studies, we first compare the performance of the proposed general group PICA model and the existing probabilistic group ICA approach. We then compare the two proposed EM algorithms and show the variational approximation EM achieves comparable accuracy to the exact EM with significantly less computation time. An fMRI data example is used to illustrate application of the proposed methods. PMID:21517789

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

DOE PAGES

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu; ...

2016-06-30

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Structure–function relationships in single molecule rectification by N-phenylbenzamide derivatives

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

Koenigsmann, Christopher; Ding, Wendu; Koepf, Matthieu

Here, we examine structure–function relationships in a series of N-phenylbenzamide (NPBA) derivatives by using computational modeling to identify molecular structures that exhibit both rectification and good conductance together with experimental studies of bias-dependent single molecule conductance and rectification behavior using the scanning tunneling microscopy break-junction technique. From a large number of computationally screened molecular diode structures, we have identified NPBA as a promising candidate, relative to the other structures that were screened. We demonstrate experimentally that conductance and rectification are both enhanced by functionalization of the NPBA 4-carboxamido-aniline moiety with electron donating methoxy groups, and are strongly correlated with themore » energy of the conducting frontier orbital relative to the Fermi level of the gold leads used in break-junction experiments.« less

Learning sorting algorithms through visualization construction

NASA Astrophysics Data System (ADS)

Cetin, Ibrahim; Andrews-Larson, Christine

2016-01-01

Recent increased interest in computational thinking poses an important question to researchers: What are the best ways to teach fundamental computing concepts to students? Visualization is suggested as one way of supporting student learning. This mixed-method study aimed to (i) examine the effect of instruction in which students constructed visualizations on students' programming achievement and students' attitudes toward computer programming, and (ii) explore how this kind of instruction supports students' learning according to their self-reported experiences in the course. The study was conducted with 58 pre-service teachers who were enrolled in their second programming class. They expect to teach information technology and computing-related courses at the primary and secondary levels. An embedded experimental model was utilized as a research design. Students in the experimental group were given instruction that required students to construct visualizations related to sorting, whereas students in the control group viewed pre-made visualizations. After the instructional intervention, eight students from each group were selected for semi-structured interviews. The results showed that the intervention based on visualization construction resulted in significantly better acquisition of sorting concepts. However, there was no significant difference between the groups with respect to students' attitudes toward computer programming. Qualitative data analysis indicated that students in the experimental group constructed necessary abstractions through their engagement in visualization construction activities. The authors of this study argue that the students' active engagement in the visualization construction activities explains only one side of students' success. The other side can be explained through the instructional approach, constructionism in this case, used to design instruction. The conclusions and implications of this study can be used by researchers and instructors dealing with computational thinking.

Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures.

PubMed

Yesselman, Joseph D; Horowitz, Scott; Brooks, Charles L; Trievel, Raymond C

2015-03-01

The propensity of backbone Cα atoms to engage in carbon-oxygen (CH · · · O) hydrogen bonding is well-appreciated in protein structure, but side chain CH · · · O hydrogen bonding remains largely uncharacterized. The extent to which side chain methyl groups in proteins participate in CH · · · O hydrogen bonding is examined through a survey of neutron crystal structures, quantum chemistry calculations, and molecular dynamics simulations. Using these approaches, methyl groups were observed to form stabilizing CH · · · O hydrogen bonds within protein structure that are maintained through protein dynamics and participate in correlated motion. Collectively, these findings illustrate that side chain methyl CH · · · O hydrogen bonding contributes to the energetics of protein structure and folding. © 2014 Wiley Periodicals, Inc.

Computational evidence for stable inorganic fullerene-like structures of ceramic and semiconductor materials

NASA Astrophysics Data System (ADS)

Chang, Ch; Patzer, A. B. C.; Sedlmayr, E.; Steinke, T.; Sülzle, D.

2001-12-01

Theoretical electronic structure techniques have become an indispensible and powerful means for predicting molecular properties and designing new materials. Based on a density functional approach and guided by geometric considerations we provide evidence for some specific inorganic fullerene-like cage molecules of ceramic and semiconductor materials which exhibit high energetic stability and point group symmetry as well as nearly perfect spherical shape.

Structured Reflection Breaks Embedded in an Online Course--Effects on Learning Experience, Time on Task and Performance

ERIC Educational Resources Information Center

Verpoorten, Dominique; Westera, Wim

2016-01-01

The purpose of this article is to gain an insight into the effects of practicing short, frequent, and structured reflection breaks interspersed with the learning material in a computer-based course. To that end, the study sets up a standardized control trial with two groups of secondary school pupils. The study shows that while performance is not…

Effect of Valence of Counterions on the Structure of Charged Membranes, a Computer Simulation Study

NASA Astrophysics Data System (ADS)

Qiao, Baofu; Olvera de La Cruz, Monica

2012-02-01

Phospholipids have been investigated for a long period, due to its ability of self-assembling into bilayer structures which resemble biological membranes. But most of the studies have been limited on the neutral phosphatidylcholine based lipids. The understanding of charged membranes (e.g., phosphatidylserine) is very limited due to the repulsion between the charged groups on lipids. In the present work, we investigated the effect of different counter-ions on the structures of charged membranes formed by 1,2-dilauroyl-sn-glycoro-3-phospho-L-serine. Three kinds of counterions were investigated, from monovalent, to divalent, to trivalent ions. Molecular dynamics simulations were performed at all-atom level. We have calculated the area per lipid. And the interaction between counterions and COO^- groups was found to dominate over that between counterions and PO4^- groups.

Establishing a group of endpoints to support collective operations without specifying unique identifiers for any endpoints

DOEpatents

Archer, Charles J.; Blocksom, Michael A.; Ratterman, Joseph D.; Smith, Brian E.; Xue, Hanghon

2016-02-02

A parallel computer executes a number of tasks, each task includes a number of endpoints and the endpoints are configured to support collective operations. In such a parallel computer, establishing a group of endpoints receiving a user specification of a set of endpoints included in a global collection of endpoints, where the user specification defines the set in accordance with a predefined virtual representation of the endpoints, the predefined virtual representation is a data structure setting forth an organization of tasks and endpoints included in the global collection of endpoints and the user specification defines the set of endpoints without a user specification of a particular endpoint; and defining a group of endpoints in dependence upon the predefined virtual representation of the endpoints and the user specification.

Computational Methods for Control and Estimation of Distributed System

DTIC Science & Technology

1988-08-01

prey example. [1987, August] Estimation of Nonlinearities in Parabolic Models for Growth, Predation and Dispersal of Populations. S a ON A VARIATIONAL ...NOTATION 17. COSATI CODES 18. SUBJECT TERMS (Continue on reverse if necessary and identify by block number) FIELD GROUP SUB-GROUP 19. ABSTRACT (Continue...techniques for infinite dimensional systems. (v) Control and stabilization of visco-elastic structures. (vi) Approximation in delay and Volterra type

Experimental and Theoretical Study of Thermodynamics of the Reaction of Titania and Water at High Temperatures

NASA Technical Reports Server (NTRS)

Nguyen, Quynhgiao N.; Myers, Dwight L.; Jacobson, Nathan S.; Opila, Elizabeth J.

2014-01-01

The transpiration method was used to determine the volatility of titanium dioxide (TiO2) in water vapor-containing environments at temperatures between 1473 and 1673 K. Water contents ranged from 0 to 76 mole % in oxygen or argon carrier gases for 20 to 250 hr exposure times. Results indicate that oxygen is not a key contributor to volatilization and the primary reaction for volatilization in this temperature range is: TiO2(s) + H2O(g) = TiO(OH)2(g). Data were analyzed with both the second and third law methods to extract an enthalpy and entropy of formation. The geometry and vibrational frequencies of TiO(OH)2(g) were computed using B3LYP density functional theory, and the enthalpy of formation was computed using the coupled-cluster singles and doubles method with a perturbative correction for connected triple substitutions [CCSD(T)]. Thermal functions are calculated using both a structure with bent and linear hydroxyl groups. Calculated second and third heats show closer agreement with the linear hydroxyl group, suggesting more experimental and computational spectroscopic and structural work is needed on this system.

Aromatic hydrazones derived from nicotinic acid hydrazide as fluorimetric pH sensing molecules: Structural analysis by computational and spectroscopic methods in solid phase and in solution

NASA Astrophysics Data System (ADS)

Benković, T.; Kenđel, A.; Parlov-Vuković, J.; Kontrec, D.; Chiş, V.; Miljanić, S.; Galić, N.

2018-02-01

Structural analyses of aroylhydrazones were performed by computational and spectroscopic methods (solid state NMR, 1 and 2D NMR spectroscopy, FT-IR (ATR) spectroscopy, Raman spectroscopy, UV-Vis spectrometry and spectrofluorimetry) in solid state and in solution. The studied compounds were N‧-(2,3-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (1), N‧-(2,5-dihydroxyphenylmethylidene)-3-pyridinecarbohydrazide (2), N‧-(3-chloro-2-hydroxy-phenylmethylidene)-3-pyridinecarbohydrazide (3), and N‧-(2-hydroxy-4-methoxyphenyl-methylidene)-3-pyridinecarbohydrazide (4). Both in solid state and in solution, all compounds were in ketoamine form (form I, sbnd COsbnd NHsbnd Ndbnd Csbnd), stabilized by intramolecular H-bond between hydroxyl proton and nitrogen atom of the Cdbnd N group. In solid state, the Cdbnd O group of 1-4 were involved in additional intermolecular H-bond between closely packed molecules. Among hydrazones studied, the chloro- and methoxy-derivatives have shown pH dependent and reversible fluorescence emission connected to deprotonation/protonation of salicylidene part of the molecules. All findings acquired by experimental methods (NMR, IR, Raman, and UV-Vis spectra) were in excellent agreement with those obtained by computational methods.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise a formalized graphical modeling language, often used to describe computation occurring within biochemical and genetic regulatory networks, but the semantics may be interpreted in different ways in the realm of automata. Therefore, there are several different ways to turn a Petri net into a state-transition automaton. Here, we systematically investigate different conversion methods and describe cases where they may yield radically different algebraic structures. We focus on the existence of group components of the corresponding transformation semigroups, as these reflect symmetries of the computation occurring within the biological system under study. Results are illustrated by applications to the Petri net modelling of intermediary metabolism. Petri nets with inhibition are shown to be computationally rich, regardless of the particular interpretation method. Along these lines we provide a mathematical argument suggesting a reason for the apparent all-pervasiveness of inhibitory connections in living systems.

"Let's get physical": advantages of a physical model over 3D computer models and textbooks in learning imaging anatomy.

PubMed

Preece, Daniel; Williams, Sarah B; Lam, Richard; Weller, Renate

2013-01-01

Three-dimensional (3D) information plays an important part in medical and veterinary education. Appreciating complex 3D spatial relationships requires a strong foundational understanding of anatomy and mental 3D visualization skills. Novel learning resources have been introduced to anatomy training to achieve this. Objective evaluation of their comparative efficacies remains scarce in the literature. This study developed and evaluated the use of a physical model in demonstrating the complex spatial relationships of the equine foot. It was hypothesized that the newly developed physical model would be more effective for students to learn magnetic resonance imaging (MRI) anatomy of the foot than textbooks or computer-based 3D models. Third year veterinary medicine students were randomly assigned to one of three teaching aid groups (physical model; textbooks; 3D computer model). The comparative efficacies of the three teaching aids were assessed through students' abilities to identify anatomical structures on MR images. Overall mean MRI assessment scores were significantly higher in students utilizing the physical model (86.39%) compared with students using textbooks (62.61%) and the 3D computer model (63.68%) (P < 0.001), with no significant difference between the textbook and 3D computer model groups (P = 0.685). Student feedback was also more positive in the physical model group compared with both the textbook and 3D computer model groups. Our results suggest that physical models may hold a significant advantage over alternative learning resources in enhancing visuospatial and 3D understanding of complex anatomical architecture, and that 3D computer models have significant limitations with regards to 3D learning. © 2013 American Association of Anatomists.

Structure based alignment and clustering of proteins (STRALCP)

DOEpatents

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.

Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA

PubMed Central

Xia, Fei; Dou, Yong; Zhou, Xingming; Yang, Xuejun; Xu, Jiaqing; Zhang, Yang

2009-01-01

Background In the field of RNA secondary structure prediction, the RNAalifold algorithm is one of the most popular methods using free energy minimization. However, general-purpose computers including parallel computers or multi-core computers exhibit parallel efficiency of no more than 50%. Field Programmable Gate-Array (FPGA) chips provide a new approach to accelerate RNAalifold by exploiting fine-grained custom design. Results RNAalifold shows complicated data dependences, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master Processing Element (PE) and multiple slave PEs for fine grain hardware implementation on FPGA. We exploit data reuse schemes to reduce the need to load energy matrices from external memory. We also propose several methods to reduce energy table parameter size by 80%. Conclusion To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete RNAalifold algorithm. The experimental results show a factor of 12.2 speedup over the RNAalifold (ViennaPackage – 1.6.5) software for a group of aligned RNA sequences with 2981-residue running on a Personal Computer (PC) platform with Pentium 4 2.6 GHz CPU. PMID:19208138

Quantum Monte Carlo Endstation for Petascale Computing

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

Lubos Mitas

2011-01-26

NCSU research group has been focused on accomplising the key goals of this initiative: establishing new generation of quantum Monte Carlo (QMC) computational tools as a part of Endstation petaflop initiative for use at the DOE ORNL computational facilities and for use by computational electronic structure community at large; carrying out high accuracy quantum Monte Carlo demonstration projects in application of these tools to the forefront electronic structure problems in molecular and solid systems; expanding the impact of QMC methods and approaches; explaining and enhancing the impact of these advanced computational approaches. In particular, we have developed quantum Monte Carlomore » code (QWalk, www.qwalk.org) which was significantly expanded and optimized using funds from this support and at present became an actively used tool in the petascale regime by ORNL researchers and beyond. These developments have been built upon efforts undertaken by the PI's group and collaborators over the period of the last decade. The code was optimized and tested extensively on a number of parallel architectures including petaflop ORNL Jaguar machine. We have developed and redesigned a number of code modules such as evaluation of wave functions and orbitals, calculations of pfaffians and introduction of backflow coordinates together with overall organization of the code and random walker distribution over multicore architectures. We have addressed several bottlenecks such as load balancing and verified efficiency and accuracy of the calculations with the other groups of the Endstation team. The QWalk package contains about 50,000 lines of high quality object-oriented C++ and includes also interfaces to data files from other conventional electronic structure codes such as Gamess, Gaussian, Crystal and others. This grant supported PI for one month during summers, a full-time postdoc and partially three graduate students over the period of the grant duration, it has resulted in 13 published papers, 15 invited talks and lectures nationally and internationally. My former graduate student and postdoc Dr. Michal Bajdich, who was supported byt this grant, is currently a postdoc with ORNL in the group of Dr. F. Reboredo and Dr. P. Kent and is using the developed tools in a number of DOE projects. The QWalk package has become a truly important research tool used by the electronic structure community and has attracted several new developers in other research groups. Our tools use several types of correlated wavefunction approaches, variational, diffusion and reptation methods, large-scale optimization methods for wavefunctions and enables to calculate energy differences such as cohesion, electronic gaps, but also densities and other properties, using multiple runs one can obtain equations of state for given structures and beyond. Our codes use efficient numerical and Monte Carlo strategies (high accuracy numerical orbitals, multi-reference wave functions, highly accurate correlation factors, pairing orbitals, force biased and correlated sampling Monte Carlo), are robustly parallelized and enable to run on tens of thousands cores very efficiently. Our demonstration applications were focused on the challenging research problems in several fields of materials science such as transition metal solids. We note that our study of FeO solid was the first QMC calculation of transition metal oxides at high pressures.« less

An E-payment system based on quantum group signature

NASA Astrophysics Data System (ADS)

Xiaojun, Wen

2010-12-01

Security and anonymity are essential to E-payment systems. However, existing E-payment systems will easily be broken into soon with the emergence of quantum computers. In this paper, we propose an E-payment system based on quantum group signature. In contrast to classical E-payment systems, our quantum E-payment system can protect not only the users' anonymity but also the inner structure of customer groups. Because of adopting the two techniques of quantum key distribution, a one-time pad and quantum group signature, unconditional security of our E-payment system is guaranteed.

Computations involving differential operators and their actions on functions

NASA Technical Reports Server (NTRS)

Crouch, Peter E.; Grossman, Robert; Larson, Richard

1991-01-01

The algorithms derived by Grossmann and Larson (1989) are further developed for rewriting expressions involving differential operators. The differential operators involved arise in the local analysis of nonlinear dynamical systems. These algorithms are extended in two different directions: the algorithms are generalized so that they apply to differential operators on groups and the data structures and algorithms are developed to compute symbolically the action of differential operators on functions. Both of these generalizations are needed for applications.

Ascent Aerodynamic Pressure Distributions on WB001

NASA Technical Reports Server (NTRS)

Vu, B.; Ruf, J.; Canabal, F.; Brunty, J.

1996-01-01

To support the reusable launch vehicle concept study, the aerodynamic data and surface pressure for WB001 were predicted using three computational fluid dynamic (CFD) codes at several flow conditions between code to code and code to aerodynamic database as well as available experimental data. A set of particular solutions have been selected and recommended for use in preliminary conceptual designs. These computational fluid dynamic (CFD) results have also been provided to the structure group for wing loading analysis.

Computational Phenotyping in Psychiatry: A Worked Example

PubMed Central

2016-01-01

Abstract Computational psychiatry is a rapidly emerging field that uses model-based quantities to infer the behavioral and neuronal abnormalities that underlie psychopathology. If successful, this approach promises key insights into (pathological) brain function as well as a more mechanistic and quantitative approach to psychiatric nosology—structuring therapeutic interventions and predicting response and relapse. The basic procedure in computational psychiatry is to build a computational model that formalizes a behavioral or neuronal process. Measured behavioral (or neuronal) responses are then used to infer the model parameters of a single subject or a group of subjects. Here, we provide an illustrative overview over this process, starting from the modeling of choice behavior in a specific task, simulating data, and then inverting that model to estimate group effects. Finally, we illustrate cross-validation to assess whether between-subject variables (e.g., diagnosis) can be recovered successfully. Our worked example uses a simple two-step maze task and a model of choice behavior based on (active) inference and Markov decision processes. The procedural steps and routines we illustrate are not restricted to a specific field of research or particular computational model but can, in principle, be applied in many domains of computational psychiatry. PMID:27517087

Computational Phenotyping in Psychiatry: A Worked Example.

PubMed

Schwartenbeck, Philipp; Friston, Karl

2016-01-01

Computational psychiatry is a rapidly emerging field that uses model-based quantities to infer the behavioral and neuronal abnormalities that underlie psychopathology. If successful, this approach promises key insights into (pathological) brain function as well as a more mechanistic and quantitative approach to psychiatric nosology-structuring therapeutic interventions and predicting response and relapse. The basic procedure in computational psychiatry is to build a computational model that formalizes a behavioral or neuronal process. Measured behavioral (or neuronal) responses are then used to infer the model parameters of a single subject or a group of subjects. Here, we provide an illustrative overview over this process, starting from the modeling of choice behavior in a specific task, simulating data, and then inverting that model to estimate group effects. Finally, we illustrate cross-validation to assess whether between-subject variables (e.g., diagnosis) can be recovered successfully. Our worked example uses a simple two-step maze task and a model of choice behavior based on (active) inference and Markov decision processes. The procedural steps and routines we illustrate are not restricted to a specific field of research or particular computational model but can, in principle, be applied in many domains of computational psychiatry.

First-principles study of crystal structure, elastic stiffness constants, piezoelectric constants, and spontaneous polarization of orthorhombic Pna21-M2O3 (M = Al, Ga, In, Sc, Y)

NASA Astrophysics Data System (ADS)

Shimada, Kazuhiro

2018-03-01

We perform first-principles calculations to investigate the crystal structure, elastic and piezoelectric properties, and spontaneous polarization of orthorhombic M2O3 (M = Al, Ga, In, Sc, Y) with Pna21 space group based on density functional theory. The lattice parameters, full elastic stiffness constants, piezoelectric stress and strain constants, and spontaneous polarization are successfully predicted. Comparison with available experimental and computational results indicates the validity of our computational results. Detailed analysis of the results clarifies the difference in the bonding character and the origin of the strong piezoelectric response and large spontaneous polarization.

Accurate critical pressures for structural phase transitions of group IV, III-V, and II-VI compounds from the SCAN density functional

NASA Astrophysics Data System (ADS)

Shahi, Chandra; Sun, Jianwei; Perdew, John P.

2018-03-01

Most of the group IV, III-V, and II-VI compounds crystallize in semiconductor structures under ambient conditions. Upon application of pressure, they undergo structural phase transitions to more closely packed structures, sometimes metallic phases. We have performed density functional calculations using projector augmented wave (PAW) pseudopotentials to determine the transition pressures for these transitions within the local density approximation (LDA), the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA), and the strongly constrained and appropriately normed (SCAN) meta-GGA. LDA underestimates the transition pressure for most of the studied materials. PBE under- or overestimates in many cases. SCAN typically corrects the errors of LDA and PBE for the transition pressure. The accuracy of SCAN is comparable to that of computationally expensive methods like the hybrid functional HSE06, the random phase approximation (RPA), and quantum Monte Carlo (QMC), in cases where calculations with these methods have been reported, but at a more modest computational cost. The improvement from LDA to PBE to SCAN is especially clearcut and dramatic for covalent semiconductor-metal transitions, as for Si and Ge, where it reflects the increasing relative stabilization of the covalent semiconducting phases under increasing functional sophistication.

Structured Ordinary Least Squares: A Sufficient Dimension Reduction approach for regressions with partitioned predictors and heterogeneous units.

PubMed

Liu, Yang; Chiaromonte, Francesca; Li, Bing

2017-06-01

In many scientific and engineering fields, advanced experimental and computing technologies are producing data that are not just high dimensional, but also internally structured. For instance, statistical units may have heterogeneous origins from distinct studies or subpopulations, and features may be naturally partitioned based on experimental platforms generating them, or on information available about their roles in a given phenomenon. In a regression analysis, exploiting this known structure in the predictor dimension reduction stage that precedes modeling can be an effective way to integrate diverse data. To pursue this, we propose a novel Sufficient Dimension Reduction (SDR) approach that we call structured Ordinary Least Squares (sOLS). This combines ideas from existing SDR literature to merge reductions performed within groups of samples and/or predictors. In particular, it leads to a version of OLS for grouped predictors that requires far less computation than recently proposed groupwise SDR procedures, and provides an informal yet effective variable selection tool in these settings. We demonstrate the performance of sOLS by simulation and present a first application to genomic data. The R package "sSDR," publicly available on CRAN, includes all procedures necessary to implement the sOLS approach. © 2016, The International Biometric Society.

On the solvation structure of dimethylsulfoxide/water around the phosphatidylcholine head group in solution

NASA Astrophysics Data System (ADS)

Dabkowska, Aleksandra P.; Foglia, Fabrizia; Lawrence, M. Jayne; Lorenz, Christian D.; McLain, Sylvia E.

2011-12-01

The solution structure of the phosphocholine (PC) head group in 1,2-dipropionyl-sn-glycero-3-phosphocholine (C3-PC) in 30 mol. % dimethylsulfoxide (DMSO)-water solutions has been determined by using neutron diffraction enhanced with isotopic substitution in combination with computer simulation techniques. By investigating the atomic scale hydration structure around the PC head group, a unique description of the displacement of water molecules by DMSO molecules is detailed around various locations of the head group. Specifically, DMSO molecules were found to be the most prevalent around the onium portion of the head group, with the dipoles of the DMSO molecules being aligned where the negatively charged oxygen can interact strongly with the positively charged lipid group. The phosphate group is also partially dehydrated by the presence of the DMSO molecules. However, around this group the bulkier positive end of the DMSO dipole is interacting with negatively charged groups of the lipid head group, the DMSO layer shows no obvious ordering as it cannot form hydrogen bonds with the oxygen atoms in the PO4 group such as water molecules can. Interestingly, DMSO-water contacts have also increased in the presence of the lipid molecule relative to DMSO-water contacts observed in pure DMSO/water solutions at similar concentrations.

Optical Fourier diffractometry applied to degraded bone structure recognition

NASA Astrophysics Data System (ADS)

Galas, Jacek; Godwod, Krzysztof; Szawdyn, Jacek; Sawicki, Andrzej

1993-09-01

Image processing and recognition methods are useful in many fields. This paper presents the hybrid optical and digital method applied to recognition of pathological changes in bones involved by metabolic bone diseases. The trabecular bone structure, registered by x ray on the photographic film, is analyzed in the new type of computer controlled diffractometer. The set of image parameters, extracted from diffractogram, is evaluated by statistical analysis. The synthetic image descriptors in discriminant space, constructed on the base of 3 training groups of images (control, osteoporosis, and osteomalacia groups) by discriminant analysis, allow us to recognize bone samples with degraded bone structure and to recognize the disease. About 89% of the images were classified correctly. This method after optimization process will be verified in medical investigations.

Working memory training and semantic structuring improves remembering future events, not past events.

PubMed

Richter, Kim Merle; Mödden, Claudia; Eling, Paul; Hildebrandt, Helmut

2015-01-01

Objectives. Memory training in combination with practice in semantic structuring and word fluency has been shown to improve memory performance. This study investigated the efficacy of a working memory training combined with exercises in semantic structuring and word fluency and examined whether training effects generalize to other cognitive tasks. Methods. In this double-blind randomized control study, 36 patients with memory impairments following brain damage were allocated to either the experimental or the active control condition, with both groups receiving 9 hours of therapy. The experimental group received a computer-based working memory training and exercises in word fluency and semantic structuring. The control group received the standard memory therapy provided in the rehabilitation center. Patients were tested on a neuropsychological test battery before and after therapy, resulting in composite scores for working memory; immediate, delayed, and prospective memory; word fluency; and attention. Results. The experimental group improved significantly in working memory and word fluency. The training effects also generalized to prospective memory tasks. No specific effect on episodic memory could be demonstrated. Conclusion. Combined treatment of working memory training with exercises in semantic structuring is an effective method for cognitive rehabilitation of organic memory impairment. © The Author(s) 2014.

Renewing Professional Organizations and Action Learning

ERIC Educational Resources Information Center

Mullen, Carol A.

2011-01-01

This account concerns the renewal of established professional organizations though action learning. In order to revitalize one national organization, an executive group of leaders committed to co-leading and co-learning through a friendly, computer-supported governance structure. Manifestations of our work together were an accelerated…

Alternative expression of the Bloch wave group velocity in loss-less periodic media using the electromagnetic field energy

NASA Astrophysics Data System (ADS)

Deparis, Olivier; Lambin, Philippe

2018-01-01

In periodic optical media, the group velocity is defined as the gradient with respect to wave-vector of the corresponding Bloch mode frequency dispersion curve, forming the photonic band structure. Instead of deducing it from the numerically computed photonic crystal band structure, the group velocity can be calculated directly from the integral of the Poynting vector over the crystal unit cell, the physical meaning of which is immediately perceivable. The related formula, which can be regarded as the application of Hellmann-Feynman theorem to electromagnetism, has been reported previously though without proof. We provide hereafter a full derivation of that formula starting from Maxwell's equations and we discuss its usefulness in photonics.

A route to possible civil engineering materials: the case of high-pressure phases of lime

NASA Astrophysics Data System (ADS)

Bouibes, A.; Zaoui, A.

2015-07-01

Lime system has a chemical composition CaO, which is known as thermodynamically stable. The purpose here is to explore further possible phases under pressure, by means of variable-composition ab initio evolutionary algorithm. The present investigation shows surprisingly new stable compounds of lime. At ambient pressure we predict, in addition to CaO, CaO2 as new thermodynamically stable compound. The latter goes through two phases transition from C2/c space group structure to Pna21 at 1.5 GPa, and Pna21 space group structure to I4/mcm at 23.4 GPa. Under increasing pressure, further compounds such as CaO3 become the most stable and stabilize in P-421m space group structure above 65 GPa. For the necessary knowledge of the new predicted compounds, we have computed their mechanical and electronic properties in order to show and to explain the main reasons leading to the structural changes.

A route to possible civil engineering materials: the case of high-pressure phases of lime.

PubMed

Bouibes, A; Zaoui, A

2015-07-23

Lime system has a chemical composition CaO, which is known as thermodynamically stable. The purpose here is to explore further possible phases under pressure, by means of variable-composition ab initio evolutionary algorithm. The present investigation shows surprisingly new stable compounds of lime. At ambient pressure we predict, in addition to CaO, CaO2 as new thermodynamically stable compound. The latter goes through two phases transition from C2/c space group structure to Pna21 at 1.5 GPa, and Pna21 space group structure to I4/mcm at 23.4 GPa. Under increasing pressure, further compounds such as CaO3 become the most stable and stabilize in P-421m space group structure above 65 GPa. For the necessary knowledge of the new predicted compounds, we have computed their mechanical and electronic properties in order to show and to explain the main reasons leading to the structural changes.

Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery.

PubMed

St-Gallay, Steve A; Sambrook-Smith, Colin P

2017-03-01

Computer-aided drug design encompasses a wide variety of tools and techniques, and can be implemented with a range of organisational structures and focus in different organisations. Here we outline the computational chemistry skills within Sygnature Discovery, along with the software and hardware at our disposal, and briefly discuss the methods that are not employed and why. The goal of the group is to provide support for design and analysis in order to improve the quality of compounds synthesised and reduce the timelines of drug discovery projects, and we reveal how this is achieved at Sygnature. Impact on medicinal chemistry is vital to demonstrating the value of computational chemistry, and we discuss the approaches taken to influence the list of compounds for synthesis, and how we recognise success. Finally we touch on some of the areas being developed within the team in order to provide further value to the projects and clients.

Effects of four instruments on coronal pre-enlargement by using cone beam computed tomography.

PubMed

Sanfelice, Cintia Mussoline; da Costa, Fernanda Botega; Reis Só, Marcus Vinícius; Vier-Pelisser, Fabiana; Souza Bier, Carlos Alexandre; Grecca, Fabiana Soares

2010-05-01

This ex vivo study used cone beam computed tomography to evaluate the amount of dentin removal from the distal wall of the mesial canal of human mandibular first molars caused by 4 instruments used to flare the cervical third. Thirty-two mesial roots were divided into 4 groups prepared by using ProTaper, K3, Gates-Glidden, or LA Axxess. The dentin thickness of the distal cervical wall of mesial canals was measured before and after the preparation by using computed tomography and Adobe Photoshop software. There was no statistically significant difference between the study groups (P > 05). All the instruments used for cervical preparation seemed to be safe and did not damage the dentin structure of the distal wall of mesial root canals of mandibular molars. Copyright (c) 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery

NASA Astrophysics Data System (ADS)

St-Gallay, Steve A.; Sambrook-Smith, Colin P.

2017-03-01

Computer-aided drug design encompasses a wide variety of tools and techniques, and can be implemented with a range of organisational structures and focus in different organisations. Here we outline the computational chemistry skills within Sygnature Discovery, along with the software and hardware at our disposal, and briefly discuss the methods that are not employed and why. The goal of the group is to provide support for design and analysis in order to improve the quality of compounds synthesised and reduce the timelines of drug discovery projects, and we reveal how this is achieved at Sygnature. Impact on medicinal chemistry is vital to demonstrating the value of computational chemistry, and we discuss the approaches taken to influence the list of compounds for synthesis, and how we recognise success. Finally we touch on some of the areas being developed within the team in order to provide further value to the projects and clients.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

NASA Astrophysics Data System (ADS)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

Application of the Hughes-LIU algorithm to the 2-dimensional heat equation

NASA Technical Reports Server (NTRS)

Malkus, D. S.; Reichmann, P. I.; Haftka, R. T.

1982-01-01

An implicit explicit algorithm for the solution of transient problems in structural dynamics is described. The method involved dividing the finite elements into implicit and explicit groups while automatically satisfying the conditions. This algorithm is applied to the solution of the linear, transient, two dimensional heat equation subject to an initial condition derived from the soluton of a steady state problem over an L-shaped region made up of a good conductor and an insulating material. Using the IIT/PRIME computer with virtual memory, a FORTRAN computer program code was developed to make accuracy, stability, and cost comparisons among the fully explicit Euler, the Hughes-Liu, and the fully implicit Crank-Nicholson algorithms. The Hughes-Liu claim that the explicit group governs the stability of the entire region while maintaining the unconditional stability of the implicit group is illustrated.

AMPX: a modular code system for generating coupled multigroup neutron-gamma libraries from ENDF/B

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

Greene, N.M.; Lucius, J.L.; Petrie, L.M.

1976-03-01

AMPX is a modular system for producing coupled multigroup neutron-gamma cross section sets. Basic neutron and gamma cross-section data for AMPX are obtained from ENDF/B libraries. Most commonly used operations required to generate and collapse multigroup cross-section sets are provided in the system. AMPX is flexibly dimensioned; neutron group structures, and gamma group structures, and expansion orders to represent anisotropic processes are all arbitrary and limited only by available computer core and budget. The basic processes provided will (1) generate multigroup neutron cross sections; (2) generate multigroup gamma cross sections; (3) generate gamma yields for gamma-producing neutron interactions; (4) combinemore » neutron cross sections, gamma cross sections, and gamma yields into final ''coupled sets''; (5) perform one-dimensional discrete ordinates transport or diffusion theory calculations for neutrons and gammas and, on option, collapse the cross sections to a broad-group structure, using the one-dimensional results as weighting functions; (6) plot cross sections, on option, to facilitate the ''evaluation'' of a particular multigroup set of data; (7) update and maintain multigroup cross section libraries in such a manner as to make it not only easy to combine new data with previously processed data but also to do it in a single pass on the computer; and (8) output multigroup cross sections in convenient formats for other codes. (auth)« less

Changes in bone macro- and microstructure in diabetic obese mice revealed by high resolution microfocus X-ray computed tomography

NASA Astrophysics Data System (ADS)

Kerckhofs, G.; Durand, M.; Vangoitsenhoven, R.; Marin, C.; van der Schueren, B.; Carmeliet, G.; Luyten, F. P.; Geris, L.; Vandamme, K.

2016-10-01

High resolution microfocus X-ray computed tomography (HR-microCT) was employed to characterize the structural alterations of the cortical and trabecular bone in a mouse model of obesity-driven type 2 diabetes (T2DM). C57Bl/6J mice were randomly assigned for 14 weeks to either a control diet-fed (CTRL) or a high fat diet (HFD)-fed group developing obesity, hyperglycaemia and insulin resistance. The HFD group showed an increased trabecular thickness and a decreased trabecular number compared to CTRL animals. Midshaft tibia intracortical porosity was assessed at two spatial image resolutions. At 2 μm scale, no change was observed in the intracortical structure. At 1 μm scale, a decrease in the cortical vascular porosity of the HFD bone was evidenced. The study of a group of 8 week old animals corresponding to animals at the start of the diet challenge revealed that the decreased vascular porosity was T2DM-dependant and not related to the ageing process. Our results offer an unprecedented ultra-characterization of the T2DM compromised skeletal micro-architecture and highlight an unrevealed T2DM-related decrease in the cortical vascular porosity, potentially affecting the bone health and fragility. Additionally, it provides some insights into the technical challenge facing the assessment of the rodent bone structure using HR-microCT imaging.

Characterizing executive functioning in older special populations: from cognitively elite to cognitively impaired.

PubMed

de Frias, Cindy M; Dixon, Roger A; Strauss, Esther

2009-11-01

The authors examined the structure and invariance of executive functions (EF) across (a) a continuum of cognitive status in 3 groups of older adults (cognitively elite [CE], cognitively normal [CN], and cognitively impaired [CI]) and (b) a 3-year longitudinal interval. Using latent variable analyses (LISREL 8.80), the authors tested 3-factor models ("Inhibition": Hayling [Burgess & Shallice, 1997], Stroop [Regard, 1981]; "Shifting": Brixton [Burgess & Shallice, 1997], Color Trails [D'Elia et al., 1996]; and "Updating": Reading and Computational Span [Salthouse & Babcock, 1991]) and 1-factor models within each group. Participants (initial N = 570; 53-90 years) were from the Victoria Longitudinal Study (Sample 3, Waves 1 and 2). Cross-sectionally, the authors observed a 3-factor EF structure especially for the CE group and 1-factor solutions for all 3 groups. Longitudinally, temporal invariance was supported for the 3-factor model (CE and CN groups) and the 1-factor model (CI and CN groups). Subgroups with higher cognitive status and greater 3-year stability performed better on EF factors than corresponding groups with lower cognitive status and less stability. Studies of EF structure, performance, dedifferentiation, and dysfunction will benefit from considering initial cognitive status and longitudinal stability.

Image understanding systems based on the unifying representation of perceptual and conceptual information and the solution of mid-level and high-level vision problems

NASA Astrophysics Data System (ADS)

Kuvychko, Igor

2001-10-01

Vision is a part of a larger information system that converts visual information into knowledge structures. These structures drive vision process, resolving ambiguity and uncertainty via feedback, and provide image understanding, that is an interpretation of visual information in terms of such knowledge models. A computer vision system based on such principles requires unifying representation of perceptual and conceptual information. Computer simulation models are built on the basis of graphs/networks. The ability of human brain to emulate similar graph/networks models is found. That means a very important shift of paradigm in our knowledge about brain from neural networks to the cortical software. Starting from the primary visual areas, brain analyzes an image as a graph-type spatial structure. Primary areas provide active fusion of image features on a spatial grid-like structure, where nodes are cortical columns. The spatial combination of different neighbor features cannot be described as a statistical/integral characteristic of the analyzed region, but uniquely characterizes such region itself. Spatial logic and topology naturally present in such structures. Mid-level vision processes like clustering, perceptual grouping, multilevel hierarchical compression, separation of figure from ground, etc. are special kinds of graph/network transformations. They convert low-level image structure into the set of more abstract ones, which represent objects and visual scene, making them easy for analysis by higher-level knowledge structures. Higher-level vision phenomena like shape from shading, occlusion, etc. are results of such analysis. Such approach gives opportunity not only to explain frequently unexplainable results of the cognitive science, but also to create intelligent computer vision systems that simulate perceptional processes in both what and where visual pathways. Such systems can open new horizons for robotic and computer vision industries.

A model for evolution of overlapping community networks

NASA Astrophysics Data System (ADS)

Karan, Rituraj; Biswal, Bibhu

2017-05-01

A model is proposed for the evolution of network topology in social networks with overlapping community structure. Starting from an initial community structure that is defined in terms of group affiliations, the model postulates that the subsequent growth and loss of connections is similar to the Hebbian learning and unlearning in the brain and is governed by two dominant factors: the strength and frequency of interaction between the members, and the degree of overlap between different communities. The temporal evolution from an initial community structure to the current network topology can be described based on these two parameters. It is possible to quantify the growth occurred so far and predict the final stationary state to which the network is likely to evolve. Applications in epidemiology or the spread of email virus in a computer network as well as finding specific target nodes to control it are envisaged. While facing the challenge of collecting and analyzing large-scale time-resolved data on social groups and communities one faces the most basic questions: how do communities evolve in time? This work aims to address this issue by developing a mathematical model for the evolution of community networks and studying it through computer simulation.

A Computational Study of Structure and Reactivity of N-Substitued-4-Piperidones Curcumin Analogues and Their Radical Anions.

PubMed

Martínez-Cifuentes, Maximiliano; Weiss-López, Boris; Araya-Maturana, Ramiro

2016-12-02

In this work, a computational study of a series of N -substitued-4-piperidones curcumin analogues is presented. The molecular structure of the neutral molecules and their radical anions, as well as their reactivity, are investigated. N -substituents include methyl and benzyl groups, while substituents on the aromatic rings cover electron-donor and electron-acceptor groups. Substitutions at the nitrogen atom do not significantly affect the geometry and frontier molecular orbitals (FMO) energies of these molecules. On the other hand, substituents on the aromatic rings modify the distribution of FMO. In addition, they influence the capability of these molecules to attach an additional electron, which was studied through adiabatic (AEA) and vertical electron affinities (VEA), as well as vertical detachment energy (VDE). To study electrophilic properties of these structures, local reactivity indices, such as Fukui ( f ⁺) and Parr ( P ⁺) functions, were calculated, and show the influence of the aromatic rings substituents on the reactivity of α,β-unsaturated ketones towards nucleophilic attack. This study has potential implications for the design of curcumin analogues based on a 4-piperidone core with desired reactivity.

SASS: A symmetry adapted stochastic search algorithm exploiting site symmetry

NASA Astrophysics Data System (ADS)

Wheeler, Steven E.; Schleyer, Paul v. R.; Schaefer, Henry F.

2007-03-01

A simple symmetry adapted search algorithm (SASS) exploiting point group symmetry increases the efficiency of systematic explorations of complex quantum mechanical potential energy surfaces. In contrast to previously described stochastic approaches, which do not employ symmetry, candidate structures are generated within simple point groups, such as C2, Cs, and C2v. This facilitates efficient sampling of the 3N-6 Pople's dimensional configuration space and increases the speed and effectiveness of quantum chemical geometry optimizations. Pople's concept of framework groups [J. Am. Chem. Soc. 102, 4615 (1980)] is used to partition the configuration space into structures spanning all possible distributions of sets of symmetry equivalent atoms. This provides an efficient means of computing all structures of a given symmetry with minimum redundancy. This approach also is advantageous for generating initial structures for global optimizations via genetic algorithm and other stochastic global search techniques. Application of the SASS method is illustrated by locating 14 low-lying stationary points on the cc-pwCVDZ ROCCSD(T) potential energy surface of Li5H2. The global minimum structure is identified, along with many unique, nonintuitive, energetically favorable isomers.

Structural and vibrational study of a neurotransmitter molecule: Dopamine [4-(2-aminoethyl) benzene-1,2-diol].

PubMed

Jha, Omkant; Yadav, T K; Yadav, R A

2018-01-15

Structural and vibrational studies for the most stable conformer of dopamine {4-(2-Aminoethyl) benzene-1, 2-diol} have been carried out at the DFT/B3LYP/6-311++G** level using the Gaussian 09 software. The IR and Raman spectra have been recorded and analyzed in light of the computed vibrational parameters using the DFT and the PEDs computed with the help of the GAR2PED software. Some of the fundamentals have considerably changed frequencies in going from benzene to dopamine. Except the rocking and wagging modes of the NH 2 group the other four modes are pure group modes. The rocking and wagging modes of the NH 2 group show mixing with the other modes. The two OH stretching vibrations are highly localized modes. The Kekule phenyl ring stretching mode is found to remain almost unchanged. The HOMO-LUMO study suggests the existence of charge transfer within the molecule and the energy gap supports the pharmacological active property of the dopamine molecule. The NBO analysis has been carried out to understand the proper and improper hydrogen bonding. Copyright © 2017. Published by Elsevier B.V.

Modulation of phase transition of thermosensitive liposomes with leucine zipper-structured lipopeptides.

PubMed

Xu, Xiejun; Xiao, Xingqing; Wang, Yiming; Xu, Shouhong; Liu, Honglai

2018-06-13

Targeted therapy for cancer requires thermosensitive components in drug carriers for controlled drug release against viral cells. The conformational transition characteristic of leucine zipper-structured lipopeptides is utilized in our lab to modulate the phase transition temperature of liposomes, thus achieving temperature-responsive control. In this study, we computationally examined the conformational transition behaviors of leucine zipper-structured lipopeptides that were modified at the N-terminus by distinct functional groups. The conformational transition temperatures of these lipopeptides were determined by structural analysis of the implicit-solvent replica exchange molecular dynamics simulation trajectories using the dihedral angle principal component analysis and the dictionary of protein secondary structure method. Our calculations revealed that the computed transition temperatures of the lipopeptides are in good agreement with the experimental measurements. The effect of hydrogen bonds on the conformational stability of the lipopeptide dimers was examined in conventional explicit-solvent molecular dynamics simulations. A quantitative correlation of the degree of structural dissociation of the dimers and their binding strength is well described by an exponential fit of the binding free energies to the conformation transition temperatures of the lipopeptides.

