Science.gov

Sample records for combined computational chemistry

  1. Computational chemistry

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.

    1987-01-01

    With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.

  2. Combined use of computational chemistry and chemoinformatics methods for chemical discovery

    NASA Astrophysics Data System (ADS)

    Sugimoto, Manabu; Ideo, Toshihiro; Iwane, Ryo

    2015-12-01

    Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of "cancer". Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be "cancer"-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of the density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.

  3. Combined use of computational chemistry and chemoinformatics methods for chemical discovery

    SciTech Connect

    Sugimoto, Manabu; Ideo, Toshihiro; Iwane, Ryo

    2015-12-31

    Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of “cancer”. Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be “cancer”-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of the density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.

  4. Computational quantum chemistry website

    SciTech Connect

    1997-08-22

    This report contains the contents of a web page related to research on the development of quantum chemistry methods for computational thermochemistry and the application of quantum chemistry methods to problems in material chemistry and chemical sciences. Research programs highlighted include: Gaussian-2 theory; Density functional theory; Molecular sieve materials; Diamond thin-film growth from buckyball precursors; Electronic structure calculations on lithium polymer electrolytes; Long-distance electronic coupling in donor/acceptor molecules; and Computational studies of NOx reactions in radioactive waste storage.

  5. Computational chemistry research

    NASA Technical Reports Server (NTRS)

    Levin, Eugene

    1987-01-01

    Task 41 is composed of two parts: (1) analysis and design studies related to the Numerical Aerodynamic Simulation (NAS) Extended Operating Configuration (EOC) and (2) computational chemistry. During the first half of 1987, Dr. Levin served as a member of an advanced system planning team to establish the requirements, goals, and principal technical characteristics of the NAS EOC. A paper entitled 'Scaling of Data Communications for an Advanced Supercomputer Network' is included. The high temperature transport properties (such as viscosity, thermal conductivity, etc.) of the major constituents of air (oxygen and nitrogen) were correctly determined. The results of prior ab initio computer solutions of the Schroedinger equation were combined with the best available experimental data to obtain complete interaction potentials for both neutral and ion-atom collision partners. These potentials were then used in a computer program to evaluate the collision cross-sections from which the transport properties could be determined. A paper entitled 'High Temperature Transport Properties of Air' is included.

  6. Extensible Computational Chemistry Environment

    2012-08-09

    ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing themore » power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of the inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less

  7. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    PubMed

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

  8. Computational Chemistry and Lubrication

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.

    1998-01-01

    Members of NASA Lewis Research Center's Tribology and Surface Science Branch are applying high-level computational chemistry techniques to the development of new lubrication systems for space applications and for future advanced aircraft engines. The next generation of gas turbine engines will require a liquid lubricant to function at temperatures in excess of 350 C in oxidizing environments. Conventional hydrocarbon-based lubricants are incapable of operating in these extreme environments, but a class of compounds known as the perfluoropolyether (PFAE) liquids (see the preceding illustration) shows promise for such applications. These commercially available products are already being used as lubricants in conditions where low vapor pressure and chemical stability are crucial, such as in satellite bearings and composite disk platters. At higher temperatures, however, these compounds undergo a decomposition process that is assisted (catalyzed) by metal and metal oxide bearing surfaces. This decomposition process severely limits the applicability of PFAE's at higher temperatures. A great deal of laboratory experimentation has revealed that the extent of fluid degradation depends on the chemical properties of the bearing surface materials. Lubrication engineers would like to understand the chemical breakdown mechanism to design a less vulnerable PFAE or to develop a chemical additive to block this degradation.

  9. Recent computational chemistry

    SciTech Connect

    Onishi, Taku

    2015-12-31

    Now we can investigate quantum phenomena for the real materials and molecules, and can design functional materials by computation, due to the previous developments of quantum theory and calculation methods. As there still exist the limit and problem in theory, the cooperation between theory and computation is getting more important to clarify the unknown quantum mechanism, and discover more efficient functional materials. It would be next-generation standard. Finally, our theoretical methodology for boundary solid is introduced.

  10. Cuby: An integrative framework for computational chemistry.

    PubMed

    Řezáč, Jan

    2016-05-15

    Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high-level, object-oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz. © 2016 Wiley Periodicals, Inc. PMID:26841135

  11. Cuby: An integrative framework for computational chemistry.

    PubMed

    Řezáč, Jan

    2016-05-15

    Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high-level, object-oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz. © 2016 Wiley Periodicals, Inc.

  12. Collaborative Physical Chemistry Projects Involving Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Whisnant, David M.; Howe, Jerry J.; Lever, Lisa S.

    2000-02-01

    The physical chemistry classes from three colleges have collaborated on two computational chemistry projects using Quantum CAChe 3.0 and Gaussian 94W running on Pentium II PCs. Online communication by email and the World Wide Web was an important part of the collaboration. In the first project, students used molecular modeling to predict benzene derivatives that might be possible hair dyes. They used PM3 and ZINDO calculations to predict the electronic spectra of the molecules and tested the predicted spectra by comparing some with experimental measurements. They also did literature searches for real hair dyes and possible health effects. In the final phase of the project they proposed a synthetic pathway for one compound. In the second project the students were asked to predict which isomer of a small carbon cluster (C3, C4, or C5) was responsible for a series of IR lines observed in the spectrum of a carbon star. After preliminary PM3 calculations, they used ab initio calculations at the HF/6-31G(d) and MP2/6-31G(d) level to model the molecules and predict their vibrational frequencies and rotational constants. A comparison of the predictions with the experimental spectra suggested that the linear isomer of the C5 molecule was responsible for the lines.

  13. Advancing manufacturing through computational chemistry

    SciTech Connect

    Noid, D.W.; Sumpter, B.G.; Tuzun, R.E.

    1995-12-31

    The capabilities of nanotechnology and computational chemistry are reaching a point of convergence. New computer hardware and novel computational methods have created opportunities to test proposed nanometer-scale devices, investigate molecular manufacturing and model and predict properties of new materials. Experimental methods are also beginning to provide new capabilities that make the possibility of manufacturing various devices with atomic precision tangible. In this paper, we will discuss some of the novel computational methods we have used in molecular dynamics simulations of polymer processes, neural network predictions of new materials, and simulations of proposed nano-bearings and fluid dynamics in nano- sized devices.

  14. Outlook Bright for Computers in Chemistry.

    ERIC Educational Resources Information Center

    Baum, Rudy M.

    1981-01-01

    Discusses the recent decision to close down the National Resource for Computation in Chemistry (NRCC), implications of that decision, and various alternatives in the field of computational chemistry. (CS)

  15. ATOMIC-SCALE DESIGN OF IRON FISCHER-TROPSCH CATALYSTS: A COMBINED COMPUTATIONAL CHEMISTRY, EXPERIMENTAL, AND MICROKINETIC MODELING APPROACH

    SciTech Connect

    Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale; Rahul P. Nabar; Calvin H. Bartholomew; Hu Zou; Brian Critchfield

    2005-03-22

    Efforts during this first year focused on four areas: (1) searching/summarizing published FTS mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) construction of mass spectrometer-TPD and Berty CSTR reactor systems; (3) preparation and characterization of unsupported iron and alumina-supported iron catalysts at various iron loadings (4) Determination of thermochemical parameters such as binding energies of reactive intermediates, heat of FTS elementary reaction steps, and kinetic parameters such as activation energies, and frequency factors of FTS elementary reaction steps on a number of model surfaces. Literature describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts was compiled in a draft review. Construction of the mass spectrometer-TPD system is 90% complete and of a Berty CSTR reactor system 98% complete. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by nonaqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2}, thus ideal for kinetic and mechanistic studies. The alumina-supported iron catalysts will be used for kinetic and mechanistic studies. In the coming year, adsorption/desorption properties, rates of elementary steps, and global reaction rates will be measured for these catalysts, with and without promoters, providing a database for understanding effects of dispersion, metal loading, and support on elementary kinetic parameters and for validation of computational models that incorporate effects of surface structure and promoters. Furthermore, using state-of-the-art self-consistent Density Functional Theory (DFT) methods, we have extensively studied the thermochemistry and kinetics of various elementary steps on

  16. Atomic-Scale Design of Iron Fischer-Tropsch Catalysts: A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

    SciTech Connect

    Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale; Rahul P. Nabar; Calvin H. Bartholomew; Hu Zou; Brian Critchfield

    2006-03-03

    rate-determining steps. In the coming year, studies will focus on quantitative determination of the rates of kinetically-relevant elementary steps on Fe catalysts with/without K and Pt promoters and at various levels of Al{sub 2}O{sub 3} support, providing a database for understanding (1) effects of promoter and support on elementary kinetic parameters and (2) for validation of computational models that incorporate effects of surface structure and promoters. Kinetic parameters will be incorporated into a microkinetics model, enabling prediction of rate without invoking assumptions, e.g. of a rate-determining step or a most-abundant surface intermediate. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on two model surfaces: (1) Fe(110) with 1/4 ML subsurface carbon, and (2) Fe(110) with 1/4 ML Pt adatoms. Reaction networks for FTS on these systems were characterized in full detail by evaluating the thermodynamics and kinetics of each elementary step. We discovered that subsurface C stabilizes all the reactive intermediates, in contrast to Pt, which destabilizes most of them. A comparative study of the reactivities of the modified-Fe surfaces against pure Fe is expected to yield a more comprehensive understanding of promotion mechanisms for FTS on Fe.