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures

PubMed Central

Manolakos, Elias S.

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub. PMID:26605332

Efficient Multicriteria Protein Structure Comparison on Modern Processor Architectures.

PubMed

Sharma, Anuj; Manolakos, Elias S

2015-01-01

Fast increasing computational demand for all-to-all protein structures comparison (PSC) is a result of three confounding factors: rapidly expanding structural proteomics databases, high computational complexity of pairwise protein comparison algorithms, and the trend in the domain towards using multiple criteria for protein structures comparison (MCPSC) and combining results. We have developed a software framework that exploits many-core and multicore CPUs to implement efficient parallel MCPSC in modern processors based on three popular PSC methods, namely, TMalign, CE, and USM. We evaluate and compare the performance and efficiency of the two parallel MCPSC implementations using Intel's experimental many-core Single-Chip Cloud Computer (SCC) as well as Intel's Core i7 multicore processor. We show that the 48-core SCC is more efficient than the latest generation Core i7, achieving a speedup factor of 42 (efficiency of 0.9), making many-core processors an exciting emerging technology for large-scale structural proteomics. We compare and contrast the performance of the two processors on several datasets and also show that MCPSC outperforms its component methods in grouping related domains, achieving a high F-measure of 0.91 on the benchmark CK34 dataset. The software implementation for protein structure comparison using the three methods and combined MCPSC, along with the developed underlying rckskel algorithmic skeletons library, is available via GitHub.

Theoretical study on the vibrational spectra of methoxy- and formyl-dihydroxy- trans-stilbenes and their hydrolytic equilibria

NASA Astrophysics Data System (ADS)

Molnár, Viktor; Billes, Ferenc; Tyihák, Ernő; Mikosch, Hans

2008-02-01

Compounds formed by exchanging one of the resveratrol hydroxy groups to methoxy or formyl groups are biologically important. Quantum chemical DFT calculations were applied for the simulation of some of their properties. Their optimized structures and charge distributions were computed. Based on the calculated vibrational force constants and optimized molecular structure infrared and Raman spectra were calculated. The characteristics of the vibrational modes were determined by normal coordinate analysis. Applying the calculated thermodynamic functions also for resveratrol, methanol, formaldehyde and water, thermodynamic equilibria were calculated for the equilibria between resveratrol and its methyl and formyl substituted derivatives, respectively.

The 'partial resonance' of the ring in the NLO crystal melaminium formate: study using vibrational spectra, DFT, HOMO-LUMO and MESP mapping.

PubMed

Binoy, J; Marchewka, M K; Jayakumar, V S

2013-03-01

The molecular geometry and vibrational spectral investigations of melaminium formate, a potential material known for toxicity and NLO activity, has been performed. The FT IR and FT Raman spectral investigations of melaminium formate is performed aided by the computed spectra of melaminium formate, triazine, melamine, melaminium and formate ion, along with bond orders and PED, computed using the density functional method (B3LYP) with 6-31G(d) basis set and XRD data, to reveal intermolecular interactions of amino groups with neighbor formula units in the crystal, intramolecular H⋯H repulsion of amino group hydrogen with protonating hydrogen, consequent loss of resonance in the melaminium ring, restriction of resonance to N(3)C(1)N(1) moiety leading to special type resonance of the ring and the resonance structure of CO(2) group of formate ion. The 3D matrix of hyperpolarizability tensor components has been computed to quantify NLO activity of melamine, melaminium and melaminium formate and the hyperpolarizability enhancement is analyzed using computed plots of HOMO and LUMO orbitals. A new mechanism of proton transfer responsible for NLO activity has been suggested, based on anomalous IR spectral bands in the high wavenumber region. The computed MEP contour maps have been used to analyze the interaction of melaminium and formate ions in the crystal. Copyright © 2012 Elsevier B.V. All rights reserved.

The `partial resonance' of the ring in the NLO crystal melaminium formate: Study using vibrational spectra, DFT, HOMO-LUMO and MESP mapping

NASA Astrophysics Data System (ADS)

Binoy, J.; Marchewka, M. K.; Jayakumar, V. S.

2013-03-01

The molecular geometry and vibrational spectral investigations of melaminium formate, a potential material known for toxicity and NLO activity, has been performed. The FT IR and FT Raman spectral investigations of melaminium formate is performed aided by the computed spectra of melaminium formate, triazine, melamine, melaminium and formate ion, along with bond orders and PED, computed using the density functional method (B3LYP) with 6-31G(d) basis set and XRD data, to reveal intermolecular interactions of amino groups with neighbor formula units in the crystal, intramolecular H⋯H repulsion of amino group hydrogen with protonating hydrogen, consequent loss of resonance in the melaminium ring, restriction of resonance to N3C1N1 moiety leading to special type resonance of the ring and the resonance structure of CO2 group of formate ion. The 3D matrix of hyperpolarizability tensor components has been computed to quantify NLO activity of melamine, melaminium and melaminium formate and the hyperpolarizability enhancement is analyzed using computed plots of HOMO and LUMO orbitals. A new mechanism of proton transfer responsible for NLO activity has been suggested, based on anomalous IR spectral bands in the high wavenumber region. The computed MEP contour maps have been used to analyze the interaction of melaminium and formate ions in the crystal.

Summary Report of Working Group 2: Computation

NASA Astrophysics Data System (ADS)

Stoltz, P. H.; Tsung, R. S.

2009-01-01

The working group on computation addressed three physics areas: (i) plasma-based accelerators (laser-driven and beam-driven), (ii) high gradient structure-based accelerators, and (iii) electron beam sources and transport [1]. Highlights of the talks in these areas included new models of breakdown on the microscopic scale, new three-dimensional multipacting calculations with both finite difference and finite element codes, and detailed comparisons of new electron gun models with standard models such as PARMELA. The group also addressed two areas of advances in computation: (i) new algorithms, including simulation in a Lorentz-boosted frame that can reduce computation time orders of magnitude, and (ii) new hardware architectures, like graphics processing units and Cell processors that promise dramatic increases in computing power. Highlights of the talks in these areas included results from the first large-scale parallel finite element particle-in-cell code (PIC), many order-of-magnitude speedup of, and details of porting the VPIC code to the Roadrunner supercomputer. The working group featured two plenary talks, one by Brian Albright of Los Alamos National Laboratory on the performance of the VPIC code on the Roadrunner supercomputer, and one by David Bruhwiler of Tech-X Corporation on recent advances in computation for advanced accelerators. Highlights of the talk by Albright included the first one trillion particle simulations, a sustained performance of 0.3 petaflops, and an eight times speedup of science calculations, including back-scatter in laser-plasma interaction. Highlights of the talk by Bruhwiler included simulations of 10 GeV accelerator laser wakefield stages including external injection, new developments in electromagnetic simulations of electron guns using finite difference and finite element approaches.

Summary Report of Working Group 2: Computation

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

Stoltz, P. H.; Tsung, R. S.

2009-01-22

The working group on computation addressed three physics areas: (i) plasma-based accelerators (laser-driven and beam-driven), (ii) high gradient structure-based accelerators, and (iii) electron beam sources and transport [1]. Highlights of the talks in these areas included new models of breakdown on the microscopic scale, new three-dimensional multipacting calculations with both finite difference and finite element codes, and detailed comparisons of new electron gun models with standard models such as PARMELA. The group also addressed two areas of advances in computation: (i) new algorithms, including simulation in a Lorentz-boosted frame that can reduce computation time orders of magnitude, and (ii) newmore » hardware architectures, like graphics processing units and Cell processors that promise dramatic increases in computing power. Highlights of the talks in these areas included results from the first large-scale parallel finite element particle-in-cell code (PIC), many order-of-magnitude speedup of, and details of porting the VPIC code to the Roadrunner supercomputer. The working group featured two plenary talks, one by Brian Albright of Los Alamos National Laboratory on the performance of the VPIC code on the Roadrunner supercomputer, and one by David Bruhwiler of Tech-X Corporation on recent advances in computation for advanced accelerators. Highlights of the talk by Albright included the first one trillion particle simulations, a sustained performance of 0.3 petaflops, and an eight times speedup of science calculations, including back-scatter in laser-plasma interaction. Highlights of the talk by Bruhwiler included simulations of 10 GeV accelerator laser wakefield stages including external injection, new developments in electromagnetic simulations of electron guns using finite difference and finite element approaches.« less

Studies of QCD structure in high-energy collisions

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

Nadolsky, Pavel M.

2016-06-26

”Studies of QCD structure in high-energy collisions” is a research project in theoretical particle physics at Southern Methodist University funded by US DOE Award DE-SC0013681. The award furnished bridge funding for one year (2015/04/15-2016/03/31) between the periods funded by Nadolsky’s DOE Early Career Research Award DE-SC0003870 (in 2010-2015) and a DOE grant DE-SC0010129 for SMU Department of Physics (starting in April 2016). The primary objective of the research is to provide theoretical predictions for Run-2 of the CERN Large Hadron Collider (LHC). The LHC physics program relies on state-of-the-art predictions in the field of quantum chromodynamics. The main effort ofmore » our group went into the global analysis of parton distribution functions (PDFs) employed by the bulk of LHC computations. Parton distributions describe internal structure of protons during ultrarelivistic collisions. A new generation of CTEQ parton distribution functions (PDFs), CT14, was released in summer 2015 and quickly adopted by the HEP community. The new CT14 parametrizations of PDFs were obtained using benchmarked NNLO calculations and latest data from LHC and Tevatron experiments. The group developed advanced methods for the PDF analysis and estimation of uncertainties in LHC predictions associated with the PDFs. We invented and refined a new ’meta-parametrization’ technique that streamlines usage of PDFs in Higgs boson production and other numerous LHC processes, by combining PDFs from various groups using multivariate stochastic sampling. In 2015, the PDF4LHC working group recommended to LHC experimental collaborations to use ’meta-parametrizations’ as a standard technique for computing PDF uncertainties. Finally, to include new QCD processes into the global fits, our group worked on several (N)NNLO calculations.« less

Interactive computer programs for the graphic analysis of nucleotide sequence data.

PubMed Central

Luckow, V A; Littlewood, R K; Rownd, R H

1984-01-01

A group of interactive computer programs have been developed which aid in the collection and graphical analysis of nucleotide and protein sequence data. The programs perform the following basic functions: a) enter, edit, list, and rearrange sequence data; b) permit automatic entry of nucleotide sequence data directly from an autoradiograph into the computer; c) search for restriction sites or other specified patterns and plot a linear or circular restriction map, or print their locations; d) plot base composition; e) analyze homology between sequences by plotting a two-dimensional graphic matrix; and f) aid in plotting predicted secondary structures of RNA molecules. PMID:6546437

Computational Design of Metal Ion Sequestering Agents

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

Hay, Benjamin P.; Rapko, Brian M.

Organic ligands that exhibit a high degree of metal ion recognition are essential precursors for developing separation processes and sensors for metal ions. Since the beginning of the nuclear era, much research has focused on discovering ligands that target specific radionuclides. Members of the Group 1A and 2A cations (e.g., Cs, Sr, Ra) and the f-block metals (actinides and lanthanides) are of primary concern to DOE. Although there has been some success in identifying ligand architectures that exhibit a degree of metal ion recognition, the ability to control binding affinity and selectivity remains a significant challenge. The traditional approach formore » discovering such ligands has involved lengthy programs of organic synthesis and testing that, in the absence of reliable methods for screening compounds before synthesis, have resulted in much wasted research effort. This project seeks to enhance and strengthen the traditional approach through computer-aided design of new and improved host molecules. Accurate electronic structure calculations are coupled with experimental data to provide fundamental information about ligand structure and the nature of metal-donor group interactions (design criteria). This fundamental information then is used in a molecular mechanics model (MM) that helps us rapidly screen proposed ligand architectures and select the best members from a set of potential candidates. By using combinatorial methods, molecule building software has been developed that generates large numbers of candidate architectures for a given set of donor groups. The specific goals of this project are: • further understand the structural and energetic aspects of individual donor group- metal ion interactions and incorporate this information within the MM framework • further develop and evaluate approaches for correlating ligand structure with reactivity toward metal ions, in other words, screening capability • use molecule structure building software to generate large numbers of candidate ligand architectures for given sets of donor groups • screen candidates and identify ligand architectures that will exhibit enhanced metal ion recognition. These new capabilities are being applied to ligand systems identified under other DOEsponsored projects where studies have suggested that modifying existing architectures will lead to dramatic enhancements in metal ion binding affinity and selectivity. With this in mind, we are collaborating with Professors R. T. Paine (University of New Mexico), K. N. Raymond (University of California, Berkeley), and J. E. Hutchison (University of Oregon), and Dr. B. A. Moyer (Oak Ridge National Laboratory) to obtain experimental validation of the predicted new ligand structures. Successful completion of this study will yield molecular-level insight into the role that ligand architecture plays in controlling metal ion complexation and will provide a computational approach to ligand design.« less

Zoaramine, a zoanthamine-like alkaloid with a new skeleton.

PubMed

Cen-Pacheco, Francisco; Norte, Manuel; Fernández, José J; Daranas, Antonio Hernández

2014-06-06

Chemical investigation of an Atlantic variety of Zoanthus sp. led to the isolation of two new metabolites, zoaramine and zoarenone. Their structures were deduced by the use of NMR spectroscopy and computational calculation of (1)H and (13)C chemical shifts. The core of these novel compounds resembles the structure of norzoanthamine alkaloids, and their isolation represents an important step toward a better understanding of the biogenetic origin of this group of antiosteoporotic molecules.

Computationally Driven Two-Dimensional Materials Design: What Is Next?

DOE PAGES

Pan, Jie; Lany, Stephan; Qi, Yue

2017-07-17

Two-dimensional (2D) materials offer many key advantages to innovative applications, such as spintronics and quantum information processing. Theoretical computations have accelerated 2D materials design. In this issue of ACS Nano, Kumar et al. report that ferromagnetism can be achieved in functionalized nitride MXene based on first-principles calculations. Their computational results shed light on a potentially vast group of materials for the realization of 2D magnets. In this Perspective, we briefly summarize the promising properties of 2D materials and the role theory has played in predicting these properties. Additionally, we discuss challenges and opportunities to boost the power of computation formore » the prediction of the 'structure-property-process (synthesizability)' relationship of 2D materials.« less

irGPU.proton.Net: Irregular strong charge interaction networks of protonatable groups in protein molecules--a GPU solver using the fast multipole method and statistical thermodynamics.

PubMed

Kantardjiev, Alexander A

2015-04-05

A cluster of strongly interacting ionization groups in protein molecules with irregular ionization behavior is suggestive for specific structure-function relationship. However, their computational treatment is unconventional (e.g., lack of convergence in naive self-consistent iterative algorithm). The stringent evaluation requires evaluation of Boltzmann averaged statistical mechanics sums and electrostatic energy estimation for each microstate. irGPU: Irregular strong interactions in proteins--a GPU solver is novel solution to a versatile problem in protein biophysics--atypical protonation behavior of coupled groups. The computational severity of the problem is alleviated by parallelization (via GPU kernels) which is applied for the electrostatic interaction evaluation (including explicit electrostatics via the fast multipole method) as well as statistical mechanics sums (partition function) estimation. Special attention is given to the ease of the service and encapsulation of theoretical details without sacrificing rigor of computational procedures. irGPU is not just a solution-in-principle but a promising practical application with potential to entice community into deeper understanding of principles governing biomolecule mechanisms. © 2015 Wiley Periodicals, Inc.

Spatial Guilds in the Serengeti Food Web Revealed by a Bayesian Group Model

PubMed Central

Baskerville, Edward B.; Dobson, Andy P.; Bedford, Trevor; Allesina, Stefano; Anderson, T. Michael; Pascual, Mercedes

2011-01-01

Food webs, networks of feeding relationships in an ecosystem, provide fundamental insights into mechanisms that determine ecosystem stability and persistence. A standard approach in food-web analysis, and network analysis in general, has been to identify compartments, or modules, defined by many links within compartments and few links between them. This approach can identify large habitat boundaries in the network but may fail to identify other important structures. Empirical analyses of food webs have been further limited by low-resolution data for primary producers. In this paper, we present a Bayesian computational method for identifying group structure using a flexible definition that can describe both functional trophic roles and standard compartments. We apply this method to a newly compiled plant-mammal food web from the Serengeti ecosystem that includes high taxonomic resolution at the plant level, allowing a simultaneous examination of the signature of both habitat and trophic roles in network structure. We find that groups at the plant level reflect habitat structure, coupled at higher trophic levels by groups of herbivores, which are in turn coupled by carnivore groups. Thus the group structure of the Serengeti web represents a mixture of trophic guild structure and spatial pattern, in contrast to the standard compartments typically identified. The network topology supports recent ideas on spatial coupling and energy channels in ecosystems that have been proposed as important for persistence. Furthermore, our Bayesian approach provides a powerful, flexible framework for the study of network structure, and we believe it will prove instrumental in a variety of biological contexts. PMID:22219719

High Performance Semantic Factoring of Giga-Scale Semantic Graph Databases

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

Joslyn, Cliff A.; Adolf, Robert D.; Al-Saffar, Sinan

2010-10-04

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors.« less

Dynamical networks of influence in small group discussions.

PubMed

Moussaïd, Mehdi; Noriega Campero, Alejandro; Almaatouq, Abdullah

2018-01-01

In many domains of life, business and management, numerous problems are addressed by small groups of individuals engaged in face-to-face discussions. While research in social psychology has a long history of studying the determinants of small group performances, the internal dynamics that govern a group discussion are not yet well understood. Here, we rely on computational methods based on network analyses and opinion dynamics to describe how individuals influence each other during a group discussion. We consider the situation in which a small group of three individuals engages in a discussion to solve an estimation task. We propose a model describing how group members gradually influence each other and revise their judgments over the course of the discussion. The main component of the model is an influence network-a weighted, directed graph that determines the extent to which individuals influence each other during the discussion. In simulations, we first study the optimal structure of the influence network that yields the best group performances. Then, we implement a social learning process by which individuals adapt to the past performance of their peers, thereby affecting the structure of the influence network in the long run. We explore the mechanisms underlying the emergence of efficient or maladaptive networks and show that the influence network can converge towards the optimal one, but only when individuals exhibit a social discounting bias by downgrading the relative performances of their peers. Finally, we find a late-speaker effect, whereby individuals who speak later in the discussion are perceived more positively in the long run and are thus more influential. The numerous predictions of the model can serve as a basis for future experiments, and this work opens research on small group discussion to computational social sciences.

Dynamical networks of influence in small group discussions

PubMed Central

Noriega Campero, Alejandro; Almaatouq, Abdullah

2018-01-01

In many domains of life, business and management, numerous problems are addressed by small groups of individuals engaged in face-to-face discussions. While research in social psychology has a long history of studying the determinants of small group performances, the internal dynamics that govern a group discussion are not yet well understood. Here, we rely on computational methods based on network analyses and opinion dynamics to describe how individuals influence each other during a group discussion. We consider the situation in which a small group of three individuals engages in a discussion to solve an estimation task. We propose a model describing how group members gradually influence each other and revise their judgments over the course of the discussion. The main component of the model is an influence network—a weighted, directed graph that determines the extent to which individuals influence each other during the discussion. In simulations, we first study the optimal structure of the influence network that yields the best group performances. Then, we implement a social learning process by which individuals adapt to the past performance of their peers, thereby affecting the structure of the influence network in the long run. We explore the mechanisms underlying the emergence of efficient or maladaptive networks and show that the influence network can converge towards the optimal one, but only when individuals exhibit a social discounting bias by downgrading the relative performances of their peers. Finally, we find a late-speaker effect, whereby individuals who speak later in the discussion are perceived more positively in the long run and are thus more influential. The numerous predictions of the model can serve as a basis for future experiments, and this work opens research on small group discussion to computational social sciences. PMID:29338013

LXtoo: an integrated live Linux distribution for the bioinformatics community

PubMed Central

2012-01-01

Background Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Findings Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. Conclusions LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo. PMID:22813356

LXtoo: an integrated live Linux distribution for the bioinformatics community.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Meng, Xiao-Hua; He, Qing-Yu

2012-07-19

Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.

PubMed

Takashima, S

2001-04-05

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.

A Group Intelligence-Based Asynchronous Argumentation Learning-Assistance Platform

ERIC Educational Resources Information Center

Huang, Chenn-Jung; Chang, Shun-Chih; Chen, Heng-Ming; Tseng, Jhe-Hao; Chien, Sheng-Yuan

2016-01-01

Structured argumentation support environments have been built and used in scientific discourse in the literature. However, to the best our knowledge, there is no research work in the literature examining whether student's knowledge has grown during learning activities with asynchronous argumentation. In this work, an intelligent computer-supported…

Understanding Phylogenies in Biology: The Influence of a Gestalt Perceptual Principle

ERIC Educational Resources Information Center

Novick, Laura R.; Catley, Kefyn M.

2007-01-01

Cladograms, hierarchical diagrams depicting evolutionary histories among (groups of) species, are commonly drawn in 2 informationally equivalent formats--tree and ladder. The authors hypothesize that these formats are not computationally equivalent because the Gestalt principle of good continuation obscures the hierarchical structure of ladders.…

Receptor Surface Models in the Classroom: Introducing Molecular Modeling to Students in a 3-D World

ERIC Educational Resources Information Center

Geldenhuys, Werner J.; Hayes, Michael; Van der Schyf, Cornelis J.; Allen, David D.; Malan, Sarel F.

2007-01-01

A simple, novel and generally applicable method to demonstrate structure-activity associations of a group of biologically interesting compounds in relation to receptor binding is described. This method is useful for undergraduates and graduate students in medicinal chemistry and computer modeling programs.

A Cloud Computing Approach to Personal Risk Management: The Open Hazards Group

NASA Astrophysics Data System (ADS)

Graves, W. R.; Holliday, J. R.; Rundle, J. B.

2010-12-01

According to the California Earthquake Authority, only about 12% of current California residences are covered by any form of earthquake insurance, down from about 30% in 1996 following the 1994, M6.7 Northridge earthquake. Part of the reason for this decreasing rate of insurance uptake is the high deductible, either 10% or 15% of the value of the structure, and the relatively high cost of the premiums, as much as thousands of dollars per year. The earthquake insurance industry is composed of the CEA, a public-private partnership; modeling companies that produce damage and loss models similar to the FEMA HAZUS model; and financial companies such as the insurance, reinsurance, and investment banking companies in New York, London, the Cayman Islands, Zurich, Dubai, Singapore, and elsewhere. In setting earthquake insurance rates, financial companies rely on models like HAZUS, that calculate on risk and exposure. In California, the process begins with an official earthquake forecast by the Working Group on California Earthquake Probabilities. Modeling companies use these 30 year earthquake probabilities as inputs to their attenuation and damage models to estimate the possible damage factors from scenario earthquakes. Economic loss is then estimated from processes such as structural failure, lost economic activity, demand surge, and fire following the earthquake. Once the potential losses are known, rates can be set so that a target ruin probability of less than 1% or so can be assured. Open Hazards Group was founded with the idea that the global public might be interested in a personal estimate of earthquake risk, computed using data supplied by the public, with models running in a cloud computing environment. These models process data from the ANSS catalog, updated at least daily, to produce rupture forecasts that are backtested with standard Reliability/Attributes and Receiver Operating Characteristic tests, among others. Models for attenuation and structural damage are then used in a computationally efficient workflow to produce real-time estimates of damage and loss for individual structures. All models are based on techniques that either have been published in the literature or will soon be published. Using these results, members of the public can gain an appreciation of their risk of exposure to damage from destructive earthquakes, information that has heretofore only been available to a few members of the financial and insurance industries.

Characteristics of middle and upper tropospheric clouds as deduced from rawinsonde data

NASA Technical Reports Server (NTRS)

Starr, D. D. O.; Cox, S. K.

1982-01-01

The static environment of middle and upper tropospheric clouds is characterized. Computed relative humidity with respect to ice is used to diagnose the presence of cloud layer. The deduced seasonal mean cloud cover estimates based on this technique are shown to be reasonable. The cases are stratified by season and pressure thickness, and the dry static stability, vertical wind speed shear, and Richardson number are computed for three layers for each case. Mean values for each parameter are presented for each stratification and layer. The relative frequency of occurrence of various structures is presented for each stratification. The observed values of each parameter and the observed structure of each parameter are quite variable. Structures corresponding to any of a number of different conceptual models may be found. Moist adiabatic conditions are not commonly observed and the stratification based on thickness yields substantially different results for each group.

Analysis of Harmonic Vibration of Cable-Stayed Footbridge under the Influence of Changes of the Cables Tension

NASA Astrophysics Data System (ADS)

Pakos, Wojciech

2015-09-01

The paper presents numerical analysis of harmonically excited vibration of a cable-stayed footbridge caused by a load function simulating crouching (squats) while changing the static tension in chosen cables. The intentional synchronized motion (e.g., squats) of a single person or group of persons on the footbridge with a frequency close to the natural frequency of the structure may lead to the resonant vibrations with large amplitudes. The appropriate tension changes in some cables cause detuning of resonance on account of stiffness changes of structures and hence detuning in the natural frequency that is close to the excitation frequency. The research was carried out on a 3D computer model of a real structure - a cable-stayed steel footbridge in Leśnica, a quarter of Wrocław, Poland, with the help of standard computer software based on FEM COSMOS/M System.

Simulation of the communication system between an AUV group and a surface station

NASA Astrophysics Data System (ADS)

Burtovaya, D.; Demin, A.; Demeshko, M.; Moiseev, A.; Kudryashova, A.

2017-01-01

An object model for simulation of the communications system of an autonomous underwater vehicles (AUV) group with a surface station is proposed in the paper. Implementation of the model is made on the basis of the software package “Object Distribution Simulation”. All structural relationships and behavior details are described. The application was developed on the basis of the proposed model and is now used for computational experiments on the simulation of the communications system between the autonomous underwater vehicles group and a surface station.

Effective-field renormalization-group method for Ising systems

NASA Astrophysics Data System (ADS)

Fittipaldi, I. P.; De Albuquerque, D. F.

1992-02-01

A new applicable effective-field renormalization-group (ERFG) scheme for computing critical properties of Ising spins systems is proposed and used to study the phase diagrams of a quenched bond-mixed spin Ising model on square and Kagomé lattices. The present EFRG approach yields results which improves substantially on those obtained from standard mean-field renormalization-group (MFRG) method. In particular, it is shown that the EFRG scheme correctly distinguishes the geometry of the lattice structure even when working with the smallest possible clusters, namely N'=1 and N=2.

The effect of degree of immersion upon learning performance in virtual reality simulations for medical education.

PubMed

Gutiérrez, Fátima; Pierce, Jennifer; Vergara, Víctor M; Coulter, Robert; Saland, Linda; Caudell, Thomas P; Goldsmith, Timothy E; Alverson, Dale C

2007-01-01

Simulations are being used in education and training to enhance understanding, improve performance, and assess competence. However, it is important to measure the performance of these simulations as learning and training tools. This study examined and compared knowledge acquisition using a knowledge structure design. The subjects were first-year medical students at The University of New Mexico School of Medicine. One group used a fully immersed virtual reality (VR) environment using a head mounted display (HMD) and another group used a partially immersed (computer screen) VR environment. The study aims were to determine whether there were significant differences between the two groups as measured by changes in knowledge structure before and after the VR simulation experience. The results showed that both groups benefited from the VR simulation training as measured by the significant increased similarity to the expert knowledge network after the training experience. However, the immersed group showed a significantly higher gain than the partially immersed group. This study demonstrated a positive effect of VR simulation on learning as reflected by improvements in knowledge structure but an enhanced effect of full-immersion using a HMD vs. a screen-based VR system.

Doping effect on the structural properties of Cu1-x(Ni, Zn, Al and Fe)xO samples (0

NASA Astrophysics Data System (ADS)

Amaral, J. B.; Araujo, R. M.; Pedra, P. P.; Meneses, C. T.; Duque, J. G. S.; dos S. Rezende, M. V.

2016-09-01

In this work, the effect of insertion of transition metal, TM (=Ni, Zn, Al and Fe), ions in Cu1-xTMxO samples (0

Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives

PubMed Central

Liu, Biao; Conroy, Jeffrey M.; Morrison, Carl D.; Odunsi, Adekunle O.; Qin, Maochun; Wei, Lei; Trump, Donald L.; Johnson, Candace S.; Liu, Song; Wang, Jianmin

2015-01-01

Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome. PMID:25849937

Programming new geometry restraints: Parallelity of atomic groups

DOE PAGES

Sobolev, Oleg V.; Afonine, Pavel V.; Adams, Paul D.; ...

2015-08-01

Improvements in structural biology methods, in particular crystallography and cryo-electron microscopy, have created an increased demand for the refinement of atomic models against low-resolution experimental data. One way to compensate for the lack of high-resolution experimental data is to use a priori information about model geometry that can be utilized in refinement in the form of stereochemical restraints or constraints. Here, the definition and calculation of the restraints that can be imposed on planar atomic groups, in particular the angle between such groups, are described. Detailed derivations of the restraint targets and their gradients are provided so that they canmore » be readily implemented in other contexts. Practical implementations of the restraints, and of associated data structures, in the Computational Crystallography Toolbox( cctbx) are presented.« less

Morphologic evaluation and classification of facial asymmetry using 3-dimensional computed tomography.

PubMed

Baek, Chaehwan; Paeng, Jun-Young; Lee, Janice S; Hong, Jongrak

2012-05-01

A systematic classification is needed for the diagnosis and surgical treatment of facial asymmetry. The purposes of this study were to analyze the skeletal structures of patients with facial asymmetry and to objectively classify these patients into groups according to these structural characteristics. Patients with facial asymmetry and recent computed tomographic images from 2005 through 2009 were included in this study, which was approved by the institutional review board. Linear measurements, angles, and reference planes on 3-dimensional computed tomograms were obtained, including maxillary (upper midline deviation, maxilla canting, and arch form discrepancy) and mandibular (menton deviation, gonion to midsagittal plane, ramus height, and frontal ramus inclination) measurements. All measurements were analyzed using paired t tests with Bonferroni correction followed by K-means cluster analysis using SPSS 13.0 to determine an objective classification of facial asymmetry in the enrolled patients. Kruskal-Wallis test was performed to verify differences among clustered groups. P < .05 was considered statistically significant. Forty-three patients (18 male, 25 female) were included in the study. They were classified into 4 groups based on cluster analysis. Their mean age was 24.3 ± 4.4 years. Group 1 included subjects (44% of patients) with asymmetry caused by a shift or lateralization of the mandibular body. Group 2 included subjects (39%) with a significant difference between the left and right ramus height with menton deviation to the short side. Group 3 included subjects (12%) with atypical asymmetry, including deviation of the menton to the short side, prominence of the angle/gonion on the larger side, and reverse maxillary canting. Group 4 included subjects (5%) with severe maxillary canting, ramus height differences, and menton deviation to the short side. In this study, patients with asymmetry were classified into 4 statistically distinct groups according to their anatomic features. This diagnostic classification method will assist in treatment planning for patients with facial asymmetry and may be used to explore the etiology of these variants of facial asymmetry. Copyright © 2012 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

Relativistic Few-Body Hadronic Physics Calculations

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

Polyzou, Wayne

2016-06-20

The goal of this research proposal was to use ``few-body'' methods to understand the structure and reactions of systems of interacting hadrons (neutrons, protons, mesons, quarks) over a broad range of energy scales. Realistic mathematical models of few-hadron systems have the advantage that they are sufficiently simple that they can be solved with mathematically controlled errors. These systems are also simple enough that it is possible to perform complete accurate experimental measurements on these systems. Comparison between theory and experiment puts strong constraints on the structure of the models. Even though these systems are ``simple'', both the experiments and computationsmore » push the limits of technology. The important property of ``few-body'' systems is that the ``cluster property'' implies that the interactions that appear in few-body systems are identical to the interactions that appear in complicated many-body systems. Of particular interest are models that correctly describe physics at distance scales that are sensitive to the internal structure of the individual nucleons. The Heisenberg uncertainty principle implies that in order to be sensitive to physics on distance scales that are a fraction of the proton or neutron radius, a relativistic treatment of quantum mechanics is necessary. The research supported by this grant involved 30 years of effort devoted to studying all aspects of interacting two and three-body systems. Realistic interactions were used to compute bound states of two- and three-nucleon, and two- and three-quark systems. Scattering observables for these systems were computed for a broad range of energies - from zero energy scattering to few GeV scattering, where experimental evidence of sub-nucleon degrees of freedom is beginning to appear. Benchmark calculations were produced, which when compared with calculations of other groups provided an essential check on these complicated calculations. In addition to computing bound state properties and scattering cross section, we also computed electron scattering cross sections in few-nucleon and few-quark systems, which are sensitive to the electric currents in these systems. We produced the definitive review on article on relativistic quantum mechanics, which and been used by many groups. In addition we developed and tested many computational techniques are used by other groups. Many of these techniques have applications in other areas of physics. The research benefited by collaborations with physicists from many different institutions and countries. It also involved working with seventeen undergraduate and graduate students.« less

Effects of Different Types of Cognitive Training on Cognitive Function, Brain Structure, and Driving Safety in Senior Daily Drivers: A Pilot Study.

PubMed

Nozawa, Takayuki; Taki, Yasuyuki; Kanno, Akitake; Akimoto, Yoritaka; Ihara, Mizuki; Yokoyama, Ryoichi; Kotozaki, Yuka; Nouchi, Rui; Sekiguchi, Atsushi; Takeuchi, Hikaru; Miyauchi, Carlos Makoto; Ogawa, Takeshi; Goto, Takakuni; Sunda, Takashi; Shimizu, Toshiyuki; Tozuka, Eiji; Hirose, Satoru; Nanbu, Tatsuyoshi; Kawashima, Ryuta

2015-01-01

Increasing proportion of the elderly in the driving population raises the importance of assuring their safety. We explored the effects of three different types of cognitive training on the cognitive function, brain structure, and driving safety of the elderly. Thirty-seven healthy elderly daily drivers were randomly assigned to one of three training groups: Group V trained in a vehicle with a newly developed onboard cognitive training program, Group P trained with a similar program but on a personal computer, and Group C trained to solve a crossword puzzle. Before and after the 8-week training period, they underwent neuropsychological tests, structural brain magnetic resonance imaging, and driving safety tests. For cognitive function, only Group V showed significant improvements in processing speed and working memory. For driving safety, Group V showed significant improvements both in the driving aptitude test and in the on-road evaluations. Group P showed no significant improvements in either test, and Group C showed significant improvements in the driving aptitude but not in the on-road evaluations. The results support the effectiveness of the onboard training program in enhancing the elderly's abilities to drive safely and the potential advantages of a multimodal training approach.

Effects of Different Types of Cognitive Training on Cognitive Function, Brain Structure, and Driving Safety in Senior Daily Drivers: A Pilot Study

PubMed Central

Taki, Yasuyuki; Kanno, Akitake; Akimoto, Yoritaka; Ihara, Mizuki; Yokoyama, Ryoichi; Kotozaki, Yuka; Sekiguchi, Atsushi; Takeuchi, Hikaru; Miyauchi, Carlos Makoto; Ogawa, Takeshi; Goto, Takakuni; Sunda, Takashi; Shimizu, Toshiyuki; Tozuka, Eiji; Hirose, Satoru; Nanbu, Tatsuyoshi; Kawashima, Ryuta

2015-01-01

Background. Increasing proportion of the elderly in the driving population raises the importance of assuring their safety. We explored the effects of three different types of cognitive training on the cognitive function, brain structure, and driving safety of the elderly. Methods. Thirty-seven healthy elderly daily drivers were randomly assigned to one of three training groups: Group V trained in a vehicle with a newly developed onboard cognitive training program, Group P trained with a similar program but on a personal computer, and Group C trained to solve a crossword puzzle. Before and after the 8-week training period, they underwent neuropsychological tests, structural brain magnetic resonance imaging, and driving safety tests. Results. For cognitive function, only Group V showed significant improvements in processing speed and working memory. For driving safety, Group V showed significant improvements both in the driving aptitude test and in the on-road evaluations. Group P showed no significant improvements in either test, and Group C showed significant improvements in the driving aptitude but not in the on-road evaluations. Conclusion. The results support the effectiveness of the onboard training program in enhancing the elderly's abilities to drive safely and the potential advantages of a multimodal training approach. PMID:26161000

Comparison of traditional methods with 3D computer models in the instruction of hepatobiliary anatomy.

PubMed

Keedy, Alexander W; Durack, Jeremy C; Sandhu, Parmbir; Chen, Eric M; O'Sullivan, Patricia S; Breiman, Richard S

2011-01-01

This study was designed to determine whether an interactive three-dimensional presentation depicting liver and biliary anatomy is more effective for teaching medical students than a traditional textbook format presentation of the same material. Forty-six medical students volunteered for participation in this study. Baseline demographic information, spatial ability, and knowledge of relevant anatomy were measured. Participants were randomized into two groups and presented with a computer-based interactive learning module comprised of animations and still images to highlight various anatomical structures (3D group), or a computer-based text document containing the same images and text without animation or interactive features (2D group). Following each teaching module, students completed a satisfaction survey and nine-item anatomic knowledge post-test. The 3D group scored higher on the post-test than the 2D group, with a mean score of 74% and 64%, respectively; however, when baseline differences in pretest scores were accounted for, this difference was not statistically significant (P = 0.33). Spatial ability did not statistically significantly correlate with post-test scores for the 3D group or the 2D group. In the post-test satisfaction survey the 3D group expressed a statistically significantly higher overall satisfaction rating compared to students in the 2D control group (4.5 versus 3.7 out of 5, P = 0.02). While the interactive 3D multimedia module received higher satisfaction ratings from students, it neither enhanced nor inhibited learning of complex hepatobiliary anatomy compared to an informationally equivalent traditional textbook style approach. . Copyright © 2011 American Association of Anatomists.

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.

Optical properties of boron-group (V) hexagonal nanowires: DFT investigation

NASA Astrophysics Data System (ADS)

Santhibhushan, B.; Soni, Mahesh; Srivastava, Anurag

2017-07-01

The paper presents structural, electronic and optical properties of boron-group V hexagonal nanowires (h-NW) within the framework of density functional theory. The h-NW of boron-group V compounds with an analogous diameter of 12 Å have been designed in (1 1 1) plane. Stability analysis performed through formation energies reveal that, the stability of these structures decreases with increasing atomic number of the group V element. The band nature predicts that these nanowires are good electrical conductors. Optical behaviour of the nanowires has been analysed through absorption coefficient, reflectivity, refractive index, optical conductivity and electron energy loss spectrum (EELS), that are computed from the frequency-dependent complex dielectric function. The analysis reveals high reactivity of BP and BAs h-NWs to the incident light especially in the IR and visible ranges, and the optical transparency of BN h-NW in the visible and UV ranges.

Structural Isosteres of Phosphate Groups in the Protein Data Bank.

PubMed

Zhang, Yuezhou; Borrel, Alexandre; Ghemtio, Leo; Regad, Leslie; Boije Af Gennäs, Gustav; Camproux, Anne-Claude; Yli-Kauhaluoma, Jari; Xhaard, Henri

2017-03-27

We developed a computational workflow to mine the Protein Data Bank for isosteric replacements that exist in different binding site environments but have not necessarily been identified and exploited in compound design. Taking phosphate groups as examples, the workflow was used to construct 157 data sets, each composed of a reference protein complexed with AMP, ADP, ATP, or pyrophosphate as well other ligands. Phosphate binding sites appear to have a high hydration content and large size, resulting in U-shaped bioactive conformations recurrently found across unrelated protein families. A total of 16 413 replacements were extracted, filtered for a significant structural overlap on phosphate groups, and sorted according to their SMILES codes. In addition to the classical isosteres of phosphate, such as carboxylate, sulfone, or sulfonamide, unexpected replacements that do not conserve charge or polarity, such as aryl, aliphatic, or positively charged groups, were found.

Proposed Use of the Computer as a Tool to Aid Analysis of Properties of Materials in Fixators of Spine

PubMed Central

Santos, Antonio; Moreira, Fernando

2014-01-01

With objective of analyzing the mechanical behavior of the internal fixators of spine and of the bony structure, the pieces and the group were made (it structures bony x internal fixator) with the aid a software of solid modeling. The materials used in the rehearsals had been the titanium, now in the market and a castor oil polyurethane destined to the development of you implant bony. PMID:24825938

Computation and brain processes, with special reference to neuroendocrine systems.

PubMed

Toni, Roberto; Spaletta, Giulia; Casa, Claudia Della; Ravera, Simone; Sandri, Giorgio

2007-01-01

The development of neural networks and brain automata has made neuroscientists aware that the performance limits of these brain-like devices lies, at least in part, in their computational power. The computational basis of a. standard cybernetic design, in fact, refers to that of a discrete and finite state machine or Turing Machine (TM). In contrast, it has been suggested that a number of human cerebral activites, from feedback controls up to mental processes, rely on a mixing of both finitary, digital-like and infinitary, continuous-like procedures. Therefore, the central nervous system (CNS) of man would exploit a form of computation going beyond that of a TM. This "non conventional" computation has been called hybrid computation. Some basic structures for hybrid brain computation are believed to be the brain computational maps, in which both Turing-like (digital) computation and continuous (analog) forms of calculus might occur. The cerebral cortex and brain stem appears primary candidate for this processing. However, also neuroendocrine structures like the hypothalamus are believed to exhibit hybrid computional processes, and might give rise to computational maps. Current theories on neural activity, including wiring and volume transmission, neuronal group selection and dynamic evolving models of brain automata, bring fuel to the existence of natural hybrid computation, stressing a cooperation between discrete and continuous forms of communication in the CNS. In addition, the recent advent of neuromorphic chips, like those to restore activity in damaged retina and visual cortex, suggests that assumption of a discrete-continuum polarity in designing biocompatible neural circuitries is crucial for their ensuing performance. In these bionic structures, in fact, a correspondence exists between the original anatomical architecture and synthetic wiring of the chip, resulting in a correspondence between natural and cybernetic neural activity. Thus, chip "form" provides a continuum essential to chip "function". We conclude that it is reasonable to predict the existence of hybrid computational processes in the course of many human, brain integrating activities, urging development of cybernetic approaches based on this modelling for adequate reproduction of a variety of cerebral performances.

One-dimensional super Calabi-Yau manifolds and their mirrors

NASA Astrophysics Data System (ADS)

Noja, S.; Cacciatori, S. L.; Piazza, F. Dalla; Marrani, A.; Re, R.

2017-04-01

We apply a definition of generalised super Calabi-Yau variety (SCY) to supermanifolds of complex dimension one. One of our results is that there are two SCY's having reduced manifold equal to P^1, namely the projective super space P^{.1|2} and the weighted projective super space W{P}_{(2)}^{.1|1} . Then we compute the corresponding sheaf cohomology of superforms, showing that the cohomology with picture number one is infinite dimensional, while the de Rham cohomology, which is what matters from a physical point of view, remains finite dimensional. Moreover, we provide the complete real and holomorphic de Rham cohomology for generic projective super spaces {P}^{.n|m} . We also determine the automorphism groups: these always match the dimension of the projective super group with the only exception of {P}^{.1|2} , whose automorphism group turns out to be larger than the projective super group. By considering the cohomology of the super tangent sheaf, we compute the deformations of {P}^{.1|m} , discovering that the presence of a fermionic structure allows for deformations even if the reduced manifold is rigid. Finally, we show that {P}^{.1|2} is self-mirror, whereas W{P}_{(2)}^{.1|1} has a zero dimensional mirror. Also, the mirror map for {P}^{.1|2} naturally endows it with a structure of N = 2 super Riemann surface.

Molecular Simulations of Carbohydrates with a Fucose-Binding Burkholderia ambifaria Lectin Suggest Modulation by Surface Residues Outside the Fucose-Binding Pocket

PubMed Central

Dingjan, Tamir; Imberty, Anne; Pérez, Serge; Yuriev, Elizabeth; Ramsland, Paul A.