  17. Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

    SciTech Connect

    Manos Mavrikakis; James Dumesic; Rahul Nabar; Calvin Bartholonew; Hu Zou; Uchenna Paul

    2008-09-29

    This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient

  18. Computational Chemistry Comparison and Benchmark Database

    National Institute of Standards and Technology Data Gateway

    SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

  19. Plug Pulled on Chemistry Computer Center.

    ERIC Educational Resources Information Center

    Robinson, Arthur L.

    1980-01-01

    Discusses the controversy surrounding the initial decision to establish, and the current decision to phase out, the National Resource for Computation in Chemistry (NRCC), a computational chemistry center jointly sponsored by the National Science Foundation and the Department of Energy. (CS)

  20. Exploiting Locality in Quantum Computation for Quantum Chemistry.

    PubMed

    McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

    2014-12-18

    Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

  1. Parallel computing in atmospheric chemistry models

    SciTech Connect

    Rotman, D.

    1996-02-01

    Studies of atmospheric chemistry are of high scientific interest, involve computations that are complex and intense, and require enormous amounts of I/O. Current supercomputer computational capabilities are limiting the studies of stratospheric and tropospheric chemistry and will certainly not be able to handle the upcoming coupled chemistry/climate models. To enable such calculations, the authors have developed a computing framework that allows computations on a wide range of computational platforms, including massively parallel machines. Because of the fast paced changes in this field, the modeling framework and scientific modules have been developed to be highly portable and efficient. Here, the authors present the important features of the framework and focus on the atmospheric chemistry module, named IMPACT, and its capabilities. Applications of IMPACT to aircraft studies will be presented.

  2. Computing Advances in the Teaching of Chemistry.

    ERIC Educational Resources Information Center

    Baskett, W. P.; Matthews, G. P.

    1984-01-01

    Discusses three trends in computer-oriented chemistry instruction: (1) availability of interfaces to integrate computers with experiments; (2) impact of the development of higher resolution graphics and greater memory capacity; and (3) role of videodisc technology on computer assisted instruction. Includes program listings for auto-titration and…

  3. Computational Chemistry Using Modern Electronic Structure Methods

    ERIC Educational Resources Information Center

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

    2007-01-01

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

  4. Formulating and Solving Problems in Computational Chemistry.

    ERIC Educational Resources Information Center

    Norris, A. C.

    1980-01-01

    Considered are the main elements of computational chemistry problems and how these elements can be used to formulate the problems mathematically. Techniques that are useful in devising an appropriate solution are also considered. (Author/TG)

  5. Disciplines, models, and computers: the path to computational quantum chemistry.

    PubMed

    Lenhard, Johannes

    2014-12-01

    Many disciplines and scientific fields have undergone a computational turn in the past several decades. This paper analyzes this sort of turn by investigating the case of computational quantum chemistry. The main claim is that the transformation from quantum to computational quantum chemistry involved changes in three dimensions. First, on the side of instrumentation, small computers and a networked infrastructure took over the lead from centralized mainframe architecture. Second, a new conception of computational modeling became feasible and assumed a crucial role. And third, the field of computa- tional quantum chemistry became organized in a market-like fashion and this market is much bigger than the number of quantum theory experts. These claims will be substantiated by an investigation of the so-called density functional theory (DFT), the arguably pivotal theory in the turn to computational quantum chemistry around 1990.

  6. Perspectives on Computational Organic Chemistry

    PubMed Central

    Streitwieser, Andrew

    2009-01-01

    The author reviews how his early love for theoretical organic chemistry led to experimental research and the extended search for quantitative correlations between experiment and quantum calculations. The experimental work led to ion pair acidities of alkali-organic compounds and most recently to equilibria and reactions of lithium and cesium enolates in THF. This chemistry is now being modeled by ab initio calculations. An important consideration is the treatment of solvation in which coordination of the alkali cation with the ether solvent plays a major role. PMID:19518150

  7. Integrating Computational Chemistry into the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Johnson, Lewis E.; Engel, Thomas

    2011-01-01

    Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

  8. Computational Chemistry of Adhesive Bonds

    NASA Technical Reports Server (NTRS)

    Phillips, Donald H.

    1999-01-01

    This investigation is intended to determine the electrical mechanical, and chemical properties of adhesive bonds at the molecular level. The initial determinations will be followed by investigations of the effects of environmental effects on the chemistry and properties of the bond layer.

  9. Medicinal electrochemistry: integration of electrochemistry, medicinal chemistry and computational chemistry.

    PubMed

    Almeida, M O; Maltarollo, V G; de Toledo, R A; Shim, H; Santos, M C; Honorio, K M

    2014-01-01

    Over the last centuries, there were many important discoveries in medicine that were crucial for gaining a better understanding of several physiological processes. Molecular modelling techniques are powerful tools that have been successfully used to analyse and interface medicinal chemistry studies with electrochemical experimental results. This special combination can help to comprehend medicinal chemistry problems, such as predicting biological activity and understanding drug action mechanisms. Electrochemistry has provided better comprehension of biological reactions and, as a result of many technological improvements, the combination of electrochemical techniques and biosensors has become an appealing choice for pharmaceutical and biomedical analyses. Therefore, this review will briefly outline the present scope and future advances related to the integration of electrochemical and medicinal chemistry approaches based on various applications from recent studies. PMID:24533810

  10. Medicinal electrochemistry: integration of electrochemistry, medicinal chemistry and computational chemistry.

    PubMed

    Almeida, M O; Maltarollo, V G; de Toledo, R A; Shim, H; Santos, M C; Honorio, K M

    2014-01-01

    Over the last centuries, there were many important discoveries in medicine that were crucial for gaining a better understanding of several physiological processes. Molecular modelling techniques are powerful tools that have been successfully used to analyse and interface medicinal chemistry studies with electrochemical experimental results. This special combination can help to comprehend medicinal chemistry problems, such as predicting biological activity and understanding drug action mechanisms. Electrochemistry has provided better comprehension of biological reactions and, as a result of many technological improvements, the combination of electrochemical techniques and biosensors has become an appealing choice for pharmaceutical and biomedical analyses. Therefore, this review will briefly outline the present scope and future advances related to the integration of electrochemical and medicinal chemistry approaches based on various applications from recent studies.

  11. Selected new developments in computational chemistry.

    PubMed Central

    Darden, T A; Bartolotti, L; Pedersen, L G

    1996-01-01

    Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry. Images Figure 1. PMID:8722111

  12. Computational chemistry and aeroassisted orbital transfer vehicles

    NASA Technical Reports Server (NTRS)

    Cooper, D. M.; Jaffe, R. L.; Arnold, J. O.

    1985-01-01

    An analysis of the radiative heating phenomena encountered during a typical aeroassisted orbital transfer vehicle (AOTV) trajectory was made to determine the potential impact of computational chemistry on AOTV design technology. Both equilibrium and nonequilibrium radiation mechanisms were considered. This analysis showed that computational chemistry can be used to predict (1) radiative intensity factors and spectroscopic data; (2) the excitation rates of both atoms and molecules; (3) high-temperature reaction rate constants for metathesis and charge exchange reactions; (4) particle ionization and neutralization rates and cross sections; and (5) spectral line widths.

  13. THE INTEGRATED USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY, AND VIRTUAL REALITY TO PREDICT THE CHEMICAL REACTIVITY OF ENVIRONMENTAL SURFACES

    EPA Science Inventory

    In the last decade three new techniques scanning probe microscopy (SPM), virtual reality (YR) and computational chemistry ave emerged with the combined capability of a priori predicting the chemically reactivity of environmental surfaces. Computational chemistry provides the cap...

  14. Computational Chemistry Studies on the Carbene Hydroxymethylene

    ERIC Educational Resources Information Center

    Marzzacco, Charles J.; Baum, J. Clayton

    2011-01-01

    A density functional theory computational chemistry exercise on the structure and vibrational spectrum of the carbene hydroxymethylene is presented. The potential energy curve for the decomposition reaction of the carbene to formaldehyde and the geometry of the transition state are explored. The results are in good agreement with recent…

  15. Computational chemistry on commodity-type computers.

    PubMed

    Nicklaus, M C; Williams, R W; Bienfait, B; Billings, E S; Hodoscek, M

    1998-01-01

    A number of inexpensive computers were benchmarked with the ab initio program Gaussian 94, using both small standard test jobs and larger density functional (DFT) calculations. Several varieties of Pentium (x86) and Alpha CPU based systems were tested. Most of them were running under the open source code operating system Linux. They were compared with several workstations and supercomputers. The most powerful of today's commodity-type processors surpassed current supercomputers in speed. The choice of compilers and compilation options was often found to have a larger influence on job CPU times than details of the hardware. Especially on the x86 type machines, the jobs always ran faster the less memory (RAM) they were given. The fastest machine on a per-CPU basis was an Alpha/Linux system. For the DFT calculation, it was close to twice as fast as a Cray J90 supercomputer. PMID:9770303

  16. Algorithms versus architectures for computational chemistry

    NASA Technical Reports Server (NTRS)

    Partridge, H.; Bauschlicher, C. W., Jr.

    1986-01-01

    The algorithms employed are computationally intensive and, as a result, increased performance (both algorithmic and architectural) is required to improve accuracy and to treat larger molecular systems. Several benchmark quantum chemistry codes are examined on a variety of architectures. While these codes are only a small portion of a typical quantum chemistry library, they illustrate many of the computationally intensive kernels and data manipulation requirements of some applications. Furthermore, understanding the performance of the existing algorithm on present and proposed supercomputers serves as a guide for future programs and algorithm development. The algorithms investigated are: (1) a sparse symmetric matrix vector product; (2) a four index integral transformation; and (3) the calculation of diatomic two electron Slater integrals. The vectorization strategies are examined for these algorithms for both the Cyber 205 and Cray XMP. In addition, multiprocessor implementations of the algorithms are looked at on the Cray XMP and on the MIT static data flow machine proposed by DENNIS.

  17. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    PubMed

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution. PMID:26907588

  18. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    PubMed

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution.

  19. Mathematical challenges from theoretical/computational chemistry

    SciTech Connect

    1995-12-31

    The committee believes that this report has relevance and potentially valuable suggestions for a wide range of readers. Target audiences include: graduate departments in the mathematical and chemical sciences; federal and private agencies that fund research in the mathematical and chemical sciences; selected industrial and government research and development laboratories; developers of software and hardware for computational chemistry; and selected individual researchers. Chapter 2 of this report covers some history of computational chemistry for the nonspecialist, while Chapter 3 illustrates the fruits of some past successful cross-fertilization between mathematical scientists and computational/theoretical chemists. In Chapter 4 the committee has assembled a representative, but not exhaustive, survey of research opportunities. Most of these are descriptions of important open problems in computational/theoretical chemistry that could gain much from the efforts of innovative mathematical scientists, written so as to be accessible introductions to the nonspecialist. Chapter 5 is an assessment, necessarily subjective, of cultural differences that must be overcome if collaborative work is to be encouraged between the mathematical and the chemical communities. Finally, the report ends with a brief list of conclusions and recommendations that, if followed, could promote accelerated progress at this interface. Recognizing that bothersome language issues can inhibit prospects for collaborative research at the interface between distinctive disciplines, the committee has attempted throughout to maintain an accessible style, in part by using illustrative boxes, and has included at the end of the report a glossary of technical terms that may be familiar to only a subset of the target audiences listed above.

  20. Integrating Computational Chemistry into a Course in Classical Thermodynamics

    ERIC Educational Resources Information Center

    Martini, Sheridan R.; Hartzell, Cynthia J.

    2015-01-01

    Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

  1. Integrating Computational Chemistry into the Physical Chemistry Laboratory Curriculum: A Wet Lab/Dry Lab Approach

    ERIC Educational Resources Information Center

    Karpen, Mary E.; Henderleiter, Julie; Schaertel, Stephanie A.

    2004-01-01

    The usage of computational chemistry in a pedagogically effective manner in the undergraduate chemistry curriculum is described. The changes instituted for an effective course structure and the assessment of the course efficacy are discussed.

  2. Introducing the Practical Aspects of Computational Chemistry to Undergraduate Chemistry Students

    ERIC Educational Resources Information Center

    Pearson, Jason K.

    2007-01-01

    Various efforts are being made to introduce the different physical aspects and uses of computational chemistry to the undergraduate chemistry students. A new laboratory approach that demonstrates all such aspects via experiments has been devised for the purpose.

  3. Scalable Computational Chemistry: New Developments and Applications

    SciTech Connect

    Yuri Alexeev

    2002-12-31

    The computational part of the thesis is the investigation of titanium chloride (II) as a potential catalyst for the bis-silylation reaction of ethylene with hexaclorodisilane at different levels of theory. Bis-silylation is an important reaction for producing bis(silyl) compounds and new C-Si bonds, which can serve as monomers for silicon containing polymers and silicon carbides. Ab initio calculations on the steps involved in a proposed mechanism are presented. This choice of reactants allows them to study this reaction at reliable levels of theory without compromising accuracy. The calculations indicate that this is a highly exothermic barrierless reaction. The TiCl{sub 2} catalyst removes a 50 kcal/mol activation energy barrier required for the reaction without the catalyst. The first step is interaction of TiCl{sub 2} with ethylene to form an intermediate that is 60 kcal/mol below the energy of the reactants. This is the driving force for the entire reaction. Dynamic correlation plays a significant role because RHF calculations indicate that the net barrier for the catalyzed reaction is 50 kcal/mol. They conclude that divalent Ti has the potential to become an important industrial catalyst for silylation reactions. In the programming part of the thesis, parallelization of different quantum chemistry methods is presented. The parallelization of code is becoming important aspects of quantum chemistry code development. Two trends contribute to it: the overall desire to study large chemical systems and the desire to employ highly correlated methods which are usually computationally and memory expensive. In the presented distributed data algorithms computation is parallelized and the largest arrays are evenly distributed among CPUs. First, the parallelization of the Hartree-Fock self-consistent field (SCF) method is considered. SCF method is the most common starting point for more accurate calculations. The Fock build (sub step of SCF) from AO integrals is also

  4. JACOB: An Enterprise Framework for Computational Chemistry

    PubMed Central

    Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

    2013-01-01

    Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: http://www.wallerlab.org/jacob. © 2013 Wiley Periodicals, Inc. PMID:23553271

  5. Coping with polypharmacology by computational medicinal chemistry.

    PubMed

    Schneider, Gisbert; Reker, Daniel; Rodrigues, Tiago; Schneider, Petra

    2014-09-01

    Predicting the macromolecular targets of drug-like molecules has become everyday practice in medicinal chemistry. We present an overview of our recent research activities in the area of polypharmacology-guided drug design. A focus is put on the self-organizing map (SOM) as a tool for compound clustering and visualization. We show how the SOM can be efficiently used for target-panel prediction, drug re-purposing, and the design of focused compound libraries. We also present the concept of virtual organic synthesis in combination with quantitative estimates of ligand-receptor binding, which we used for de novo designing target-selective ligands. We expect these and related approaches to enable the future discovery of personalized medicines.