2017-01-01

Burkholderia ambifaria is an opportunistic respiratory pathogen belonging to the Burkholderia cepacia complex, a collection of species responsible for the rapidly fatal cepacia syndrome in cystic fibrosis patients. A fucose-binding lectin identified in the B. ambifaria genome, BambL, is able to adhere to lung tissue, and may play a role in respiratory infection. X-ray crystallography has revealed the bound complex structures for four fucosylated human blood group epitopes (blood group B, H type 1, H type 2, and Lex determinants). The present study employed computational approaches, including docking and molecular dynamics (MD), to extend the structural analysis of BambL-oligosaccharide complexes to include four additional blood group saccharides (A, Lea, Leb, and Ley) and a library of blood-group-related carbohydrates. Carbohydrate recognition is dominated by interactions with fucose via a hydrogen-bonding network involving Arg15, Glu26, Ala38, and Trp79 and a stacking interaction with Trp74. Additional hydrogen bonds to non-fucose residues are formed with Asp30, Tyr35, Thr36, and Trp74. BambL recognition is dominated by interactions with fucose, but also features interactions with other parts of the ligands that may modulate specificity or affinity. The detailed computational characterization of the BambL carbohydrate-binding site provides guidelines for the future design of lectin inhibitors. PMID:28680402

Changes in bone macro- and microstructure in diabetic obese mice revealed by high resolution microfocus X-ray computed tomography

PubMed Central

Kerckhofs, G.; Durand, M.; Vangoitsenhoven, R.; Marin, C.; Van der Schueren, B.; Carmeliet, G.; Luyten, F. P.; Geris, L.; Vandamme, K.

2016-01-01

High resolution microfocus X-ray computed tomography (HR-microCT) was employed to characterize the structural alterations of the cortical and trabecular bone in a mouse model of obesity-driven type 2 diabetes (T2DM). C57Bl/6J mice were randomly assigned for 14 weeks to either a control diet-fed (CTRL) or a high fat diet (HFD)-fed group developing obesity, hyperglycaemia and insulin resistance. The HFD group showed an increased trabecular thickness and a decreased trabecular number compared to CTRL animals. Midshaft tibia intracortical porosity was assessed at two spatial image resolutions. At 2 μm scale, no change was observed in the intracortical structure. At 1 μm scale, a decrease in the cortical vascular porosity of the HFD bone was evidenced. The study of a group of 8 week old animals corresponding to animals at the start of the diet challenge revealed that the decreased vascular porosity was T2DM-dependant and not related to the ageing process. Our results offer an unprecedented ultra-characterization of the T2DM compromised skeletal micro-architecture and highlight an unrevealed T2DM-related decrease in the cortical vascular porosity, potentially affecting the bone health and fragility. Additionally, it provides some insights into the technical challenge facing the assessment of the rodent bone structure using HR-microCT imaging. PMID:27759061

A modification in the technique of computing average lengths from the scales of fishes

USGS Publications Warehouse

Van Oosten, John

1953-01-01

In virtually all the studies that employ scales, otollths, or bony structures to obtain the growth history of fishes, it has been the custom to compute lengths for each individual fish and from these data obtain the average growth rates for any particular group. This method involves a considerable amount of mathematical manipulation, time, and effort. Theoretically it should be possible to obtain the same information simply by averaging the scale measurements for each year of life and the length of the fish employed and computing the average lengths from these data. This method would eliminate all calculations for individual fish. Although Van Oosten (1929: 338) pointed out many years ago the validity of this method of computation, his statements apparently have been overlooked by subsequent investigators.

Sublaminate- or ply-level analysis of composites and strain energy release rates of end-notch and mixed-mode fracture specimens

NASA Technical Reports Server (NTRS)

Valisetty, Rao R.; Chamis, Christos C.

1988-01-01

The sublaminate or ply-level analysis of composite structures is presently undertaken by a computational procedure yielding the stresses in regions affected by delaminations, transverse cracks, and discontinuities that are related to material properties, geometries, and loads. Attention is given to layers or groups of layers that are immediately affected by flaws; these are analyzed as if they were homogeneous bodies in equilibrium, in isolation from the rest of the laminate. Computed stresses agree with those from a three-dimensional FEM analysis.

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.

MODY - calculation of ordered structures by symmetry-adapted functions

NASA Astrophysics Data System (ADS)

Białas, Franciszek; Pytlik, Lucjan; Sikora, Wiesława

2016-01-01

In this paper we focus on the new version of computer program MODY for calculations of symmetryadapted functions based on the theory of groups and representations. The choice of such a functional frame of coordinates for description of ordered structures leads to a minimal number of parameters which must be used for presentation of such structures and investigations of their properties. The aim of this work is to find those parameters, which are coefficients of a linear combination of calculated functions, leading to construction of different types of structure ordering with a given symmetry. A spreadsheet script for simplification of this work has been created and attached to the program.

Waves in a plane graphene - dielectric waveguide structure

NASA Astrophysics Data System (ADS)

Evseev, Dmitry A.; Eliseeva, Svetlana V.; Sementsov, Dmitry I.

2017-10-01

The features of the guided TE modes propagation have been investigated on the basis of computer simulations in a planar structure consisting of a set of alternating layers of dielectric and graphene. Within the framework of the effective medium approximation, the dispersion relations have been received for symmetric and antisymmetric waveguide modes, determined by the frequency range of their existence. The wave field distribution by structure, frequency dependences of the constants of propagation and transverse components of the wave vectors, as well as group and phase velocities of waveguide modes have been obtained, the effect of the graphene part in a structure on the waveguide mode behavior has been shown.

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Microstructures and properties of cancellous bone of avascular necrosis of femoral heads

NASA Astrophysics Data System (ADS)

Yao, Xuefeng; Wang, Peng; Dai, Ruchun; Yeh, Hsien Yang

2010-03-01

The aim of this study is to investigate microscopic structure and characterize cancellous bone of avascular necrosis of the femoral head (ANFH). The rabbit model of the ANFH is established. The histopathologic features are studied successfully. The differences between the steroid-injection group (S.G.) and the controlled group (C.G.) are examined, including the weight of rabbits, the hematological examination and the three-dimensional structures. It is found that the plasma levels of cholesterol (CHO), high-density lipoprotein (HDL) and low-density lipoprotein (LDL) in S.G. are lower than those in C.G. when the triglyceride (TG) increased in the S.G.; but the bone mineral content (BMC) and the structural model index (SMI) of the organ and tissue decreased significantly in S.G. Three-dimensional structures of the femoral head are obtained using micro-computed tomography (CT) scanning and the mechanical model is established to analyze the influences of these structural changes on the mechanical properties of the cancellous bone.

Future networking and cooperation summary of discussion

Treesearch

Roger R. Bay

1993-01-01

At the end of the workshop, I led a lightly structured and informal discussion concerning methods of continuing and improving communications and cooperation among workshop participants. The group specifically ad-dressed three areas: maintaining informal one-on-one direct contacts, improving the use of the ADAP computer system for mail, and the desirability of starting...

SPAR reference manual

NASA Technical Reports Server (NTRS)

Whetstone, W. D.

1976-01-01

The functions and operating rules of the SPAR system, which is a group of computer programs used primarily to perform stress, buckling, and vibrational analyses of linear finite element systems, were given. The following subject areas were discussed: basic information, structure definition, format system matrix processors, utility programs, static solutions, stresses, sparse matrix eigensolver, dynamic response, graphics, and substructure processors.

Computer-Based Learning: Graphical Integration of Whole and Sectional Neuroanatomy Improves Long-Term Retention

ERIC Educational Resources Information Center

Naaz, Farah; Chariker, Julia H.; Pani, John R.

2014-01-01

A study was conducted to test the hypothesis that instruction with graphically integrated representations of whole and sectional neuroanatomy is especially effective for learning to recognize neural structures in sectional imagery (such as magnetic resonance imaging [MRI]). Neuroanatomy was taught to two groups of participants using computer…

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Segmentations of the cartilaginous skeletons of chondrichthyan fishes by the use of state-of-the-art computed tomography

PubMed Central

McQuiston, Andrew D; Crawford, Callie; Schoepf, U Joseph; Varga-Szemes, Akos; Canstein, Christian; Renker, Matthias; De Cecco, Carlo N; Baumann, Stefan; Naylor, Gavin J P

2017-01-01

AIM To apply dual-source multidetector computed tomography (DSCT) scanning technology in conjunction with computationally assisted segmentation in order to explore and document skeletal variation that has occurred over the course of evolution. METHODS We examined 4 divergent species of elasmobranchs with high-resolution 3rd generation DSCT. The formalin prepared species examined were: Aptychotrema vincentiana, Mitsukurina owstoni, Negaprion brevirostris and Dactylobatus armatus. RESULTS All three structures of the hyoid arch (hyomandibular, ceratohyal, and basihyal) were clearly visible whereas in the two batoids, the hyomandibular was the prominent feature, the ceratohyal was not visible and the basihyal was more reduced and closer to the gill arches. The general shape of the puboischiadic bar, or pelvic girdle, illustrated a closer relationship between the two sharks and the two batoids than between the two groups. CONCLUSION In exquisite detail, DSCT imaging revealed important morphological variations in various common structures in the four elasmobranch specimens studied, providing insights into their evolutionary diversification. PMID:28529682

Molecular Structure and Free Energy Landscape for Electron Transport in the Deca-Heme Cytochrome MtrF

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

Breuer, Marian; Zarzycki, Piotr P.; Shi, Liang

2012-12-01

The free energy profile for electron flow through the bacterial deca-heme cytochrome MtrF has been computed using thermodynamic integration and classical molecular dynamics. The extensive calculations on two versions of the structure help validate the method and results, because differences in the profiles can be related to differences in the charged amino acids local to specific heme groups. First estimates of reorganization free energies λ yield a range consistent with expectations for partially solvent exposed cofactors, and reveal an activation energy range surmountable for electron flow. Future work will aim at increasing the accuracy of λ with polarizable force fieldmore » dynamics and quantum chemical energy gap calculations, as well as quantum chemical computation of electronic coupling matrix elements.« less

High performance semantic factoring of giga-scale semantic graph databases.

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

al-Saffar, Sinan; Adolf, Bob; Haglin, David

2010-10-01

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors, including basic properties, connected components, namespace interaction, and typed paths.« less

Inequality measures perform differently in global and local assessments: An exploratory computational experiment

NASA Astrophysics Data System (ADS)

Chiang, Yen-Sheng

2015-11-01

Inequality measures are widely used in both the academia and public media to help us understand how incomes and wealth are distributed. They can be used to assess the distribution of a whole society-global inequality-as well as inequality of actors' referent networks-local inequality. How different is local inequality from global inequality? Formalizing the structure of reference groups as a network, the paper conducted a computational experiment to see how the structure of complex networks influences the difference between global and local inequality assessed by a selection of inequality measures. It was found that local inequality tends to be higher than global inequality when population size is large; network is dense and heterophilously assorted, and income distribution is less dispersed. The implications of the simulation findings are discussed.

Computational structural mechanics engine structures computational simulator

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The Computational Structural Mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures.

Spectroscopic and first principles investigation on 4-[(4-pyridinylmethylene)amino]-benzoic acid bearing pyridyl and carboxyl anchoring groups

NASA Astrophysics Data System (ADS)

Zhang, Lei; Wang, Qiaoyi

2018-03-01

We report a combined experimental and computational investigation on the structure and photophysics of 4-[(4-pyridinylmethylene)amino]-benzoic acid, a functional molecule bearing two anchoring groups for attachment onto a TiO2 surface and perovskite surface, for potential solar cell application. This molecule possesses interesting adsorption properties in perovskite solar cell because the pyridyl group serves as the Lewis base and targets Lewis acidic sites in the perovskite surface, while the carboxyl group targets TiO2 surface, improving the coupling between the perovskite surface and the TiO2 surface. The electronic structures of the molecule and its photochemistry are revealed by the UV-vis absorption spectra and the fluorescence spectra under visible light irradiation, which are combined with density functional theory (DFT) and time-dependent density functional theory (TDDFT) analysis. Considering the bi-anchoring groups and the conjugated π system embedded in the molecule, we anticipate it can molecular engineer the TiO2/perovskite interface in perovskite solar cell.

Computational Aeroacoustics: An Overview

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.

2003-01-01

An overview of recent advances in computational aeroacoustics (CAA) is presented. CAA algorithms must not be dispersive and dissipative. It should propagate waves supported by the Euler equations with the correct group velocities. Computation domains are inevitably finite in size. To avoid the reflection of acoustic and other outgoing waves at the boundaries of the computation domain, it is required that special boundary conditions be imposed at the boundary region. These boundary conditions either absorb all the outgoing waves without reflection or allow the waves to exit smoothly. High-order schemes, invariably, supports spurious short waves. These spurious waves tend to pollute the numerical solution. They must be selectively damped or filtered out. All these issues and relevant computation methods are briefly reviewed. Jet screech tones are known to have caused structural fatigue in military combat aircrafts. Numerical simulation of the jet screech phenomenon is presented as an example of a successful application of CAA.

Social Network Theory in Engineering Education

NASA Astrophysics Data System (ADS)

Simon, Peter A.

Collaborative groups are important both in the learning environment of engineering education and, in the real world, the business of engineering design. Selecting appropriate individuals to form an effective group and monitoring a group's progress are important aspects of successful task performance. This exploratory study looked at using the concepts of cognitive social structures, structural balance, and centrality from social network analysis as well as the measures of emotional intelligence. The concepts were used to analyze potential team members to examine if an individual's ability to perceive emotion in others and the self and to use, understand, and manage those emotions are a factor in a group's performance. The students from a capstone design course in computer engineering were used as volunteer subjects. They were formed into groups and assigned a design exercise to determine whether and which of the above-mentioned tools would be effective in both selecting teams and predicting the quality of the resultant design. The results were inconclusive with the exception of an individual's ability to accurately perceive emotions. The instruments that were successful were the Self-Monitoring scale and the accuracy scores derived from cognitive social structures and Level IV of network levels of analysis.

The collaboration of grouping laws in vision.

PubMed

Grompone von Gioi, Rafael; Delon, Julie; Morel, Jean-Michel

2012-01-01

Gestalt theory gives a list of geometric grouping laws that could in principle give a complete account of human image perception. Based on an extensive thesaurus of clever graphical images, this theory discusses how grouping laws collaborate, and conflict toward a global image understanding. Unfortunately, as shown in the bibliographical analysis herewith, the attempts to formalize the grouping laws in computer vision and psychophysics have at best succeeded to compute individual partial structures (or partial gestalts), such as alignments or symmetries. Nevertheless, we show here that a never formalized clever Gestalt experimental procedure, the Nachzeichnung suggests a numerical set up to implement and test the collaboration of partial gestalts. The new computational procedure proposed here analyzes a digital image, and performs a numerical simulation that we call Nachtanz or Gestaltic dance. In this dance, the analyzed digital image is gradually deformed in a random way, but maintaining the detected partial gestalts. The resulting dancing images should be perceptually indistinguishable if and only if the grouping process was complete. Like the Nachzeichnung, the Nachtanz permits a visual exploration of the degrees of freedom still available to a figure after all partial groups (or gestalts) have been detected. In the new proposed procedure, instead of drawing themselves, subjects will be shown samples of the automatic Gestalt dances and required to evaluate if the figures are similar. Several numerical preliminary results with this new Gestaltic experimental setup are thoroughly discussed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Link failure detection in a parallel computer

DOEpatents

Archer, Charles J.; Blocksome, Michael A.; Megerian, Mark G.; Smith, Brian E.

2010-11-09

Methods, apparatus, and products are disclosed for link failure detection in a parallel computer including compute nodes connected in a rectangular mesh network, each pair of adjacent compute nodes in the rectangular mesh network connected together using a pair of links, that includes: assigning each compute node to either a first group or a second group such that adjacent compute nodes in the rectangular mesh network are assigned to different groups; sending, by each of the compute nodes assigned to the first group, a first test message to each adjacent compute node assigned to the second group; determining, by each of the compute nodes assigned to the second group, whether the first test message was received from each adjacent compute node assigned to the first group; and notifying a user, by each of the compute nodes assigned to the second group, whether the first test message was received.

Robust peptide bundles designed computationally

NASA Astrophysics Data System (ADS)

Haider, Michael; Zhang, Huixi Violet; Kiick, Kristi; Saven, Jeffery; Pochan, Darrin

Peptides are ideal candidates for the design and controlled assembly of nanoscale materials due to their potential to assemble with atomistic precision as in biological systems. Unlike other work utilizing natural proteins and structural motifs, this effort is completely de novo in order to build arbitrary structures with desired size for the specific placement and separation of functional groups. We have successfully computationally designed soluble, coiled coil, peptide, tetramer bundles which are robust and stable. Using circular dichroism we demonstrated the thermal stability of these bundles as well as confirmed their alpha helical and coiled coil nature. The stability of these bundles arises from the computational design of the coiled coil interior core residues. The coiled coil tetramer was confirmed to be the dominant species by analytical ultra-centrifugation sedimentation studies. We also established how these bundles behave in solution using small angle neutron scattering. The form factor of the bundles is well represented by a cylinder model and their behavior at high concentrations is modeled using a structure factor for aggregates of the cylinders. All of these experiments support our claim that the designed coiled coil bundles were achieved in solution. NSF DMREF 1234161.

Synthesis, spectroscopic and computational characterization of the tautomerism of pyrazoline derivatives from chalcones

NASA Astrophysics Data System (ADS)

Miguel, Fábio Balbino; Dantas, Juliana Arantes; Amorim, Stefany; Andrade, Gustavo F. S.; Costa, Luiz Antônio Sodré; Couri, Mara Rubia Costa

2016-01-01

In the present study a series of novel pyrazolines derivatives has been synthesized, and their structures assigned on the basis of FT-Raman, 1H and 13C NMR spectral data and computational DFT calculations. A joint computational study using B3LYP/6-311G(2d,2p) density functional theory and FT-Raman investigation on the tautomerism of 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carbothioamide and 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carboxamide are presented. The structures were characterized as a minimum in the potential energy surface using DFT. The calculated Raman and NMR spectra were of such remarkable agreement to the experimental results that the equilibrium between tautomeric forms has been discussed in detail. Our study suggests the existence of tautomers, the carboxamide/carbothioamide group may tautomerize, in the solid state or in solution. Thermodynamic data calculated suggests that the R(Cdbnd S)NH2 and R(Cdbnd O)NH2 species are more stable than the R(Cdbnd NH)SH and R(Cdbnd NH)OH species. Additionally, results found for the 1H NMR shifting, pointed out to which structure is present.

Structural analysis of natural textures.

PubMed

Vilnrotter, F M; Nevatia, R; Price, K E

1986-01-01

Many textures can be described structurally, in terms of the individual textural elements and their spatial relationships. This paper describes a system to generate useful descriptions of natural textures in these terms. The basic approach is to determine an initial, partial description of the elements using edge features. This description controls the extraction of the texture elements. The elements are grouped by type, and spatial relationships between elements are computed. The descriptions are shown to be useful for recognition of the textures, and for reconstruction of periodic textures.

Structure, bonding, and reactivity of reactant complexes and key intermediates.

PubMed

Soriano, Elena; Marco-Contelles, José

2011-01-01

Complexes of Pt and Au (gold(III) and cationic gold(I)) have shown an exceptional ability to promote a variety of organic transformations of unsaturated precursors due to their peculiar Lewis acid properties: the alkynophilic character of these soft metals and the π-acid activation of unsaturated groups promotes the intra- or intermolecular attack of a nucleophile. In this chapter we summarize the computational data reported on the structure, bonding, and reactivity of the reactant π-complexes and also on the key intermediate species.

Image/video understanding systems based on network-symbolic models

NASA Astrophysics Data System (ADS)

Kuvich, Gary

2004-03-01

Vision is a part of a larger information system that converts visual information into knowledge structures. These structures drive vision process, resolve ambiguity and uncertainty via feedback projections, and provide image understanding that is an interpretation of visual information in terms of such knowledge models. Computer simulation models are built on the basis of graphs/networks. The ability of human brain to emulate similar graph/network models is found. Symbols, predicates and grammars naturally emerge in such networks, and logic is simply a way of restructuring such models. Brain analyzes an image as a graph-type relational structure created via multilevel hierarchical compression of visual information. Primary areas provide active fusion of image features on a spatial grid-like structure, where nodes are cortical columns. Spatial logic and topology naturally present in such structures. Mid-level vision processes like perceptual grouping, separation of figure from ground, are special kinds of network transformations. They convert primary image structure into the set of more abstract ones, which represent objects and visual scene, making them easy for analysis by higher-level knowledge structures. Higher-level vision phenomena are results of such analysis. Composition of network-symbolic models combines learning, classification, and analogy together with higher-level model-based reasoning into a single framework, and it works similar to frames and agents. Computational intelligence methods transform images into model-based knowledge representation. Based on such principles, an Image/Video Understanding system can convert images into the knowledge models, and resolve uncertainty and ambiguity. This allows creating intelligent computer vision systems for design and manufacturing.

A Qualitative Analysis of NASA’s Human Computer Interaction Group Examining the Root Causes of Focusing on Derivative System Improvements Versus Core User Needs

DTIC Science & Technology

2017-12-01

emphasis on meeting deliverable dates over a focus on customer service and user experience, a common finding in McGrath and MacMillan’s (2000) research...including suggestions for reducing this burden, to Washington headquarters Services , Directorate for Information Operations and Reports, 1215...structure, process improvements, and training needs as the group prepares to support the retirement of the International Space Station in the 2020s and

Program for User-Friendly Management of Input and Output Data Sets

NASA Technical Reports Server (NTRS)

Klimeck, Gerhard

2003-01-01

A computer program manages large, hierarchical sets of input and output (I/O) parameters (typically, sequences of alphanumeric data) involved in computational simulations in a variety of technological disciplines. This program represents sets of parameters as structures coded in object-oriented but otherwise standard American National Standards Institute C language. Each structure contains a group of I/O parameters that make sense as a unit in the simulation program with which this program is used. The addition of options and/or elements to sets of parameters amounts to the addition of new elements to data structures. By association of child data generated in response to a particular user input, a hierarchical ordering of input parameters can be achieved. Associated with child data structures are the creation and description mechanisms within the parent data structures. Child data structures can spawn further child data structures. In this program, the creation and representation of a sequence of data structures is effected by one line of code that looks for children of a sequence of structures until there are no more children to be found. A linked list of structures is created dynamically and is completely represented in the data structures themselves. Such hierarchical data presentation can guide users through otherwise complex setup procedures and it can be integrated within a variety of graphical representations.

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

PubMed

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

PubMed Central

Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

EKPD: a hierarchical database of eukaryotic protein kinases and protein phosphatases.

PubMed

Wang, Yongbo; Liu, Zexian; Cheng, Han; Gao, Tianshun; Pan, Zhicheng; Yang, Qing; Guo, Anyuan; Xue, Yu

2014-01-01

We present here EKPD (http://ekpd.biocuckoo.org), a hierarchical database of eukaryotic protein kinases (PKs) and protein phosphatases (PPs), the key molecules responsible for the reversible phosphorylation of proteins that are involved in almost all aspects of biological processes. As extensive experimental and computational efforts have been carried out to identify PKs and PPs, an integrative resource with detailed classification and annotation information would be of great value for both experimentalists and computational biologists. In this work, we first collected 1855 PKs and 347 PPs from the scientific literature and various public databases. Based on previously established rationales, we classified all of the known PKs and PPs into a hierarchical structure with three levels, i.e. group, family and individual PK/PP. There are 10 groups with 149 families for the PKs and 10 groups with 33 families for the PPs. We constructed 139 and 27 Hidden Markov Model profiles for PK and PP families, respectively. Then we systematically characterized ∼50,000 PKs and >10,000 PPs in eukaryotes. In addition, >500 PKs and >400 PPs were computationally identified by ortholog search. Finally, the online service of the EKPD database was implemented in PHP + MySQL + JavaScript.

Decision Accuracy in Computer-Mediated versus Face-to-Face Decision-Making Teams.

PubMed

Hedlund; Ilgen; Hollenbeck

1998-10-01

Changes in the way organizations are structured and advances in communication technologies are two factors that have altered the conditions under which group decisions are made. Decisions are increasingly made by teams that have a hierarchical structure and whose members have different areas of expertise. In addition, many decisions are no longer made via strictly face-to-face interaction. The present study examines the effects of two modes of communication (face-to-face or computer-mediated) on the accuracy of teams' decisions. The teams are characterized by a hierarchical structure and their members differ in expertise consistent with the framework outlined in the Multilevel Theory of team decision making presented by Hollenbeck, Ilgen, Sego, Hedlund, Major, and Phillips (1995). Sixty-four four-person teams worked for 3 h on a computer simulation interacting either face-to-face (FtF) or over a computer network. The communication mode had mixed effects on team processes in that members of FtF teams were better informed and made recommendations that were more predictive of the correct team decision, but leaders of CM teams were better able to differentiate staff members on the quality of their decisions. Controlling for the negative impact of FtF communication on staff member differentiation increased the beneficial effect of the FtF mode on overall decision making accuracy. Copyright 1998 Academic Press.

Group I introns are widespread in archaea.

PubMed

Nawrocki, Eric P; Jones, Thomas A; Eddy, Sean R

2018-05-18

Group I catalytic introns have been found in bacterial, viral, organellar, and some eukaryotic genomes, but not in archaea. All known archaeal introns are bulge-helix-bulge (BHB) introns, with the exception of a few group II introns. It has been proposed that BHB introns arose from extinct group I intron ancestors, much like eukaryotic spliceosomal introns are thought to have descended from group II introns. However, group I introns have little sequence conservation, making them difficult to detect with standard sequence similarity searches. Taking advantage of recent improvements in a computational homology search method that accounts for both conserved sequence and RNA secondary structure, we have identified 39 group I introns in a wide range of archaeal phyla, including examples of group I introns and BHB introns in the same host gene.

International Journal of Quantum Chemistry. Quantum Chemistry Symposium Number 26: Proceedings of the International Symposium on Atomic, Molecular, and Condensed Matter Theory and Computational Methods Held in St. Augustine, Florida on 14-21 March 1992

DTIC Science & Technology

1993-02-01

Spectrum The vibrational IR spectra of formaldeh.de and its deuterated species have been measured by a number of groups and analyzed in several studies ... studies [23-28]. The order of the frontier (r) orbitals, a textbook example for simple group theory arguments, is determined by the high symmetry (Dy...simplexes will give a structure with octahedral symmetr\\ since the subgroup of the Coxeter group which leaves one component of a four -vector invariant

Validation of learning style measures: implications for medical education practice.

PubMed

Chapman, Dane M; Calhoun, Judith G

2006-06-01

It is unclear which learners would most benefit from the more individualised, student-structured, interactive approaches characteristic of problem-based and computer-assisted learning. The validity of learning style measures is uncertain, and there is no unifying learning style construct identified to predict such learners. This study was conducted to validate learning style constructs and to identify the learners most likely to benefit from problem-based and computer-assisted curricula. Using a cross-sectional design, 3 established learning style inventories were administered to 97 post-Year 2 medical students. Cognitive personality was measured by the Group Embedded Figures Test, information processing by the Learning Styles Inventory, and instructional preference by the Learning Preference Inventory. The 11 subscales from the 3 inventories were factor-analysed to identify common learning constructs and to verify construct validity. Concurrent validity was determined by intercorrelations of the 11 subscales. A total of 94 pre-clinical medical students completed all 3 inventories. Five meaningful learning style constructs were derived from the 11 subscales: student- versus teacher-structured learning; concrete versus abstract learning; passive versus active learning; individual versus group learning, and field-dependence versus field-independence. The concurrent validity of 10 of 11 subscales was supported by correlation analysis. Medical students most likely to thrive in a problem-based or computer-assisted learning environment would be expected to score highly on abstract, active and individual learning constructs and would be more field-independent. Learning style measures were validated in a medical student population and learning constructs were established for identifying learners who would most likely benefit from a problem-based or computer-assisted curriculum.

A comparative study for image quality and radiation dose of a cone beam computed tomography scanner and a multislice computed tomography scanner for paranasal sinus imaging.

PubMed

De Cock, Jens; Zanca, Federica; Canning, John; Pauwels, Ruben; Hermans, Robert

2015-07-01

To evaluate image quality and radiation dose of a state of the art cone beam computed tomography (CBCT) system and a multislice computed tomography (MSCT) system in patients with sinonasal poliposis. In this retrospective study two radiologists evaluated 57 patients with sinonasal poliposis who underwent a CBCT or MSCT sinus examination, along with a control group of 90 patients with normal radiological findings. Tissue doses were measured using a phantom model with thermoluminescent dosimeters (TLD). Overall image quality in CBCT was scored significantly higher than in MSCT in patients with normal radiologic findings (p-value: 0.00001). In patients with sinonasal poliposis, MSCT scored significantly higher than CBCT (p-value: 0.00001). The average effective dose for MSCT was 42% higher compared to CBCT (108 μSv vs 63 μSv). CBCT and MSCT are both suited for the evaluation of sinonasal poliposis. In patients with sinonasal poliposis, clinically important structures of the paranasal sinuses can be better delineated with MSCT, whereas in patients without sinonasal poliposis, CBCT turns out to define the important structures of the sinonasal region better. However, given the lower radiation dose, CBCT can be considered for the evaluation of the sinonasal structures in patients with sinonasal poliposis. • CBCT and MSCT are both suited for evaluation of sinonasal poliposis. • Effective dose for MSCT was 42% higher compared to CBCT. • In patients with sinonasal poliposis, clinically important anatomical structures are better delineated with MSCT. • In patients with normal radiological findings, clinically important anatomical structures are better delineated with CBCT.

Brain structural changes following adaptive cognitive training assessed by Tensor-Based Morphometry (TBM)

PubMed Central

Colom, Roberto; Hua, Xue; Martínez, Kenia; Burgaleta, Miguel; Román, Francisco J.; Gunter, Jeffrey L.; Carmona, Susanna; Jaeggi, Susanne M.; Thompson, Paul M.

2016-01-01

Tensor-Based Morphometry (TBM) allows the automatic mapping of brain changes across time building 3D deformation maps. This technique has been applied for tracking brain degeneration in Alzheimer's and other neurodegenerative diseases with high sensitivity and reliability. Here we applied TBM to quantify changes in brain structure after completing a challenging adaptive cognitive training program based on the n-back task. Twenty-six young women completed twenty-four training sessions across twelve weeks and they showed, on average, large cognitive improvements. High-resolution MRI scans were obtained before and after training. The computed longitudinal deformation maps were analyzed for answering three questions: (a) Are there differential brain structural changes in the training group as compared with a matched control group? (b) Are these changes related to performance differences in the training program? (c) Are standardized changes in a set of psychological factors (fluid and crystallized intelligence, working memory, and attention control) measured before and after training, related to structural changes in the brain? Results showed (a) greater structural changes for the training group in the temporal lobe, (b) a negative correlation between these changes and performance across training sessions (the greater the structural change, the lower the cognitive performance improvements), and (c) negligible effects regarding the psychological factors measured before and after training. PMID:27477628

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.

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations.

PubMed

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika

2018-05-30

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

CSM research: Methods and application studies

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

1989-01-01

Computational mechanics is that discipline of applied science and engineering devoted to the study of physical phenomena by means of computational methods based on mathematical modeling and simulation, utilizing digital computers. The discipline combines theoretical and applied mechanics, approximation theory, numerical analysis, and computer science. Computational mechanics has had a major impact on engineering analysis and design. When applied to structural mechanics, the discipline is referred to herein as computational structural mechanics. Complex structures being considered by NASA for the 1990's include composite primary aircraft structures and the space station. These structures will be much more difficult to analyze than today's structures and necessitate a major upgrade in computerized structural analysis technology. NASA has initiated a research activity in structural analysis called Computational Structural Mechanics (CSM). The broad objective of the CSM activity is to develop advanced structural analysis technology that will exploit modern and emerging computers, such as those with vector and/or parallel processing capabilities. Here, the current research directions for the Methods and Application Studies Team of the Langley CSM activity are described.

Evaluation of a 'virtual' approach to commissioning health research.

PubMed

McCourt, Christine A; Morgan, Philip A; Youll, Penny

2006-10-18

The objective of this study was to evaluate the implementation of a 'virtual' (computer-mediated) approach to health research commissioning. This had been introduced experimentally in a DOH programme--the 'Health of Londoners Programme'--in order to assess whether is could enhance the accessibility, transparency and effectiveness of commissioning health research. The study described here was commissioned to evaluate this novel approach, addressing these key questions. A naturalistic-experimental approach was combined with principles of action research. The different commissioning groups within the programme were randomly allocated to either the traditional face-to-face mode or the novel 'virtual' mode. Mainly qualitative data were gathered including observation of all (virtual and face-to-face) commissioning meetings; semi-structured interviews with a purposive sample of participants (n = 32/66); structured questionnaires and interviews with lead researchers of early commissioned projects. All members of the commissioning groups were invited to participate in collaborative enquiry groups which participated actively in the analysis process. The virtual process functioned as intended, reaching timely and relatively transparent decisions that participants had confidence in. Despite the potential for greater access using a virtual approach, few differences were found in practice. Key advantages included physical access, a more flexible and extended time period for discussion, reflection and information gathering and a more transparent decision-making process. Key challenges were the reduction of social cues available in a computer-mediated medium that require novel ways of ensuring appropriate dialogue, feedback and interaction. However, in both modes, the process was influenced by a range of factors and was not technology driven. There is potential for using computer-mediated communication within the research commissioning process. This may enhance access, effectiveness and transparency of decision-making but further development is needed for this to be fully realised, including attention to process as well as the computer-mediated medium.

Evaluation of a 'virtual' approach to commissioning health research

PubMed Central

McCourt, Christine A; Morgan, Philip A; Youll, Penny

2006-01-01

Background The objective of this study was to evaluate the implementation of a 'virtual' (computer-mediated) approach to health research commissioning. This had been introduced experimentally in a DOH programme – the 'Health of Londoners Programme' – in order to assess whether is could enhance the accessibility, transparency and effectiveness of commissioning health research. The study described here was commissioned to evaluate this novel approach, addressing these key questions. Methods A naturalistic-experimental approach was combined with principles of action research. The different commissioning groups within the programme were randomly allocated to either the traditional face-to-face mode or the novel 'virtual' mode. Mainly qualitative data were gathered including observation of all (virtual and face-to-face) commissioning meetings; semi-structured interviews with a purposive sample of participants (n = 32/66); structured questionnaires and interviews with lead researchers of early commissioned projects. All members of the commissioning groups were invited to participate in collaborative enquiry groups which participated actively in the analysis process. Results The virtual process functioned as intended, reaching timely and relatively transparent decisions that participants had confidence in. Despite the potential for greater access using a virtual approach, few differences were found in practice. Key advantages included physical access, a more flexible and extended time period for discussion, reflection and information gathering and a more transparent decision-making process. Key challenges were the reduction of social cues available in a computer-mediated medium that require novel ways of ensuring appropriate dialogue, feedback and interaction. However, in both modes, the process was influenced by a range of factors and was not technology driven. Conclusion There is potential for using computer-mediated communication within the research commissioning process. This may enhance access, effectiveness and transparency of decision-making but further development is needed for this to be fully realised, including attention to process as well as the computer-mediated medium. PMID:17049079

A COMPUTER MODELING STUDY OF BINDING PROPERTIES OF CHIRAL NUCLEOPEPTIDE FOR BIOMEDICAL APPLICATIONS.

PubMed

Pirtskhalava, M; Egoyan, A; Mirtskhulava, M; Roviello, G

2017-12-01

Nucleopeptides often show interesting properties of molecular binding that render them good candidates for development of innovative drugs for anticancer and antiviral therapies. In this work we present results of computer modeling of interactions between the molecules of hexathymine nucleopeptide (T6) and poly rA RNA (A18). The results of geometry optimization calculated using Hyperchem software and our own computer program for molecular docking show that molecules establish stable complexes due to the complementary-nucleobase interaction and the electrostatic interaction between the negative phosphate group of poly rA and the positively-charged residues present in the cationic nucleopeptide structure. Computer modeling makes it possible to find the optimal binding configuration of the molecules of a nucleopeptide and poly rA RNA and to estimate the binding energy between the molecules.

Radical bonding: structure and stability of bis(phenalenyl) complexes of divalent metals from across the periodic table.

PubMed

Craciun, Smaranda; Donald, Kelling J

2009-07-06

We examine the bonding possibilities of the bis(phenalenyl) MP(2) sandwich complexes of the divalent metals M = Be, Mg, Ca, Sr, Ba, Zn, Cd, and Hg, at the B3LYP level of theory. The outcome is an extraordinarily diverse class of low symmetry bis(phenalenyl)metal complexes in which bonding preferences and binding enthalpies differ dramatically. The lowest energy group 2 metal MP(2) complexes include an intriguing eta(1),eta(3) BeP(2) structure, and bent eta(6),eta(6) systems for M = Ca, Sr, and Ba. The group 12 bis(phenalenyl) complexes are thermodynamically unstable eta(1),eta(1) slip-sandwich structures. To better understand changes in the structural preferences going from the (eta(6),eta(6)) group 2 to the (eta(1),eta(1)) group 12 complexes, we explored the bonding in the bis(phenalenyl) complexes of transition metals with stable +2 oxidations states between Ca and Zn in period 4. The computed binding enthalpies are large and negative for nearly all of the minimum energy bis(phenalenyl) complexes of the group 2 and the transition metals; they are tiny for MgP(2), and are quite positive for the group 12 systems. The structural preferences and stability of the complexes is a subtle negotiation of several influences: the (un)availability of (n - 1)d and np, orbitals for bonding, the cost of the rehybridization at carbon sites in the phenalenyl rings in preparation for bonding to the metals, and the (P---P) interaction between the phenalenyl radicals.

Making electronic mail accessible: perspectives of people with acquired cognitive impairments, caregivers and professionals.

PubMed

Todis, B; Sohlberg, M M; Hood, D; Fickas, S

2005-06-01

The primary objective of this study was to better understand the technology needs, barriers and strategies of individuals with acquired cognitive impairments (ACI) in order to design and modify technologies with potential for alleviating the diminished independence and social isolation common in this population. The authors hypothesized that (1) higher rates of computer use would be reported by younger, more highly educated individuals with ACI, those with less severe injuries and those with previous computer experience; (2) A low percentage of survey respondents would own their own computers; and (3) People with ACI would experience social isolation and report low frequency of connecting with important people who live far away. A total of 133 individuals with ACI, professionals and care providers completed the survey. To gain more specific information, seven focus groups were conducted with 66 individuals with ACI and 20 care providers. Finally, 10 current email users participated in structured conversations, detailing their strategies for using email. The survey revealed that 80% of subjects with ACI reported owning a computer. Age and education were not predictors of computer use, but individuals whose ACI was the result of more severe injuries were less likely to use computers. As expected, respondents reported that maintaining contact with distant loved ones is problematic. The focus groups and conversations provided more detail about the communication needs of the population and the relative advantages and disadvantages of email compared with telephone and mail. Participants also identified barriers to email use they had encountered or feared they would encounter when using email. A number of accommodations to overcome these barriers were suggested. The results of the survey, focus groups and conversations confirmed the utility of email and other technologies for people with ACI and the need to make these technologies more accessible. The results and suggestions provided by the focus groups and interviews are being used in the design of Think and Link, an email interface for use by individuals with ACI.

DFT studies of the hydrated carbohydrate, glucose: optimization and DFTMD simulations of ten explicit waters superimposed with an implicit solvation method, COSMO

USDA-ARS?s Scientific Manuscript database

One of the most important and least understood properties of carbohydrates is their conformational profile in solution. The study of carbohydrates in solution is a most difficult computational problem, a result of the many soft conformational variables (hydroxyl groups) inherent in the structures of...

Measuring the Impact of Haptic Feedback Using the SOLO Taxonomy

ERIC Educational Resources Information Center

Minogue, James; Jones, Gail

2009-01-01

The application of Biggs' and Collis' Structure of Observed Learning Outcomes taxonomy in the evaluation of student learning about cell membrane transport via a computer-based learning environment is described in this study. Pre-test-post-test comparisons of student outcome data (n = 80) were made across two groups of randomly assigned students:…

Modification and Factor Analysis of the Grief Experience Inventory in Non-Death Loss/Bereavement Situations.

ERIC Educational Resources Information Center

Zinner, Ellen S.; And Others

1991-01-01

Administered Grief Experience Inventory (GEI) to 102 mothers of brain-injured adolescents and young adults across 3 years postinjury. Factor analysis of data was computed and compared to factors derived from original GEI General Reference Group (n=135). Found strikingly similar factor structures between modified nondeath form and original GEI.…

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

To cut or not to cut? Assessing the modular structure of brain networks.

PubMed

Chang, Yu-Teng; Pantazis, Dimitrios; Leahy, Richard M

2014-05-01

A wealth of methods has been developed to identify natural divisions of brain networks into groups or modules, with one of the most prominent being modularity. Compared with the popularity of methods to detect community structure, only a few methods exist to statistically control for spurious modules, relying almost exclusively on resampling techniques. It is well known that even random networks can exhibit high modularity because of incidental concentration of edges, even though they have no underlying organizational structure. Consequently, interpretation of community structure is confounded by the lack of principled and computationally tractable approaches to statistically control for spurious modules. In this paper we show that the modularity of random networks follows a transformed version of the Tracy-Widom distribution, providing for the first time a link between module detection and random matrix theory. We compute parametric formulas for the distribution of modularity for random networks as a function of network size and edge variance, and show that we can efficiently control for false positives in brain and other real-world networks. Copyright © 2014 Elsevier Inc. All rights reserved.

Ecologic study of children's use of a computer nutrition education program.

PubMed

Matheson, D; Achterberg, C

2001-01-01

The purpose of this research was to describe the context created by students as they worked in groups on a nutrition computer-assisted instruction (CAI) program. Students worked on the program in groups of three. Observational methods were used to collect data from students in two sixth-grade classrooms that were part of an experimental program designed to restructure the educational process. Thirty-two students, from 12 groups, were observed as they completed the program. The groups were assigned by the teachers according to standard principles of cooperative learning. Students completed "Ship to Shore," a program designed specifically for this research. The program required three to five 50-minute classroom periods to complete. The objectives of the program were to change children's knowledge structure of basic nutrition concepts and to increase children's critical thinking skills related to nutrition concepts. We collected observational data focused on three domains: (1) student-computer interaction, (2) student-student interaction, and (3) students' thinking and learning skills. Grounded theory methods were used to analyze the data. Specifically, the constant-comparative method was used to develop open coding categories, defined by properties and described by dimensions. The open coding categories were in turn used in axial coding to differentiate students' learning styles. Five styles of student interaction were defined. These included (1) dominant directors (n = 6; 19%), (2) passive actors (n = 5; 16%), (3) action-oriented students (n = 7; 22%), (4) content-oriented students (n = 8; 25%), and (5) problem solvers (n = 5; 16%). The "student style" groups were somewhat gender specific. The dominant directors and passive actors were girls and the action-oriented and content-oriented students were boys. The problem solvers group was mixed gender. Children's responses to computer-based nutrition education are highly variable. Based on the results of this research, nutrition educators may recommend that nutrition CAI programs be implemented in mixed gender groups.