  6. Computational Chemistry in the Pharmaceutical Industry: From Childhood to Adolescence.

    PubMed

    Hillisch, Alexander; Heinrich, Nikolaus; Wild, Hanno

    2015-12-01

    Computational chemistry within the pharmaceutical industry has grown into a field that proactively contributes to many aspects of drug design, including target selection and lead identification and optimization. While methodological advancements have been key to this development, organizational developments have been crucial to our success as well. In particular, the interaction between computational and medicinal chemistry and the integration of computational chemistry into the entire drug discovery process have been invaluable. Over the past ten years we have shaped and developed a highly efficient computational chemistry group for small-molecule drug discovery at Bayer HealthCare that has significantly impacted the clinical development pipeline. In this article we describe the setup and tasks of the computational group and discuss external collaborations. We explain what we have found to be the most valuable and productive methods and discuss future directions for computational chemistry method development. We share this information with the hope of igniting interesting discussions around this topic.

  7. Computationally efficient implementation of combustion chemistry in parallel PDF calculations

    NASA Astrophysics Data System (ADS)

    Lu, Liuyan; Lantz, Steven R.; Ren, Zhuyin; Pope, Stephen B.

    2009-08-01

    In parallel calculations of combustion processes with realistic chemistry, the serial in situ adaptive tabulation (ISAT) algorithm [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combustion Theory and Modelling, 1 (1997) 41-63; L. Lu, S.B. Pope, An improved algorithm for in situ adaptive tabulation, Journal of Computational Physics 228 (2009) 361-386] substantially speeds up the chemistry calculations on each processor. To improve the parallel efficiency of large ensembles of such calculations in parallel computations, in this work, the ISAT algorithm is extended to the multi-processor environment, with the aim of minimizing the wall clock time required for the whole ensemble. Parallel ISAT strategies are developed by combining the existing serial ISAT algorithm with different distribution strategies, namely purely local processing (PLP), uniformly random distribution (URAN), and preferential distribution (PREF). The distribution strategies enable the queued load redistribution of chemistry calculations among processors using message passing. They are implemented in the software x2f_mpi, which is a Fortran 95 library for facilitating many parallel evaluations of a general vector function. The relative performance of the parallel ISAT strategies is investigated in different computational regimes via the PDF calculations of multiple partially stirred reactors burning methane/air mixtures. The results show that the performance of ISAT with a fixed distribution strategy strongly depends on certain computational regimes, based on how much memory is available and how much overlap exists between tabulated information on different processors. No one fixed strategy consistently achieves good performance in all the regimes. Therefore, an adaptive distribution strategy, which blends PLP, URAN and PREF, is devised and implemented. It yields consistently good performance in all regimes. In the adaptive parallel

  8. Combining experimental and computational studies to understand and predict reactivities of relevance to homogeneous catalysis.

    PubMed

    Tsang, Althea S-K; Sanhueza, Italo A; Schoenebeck, Franziska

    2014-12-01

    This article showcases three major uses of computational chemistry in reactivity studies: the application after, in combination with, and before experiment. Following a brief introduction of suitable computational tools, challenges and opportunities in the implementation of computational chemistry in reactivity studies are discussed, exemplified with selected case studies from our and other laboratories.

  9. Computing protein infrared spectroscopy with quantum chemistry.

    PubMed

    Besley, Nicholas A

    2007-12-15

    Quantum chemistry is a field of science that has undergone unprecedented advances in the last 50 years. From the pioneering work of Boys in the 1950s, quantum chemistry has evolved from being regarded as a specialized and esoteric discipline to a widely used tool that underpins much of the current research in chemistry today. This achievement was recognized with the award of the 1998 Nobel Prize in Chemistry to John Pople and Walter Kohn. As the new millennium unfolds, quantum chemistry stands at the forefront of an exciting new era. Quantitative calculations on systems of the magnitude of proteins are becoming a realistic possibility, an achievement that would have been unimaginable to the early pioneers of quantum chemistry. In this article we will describe ongoing work towards this goal, focusing on the calculation of protein infrared amide bands directly with quantum chemical methods.

  10. Molecular Modeling and Computational Chemistry at Humboldt State University.

    ERIC Educational Resources Information Center

    Paselk, Richard A.; Zoellner, Robert W.

    2002-01-01

    Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

  11. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery.

    PubMed

    Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G; Mendoza-Sanchez, Rodrigo; Corbeil, Christopher R; Weill, Nathanael; Campagna-Slater, Valérie; Moitessier, Nicolas

    2012-01-23

    As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.

  12. Computer-Based Learning in Chemistry Classes

    ERIC Educational Resources Information Center

    Pietzner, Verena

    2014-01-01

    Currently not many people would doubt that computers play an essential role in both public and private life in many countries. However, somewhat surprisingly, evidence of computer use is difficult to find in German state schools although other countries have managed to implement computer-based teaching and learning in their schools. This paper…

  13. From computational quantum chemistry to computational biology: experiments and computations are (full) partners.

    PubMed

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  14. PERSPECTIVE: From computational quantum chemistry to computational biology: experiments and computations are (full) partners

    NASA Astrophysics Data System (ADS)

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  15. Computational solution of atmospheric chemistry problems

    NASA Technical Reports Server (NTRS)

    Jafri, J.; Ake, R. L.

    1986-01-01

    Extensive studies were performed on problems of interest in atmospheric chemistry. In addition to several minor projects, four major projects were performed and described (theoretical studies of ground and low-lying excited states of ClO2; ground and excited state potential energy surfaces of the methyl peroxy radical; electronic states ot the FO radical; and theoretical studies S02 (H2O) (sub n)).

  16. Computational chemistry, systems biology and toxicology. Harnessing the chemistry of life: revolutionizing toxicology. a commentary.

    PubMed

    Kimber, Ian; Humphris, Colin; Westmoreland, Carl; Alepee, Nathalie; Negro, Gianni Dal; Manou, Irene

    2011-04-01

    There is a continuing interest in, and increasing imperatives for, the development of alternative methods for toxicological evaluations that do not require the use of animals. Although a significant investment has resulted in some achievements, progress has been patchy and there remain many challenges. Among the most significant hurdles is developing non-animal methods that would permit assessment of the potential for a chemical or drug to cause adverse health effects following repeated systemic exposure. Developing approaches to address this challenge has been one of the objectives of the European Partnership for Alternative Approaches to Animal Testing (EPAA). The EPAA is a unique partnership between the European Commission and industry that has interests in all aspects of reducing, refining and replacing the use of animals (the '3Rs'). One possible strategy that emerged from a broad scientific debate sponsored by the EPAA was the opportunity for developing entirely new paradigms for toxicity testing based upon harnessing the increasing power of computational chemistry in combination with advanced systems biology. This brief commentary summarizes a workshop organized by the EPAA in 2010, that had the ambitious title of 'Harnessing the Chemistry of Life: Revolutionizing Toxicology'. At that workshop international experts in chemistry, systems biology and toxicology sought to map out how best developments in these sciences could be exploited to design new strategies for toxicity testing using adverse effects in the liver as an initial focus of attention. Here we describe the workshop design and outputs, the primary purpose being to stimulate debate about the need to align different areas of science with toxicology if new and truly innovative approaches to toxicity testing are to be developed.

  17. Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.

    ERIC Educational Resources Information Center

    Albee, David; Jones, Edward

    1989-01-01

    Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)

  18. A Program of Computational Chemistry Exercises for the First-Semester General Chemistry Course

    ERIC Educational Resources Information Center

    Feller, Scott E.; Dallinger, Richard F.; McKinney, Paul Caylor

    2004-01-01

    The computer systems available for molecular modeling are described, along with a discussion of a molecular modeling program created and supported by computational techniques for the first-semester general chemistry course. Various exercises are listed, which direct the learner from a beginner's course in software practice to more complex…

  19. Interdisciplinary Educational Collaborations: Chemistry and Computer Science

    ERIC Educational Resources Information Center

    Haines, Ronald S.; Woo, Daniel T.; Hudson, Benjamin T.; Mori, Joji C.; Ngan, Evey S. M.; Pak, Wing-Yee

    2007-01-01

    Research collaborations between chemists and other scientists resulted in significant outcomes such as development of software. Such collaboration provided a realistic learning experience for computer science students.