Rotational spectroscopy of antipyretics: Conformation, structure, and internal dynamics of phenazone

NASA Astrophysics Data System (ADS)

Écija, Patricia; Cocinero, Emilio J.; Lesarri, Alberto; Fernández, José A.; Caminati, Walther; Castaño, Fernando

2013-03-01

The conformational and structural preferences of phenazone (antipyrine), the prototype of non-opioid pyrazolone antipyretics, have been probed in a supersonic jet expansion using rotational spectroscopy. The conformational landscape of the two-ring assembly was first explored computationally, but only a single conformer was predicted, with the N-phenyl and N-methyl groups on opposite sides of the pyrazolone ring. Consistently, the microwave spectrum evidenced a rotational signature arising from a single molecular structure. The spectrum exhibited very complicated fine and hyperfine patterns (not resolvable with any other spectroscopic technique) originated by the simultaneous coupling of the methyl group internal rotation and the spins of the two 14N nuclei with the overall rotation. The internal rotation tunnelling was ascribed to the C-CH3 group and the barrier height established experimentally (7.13(10) kJ mol-1). The internal rotation of the N-CH3 group has a lower limit of 9.4 kJ mol-1. The structure of the molecule was determined from the rotational parameters, with the phenyl group elevated ca. 25° with respect to the average plane of the pyrazolic moiety and a phenyl torsion of ca. 52°. The origin of the conformational preferences is discussed in terms of the competition between intramolecular C-H⋯N and C-H⋯O weak hydrogen bonds.

Design and evaluation of a computer game to promote a healthy diet for young adults.

PubMed

Peng, Wei

2009-03-01

This article reports the development and evaluation of a computer game (RightWay Café) as a special medium to promote a healthy diet for young adults. Structural features of computer games, such as interactive tailoring, role playing, the element of fun, and narrative, were operationalized in the RightWay Café game to afford behavior rehearsal in a safe and entertaining way. Theories such as the health belief model, social cognitive theory, and theory of reasoned action guided the content design of the game to influence mediators of behavior change, including self-efficacy, perceived benefits, perceived barriers, and behavior change intention. A randomized controlled evaluation study with pretest, posttest, and follow-up design demonstrated that this game was effective in teaching nutrition and weight management knowledge and increasing people's self-efficacy and perceived benefits of healthy eating, as well as their intention to be on a healthy diet. Limited long-term effects were also found: participants in the game-playing group had greater self-efficacy than participants in the control group after 1 month. This study validates the computer game-based approach to health promotion for young adults. Limitations and implications are also discussed.

Computation of statistical secondary structure of nucleic acids.

PubMed Central

Yamamoto, K; Kitamura, Y; Yoshikura, H

1984-01-01

This paper presents a computer analysis of statistical secondary structure of nucleic acids. For a given single stranded nucleic acid, we generated "structure map" which included all the annealing structures in the sequence. The map was transformed into "energy map" by rough approximation; here, the energy level of every pairing structure consisting of more than 2 successive nucleic acid pairs was calculated. By using the "energy map", the probability of occurrence of each annealed structure was computed, i.e., the structure was computed statistically. The basis of computation was the 8-queen problem in the chess game. The validity of our computer programme was checked by computing tRNA structure which has been well established. Successful application of this programme to small nuclear RNAs of various origins is demonstrated. PMID:6198622

COMPUTATION OF ℛ IN AGE-STRUCTURED EPIDEMIOLOGICAL MODELS WITH MATERNAL AND TEMPORARY IMMUNITY.

PubMed

Feng, Zhilan; Han, Qing; Qiu, Zhipeng; Hill, Andrew N; Glasser, John W

2016-03-01

For infectious diseases such as pertussis, susceptibility is determined by immunity, which is chronological age-dependent. We consider an age-structured epidemiological model that accounts for both passively acquired maternal antibodies that decay and active immunity that wanes, permitting reinfection. The model is a 6-dimensional system of partial differential equations (PDE). By assuming constant rates within each age-group, the PDE system can be reduced to an ordinary differential equation (ODE) system with aging from one age-group to the next. We derive formulae for the effective reproduction number ℛ and provide their biological interpretation in some special cases. We show that the disease-free equilibrium is stable when ℛ < 1 and unstable if ℛ > 1.

A Computationally Efficient Method for Polyphonic Pitch Estimation

NASA Astrophysics Data System (ADS)

Zhou, Ruohua; Reiss, Joshua D.; Mattavelli, Marco; Zoia, Giorgio

2009-12-01

This paper presents a computationally efficient method for polyphonic pitch estimation. The method employs the Fast Resonator Time-Frequency Image (RTFI) as the basic time-frequency analysis tool. The approach is composed of two main stages. First, a preliminary pitch estimation is obtained by means of a simple peak-picking procedure in the pitch energy spectrum. Such spectrum is calculated from the original RTFI energy spectrum according to harmonic grouping principles. Then the incorrect estimations are removed according to spectral irregularity and knowledge of the harmonic structures of the music notes played on commonly used music instruments. The new approach is compared with a variety of other frame-based polyphonic pitch estimation methods, and results demonstrate the high performance and computational efficiency of the approach.

Electronic Circular Dichroism of [16]Helicene With Simplified TD-DFT: Beyond the Single Structure Approach.

PubMed

Bannwarth, Christoph; Seibert, Jakob; Grimme, Stefan

2016-05-01

The electronic circular dichroism (ECD) spectrum of the recently synthesized [16]helicene and a derivative comprising two triisopropylsilyloxy protection groups was computed by means of the very efficient simplified time-dependent density functional theory (sTD-DFT) approach. Different from many previous ECD studies of helicenes, nonequilibrium structure effects were accounted for by computing ECD spectra on "snapshots" obtained from a molecular dynamics (MD) simulation including solvent molecules. The trajectories are based on a molecule specific classical potential as obtained from the recently developed quantum chemically derived force field (QMDFF) scheme. The reduced computational cost in the MD simulation due to the use of the QMDFF (compared to ab-initio MD) as well as the sTD-DFT approach make realistic spectral simulations feasible for these compounds that comprise more than 100 atoms. While the ECD spectra of [16]helicene and its derivative computed vertically on the respective gas phase, equilibrium geometries show noticeable differences, these are "washed" out when nonequilibrium structures are taken into account. The computed spectra with two recommended density functionals (ωB97X and BHLYP) and extended basis sets compare very well with the experimental one. In addition we provide an estimate for the missing absolute intensities of the latter. The approach presented here could also be used in future studies to capture nonequilibrium effects, but also to systematically average ECD spectra over different conformations in more flexible molecules. Chirality 28:365-369, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

System technology analysis of aeroassisted orbital transfer vehicles: Moderate lift/drag (0.75-1.5). Volume 3: Cost estimates and work breakdown structure/dictionary, phase 1 and 2

NASA Technical Reports Server (NTRS)

1985-01-01

Technology payoffs of representative ground based (Phase 1) and space based (Phase 2) mid lift/drag ratio aeroassisted orbit transfer vehicles (AOTV) were assessed and prioritized. A narrative summary of the cost estimates and work breakdown structure/dictionary for both study phases is presented. Costs were estimated using the Grumman Space Programs Algorithm for Cost Estimating (SPACE) computer program and results are given for four AOTV configurations. The work breakdown structure follows the standard of the joint government/industry Space Systems Cost Analysis Group (SSCAG). A table is provided which shows cost estimates for each work breakdown structure element.

Computer and internet use in a community health clinic population.

PubMed

Peterson, Neeraja B; Dwyer, Kathleen A; Mulvaney, Shelagh A

2009-01-01

To determine if patients from a community health clinic have access to computers and/or the Internet and if they believe a computer is useful in their medical care. A convenience sample of 100 subjects, aged 50 years and older, from a community health clinic in Nashville, Tennessee, completed a structured interview and a health literacy assessment. Of the 100 participants, 40 did not have any computer access, 27 had computer but not Internet access, and 33 had Internet access. Participants with computer access (with or without Internet) had higher incomes, higher educational status, and higher literacy status than those without computer access. Of participants reporting current computer use (n = 54), 33% reported never using their computer to look up health and medical information. Of those who "never'' used their computer for this activity, 54% reported they did not have Internet connectivity, whereas 31% reported they did not know how to use the Internet. Although this group of individuals reported that they were comfortable using a computer (77%), they reported being uncomfortable with accessing the Internet (53%). Not only does access to computers and the Internet need to be improved before widespread use by patients, but computer users will need to be instructed on how to navigate the Internet.

ACToR Chemical Structure processing using Open Source ...

EPA Pesticide Factsheets

ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

The Million-Body Problem: Particle Simulations in Astrophysics

ScienceCinema

Rasio, Fred

2018-05-21

Computer simulations using particles play a key role in astrophysics. They are widely used to study problems across the entire range of astrophysical scales, from the dynamics of stars, gaseous nebulae, and galaxies, to the formation of the largest-scale structures in the universe. The 'particles' can be anything from elementary particles to macroscopic fluid elements, entire stars, or even entire galaxies. Using particle simulations as a common thread, this talk will present an overview of computational astrophysics research currently done in our theory group at Northwestern. Topics will include stellar collisions and the gravothermal catastrophe in dense star clusters.

Computational Material Modeling of Hydrated Cement Paste Calcium Silicate Hydrate (C-S-H) Chemistry Structure - Influence of Magnesium Exchange on Mechanical Stiffness: C-S-H Jennite

DTIC Science & Technology

2015-04-27

MODELING OF C-S-H Material chemistry level modeling following the principles and techniques commonly grouped under Computational Material Science is...Henmi, C. and Kusachi, I. Monoclinic tobermorite from fuka, bitchu-cho, Okoyama Perfecture. Japan J. Min. Petr. Econ . Geol. (1989)84:374-379. [22...31] Liu, Y. et al. First principles study of the stability and mechanical properties of MC (M=Ti, V, Zr, Nb, Hf and Ta) compounds. Journal of Alloys and Compounds. (2014) 582:500-504. 10

Use of a personal computer for the real-time reception and analysis of data from a sounding rocket experiment

NASA Technical Reports Server (NTRS)

Herrick, W. D.; Penegor, G. T.; Cotton, D. M.; Kaplan, G. C.; Chakrabarti, S.

1990-01-01

In September 1988 the Earth and Planetary Atmospheres Group of the Space Sciences Laboratory of the University of California at Berkeley flew an experiment on a high-altitude sounding rocket launched from the NASA Wallops Flight Facility in Virginia. The experiment, BEARS (Berkeley EUV Airglow Rocket Spectrometer), was designed to obtain spectroscopic data on the composition and structure of the earth's upper atmosphere. Consideration is given to the objectives of the BEARS experiment; the computer interface and software; the use of remote data transmission; and calibration, integration, and flight operations.

Average waiting time in FDDI networks with local priorities

NASA Technical Reports Server (NTRS)

Gercek, Gokhan

1994-01-01

A method is introduced to compute the average queuing delay experienced by different priority group messages in an FDDI node. It is assumed that no FDDI MAC layer priorities are used. Instead, a priority structure is introduced to the messages at a higher protocol layer (e.g. network layer) locally. Such a method was planned to be used in Space Station Freedom FDDI network. Conservation of the average waiting time is used as the key concept in computing average queuing delays. It is shown that local priority assignments are feasable specially when the traffic distribution is asymmetric in the FDDI network.

Density functional theory analysis of the impact of steric interaction on the function of switchable polarity solvents

DOE PAGES

McNally, Joshua S.; Noll, Bruce; Orme, Christopher J.; ...

2015-05-04

Here, a density functional theory (DFT) analysis has been performed to explore the impact of steric interactions on the function of switchable polarity solvents (SPS) and their implications on a quantitative structure-activity relationship (QSAR) model previously proposed for SPS. An x-ray crystal structure of the N,N-dimethylcyclohexylammonium bicarbonate (Hdmcha) salt has been solved as an asymmetric unit containing two cation/anion pairs, with a hydrogen bonding interaction observed between the bicarbonate anions, as well as between the cation and anion in each pair. DFT calculations provide an optimized structure of Hdmcha that closely resembles experimental data and reproduces the cation/anion interaction withmore » the inclusion of a dielectric field. Relaxed potential energy surface (PES) scans have been performed on Hdmcha-based computational model compounds, differing in the size of functional group bonded to the nitrogen center, to assess the steric impact of the group on the relative energy and structural properties of the compound. Results suggest that both the length and amount of branching associated with the substituent impact the energetic limitations on rotation of the group along the N-R bond and NC-R bond, and disrupt the energy minimized position of the hydrogen bonded bicarbonate group. The largest interaction resulted from functional groups that featured five bonds between the ammonium proton and a proton on a functional group with the freedom of rotation to form a pseudo-six membered ring which included both protons.« less

Gauge backgrounds and zero-mode counting in F-theory

NASA Astrophysics Data System (ADS)

Bies, Martin; Mayrhofer, Christoph; Weigand, Timo

2017-11-01

Computing the exact spectrum of charged massless matter is a crucial step towards understanding the effective field theory describing F-theory vacua in four dimensions. In this work we further develop a coherent framework to determine the charged massless matter in F-theory compactified on elliptic fourfolds, and demonstrate its application in a concrete example. The gauge background is represented, via duality with M-theory, by algebraic cycles modulo rational equivalence. Intersection theory within the Chow ring allows us to extract coherent sheaves on the base of the elliptic fibration whose cohomology groups encode the charged zero-mode spectrum. The dimensions of these cohomology groups are computed with the help of modern techniques from algebraic geometry, which we implement in the software gap. We exemplify this approach in models with an Abelian and non-Abelian gauge group and observe jumps in the exact massless spectrum as the complex structure moduli are varied. An extended mathematical appendix gives a self-contained introduction to the algebro-geometric concepts underlying our framework.

Analysis on Multicast Routing Protocols for Mobile Ad Hoc Networks

NASA Astrophysics Data System (ADS)

Xiang, Ma

As the Mobile Ad Hoc Networks technologies face a series of challenges like dynamic changes of topological structure, existence of unidirectional channel, limited wireless transmission bandwidth, the capability limitations of mobile termination and etc, therefore, the research to mobile Ad Hoc network routings inevitablely undertake a more important task than those to other networks. Multicast is a mode of communication transmission oriented to group computing, which sends the data to a group of host computers by using single source address. In a typical mobile Ad Hoc Network environment, multicast has a significant meaning. On the one hand, the users of mobile Ad Hoc Network usually need to form collaborative working groups; on the other hand, this is also an important means of fully using the broadcast performances of wireless communication and effectively using the limited wireless channel resources. This paper summarizes and comparatively analyzes the routing mechanisms of various existing multicast routing protocols according to the characteristics of mobile Ad Hoc network.

In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects

PubMed Central

Cronin, Mark T.D.; Enoch, Steven J.; Mellor, Claire L.; Przybylak, Katarzyna R.; Richarz, Andrea-Nicole; Madden, Judith C.

2017-01-01

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given. PMID:28744348

Crystal-Packing Trends for a Series of 6,9,12,15,18-Pentaaryl-1-hydro[60]fullerenes

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

Kennedy, Robert D.; Halim, Merissa; Khan, Saeed I.

2012-06-11

The relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes and the solid-state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic “badminton shuttlecock” shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non-stacked structures with, for example, dimeric, layered, diamondoid, or feather-in-cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shaped para-substituents on the aryl groups. The seriesmore » of pentaarylfullerenes was characterized by single-crystal X-ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.« less

Are structural properties of dendrimers sensitive to the symmetry of branching? Computer simulation of lysine dendrimers

NASA Astrophysics Data System (ADS)

Falkovich, S.; Markelov, D.; Neelov, I.; Darinskii, A.

2013-08-01

Poly-L-lysine (PLL) dendrimers are promising systems for biomedical applications due to their biocompatibility. These dendrimers have a specific topology: two spacers of different lengths come out of each branching point and thus the branching is asymmetric. Because of this asymmetry terminal groups are located at branches of different lengths, unlike dendrimers with a symmetric branching. This paper presents the results of the first systematic molecular dynamics simulation of such asymmetric PLL dendrimers. It is shown that PLL dendrimers are porous molecules with all terminal groups equally accessible to water. We have found that in spite of an asymmetry of branching the general structural characteristics of PLL dendrimers are rather similar to those of dendrimers with symmetric branching. We have also found that the structural characteristics of PLL dendrimers obey the general laws for dendrimers and that their electrostatic properties agree with the predictions of a general analytic theory.

In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects.

PubMed

Cronin, Mark T D; Enoch, Steven J; Mellor, Claire L; Przybylak, Katarzyna R; Richarz, Andrea-Nicole; Madden, Judith C

2017-07-01

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given.

Photophysical properties of Schiff's bases from 3-(1,3-benzothiazol-2-yl)-2-hydroxy naphthalene-1-carbaldehyde.

PubMed

Satam, Manjaree A; Telore, Rahul D; Sekar, Nagaiyan

2014-11-11

A series of novel Schiff's bases have been synthesized from 3-(1,3-benzothiazol-2-yl)-2-hydroxynaphthalene-1-carbaldehyde. The presence of hydroxyl group ortho to the benzothiazolyl group as well as the imine linkage lead to the occurrence of excited state intramolecular proton transfer process. The computational strategy was used to study the ESIPT process of the synthesized Schiff's bases, which revealed surprisingly that the keto form predominantly exists in the ground state contradicting the ESIPT process. Density functional theory and time dependent density functional theory have been used to investigate the structural parameters and photophysical properties in different solvents of one of the Schiff's bases. The experimental results correlate well with the computed results. All Schiff's bases show good thermal stability. Copyright © 2014 Elsevier B.V. All rights reserved.

Self-assembly in densely grafted macromolecules with amphiphilic monomer units: diagram of states.

PubMed

Lazutin, A A; Vasilevskaya, V V; Khokhlov, A R

2017-11-22

By means of computer modelling, the self-organization of dense planar brushes of macromolecules with amphiphilic monomer units was addressed and their state diagram was constructed. The diagram of states includes the following regions: disordered position of monomer units with respect to each other, strands composed of a few polymer chains and lamellae with different domain spacing. The transformation of lamellae structures with different domain spacing occurred within the intermediate region and could proceed through the formation of so-called parking garage structures. The parking garage structure joins the lamellae with large (on the top of the brushes) and small (close to the grafted surface) domain spacing, which appears like a system of inclined locally parallel layers connected with each other by bridges. The parking garage structures were observed for incompatible A and B groups in selective solvents, which result in aggregation of the side B groups and dense packing of amphiphilic macromolecules in the restricted volume of the planar brushes.

Computer-Based Cognitive Training for Executive Functions after Stroke: A Systematic Review

PubMed Central

van de Ven, Renate M.; Murre, Jaap M. J.; Veltman, Dick J.; Schmand, Ben A.

2016-01-01

Background: Stroke commonly results in cognitive impairments in working memory, attention, and executive function, which may be restored with appropriate training programs. Our aim was to systematically review the evidence for computer-based cognitive training of executive dysfunctions. Methods: Studies were included if they concerned adults who had suffered stroke or other types of acquired brain injury, if the intervention was computer training of executive functions, and if the outcome was related to executive functioning. We searched in MEDLINE, PsycINFO, Web of Science, and The Cochrane Library. Study quality was evaluated based on the CONSORT Statement. Treatment effect was evaluated based on differences compared to pre-treatment and/or to a control group. Results: Twenty studies were included. Two were randomized controlled trials that used an active control group. The other studies included multiple baselines, a passive control group, or were uncontrolled. Improvements were observed in tasks similar to the training (near transfer) and in tasks dissimilar to the training (far transfer). However, these effects were not larger in trained than in active control groups. Two studies evaluated neural effects and found changes in both functional and structural connectivity. Most studies suffered from methodological limitations (e.g., lack of an active control group and no adjustment for multiple testing) hampering differentiation of training effects from spontaneous recovery, retest effects, and placebo effects. Conclusions: The positive findings of most studies, including neural changes, warrant continuation of research in this field, but only if its methodological limitations are addressed. PMID:27148007

Mixed-Timescale Per-Group Hybrid Precoding for Multiuser Massive MIMO Systems

NASA Astrophysics Data System (ADS)

Teng, Yinglei; Wei, Min; Liu, An; Lau, Vincent; Zhang, Yong

2018-05-01

Considering the expensive radio frequency (RF) chain, huge training overhead and feedback burden issues in massive MIMO, in this letter, we propose a mixed-timescale per-group hybrid precoding (MPHP) scheme under an adaptive partially-connected RF precoding structure (PRPS), where the RF precoder is implemented using an adaptive connection network (ACN) and M analog phase shifters (APSs), where M is the number of antennas at the base station (BS). Exploiting the mixed-time stage channel state information (CSI) structure, the joint-design of ACN and APSs is formulated as a statistical signal-to-leakage-and-noise ratio (SSLNR) maximization problem, and a heuristic group RF precoding (GRFP) algorithm is proposed to provide a near-optimal solution. Simulation results show that the proposed design advances at better energy efficiency (EE) and lower hardware cost, CSI signaling overhead and computational complexity than the conventional hybrid precoding (HP) schemes.

Error-correction coding for digital communications

NASA Astrophysics Data System (ADS)

Clark, G. C., Jr.; Cain, J. B.

This book is written for the design engineer who must build the coding and decoding equipment and for the communication system engineer who must incorporate this equipment into a system. It is also suitable as a senior-level or first-year graduate text for an introductory one-semester course in coding theory. Fundamental concepts of coding are discussed along with group codes, taking into account basic principles, practical constraints, performance computations, coding bounds, generalized parity check codes, polynomial codes, and important classes of group codes. Other topics explored are related to simple nonalgebraic decoding techniques for group codes, soft decision decoding of block codes, algebraic techniques for multiple error correction, the convolutional code structure and Viterbi decoding, syndrome decoding techniques, and sequential decoding techniques. System applications are also considered, giving attention to concatenated codes, coding for the white Gaussian noise channel, interleaver structures for coded systems, and coding for burst noise channels.

Super-resolution Doppler beam sharpening method using fast iterative adaptive approach-based spectral estimation

NASA Astrophysics Data System (ADS)

Mao, Deqing; Zhang, Yin; Zhang, Yongchao; Huang, Yulin; Yang, Jianyu

2018-01-01

Doppler beam sharpening (DBS) is a critical technology for airborne radar ground mapping in forward-squint region. In conventional DBS technology, the narrow-band Doppler filter groups formed by fast Fourier transform (FFT) method suffer from low spectral resolution and high side lobe levels. The iterative adaptive approach (IAA), based on the weighted least squares (WLS), is applied to the DBS imaging applications, forming narrower Doppler filter groups than the FFT with lower side lobe levels. Regrettably, the IAA is iterative, and requires matrix multiplication and inverse operation when forming the covariance matrix, its inverse and traversing the WLS estimate for each sampling point, resulting in a notably high computational complexity for cubic time. We propose a fast IAA (FIAA)-based super-resolution DBS imaging method, taking advantage of the rich matrix structures of the classical narrow-band filtering. First, we formulate the covariance matrix via the FFT instead of the conventional matrix multiplication operation, based on the typical Fourier structure of the steering matrix. Then, by exploiting the Gohberg-Semencul representation, the inverse of the Toeplitz covariance matrix is computed by the celebrated Levinson-Durbin (LD) and Toeplitz-vector algorithm. Finally, the FFT and fast Toeplitz-vector algorithm are further used to traverse the WLS estimates based on the data-dependent trigonometric polynomials. The method uses the Hermitian feature of the echo autocorrelation matrix R to achieve its fast solution and uses the Toeplitz structure of R to realize its fast inversion. The proposed method enjoys a lower computational complexity without performance loss compared with the conventional IAA-based super-resolution DBS imaging method. The results based on simulations and measured data verify the imaging performance and the operational efficiency.

Providing nearest neighbor point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer

DOEpatents

Archer, Charles J.; Faraj, Ahmad A.; Inglett, Todd A.; Ratterman, Joseph D.

2012-10-23

Methods, apparatus, and products are disclosed for providing nearest neighbor point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer, each compute node connected to each adjacent compute node in the global combining network through a link, that include: identifying each link in the global combining network for each compute node of the operational group; designating one of a plurality of point-to-point class routing identifiers for each link such that no compute node in the operational group is connected to two adjacent compute nodes in the operational group with links designated for the same class routing identifiers; and configuring each compute node of the operational group for point-to-point communications with each adjacent compute node in the global combining network through the link between that compute node and that adjacent compute node using that link's designated class routing identifier.

Computational insight into the reaction intermediates in the glycosylation reaction assisted by donor heteroatoms.

PubMed

Bravo, Fernando; Viso, Antonio; Alcázar, Eva; Molas, Pineda; Bo, Carles; Castillón, Sergio

2003-02-07

We studied the geometric and electronic structure of several cations (9 and 18-23) that are usually proposed as intermediates for glycosylation reactions using DFT methods. For ions 9 and 18-23 the geometries obtained corresponded to an open ion (6b type) irrespective of the exocyclic heteroatom (S, Se, I) and the size of the cycle (furanoses as well as pyranoses). We studied how substituents bonded to the exocyclic heteroatom (R in SR and SeR) affect the structure of ions and found that the geometry approached that of episulfonium and episelenonium ions (6a type) when the substituents were electron donors. The tert-butyl group and the 2,4,6-trimethyl- and 2,4,6-trimethoxyphenyl and trimethylsilyl groups produced the strongest of these effects. The presence of an electron-withdrawing group (CO-CF(3)) bonded to the hydroxymethyl group produced a similar but weaker effect. We analyzed this behavior in terms of molecular orbital interactions.

PREFACE: 4th Workshop on Theory, Modelling and Computational Methods for Semiconductors (TMCSIV)

NASA Astrophysics Data System (ADS)

Tomić, Stanko; Probert, Matt; Migliorato, Max; Pal, Joydeep

2014-06-01

These conference proceedings contain the written papers of the contributions presented at the 4th International Conference on Theory, Modelling and Computational Methods for Semiconductor materials and nanostructures. The conference was held at the MediaCityUK, University of Salford, Manchester, UK on 22-24 January 2014. The previous conferences in this series took place in 2012 at the University of Leeds, in 2010 at St William's College, York and in 2008 at the University of Manchester, UK. The development of high-performance computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational, optical and electronic properties of semiconductors and their hetero- and nano-structures. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in semiconductor science and technology, where there is substantial potential for time-saving in R&D. Theoretical approaches represented in this meeting included: Density Functional Theory, Semi-empirical Electronic Structure Methods, Multi-scale Approaches, Modelling of PV devices, Electron Transport, and Graphene. Topics included, but were not limited to: Optical Properties of Quantum Nanostructures including Colloids and Nanotubes, Plasmonics, Magnetic Semiconductors, Photonic Structures, and Electronic Devices. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the theoretical modelling of Group IV, III-V and II-VI semiconductors, as well as students, postdocs and early-career researchers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students, with several lectures given by recognized experts in various theoretical approaches. The following two days showcased some of the best theoretical research carried out in the UK in this field, with several contributions also from representatives of renowned theoretical groups from many European countries (Spain, France, Ireland, Germany, Switzerland, Luxemburg, Norway, Italy, Poland, Denmark, Sweden, Serbia, etc.), as well as Asia (Iran, Japan) and USA. We would like to thank all participants for making this a very successful meeting and for their contribution to the conference programme and these proceedings. We would also like to acknowledge the financial support from the Institute of Physics (Semiconductor Physics Group and Computational Physics Group), EPSRC-UK, the CECAM UK-Hartree Node, CCP9, and Quantum Wise (distributors of Atomistix). The Editors Acknowledgments Conference Organising Committee: Stanko Tomić (Chair, University of Salford) Matt Probert (University of York) Max Migliorato (University of Manchester) Joydeep Pal (University of Manchester) Programme Committee: David Whittaker (University of Sheffield, UK) John Robertson (University of Cambridge, UK) Risto Nieminen (Helsinki University of Technology Finland) Eoin O'Reilly (Tyndall Institute Cork Republic of Ireland) Marco Califano (University of Leeds, UK) Stewart Clark (University of Durham, UK) Stanko Tomić (University of Salford, UK) Mauro Pereira (Sheffield Hallam University, UK) Aldo Di Carlo (University of Rome ''Tor Vergata,'' Italy) Lev Kantorovich (King's College London, UK) Mervin Roy (University of Leicester, UK) Ben Hourahine (University of Strathclyde, UK) Rita Magri (University of Modena and Reggio Emilia, Italy) Zoran Ikonic (University of Leeds) John Barker (University of Glasgow) The proceedings were edited and compiled by Joydeep Pal, Max Migliorato and Stanko Tomić.

Climate Modeling Computing Needs Assessment

NASA Astrophysics Data System (ADS)

Petraska, K. E.; McCabe, J. D.

2011-12-01

This paper discusses early findings of an assessment of computing needs for NASA science, engineering and flight communities. The purpose of this assessment is to document a comprehensive set of computing needs that will allow us to better evaluate whether our computing assets are adequately structured to meet evolving demand. The early results are interesting, already pointing out improvements we can make today to get more out of the computing capacity we have, as well as potential game changing innovations for the future in how we apply information technology to science computing. Our objective is to learn how to leverage our resources in the best way possible to do more science for less money. Our approach in this assessment is threefold: Development of use case studies for science workflows; Creating a taxonomy and structure for describing science computing requirements; and characterizing agency computing, analysis, and visualization resources. As projects evolve, science data sets increase in a number of ways: in size, scope, timelines, complexity, and fidelity. Generating, processing, moving, and analyzing these data sets places distinct and discernable requirements on underlying computing, analysis, storage, and visualization systems. The initial focus group for this assessment is the Earth Science modeling community within NASA's Science Mission Directorate (SMD). As the assessment evolves, this focus will expand to other science communities across the agency. We will discuss our use cases, our framework for requirements and our characterizations, as well as our interview process, what we learned and how we plan to improve our materials after using them in the first round of interviews in the Earth Science Modeling community. We will describe our plans for how to expand this assessment, first into the Earth Science data analysis and remote sensing communities, and then throughout the full community of science, engineering and flight at NASA.

Methodes d'optimisation des parametres 2D du reflecteur dans un reacteur a eau pressurisee

NASA Astrophysics Data System (ADS)

Clerc, Thomas

With a third of the reactors in activity, the Pressurized Water Reactor (PWR) is today the most used reactor design in the world. This technology equips all the 19 EDF power plants. PWRs fit into the category of thermal reactors, because it is mainly the thermal neutrons that contribute to the fission reaction. The pressurized light water is both used as the moderator of the reaction and as the coolant. The active part of the core is composed of uranium, slightly enriched in uranium 235. The reflector is a region surrounding the active core, and containing mostly water and stainless steel. The purpose of the reflector is to protect the vessel from radiations, and also to slow down the neutrons and reflect them into the core. Given that the neutrons participate to the reaction of fission, the study of their behavior within the core is capital to understand the general functioning of how the reactor works. The neutrons behavior is ruled by the transport equation, which is very complex to solve numerically, and requires very long calculation. This is the reason why the core codes that will be used in this study solve simplified equations to approach the neutrons behavior in the core, in an acceptable calculation time. In particular, we will focus our study on the diffusion equation and approximated transport equations, such as SPN or S N equations. The physical properties of the reflector are radically different from those of the fissile core, and this structural change causes important tilt in the neutron flux at the core/reflector interface. This is why it is very important to accurately design the reflector, in order to precisely recover the neutrons behavior over the whole core. Existing reflector calculation techniques are based on the Lefebvre-Lebigot method. This method is only valid if the energy continuum of the neutrons is discretized in two energy groups, and if the diffusion equation is used. The method leads to the calculation of a homogeneous reflector. The aim of this study is to create a computational scheme able to compute the parameters of heterogeneous, multi-group reflectors, with both diffusion and SPN/SN operators. For this purpose, two computational schemes are designed to perform such a reflector calculation. The strategy used in both schemes is to minimize the discrepancies between a power distribution computed with a core code and a reference distribution, which will be obtained with an APOLLO2 calculation based on the method Method Of Characteristics (MOC). In both computational schemes, the optimization parameters, also called control variables, are the diffusion coefficients in each zone of the reflector, for diffusion calculations, and the P-1 corrected macroscopic total cross-sections in each zone of the reflector, for SPN/SN calculations (or correction factors on these parameters). After a first validation of our computational schemes, the results are computed, always by optimizing the fast diffusion coefficient for each zone of the reflector. All the tools of the data assimilation have been used to reflect the different behavior of the solvers in the different parts of the core. Moreover, the reflector is refined in six separated zones, corresponding to the physical structure of the reflector. There will be then six control variables for the optimization algorithms. [special characters omitted]. Our computational schemes are then able to compute heterogeneous, 2-group or multi-group reflectors, using diffusion or SPN/SN operators. The optimization performed reduces the discrepancies distribution between the power computed with the core codes and the reference power. However, there are two main limitations to this study: first the homogeneous modeling of the reflector assemblies doesn't allow to properly describe its physical structure near the core/reflector interface. Moreover, the fissile assemblies are modeled in infinite medium, and this model reaches its limit at the core/reflector interface. These two problems should be tackled in future studies. (Abstract shortened by UMI.).

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

Feature-Based Morphometry: Discovering Group-related Anatomical Patterns

PubMed Central

Toews, Matthew; Wells, William; Collins, D. Louis; Arbel, Tal

2015-01-01

This paper presents feature-based morphometry (FBM), a new, fully data-driven technique for discovering patterns of group-related anatomical structure in volumetric imagery. In contrast to most morphometry methods which assume one-to-one correspondence between subjects, FBM explicitly aims to identify distinctive anatomical patterns that may only be present in subsets of subjects, due to disease or anatomical variability. The image is modeled as a collage of generic, localized image features that need not be present in all subjects. Scale-space theory is applied to analyze image features at the characteristic scale of underlying anatomical structures, instead of at arbitrary scales such as global or voxel-level. A probabilistic model describes features in terms of their appearance, geometry, and relationship to subject groups, and is automatically learned from a set of subject images and group labels. Features resulting from learning correspond to group-related anatomical structures that can potentially be used as image biomarkers of disease or as a basis for computer-aided diagnosis. The relationship between features and groups is quantified by the likelihood of feature occurrence within a specific group vs. the rest of the population, and feature significance is quantified in terms of the false discovery rate. Experiments validate FBM clinically in the analysis of normal (NC) and Alzheimer's (AD) brain images using the freely available OASIS database. FBM automatically identifies known structural differences between NC and AD subjects in a fully data-driven fashion, and an equal error classification rate of 0.80 is achieved for subjects aged 60-80 years exhibiting mild AD (CDR=1). PMID:19853047

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.

Structures and bonding of C2X2Y q (X=Si,Ge,Sn,Pb; Y=C,Si,Ge,Sn,Pb; q = +1,0,-1): π-type templates for planar tetracoordinate heavier group 14 atoms

NASA Astrophysics Data System (ADS)

Yu, Shuang; Sui, Jing-jing; Xu, Jing; Ding, Yi-hong

2018-05-01

Contrasting the big family of the planar tetracoordinate carbon (ptC), species featuring the planar tetracoordinate heavier group element M (ptM) have been largely limited. Effective structural frameworks to accommodate such ptM centres are thus highly desired. In the present article, we report an extensive computational study on 60 pentatomic systems C2X2Yq (X=Si,Ge,Sn,Pb; Y=C,Si,Ge,Sn,Pb; q = +1,0,-1) covering both the low and high spin states. Up to 34 systems were shown to have the very low-lying singlet planar tetracoordinate heavier group 14 (ptM with M=Si,Ge,Sn,Pb) structures bearing the 19 (q = +1), 20 (q = 0) and 21 (q = -1) valence electrons (ve). Structural and bonding analysis confirmed the effectiveness of the inherent π-type ligand skeleton XCCX or XCCY that each have several sets of π-bonding orbitals to stabilise the ptM centre. The structural and bonding motifs of these ptMs differ greatly from the classic ptMs, which have the σ-type ligand skeleton, smaller number of valence electrons (≤18ve), and the centre → ligand π-delocalisation.

The effectiveness of using multimedia computer simulations coupled with social constructivist pedagogy in a college introductory physics classroom

NASA Astrophysics Data System (ADS)

Chou, Chiu-Hsiang

Electricity and Magnetism is legendarily considered a subject incomprehensible to the students in the college introductory level. From a social constructivist perspective, learners are encouraged to assess the quantity and the quality of prior knowledge in a subject domain and to co-construct shared knowledge and understanding by implementing and building on each other's ideas. They become challenged by new data and perspectives thus stimulate a reconceptualization of knowledge and to be actively engaged in discovering new meanings based on experiences grounded in the real-world phenomena they are expected to learn. This process is categorized as a conceptual change learning environment and can facilitate learning of E & M. Computer simulations are an excellent tool to assist the teacher and leaner in achieving these goals and were used in this study. This study examined the effectiveness of computer simulations within a conceptual change learning environment and compared it to more lecture-centered, traditional ways of teaching E & M. An experimental and control group were compared and the following differences were observed. Statistic analyses were done with ANOVA (F-test). The results indicated that the treatment group significantly outperformed the control group on the achievement test, F(1,54) = 12.34, p <.05 and the treatment group had a higher rate of improvement than the control group on two subscales: Isolation of Variables and Abstract Transformation. The results from the Maryland Physics Expectations Survey (MPEX) showed that the treatment students became more field independent and were aware of more fundamental role played by physics concepts in complex problem solving. The protocol analysis of structured interviews revealed that students in the treatment group tended to visualize the problem from different aspects and articulated what they thought in a more scientific approach. Responses to the instructional evaluation questionnaire indicated overwhelming positive ratings of appropriateness and instructional effectiveness of computer simulation instruction. In conclusion, the CSI developed and evaluated in this study provided opportunities for students to refine their preconceptions and practice using new understandings. It suggests substantial promise for the computer simulation in a classroom environment.

Computational identification of potent inhibitors for Streptomycin 3″-adenylyltransferase of Serratia marcescens.

PubMed

Prabhu, Dhamodharan; Vidhyavathi, Ramasamy; Jeyakanthan, Jeyaraman

2017-02-01

Serratia marcescens is an opportunistic pathogen responsible for the respiratory and urinary tract infections in humans. The antibiotic resistance mechanism of S. marcescens is mediated through aminoglycoside modification enzyme that transfer adenyl group from substrate to antibiotic through regiospecific transfers for the inactivation of antibiotics. Streptomycin 3 ″ -adenylyltransferase acts on the 3' position of the antibiotic and considered as a novel drug target to overcome bacterial antibiotic resistance. Till now, there is no experimentally solved crystal structure of Streptomycin 3″-adenylyltransferase in S. marcescens. Hence, the present study was initiated to construct the three dimensional structure of Streptomycin 3″-adenylyltransferase in order to understand the binding mechanism. The modeled structure was subjected to structure-based virtual screening to identify potent compounds from the five chemical structure databases. Furthermore, different computational methods such as molecular docking, molecular dynamics simulations, ADME toxicity assessment, free energy and density functional theory calculations predicted the structural, binding and pharmacokinetic properties of the best five compounds. Overall, the results suggested that stable binding confirmation of the five potent compounds were mediated through hydrophobic, π-π stacking, salt bridges and hydrogen bond interactions. The identified compounds could pave way for the development of anti-pathogenic agents as potential drug entities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computerized modeling techniques predict the 3D structure of H₄R: facts and fiction.

PubMed

Zaid, Hilal; Ismael-Shanak, Siba; Michaeli, Amit; Rayan, Anwar

2012-01-01

The functional characterization of proteins presents a daily challenge r biochemical, medical and computational sciences, especially when the structures are undetermined empirically, as in the case of the Histamine H4 Receptor (H₄R). H₄R is a member of the GPCR superfamily that plays a vital role in immune and inflammatory responses. To date, the concept of GPCRs modeling is highlighted in textbooks and pharmaceutical pamphlets, and this group of proteins has been the subject of almost 3500 publications in the scientific literature. The dynamic nature of determining the GPCRs structure was elucidated through elegant and creative modeling methodologies, implemented by many groups around the world. H₄R which belongs to the GPCR family was cloned in 2000; understandably, its biological activity was reported only 65 times in pubmed. Here we attempt to cover the fundamental concepts of H₄R structure modeling and its implementation in drug discovery, especially those that have been experimentally tested and to highlight some ideas that are currently being discussed on the dynamic nature of H₄R and GPCRs computerized techniques for 3D structure modeling.

Structural mechanism underlying capsaicin binding and activation of TRPV1 ion channel

PubMed Central

Cheng, Wei; Yang, Wei; Yu, Peilin; Song, Zhenzhen; Yarov-Yarovoy, Vladimir; Zheng, Jie

2015-01-01

Capsaicin bestows spiciness by activating TRPV1 channel with exquisite potency and selectivity. Capsaicin-bound channel structure was previously resolved by cryo-EM at 4.2-to-4.5 Å resolution, however important details required for mechanistic understandings are unavailable: capsaicin was registered as a small electron density, reflecting neither its chemical structure nor specific ligand-channel interactions. We obtained the missing atomic-level details by iterative computation, which were confirmed by systematic site-specific functional tests. We observed that the bound capsaicin takes “tail-up, head-down” configurations. The vanillyl and amide groups form specific interactions to anchor its bound position, while the aliphatic tail may sample a range of conformations, making it invisible in cryo-EM images. Capsaicin stabilizes the open state by “pull-and-contact” interactions between the vanillyl group and the S4-S5 linker. Our study provided a structural mechanism for the agonistic function of capsaicin and its analogs, and demonstrated an effective approach to obtain atomic level information from cryo-EM structures. PMID:26053297

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

The influence of care provider access to structural empowerment on individualized care in long-term-care facilities.

PubMed

Caspar, Sienna; O'Rourke, Norm

2008-07-01

Implementing management initiatives that enable formal caregivers to provide quality, individualized care to older adults in long-term-care (LTC) facilities is increasingly important given that the number of LTC residents is projected to triple by 2031. The objective of this study was to explore the relationship between care provider access to structural empowerment and the provision of individualized care in LTC. We computed structural equation models separately for registered nurses and licensed practical nurses (n = 242) and care aides (n = 326) to examine the relationship between access to empowerment structures (i.e., informal power, formal power, information, support, resources, opportunity) and the provision of individualized care. We subsequently undertook invariance analyses to determine if the association between empowerment structures and reported provision of individualized care differed between caregiver groups. Access to structural empowerment had a statistically significant, positive association with provision of individualized care for both groups. For registered nurses/licensed practical nurses and care aides, empowerment explained 50% and 45% of observed variance in individualized care, respectively. These notable percentages did not differ significantly between caregiver groups. Of the empowerment structures, support, especially in the form of access to educational opportunities and recognition for a job well done, seems to be particularly significant to care providers. Findings from this study suggest that provision of individualized care in LTC may be enhanced when formal caregivers have appreciable access to empowerment structures.

Surveying Requirements Meeting Management Sessions, 1-5 February 1982,

DTIC Science & Technology

1983-02-01

organized and conducted by the Engineering Division, Directorate of Civil Works, Office of the Chief of Engineers, to improve management and...Development) 1. Technical User Groups Overview - M. K. Miles, OCE 2. Organizing a Successful Computer Aided Applications Program - Dr. N. Radhakrishnan...2. Organization Structure 3. In-House Capabilities 4. Expertise Requirements 5. Professionalism TUESDAY-2 FEBRUARY No Management Activities WEDNESDAY

Setting the Scope of Concept Inventories for Introductory Computing Subjects

ERIC Educational Resources Information Center

Goldman, Ken; Gross, Paul; Heeren, Cinda; Herman, Geoffrey L.; Kaczmarczyk, Lisa; Loui, Michael C.; Zilles, Craig

2010-01-01

A concept inventory is a standardized assessment tool intended to evaluate a student's understanding of the core concepts of a topic. In order to create a concept inventory it is necessary to accurately identify these core concepts. A Delphi process is a structured multi-step process that uses a group of experts to achieve a consensus opinion. We…

Spherical sila- and germa-homoaromaticity.

PubMed

Chen, Zhongfang; Hirsch, Andreas; Nagase, Shigeru; Thiel, Walter; Schleyer, Paul von Ragué

2003-12-17

Guided by the 2(N + 1)2 electron-counting rule for spherical aromatic molecules, we have designed various spherical sila- and germa-homoaromatic systems rich in group 14 elements. Their aromaticity is revealed by density-functional computations of their structures and the nucleus-independent chemical shifts (NICS). Besides the formerly used endohedral inclusion strategy, spherical homoaromaticity is another way to stabilize silicon and germanium clusters.