  20. Software and resources for computational medicinal chemistry

    PubMed Central

    Liao, Chenzhong; Sitzmann, Markus; Pugliese, Angelo; Nicklaus, Marc C

    2011-01-01

    Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools. PMID:21707404

  1. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  2. Towards quantum chemistry on a quantum computer.

    PubMed

    Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

    2010-02-01

    Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications. PMID:21124400

  3. Virtual drug discovery: beyond computational chemistry?

    PubMed

    Gilardoni, Francois; Arvanites, Anthony C

    2010-02-01

    This editorial looks at how a fully integrated structure that performs all aspects in the drug discovery process, under one company, is slowly disappearing. The steps in the drug discovery paradigm have been slowly increasing toward virtuality or outsourcing at various phases of product development in a company's candidate pipeline. Each step in the process, such as target identification and validation and medicinal chemistry, can be managed by scientific teams within a 'virtual' company. Pharmaceutical companies to biotechnology start-ups have been quick in adopting this new research and development business strategy in order to gain flexibility, access the best technologies and technical expertise, and decrease product developmental costs. In today's financial climate, the term virtual drug discovery has an organizational meaning. It represents the next evolutionary step in outsourcing drug development.

  4. National Resource for Computation in Chemistry (NRCC). Attached scientific processors for chemical computations: a report to the chemistry community

    SciTech Connect

    Ostlund, N.S.

    1980-01-01

    The demands of chemists for computational resources are well known and have been amply documented. The best and most cost-effective means of providing these resources is still open to discussion, however. This report surveys the field of attached scientific processors (array processors) and attempts to indicate their present and possible future use in computational chemistry. Array processors have the possibility of providing very cost-effective computation. This report attempts to provide information that will assist chemists who might be considering the use of an array processor for their computations. It describes the general ideas and concepts involved in using array processors, the commercial products that are available, and the experiences reported by those currently using them. In surveying the field of array processors, the author makes certain recommendations regarding their use in computational chemistry. 5 figures, 1 table (RWR)

  5. Writing and Computing across the USM Chemistry Curriculum

    NASA Astrophysics Data System (ADS)

    Gordon, Nancy R.; Newton, Thomas A.; Rhodes, Gale; Ricci, John S.; Stebbins, Richard G.; Tracy, Henry J.

    2001-01-01

    The faculty of the University of Southern Maine believes the ability to communicate effectively is one of the most important skills required of successful chemists. To help students achieve that goal, the faculty has developed a Writing and Computer Program consisting of writing and computer assignments of gradually increasing sophistication for all our laboratory courses. The assignments build in complexity until, at the junior level, students are writing full journal-quality laboratory reports. Computer assignments also increase in difficulty as students attack more complicated subjects. We have found the program easy to initiate and our part-time faculty concurs as well. The Writing and Computing across the Curriculum Program also serves to unite the entire chemistry curriculum. We believe the program is helping to reverse what the USM chemistry faculty and other educators have found to be a steady deterioration in the writing skills of many of today's students.

  6. Investigating the Effectiveness of Computer Simulations for Chemistry Learning

    ERIC Educational Resources Information Center

    Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

    2012-01-01

    Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

  7. Incorporating Computational Chemistry into the Chemical Engineering Curriculum

    ERIC Educational Resources Information Center

    Wilcox, Jennifer

    2006-01-01

    A graduate-level computational chemistry course was designed and developed and carried out in the Department of Chemical Engineering at Worcester Polytechnic Institute in the Fall of 2005. The thrust of the course was a reaction assignment that led students through a series of steps, beginning with energetic predictions based upon fundamental…

  8. Dissociation of the Ethyl Radical: An Exercise in Computational Chemistry

    ERIC Educational Resources Information Center

    Nassabeh, Nahal; Tran, Mark; Fleming, Patrick E.

    2014-01-01

    A set of exercises for use in a typical physical chemistry laboratory course are described, modeling the unimolecular dissociation of the ethyl radical to form ethylene and atomic hydrogen. Students analyze the computational results both qualitatively and quantitatively. Qualitative structural changes are compared to approximate predicted values…

  9. A Computer Assisted Problem Solving Method for Beginning Chemistry Students.

    ERIC Educational Resources Information Center

    Powers, Michael H.

    1984-01-01

    Outlines a problem-solving method for beginning chemistry students that utilizes specific, concrete steps as well as computer-assisted tutorials. The method involves an approach referred to as the Factor-Unit Method coupled with a graphical "road map" which allows students to trace problems from start to finish. (JN)

  10. Applied Computational Chemistry for the Blind and Visually Impaired

    ERIC Educational Resources Information Center

    Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

    2012-01-01

    We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

  11. Integration of Computational Chemistry into the Undergraduate Organic Chemistry Laboratory Curriculum

    ERIC Educational Resources Information Center

    Esselman, Brian J.; Hill, Nicholas J.

    2016-01-01

    Advances in software and hardware have promoted the use of computational chemistry in all branches of chemical research to probe important chemical concepts and to support experimentation. Consequently, it has become imperative that students in the modern undergraduate curriculum become adept at performing simple calculations using computational…

  12. Developing and Using Conceptual Computer Animations for Chemistry Instruction

    NASA Astrophysics Data System (ADS)

    Burke, K. A.; Greenbowe, Thomas J.; Windschitl, Mark A.

    1998-12-01

    Multimedia technology has advanced rapidly within the past two years providing an opportunity for chemistry instructors to develop and use their own computer animations. Conceptual computer animations are designed to help students understand the basic concept or principle of a dynamic chemical process. This paper discusses several issues surrounding the development and use of instructional conceptual computer animations. If possible, an animation sequence should be linked to a lecture demonstration, thereby assisting in the presentation of all three levels of representation: microscopic, macroscopic and symbolic. Computer animations provide instructors with a vehicle for presenting topics from the particulate nature of matter view and a technique for teaching for conceptual understanding. A design team consisting of individuals who have knowledge or expertise in the content area, instructional design, computer animation techniques, and graphic and sound production should work with the chemistry instructor to develop and produce the animation sequences. Various software tools for drawing, animating, and incorporating audio tracks along with the animation are discussed. Aspects of effective computer anmation are listed. Techniques for 24-hour student access to instructional computer animations through the internet via the World Wide Web, as well as to a local file servers through the intranet are mentioned. Chemistry instructors who develop computer animations or multimedia presentations must be aware of copyright laws pertaining to the educational use and distribution of images, pictures, illustrations, and sounds. Using computer animations does take additonal time in lecture. However instructors must decide whether they want to "cover" or "uncover" material. The inclusion of computer animations is consistent with reports from the ACS task force that emphasizes "less is more" in terms of curriculum reform.

  13. Computational Tools To Model Halogen Bonds in Medicinal Chemistry.

    PubMed

    Ford, Melissa Coates; Ho, P Shing

    2016-03-10

    The use of halogens in therapeutics dates back to the earliest days of medicine when seaweed was used as a source of iodine to treat goiters. The incorporation of halogens to improve the potency of drugs is now fairly standard in medicinal chemistry. In the past decade, halogens have been recognized as direct participants in defining the affinity of inhibitors through a noncovalent interaction called the halogen bond or X-bond. Incorporating X-bonding into structure-based drug design requires computational models for the anisotropic distribution of charge and the nonspherical shape of halogens, which lead to their highly directional geometries and stabilizing energies. We review here current successes and challenges in developing computational methods to introduce X-bonding into lead compound discovery and optimization during drug development. This fast-growing field will push further development of more accurate and efficient computational tools to accelerate the exploitation of halogens in medicinal chemistry.