Views of Students', Teachers' and Parents' on the Tablet Computer Usage in Education

ERIC Educational Resources Information Center

Soykan, Emrah

2015-01-01

This study aims at identification of views of teachers, students and their parents at Near East College in North Cyprus on use of tablets in education. The research is a descriptive case study. In collection of data, semi-structured interviews appropriate for qualitative research methods are used. Study group for this research is composed of high…

Software Engineering Guidebook

NASA Technical Reports Server (NTRS)

Connell, John; Wenneson, Greg

1993-01-01

The Software Engineering Guidebook describes SEPG (Software Engineering Process Group) supported processes and techniques for engineering quality software in NASA environments. Three process models are supported: structured, object-oriented, and evolutionary rapid-prototyping. The guidebook covers software life-cycles, engineering, assurance, and configuration management. The guidebook is written for managers and engineers who manage, develop, enhance, and/or maintain software under the Computer Software Services Contract.

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

PubMed

Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

2015-12-10

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

The impact of technology on the enactment of inquiry in a technology enthusiast's sixth grade science classroom

NASA Astrophysics Data System (ADS)

Waight, Noemi; Abd-El-Khalick, Fouad

2007-01-01

This study investigated the impact of the use of computer technology on the enactment of inquiry in a sixth grade science classroom. Participants were 42 students (38% female) enrolled in two sections of the classroom and taught by a technology-enthusiast instructor. Data were collected over the course of 4 months during which several inquiry activities were completed, some of which were supported with the use of technology. Non-participant observation, classroom videotaping, and semi-structured and critical-incident interviews were used to collect data. The results indicated that the technology in use worked to restrict rather than promote inquiry in the participant classroom. In the presence of computers, group activities became more structured with a focus on sharing tasks and accounting for individual responsibility, and less time was dedicated to group discourse with a marked decrease in critical, meaning-making discourse. The views and beliefs of teachers and students in relation to their specific contexts moderate the potential of technology in supporting inquiry teaching and learning and should be factored both in teacher training and attempts to integrate technology in science teaching.

One-dimensional continuum electronic structure with the density-matrix renormalization group and its implications for density-functional theory.

PubMed

Stoudenmire, E M; Wagner, Lucas O; White, Steven R; Burke, Kieron

2012-08-03

We extend the density matrix renormalization group to compute exact ground states of continuum many-electron systems in one dimension with long-range interactions. We find the exact ground state of a chain of 100 strongly correlated artificial hydrogen atoms. The method can be used to simulate 1D cold atom systems and to study density-functional theory in an exact setting. To illustrate, we find an interacting, extended system which is an insulator but whose Kohn-Sham system is metallic.

Challenging Density Functional Theory Calculations with Hemes and Porphyrins.

PubMed

de Visser, Sam P; Stillman, Martin J

2016-04-07

In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol(-1)). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties.

Embedding global and collective in a torus network with message class map based tree path selection

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

Chen, Dong; Coteus, Paul W.; Eisley, Noel A.

Embodiments of the invention provide a method, system and computer program product for embedding a global barrier and global interrupt network in a parallel computer system organized as a torus network. The computer system includes a multitude of nodes. In one embodiment, the method comprises taking inputs from a set of receivers of the nodes, dividing the inputs from the receivers into a plurality of classes, combining the inputs of each of the classes to obtain a result, and sending said result to a set of senders of the nodes. Embodiments of the invention provide a method, system and computermore » program product for embedding a collective network in a parallel computer system organized as a torus network. In one embodiment, the method comprises adding to a torus network a central collective logic to route messages among at least a group of nodes in a tree structure.« less

Users' evaluation of the Navy Computer-Assisted Medical Diagnosis System.

PubMed

Merrill, L L; Pearsall, D M; Gauker, E D

1996-01-01

U.S. Navy Independent Duty Corpsmen (IDCs) aboard small ships and submarines are responsible for all clinical and related health care duties while at sea. During deployment, life-threatening illnesses sometimes require evacuation to a shore-based treatment facility. At-sea evacuations are dangerous, expensive, and may compromise the mission of the vessel. Therefore, Group Medical Officers and IDCs were trained to use the Navy Computer-Assisted Medical Diagnosis (NCAMD) system during deployment. They were then surveyed to evaluate the NCAMD system. Their responses show that NCAMD is a cost-efficient, user-friendly package. It is easy to learn, and is especially valuable for training in the diagnosis of chest and abdominal complaints. However, the delivery of patient care at sea would significantly improve if computer hardware were upgraded to current industry standards. Also, adding various computer peripheral devices, structured forms, and reference materials to the at-sea clinician's resources could enhance shipboard patient care.

Data communication network at the ASRM facility

NASA Technical Reports Server (NTRS)

Moorhead, Robert J., II; Smith, Wayne D.; Nirgudkar, Ravi; Zhu, Zhifan; Robinson, Walter

1993-01-01

The main objective of the report is to present the overall communication network structure for the Advanced Solid Rocket Motor (ASRM) facility being built at Yellow Creek near Iuka, Mississippi. This report is compiled using information received from NASA/MSFC, LMSC, AAD, and RUST Inc. As per the information gathered, the overall network structure will have one logical FDDI ring acting as a backbone for the whole complex. The buildings will be grouped into two categories viz. manufacturing critical and manufacturing non-critical. The manufacturing critical buildings will be connected via FDDI to the Operational Information System (OIS) in the main computing center in B 1000. The manufacturing non-critical buildings will be connected by 10BASE-FL to the Business Information System (BIS) in the main computing center. The workcells will be connected to the Area Supervisory Computers (ASCs) through the nearest manufacturing critical hub and one of the OIS hubs. The network structure described in this report will be the basis for simulations to be carried out next year. The Comdisco's Block Oriented Network Simulator (BONeS) will be used for the network simulation. The main aim of the simulations will be to evaluate the loading of the OIS, the BIS, the ASCs, and the network links by the traffic generated by the workstations and workcells throughout the site.

Synthesis, spectroscopic and computational characterization of the tautomerism of pyrazoline derivatives from chalcones.

PubMed

Miguel, Fábio Balbino; Dantas, Juliana Arantes; Amorim, Stefany; Andrade, Gustavo F S; Costa, Luiz Antônio Sodré; Couri, Mara Rubia Costa

2016-01-05

In the present study a series of novel pyrazolines derivatives has been synthesized, and their structures assigned on the basis of FT-Raman, (1)H and (13)C NMR spectral data and computational DFT calculations. A joint computational study using B3LYP/6-311G(2d,2p) density functional theory and FT-Raman investigation on the tautomerism of 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carbothioamide and 3-(4-substituted-phenyl)-4,5-dihydro-5-(4-substituted-phenyl)pyrazole-1-carboxamide are presented. The structures were characterized as a minimum in the potential energy surface using DFT. The calculated Raman and NMR spectra were of such remarkable agreement to the experimental results that the equilibrium between tautomeric forms has been discussed in detail. Our study suggests the existence of tautomers, the carboxamide/carbothioamide group may tautomerize, in the solid state or in solution. Thermodynamic data calculated suggests that the R(CS)NH2 and R(CO)NH2 species are more stable than the R(CNH)SH and R(CNH)OH species. Additionally, results found for the (1)H NMR shifting, pointed out to which structure is present. Copyright © 2015 Elsevier B.V. All rights reserved.

Data communication network at the ASRM facility

NASA Astrophysics Data System (ADS)

Moorhead, Robert J., II; Smith, Wayne D.; Nirgudkar, Ravi; Zhu, Zhifan; Robinson, Walter

1993-02-01

The main objective of the report is to present the overall communication network structure for the Advanced Solid Rocket Motor (ASRM) facility being built at Yellow Creek near Iuka, Mississippi. This report is compiled using information received from NASA/MSFC, LMSC, AAD, and RUST Inc. As per the information gathered, the overall network structure will have one logical FDDI ring acting as a backbone for the whole complex. The buildings will be grouped into two categories viz. manufacturing critical and manufacturing non-critical. The manufacturing critical buildings will be connected via FDDI to the Operational Information System (OIS) in the main computing center in B 1000. The manufacturing non-critical buildings will be connected by 10BASE-FL to the Business Information System (BIS) in the main computing center. The workcells will be connected to the Area Supervisory Computers (ASCs) through the nearest manufacturing critical hub and one of the OIS hubs. The network structure described in this report will be the basis for simulations to be carried out next year. The Comdisco's Block Oriented Network Simulator (BONeS) will be used for the network simulation. The main aim of the simulations will be to evaluate the loading of the OIS, the BIS, the ASCs, and the network links by the traffic generated by the workstations and workcells throughout the site.

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 structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

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

Suresh, Niraj; Stephens, Sean A.; Adams, Lexor

Plant roots play a critical role in plant-soil-microbe interactions that occur in the rhizosphere, as well as processes with important implications to climate change and forest management. Quantitative size information on roots in their native environment is invaluable for studying root growth and environmental processes involving the plant. X ray computed tomography (XCT) has been demonstrated to be an effective tool for in situ root scanning and analysis. Our group at the Environmental Molecular Sciences Laboratory (EMSL) has developed an XCT-based tool to image and quantitatively analyze plant root structures in their native soil environment. XCT data collected on amore » Prairie dropseed (Sporobolus heterolepis) specimen was used to visualize its root structure. A combination of open-source software RooTrak and DDV were employed to segment the root from the soil, and calculate its isosurface, respectively. Our own computer script named 3DRoot-SV was developed and used to calculate root volume and surface area from a triangular mesh. The process utilizing a unique combination of tools, from imaging to quantitative root analysis, including the 3DRoot-SV computer script, is described.« less

Use of laser 3D surface digitizer in data collection and 3D modeling of anatomical structures

NASA Astrophysics Data System (ADS)

Tse, Kelly; Van Der Wall, Hans; Vu, Dzung H.

2006-02-01

A laser digitizer (Konica-Minolta Vivid 910) is used to obtain 3-dimensional surface scans of anatomical structures with a maximum resolution of 0.1mm. Placing the specimen on a turntable allows multiple scans allaround because the scanner only captures data from the portion facing its lens. A computer model is generated using 3D modeling software such as Geomagic. The 3D model can be manipulated on screen for repeated analysis of anatomical features, a useful capability when the specimens are rare or inaccessible (museum collection, fossils, imprints in rock formation.). As accurate measurements can be performed on the computer model, instead of taking measurements on actual specimens only at the archeological excavation site e.g., a variety of quantitative data can be later obtained on the computer model in the laboratory as new ideas come to mind. Our group had used a mechanical contact digitizer (Microscribe) for this purpose, but with the surface digitizer, we have been obtaining data sets more accurately and more quickly.

Towards data warehousing and mining of protein unfolding simulation data.

PubMed

Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

2005-10-01

The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

Theoretical Investigations of Well-Defined Graphene Nanostructures: Catalysis, Spectroscopy, and Development of Novel Fragment-Based Models

NASA Astrophysics Data System (ADS)

Noffke, Benjamin W.

Carbon materials have the potential to replace some precious metals in renewable energy applications. These materials are particularly attractive because of the elemental abundance and relatively low nuclear mass of carbon, implying economically feasible and lightweight materials. Targeted design of carbon materials is hindered by the lack of fundamental understanding that is required to tailor their properties for the desired application. However, most available synthetic methods to create carbon materials involve harsh conditions that limit the control of the resulting structure. Without a well-defined structure, the system is too complex and fundamental studies cannot be definitive. This work seeks to gain fundamental understanding through the development and application of efficient computational models for these systems, in conjunction with experiments performed on soluble, well-defined graphene nanostructures prepared by our group using a bottom-up synthetic approach. Theory is used to determine mechanistic details for well-defined carbon systems in applications of catalysis and electrochemical transformations. The resulting computational models do well to explain previous observations of carbon materials and provide suggestions for future directions. However, as the system size of the nanostructures gets larger, the computational cost can become prohibitive. To reduce the computational scaling of quantum chemical calculations, a new fragmentation scheme has been developed that addresses the challenges of fragmenting conjugated molecules. By selecting fragments that retain important structural characteristics in graphene, a more efficient method is achieved. The new method paves the way for an automated, systematic fragmentation scheme of graphene molecules.

Neutron radiation damage studies in the structural materials of a 500 MWe fast breeder reactor using DPA cross-sections from ENDF / B-VII.1

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Bachchan, Abhitab; Pandikumar, G.; Ganesan, S.

2018-04-01

The radiation damage in the structural materials of a 500 MWe Indian prototype fast breeder reactor (PFBR) is re-assessed by computing the neutron displacement per atom (dpa) cross-sections from the recent nuclear data library evaluated by the USA, ENDF / B-VII.1, wherein revisions were taken place in the new evaluations of basic nuclear data because of using the state-of-the-art neutron cross-section experiments, nuclear model-based predictions and modern data evaluation techniques. An indigenous computer code, computation of radiation damage (CRaD), is developed at our centre to compute primary-knock-on atom (PKA) spectra and displacement cross-sections of materials both in point-wise and any chosen group structure from the evaluated nuclear data libraries. The new radiation damage model, athermal recombination-corrected displacement per atom (arc-dpa), developed based on molecular dynamics simulations is also incorporated in our study. This work is the result of our earlier initiatives to overcome some of the limitations experienced while using codes like RECOIL, SPECTER and NJOY 2016, to estimate radiation damage. Agreement of CRaD results with other codes and ASTM standard for Fe dpa cross-section is found good. The present estimate of total dpa in D-9 steel of PFBR necessitates renormalisation of experimental correlations of dpa and radiation damage to ensure consistency of damage prediction with ENDF / B-VII.1 library.

Modeling Chagas Disease at Population Level to Explain Venezuela's Real Data

PubMed Central

González-Parra, Gilberto; Chen-Charpentier, Benito M.; Bermúdez, Moises

2015-01-01

Objectives In this paper we present an age-structured epidemiological model for Chagas disease. This model includes the interactions between human and vector populations that transmit Chagas disease. Methods The human population is divided into age groups since the proportion of infected individuals in this population changes with age as shown by real prevalence data. Moreover, the age-structured model allows more accurate information regarding the prevalence, which can help to design more specific control programs. We apply this proposed model to data from the country of Venezuela for two periods, 1961–1971, and 1961–1991 taking into account real demographic data for these periods. Results Numerical computer simulations are presented to show the suitability of the age-structured model to explain the real data regarding prevalence of Chagas disease in each of the age groups. In addition, a numerical simulation varying the death rate of the vector is done to illustrate prevention and control strategies against Chagas disease. Conclusion The proposed model can be used to determine the effect of control strategies in different age groups. PMID:26929912

Neutron powder diffraction and molecular simulation study of the structural evolution of ammonia borane from 15 to 340 K.

PubMed

Hess, Nancy J; Schenter, Gregory K; Hartman, Michael R; Daemen, Luc L; Proffen, Thomas; Kathmann, Shawn M; Mundy, Christopher J; Hartl, Monika; Heldebrant, David J; Stowe, Ashley C; Autrey, Tom

2009-05-14

The structural behavior of (11)B-, (2)H-enriched ammonia borane, ND(3)(11)BD(3), over the temperature range from 15 to 340 K was investigated using a combination of neutron powder diffraction and ab initio molecular dynamics simulations. In the low temperature orthorhombic phase, the progressive displacement of the borane group under the amine group was observed leading to the alignment of the B-N bond near parallel to the c-axis. The orthorhombic to tetragonal structural phase transition at 225 K is marked by dramatic change in the dynamics of both the amine and borane group. The resulting hydrogen disorder is problematic to extract from the metrics provided by Rietveld refinement but is readily apparent in molecular dynamics simulation and in difference Fourier transform maps. At the phase transition, Rietveld refinement does indicate a disruption of one of two dihydrogen bonds that link adjacent ammonia borane molecules. Metrics determined by Rietveld refinement are in excellent agreement with those determined from molecular simulation. This study highlights the valuable insights added by coupled experimental and computational studies.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1988-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.

Conformational responses to changes in the state of ionization of titrable groups in proteins

NASA Astrophysics Data System (ADS)

Richman, Daniel Eric

Electrostatic energy links the structural properties of proteins with some of their important biological functions, including catalysis, energy transduction, and binding and recognition. Accurate calculation of electrostatic energy is essential for predicting and for analyzing function from structure. All proteins have many ionizable residues at the protein-water interface. These groups tend to have ionization equilibria (pK a values) shifted slightly relative to their values in water. In contrast, groups buried in the hydrophobic interior usually have highly anomalous p Ka values. These shifts are what structure-based calculations have to reproduce to allow examination of contributions from electrostatics to stability, solubility and interactions of proteins. Electrostatic energies are challenging to calculate accurately because proteins are heterogeneous dielectric materials. Any individual ionizable group can experience very different local environments with different dielectric properties. The studies in this thesis examine the hypothesis that proteins reorganize concomitant with changes in their state of ionization. It appears that the pKa value measured experimentally reflects the average of pKa values experienced in the different electrostatic environments corresponding to different conformational microstates. Current computational models fail to sample conformational reorganization of the backbone correctly. Staphyloccocal nuclease (SNase) was used as a model protein in nuclear magnetic resonance (NMR) spectroscopy studies to characterize the conformational rearrangements of the protein coupled to changes in the ionization state of titrable groups. One set of experiments tests the hypothesis that proton binding to surface Asp and Glu side chains drives local unfolding by stabilizing less-native, more water-solvated conformations in which the side chains have normalized pKa values. Increased backbone flexibility in the ps-ns timescale, hydrogen bond (H-bond) breaking on at least the mus timescale, and segmental unfolding were detected near titrating groups as pH decreased into the acidic range. The study identified local structural features and stabilities that modulate the magnitude of electrostatic effects. The data demonstrate that computational approaches to pK a calculations for surface groups must account for local fluctuations spanning a wide range of timescales. A comparative NMR spectroscopy study with the L25K and L125K variants of SNase, each with a Lys residue buried in the hydrophobic interior of the protein, determined locations, timescales, and amplitudes of backbone conformational reorganization coupled with ionization of the buried Lys residues. The L25K protein exhibited an ensemble of local fluctuations of the beta barrel in the hundreds of mus timescale and an ensemble of subglobally unfolded beta-barrel states in the hundreds of ms timescale with strong pH dependence. The L125K protein exhibited fluctuations of the helix around site 125 in the mus timescale, with negligible pH dependence. These data illustrate the diverse timescales and local structural properties of conformational reorganization coupled to ionization of buried groups, and the challenge to structure-based electrostatics calculations, which must capture these long-timescale processes.

Brain structural changes following adaptive cognitive training assessed by Tensor-Based Morphometry (TBM).

PubMed

Colom, Roberto; Hua, Xue; Martínez, Kenia; Burgaleta, Miguel; Román, Francisco J; Gunter, Jeffrey L; Carmona, Susanna; Jaeggi, Susanne M; Thompson, Paul M

2016-10-01

Tensor-Based Morphometry (TBM) allows the automatic mapping of brain changes across time building 3D deformation maps. This technique has been applied for tracking brain degeneration in Alzheimer's and other neurodegenerative diseases with high sensitivity and reliability. Here we applied TBM to quantify changes in brain structure after completing a challenging adaptive cognitive training program based on the n-back task. Twenty-six young women completed twenty-four training sessions across twelve weeks and they showed, on average, large cognitive improvements. High-resolution MRI scans were obtained before and after training. The computed longitudinal deformation maps were analyzed for answering three questions: (a) Are there differential brain structural changes in the training group as compared with a matched control group? (b) Are these changes related to performance differences in the training program? (c) Are standardized changes in a set of psychological factors (fluid and crystallized intelligence, working memory, and attention control) measured before and after training, related to structural changes in the brain? Results showed (a) greater structural changes for the training group in the temporal lobe, (b) a negative correlation between these changes and performance across training sessions (the greater the structural change, the lower the cognitive performance improvements), and (c) negligible effects regarding the psychological factors measured before and after training. Copyright © 2016 Elsevier Ltd. All rights reserved.

Embedding global barrier and collective in torus network with each node combining input from receivers according to class map for output to senders

DOEpatents

Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Heidelberger, Philip; Senger, Robert M; Salapura, Valentina; Steinmacher-Burow, Burkhard; Sugawara, Yutaka; Takken, Todd E

2013-08-27

Embodiments of the invention provide a method, system and computer program product for embedding a global barrier and global interrupt network in a parallel computer system organized as a torus network. The computer system includes a multitude of nodes. In one embodiment, the method comprises taking inputs from a set of receivers of the nodes, dividing the inputs from the receivers into a plurality of classes, combining the inputs of each of the classes to obtain a result, and sending said result to a set of senders of the nodes. Embodiments of the invention provide a method, system and computer program product for embedding a collective network in a parallel computer system organized as a torus network. In one embodiment, the method comprises adding to a torus network a central collective logic to route messages among at least a group of nodes in a tree structure.

Lie group model neuromorphic geometric engine for real-time terrain reconstruction from stereoscopic aerial photos

NASA Astrophysics Data System (ADS)

Tsao, Thomas R.; Tsao, Doris

1997-04-01

In the 1980's, neurobiologist suggested a simple mechanism in primate visual cortex for maintaining a stable and invariant representation of a moving object. The receptive field of visual neurons has real-time transforms in response to motion, to maintain a stable representation. When the visual stimulus is changed due to motion, the geometric transform of the stimulus triggers a dual transform of the receptive field. This dual transform in the receptive fields compensates geometric variation in the stimulus. This process can be modelled using a Lie group method. The massive array of affine parameter sensing circuits will function as a smart sensor tightly coupled to the passive imaging sensor (retina). Neural geometric engine is a neuromorphic computing device simulating our Lie group model of spatial perception of primate's primal visual cortex. We have developed the computer simulation and experimented on realistic and synthetic image data, and performed a preliminary research of using analog VLSI technology for implementation of the neural geometric engine. We have benchmark tested on DMA's terrain data with their result and have built an analog integrated circuit to verify the computational structure of the engine. When fully implemented on ANALOG VLSI chip, we will be able to accurately reconstruct a 3D terrain surface in real-time from stereoscopic imagery.

Effect of computer radiation on weight and oxidant-antioxidant status of mice.

PubMed

Pei, Xuexian; Gu, Qijun; Ye, Dongdong; Wang, Yang; Zou, Xu; He, Lianping; Jin, Yuelong; Yao, Yingshui

2014-10-20

To explore the effects of computer radiation on weight and oxidant-antioxidant status of mice, and further to confirm that whether vitamin C has protective effects on computer radiation. Sixty Male adult ICR mice were randomly divided into six groups. each group give different treatment as follows: group A was control, group B given vitamin C intake, group C given 8 h/day computer radiation exposure, group D given vitamin C intake and 8 h/day computer radiation group E given 16 h/day computer radiation exposure, group F given vitamin C intake plus exposure to 16 h/day computer radiation. After seven weeks, mice was executed to collect the blood samples, for detecting total antioxidant capacity (T-AOC) and alkaline phosphatases (ALP)content in serum or liver tissue were determined by ELISA. No difference was found for the change of weight among six groups at different week. In the group C, D and F, the liver tissue T-AOC level were higher than the group A. In the group B, C and E, the serum ALP level were lower than the group A (P<0.05). The study indicate that computer radiation may have an adverse effect on T-AOC and ALP level of mice, and vitamin C have protective effect against computer radiation. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Zero-point corrections for isotropic coupling constants for cyclohexadienyl radical, C₆H₇ and C₆H₆Mu: beyond the bond length change approximation.

PubMed

Hudson, Bruce S; Chafetz, Suzanne K

2013-04-25

Zero-point vibrational level averaging for electron spin resonance (ESR) and muon spin resonance (µSR) hyperfine coupling constants (HFCCs) are computed for H and Mu isotopomers of the cyclohexadienyl radical. A local mode approximation previously developed for computation of the effect of replacement of H by D on ¹³C-NMR chemical shifts is used. DFT methods are used to compute the change in energy and HFCCs when the geometry is changed from the equilibrium values for the stretch and both bend degrees of freedom. This variation is then averaged over the probability distribution for each degree of freedom. The method is tested using data for the methylene group of C₆H₇, cyclohexadienyl radical and its Mu analog. Good agreement is found for the difference between the HFCCs for Mu and H of CHMu and that for H of CHMu and CH₂ of the parent radical methylene group. All three of these HFCCs are the same in the absence of the zero point average, a one-parameter fit of the static HFCC, a(0), can be computed. That value, 45.2 Gauss, is compared to the results of several fixed geometry electronic structure computations. The HFCC values for the ortho, meta and para H atoms are then discussed.

Distributions of methyl group rotational barriers in polycrystalline organic solids

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

Beckmann, Peter A., E-mail: pbeckman@brynmawr.edu, E-mail: wangxianlong@uestc.edu.cn; Conn, Kathleen G.; Division of Education and Human Services, Neumann University, One Neumann Drive, Aston, Pennsylvania 19014-1298

We bring together solid state {sup 1}H spin-lattice relaxation rate measurements, scanning electron microscopy, single crystal X-ray diffraction, and electronic structure calculations for two methyl substituted organic compounds to investigate methyl group (CH{sub 3}) rotational dynamics in the solid state. Methyl group rotational barrier heights are computed using electronic structure calculations, both in isolated molecules and in molecular clusters mimicking a perfect single crystal environment. The calculations are performed on suitable clusters built from the X-ray diffraction studies. These calculations allow for an estimate of the intramolecular and the intermolecular contributions to the barrier heights. The {sup 1}H relaxation measurements,more » on the other hand, are performed with polycrystalline samples which have been investigated with scanning electron microscopy. The {sup 1}H relaxation measurements are best fitted with a distribution of activation energies for methyl group rotation and we propose, based on the scanning electron microscopy images, that this distribution arises from molecules near crystallite surfaces or near other crystal imperfections (vacancies, dislocations, etc.). An activation energy characterizing this distribution is compared with a barrier height determined from the electronic structure calculations and a consistent model for methyl group rotation is developed. The compounds are 1,6-dimethylphenanthrene and 1,8-dimethylphenanthrene and the methyl group barriers being discussed and compared are in the 2–12 kJ mol{sup −1} range.« less

Computer-based multisensory learning in children with developmental dyslexia.

PubMed

Kast, Monika; Meyer, Martin; Vögeli, Christian; Gross, Markus; Jäncke, Lutz

2007-01-01

Several attempts have been made to remediate developmental dyslexia using various training environments. Based on the well-known retrieval structure model, the memory strength of phonemes and graphemes should be strengthened by visual and auditory associations between graphemes and phonemes. Using specifically designed training software, we examined whether establishing a multitude of visuo-auditory associations might help to mitigate writing errors in children with developmental dyslexia. Forty-three children with developmental dyslexia and 37 carefully matched normal reading children performed a computer-based writing training (15-20 minutes 4 days a week) for three months with the aim to recode a sequential textual input string into a multi-sensory representation comprising visual and auditory codes (including musical tones). The study included four matched groups: a group of children with developmental dyslexia (n=20) and a control group (n=18) practiced with the training software in the first period (3 months, 15-20 minutes 4 days a week), while a second group of children with developmental dyslexia (n=23) (waiting group) and a second control group (n=19) received no training during the first period. In the second period the children with developmental dyslexia and controls who did not receive training during the first period now took part in the training. Children with developmental dyslexia who did not perform computer-based training during the first period hardly improved their writing skills (post-pre improvement of 0-9%), the dyslexic children receiving training strongly improved their writing skills (post-pre improvement of 19-35%). The group who did the training during the second period also revealed improvement of writing skills (post-pre improvement of 27-35%). Interestingly, we noticed a strong transfer from trained to non-trained words in that the children who underwent the training were also better able to write words correctly that were not part of the training software. In addition, even non-impaired readers and writers (controls) benefited from this training. Three-month of visual-auditory multimedia training strongly improved writing skills in children with developmental dyslexia and non-dyslexic children. Thus, according to the retrieval structure model, multi-sensory training using visual and auditory cues enhances writing performance in children with developmental dyslexia and non-dyslexic children.

Effects of computer monitor-emitted radiation on oxidant/antioxidant balance in cornea and lens from rats

PubMed Central

Namuslu, Mehmet; Devrim, Erdinç; Durak, İlker

2009-01-01

Purpose This study aims to investigate the possible effects of computer monitor-emitted radiation on the oxidant/antioxidant balance in corneal and lens tissues and to observe any protective effects of vitamin C (vit C). Methods Four groups (PC monitor, PC monitor plus vitamin C, vitamin C, and control) each consisting of ten Wistar rats were studied. The study lasted for three weeks. Vitamin C was administered in oral doses of 250 mg/kg/day. The computer and computer plus vitamin C groups were exposed to computer monitors while the other groups were not. Malondialdehyde (MDA) levels and superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT) activities were measured in corneal and lens tissues of the rats. Results In corneal tissue, MDA levels and CAT activity were found to increase in the computer group compared with the control group. In the computer plus vitamin C group, MDA level, SOD, and GSH-Px activities were higher and CAT activity lower than those in the computer and control groups. Regarding lens tissue, in the computer group, MDA levels and GSH-Px activity were found to increase, as compared to the control and computer plus vitamin C groups, and SOD activity was higher than that of the control group. In the computer plus vitamin C group, SOD activity was found to be higher and CAT activity to be lower than those in the control group. Conclusion The results of this study suggest that computer-monitor radiation leads to oxidative stress in the corneal and lens tissues, and that vitamin C may prevent oxidative effects in the lens. PMID:19960068

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.

A Summary of Numerous Strain-Gage Load Calibrations on Aircraft Wings and Tails in a Technological Format

NASA Technical Reports Server (NTRS)

Jenkins, Jerald M.; DeAngelis, V. Michael

1997-01-01

Fifteen aircraft structures that were calibrated for flight loads using strain gages are examined. The primary purpose of this paper is to document important examples of load calibrations on airplanes during the past four decades. The emphasis is placed on studying the physical procedures of calibrating strain-gaged structures and all the supporting analyses and computational techniques that have been used. The results and experiences obtained from actual data from 14 structures (on 13 airplanes and 1 laboratory test structure) are presented. This group of structures includes fins, tails, and wings with a wide variety of aspect ratios. Straight- wing, swept-wing, and delta-wing configurations are studied. Some of the structures have skin-dominant construction; others are spar-dominant. Anisotropic materials, heat shields, corrugated components, nonorthogonal primary structures, and truss-type structures are particular characteristics that are included.

Grid site availability evaluation and monitoring at CMS

DOE PAGES

Lyons, Gaston; Maciulaitis, Rokas; Bagliesi, Giuseppe; ...

2017-10-01

The Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) uses distributed grid computing to store, process, and analyse the vast quantity of scientific data recorded every year. The computing resources are grouped into sites and organized in a tiered structure. Each site provides computing and storage to the CMS computing grid. Over a hundred sites worldwide contribute with resources from hundred to well over ten thousand computing cores and storage from tens of TBytes to tens of PBytes. In such a large computing setup scheduled and unscheduled outages occur continually and are not allowed to significantly impactmore » data handling, processing, and analysis. Unscheduled capacity and performance reductions need to be detected promptly and corrected. CMS developed a sophisticated site evaluation and monitoring system for Run 1 of the LHC based on tools of the Worldwide LHC Computing Grid. For Run 2 of the LHC the site evaluation and monitoring system is being overhauled to enable faster detection/reaction to failures and a more dynamic handling of computing resources. Furthermore, enhancements to better distinguish site from central service issues and to make evaluations more transparent and informative to site support staff are planned.« less

Grid site availability evaluation and monitoring at CMS

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

Lyons, Gaston; Maciulaitis, Rokas; Bagliesi, Giuseppe

The Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) uses distributed grid computing to store, process, and analyse the vast quantity of scientific data recorded every year. The computing resources are grouped into sites and organized in a tiered structure. Each site provides computing and storage to the CMS computing grid. Over a hundred sites worldwide contribute with resources from hundred to well over ten thousand computing cores and storage from tens of TBytes to tens of PBytes. In such a large computing setup scheduled and unscheduled outages occur continually and are not allowed to significantly impactmore » data handling, processing, and analysis. Unscheduled capacity and performance reductions need to be detected promptly and corrected. CMS developed a sophisticated site evaluation and monitoring system for Run 1 of the LHC based on tools of the Worldwide LHC Computing Grid. For Run 2 of the LHC the site evaluation and monitoring system is being overhauled to enable faster detection/reaction to failures and a more dynamic handling of computing resources. Furthermore, enhancements to better distinguish site from central service issues and to make evaluations more transparent and informative to site support staff are planned.« less

Grid site availability evaluation and monitoring at CMS

NASA Astrophysics Data System (ADS)

Lyons, Gaston; Maciulaitis, Rokas; Bagliesi, Giuseppe; Lammel, Stephan; Sciabà, Andrea

2017-10-01

The Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) uses distributed grid computing to store, process, and analyse the vast quantity of scientific data recorded every year. The computing resources are grouped into sites and organized in a tiered structure. Each site provides computing and storage to the CMS computing grid. Over a hundred sites worldwide contribute with resources from hundred to well over ten thousand computing cores and storage from tens of TBytes to tens of PBytes. In such a large computing setup scheduled and unscheduled outages occur continually and are not allowed to significantly impact data handling, processing, and analysis. Unscheduled capacity and performance reductions need to be detected promptly and corrected. CMS developed a sophisticated site evaluation and monitoring system for Run 1 of the LHC based on tools of the Worldwide LHC Computing Grid. For Run 2 of the LHC the site evaluation and monitoring system is being overhauled to enable faster detection/reaction to failures and a more dynamic handling of computing resources. Enhancements to better distinguish site from central service issues and to make evaluations more transparent and informative to site support staff are planned.

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.

Method and structure for skewed block-cyclic distribution of lower-dimensional data arrays in higher-dimensional processor grids

DOEpatents

Chatterjee, Siddhartha [Yorktown Heights, NY; Gunnels, John A [Brewster, NY

2011-11-08

A method and structure of distributing elements of an array of data in a computer memory to a specific processor of a multi-dimensional mesh of parallel processors includes designating a distribution of elements of at least a portion of the array to be executed by specific processors in the multi-dimensional mesh of parallel processors. The pattern of the designating includes a cyclical repetitive pattern of the parallel processor mesh, as modified to have a skew in at least one dimension so that both a row of data in the array and a column of data in the array map to respective contiguous groupings of the processors such that a dimension of the contiguous groupings is greater than one.

Freshman year computer engineering students' experiences for flipped physics lab class: An action research

NASA Astrophysics Data System (ADS)

Akı, Fatma Nur; Gürel, Zeynep

2017-02-01

The purpose of this research is to determine the university students' learning experiences about flipped-physics laboratory class. The research has been completed during the fall semester of 2015 at Computer Engineering Department of Istanbul Commerce University. In this research, also known as a teacher qualitative research design, action research method is preferred to use. The participants are ten people, including seven freshman and three junior year students of Computer Engineering Department. The research data was collected at the end of the semester with the focus group interview which includes structured and open-ended questions. And data was evaluated with categorical content analysis. According to the results, students have some similar and different learning experiences to flipped education method for physics laboratory class.

Diversity of Streptomyces spp. in Eastern Himalayan region – computational RNomics approach to phylogeny

PubMed Central

Bhattacharjee, Kaushik; Banerjee, Subhro; Joshi, Santa Ram

2012-01-01

Isolation and characterization of actinomycetes from soil samples from altitudinal gradient of North-East India were investigated for computational RNomics based phylogeny. A total of 52 diverse isolates of Streptomyces from the soil samples were isolated on four different media and from these 6 isolates were selected on the basis of cultural characteristics, microscopic and biochemical studies. Sequencing of 16S rDNA of the selected isolates identified them to belong to six different species of Streptomyces. The molecular morphometric and physico-kinetic analysis of 16S rRNA sequences were performed to predict the diversity of the genus. The computational RNomics study revealed the significance of the structural RNA based phylogenetic analysis in a relatively diverse group of Streptomyces. PMID:22829729

Rational design of an enzyme mutant for anti-cocaine therapeutics

NASA Astrophysics Data System (ADS)

Zheng, Fang; Zhan, Chang-Guo

2008-09-01

(-)-Cocaine is a widely abused drug and there is no available anti-cocaine therapeutic. The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority. An ideal anti-cocaine medication would be to accelerate (-)-cocaine metabolism producing biologically inactive metabolites. The main metabolic pathway of cocaine in body is the hydrolysis at its benzoyl ester group. Reviewed in this article is the state-of-the-art computational design of high-activity mutants of human butyrylcholinesterase (BChE) against (-)-cocaine. The computational design of BChE mutants have been based on not only the structure of the enzyme, but also the detailed catalytic mechanisms for BChE-catalyzed hydrolysis of (-)-cocaine and (+)-cocaine. Computational studies of the detailed catalytic mechanisms and the structure-and-mechanism-based computational design have been carried out through the combined use of a variety of state-of-the-art techniques of molecular modeling. By using the computational insights into the catalytic mechanisms, a recently developed unique computational design strategy based on the simulation of the rate-determining transition state has been employed to design high-activity mutants of human BChE for hydrolysis of (-)-cocaine, leading to the exciting discovery of BChE mutants with a considerably improved catalytic efficiency against (-)-cocaine. One of the discovered BChE mutants (i.e., A199S/S287G/A328W/Y332G) has a ˜456-fold improved catalytic efficiency against (-)-cocaine. The encouraging outcome of the computational design and discovery effort demonstrates that the unique computational design approach based on the transition-state simulation is promising for rational enzyme redesign and drug discovery.

Migration of the CERN IT Data Centre Support System to ServiceNow

NASA Astrophysics Data System (ADS)

Alvarez Alonso, R.; Arneodo, G.; Barring, O.; Bonfillou, E.; Coelho dos Santos, M.; Dore, V.; Lefebure, V.; Fedorko, I.; Grossir, A.; Hefferman, J.; Mendez Lorenzo, P.; Moller, M.; Pera Mira, O.; Salter, W.; Trevisani, F.; Toteva, Z.

2014-06-01

The large potential and flexibility of the ServiceNow infrastructure based on "best practises" methods is allowing the migration of some of the ticketing systems traditionally used for the monitoring of the servers and services available at the CERN IT Computer Centre. This migration enables the standardization and globalization of the ticketing and control systems implementing a generic system extensible to other departments and users. One of the activities of the Service Management project together with the Computing Facilities group has been the migration of the ITCM structure based on Remedy to ServiceNow within the context of one of the ITIL processes called Event Management. The experience gained during the first months of operation has been instrumental towards the migration to ServiceNow of other service monitoring systems and databases. The usage of this structure is also extended to the service tracking at the Wigner Centre in Budapest.

Density functional theory based screening of ternary alkali-transition metal borohydrides: A computational material design project

NASA Astrophysics Data System (ADS)

Hummelshøj, J. S.; Landis, D. D.; Voss, J.; Jiang, T.; Tekin, A.; Bork, N.; Dułak, M.; Mortensen, J. J.; Adamska, L.; Andersin, J.; Baran, J. D.; Barmparis, G. D.; Bell, F.; Bezanilla, A. L.; Bjork, J.; Björketun, M. E.; Bleken, F.; Buchter, F.; Bürkle, M.; Burton, P. D.; Buus, B. B.; Calborean, A.; Calle-Vallejo, F.; Casolo, S.; Chandler, B. D.; Chi, D. H.; Czekaj, I.; Datta, S.; Datye, A.; DeLaRiva, A.; Despoja, V.; Dobrin, S.; Engelund, M.; Ferrighi, L.; Frondelius, P.; Fu, Q.; Fuentes, A.; Fürst, J.; García-Fuente, A.; Gavnholt, J.; Goeke, R.; Gudmundsdottir, S.; Hammond, K. D.; Hansen, H. A.; Hibbitts, D.; Hobi, E.; Howalt, J. G.; Hruby, S. L.; Huth, A.; Isaeva, L.; Jelic, J.; Jensen, I. J. T.; Kacprzak, K. A.; Kelkkanen, A.; Kelsey, D.; Kesanakurthi, D. S.; Kleis, J.; Klüpfel, P. J.; Konstantinov, I.; Korytar, R.; Koskinen, P.; Krishna, C.; Kunkes, E.; Larsen, A. H.; Lastra, J. M. G.; Lin, H.; Lopez-Acevedo, O.; Mantega, M.; Martínez, J. I.; Mesa, I. N.; Mowbray, D. J.; Mýrdal, J. S. G.; Natanzon, Y.; Nistor, A.; Olsen, T.; Park, H.; Pedroza, L. S.; Petzold, V.; Plaisance, C.; Rasmussen, J. A.; Ren, H.; Rizzi, M.; Ronco, A. S.; Rostgaard, C.; Saadi, S.; Salguero, L. A.; Santos, E. J. G.; Schoenhalz, A. L.; Shen, J.; Smedemand, M.; Stausholm-Møller, O. J.; Stibius, M.; Strange, M.; Su, H. B.; Temel, B.; Toftelund, A.; Tripkovic, V.; Vanin, M.; Viswanathan, V.; Vojvodic, A.; Wang, S.; Wellendorff, J.; Thygesen, K. S.; Rossmeisl, J.; Bligaard, T.; Jacobsen, K. W.; Nørskov, J. K.; Vegge, T.

2009-07-01

We present a computational screening study of ternary metal borohydrides for reversible hydrogen storage based on density functional theory. We investigate the stability and decomposition of alloys containing 1 alkali metal atom, Li, Na, or K (M1); and 1 alkali, alkaline earth or 3d/4d transition metal atom (M2) plus two to five (BH4)- groups, i.e., M1M2(BH4)2-5, using a number of model structures with trigonal, tetrahedral, octahedral, and free coordination of the metal borohydride complexes. Of the over 700 investigated structures, about 20 were predicted to form potentially stable alloys with promising decomposition energies. The M1(Al/Mn/Fe)(BH4)4, (Li/Na)Zn(BH4)3, and (Na/K)(Ni/Co)(BH4)3 alloys are found to be the most promising, followed by selected M1(Nb/Rh)(BH4)4 alloys.

An expert system for prediction of chemical toxicity

USGS Publications Warehouse

Hickey, James P.; Aldridge, Andrew J.; Passino-Reader, Dora R.; Frank, Anthony M.

1992-01-01

The National Fisheries Research Center- Great Lakes has developed an interactive computer program that uses the structure of an organic molecule to predict its acute toxicity to four aquatic species. The expert system software, written in the muLISP language, identifies the skeletal structures and substituent groups of an organic molecule from a user-supplied standard chemical notation known as a SMILES string, and then generates values for four solvatochromic parameters. Multiple regression equations relate these parameters to the toxicities (expressed as log10LC50s and log10EC50s, along with 95% confidence intervals) for four species. The system is demonstrated by prediction of toxicity for anilide-type pesticides to the fathead minnow (Pimephales promelas). This software is designed for use on an IBM-compatible personal computer by personnel with minimal toxicology background for rapid estimation of chemical toxicity. The system has numerous applications, with much potential for use in the pharmaceutical industry

Representing exact number visually using mental abacus.

PubMed

Frank, Michael C; Barner, David

2012-02-01

Mental abacus (MA) is a system for performing rapid and precise arithmetic by manipulating a mental representation of an abacus, a physical calculation device. Previous work has speculated that MA is based on visual imagery, suggesting that it might be a method of representing exact number nonlinguistically, but given the limitations on visual working memory, it is unknown how MA structures could be stored. We investigated the structure of the representations underlying MA in a group of children in India. Our results suggest that MA is represented in visual working memory by splitting the abacus into a series of columns, each of which is independently stored as a unit with its own detailed substructure. In addition, we show that the computations of practiced MA users (but not those of control participants) are relatively insensitive to verbal interference, consistent with the hypothesis that MA is a nonlinguistic format for exact numerical computation.

CCP4i2: the new graphical user interface to the CCP4 program suite.

PubMed

Potterton, Liz; Agirre, Jon; Ballard, Charles; Cowtan, Kevin; Dodson, Eleanor; Evans, Phil R; Jenkins, Huw T; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J; Nicholls, Robert A; Noble, Martin; Pannu, Navraj S; Roth, Christian; Sheldrick, George; Skubak, Pavol; Turkenburg, Johan; Uski, Ville; von Delft, Frank; Waterman, David; Wilson, Keith; Winn, Martyn; Wojdyr, Marcin

2018-02-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures.

Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

PubMed Central

Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.; Bartashevich, Ekaterina; Boerrigter, Stephan X. M.; Braun, Doris E.; Cruz-Cabeza, Aurora J.; Day, Graeme M.; Della Valle, Raffaele G.; Desiraju, Gautam R.; van Eijck, Bouke P.; Facelli, Julio C.; Ferraro, Marta B.; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W. M.; Hofmann, Fridolin; Jose, K. V. Jovan; Karamertzanis, Panagiotis G.; Kazantsev, Andrei V.; Kendrick, John; Kuleshova, Liudmila N.; Leusen, Frank J. J.; Maleev, Andrey V.; Misquitta, Alston J.; Mohamed, Sharmarke; Needs, Richard J.; Neumann, Marcus A.; Nikylov, Denis; Orendt, Anita M.; Pal, Rumpa; Pantelides, Constantinos C.; Pickard, Chris J.; Price, Louise S.; Price, Sarah L.; Scheraga, Harold A.; van de Streek, Jacco; Thakur, Tejender S.; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K.

2011-01-01

Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

The 6th International Conference on Computer Science and Computational Mathematics (ICCSCM 2017)

NASA Astrophysics Data System (ADS)

2017-09-01

The ICCSCM 2017 (The 6th International Conference on Computer Science and Computational Mathematics) has aimed to provide a platform to discuss computer science and mathematics related issues including Algebraic Geometry, Algebraic Topology, Approximation Theory, Calculus of Variations, Category Theory; Homological Algebra, Coding Theory, Combinatorics, Control Theory, Cryptology, Geometry, Difference and Functional Equations, Discrete Mathematics, Dynamical Systems and Ergodic Theory, Field Theory and Polynomials, Fluid Mechanics and Solid Mechanics, Fourier Analysis, Functional Analysis, Functions of a Complex Variable, Fuzzy Mathematics, Game Theory, General Algebraic Systems, Graph Theory, Group Theory and Generalizations, Image Processing, Signal Processing and Tomography, Information Fusion, Integral Equations, Lattices, Algebraic Structures, Linear and Multilinear Algebra; Matrix Theory, Mathematical Biology and Other Natural Sciences, Mathematical Economics and Financial Mathematics, Mathematical Physics, Measure Theory and Integration, Neutrosophic Mathematics, Number Theory, Numerical Analysis, Operations Research, Optimization, Operator Theory, Ordinary and Partial Differential Equations, Potential Theory, Real Functions, Rings and Algebras, Statistical Mechanics, Structure Of Matter, Topological Groups, Wavelets and Wavelet Transforms, 3G/4G Network Evolutions, Ad-Hoc, Mobile, Wireless Networks and Mobile Computing, Agent Computing & Multi-Agents Systems, All topics related Image/Signal Processing, Any topics related Computer Networks, Any topics related ISO SC-27 and SC- 17 standards, Any topics related PKI(Public Key Intrastructures), Artifial Intelligences(A.I.) & Pattern/Image Recognitions, Authentication/Authorization Issues, Biometric authentication and algorithms, CDMA/GSM Communication Protocols, Combinatorics, Graph Theory, and Analysis of Algorithms, Cryptography and Foundation of Computer Security, Data Base(D.B.) Management & Information Retrievals, Data Mining, Web Image Mining, & Applications, Defining Spectrum Rights and Open Spectrum Solutions, E-Comerce, Ubiquitous, RFID, Applications, Fingerprint/Hand/Biometrics Recognitions and Technologies, Foundations of High-performance Computing, IC-card Security, OTP, and Key Management Issues, IDS/Firewall, Anti-Spam mail, Anti-virus issues, Mobile Computing for E-Commerce, Network Security Applications, Neural Networks and Biomedical Simulations, Quality of Services and Communication Protocols, Quantum Computing, Coding, and Error Controls, Satellite and Optical Communication Systems, Theory of Parallel Processing and Distributed Computing, Virtual Visions, 3-D Object Retrievals, & Virtual Simulations, Wireless Access Security, etc. The success of ICCSCM 2017 is reflected in the received papers from authors around the world from several countries which allows a highly multinational and multicultural idea and experience exchange. The accepted papers of ICCSCM 2017 are published in this Book. Please check http://www.iccscm.com for further news. A conference such as ICCSCM 2017 can only become successful using a team effort, so herewith we want to thank the International Technical Committee and the Reviewers for their efforts in the review process as well as their valuable advices. We are thankful to all those who contributed to the success of ICCSCM 2017. The Secretary

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.

Resolution acuity versus recognition acuity with Landolt-style optotypes.

PubMed

Heinrich, Sven P; Bach, Michael

2013-09-01

International standards define acuity as the reciprocal of the threshold gap size of a Landolt C optotype. However, the literature is inconsistent as to what type of acuity is measured with Landolt Cs. The present study addresses this question more directly than previous studies by quantifying the effect of an inherent luminance artifact in Landolt-style optotypes. Two groups of modified optotypes were used. In the first group, each optotype had a single gap structure with the same average luminance. Between optotypes, the gap structures differed in their degree of fineness. In the second group of optotypes, a standard gap was always present, defining the orientation of the optotype. Additional gap structures of the same average luminance, but different fineness, were inserted at the remaining potential gap locations, thereby balancing luminance across potential gap locations. Visual acuity measures were obtained for each optotype variant, using a computer-based test employing a staircase procedure. Similar acuity values were obtained for all optotypes of the first group, and for standard Landolt Cs, irrespective of the fineness of the gap structure. With luminance-balanced optotypes of the second group, measured acuity was halved, compared to standard optotypes. The results support the view that it is recognition acuity, rather than resolution acuity, which is measured with standard Landolt-style optotypes, with the imbalanced luminance distribution serving as a cue. Luminance-balanced optotypes may help to obtain a more veridical estimate of resolution acuity, although recognition acuity may be more relevant in daily living.

PREFACE: 3rd Workshop on Theory, Modelling and Computational Methods for Semiconductors (TMCSIII)

NASA Astrophysics Data System (ADS)

Califano, Marco; Migliorato, Max; Probert, Matt

2012-05-01

These conference proceedings contain the written papers of the contributions presented at the 3rd International Conference on Theory, Modelling and Computational Methods for Semiconductor materials and nanostructures. The conference was held at the School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK on 18-20 January 2012. The previous conferences in this series took place in 2010 at St William's College, York and in 2008 at the University of Manchester, UK. The development of high-speed computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational, optical and electronic properties of semiconductors and their hetero- and nano-structures. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in semiconductor science and technology, where there is substantial potential for time-saving in R&D. Theoretical approaches represented in this meeting included: Density Functional Theory, Tight Binding, Semiempirical Pseudopotential Methods, Effective Mass Models, Empirical Potential Methods and Multiscale Approaches. Topics included, but were not limited to: Optical and Transport Properties of Quantum Nanostructures including Colloids and Nanotubes, Plasmonics, Magnetic Semiconductors, Graphene, Lasers, Photonic Structures, Photovoltaic and Electronic Devices. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the theoretical modelling of Group IV, III-V and II-VI semiconductors, as well as students, postdocs and early-career researchers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students, with several lectures given by recognised experts in various theoretical approaches. The following two days showcased some of the best theoretical research carried out in the UK in this field, with several contributions also from representatives of renowned theoretical groups from many European countries (Spain, France, Ireland, Germany, Italy, Poland, Denmark, Sweden, Serbia, Greece, etc.), as well as Asia (India) and Africa (Algeria, Tunisia and South Africa). We would like to thank all participants for making this a very successful meeting and for their contribution to the conference programme and these proceedings. We would also like to acknowledge the financial support from the Institute of Physics (Computational Physics group and Semiconductor Physics group), and QuantumWise (distributors of Atomistix). The Editors Acknowledgments Conference Organising Committee: Marco Califano (University of Leeds) Max Migliorato (University of Manchester) Matt Probert (University of York) Programme Committee: Stewart Clark (University of Durham) Aldo Di Carlo (University of Rome 'Tor Vergata', Italy) Ben Hourahine (University of Strathclyde) Lev Kantorovich (King's College London) Risto Nieminen (Helsinki University of Technology, Finland) Eoin O'Reilly (Tyndall Institute Cork, Republic of Ireland) Mauro Pereira (Sheffield Hallam University) John Robertson (University of Cambridge) Mervin Roy (University of Leicester) Stanko Tomic (University of Salford) David Whittaker (University of Sheffield) The proceedings were edited and compiled by Marco Califano, Max Migliorato and Matt Probert.

A Validation Framework for the Long Term Preservation of High Energy Physics Data

NASA Astrophysics Data System (ADS)

Ozerov, Dmitri; South, David M.

2014-06-01

The study group on data preservation in high energy physics, DPHEP, is moving to a new collaboration structure, which will focus on the implementation of preservation projects, such as those described in the group's large scale report published in 2012. One such project is the development of a validation framework, which checks the compatibility of evolving computing environments and technologies with the experiments software for as long as possible, with the aim of substantially extending the lifetime of the analysis software, and hence of the usability of the data. The framework is designed to automatically test and validate the software and data of an experiment against changes and upgrades to the computing environment, as well as changes to the experiment software itself. Technically, this is realised using a framework capable of hosting a number of virtual machine images, built with different configurations of operating systems and the relevant software, including any necessary external dependencies.

Performance Enhancement Strategies for Multi-Block Overset Grid CFD Applications

NASA Technical Reports Server (NTRS)

Djomehri, M. Jahed; Biswas, Rupak

2003-01-01

The overset grid methodology has significantly reduced time-to-solution of highfidelity computational fluid dynamics (CFD) simulations about complex aerospace configurations. The solution process resolves the geometrical complexity of the problem domain by using separately generated but overlapping structured discretization grids that periodically exchange information through interpolation. However, high performance computations of such large-scale realistic applications must be handled efficiently on state-of-the-art parallel supercomputers. This paper analyzes the effects of various performance enhancement strategies on the parallel efficiency of an overset grid Navier-Stokes CFD application running on an SGI Origin2000 machinc. Specifically, the role of asynchronous communication, grid splitting, and grid grouping strategies are presented and discussed. Details of a sophisticated graph partitioning technique for grid grouping are also provided. Results indicate that performance depends critically on the level of latency hiding and the quality of load balancing across the processors.

Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures.

PubMed

Gupta, Dinesh C; Bhat, Idris Hamid

2013-12-01

The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (B2 phase) with space group Pm-3m. Hubbard-U and spin-orbit coupling were included to predict correctly the semiconducting band gap of LuN. Under compression, these materials undergo first-order structural transitions from B1 to B2 phases at 241, 98, 56.82, 25.2 and 32.3 GPa, respectively. The computed elastic properties show that LuBi is ductile by nature. The electronic structure calculations show that LuN is semiconductor at ambient conditions with an indirect band gap of 1.55 eV while other Lu-pnictides are metallic. It was observed that LuN shows metallization at high pressures. The structural properties, viz, equilibrium lattice constant, bulk modulus and its pressure derivative, transition pressure, equation of state, volume collapse, band gap and elastic moduli, show good agreement with available data.

Bridging the digital divide by increasing computer and cancer literacy: community technology centers for head-start parents and families.

PubMed

Salovey, Peter; Williams-Piehota, Pamela; Mowad, Linda; Moret, Marta Elisa; Edlund, Denielle; Andersen, Judith

2009-01-01

This article describes the establishment of two community technology centers affiliated with Head Start early childhood education programs focused especially on Latino and African American parents of children enrolled in Head Start. A 6-hour course concerned with computer and cancer literacy was presented to 120 parents and other community residents who earned a free, refurbished, Internet-ready computer after completing the program. Focus groups provided the basis for designing the structure and content of the course and modifying it during the project period. An outcomes-based assessment comparing program participants with 70 nonparticipants at baseline, immediately after the course ended, and 3 months later suggested that the program increased knowledge about computers and their use, knowledge about cancer and its prevention, and computer use including health information-seeking via the Internet. The creation of community computer technology centers requires the availability of secure space, capacity of a community partner to oversee project implementation, and resources of this partner to ensure sustainability beyond core funding.

Assessment of jawbone trabecular bone structure amongst osteoporotic women by cone-beam computed tomography: the OSTEOSYR project.

PubMed

Barngkgei, Imad; Al Haffar, Iyad; Shaarani, Eyad; Khattab, Razan; Mashlah, Ammar

2016-11-01

To assess the trabecular bone structure of jawbones and the dens (the odontoid process of the second cervical vertebra) amongst osteoporotic and nonosteoporotic women using cone-beam computed tomography (CBCT). Analysis of the dens trabecular bone structure aimed to test the validity of CBCT in such analysis. Thirty-eight women who went under dual-energy X-ray absorptiometry (DXA) examination were scanned by CBCT. Cuboids from different areas of jawbones and the dens were extracted from each scan. Trabecular thickness (Tb.Th), trabecular separation (Tb.S), bone volume fraction (BV/TV), specific bone surface (BS/TV) and connectivity density were calculated. Student's t-test, Pearson correlation, and logistic regression analysis were used to explore differences in these measures between groups. Jawbone-derived measures showed insignificant differences (P > 0.05) between osteoporotic and non-osteoporotic groups, and weak correlations with femoral neck and lumbar vertebrae T-scores (r ≤ 0.4). Dens-derived measures, however, resulted in the opposite (r = 0.34-0.38 [P value = 0.02-0.036] and r = 0.48-0.61 [P value ≤ 0.003]) and the highest accuracy of osteoporosis prediction: 84.2% and 78.9% respectively. Trabecular bone structure of the mandible and maxilla is not affected in osteoporosis as assessed by CBCT. Dens trabecular bone analysis revealed the opposite, so some trabecular bone measures may be assessed by CBCT, which may aid in predicting osteoporosis. © 2015 Wiley Publishing Asia Pty Ltd.

Evolutionary profiles from the QR factorization of multiple sequence alignments

PubMed Central

Sethi, Anurag; O'Donoghue, Patrick; Luthey-Schulten, Zaida

2005-01-01

We present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. The method, based on the multidimensional QR factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of proteins. We observe a general trend that these smaller, more evolutionarily balanced profiles have comparable and, in many cases, better performance in database searches than conventional profiles containing hundreds of sequences, constructed in an iterative and computationally intensive procedure. For more diverse families or superfamilies, with sequence identity <30%, structural alignments, based purely on the geometry of the protein structures, provide better alignments than pure sequence-based methods. Merging the structure and sequence information allows the construction of accurate profiles for distantly related groups. These structure-based profiles outperformed other sequence-based methods for finding distant homologs and were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. Phylogenetic analysis showed the putative class II CysRSs to be a monophyletic group and homology modeling revealed a constellation of active site residues similar to that in the known class I CysRS. PMID:15741270

Enlist micros: Training science teachers to use microcomputers

NASA Astrophysics Data System (ADS)

Baird, William E.; Ellis, James D.; Kuerbis, Paul J.

A National Science Foundation grant to the Biological Sciences Curriculum Study (BSCS) at The Colorado College supported the design and production of training materials to encourage literacy of science teachers in the use of microcomputers. ENLIST Micros is based on results of a national needs assessment that identified 22 compentencies needed by K-12 science teachers to use microcomputers for instruction. A writing team developed the 16-hour training program in the summer of 1985, and field-test coordinators tested it with 18 preservice or in-service groups during the 1985-86 academic year at 15 sites within the United States. The training materials consist of video programs, interactive computer disks for the Apple II series microcomputer, a training manual for participants, and a guide for the group leader. The experimental materials address major areas of educational computing: awareness, applications, implementation, evaluation, and resources. Each chapter contains activities developed for this program, such as viewing video segments of science teachers who are using computers effectively and running commercial science and training courseware. Role playing and small-group interaction help the teachers overcome their reluctance to use computers and plan for effective implementation of microcomputers in the school. This study examines the implementation of educational computing among 47 science teachers who completed the ENLIST Micros training at a southern university. We present results of formative evaluation for that site. Results indicate that both elementary and secondary teachers benefit from the training program and demonstrate gains in attitudes toward computer use. Participating teachers said that the program met its stated objectives and helped them obtain needed skills. Only 33 percent of these teachers, however, reported using computers one year after the training. In June 1986, the BSCS initiated a follow up to the ENLIST Micros curriculum to develop, evaluate, and disseminate a complete model of teacher enhancement for educational computing in the sciences. In that project, we use the ENLIST Micros curriculum as the first step in a training process. The project includes seminars that introduce additional skills: It contains provisions for sharing among participants, monitors use of computers in participants' classrooms, provides structured coaching of participants' use of computers in their classrooms, and offers planned observations of peers using computers in their science teaching.

Image processing for cryogenic transmission electron microscopy of symmetry-mismatched complexes.

PubMed

Huiskonen, Juha T

2018-02-08

Cryogenic transmission electron microscopy (cryo-TEM) is a high-resolution biological imaging method, whereby biological samples, such as purified proteins, macromolecular complexes, viral particles, organelles and cells, are embedded in vitreous ice preserving their native structures. Due to sensitivity of biological materials to the electron beam of the microscope, only relatively low electron doses can be applied during imaging. As a result, the signal arising from the structure of interest is overpowered by noise in the images. To increase the signal-to-noise ratio, different image processing-based strategies that aim at coherent averaging of signal have been devised. In such strategies, images are generally assumed to arise from multiple identical copies of the structure. Prior to averaging, the images must be grouped according to the view of the structure they represent and images representing the same view must be simultaneously aligned relatively to each other. For computational reconstruction of the three-dimensional structure, images must contain different views of the original structure. Structures with multiple symmetry-related substructures are advantageous in averaging approaches because each image provides multiple views of the substructures. However, the symmetry assumption may be valid for only parts of the structure, leading to incoherent averaging of the other parts. Several image processing approaches have been adapted to tackle symmetry-mismatched substructures with increasing success. Such structures are ubiquitous in nature and further computational method development is needed to understanding their biological functions. ©2018 The Author(s).

Extratympanic observation of middle ear structure using a refractive index matching material (glycerol) and an infrared camera.

PubMed

Kong, Soo-Keun; Chon, Kyong-Myong; Goh, Eui-Kyung; Lee, Il-Woo; Wang, Soo-Geun

2014-05-01

High-resolution computed tomography has been used mainly in the diagnosis of middle ear disease, such as high-jugular bulb, congenital cholesteatoma, and ossicular disruption. However, certain diagnoses are confirmed through exploratory tympanotomy. There are few noninvasive methods available to observe the middle ear. The purpose of this study was to investigate the effect of glycerol as a refractive index matching material and an infrared (IR) camera system for extratympanic observation. 30% glycerol was used as a refractive index matching material in five fresh cadavers. Each material was divided into four subgroups; GN (glycerol no) group, GO (glycerol out) group, GI (glycerol in) group, and GB (glycerol both) group. A printed letter and middle ear structures on the inside tympanic membrane were observed using a visible and IR ray camera system. In the GB group, there were marked a transilluminated letter or an ossicle on the inside tympanic membrane. In particular, a footplate of stapes was even transilluminated using the IR camera system in the GB group. This method can be useful in the diagnosis of diseases of the middle ear if it is clinically applied through further studies.

Extratympanic observation of middle ear structure using a refractive index matching material (glycerol) and an infrared camera

NASA Astrophysics Data System (ADS)

Kong, Soo-Keun; Chon, Kyong-Myong; Goh, Eui-Kyung; Lee, Il-Woo; Wang, Soo-Geun

2014-05-01

High-resolution computed tomography has been used mainly in the diagnosis of middle ear disease, such as high-jugular bulb, congenital cholesteatoma, and ossicular disruption. However, certain diagnoses are confirmed through exploratory tympanotomy. There are few noninvasive methods available to observe the middle ear. The purpose of this study was to investigate the effect of glycerol as a refractive index matching material and an infrared (IR) camera system for extratympanic observation. 30% glycerol was used as a refractive index matching material in five fresh cadavers. Each material was divided into four subgroups; GN (glycerol no) group, GO (glycerol out) group, GI (glycerol in) group, and GB (glycerol both) group. A printed letter and middle ear structures on the inside tympanic membrane were observed using a visible and IR ray camera system. In the GB group, there were marked a transilluminated letter or an ossicle on the inside tympanic membrane. In particular, a footplate of stapes was even transilluminated using the IR camera system in the GB group. This method can be useful in the diagnosis of diseases of the middle ear if it is clinically applied through further studies.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

PREFACE: Theory, Modelling and Computational methods for Semiconductors

NASA Astrophysics Data System (ADS)

Migliorato, Max; Probert, Matt

2010-04-01

These conference proceedings contain the written papers of the contributions presented at the 2nd International Conference on: Theory, Modelling and Computational methods for Semiconductors. The conference was held at the St Williams College, York, UK on 13th-15th Jan 2010. The previous conference in this series took place in 2008 at the University of Manchester, UK. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in Semiconductor science and technology, where there is a substantial potential for time saving in R&D. The development of high speed computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational and electronic properties of semiconductors and their heterostructures. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the field of theory of group IV, III-V and II-VI semiconductors together with postdocs and students in the early stages of their careers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students at this influential point in their careers. We would like to thank all participants for their contribution to the conference programme and these proceedings. We would also like to acknowledge the financial support from the Institute of Physics (Computational Physics group and Semiconductor Physics group), the UK Car-Parrinello Consortium, Accelrys (distributors of Materials Studio) and Quantumwise (distributors of Atomistix). The Editors Acknowledgements Conference Organising Committee: Dr Matt Probert (University of York) and Dr Max Migliorato (University of Manchester) Programme Committee: Dr Marco Califano (University of Leeds), Dr Jacob Gavartin (Accelrys Ltd, Cambridge), Dr Stanko Tomic (STFC Daresbury Laboratory), Dr Gabi Slavcheva (Imperial College London) Proceedings edited and compiled by Dr Max Migliorato and Dr Matt Probert

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

Diffusion in Stellar Envelopes

NASA Astrophysics Data System (ADS)

Seaton, M. J.

Abundances in stellar atmospheres can depend on diffusive movements in much deeper layers of stellar envelopes. Diffusion in envelopes is also of interest in that it can lead to changes in opacities and hence to the structures of stars. For envelopes the radiative accelerations grad can be expressed in terms of quantities which depend only on temperatures, densities and chemical compositions. Computations have been made for the elements C, N, O, Ne, Na, Mg, Al, Si, S, Ar, Ca, Cr, Mn, Fe and Ni and tables are being made generally available through CDS (Strasbourg). Some results from those computations will be presented. The computed values of grad are used to study diffusion of iron-group elements in envelopes of HgMn stars. It is shown that one can define a value tau_0 of the Rosseland-mean optical depth tau such that diffusive movements for tau >= tau_0 do not depend on those for tau <= tau_0. For Cr and Mn we obtain solutions with tau_0 = 1 and are able to make some meaningful comparisons of abundances, as computed and as observed in atmospheres. For Fe we find that diffusive movements are slowed down in regions of T ~= 10^5 K where the dominant ionisation stages are near argon-like. Diffusion of Fe-group elements can produce substantial changes in opacities.

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.

Maximal Neighbor Similarity Reveals Real Communities in Networks

PubMed Central

Žalik, Krista Rizman

2015-01-01

An important problem in the analysis of network data is the detection of groups of densely interconnected nodes also called modules or communities. Community structure reveals functions and organizations of networks. Currently used algorithms for community detection in large-scale real-world networks are computationally expensive or require a priori information such as the number or sizes of communities or are not able to give the same resulting partition in multiple runs. In this paper we investigate a simple and fast algorithm that uses the network structure alone and requires neither optimization of pre-defined objective function nor information about number of communities. We propose a bottom up community detection algorithm in which starting from communities consisting of adjacent pairs of nodes and their maximal similar neighbors we find real communities. We show that the overall advantage of the proposed algorithm compared to the other community detection algorithms is its simple nature, low computational cost and its very high accuracy in detection communities of different sizes also in networks with blurred modularity structure consisting of poorly separated communities. All communities identified by the proposed method for facebook network and E-Coli transcriptional regulatory network have strong structural and functional coherence. PMID:26680448

The effect of introducing computers into an introductory physics problem-solving laboratory

NASA Astrophysics Data System (ADS)

McCullough, Laura Ellen

2000-10-01

Computers are appearing in every type of classroom across the country. Yet they often appear without benefit of studying their effects. The research that is available on computer use in classrooms has found mixed results, and often ignores the theoretical and instructional contexts of the computer in the classroom. The University of Minnesota's physics department employs a cooperative-group problem solving pedagogy, based on a cognitive apprenticeship instructional model, in its calculus-based introductory physics course. This study was designed to determine possible negative effects of introducing a computerized data-acquisition and analysis tool into this pedagogy as a problem-solving tool for students to use in laboratory. To determine the effects of the computer tool, two quasi-experimental treatment groups were selected. The computer-tool group (N = 170) used a tool, designed for this study (VideoTool), to collect and analyze motion data in the laboratory. The control group (N = 170) used traditional non-computer equipment (spark tapes and Polaroid(TM) film). The curriculum was kept as similar as possible for the two groups. During the ten week academic quarter, groups were examined for effects on performance on conceptual tests and grades, attitudes towards the laboratory and the laboratory tools, and behaviors within cooperative groups. Possible interactions with gender were also examined. Few differences were found between the control and computer-tool groups. The control group received slightly higher scores on one conceptual test, but this difference was not educationally significant. The computer-tool group had slightly more positive attitudes towards using the computer tool than their counterparts had towards the traditional tools. The computer-tool group also perceived that they spoke more frequently about physics misunderstandings, while the control group felt that they discussed equipment difficulties more often. This perceptual difference interacted with gender, with the men in the control group more likely to discuss equipment difficulties than any other group. Overall, the differences between the control and quasi-experimental groups were minimal. It was concluded that carefully replacing traditional data collection and analysis tools with a computer tool had no negative effects on achievement, attitude, group behavior, and did not interact with gender.

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.

Hypersonic transport aircraft

NASA Technical Reports Server (NTRS)

1987-01-01

A hypersonic transport aircraft design project was selected as a result of interactions with NASA Lewis Research Center personnel and fits the Presidential concept of the Orient Express. The Graduate Teaching Assistant (GTA) and an undergraduate student worked at the NASA Lewis Research Center during the 1986 summer conducting a literature survey, and relevant literature and useful software were collected. The computer software was implemented in the Computer Aided Design Laboratory of the Mechanical and Aerospace Engineering Department. In addition to the lectures by the three instructors, a series of guest lectures was conducted. The first of these lectures 'Anywhere in the World in Two Hours' was delivered by R. Luidens of NASA Lewis Center. In addition, videotaped copies of relevant seminars obtained from NASA Lewis were also featured. The first assignment was to individually research and develop the mission requirements and to discuss the findings with the class. The class in consultation with the instructors then developed a set of unified mission requirements. Then the class was divided into three design groups (1) Aerodynamics Group, (2) Propulsion Group, and (3) Structures and Thermal Analyses Group. The groups worked on their respective design areas and interacted with each other to finally come up with an integrated conceptual design. The three faculty members and the GTA acted as the resource persons for the three groups and aided in the integration of the individual group designs into the final design of a hypersonic aircraft.

Crown traits of coniferous trees and their relation to shade tolerance can differ with leaf type: a biophysical demonstration using computed tomography scanning data.

PubMed

Dutilleul, Pierre; Han, Liwen; Valladares, Fernando; Messier, Christian

2015-01-01

Plant light interception and shade tolerance are intrinsically related in that they involve structural, morphological and physiological adaptations to manage light capture for photosynthetic utilization, in order to sustain survival, development and reproduction. At the scale of small-size trees, crown traits related to structural geometry of branching pattern and space occupancy through phyllotaxis can be accurately evaluated in 3D, using computed tomography (CT) scanning data. We demonstrate this by scrutinizing the crowns of 15 potted miniature conifers of different species or varieties, classified in two groups based on leaf type (10 needlelike, 5 scalelike); we also test whether mean values of crown traits measured from CT scanning data and correlations with a shade tolerance index (STI) differ between groups. Seven crown traits, including fractal dimensions (FD1: smaller scales, FD2: larger scales) and leaf areas, were evaluated for all 15 miniature conifers; an average silhouette-to-total-area ratio was also calculated for each of the 10 needlelike-leaf conifers. Between-group differences in mean values are significant (P < 0.05) for STI, FD1, FD2, and the average leaf area displayed (ĀD). Between-group differences in sign and strength of correlations are observed. For example, the correlation between STI and FD1 is negative and significant (P < 0.10) for the needlelike-leaf group, but is positive and significant (P < 0.05) for the miniature conifers with scalelike leaves, which had lower STI and higher FD1 on average in our study; the positive correlation between STI and ĀD is significant (P < 0.05) for the scalelike-leaf group, and very moderate for the needlelike-leaf one. A contrasting physical attachment of the leaves to branches may explain part of the between-group differences. Our findings open new avenues for the understanding of fundamental plant growth processes; the information gained could be included in a multi-scale approach to tree crown modeling.

Research Needs for Human Factors

DTIC Science & Technology

1983-01-01

their relative merits. Until such comparisons are made, practitioners will continue to advocate their own products without a basis for choice among ...judgments among a group of experts; (2) formulating questions for "experts in a way that is compatible with their mental structures or "cognitive...system* Typically the operators work in teams and control compute3, which in turn mediate information flow among various automatic components. Other

Determination of Physical Properties of Ionic Liquids Using Molecular Simulations

DTIC Science & Technology

2010-08-20

That is, most groups rely on relatively short (100-500 ps) simulations and evaluate the viscosity via conventional Green - Kubo integration . In this...and can contribute to higher than expected viscosities . The liquid structure of the energetic ionic liquid 2-hydroxyethylhydrizinium nitrate was...claimed previously that neglect of polarizability leads to inaccuracies in the computed transport properties of ionic liquids such as viscosities

Program Helps Decompose Complex Design Systems

NASA Technical Reports Server (NTRS)

Rogers, James L., Jr.; Hall, Laura E.

1994-01-01

DeMAID (A Design Manager's Aid for Intelligent Decomposition) computer program is knowledge-based software system for ordering sequence of modules and identifying possible multilevel structure for design problem. Groups modular subsystems on basis of interactions among them. Saves considerable money and time in total design process, particularly in new design problem in which order of modules has not been defined. Available in two machine versions: Macintosh and Sun.

Recognition of Computer Viruses by Detecting Their Gene of Self Replication

DTIC Science & Technology

2006-03-01

etection A pproach ................................................................................................. 6 1.4.1 The syntactic analysis m...Therefore a group of instructions acting together in the right order have to be identified for the gene of self-replication to be obvious in a...its first system call NtCreateFile, while the outputs of NtWriteFile become its output arguments. These four blocks form the final structure - The Gene

Quantum chemical parameters in QSAR: what do I use when?

USGS Publications Warehouse

Hickey, James P.; Ostrander, Gary K.

1996-01-01

This chapter provides a brief overview of the numerous quantum chemical parameters that have been/are currently being used in quantitative structure activity relationships (QSAR), along with a representative bibliography. The parameters will be grouped according to their mechanistic interpretations, and representative biological and physical chemical applications will be mentioned. Parmater computation methods and the appropriate software are highlighted, as are sources for software.

Structure Elucidation of Mixed-Linker Zeolitic Imidazolate Frameworks by Solid-State (1)H CRAMPS NMR Spectroscopy and Computational Modeling.

PubMed

Jayachandrababu, Krishna C; Verploegh, Ross J; Leisen, Johannes; Nieuwendaal, Ryan C; Sholl, David S; Nair, Sankar

2016-06-15

Mixed-linker zeolitic imidazolate frameworks (ZIFs) are nanoporous materials that exhibit continuous and controllable tunability of properties like effective pore size, hydrophobicity, and organophilicity. The structure of mixed-linker ZIFs has been studied on macroscopic scales using gravimetric and spectroscopic techniques. However, it has so far not been possible to obtain information on unit-cell-level linker distribution, an understanding of which is key to predicting and controlling their adsorption and diffusion properties. We demonstrate the use of (1)H combined rotation and multiple pulse spectroscopy (CRAMPS) NMR spin exchange measurements in combination with computational modeling to elucidate potential structures of mixed-linker ZIFs, particularly the ZIF 8-90 series. All of the compositions studied have structures that have linkers mixed at a unit-cell-level as opposed to separated or highly clustered phases within the same crystal. Direct experimental observations of linker mixing were accomplished by measuring the proton spin exchange behavior between functional groups on the linkers. The data were then fitted to a kinetic spin exchange model using proton positions from candidate mixed-linker ZIF structures that were generated computationally using the short-range order (SRO) parameter as a measure of the ordering, clustering, or randomization of the linkers. The present method offers the advantages of sensitivity without requiring isotope enrichment, a straightforward NMR pulse sequence, and an analysis framework that allows one to relate spin diffusion behavior to proposed atomic positions. We find that structures close to equimolar composition of the two linkers show a greater tendency for linker clustering than what would be predicted based on random models. Using computational modeling we have also shown how the window-type distribution in experimentally synthesized mixed-linker ZIF-8-90 materials varies as a function of their composition. The structural information thus obtained can be further used for predicting, screening, or understanding the tunable adsorption and diffusion behavior of mixed-linker ZIFs, for which the knowledge of linker distributions in the framework is expected to be important.

Causal Learning with Local Computations

ERIC Educational Resources Information Center

Fernbach, Philip M.; Sloman, Steven A.

2009-01-01

The authors proposed and tested a psychological theory of causal structure learning based on local computations. Local computations simplify complex learning problems via cues available on individual trials to update a single causal structure hypothesis. Structural inferences from local computations make minimal demands on memory, require…

Target recognition and scene interpretation in image/video understanding systems based on network-symbolic models

NASA Astrophysics Data System (ADS)

Kuvich, Gary

2004-08-01

Vision is only a part of a system that converts visual information into knowledge structures. These structures drive the vision process, resolving ambiguity and uncertainty via feedback, and provide image understanding, which is an interpretation of visual information in terms of these knowledge models. These mechanisms provide a reliable recognition if the object is occluded or cannot be recognized as a whole. It is hard to split the entire system apart, and reliable solutions to the target recognition problems are possible only within the solution of a more generic Image Understanding Problem. Brain reduces informational and computational complexities, using implicit symbolic coding of features, hierarchical compression, and selective processing of visual information. Biologically inspired Network-Symbolic representation, where both systematic structural/logical methods and neural/statistical methods are parts of a single mechanism, is the most feasible for such models. It converts visual information into relational Network-Symbolic structures, avoiding artificial precise computations of 3-dimensional models. Network-Symbolic Transformations derive abstract structures, which allows for invariant recognition of an object as exemplar of a class. Active vision helps creating consistent models. Attention, separation of figure from ground and perceptual grouping are special kinds of network-symbolic transformations. Such Image/Video Understanding Systems will be reliably recognizing targets.

Influence of Heat Treatment of Nickel-Titanium Rotary Endodontic Instruments on Apical Preparation: A Micro-Computed Tomographic Study.

PubMed

de Almeida, Bernardo Corrêa; Ormiga, Fabíola; de Araújo, Marcos César Pimenta; Lopes, Ricardo Tadeu; Lima, Inayá Corrêa Barbosa; dos Santos, Bernardo Camargo; Gusman, Heloisa

2015-12-01

The aim of this study was to make a 3-dimensional comparison of the canal transportation and changes in apical geometry using micro-computed tomographic imaging after canal preparation with K3 (SybronEndo, Orange, CA) and K3XF (SybronEndo) file systems. Twenty-eight mandibular molars were randomly divided into 2 groups according to the rotary system used in instrumentation: K3 or K3XF. The specimens were scanned by micro-computed tomographic imaging before and after instrumentation. Images before and after instrumentation from each group were compared with regard to canal volume, surface area, and structure model index (SMI) (paired t test, P < .05). After instrumentation, the canals from each group were compared regarding the changes in volume, surface area, SMI, and canal transportation in the last 4 apical mm (t test, P < .05). Instrumentation with the 2 rotary systems significantly changed the canal volume, surface area, and SMI (P < .05). There were no significant differences between instrument types concerning these parameters (P > .05). There were no significant differences between the 2 groups with regard to canal transportation in the last 4 apical mm (P > .05). Both rotary systems showed adequate canal preparations with reduced values of canal transportation. Heat treatment did not influence changes in root canal geometry in the apical region. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

On Topological Indices of Certain Dendrimer Structures

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Bashir, Yasir; Ahmad, Safyan; Gao, Wei

2017-05-01

A topological index can be considered as transformation of chemical structure in to real number. In QSAR/QSPR study, physicochemical properties and topological indices such as Randić, Zagreb, atom-bond connectivity ABC, and geometric-arithmetic GA index are used to predict the bioactivity of chemical compounds. Dendrimers are highly branched, star-shaped macromolecules with nanometer-scale dimensions. Dendrimers are defined by three components: a central core, an interior dendritic structure (the branches), and an exterior surface with functional surface groups. In this paper we determine generalised Randić, general Zagreb, general sum-connectivity indices of poly(propyl) ether imine, porphyrin, and zinc-Porphyrin dendrimers. We also compute ABC and GA indices of these families of dendrimers.

Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika; Wawer, Iwona

2016-06-01

In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

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.

Bayesian Group Bridge for Bi-level Variable Selection.

PubMed

Mallick, Himel; Yi, Nengjun

2017-06-01

A Bayesian bi-level variable selection method (BAGB: Bayesian Analysis of Group Bridge) is developed for regularized regression and classification. This new development is motivated by grouped data, where generic variables can be divided into multiple groups, with variables in the same group being mechanistically related or statistically correlated. As an alternative to frequentist group variable selection methods, BAGB incorporates structural information among predictors through a group-wise shrinkage prior. Posterior computation proceeds via an efficient MCMC algorithm. In addition to the usual ease-of-interpretation of hierarchical linear models, the Bayesian formulation produces valid standard errors, a feature that is notably absent in the frequentist framework. Empirical evidence of the attractiveness of the method is illustrated by extensive Monte Carlo simulations and real data analysis. Finally, several extensions of this new approach are presented, providing a unified framework for bi-level variable selection in general models with flexible penalties.

Large Scale Structures in the GOODS-SOUTH Field up to z~2.5

NASA Astrophysics Data System (ADS)

Trevese, D.; Castellano, M.; Salimbeni, S.; Pentericci, L.; Fiore, F.

2009-05-01

We apply a density evaluation technique based on photometric redshifts, developed by our group, to estimate galaxy space density on the deep (z450~26) multi-wavelength GOODS-MUSIC catalogue. We find several groups and clusters in the redshift range 0.4-2.5. We present here an outline of the X-ray properties of our cluster sample as computed from the Chandra 2Ms data. A group at z = 0.96 could be associated to an extended X-ray source, while two clusters with masses of few times 1014Msolar have upper limits on their X-ray emission significantly lower than expected from their optical properties.

The use of computer simulations in whole-class versus small-group settings

NASA Astrophysics Data System (ADS)

Smetana, Lara Kathleen

This study explored the use of computer simulations in a whole-class as compared to small-group setting. Specific consideration was given to the nature and impact of classroom conversations and interactions when computer simulations were incorporated into a high school chemistry course. This investigation fills a need for qualitative research that focuses on the social dimensions of actual classrooms. Participants included a novice chemistry teacher experienced in the use of educational technologies and two honors chemistry classes. The study was conducted in a rural school in the south-Atlantic United States at the end of the fall 2007 semester. The study took place during one instructional unit on atomic structure. Data collection allowed for triangulation of evidence from a variety of sources approximately 24 hours of video- and audio-taped classroom observations, supplemented with the researcher's field notes and analytic journal; miscellaneous classroom artifacts such as class notes, worksheets, and assignments; open-ended pre- and post-assessments; student exit interviews; teacher entrance, exit and informal interviews. Four web-based simulations were used, three of which were from the ExploreLearning collection. Assessments were analyzed using descriptive statistics and classroom observations, artifacts and interviews were analyzed using Erickson's (1986) guidelines for analytic induction. Conversational analysis was guided by methods outlined by Erickson (1982). Findings indicated (a) the teacher effectively incorporated simulations in both settings (b) students in both groups significantly improved their understanding of the chemistry concepts (c) there was no statistically significant difference between groups' achievement (d) there was more frequent exploratory talk in the whole-class group (e) there were more frequent and meaningful teacher-student interactions in the whole-class group (f) additional learning experiences not measured on the assessment resulted from conversations and interactions in the whole-class setting (g) the potential benefits of exploratory talk in the whole-class setting were not fully realized. These findings suggest that both whole-class and small-group settings are appropriate for using computer simulations in science. The effective incorporation of simulations into whole-class instruction may provide a solution to the dilemma of technology penetration versus integration in today's classrooms.

Software tools for interactive instruction in radiologic anatomy.

PubMed

Alvarez, Antonio; Gold, Garry E; Tobin, Brian; Desser, Terry S

2006-04-01

To promote active learning in an introductory Radiologic Anatomy course through the use of computer-based exercises. DICOM datasets from our hospital PACS system were transferred to a networked cluster of desktop computers in a medical school classroom. Medical students in the Radiologic Anatomy course were divided into four small groups and assigned to work on a clinical case for 45 minutes. The groups used iPACS viewer software, a free DICOM viewer, to view images and annotate anatomic structures. The classroom instructor monitored and displayed each group's work sequentially on the master screen by running SynchronEyes, a software tool for controlling PC desktops remotely. Students were able to execute the assigned tasks using the iPACS software with minimal oversight or instruction. Course instructors displayed each group's work on the main display screen of the classroom as the students presented the rationale for their decisions. The interactive component of the course received high ratings from the students and overall course ratings were higher than in prior years when the course was given solely in lecture format. DICOM viewing software is an excellent tool for enabling students to learn radiologic anatomy from real-life clinical datasets. Interactive exercises performed in groups can be powerful tools for stimulating students to learn radiologic anatomy.

Conformation, structure and molecular solvation: a spectroscopic and computational study of 2-phenoxy ethanol and its singly and multiply hydrated clusters

NASA Astrophysics Data System (ADS)

Macleod, Neil A.; Simons, John P.

2002-10-01

The conformational landscapes of 2-phenoxy ethanol (POX) and its hydrated clusters have been studied in the gas-phase, providing a model for pharmaceutical β-blockers. A combination of experimental techniques, including resonant two-photon ionisation (R2PI), laser-induced-fluorescence (LIF) and resonant ion-dip infra-red spectroscopy (RIDIRS), coupled with high-level ab initio calculations has allowed the assignment of the individually resolved spectral features to discrete conformational and supra-molecular structures. Assignments were made by comparison of experimental vibrational spectra and partially resolved ultra-violet rotational band contours with those predicted from quantum chemical calculations. The isolated molecule displays a solitary structure with an extended geometry of the side-chain which is stabilised by an intramolecular hydrogen-bond between the alcohol (proton donor) and the ether (proton acceptor) groups of the side-chain. In singly hydrated clusters the water molecule is accommodated by insertion into the intramolecular hydrogen-bond. In the doubly hydrated and higher clusters cyclic structures are generated which incorporate both the water molecules and the terminal OH group of the side-chain; additional (weak) hydrogen bonded interactions with the phenoxy group provide a degree of selectivity but essentially, the water 'droplet' forms on the end of the alcohol side-chain.

Molecular Modeling of a Probe in 2D IR Spectroscopy

NASA Astrophysics Data System (ADS)

Cooper, Anthony; Larini, Luca

Proteins must adopt a precise three dimensional structure in the folding process in order to perform its designated function. Although much has been learned about folding, there are still many details in structural dynamics that are difficult to characterize by existing experimental techniques. In order to overcome these challenges, novel infrared and fluorescent spectroscopic techniques have recently been employed to probe the molecular structure at the atomistic scale. These techniques rely on the spectroscopic properties of the nitrile group attached to a phenylalanine. In this study, we model this probe and we compute its properties in different solvents. This is done by performing Molecular Dynamics simulations with a PheCN solvated in water, urea and TMAO. We measure the decay rate of the vibrational stretching of the CN group in order to characterize the effects of different solvents on the local structure of the molecule. This data can be used to identify non-trivial conformational changes of the protein in the folding process. Preliminary results show agreement with current experimental data on 2D IR spectroscopy.