  14. How changes in computer technology are revolutionizing the practice of chemistry.

    PubMed

    Levy, G C

    1988-11-01

    During the early 1980s, two major developments in computer technology changed the way chemists approached their science. The advent of the micropressor and then the PC changed experimental chemistry, while the availability of two classes of computer, the superminicomputer and supercomputer, greatly influenced computational chemistry. In the past two years, graphics workstation computers have begun to affect the practice of chemistry by combining fast, high-resolution, multiwindow graphics with superminicomputer power. In 1988, the advent of a new class of computer--the graphics supercomputer--offers extraordinary promise to both theoretician and experimentalist. In these systems, near-Cray compute power is combined with ultrahigh-speed 3-dimensional graphics for unparalleled visualization of molecular processes and other complex events. This is made practical not just by computing and graphics power but by use of ultrahigh internal bandwidths inside the graphics supercomputers. Another major development in scientific computing is the evolving concept of the laboratory computer network. Current network designs include hierarchical configurations incorporating various levels of computers--through supercomputers--either locally or via national or regional networks. New software methods are also having impact on chemical research, allowing, for example, the scientist to better abstract information from noisy or incomplete experimental data. Use of parallelism (multiple CPUs) in new design workstation computers will extend their power, by the early 1990s, past that of current supercomputer mainframes. Within five years the chemist will have $10 million of 1985 computer power on his desk, for considerably less than $100,000, along with visualization tools and software only dreamed of in 1985.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3235470

  15. ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

    EPA Science Inventory

    Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...

  16. Gabedit--a graphical user interface for computational chemistry softwares.

    PubMed

    Allouche, Abdul-Rahman

    2011-01-15

    Gabedit is a freeware graphical user interface, offering preprocessing and postprocessing adapted (to date) to nine computational chemistry software packages. It includes tools for editing, displaying, analyzing, converting, and animating molecular systems. A conformational search tool is implemented using a molecular mechanics or a semiempirical potential. Input files can be generated for the computational chemistry software supported by Gabedit. Some molecular properties of interest are processed directly from the output of the computational chemistry programs; others are calculated by Gabedit before display. Molecular orbitals, electron density, electrostatic potential, nuclear magnetic resonance shielding density, and any other volumetric data properties can be displayed. It can display electronic circular dichroism, UV-visible, infrared, and Raman-computed spectra after a convolution. Gabedit can generate a Povray file for geometry, surfaces, contours, and color-coded planes. Output can be exported to a selection of popular image and vector graphics file formats; the program can also generate a series of pictures for animation. Quantum mechanical electrostatic potentials can be calculated using the partial charges on atoms, or by solving the Poisson equation using the multigrid method. The atoms in molecule charges can also be calculated. Gabedit is platform independent. The code is distributed under free open source X11 style license and is available at http://gabedit.sourceforge.net/. PMID:20607691

  17. From transistor to trapped-ion computers for quantum chemistry.

    PubMed

    Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

    2014-01-01

    Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology. PMID:24395054

  18. Computational chemistry in Argonne`s Reactor Analysis Division

    SciTech Connect

    Gelbard, E.; Agrawal, R.; Fanning, T.

    1997-08-01

    Roughly 3 years ago work on Argonne`s Integral Fast Reactor ({open_quotes}IFR{close_quotes}) was terminated and at that time, ANL funding was redirected to a number of alternative programs. One such alternative was waste management and, since disposal of spent fuel from ANL`s EBR-II reactor presents some special problems, this seemed an appropriate area for ANL work. Methods for the treatment and disposal of spent fuel (particularly from EBR-II but also from other sources) are now under very active investigation at ANL. The very large waste form development program is mainly experimental at this point, but within the Reactor Analysis ({open_quotes}RA{close_quotes}) Division a small computational chemistry program is underway, designed to supplement the experimental program. One of the most popular proposals for the treatment of much of our high-level wastes is vitrification. As noted below, this approach has serious drawbacks for EBR-II spent fuel. ANL has proposed, instead, that spent fuel first be pretreated by a special metallurgical process which produces, as waste, chloride salts of the various fission products; these salts would then be adsorbed in zeolite A, which is subsequently bonded with glass to produce a waste form suitable for disposal. So far it has been the main mission of RA`s computational chemistry program to study the process by which leaching occurs when the glass-bonded zeolite waste form is exposed to water. It is the purpose of this paper to describe RA`s computational chemistry program, to discuss the computational techniques involved in such a program, and in general to familiarize the M. and C. Division with a computational area which is probably unfamiliar to most of its member. 11 refs., 2 figs.

  19. Turbulent reacting flow computations including turbulence-chemistry interactions

    NASA Technical Reports Server (NTRS)

    Narayan, J. R.; Girimaji, S. S.

    1992-01-01

    A two-equation (k-epsilon) turbulence model has been extended to be applicable for compressible reacting flows. A compressibility correction model based on modeling the dilatational terms in the Reynolds stress equations has been used. A turbulence-chemistry interaction model is outlined. In this model, the effects of temperature and species mass concentrations fluctuations on the species mass production rates are decoupled. The effect of temperature fluctuations is modeled via a moment model, and the effect of concentration fluctuations is included using an assumed beta-pdf model. Preliminary results obtained using this model are presented. A two-dimensional reacting mixing layer has been used as a test case. Computations are carried out using the Navier-Stokes solver SPARK using a finite rate chemistry model for hydrogen-air combustion.

  20. Introductory College Chemistry Students' Understanding of Stoichiometry: Connections between Conceptual and Computational Understandings and Instruction.

    ERIC Educational Resources Information Center

    Wolfer, Adam J.; Lederman, Norman G.

    Many studies of college chemistry students have found a gap between students' success in solving computational chemistry problems and their success in solving conceptual chemistry problems. This paper examines college students' understanding of the concept of stoichiometry, the particulate nature of matter, and chemistry problem solving. This…

  1. Development and Assessment of a Chemistry-Based Computer Video Game as a Learning Tool

    ERIC Educational Resources Information Center

    Martinez-Hernandez, Kermin Joel

    2010-01-01

    The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning…

  2. The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

    PubMed

    Thackston, Russell; Fortenberry, Ryan C

    2015-05-01

    The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. PMID:25753841

  3. The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

    PubMed

    Thackston, Russell; Fortenberry, Ryan C

    2015-05-01

    The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services.

  4. Investigating the Medium Effect in Computer-Aided Assessment of School Chemistry and College Computing National Examinations

    ERIC Educational Resources Information Center

    Ashton, Helen S.; Beevers, Cliff E.; Korabinski, Athol A.; Youngson, Martin A.

    2005-01-01

    This article presents results of a comparison between paper and computer tests of ability in Chemistry and Computing. A statistical model is employed to analyse the experimental data from almost 200 candidates. It is shown that there is no medium effect when specific traditional paper examinations in Chemistry and Computing are transferred into…

  5. Computational chemistry meets cultural heritage: challenges and perspectives.

    PubMed

    Fantacci, Simona; Amat, Anna; Sgamellotti, Antonio

    2010-06-15

    Chemistry is central to addressing topics of interest in the cultural heritage field, offering particular insight into the nature and composition of the original materials, the degradation processes that have occurred over the years, and the attendant physical and chemical changes. On the one hand, the chemical characterization of the constituting materials allows researchers to unravel the rich information enclosed in a work of art, providing insight into the manufacturing techniques and revealing aspects of artistic, chronological, historical, and sociocultural significance. On the other hand, despite the recognized contribution of computational chemistry in many branches of materials science, this tool has only recently been applied to cultural heritage, largely because of the inherent complexity of art materials. In this Account, we present a brief overview of the available computational methods, classified on the basis of accuracy level and dimension of the system to be simulated. Among the discussed methodologies, density functional theory (DFT) and time-dependent DFT represent a good compromise between accuracy and computational cost, allowing researchers to model the structural, electronic, and spectroscopic properties of complex extended systems in condensed phase. We then discuss the results of recent research devoted to the computer simulation of prototypical systems in cultural heritage, namely, indigo and Maya Blue, weld and weld lake, and the pigment minium (red lead). These studies provide insight into the basic interactions underlying the materials properties and, in some cases, permit the assignment of the material composition. We discuss properties of interest in the cultural heritage field, ranging from structural geometries and acid-base properties to IR-Raman vibrational spectra and UV-vis absorption-emission spectra (including excited-state deactivation pathways). We particularly highlight how computational chemistry applications in cultural

  6. Computational chemistry meets cultural heritage: challenges and perspectives.

    PubMed

    Fantacci, Simona; Amat, Anna; Sgamellotti, Antonio

    2010-06-15

    Chemistry is central to addressing topics of interest in the cultural heritage field, offering particular insight into the nature and composition of the original materials, the degradation processes that have occurred over the years, and the attendant physical and chemical changes. On the one hand, the chemical characterization of the constituting materials allows researchers to unravel the rich information enclosed in a work of art, providing insight into the manufacturing techniques and revealing aspects of artistic, chronological, historical, and sociocultural significance. On the other hand, despite the recognized contribution of computational chemistry in many branches of materials science, this tool has only recently been applied to cultural heritage, largely because of the inherent complexity of art materials. In this Account, we present a brief overview of the available computational methods, classified on the basis of accuracy level and dimension of the system to be simulated. Among the discussed methodologies, density functional theory (DFT) and time-dependent DFT represent a good compromise between accuracy and computational cost, allowing researchers to model the structural, electronic, and spectroscopic properties of complex extended systems in condensed phase. We then discuss the results of recent research devoted to the computer simulation of prototypical systems in cultural heritage, namely, indigo and Maya Blue, weld and weld lake, and the pigment minium (red lead). These studies provide insight into the basic interactions underlying the materials properties and, in some cases, permit the assignment of the material composition. We discuss properties of interest in the cultural heritage field, ranging from structural geometries and acid-base properties to IR-Raman vibrational spectra and UV-vis absorption-emission spectra (including excited-state deactivation pathways). We particularly highlight how computational chemistry applications in cultural

  7. Opportunities and challenges of high-performance computing in chemistry

    SciTech Connect

    Guest, M.F.; Kendall, R.A.; Nichols, J.A.

    1995-06-01

    The field of high-performance computing is developing at an extremely rapid pace. Massively parallel computers offering orders of magnitude increase in performance are under development by all the major computer vendors. Many sites now have production facilities that include massively parallel hardware. Molecular modeling methodologies (both quantum and classical) are also advancing at a brisk pace. The transition of molecular modeling software to a massively parallel computing environment offers many exciting opportunities, such as the accurate treatment of larger, more complex molecular systems in routine fashion, and a viable, cost-effective route to study physical, biological, and chemical `grand challenge` problems that are impractical on traditional vector supercomputers. This will have a broad effect on all areas of basic chemical science at academic research institutions and chemical, petroleum, and pharmaceutical industries in the United States, as well as chemical waste and environmental remediation processes. But, this transition also poses significant challenges: architectural issues (SIMD, MIMD, local memory, global memory, etc.) remain poorly understood and software development tools (compilers, debuggers, performance monitors, etc.) are not well developed. In addition, researchers that understand and wish to pursue the benefits offered by massively parallel computing are often hindered by lack of expertise, hardware, and/or information at their site. A conference and workshop organized to focus on these issues was held at the National Institute of Health, Bethesda, Maryland (February 1993). This report is the culmination of the organized workshop. The main conclusion: a drastic acceleration in the present rate of progress is required for the chemistry community to be positioned to exploit fully the emerging class of Teraflop computers, even allowing for the significant work to date by the community in developing software for parallel architectures.

  8. Theoretical Hammett Plot for the Gas-Phase Ionization of Benzoic Acid versus Phenol: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Ziegler, Blake E.

    2013-01-01

    Computational chemistry undergraduate laboratory courses are now part of the chemistry curriculum at many universities. However, there remains a lack of computational chemistry exercises available to instructors. This exercise is presented for students to develop skills using computational chemistry software while supplementing their knowledge of…

  9. Computers in Chemistry Teaching: A Bibliography and Index of CAL Packages.

    ERIC Educational Resources Information Center

    Rushby, N. J.

    This resource document lists 36 books, papers, and reports dealing with various uses of computers in chemistry instruction; and describes several computer program packages available for use in teaching undergraduate, experimental laboratory, physical, and nuclear and X-ray chemistry, including biochemistry. Each program package is presented by…

  10. Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

    ERIC Educational Resources Information Center

    Perri, M. J.; Weber, S. H.

    2014-01-01

    A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

  11. Interactive Computer Visualization in the Introductory Chemistry Curriculum

    NASA Astrophysics Data System (ADS)

    Bragin, Victoria M.

    1996-08-01

    Increasingly, chemistry instructors, especially in two-year colleges, find themselves teaching classes where there is great disparity in the academic preparation of the students and where even those students with good mathematics and basic science backgrounds have poor English language and communication skills. This project explores the use of technological innovations to facilitate learning in introductory chemistry courses by those with a poor academic background, while also challenging those prepared to master the curriculum. An additional objective is to improve the communication skills of all students. Material is presented visually and in as engaging a fashion as possible, students are provided ready access to relevant information about the course content in ways that are adapted to their individual learning styles, and collaborative learning is encouraged, especially among those who work and live at a distance from campus. The chief tactics employed are: Development of software that can be customized to meet the varying needs of individual students, courses, and instructors. Use of simulations that, while not replacing laboratory bench experiments, allow students to practice important laboratory techniques and observe the physical behavior of chemical systems. Use of software that allows students to explore the molecular basis of chemical phenomena. Use of software that allows students to display and analyze data in ways that facilitate drawing general conclusions about the quantitative relationships between observable properties. Use of the computer as a communications device. The ability to customize software is important in adapting to different learning styles and in encouraging students to learn by discovery. For example, TitrationLab was developed so that the material may merely be presented empirically or in ways in which the principles of equilibrium are demonstrated. At the advanced level, automatically generated titration curves are used to

  12. Computational investigation of rocket based combined cycle

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-bo; Wang, Zhan-xue; Liu, Zeng-wen

    2013-03-01

    Based on Computational Fluid Dynamic technology, the mixing process of Rocket Based Combined Cycle (RBCC) propulsion system is researched. The idea of RBCC propulsion system means combining rocket engine with ramjet engine effectively, which can flight from sea level to high altitude in wide Mach ranges. In order to analyze how the length of the mixing part affects mixing process, different length of mixing part are researched. As it is indicated, with a constant Mach number, increasing the length of mixing part makes main flow and second flow mix more evenly. Moreover, the length of mixing part has a slight impact on the thrust. Obviously the main consequence of increasing the length of mixing part is promoting the mix of main flow and second flow. Therefore, in order to decrease the weight of aircraft, it is of importance to reduce the length. Through comparing distribution of different cases, when working in the situation of maximum power, the flow in the nozzle of rocket engine is under expansion, while that in the nozzle is fully expanded. Nevertheless, in the case of high altitude and high Mach number, there exists a vortex in the nozzle of rocket engine because of over expansion; meanwhile, the flow in the nozzle is under expansion. Therefore, it is necessary to adjust nozzle throat area in order to increase the thrust of RBCC at high altitude.

  13. Interactive Computer Visualization in the Introductory Chemistry Curriculum

    NASA Astrophysics Data System (ADS)

    Bragin, Victoria M.

    1996-08-01

    Increasingly, chemistry instructors, especially in two-year colleges, find themselves teaching classes where there is great disparity in the academic preparation of the students and where even those students with good mathematics and basic science backgrounds have poor English language and communication skills. This project explores the use of technological innovations to facilitate learning in introductory chemistry courses by those with a poor academic background, while also challenging those prepared to master the curriculum. An additional objective is to improve the communication skills of all students. Material is presented visually and in as engaging a fashion as possible, students are provided ready access to relevant information about the course content in ways that are adapted to their individual learning styles, and collaborative learning is encouraged, especially among those who work and live at a distance from campus. The chief tactics employed are: Development of software that can be customized to meet the varying needs of individual students, courses, and instructors. Use of simulations that, while not replacing laboratory bench experiments, allow students to practice important laboratory techniques and observe the physical behavior of chemical systems. Use of software that allows students to explore the molecular basis of chemical phenomena. Use of software that allows students to display and analyze data in ways that facilitate drawing general conclusions about the quantitative relationships between observable properties. Use of the computer as a communications device. The ability to customize software is important in adapting to different learning styles and in encouraging students to learn by discovery. For example, TitrationLab was developed so that the material may merely be presented empirically or in ways in which the principles of equilibrium are demonstrated. At the advanced level, automatically generated titration curves are used to

  14. A Timesharing Computer Program for a General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Cutler, Gary L.; Drum, Donald A.

    1975-01-01

    Describes an experiment in which general and physical chemistry students can determine the heat of vaporization of a volatile substance from experimental laboratory data using timesharing techniques. (MLH)

  15. Promoting Intrinsic and Extrinsic Motivation among Chemistry Students Using Computer-Assisted Instruction

    ERIC Educational Resources Information Center

    Gambari, Isiaka A.; Gbodi, Bimpe E.; Olakanmi, Eyitao U.; Abalaka, Eneojo N.