Evaluation of multiple-scale 3D characterization for coal physical structure with DCM method and synchrotron X-ray CT.

PubMed

Wang, Haipeng; Yang, Yushuang; Yang, Jianli; Nie, Yihang; Jia, Jing; Wang, Yudan

2015-01-01

Multiscale nondestructive characterization of coal microscopic physical structure can provide important information for coal conversion and coal-bed methane extraction. In this study, the physical structure of a coal sample was investigated by synchrotron-based multiple-energy X-ray CT at three beam energies and two different spatial resolutions. A data-constrained modeling (DCM) approach was used to quantitatively characterize the multiscale compositional distributions at the two resolutions. The volume fractions of each voxel for four different composition groups were obtained at the two resolutions. Between the two resolutions, the difference for DCM computed volume fractions of coal matrix and pores is less than 0.3%, and the difference for mineral composition groups is less than 0.17%. This demonstrates that the DCM approach can account for compositions beyond the X-ray CT imaging resolution with adequate accuracy. By using DCM, it is possible to characterize a relatively large coal sample at a relatively low spatial resolution with minimal loss of the effect due to subpixel fine length scale structures.

Optimizing isotope substitution in graphene for thermal conductivity minimization by genetic algorithm driven molecular simulations

NASA Astrophysics Data System (ADS)

Davies, Michael; Ganapathysubramanian, Baskar; Balasubramanian, Ganesh

2017-03-01

We present results from a computational framework integrating genetic algorithm and molecular dynamics simulations to systematically design isotope engineered graphene structures for reduced thermal conductivity. In addition to the effect of mass disorder, our results reveal the importance of atomic distribution on thermal conductivity for the same isotopic concentration. Distinct groups of isotope-substituted graphene sheets are identified based on the atomic composition and distribution. Our results show that in structures with equiatomic compositions, the enhanced scattering by lattice vibrations results in lower thermal conductivities due to the absence of isotopic clusters.

HAL/SM system functional design specification. [systems analysis and design analysis of central processing units

NASA Technical Reports Server (NTRS)

Ross, C.; Williams, G. P. W., Jr.

1975-01-01

The functional design of a preprocessor, and subsystems is described. A structure chart and a data flow diagram are included for each subsystem. Also a group of intermodule interface definitions (one definition per module) is included immediately following the structure chart and data flow for a particular subsystem. Each of these intermodule interface definitions consists of the identification of the module, the function the module is to perform, the identification and definition of parameter interfaces to the module, and any design notes associated with the module. Also described are compilers and computer libraries.

The impact of haptic feedback on students' conceptions of the cell

NASA Astrophysics Data System (ADS)

Minogue, James

2005-07-01

The purpose of this study was to investigate the efficacy of adding haptic (sense of touch) feedback to computer generated visualizations for use in middle school science instruction. Current technology allows for the simulation of tactile and kinesthetic sensations via haptic devices and a computer interface. This study, conducted with middle school students (n = 80), explored the cognitive and affective impacts of this innovative technology on students' conceptions of the cell and the process of passive transport. A pretest-posttest control group design was used and participants were randomly assigned to one of two treatment groups (n = 40 for each). Both groups experienced the same core computer-mediated instructional program. This Cell Exploration program engaged students in a 3-D immersive environment that allowed them to actively investigate the form and function of a typical animal cell including its major organelles. The program also engaged students in a study of the structure and function of the cell membrane as it pertains to the process of passive transport and the mechanisms behind the membrane's selective permeability. As they conducted their investigations, students in the experimental group received bi-modal visual and haptic (simulated tactile and kinesthetic) feedback whereas the control group students experienced the program with only visual stimuli. A battery of assessments, including objective and open-ended written response items as well as a haptic performance assessment, were used to gather quantitative and qualitative data regarding changes in students' understandings of the cell concepts prior to and following their completion of the instructional program. Additionally, the impact of haptics on the affective domain of students' learning was assessed using a post-experience semi-structured interview and an attitudinal survey. Results showed that students from both conditions (Visual-Only and Visual + Haptic) found the instructional program interesting and engaging. Additionally, the vast majority of the students reported that they learned a lot about and were more interested in the topic due to their participation. Moreover, students who received the bi-modal (Visual + Haptic) feedback indicated that they experienced lower levels of frustration and spatial disorientation as they conducted their investigations when compared to individuals that relied solely on vision. There were no significant differences measured across the treatment groups on the cognitive assessment items. Despite this finding, the study provided valuable insight into the theoretical and practical considerations involved in the development of multimodal instructional programs.

The effects of flow on schooling Devario aequipinnatus: school structure, startle response and information transmission

PubMed Central

Chicoli, A.; Butail, S.; Lun, Y.; Bak-Coleman, J.; Coombs, S.; Paley, D.A.

2014-01-01

To assess how flow affects school structure and threat detection, startle response rates of solitary and small groups of giant danio Devario aequipinnatus were compared to visual looming stimuli in flow and no-flow conditions. The instantaneous position and heading of each D. aequipinnatus were extracted from high-speed videos. Behavioural results indicate that (1) school structure is altered in flow such that D. aequipinnatus orient upstream while spanning out in a crosswise direction, (2) the probability of at least one D. aequipinnatus detecting the visual looming stimulus is higher in flow than no flow for both solitary D. aequipinnatus and groups of eight D. aequipinnatus, however, (3) the probability of three or more individuals responding is higher in no flow than flow. Taken together, these results indicate a higher probability of stimulus detection in flow but a higher probability of internal transmission of information in no flow. Finally, results were well predicted by a computational model of collective fright response that included the probability of direct detection (based on signal detection theory) and indirect detection (i.e. via interactions between group members) of threatening stimuli. This model provides a new theoretical framework for analysing the collective transfer of information among groups of fishes and other organisms. PMID:24773538

The effects of a computer skill training programme adopting social comparison and self-efficacy enhancement strategies on self-concept and skill outcome in trainees with physical disabilities.

PubMed

Tam, S F

2000-10-15

The aim of this controlled, quasi-experimental study was to evaluate the effects of both self-efficacy enhancement and social comparison training strategy on computer skills learning and self-concept outcome of trainees with physical disabilities. The self-efficacy enhancement group comprised 16 trainees, the tutorial training group comprised 15 trainees, and there were 25 subjects in the control group. Both the self-efficacy enhancement group and the tutorial training group received a 15 week computer skills training course, including generic Chinese computer operation, Chinese word processing and Chinese desktop publishing skills. The self-efficacy enhancement group received training with tutorial instructions that incorporated self-efficacy enhancement strategies and experienced self-enhancing social comparisons. The tutorial training group received behavioural learning-based tutorials only, and the control group did not receive any training. The following measurements were employed to evaluate the outcomes: the Self-Concept Questionnaire for the Physically Disabled Hong Kong Chinese (SCQPD), the computer self-efficacy rating scale and the computer performance rating scale. The self-efficacy enhancement group showed significantly better computer skills learning outcome, total self-concept, and social self-concept than the tutorial training group. The self-efficacy enhancement group did not show significant changes in their computer self-efficacy: however, the tutorial training group showed a significant lowering of their computer self-efficacy. The training strategy that incorporated self-efficacy enhancement and positive social comparison experiences maintained the computer self-efficacy of trainees with physical disabilities. This strategy was more effective in improving the learning outcome (p = 0.01) and self-concept (p = 0.05) of the trainees than the conventional tutorial-based training strategy.

Configuring compute nodes of a parallel computer in an operational group into a plurality of independent non-overlapping collective networks

DOEpatents

Archer, Charles J.; Inglett, Todd A.; Ratterman, Joseph D.; Smith, Brian E.

2010-03-02

Methods, apparatus, and products are disclosed for configuring compute nodes of a parallel computer in an operational group into a plurality of independent non-overlapping collective networks, the compute nodes in the operational group connected together for data communications through a global combining network, that include: partitioning the compute nodes in the operational group into a plurality of non-overlapping subgroups; designating one compute node from each of the non-overlapping subgroups as a master node; and assigning, to the compute nodes in each of the non-overlapping subgroups, class routing instructions that organize the compute nodes in that non-overlapping subgroup as a collective network such that the master node is a physical root.

Computers and the Learning of Biological Concepts: Attitudes and Achievement of Nigerian Students.

ERIC Educational Resources Information Center

Jegede, Olugbemiro J.

1991-01-01

Compared attitudes toward computer use and achievement in biology for three groups of Nigerian students (n=64): (1) working alone with computer; (2) working in groups of three on the computer; (3) and a control group that received normal instruction (lecture). Students in the second group had the highest scores on attitude. No significant…

Characterization of porous glass fiber-reinforced composite (FRC) implant structures: porosity and mechanical properties.

PubMed

Ylä-Soininmäki, Anne; Moritz, Niko; Lassila, Lippo V J; Peltola, Matti; Aro, Hannu T; Vallittu, Pekka K

2013-12-01

The aim of this study was to characterize the microstructure and mechanical properties of porous fiber-reinforced composites (FRC). Implants made of the FRC structures are intended for cranial applications. The FRC specimens were prepared by impregnating E-glass fiber sheet with non-resorbable bifunctional bis-phenyl glycidyl dimethacrylate and triethylene glycol dimethacrylate resin matrix. Four groups of porous FRC specimens were prepared with a different amount of resin matrix. Control group contained specimens of fibers, which were bound together with sizing only. Microstructure of the specimens was analyzed using a micro computed tomography (micro-CT) based method. Mechanical properties of the specimens were measured with a tensile test. The amount of resin matrix in the specimens had an effect on the microstructure. Total porosity was 59.5 % (median) in the group with the lowest resin content and 11.2 % (median) in the group with the highest resin content. In control group, total porosity was 94.2 % (median). Correlations with resin content were obtained for all micro-CT based parameters except TbPf. The tensile strength of the composites was 21.3 MPa (median) in the group with the highest resin content and 43.4 MPa (median) in the group with the highest resin content. The tensile strength in control group was 18.9 MPa (median). There were strong correlations between the tensile strength of the specimens and most of the micro-CT based parameters. This experiment suggests that porous FRC structures may have the potential for use in implants for cranial bone reconstructions, provided further relevant in vitro and in vivo tests are performed.

Microwave Spectra of the Two Conformers of PROPENE-3-{d}_1 and a Semiexperimental Equilibrium Structure of Propene

NASA Astrophysics Data System (ADS)

Craig, Norman C.; Demaison, J.; Rudolph, Heinz Dieter; Gurusinghe, Ranil M.; Tubergen, Michael; Coudert, L. H.; Szalay, Peter; Császár, Attila

2017-06-01

FT microwave spectra have been observed and analyzed for the S (in-plane) and A (out-of-plane) conformers of propene-3-{d}_1 in the 10-22 GHz region. Both conformers display splittings due to deuterium quadrupole coupling; for the latter one only, a 19 MHz splitting due to internal rotation of the partially deuterated methyl group has been observed. In addition to rotational constants, the analysis yielded quadrupole coupling constants and parameters describing the tunneling splitting and its rotational dependence. Improved rotational constants for parent propene and the three ^{13}C_1 species are recently available. Use of vibration-rotation interaction constants computed at the MP2(FC)/cc-pVTZ level gave equilibrium rotational constants for these six species and for fourteen more deuterium isotopologues with diminished accuracy from early literature data. A semiexperimental equilibrium structure, r_e^{SE}, has been determined for propene by fitting fourteen structural parameters to the equilibrium rotational constants. The new r_e^{SE} structure compares well with an ab initio equilibrium structure computed with the all-electron CCSD(T)/cc-pV(Q,T)Z model and with a structure obtained using the mixed regression method with predicates and equilibrium rotational constants. N. C. Craig, P. Groner, A. R. Conrad, R. Gurusinghe, M. J. Tubergen J. Mol. Spectrosc. 248, 1-6 (2016).

Hierarchical semi-numeric method for pairwise fuzzy group decision making.

PubMed

Marimin, M; Umano, M; Hatono, I; Tamura, H

2002-01-01

Gradual improvements to a single-level semi-numeric method, i.e., linguistic labels preference representation by fuzzy sets computation for pairwise fuzzy group decision making are summarized. The method is extended to solve multiple criteria hierarchical structure pairwise fuzzy group decision-making problems. The problems are hierarchically structured into focus, criteria, and alternatives. Decision makers express their evaluations of criteria and alternatives based on each criterion by using linguistic labels. The labels are converted into and processed in triangular fuzzy numbers (TFNs). Evaluations of criteria yield relative criteria weights. Evaluations of the alternatives, based on each criterion, yield a degree of preference for each alternative or a degree of satisfaction for each preference value. By using a neat ordered weighted average (OWA) or a fuzzy weighted average operator, solutions obtained based on each criterion are aggregated into final solutions. The hierarchical semi-numeric method is suitable for solving a larger and more complex pairwise fuzzy group decision-making problem. The proposed method has been verified and applied to solve some real cases and is compared to Saaty's (1996) analytic hierarchy process (AHP) method.

Structures of Saccharomyces cerevisiae D-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition.

PubMed

Hu, Xiao-Qian; Guo, Peng-Chao; Ma, Jin-Di; Li, Wei-Fang

2013-11-01

The primary role of yeast Ara1, previously mis-annotated as a D-arabinose dehydrogenase, is to catalyze the reduction of a variety of toxic α,β-dicarbonyl compounds using NADPH as a cofactor at physiological pH levels. Here, crystal structures of Ara1 in apo and NADPH-complexed forms are presented at 2.10 and 2.00 Å resolution, respectively. Ara1 exists as a homodimer, each subunit of which adopts an (α/β)8-barrel structure and has a highly conserved cofactor-binding pocket. Structural comparison revealed that induced fit upon NADPH binding yielded an intact active-site pocket that recognizes the substrate. Moreover, the crystal structures combined with computational simulation defined an open substrate-binding site to accommodate various substrates that possess a dicarbonyl group.

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

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

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moietymore » with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. Finally, we also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.« less

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

PubMed Central

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

2016-01-01

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties. PMID:27870845

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks

DOE PAGES

Haraldsdóttir, Hulda S.; Fleming, Ronan M. T.

2016-11-21

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moietymore » with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. Finally, we also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.« less

Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks.

PubMed

Haraldsdóttir, Hulda S; Fleming, Ronan M T

2016-11-01

Conserved moieties are groups of atoms that remain intact in all reactions of a metabolic network. Identification of conserved moieties gives insight into the structure and function of metabolic networks and facilitates metabolic modelling. All moiety conservation relations can be represented as nonnegative integer vectors in the left null space of the stoichiometric matrix corresponding to a biochemical network. Algorithms exist to compute such vectors based only on reaction stoichiometry but their computational complexity has limited their application to relatively small metabolic networks. Moreover, the vectors returned by existing algorithms do not, in general, represent conservation of a specific moiety with a defined atomic structure. Here, we show that identification of conserved moieties requires data on reaction atom mappings in addition to stoichiometry. We present a novel method to identify conserved moieties in metabolic networks by graph theoretical analysis of their underlying atom transition networks. Our method returns the exact group of atoms belonging to each conserved moiety as well as the corresponding vector in the left null space of the stoichiometric matrix. It can be implemented as a pipeline of polynomial time algorithms. Our implementation completes in under five minutes on a metabolic network with more than 4,000 mass balanced reactions. The scalability of the method enables extension of existing applications for moiety conservation relations to genome-scale metabolic networks. We also give examples of new applications made possible by elucidating the atomic structure of conserved moieties.

Theoretical study on the electronic structures and phosphorescent properties of four Ir(III) complexes with different substituents on the ancillary ligand

NASA Astrophysics Data System (ADS)

Han, Deming; Shang, Xiaohong; Zhang, Gang; Zhao, Lihui

2013-12-01

The geometry structures, electronic structures, absorption and phosphorescent properties of four Ir(III) complexes {[(F2-ppy)2Ir(pta-X)], where F2-ppy = (2,4-difluoro)phenylpyridine; pta = pyridine-1,2,4-triazole; X = -CF3; -H; -CH3; -N(CH3)2}, are investigated using the density functional method. The results reveal that the electron-accepting group -CF3 has no obvious effect on absorption and emission properties, while the substitutive group -N(CH3)2 with strong electron-donating ability has obvious effect on the emission properties. The mobility of hole and electron were studied computationally based on the Marcus-Hush theory. Calculations of ionisation potential and electron affinity were used to evaluate the injection abilities of holes and electrons into these complexes. We hope that this theoretical work can provide a suitable guide to the future design and synthesis of novel phosphorescent materials for use in the organic light-emitting diodes.

Properties of a soft-core model of methanol: An integral equation theory and computer simulation study

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

Huš, Matej; Urbic, Tomaz, E-mail: tomaz.urbic@fkkt.uni-lj.si; Munaò, Gianmarco

Thermodynamic and structural properties of a coarse-grained model of methanol are examined by Monte Carlo simulations and reference interaction site model (RISM) integral equation theory. Methanol particles are described as dimers formed from an apolar Lennard-Jones sphere, mimicking the methyl group, and a sphere with a core-softened potential as the hydroxyl group. Different closure approximations of the RISM theory are compared and discussed. The liquid structure of methanol is investigated by calculating site-site radial distribution functions and static structure factors for a wide range of temperatures and densities. Results obtained show a good agreement between RISM and Monte Carlo simulations.more » The phase behavior of methanol is investigated by employing different thermodynamic routes for the calculation of the RISM free energy, drawing gas-liquid coexistence curves that match the simulation data. Preliminary indications for a putative second critical point between two different liquid phases of methanol are also discussed.« less

COINS: A composites information database system

NASA Technical Reports Server (NTRS)

Siddiqi, Shahid; Vosteen, Louis F.; Edlow, Ralph; Kwa, Teck-Seng

1992-01-01

An automated data abstraction form (ADAF) was developed to collect information on advanced fabrication processes and their related costs. The information will be collected for all components being fabricated as part of the ACT program and include in a COmposites INformation System (COINS) database. The aim of the COINS development effort is to provide future airframe preliminary design and fabrication teams with a tool through which production cost can become a deterministic variable in the design optimization process. The effort was initiated by the Structures Technology Program Office (STPO) of the NASA LaRC to implement the recommendations of a working group comprised of representatives from the commercial airframe companies. The principal working group recommendation was to re-institute collection of composite part fabrication data in a format similar to the DOD/NASA Structural Composites Fabrication Guide. The fabrication information collection form was automated with current user friendly computer technology. This work in progress paper describes the new automated form and features that make the form easy to use by an aircraft structural design-manufacturing team.

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.

The influence of phylogeny, social style, and sociodemographic factors on macaque social network structure.

PubMed

Balasubramaniam, Krishna N; Beisner, Brianne A; Berman, Carol M; De Marco, Arianna; Duboscq, Julie; Koirala, Sabina; Majolo, Bonaventura; MacIntosh, Andrew J; McFarland, Richard; Molesti, Sandra; Ogawa, Hideshi; Petit, Odile; Schino, Gabriele; Sosa, Sebastian; Sueur, Cédric; Thierry, Bernard; de Waal, Frans B M; McCowan, Brenda

2018-01-01

Among nonhuman primates, the evolutionary underpinnings of variation in social structure remain debated, with both ancestral relationships and adaptation to current conditions hypothesized to play determining roles. Here we assess whether interspecific variation in higher-order aspects of female macaque (genus: Macaca) dominance and grooming social structure show phylogenetic signals, that is, greater similarity among more closely-related species. We use a social network approach to describe higher-order characteristics of social structure, based on both direct interactions and secondary pathways that connect group members. We also ask whether network traits covary with each other, with species-typical social style grades, and/or with sociodemographic characteristics, specifically group size, sex-ratio, and current living condition (captive vs. free-living). We assembled 34-38 datasets of female-female dyadic aggression and allogrooming among captive and free-living macaques representing 10 species. We calculated dominance (transitivity, certainty), and grooming (centrality coefficient, Newman's modularity, clustering coefficient) network traits as aspects of social structure. Computations of K statistics and randomization tests on multiple phylogenies revealed moderate-strong phylogenetic signals in dominance traits, but moderate-weak signals in grooming traits. GLMMs showed that grooming traits did not covary with dominance traits and/or social style grade. Rather, modularity and clustering coefficient, but not centrality coefficient, were strongly predicted by group size and current living condition. Specifically, larger groups showed more modular networks with sparsely-connected clusters than smaller groups. Further, this effect was independent of variation in living condition, and/or sampling effort. In summary, our results reveal that female dominance networks were more phylogenetically conserved across macaque species than grooming networks, which were more labile to sociodemographic factors. Such findings narrow down the processes that influence interspecific variation in two core aspects of macaque social structure. Future directions should include using phylogeographic approaches, and addressing challenges in examining the effects of socioecological factors on primate social structure. © 2017 Wiley Periodicals, Inc.

Aeroelastic Modeling of a Nozzle Startup Transient

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2014-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a tightly coupled aeroelastic modeling algorithm by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed under the framework of modal analysis. Transient aeroelastic nozzle startup analyses at sea level were performed, and the computed transient nozzle fluid-structure interaction physics presented,

Vector-borne diseases models with residence times - A Lagrangian perspective.

PubMed

Bichara, Derdei; Castillo-Chavez, Carlos

2016-11-01

A multi-patch and multi-group modeling framework describing the dynamics of a class of diseases driven by the interactions between vectors and hosts structured by groups is formulated. Hosts' dispersal is modeled in terms of patch-residence times with the nonlinear dynamics taking into account the effective patch-host size. The residence times basic reproduction number R 0 is computed and shown to depend on the relative environmental risk of infection. The model is robust, that is, the disease free equilibrium is globally asymptotically stable (GAS) if R 0 ≤1 and a unique interior endemic equilibrium is shown to exist that is GAS whenever R 0 >1 whenever the configuration of host-vector interactions is irreducible. The effects of patchiness and groupness, a measure of host-vector heterogeneous structure, on the basic reproduction number R 0 , are explored. Numerical simulations are carried out to highlight the effects of residence times on disease prevalence. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthetic tripodal receptors for carbohydrates. Pyrrole, a hydrogen bonding partner for saccharidic hydroxyls.

PubMed

Francesconi, Oscar; Gentili, Matteo; Roelens, Stefano

2012-09-07

The carbohydrate recognition properties of synthetic tripodal receptors relying on H-bonding interactions have highlighted the crucial role played by the functional groups matching saccharidic hydroxyls. Herein, pyrrole and pyridine, which emerged as two of the most effective H-bonding groups, were quantitatively compared through their isostructural substitution within the architecture of a shape-persistent bicyclic cage receptor. NMR and ITC binding studies gave for the pyrrolic receptor a 20-fold larger affinity toward octyl-β-d-glucopyranoside in CDCl(3), demonstrating the superior recognition properties of pyrrole under conditions in which differences would depend on the intrinsic binding ability of the two groups. The three-dimensional structures of the two glucoside complexes in solution were elucidated by combined NMR and molecular mechanics computational techniques, showing that the origin of the stability difference between the two closely similar complex structures resides in the ability of pyrrole to establish shorter/stronger H-bonds with the glucosidic ligand compared to pyridine.

MrGrid: A Portable Grid Based Molecular Replacement Pipeline

PubMed Central

Reboul, Cyril F.; Androulakis, Steve G.; Phan, Jennifer M. N.; Whisstock, James C.; Goscinski, Wojtek J.; Abramson, David; Buckle, Ashley M.

2010-01-01

Background The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. Methodology/Principal Findings MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. Conclusions MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success. PMID:20386612

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.

On the role of minicomputers in structural design

NASA Technical Reports Server (NTRS)

Storaasli, O. O.

1977-01-01

Results are presented of exploratory studies on the use of a minicomputer in conjunction with large-scale computers to perform structural design tasks, including data and program management, use of interactive graphics, and computations for structural analysis and design. An assessment is made of minicomputer use for the structural model definition and checking and for interpreting results. Included are results of computational experiments demonstrating the advantages of using both a minicomputer and a large computer to solve a large aircraft structural design problem.

Data communication network at the ASRM facility

NASA Astrophysics Data System (ADS)

Moorhead, Robert J., II; Smith, Wayne D.

1993-08-01

This report describes the simulation of the overall communication network structure for the Advanced Solid Rocket Motor (ASRM) facility being built at Yellow Creek near Iuka, Mississippi as of today. The report is compiled using information received from NASA/MSFC, LMSC, AAD, and RUST Inc. As per the information gathered, the overall network structure will have one logical FDDI ring acting as a backbone for the whole complex. The buildings will be grouped into two categories viz. manufacturing intensive and manufacturing non-intensive. The manufacturing intensive buildings will be connected via FDDI to the Operational Information System (OIS) in the main computing center in B_1000. The manufacturing non-intensive buildings will be connected by 10BASE-FL to the OIS through the Business Information System (BIS) hub in the main computing center. All the devices inside B_1000 will communicate with the BIS. The workcells will be connected to the Area Supervisory Computers (ASCs) through the nearest manufacturing intensive hub and one of the OIS hubs. Comdisco's Block Oriented Network Simulator (BONeS) has been used to simulate the performance of the network. BONeS models a network topology, traffic, data structures, and protocol functions using a graphical interface. The main aim of the simulations was to evaluate the loading of the OIS, the BIS, and the ASCs, and the network links by the traffic generated by the workstations and workcells throughout the site.

Semi-automatic forensic approach using mandibular midline lingual structures as fingerprint: a pilot study.

PubMed

Shaheen, E; Mowafy, B; Politis, C; Jacobs, R

2017-12-01

Previous research proposed the use of the mandibular midline neurovascular canal structures as a forensic finger print. In their observer study, an average correct identification of 95% was reached which triggered this study. To present a semi-automatic computer recognition approach to replace the observers and to validate the accuracy of this newly proposed method. Imaging data from Computer Tomography (CT) and Cone Beam Computer Tomography (CBCT) of mandibles scanned at two different moments were collected to simulate an AM and PM situation where the first scan presented AM and the second scan was used to simulate PM. Ten cases with 20 scans were used to build a classifier which relies on voxel based matching and results with classification into one of two groups: "Unmatched" and "Matched". This protocol was then tested using five other scans out of the database. Unpaired t-testing was applied and accuracy of the computerized approach was determined. A significant difference was found between the "Unmatched" and "Matched" classes with means of 0.41 and 0.86 respectively. Furthermore, the testing phase showed an accuracy of 100%. The validation of this method pushes this protocol further to a fully automatic identification procedure for victim identification based on the mandibular midline canals structures only in cases with available AM and PM CBCT/CT data.

Data communication network at the ASRM facility

NASA Technical Reports Server (NTRS)

Moorhead, Robert J., II; Smith, Wayne D.

1993-01-01

This report describes the simulation of the overall communication network structure for the Advanced Solid Rocket Motor (ASRM) facility being built at Yellow Creek near Iuka, Mississippi as of today. The report is compiled using information received from NASA/MSFC, LMSC, AAD, and RUST Inc. As per the information gathered, the overall network structure will have one logical FDDI ring acting as a backbone for the whole complex. The buildings will be grouped into two categories viz. manufacturing intensive and manufacturing non-intensive. The manufacturing intensive buildings will be connected via FDDI to the Operational Information System (OIS) in the main computing center in B_1000. The manufacturing non-intensive buildings will be connected by 10BASE-FL to the OIS through the Business Information System (BIS) hub in the main computing center. All the devices inside B_1000 will communicate with the BIS. The workcells will be connected to the Area Supervisory Computers (ASCs) through the nearest manufacturing intensive hub and one of the OIS hubs. Comdisco's Block Oriented Network Simulator (BONeS) has been used to simulate the performance of the network. BONeS models a network topology, traffic, data structures, and protocol functions using a graphical interface. The main aim of the simulations was to evaluate the loading of the OIS, the BIS, and the ASCs, and the network links by the traffic generated by the workstations and workcells throughout the site.

An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

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

Bokatzian, Samantha S.; Stover, Michele L.; Plummer, Chelsea E.

Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at themore » phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.« less

Student construction of small molecule models using Spartan Model to explore polarity

NASA Astrophysics Data System (ADS)

Dale, Glenn Lamar

2006-12-01

This study compared the attitudes and the gains of knowledge concerning Lewis structures and polarity of molecules. The students performed a lab exercise in which they drew Lewis structures, constructed models of the molecules, determined the geometry of the molecules, and determined the polarity of the molecules. The control group students constructed models using physical ball-and-stick models. The treatment group students used Spartan Model to construct models. Students from a university and a community college participated in this study. Four lab classes at each school made up the treatment group. Five lab classes at the university and three lab classes at the community college made up the control group. The treatment group classes were selected based on available computer resources. All students in the study were given the Lab Pre Test, Lab Post Test, and the Lecture Post Test to assess the student's ability to answer questions pertaining to Lewis structures and polarity of molecules. An Attitudinal Survey assessed the attitudes of the students who participated in the study. Student interviews were performed to assess the student's attitudes towards the lab exercise. The interviews investigated attitudes about the modeling exercise, Lewis structures, and polarity of molecules. There were no significant differences in the performance of the treatment group when compared to the control group on the performance assessment instruments at the university or the community college. The treatment group students at the university had a more positive attitude about the lab activity. They believed that the lab activity helped them better understand the concepts of Lewis structure and molecular polarity. At the community college, the control group students had a more positive attitude about the lab activity. The students involved in the study believed that the lab activity helped them to understand the concepts of molecular geometry and polarity. The interviews of the treatment group students indicated that they strongly believed that the lab activity helped them better understand the concept of Lewis structures and of molecular polarity. As reflected in the interviews of the treatment group and the control group, the lab activity did not help the students be able to look at a Lewis structure and build a mental image of the molecule. The students believed the electrostatic potential plots generated by Spartan Model were very insightful into the concept of polarity. It gave them a visual representation of a difficult topic.

CCP4i2: the new graphical user interface to the CCP4 program suite

PubMed Central

Potterton, Liz; Ballard, Charles; Dodson, Eleanor; Evans, Phil R.; Keegan, Ronan; Krissinel, Eugene; Stevenson, Kyle; Lebedev, Andrey; McNicholas, Stuart J.; Noble, Martin; Pannu, Navraj S.; Roth, Christian; Sheldrick, George; Skubak, Pavol; Uski, Ville

2018-01-01

The CCP4 (Collaborative Computational Project, Number 4) software suite for macromolecular structure determination by X-ray crystallography groups brings together many programs and libraries that, by means of well established conventions, interoperate effectively without adhering to strict design guidelines. Because of this inherent flexibility, users are often presented with diverse, even divergent, choices for solving every type of problem. Recently, CCP4 introduced CCP4i2, a modern graphical interface designed to help structural biologists to navigate the process of structure determination, with an emphasis on pipelining and the streamlined presentation of results. In addition, CCP4i2 provides a framework for writing structure-solution scripts that can be built up incrementally to create increasingly automatic procedures. PMID:29533233

Exploring the Structure of Spatial Representations

PubMed Central

Madl, Tamas; Franklin, Stan; Chen, Ke; Trappl, Robert; Montaldi, Daniela

2016-01-01

It has been suggested that the map-like representations that support human spatial memory are fragmented into sub-maps with local reference frames, rather than being unitary and global. However, the principles underlying the structure of these ‘cognitive maps’ are not well understood. We propose that the structure of the representations of navigation space arises from clustering within individual psychological spaces, i.e. from a process that groups together objects that are close in these spaces. Building on the ideas of representational geometry and similarity-based representations in cognitive science, we formulate methods for learning dissimilarity functions (metrics) characterizing participants’ psychological spaces. We show that these learned metrics, together with a probabilistic model of clustering based on the Bayesian cognition paradigm, allow prediction of participants’ cognitive map structures in advance. Apart from insights into spatial representation learning in human cognition, these methods could facilitate novel computational tools capable of using human-like spatial concepts. We also compare several features influencing spatial memory structure, including spatial distance, visual similarity and functional similarity, and report strong correlations between these dimensions and the grouping probability in participants’ spatial representations, providing further support for clustering in spatial memory. PMID:27347681

[Morphochemical changes in the substantia nigra cellular structures in Parkinson's disease].

PubMed

Salkov, V N; Khudoerkov, R M; Voronkov, D N; Sobolev, V B; Kutukova, K A

to clarify the features of morphochemical changes in the substantia nigra cellular structures in Parkinson's disease. The structural characteristics of the substantia nigra were studied microscopically and quantified using computer morphometric methods at brain autopsies of individuals with Parkinson's disease who had died from intercurrent diseases and those who had no evidence of neurological disorders in their history (a control group). This investigation could clarify the features of morphochemical changes in both the neural network structures and the glial populations of the substantia nigra in Parkinson's disease. The number of neurons containing tyrosine hydroxylase (a marker of dopamine neurons) in the compact part of the substantia nigra (a ventral region) was smaller and the density distribution of Lewy bodies was higher in the patients with Parkinson's disease than in the control group. The accumulation of iron (II) compounds in the cellular elements and neuropile and the increased expression of glial fibrillary acidic protein in Parkinson's disease were more pronounced than those in the controls. Postmortem diagnosis in Parkinson's disease should be based on a full description of a set of neuronal and glial morphochemical and structural changes in the substantia nigra rather than on the identification of cellular markers for the neurodegenerative process.

Computational simulations assessment of mutations impact on streptokinase (SK) from a group G streptococci with enhanced activity - insights into the functional roles of structural dynamics flexibility of SK and stabilization of SK-μplasmin catalytic complex.

PubMed

Kazemi, Faegheh; Arab, Seyed Shahriar; Mohajel, Nasir; Keramati, Malihe; Niknam, Niloofar; Aslani, Mohammad Mehdi; Roohvand, Farzin

2018-05-28

Streptokinase (SK), a plasminogen activator (PA) that converts inactive plasminogen (Pg) to plasmin (Pm), is a protein secreted by groups A, C, and G streptococci (GAS, GCS, and GGS, respectively), with high sequence divergence and functional heterogeneity. While roles of some residual changes in altered SK functionality are shown, the underlying structural mechanisms are less known. Herein, using computational approaches, we analyzed the conformational basis for the increased activity of SK from a GGS (SKG132) isolate with four natural residual substitutions (Ile33Phe, Arg45Gln, Asn228Lys, Phe287Ile) compared to the standard GCS (SKC). Using the crystal structure of SK.Pm catalytic complex as main template SKC.μPm catalytic complex was modeled through homology modeling process and validated by several online validation servers. Subsequently, SKG132.μPm structure was constructed by altering the corresponding residual substitutions. Results of three independent MD simulations showed increased RMSF values for SKG132.μPm, indicating the enhanced structural flexibility compared to SKC.μPm, specially in 170 and 250 loops and three regions: R1 (149-161), R2 (182-215) and R3 (224-229). In parallel, the average number of Hydrogen bonds in 170 loop, R2 and R3 (especially for Asn228Lys) of SKG132 compared to that of the SKC was decreased. Accordingly, residue interaction networks (RINs) analyses indicated that Asn228Lys might induce more level of structural flexibility by generation of free Lys256, while Phe287Ile and Ile33Phe enhanced the stabilization of the SKG132.μPm catalytic complex. These results denoted the potential role of the optimal dynamic state and stabilized catalytic complex for increased PA potencies of SK as a thrombolytic drug.

Thomson backscattering diagnostics of nanosecond electron bunches in high space charge regime

NASA Astrophysics Data System (ADS)

Plachinda, Pavel

The trend over the last 50 years of down-scaling the silicon transistor to achieve faster computations has led to doubling of the number of transistors and computation speed over about every two years. However, this trend cannot be maintained due to the fundamental limitations of silicon as the main material for the semiconducting industry. Therefore, there is an active search for exploration of alternate materials. Among the possible candidates that can may be able to replace silicon is graphene which has recently gained the most attention. Unique properties of graphene include exceedingly high carrier mobility, tunable band gap, huge optical density of a monolayer, anomalous quantum Hall effect, and many others. To be suitable for microelectronic applications the material should be semiconductive, i.e. have a non-zero band gap. Pristine graphene is a semimetal, but by the virtue of doping the graphene surface with different molecules and radicals a band gap can be opened. Because the electronic properties of all materials are intimately related to their atomic structure, characterization of molecular and electronic structure of functionalizing groups is of high interest. The ab-inito (from the first principles) calculations provide a unique opportunity to study the influence of the dopants and thus allow exploration of the physical phenomena in functionalized graphene structures. This ability paves the road to probe the properties based on the intuitive structural information only. A great advantage of this approach lies in the opportunity for quick screening of various atomic structures. We conducted a series of ab-inito investigations of graphene functionalized with covalently and hapticly bound groups, and demonstrated possible practical usage of functionalized graphene for microelectronic and optical applications. This investigation showed that it is possible produce band gaps in graphene (i.e., produce semiconducting graphene) of about 1 eV, without degrading the carrier mobility. This was archived by considering the influence of those adducts on electronic band structure and conductivity properties.

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.

Structure-sequence based analysis for identification of conserved regions in proteins

DOEpatents

Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

2013-05-28

Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.

Conjunctival impression cytology in computer users.

PubMed

Kumar, S; Bansal, R; Khare, A; Malik, K P S; Malik, V K; Jain, K; Jain, C

2013-01-01

It is known that the computer users develop the features of dry eye. To study the cytological changes in the conjunctiva using conjunctival impression cytology in computer users and a control group. Fifteen eyes of computer users who had used computers for more than one year and ten eyes of an age-and-sex matched control group (those who had not used computers) were studied by conjunctival impression cytology. Conjunctival impression cytology (CIC) results in the control group were of stage 0 and stage I while the computer user group showed CIC results between stages II to stage IV. Among the computer users, the majority ( > 90 %) showed stage III and stage IV changes. We found that those who used computers daily for long hours developed more CIC changes than those who worked at the computer for a shorter daily duration. © NEPjOPH.

A Pipeline Software Architecture for NMR Spectrum Data Translation

PubMed Central

Ellis, Heidi J.C.; Weatherby, Gerard; Nowling, Ronald J.; Vyas, Jay; Fenwick, Matthew; Gryk, Michael R.

2012-01-01

The problem of formatting data so that it conforms to the required input for scientific data processing tools pervades scientific computing. The CONNecticut Joint University Research Group (CONNJUR) has developed a data translation tool based on a pipeline architecture that partially solves this problem. The CONNJUR Spectrum Translator supports data format translation for experiments that use Nuclear Magnetic Resonance to determine the structure of large protein molecules. PMID:24634607

Association between third molar agenesis and craniofacial structure development.

PubMed

Ramiro-Verdugo, Jara; De Vicente-Corominas, Elena; Montiel-Company, José María; Gandía-Franco, José Luís; Bellot-Arcís, Carlos

2015-11-01

The aim of this investigation was to study the relationship between third molar agenesis-including the number of ageneses-and craniofacial structure growth. We reviewed 305 clinical histories of patients treated at the Orthodontics Unit of the Faculty of Medicine and Dentistry at the University of Valencia in Spain. This included radiographic records of optimal quality. Of these, 40 patients who had agenesis of at least 1 third molar were included in the study group. A control group was formed with another 40 patients with all 4 third molars present. For both groups, a further criterion for inclusion was cone-beam computed tomography records. The cephalometric analysis was performed with NemoCeph 3D software (version 11.3.1.38; Nemotec, Madrid, Spain). The only significant differences between the 2 groups were in the total gonial angle and the upper gonial angle (P ≤0.05), both of which were smaller in the study group. Third molar agenesis is associated with a reduction in Jarabak's gonial angle and upper gonial angle, characteristic of patients with a more horizontal or brachyfacial skeletal pattern. No significant differences were found in other measurements. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Absolute surface energy calculations of Wurtzite (0001)/(000-1): a study of ZnO and GaN

NASA Astrophysics Data System (ADS)

Zhang, Jingzhao; Zhang, Yiou; Tse, Kinfai; Deng, Bei; Xu, Hu; Zhu, Junyi

The accurate absolute surface energies of (0001)/(000-1) surfaces of wurtzite structures are crucial in determining the thin film growth mode of important energy materials. However, the surface energies still remain to be solved due to the intrinsic difficulty of calculating dangling bond energy of asymmetrically bonded surface atoms. We used a pseudo-hydrogen passivation method to estimate the dangling bond energy and calculate the polar surfaces of ZnO and GaN. The calculations were based on the pseudo chemical potentials obtained from a set of tetrahedral clusters or simple pseudo-molecules, using density functional theory approaches, for both GGA and HSE. And the surface energies of (0001)/(000-1) surfaces of wurtzite ZnO and GaN we obtained showed relatively high self-consistencies. A wedge structure calculation with a new bottom surface passivation scheme of group I and group VII elements was also proposed and performed to show converged absolute surface energy of wurtzite ZnO polar surfaces. Part of the computing resources was provided by the High Performance Cluster Computing Centre, Hong Kong Baptist University. This work was supported by the start-up funding and direct Grant with the Project code of 4053134 at CUHK.

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

An evaluation of a computer based education program for the diagnosis and management of dementia in primary care. An international study of the transcultural adaptations necessary for European dissemination.

PubMed

Degryse, J; De Lepeleire, J; Southgate, L; Vernooij-Dassen, M; Gay, B; Heyrman, J

2009-05-01

The aim of this study is to make an inventory of the changes that are needed to make an interactive computer based training program (ICBT) with a specific educational content, acceptable to professional communities with different linguistic,cultural and health care backgrounds in different European countries. Existing educational software, written in two languages was reviewed by GPs and primary care professionals in three different countries. Reviewers worked through the program using a structured critical reading grid. A 'simple' translation of the program is not sufficient. Minor changes are needed to take account of linguistic differences and medical semantics. Major changes are needed in respect of the existing clinical guidelines in every country related to differences in the existing health care systems. ICTB programs cannot easily be used in different countries and cultures. The development of a structured educational program needs collaboration between educationalists, domain experts, information technology advisers and software engineers. Simple validation of the content by local expert groups will not guarantee the program's exportability. It is essential to involve different national expert groups at every phase of the development process in order to disseminate it in other countries.

Phytotoxicity, structural and computational analysis of 2-methyl-1,5-diarylpentadienones

NASA Astrophysics Data System (ADS)

Din, Zia Ud; Rodrigues-Filho, Edson; de Cassia Pereira, Viviane; Gualtieri, Sonia Cristina Juliano; Deflon, Victor Marcelo; da Silva Maia, Pedro Ivo; Kuznetsov, Aleksey E.

2017-08-01

In our studies aimed to produce new chemicals used in weed control, 2-methyl-1,5-diarylpentadienones were synthesized by the reaction of p-methoxybenzaldehyde, p-nitrobenzaldehyde and p-N,N-dimethylbenzaldehyde, respectively, with 2-butanone, resulting in four model compounds. The phytotoxicity of these compounds against wheat coleoptiles and Sesame seedling was observed at μM concentrations, indicating good potential for their usage in weed management in the field. Spectroscopic and computational studies were performed in order to gain understanding on their mechanisms of action and to clarify some structural complexities due existence of conformers and substituent effects. These compounds probably act as hydroxyphenylpyruvate dioxygenase inhibitors. The tested compounds were characterized by spectroscopic and single crystal X-ray diffraction analyses. Solid crystalline state of the compound A (2-Methyl-1-(p-methophyphenyl)-5-(phenyl)-diarylpentadienone) is observed in the monoclinic space group P21/c with unit cell dimensions a = 14.3366(4) Å, b = 11.3788(4) Å, c = 9.6319(3) Å, β = 96.596, V = 1560.88(9) Å3 and Z = 4. Compound C (2-Methyl-1-(p-methophyphenyl)-5-(p-nitrophenyl)-diarylpentadienone) crystallizes in the monoclinic space group P21/c with unit cell dimensions a = 17.8276(9) Å, b = 7.3627(4) Å, c = 12.9740(6) Å, β = 107.6230(10), V = 1623.04(14) Å3 and Z = 4. LC-UV-MS analysis furnished important data helpful for their characterization. The spectroscopic data and computational (DFT) analysis revealed the fact that each of the compounds A-D occurs in solution as four conformers.

Analysis of the upper massif of the craniofacial with the radial method – practical use

PubMed Central

Lepich, Tomasz; Dąbek, Józefa; Stompel, Daniel; Gielecki, Jerzy S.

2011-01-01

Introduction The analysis of the upper massif of the craniofacial (UMC) is widely used in many fields of science. The aim of the study was to create a high resolution computer system based on a digital information record and on vector graphics, that could enable dimension measuring and evaluation of craniofacial shape using the radial method. Material and methods The study was carried out on 184 skulls, in a good state of preservation, from the early middle ages. The examined skulls were fixed into Molisson's craniostat in the author's own modification. They were directed in space towards the Frankfurt plane and photographed in frontal norm with a digital camera. The parameters describing the plane and dimensional structure of the UMC and orbits were obtained thanks to the computer analysis of the function recordings picturing the craniofacial structures and using software combining raster graphics with vector graphics. Results It was compared mean values of both orbits separately for male and female groups. In female skulls the comparison of the left and right side did not show statistically significant differences. In male group, higher values were observed for the right side. Only the circularity index presented higher values for the left side. Conclusions Computer graphics with the software used for analysing digital pictures of UMC and orbits increase the precision of measurements as well as the calculation possibilities. Recognition of the face in the post mortem examination is crucial for those working on identification in anthropology and criminology laboratories. PMID:22291834

Aging of the midface bony elements: a three-dimensional computed tomographic study.

PubMed

Shaw, Robert B; Kahn, David M

2007-02-01

The face loses volume as the soft-tissue structures age. In this study, the authors demonstrate how specific bony aspects of the face change with age in both men and women and what impact this may have on the techniques used in facial cosmetic surgery. Facial bone computed tomographic scans were obtained from 60 Caucasian patients (30 women and 30 men). The authors' study population consisted of 10 male and 10 female subjects in each of three age categories. Each computed tomographic scan underwent three-dimensional reconstruction with volume rendering, and the following measurements were obtained: glabellar angle (maximal prominence of glabella to nasofrontal suture), pyriform angle (nasal bone to lateral inferior pyriform aperture), and maxillary angle (superior to inferior maxilla at the articulation of the inferior maxillary wing and alveolar arch). The pyriform aperture area was also obtained. The t test was used to identify any trends between age groups. The glabellar and maxillary angle in both the male and female subjects showed a significant decrease with increasing age. The pyriform angle did not show a significant change between age groups for either sex. There was a significant increase in pyriform aperture area from the young to the middle age group for both sexes. These results suggest that the bony elements of the midface change dramatically with age and, coupled with soft-tissue changes, lead to the appearance of the aged face.

Thyroid Hormone Indices in Computer Workers with Emphasis on the Role of Zinc Supplementation.

PubMed

Amin, Ahmed Ibrahim; Hegazy, Noha Mohamed; Ibrahim, Khadiga Salah; Mahdy-Abdallah, Heba; Hammouda, Hamdy A A; Shaban, Eman Essam

2016-06-15

This study aimed to investigate the effects of computer monitor-emitted radiation on thyroid hormones and the possible protective role of zinc supplementation. The study included three groups. The first group (group B) consisted of 42 computer workers. This group was given Zinc supplementation in the form of one tablet daily for eight weeks. The second group (group A) comprised the same 42 computer workers after zinc supplementation. A group of 63 subjects whose job does not entail computer use was recruited as a control Group (Group C). All participants filled a questionnaire including detailed medical and occupational histories. They were subjected to full clinical examination. Thyroid stimulating hormone (TSH), free triiodothyronine (FT3), free thyroxine (FT4) and zinc levels were measured in all participants. TSH, FT3, FT4 and zinc concentrations were decreased significantly in group B relative to group C. In group A, all tested parameters were improved when compared with group B. The obtained results revealed that radiation emitted from computers led to changes in TSH and thyroid hormones (FT3 and FT4) in the workers. Improvement after supplementation suggests that zinc can ameliorate hazards of such radiation on thyroid hormone indices.

Group Velocity Dispersion Curves from Wigner-Ville Distributions

NASA Astrophysics Data System (ADS)

Lloyd, Simon; Bokelmann, Goetz; Sucic, Victor

2013-04-01

With the widespread adoption of ambient noise tomography, and the increasing number of local earthquakes recorded worldwide due to dense seismic networks and many very dense temporary experiments, we consider it worthwhile to evaluate alternative Methods to measure surface wave group velocity dispersions curves. Moreover, the increased computing power of even a simple desktop computer makes it feasible to routinely use methods other than the typically employed multiple filtering technique (MFT). To that end we perform tests with synthetic and observed seismograms using the Wigner-Ville distribution (WVD) frequency time analysis, and compare dispersion curves measured with WVD and MFT with each other. Initial results suggest WVD to be at least as good as MFT at measuring dispersion, albeit at a greater computational expense. We therefore need to investigate if, and under which circumstances, WVD yields better dispersion curves than MFT, before considering routinely applying the method. As both MFT and WVD generally work well for teleseismic events and at longer periods, we explore how well the WVD method performs at shorter periods and for local events with smaller epicentral distances. Such dispersion information could potentially be beneficial for improving velocity structure resolution within the crust.

Challenging Density Functional Theory Calculations with Hemes and Porphyrins

PubMed Central

de Visser, Sam P.; Stillman, Martin J.

2016-01-01

In this paper we review recent advances in computational chemistry and specifically focus on the chemical description of heme proteins and synthetic porphyrins that act as both mimics of natural processes and technological uses. These are challenging biochemical systems involved in electron transfer as well as biocatalysis processes. In recent years computational tools have improved considerably and now can reproduce experimental spectroscopic and reactivity studies within a reasonable error margin (several kcal·mol−1). This paper gives recent examples from our groups, where we investigated heme and synthetic metal-porphyrin systems. The four case studies highlight how computational modelling can correctly reproduce experimental product distributions, predicted reactivity trends and guide interpretation of electronic structures of complex systems. The case studies focus on the calculations of a variety of spectroscopic features of porphyrins and show how computational modelling gives important insight that explains the experimental spectra and can lead to the design of porphyrins with tuned properties. PMID:27070578

Computational models of music perception and cognition I: The perceptual and cognitive processing chain

NASA Astrophysics Data System (ADS)

Purwins, Hendrik; Herrera, Perfecto; Grachten, Maarten; Hazan, Amaury; Marxer, Ricard; Serra, Xavier

2008-09-01

We present a review on perception and cognition models designed for or applicable to music. An emphasis is put on computational implementations. We include findings from different disciplines: neuroscience, psychology, cognitive science, artificial intelligence, and musicology. The article summarizes the methodology that these disciplines use to approach the phenomena of music understanding, the localization of musical processes in the brain, and the flow of cognitive operations involved in turning physical signals into musical symbols, going from the transducers to the memory systems of the brain. We discuss formal models developed to emulate, explain and predict phenomena involved in early auditory processing, pitch processing, grouping, source separation, and music structure computation. We cover generic computational architectures of attention, memory, and expectation that can be instantiated and tuned to deal with specific musical phenomena. Criteria for the evaluation of such models are presented and discussed. Thereby, we lay out the general framework that provides the basis for the discussion of domain-specific music models in Part II.

The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry.

PubMed

Johnstone, Timothy C

2014-01-08

The crystal structure of the anticancer drug oxaliplatin, [Pt( R,R- DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P2 1 , confirming the sole presence of the R , R enantiomer of the DACH ligand [M. A. Bruck et al. , Inorg. Chim. Acta , 92 (1984) 279-284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P2 1 /m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al. , Polyhedron , 22 (2003) 1529-1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt( R , R -DACH)I 2 , and a platinum(IV) derivative, trans -[Pt( R , R -DACH)(oxalate)(OH) 2 ], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R , R . A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P2 1 /m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained.

The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry

PubMed Central

Johnstone, Timothy C.

2013-01-01

The crystal structure of the anticancer drug oxaliplatin, [Pt(R,R-DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P21, confirming the sole presence of the R,R enantiomer of the DACH ligand [M. A. Bruck et al., Inorg. Chim. Acta, 92 (1984) 279–284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P21/m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al., Polyhedron, 22 (2003) 1529–1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt(R,R-DACH)I2, and a platinum(IV) derivative, trans-[Pt(R,R-DACH)(oxalate)(OH)2], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R,R. A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P21/m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained. PMID:24415827

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

PubMed

Del Galdo, Sara; Amadei, Andrea

2016-10-12

In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

Cloud-based Monte Carlo modelling of BSSRDF for the rendering of human skin appearance (Conference Presentation)

NASA Astrophysics Data System (ADS)

Doronin, Alexander; Rushmeier, Holly E.; Meglinski, Igor; Bykov, Alexander V.

2016-03-01

We present a new Monte Carlo based approach for the modelling of Bidirectional Scattering-Surface Reflectance Distribution Function (BSSRDF) for accurate rendering of human skin appearance. The variations of both skin tissues structure and the major chromophores are taken into account correspondingly to the different ethnic and age groups. The computational solution utilizes HTML5, accelerated by the graphics processing units (GPUs), and therefore is convenient for the practical use at the most of modern computer-based devices and operating systems. The results of imitation of human skin reflectance spectra, corresponding skin colours and examples of 3D faces rendering are presented and compared with the results of phantom studies.

Machine intelligence and robotics: Report of the NASA study group. Executive summary

NASA Technical Reports Server (NTRS)

1979-01-01

A brief overview of applications of machine intelligence and robotics in the space program is given. These space exploration robots, global service robots to collect data for public service use on soil conditions, sea states, global crop conditions, weather, geology, disasters, etc., from Earth orbit, space industrialization and processing technologies, and construction of large structures in space. Program options for research, advanced development, and implementation of machine intelligence and robot technology for use in program planning are discussed. A vigorous and long-range program to incorporate and keep pace with state of the art developments in computer technology, both in spaceborne and ground-based computer systems is recommended.

Open-Source, Distributed Computational Environment for Virtual Materials Exploration

DTIC Science & Technology

2015-01-01

compromising structural integrity.  For  example, advanced designs could specify advanced materials processing techniques such as heat  treatments  in specific...orchestration of execution of multiple standalone codes at varying  length scales will need advanced  high ‐performance computing (HPC) integration in...possible hooks that could be used to  coordinate larger  workflows spanning tools developed by different groups.    The  high  level approach explored

Structural basis for the mutation-induced dysfunction of human CYP2J2: a computational study.

PubMed

Cong, Shan; Ma, Xiao-Tu; Li, Yi-Xue; Wang, Jing-Fang

2013-06-24

Arachidonic acid is an essential fatty acid in cells, acting as a key inflammatory intermediate in inflammatory reactions. In cardiac tissues, CYP2J2 can adopt arachidonic acid as a major substrate to produce epoxyeicosatrienoic acids (EETs), which can protect endothelial cells from ischemic or hypoxic injuries and have been implicated in the pathogenesis of coronary artery disease and hypertension. However, some CYP2J2 polymorphisms, i.e., T143A and N404Y, significantly reduce the metabolism of arachidonic acid. Lacking experimental structural data for CYP2J2, the detailed mechanism for the mutation-induced dysfunction in the metabolism of arachidonic acid is still unknown. In the current study, three-dimensional structural models of the wild-type CYP2J2 and two mutants (T143A and N404Y) were constructed by a coordinate reconstruction approach and ab initio modeling using CYP2R1 as a template. The structural analysis of the computational models showed that the wild-type CYP2J2 exhibited a typical CYP fold with 12 alpha-helices and three beta-sheets on one side and with the heme group buried deeply inside the core. Due to the small and hydrophobic side-chain, T143A mutation could destabilize the C helix, further placing the water access channel in a closed state to prevent the escape of the produced water molecules during the catalytic processes. N404Y mutation could reposition the side-chain of Leu(378), making it no longer form a hydrogen bond with the carboxyl group of arachidonic acid. However, this hydrogen bond was essential for substrate recognition and positioning in a correct orientation.

Discriminant function analysis as tool for subsurface geologist

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

Chesser, K.

1987-05-01

Sedimentary structures such as cross-bedding control porosity, permeability, and other petrophysical properties in sandstone reservoirs. Understanding the distribution of such structures in the subsurface not only aids in the prediction of reservoir properties but also provides information about depositional environments. Discriminant function analysis (DFA) is a simple yet powerful method incorporating petrophysical data from wireline logs, core analyses, or other sources into groups that have been previously defined through direct observation of sedimentary structures in cores. Once data have been classified into meaningful groups, the geologist can predict the distribution of specific sedimentary structures or important reservoir properties in areasmore » where cores are unavailable. DFA is efficient. Given several variables, DFA will choose the best combination to discriminate among groups. The initial classification function can be computed from relatively few observations, and additional data may be included as necessary. Furthermore, DFA provides quantitative goodness-of-fit estimates for each observation. Such estimates can be used as mapping parameters or to assess risk in petroleum ventures. Petrophysical data from the Skinner sandstone of Strauss field in southeastern Kansas tested the ability of DFA to discriminate between cross-bedded and ripple-bedded sandstones. Petroleum production in Strauss field is largely restricted to the more permeable cross-bedded sandstones. DFA based on permeability correctly placed 80% of samples into cross-bedded or ripple-bedded groups. Addition of formation factor to the discriminant function increased correct classifications to 83% - a small but statistically significant gain.« less

Development of an Aeroelastic Modeling Capability for Transient Nozzle Side Load Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Zhao, Xiang; Zhang, Sijun; Chen, Yen-Sen

2013-01-01

Lateral nozzle forces are known to cause severe structural damage to any new rocket engine in development during test. While three-dimensional, transient, turbulent, chemically reacting computational fluid dynamics methodology has been demonstrated to capture major side load physics with rigid nozzles, hot-fire tests often show nozzle structure deformation during major side load events, leading to structural damages if structural strengthening measures were not taken. The modeling picture is incomplete without the capability to address the two-way responses between the structure and fluid. The objective of this study is to develop a coupled aeroelastic modeling capability by implementing the necessary structural dynamics component into an anchored computational fluid dynamics methodology. The computational fluid dynamics component is based on an unstructured-grid, pressure-based computational fluid dynamics formulation, while the computational structural dynamics component is developed in the framework of modal analysis. Transient aeroelastic nozzle startup analyses of the Block I Space Shuttle Main Engine at sea level were performed. The computed results from the aeroelastic nozzle modeling are presented.

Mid-term survival analysis of closed wedge high tibial osteotomy: A comparative study of computer-assisted and conventional techniques.

PubMed

Bae, Dae Kyung; Song, Sang Jun; Kim, Kang Il; Hur, Dong; Jeong, Ho Yeon

2016-03-01

The purpose of the present study was to compare the clinical and radiographic results and survival rates between computer-assisted and conventional closing wedge high tibial osteotomies (HTOs). Data from a consecutive cohort comprised of 75 computer-assisted HTOs and 75 conventional HTOs were retrospectively reviewed. The Knee Society knee and function scores, Hospital for Special Surgery (HSS) score and femorotibial angle (FTA) were compared between the two groups. Survival rates were also compared with procedure failure. The knee and function scores at one year postoperatively were slightly better in the computer-assisted group than those in conventional group (90.1 vs. 86.1) (82.0 vs. 76.0). The HSS scores at one year postoperatively were slightly better for the computer-assisted HTOs than those of conventional HTOs (89.5 vs. 81.8). The inlier of the postoperative FTA was wider in the computer-assisted group than that in the conventional HTO group (88.0% vs. 58.7%), and mean postoperative FTA was greater in the computer-assisted group that in the conventional HTO group (valgus 9.0° vs. valgus 7.6°, p<0.001). The five- and 10-year survival rates were 97.1% and 89.6%, respectively. No difference was detected in nine-year survival rates (p=0.369) between the two groups, although the clinical and radiographic results were better in the computer-assisted group that those in the conventional HTO group. Mid-term survival rates did not differ between computer-assisted and conventional HTOs. A comparative analysis of longer-term survival rate is required to demonstrate the long-term benefit of computer-assisted HTO. III. Copyright © 2015 Elsevier B.V. All rights reserved.

Detection and characterization of Budd-Chiari syndrome with inferior vena cava obstruction: Comparison of fixed and flexible delayed scan time of computed tomography venography.

PubMed

Zhou, Peng-Li; Wu, Gang; Han, Xin-Wei; Bi, Yong-Hua; Zhang, Wen-Guang; Wu, Zheng-Yang

2017-06-01

To compare the results of computed tomography venography (CTV) with a fixed and a flexible delayed scan time for Budd-Chiari syndrome (BCS) with inferior vena cava (IVC) obstruction. A total of 209 consecutive BCS patients with IVC obstruction underwent either a CTV with a fixed delayed scan time of 180s (n=87) or a flexible delayed scan time for good image quality according to IVC blood flow in color Doppler ultrasonography (n=122). The IVC blood flow velocity was measured using a color Doppler ultrasound prior to CT scan. Image quality was classified as either good, moderate, or poor. Image quality, surrounding structures and the morphology of the IVC obstruction were compared between the two groups using a χ 2 -test or paired or unpaired t-tests as appropriate. Inter-observer agreement was assessed using Kappa statistics. There was no significant difference in IVC blood flow velocity between the two groups. Overall image quality, surrounding structures and IVC obstruction morphology delineation on the flexible delayed scan time of CTV images were rated better relative to those obtained by fixed delayed scan time of CTV images (p<0.001). Evaluation of CTV data sets was significantly facilitated with flexible delayed scan time of CTV. There were no significant differences in Kappa statistics between Group A and Group B. The flexible delayed scan time of CTV was associated with better detection and more reliable characterization of BCS with IVC obstruction compared to a fixed delayed scan time. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of genetic population structure in Acacia caven (Leguminosae, Mimosoideae), comparing one exploratory and two Bayesian-model-based methods.

PubMed

Pometti, Carolina L; Bessega, Cecilia F; Saidman, Beatriz O; Vilardi, Juan C

2014-03-01

Bayesian clustering as implemented in STRUCTURE or GENELAND software is widely used to form genetic groups of populations or individuals. On the other hand, in order to satisfy the need for less computer-intensive approaches, multivariate analyses are specifically devoted to extracting information from large datasets. In this paper, we report the use of a dataset of AFLP markers belonging to 15 sampling sites of Acacia caven for studying the genetic structure and comparing the consistency of three methods: STRUCTURE, GENELAND and DAPC. Of these methods, DAPC was the fastest one and showed accuracy in inferring the K number of populations (K = 12 using the find.clusters option and K = 15 with a priori information of populations). GENELAND in turn, provides information on the area of membership probabilities for individuals or populations in the space, when coordinates are specified (K = 12). STRUCTURE also inferred the number of K populations and the membership probabilities of individuals based on ancestry, presenting the result K = 11 without prior information of populations and K = 15 using the LOCPRIOR option. Finally, in this work all three methods showed high consistency in estimating the population structure, inferring similar numbers of populations and the membership probabilities of individuals to each group, with a high correlation between each other.

Effects of Computer Course on Computer Self-Efficacy, Computer Attitudes and Achievements of Young Individuals in Siirt, Turkey

ERIC Educational Resources Information Center

Çelik, Halil Coskun

2015-01-01

The purpose of this study is to investigate the effects of computer courses on young individuals' computer self-efficacy, attitudes and achievement. The study group of this research included 60 unemployed young individuals (18-25 ages) in total; 30 in the experimental group and 30 in the control group. An experimental research model with pretest…

Computers in medicine: patients' attitudes

PubMed Central

Cruickshank, P. J.

1984-01-01

Data are presented from two surveys where a 26-item questionnaire was used to measure patients' attitudes to diagnostic computers and to medical computers in general. The first group of respondents were 229 patients who had been given outpatient appointments at a hospital general medical clinic specializing in gastrointestinal problems, where some had experienced a diagnostic computer in use. The second group of respondents were 416 patients attending a group general practice where there was no computer. Patients who had experience of the diagnostic computer or a personal computer had more favourable attitudes to computers in medicine as did younger people and males. The two samples of patients showed broadly similar attitudes, and a notable finding was that over half of each group believed that, with a computer around, the personal touch of the doctor would be lost. PMID:6471021

CAD-centric Computation Management System for a Virtual TBM

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

Ramakanth Munipalli; K.Y. Szema; P.Y. Huang

HyPerComp Inc. in research collaboration with TEXCEL has set out to build a Virtual Test Blanket Module (VTBM) computational system to address the need in contemporary fusion research for simulating the integrated behavior of the blanket, divertor and plasma facing components in a fusion environment. Physical phenomena to be considered in a VTBM will include fluid flow, heat transfer, mass transfer, neutronics, structural mechanics and electromagnetics. We seek to integrate well established (third-party) simulation software in various disciplines mentioned above. The integrated modeling process will enable user groups to interoperate using a common modeling platform at various stages of themore » analysis. Since CAD is at the core of the simulation (as opposed to computational meshes which are different for each problem,) VTBM will have a well developed CAD interface, governing CAD model editing, cleanup, parameter extraction, model deformation (based on simulation,) CAD-based data interpolation. In Phase-I, we built the CAD-hub of the proposed VTBM and demonstrated its use in modeling a liquid breeder blanket module with coupled MHD and structural mechanics using HIMAG and ANSYS. A complete graphical user interface of the VTBM was created, which will form the foundation of any future development. Conservative data interpolation via CAD (as opposed to mesh-based transfer), the regeneration of CAD models based upon computed deflections, are among the other highlights of phase-I activity.« less

Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology

NASA Astrophysics Data System (ADS)

Lutnick, Brendon; Tomaszewski, John E.; Sarder, Pinaki

2017-03-01

Clinical pathology relies on manual compartmentalization and quantification of biological structures, which is time consuming and often error-prone. Application of computer vision segmentation algorithms to histopathological image analysis, in contrast, can offer fast, reproducible, and accurate quantitative analysis to aid pathologists. Algorithms tunable to different biologically relevant structures can allow accurate, precise, and reproducible estimates of disease states. In this direction, we have developed a fast, unsupervised computational method for simultaneously separating all biologically relevant structures from histopathological images in multi-scale. Segmentation is achieved by solving an energy optimization problem. Representing the image as a graph, nodes (pixels) are grouped by minimizing a Potts model Hamiltonian, adopted from theoretical physics, modeling interacting electron spins. Pixel relationships (modeled as edges) are used to update the energy of the partitioned graph. By iteratively improving the clustering, the optimal number of segments is revealed. To reduce computational time, the graph is simplified using a Cantor pairing function to intelligently reduce the number of included nodes. The classified nodes are then used to train a multiclass support vector machine to apply the segmentation over the full image. Accurate segmentations of images with as many as 106 pixels can be completed only in 5 sec, allowing for attainable multi-scale visualization. To establish clinical potential, we employed our method in renal biopsies to quantitatively visualize for the first time scale variant compartments of heterogeneous intra- and extraglomerular structures simultaneously. Implications of the utility of our method extend to fields such as oncology, genomics, and non-biological problems.

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.

The neural representation of social networks.

PubMed

Weaverdyck, Miriam E; Parkinson, Carolyn

2018-05-24

The computational demands associated with navigating large, complexly bonded social groups are thought to have significantly shaped human brain evolution. Yet, research on social network representation and cognitive neuroscience have progressed largely independently. Thus, little is known about how the human brain encodes the structure of the social networks in which it is embedded. This review highlights recent work seeking to bridge this gap in understanding. While the majority of research linking social network analysis and neuroimaging has focused on relating neuroanatomy to social network size, researchers have begun to define the neural architecture that encodes social network structure, cognitive and behavioral consequences of encoding this information, and individual differences in how people represent the structure of their social world. Copyright © 2018 Elsevier Ltd. All rights reserved.

Annotated bibliography of structural equation modelling: technical work.

PubMed

Austin, J T; Wolfle, L M

1991-05-01

Researchers must be familiar with a variety of source literature to facilitate the informed use of structural equation modelling. Knowledge can be acquired through the study of an expanding literature found in a diverse set of publishing forums. We propose that structural equation modelling publications can be roughly classified into two groups: (a) technical and (b) substantive applications. Technical materials focus on the procedures rather than substantive conclusions derived from applications. The focus of this article is the former category; included are foundational/major contributions, minor contributions, critical and evaluative reviews, integrations, simulations and computer applications, precursor and historical material, and pedagogical textbooks. After a brief introduction, we annotate 294 articles in the technical category dating back to Sewall Wright (1921).

Structural behavior of composites with progressive fracture

NASA Technical Reports Server (NTRS)

Minnetyan, L.; Murthy, P. L. N.; Chamis, C. C.

1989-01-01

The objective of the study is to unify several computational tools developed for the prediction of progressive damage and fracture with efforts for the prediction of the overall response of damaged composite structures. In particular, a computational finite element model for the damaged structure is developed using a computer program as a byproduct of the analysis of progressive damage and fracture. Thus, a single computational investigation can predict progressive fracture and the resulting variation in structural properties of angleplied composites.

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

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

Structural Basis for the ABO Blood-Group Dependence of Plasmodium falciparum Rosetting

PubMed Central

Hessel, Audrey; Raynal, Bertrand; England, Patrick; Cohen, Jacques H.; Bertrand, Olivier; Peyrard, Thierry; Bentley, Graham A.; Lewit-Bentley, Anita; Mercereau-Puijalon, Odile

2012-01-01

The ABO blood group influences susceptibility to severe Plasmodium falciparum malaria. Recent evidence indicates that the protective effect of group O operates by virtue of reduced rosetting of infected red blood cells (iRBCs) with uninfected RBCs. Rosetting is mediated by a subgroup of PfEMP1 adhesins, with RBC binding being assigned to the N-terminal DBL1α1 domain. Here, we identify the ABO blood group as the main receptor for VarO rosetting, with a marked preference for group A over group B, which in turn is preferred to group O RBCs. We show that recombinant NTS-DBL1α1 and NTS-DBL1α1-CIDR1γ reproduce the VarO-iRBC blood group preference and document direct binding to blood group trisaccharides by surface plasmon resonance. More detailed RBC subgroup analysis showed preferred binding to group A1, weaker binding to groups A2 and B, and least binding to groups Ax and O. The 2.8 Å resolution crystal structure of the PfEMP1-VarO Head region, NTS-DBL1α1-CIDR1γ, reveals extensive contacts between the DBL1α1 and CIDR1γ and shows that the NTS-DBL1α1 hinge region is essential for RBC binding. Computer docking of the blood group trisaccharides and subsequent site-directed mutagenesis localized the RBC-binding site to the face opposite to the heparin-binding site of NTS-DBLα1. RBC binding involves residues that are conserved between rosette-forming PfEMP1 adhesins, opening novel opportunities for intervention against severe malaria. By deciphering the structural basis of blood group preferences in rosetting, we provide a link between ABO blood grouppolymorphisms and rosette-forming adhesins, consistent with the selective role of falciparum malaria on human genetic makeup. PMID:22807674

Laboratory manual: mineral X-ray diffraction data retrieval/plot computer program

USGS Publications Warehouse

Hauff, Phoebe L.; VanTrump, George

1976-01-01

The Mineral X-Ray Diffraction Data Retrieval/Plot Computer Program--XRDPLT (VanTrump and Hauff, 1976a) is used to retrieve and plot mineral X-ray diffraction data. The program operates on a file of mineral powder diffraction data (VanTrump and Hauff, 1976b) which contains two-theta or 'd' values, and intensities, chemical formula, mineral name, identification number, and mineral group code. XRDPLT is a machine-independent Fortran program which operates in time-sharing mode on a DEC System i0 computer and the Gerber plotter (Evenden, 1974). The program prompts the user to respond from a time-sharing terminal in a conversational format with the required input information. The program offers two major options: retrieval only; retrieval and plot. The first option retrieves mineral names, formulas, and groups from the file by identification number, by the mineral group code (a classification by chemistry or structure), or by searches based on the formula components. For example, it enables the user to search for minerals by major groups (i.e., feldspars, micas, amphiboles, oxides, phosphates, carbonates) by elemental composition (i.e., Fe, Cu, AI, Zn), or by a combination of these (i.e., all copper-bearing arsenates). The second option retrieves as the first, but also plots the retrieved 2-theta and intensity values as diagrammatic X-ray powder patterns on mylar sheets or overlays. These plots can be made using scale combinations compatible with chart recorder diffractograms and 114.59 mm powder camera films. The overlays are then used to separate or sieve out unrelated minerals until unknowns are matched and identified.

Advanced thermally stable jet fuels. Technical progress report, January 1995--March 1995

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

Schobert, H.H.; Eser, S.; Song, C.

Quantitative structure-property relationships have been applied to study the thermal stability of pure hydrocarbons typical of jet fuel components. A simple method of chemical structure description in terms of Benson groups was tested in searching for structure-property relationships for the hydrocarbons tested experimentally in this program. Molecular connectivity as a structure-based approach to chemical structure-property relationship analysis was also tested. Further development of both the experimental data base and computational methods will be necessary. Thermal decomposition studies, using glass tube reactors, were extended to two additional model compounds: n-decane and n-dodecane. Efforts on refining the deposit growth measurement and characterizationmore » of suspended matter in stressed fuels have lead to improvements in the analysis of stressed fuels. Catalytic hydrogenation and dehydrogenation studies utilizing a molybdenum sulfide catalyst are also described.« less

Analysis of the Structures and Properties of (GaSb)n (n = 4-9) Clusters through Density Functional Theory.

PubMed

Lu, Qi Liang; Luo, Qi Quan; Huang, Shou Guo; Li, Yi De; Wan, Jian Guo

2016-07-07

An optimization strategy combining global semiempirical quantum mechanical search with all-electron density functional theory was adopted to determine the lowest energy structure of (GaSb)n clusters up to n = 9. The growth pattern of the clusters differed from those of previously reported group III-V binary clusters. A cagelike configuration was found for cluster sizes n ≤ 7. The structure of (GaSb)6 deviated from that of other III-V clusters. Competition existed between core-shell and hollow cage structures of (GaSb)7. Novel noncagelike structures were energetically preferred over the cages for the (GaSb)8 and (GaSb)9 clusters. Electronic properties, such as vertical ionization potential, adiabatic electron affinities, HOMO-LUMO gaps, and average on-site charges on Ga or Sb atoms, as well as binding energies, were computed.

Causal learning with local computations.

PubMed

Fernbach, Philip M; Sloman, Steven A

2009-05-01

The authors proposed and tested a psychological theory of causal structure learning based on local computations. Local computations simplify complex learning problems via cues available on individual trials to update a single causal structure hypothesis. Structural inferences from local computations make minimal demands on memory, require relatively small amounts of data, and need not respect normative prescriptions as inferences that are principled locally may violate those principles when combined. Over a series of 3 experiments, the authors found (a) systematic inferences from small amounts of data; (b) systematic inference of extraneous causal links; (c) influence of data presentation order on inferences; and (d) error reduction through pretraining. Without pretraining, a model based on local computations fitted data better than a Bayesian structural inference model. The data suggest that local computations serve as a heuristic for learning causal structure. Copyright 2009 APA, all rights reserved.

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Computer-Mediated Collaborative Projects: Processes for Enhancing Group Development

ERIC Educational Resources Information Center

Dupin-Bryant, Pamela A.

2008-01-01

Groups are a fundamental part of the business world. Yet, as companies continue to expand internationally, a major challenge lies in promoting effective communication among employees who work in varying time zones. Global expansion often requires group collaboration through computer systems. Computer-mediated groups lead to different communicative…

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.

Reaction Mechanism Generator: Automatic construction of chemical kinetic mechanisms

NASA Astrophysics Data System (ADS)

Gao, Connie W.; Allen, Joshua W.; Green, William H.; West, Richard H.

2016-06-01

Reaction Mechanism Generator (RMG) constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react. Species thermochemistry is estimated through Benson group additivity and reaction rate coefficients are estimated using a database of known rate rules and reaction templates. At its core, RMG relies on two fundamental data structures: graphs and trees. Graphs are used to represent chemical structures, and trees are used to represent thermodynamic and kinetic data. Models are generated using a rate-based algorithm which excludes species from the model based on reaction fluxes. RMG can generate reaction mechanisms for species involving carbon, hydrogen, oxygen, sulfur, and nitrogen. It also has capabilities for estimating transport and solvation properties, and it automatically computes pressure-dependent rate coefficients and identifies chemically-activated reaction paths. RMG is an object-oriented program written in Python, which provides a stable, robust programming architecture for developing an extensible and modular code base with a large suite of unit tests. Computationally intensive functions are cythonized for speed improvements.

A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding.

PubMed

Petrov, Artem; Arzhanik, Vladimir; Makarov, Gennady; Koliasnikov, Oleg

2016-08-01

Antibodies are the family of proteins, which are responsible for antigen recognition. The computational modeling of interaction between an antigen and an antibody is very important when crystallographic structure is unavailable. In this research, we have discovered the correlation between the amino acid sequence of antibody and its specific binding characteristics on the example of the novel conservative binding motif, which consists of four residues: Arg H52, Tyr H33, Thr H59, and Glu H61. These residues are specifically oriented in the binding site and interact with each other in a specific manner. The residues of the binding motif are involved in interaction strictly with negatively charged groups of antigens, and form a binding complex. Mechanism of interaction and characteristics of the complex were also discovered. The results of this research can be used to increase the accuracy of computational antibody-antigen interaction modeling and for post-modeling quality control of the modeled structures.

Computer Modeling of the Structure and Spectra of Fluorescent Proteins

PubMed Central

Grigorenko, B.L.; Savitsky, A.P.

2009-01-01

Fluorescent proteins from the family of green fluorescent proteins are intensively used as biomarkers in living systems. The chromophore group based on the hydroxybenzylidene-imidazoline molecule, which is formed in nature from three amino-acid residues inside the protein globule and well shielded from external media, is responsible for light absorption and fluorescence. Along with the intense experimental studies of the properties of fluorescent proteins and their chromophores by biochemical, X-ray, and spectroscopic tools, in recent years, computer modeling has been used to characterize their properties and spectra. We present in this review the most interesting results of the molecular modeling of the structural parameters and optical and vibrational spectra of the chromophorecontaining domains of fluorescent proteins by methods of quantum chemistry, molecular dynamics, and combined quantum-mechanical-molecular-mechanical approaches. The main emphasis is on the correlation of theoretical and experimental data and on the predictive power of modeling, which may be useful for creating new, efficient biomarkers. PMID:22649601

Functionalization-induced changes in the structural and physical properties of amorphous polyaniline: a first-principles and molecular dynamics study.

PubMed

Chen, X P; Liang, Q H; Jiang, J K; Wong, Cell K Y; Leung, Stanley Y Y; Ye, H Y; Yang, D G; Ren, T L

2016-02-09

In this paper, we present a first-principles and molecular dynamics study to delineate the functionalization-induced changes in the local structure and the physical properties of amorphous polyaniline. The results of radial distribution function (RDF) demonstrate that introducing -SO3(-)Na(+) groups at phenyl rings leads to the structural changes in both the intrachain and interchain ordering of polyaniline at shorter distances (≤5 Å). An unique RDF feature in 1.8-2.1 Å regions is usually observed in both the interchain and intrachain RDF profiles of the -SO3(-)Na(+) substituted polymer (i.e. Na-SPANI). Comparative studies of the atom-atom pairs, bond structures, torsion angles and three-dimensional structures show that EB-PANI has much better intrachain ordering than that of Na-SPANI. In addition, investigation of the band gap, density of states (DOS), and absorption spectra indicates that the derivatization at ring do not substantially alter the inherent electronic properties but greatly change the optical properties of polyaniline. Furthermore, the computed diffusion coefficient of water in Na-SPANI is smaller than that of EB-PANI. On the other hand, the Na-SPANI shows a larger density than that of EB-PANI. The computed RDF profiles, band gaps, absorption spectra, and diffusion coefficients are in quantitative agreement with the experimental data.

Summary of talks and papers at ISCB-Asia/SCCG 2012

PubMed Central

2013-01-01

The second ISCB-Asia conference of the International Society for Computational Biology took place December 17-19, 2012, in Shenzhen, China. The conference was co-hosted by BGI as the first Shenzhen Conference on Computational Genomics (SCCG). 45 talks were presented at ISCB-Asia/SCCG 2012. The topics covered included software tools, reproducible computing, next-generation sequencing data analysis, transcription and mRNA regulation, protein structure and function, cancer genomics and personalized medicine. Nine of the proceedings track talks are included as full papers in this supplement. In this report we first give a short overview of the conference by listing some statistics and visualizing the talk abstracts as word clouds. Then we group the talks by topic and briefly summarize each one, providing references to related publications whenever possible. Finally, we close with a few comments on the success of this conference.

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.

PubMed

Brunk, Elizabeth; Ashari, Negar; Athri, Prashanth; Campomanes, Pablo; de Carvalho, F Franco; Curchod, Basile F E; Diamantis, Polydefkis; Doemer, Manuel; Garrec, Julian; Laktionov, Andrey; Micciarelli, Marco; Neri, Marilisa; Palermo, Giulia; Penfold, Thomas J; Vanni, Stefano; Tavernelli, Ivano; Rothlisberger, Ursula

2011-01-01

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells. Many of these projects are done in collaboration with experimental groups from the Institute of Chemical Sciences and Engineering (ISIC) at the EPFL.

[The computer assisted pacemaker clinic at the regional hospital of Udine (author's transl)].

PubMed

Feruglio, G A; Lestuzzi, L; Carminati, D

1978-01-01

For a close follow-up of large groups of pacemaker patients and for evaluation of long term pacing on a reliable statistical basis, many pacemaker centers in the world are now using computer systems. A patient data system with structured display records, designed to give complete, comprehensive and surveyable information and which are immediately retrievable 24 hours a day, on display or printed sets, seems to offer an ideal solution. The pacemaker clinic at the Regional Hospital of Udine has adopted this type of system. The clinic in linked to a live, on-line patient data system (G/3, Informatica Friuli-Venezia Giulia). The input and retrieval of information are made through a conventional keyboard. The input formats have fixed headings with coded alternatives and a limited space for comments in free text. The computer edits the coded information to surveyable reviews. Searches can be made on coded information and data of interest.

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.

The spectroscopic impact of interactions with the four Gouterman orbitals from peripheral decoration of porphyrins with simple electron withdrawing and donating groups.

PubMed

Zhang, Angel; Kwan, Lydia; Stillman, Martin J

2017-11-07

Tetrapyrroles are of great interest for solar cell and photodynamic therapy applications due to their structural analogy with chlorophyll, a natural photosensitizer. Unsubstituted symmetric porphyrins exhibit weak absorption in the red region which makes them unsuitable for these applications. The push-pull peripheral decoration modifies the energies of the frontier molecular orbitals, which in turn influences the tetrapyrrole's spectroscopic properties. The absorption, magnetic circular dichroism, and emission spectra were measured for four zinc tetratolylporphyrin compounds substituted peripherally with a fused dimethoxybenzo group as an electron withdrawing group (EWG) on one pyrrole and on the opposite pyrrole, a single acetamido (1), a nitro (2), a proton (3), or a benzoylamino (4) substituent. Unusually, the magnetic circular dichroism spectrum of 2 exhibited a negative A term for the lowest energy absorption band (the Q band) and its emission spectrum was also unlike those of 1, 3, and 4. A complete computational analysis was carried out to obtain the energies and electron distribution, shown by electron density surfaces, of the four Gouterman MOs. TD-DFT calculations showed that for 2, ΔLUMO was greater than ΔHOMO, which accounted for the observed negative A term. The trend in the estimated MCD A term magnitudes, normalized to the absorbance as [A/(dipole strength) BM], provides experimental confirmation of the computationally determined ratio of ΔLUMO/ΔHOMO data. The value of ΔHOMO was confirmed by the trend in oscillator strengths. A series of fictive porphyrins (F1-F5) incorporating simple push-pull substituents were designed and their electronic structures were investigated using TD-DFT calculations. The substituents in the five fictive molecules illustrate the differential effect of the donor and acceptor groups in the β-position of the pyrroles on the relative stabilities of the four Gouterman orbitals. NO 2 groups result in the greatest splitting of the LUMO pair. We show that on using strong EWGs, opposite electron donating groups result in a ΔLUMO > 0, which red-shifts the Q band and introduces a strong dipole. With the nitro and formyl EWGs, ΔLUMO becomes greater than ΔHOMO, resulting in a complex electronic structure of the Q band, recognizable by a negative A term suggesting a design objective for future photosensitizers.

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.

The Imprimatur of Europe: Turkey, Europeanization, and the European Union

DTIC Science & Technology

1994-08-01

Jasmine , Erin, and Leo, for their patience and understanding as I sat trance-like in front of the computer writing. Their contribution to this effort was...1) that the international environment is conflictual; (2) that the " essence of social reality is the group" and its present relevant manifestation...consequences in others. In essence , completely autonomous national economic structures, capable of making or taking autonomous actions, no longer exist

Computational Modeling of Multi-Scale Material Features in Cement Paste - An Overview

DTIC Science & Technology

2015-05-25

and concrete ; though commonly used are one of the most complex in terms of material morphology and structure than most materials, for example...across the multiple scales are required. In this paper, recent work from our research group on the nano to continuum level modeling of cementitious...of our research work consisting of, • Molecular Dynamics (MD) modeling for the nano scale features of the cementitious material chemistry. • Micro

Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Carnevale, V.; Raugei, S.

2009-12-01

Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

Hydrogen bonding in phytohormone-auxin (IAA) and its derivatives

NASA Astrophysics Data System (ADS)

Kojić-Prodić, Biserka; Kroon, Jan; Puntarec, Vitomir

1994-06-01

The significant importance of hydrogen bonds in biological structures and enzymatic reactions has been demonstrated in many examples. As a part of the molecular recognition study of auxins (plant growth hormones) the influence of hydrogen bonding on molecular conformation, particularly of the carboxyl group, which is one of the biologically active ligand sites, has been studied by X-ray diffraction and computational chemistry methods. The survey includes about 40 crystal structures of free auxins such as indol-3-ylacetic acid and its n-alkylated and halogenated derivatives but also bound auxins such as N-(indol-3-ylacetyl)- L-amino acids, and carbohydrate conjugates. The study includes hydrogen bonds of the NH⋯O and OH⋯O types. The classification of hydrogen bond patterns based on the discrimination between the centrosymmetric and non-centrosymmetric space groups and several examples of hydrogen bond systematics on graph set analysis are also shown.

Slow-light transmission with high group index and large normalized delay bandwidth product through successive defect rods on intrinsic photonic crystal waveguide

NASA Astrophysics Data System (ADS)

Elshahat, Sayed; Khan, Karim; Yadav, Ashish; Bibbò, Luigi; Ouyang, Zhengbiao

2018-07-01

We proposed a strategy with successive cavities as energy reservoirs of electromagnetic energy and light-speed reducers introduced in the first and second rows of rods on the walls of an intrinsic photonic crystal waveguide (PCW) for slow-light transmission in the PCW concerning applications for optical communication, optical computation and optical signal processing. Subsequently, plane-wave expansion method (PWE) is used for studying slow-light properties and finite-difference time-domain (FDTD) method to demonstrate the slow-light propagating property of our proposed structure. We obtained group index as exceedingly large as 6123 with normalized delay bandwidth product (NDBP) as high as 0.48. We designed a facile but more generalized structure that may provide a vital theoretical basis for further enhancing the storage capacity properties of slow light with wideband and high NDBP.

On the structure of an aqueous propylene glycol solution.

PubMed

Rhys, Natasha H; Gillams, Richard J; Collins, Louise E; Callear, Samantha K; Lawrence, M Jayne; McLain, Sylvia E

2016-12-14

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

On the structure of an aqueous propylene glycol solution

NASA Astrophysics Data System (ADS)

Rhys, Natasha H.; Gillams, Richard J.; Collins, Louise E.; Callear, Samantha K.; Lawrence, M. Jayne; McLain, Sylvia E.

2016-12-01

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.