    2016-01-01

    The role of computer-assisted instruction in promoting intrinsic and extrinsic motivation among Nigerian secondary school chemistry students was investigated in this study. The study employed two modes of computer-assisted instruction (computer simulation instruction and computer tutorial instructional packages) and two levels of gender (male and…

  16. Using Computational Chemistry Activities to Promote Learning and Retention in a Secondary School General Chemistry Setting

    ERIC Educational Resources Information Center

    Ochterski, Joseph W.

    2014-01-01

    This article describes the results of using state-of-the-art, research-quality software as a learning tool in a general chemistry secondary school classroom setting. I present three activities designed to introduce fundamental chemical concepts regarding molecular shape and atomic orbitals to students with little background in chemistry, such as…

  17. The effect of computer-assisted instruction on the attitudes of college students toward computers and chemistry

    NASA Astrophysics Data System (ADS)

    Cavin, Claudia S.; Cavin, E. D.; Lagowski, J. J.

    The purpose of this study was to see whether college students' attitudes toward computers and chemistry would be affected by using CAI materials in a chemistry course, and whether there would be any difference for students of different sex. Students were randomly assigned to experimental and control groups, pre- and posttests were given to both groups, and the data were analyzed using 2-way analysis of covariance. It was found that the attitude of women toward computers was improved by using CAI. No change in attitude toward chemistry was found.

  18. Using Computer Visualization Models in High School Chemistry: The Role of Teacher Beliefs.

    ERIC Educational Resources Information Center

    Robblee, Karen M.; Garik, Peter; Abegg, Gerald L.; Faux, Russell; Horwitz, Paul

    This paper discusses the role of high school chemistry teachers' beliefs in implementing computer visualization software to teach atomic and molecular structure from a quantum mechanical perspective. The informants in this study were four high school chemistry teachers with comparable academic and professional backgrounds. These teachers received…

  19. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

    ERIC Educational Resources Information Center

    Albrecht, Birgit

    2014-01-01

    The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

  20. Integrating Free Computer Software in Chemistry and Biochemistry Instruction: An International Collaboration

    ERIC Educational Resources Information Center

    Cedeno, David L.; Jones, Marjorie A.; Friesen, Jon A.; Wirtz, Mark W.; Rios, Luz Amalia; Ocampo, Gonzalo Taborda

    2010-01-01

    At the Universidad de Caldas, Manizales, Colombia, we used their new computer facilities to introduce chemistry graduate students to biochemical database mining and quantum chemistry calculations using freeware. These hands-on workshops allowed the students a strong introduction to easily accessible software and how to use this software to begin…

  1. Effects of Computer Based Learning on Students' Attitudes and Achievements towards Analytical Chemistry

    ERIC Educational Resources Information Center

    Akcay, Hüsamettin; Durmaz, Asli; Tüysüz, Cengiz; Feyzioglu, Burak

    2006-01-01

    The aim of this study was to compare the effects of computer-based learning and traditional method on students' attitudes and achievement towards analytical chemistry. Students from Chemistry Education Department at Dokuz Eylul University (D.E.U) were selected randomly and divided into three groups; two experimental (Eg-1 and Eg-2) and a control…

  2. COMPUTATIONAL CHEMISTRY: AN EMERGING TECHNOLOGY FOR SOLVING PROBLEMS IN ATMOSPHERIC CHEMISTRY

    EPA Science Inventory

    Over the past three decades, atmospheric chemistry has served as an important component in developing strategies for reducing ambient concentrations of air pollutants. Laboratory studies are carried out to investigate the key chemical reactions that determine the fates and lif...

  3. Combined Volatolomics for Monitoring of Human Body Chemistry

    NASA Astrophysics Data System (ADS)

    Broza, Yoav Y.; Zuri, Liat; Haick, Hossam

    2014-04-01

    Analysis of volatile organic compounds (VOCs) is a promising approach for non-invasive, fast and potentially inexpensive diagnostics. Here, we present a new methodology for profiling the body chemistry by using the volatile fraction of molecules in various body fluids. Using mass spectrometry and cross-reactive nanomaterial-based sensors array, we demonstrate that simultaneous VOC detection from breath and skin would provide complementary, non-correlated information of the body's volatile metabolites profile. Eventually with further wide population validation studies, such a methodology could provide more accurate monitoring of pathological changes compared to the information provided by a single body fluid. The qualitative and quantitative methods presented here offers a variety of options for novel mapping of the metabolic properties of complex organisms, including humans.

  4. Combined volatolomics for monitoring of human body chemistry.

    PubMed

    Broza, Yoav Y; Zuri, Liat; Haick, Hossam

    2014-04-09

    Analysis of volatile organic compounds (VOCs) is a promising approach for non-invasive, fast and potentially inexpensive diagnostics. Here, we present a new methodology for profiling the body chemistry by using the volatile fraction of molecules in various body fluids. Using mass spectrometry and cross-reactive nanomaterial-based sensors array, we demonstrate that simultaneous VOC detection from breath and skin would provide complementary, non-correlated information of the body's volatile metabolites profile. Eventually with further wide population validation studies, such a methodology could provide more accurate monitoring of pathological changes compared to the information provided by a single body fluid. The qualitative and quantitative methods presented here offers a variety of options for novel mapping of the metabolic properties of complex organisms, including humans.

  5. Comparison of seven packages that compute ocean carbonate chemistry

    NASA Astrophysics Data System (ADS)

    Orr, J. C.; Epitalon, J.-M.; Gattuso, J.-P.

    2014-04-01

    To study ocean acidification and the carbon cycle, marine scientists often use two measured or modeled carbonate system variables to compute others. These carbonate chemistry calculations, based on well-known thermodynamic equilibria, are now available from seven public packages: CO2SYS, csys, seacarb, swco2, CO2calc, ODV, and mocsy. We compared results from these packages using common input data and the set of equilibrium constants recommended for best practices. All packages agree within ±0.00025 units for pH and ±0.5 μmol kg-1 for CO32-, and six packages agree within ±0.2 μatm for pCO2 in terms of zonal-mean surface values. In the remaining package (csys), the surface pCO2 variable is up to 1.4 μatm lower than in other packages, but that is because it is mislabeled. When compared to surface fCO2, it differs by less than 0.2 μatm. The csys deviations in fCO2, pH, and CO32- grow with depth but remain small. Another package (swco2) also diverges significantly but only in warm deep waters as found in the Mediterranean Sea. Discrepancies between packages derive largely from their code for the equilibrium constants. Analysis of the sensitivity of each computed variable to changes in each constant showed the expected dominance of K1 and K2, while also revealing comparable sensitivity to KB, e.g., with the AT-CT input pair. Best-practice formulations for K1 and K2 are implemented consistently among packages, except those in csys deviate slightly at depth (e.g., 0.5% larger values at 4000 db) due to its pressure corrections made on the total instead of the seawater pH scale. With more recent formulations for K1 and K2 designed to cover a wider range of salinities, packages disagree more, e.g., by 8 μatm in pCO2, 1 μmol kg-1 in CO32-, and 0.006 units in pH under typical surface conditions. These discrepancies stem from packages using different sets of coefficients for the corresponding salinity dependence of the new formulations. Although each set should be

  6. Automated Fake Color Separation: Combining Computer Vision And Computer Graphics

    NASA Astrophysics Data System (ADS)

    Walters, Deborah

    1987-05-01

    A system is described for the automation of the color separation process. In current color separation systems, humans must visually segment line-art images, and using pen and ink, delineate the segments in a manner that enables a computer graphics system to be used interactively to color in each segment. The goal of this research was to remove the labor-intensive human visual segmentation, by adding rudimentary visual processing capabilities to the computer graphics system. This is possible through the use of computer vision algorithms which incorporate general knowledge about line-art, and are based on image features that are used by the human visual system in the early stages of visual processing. A major color separation company is planning the hardware implementation of a vision-graphics system based on these algorithms, and the State University of New York is applying for two patents based on this research.

  7. On the Impact of Execution Models: A Case Study in Computational Chemistry

    SciTech Connect

    Chavarría-Miranda, Daniel; Halappanavar, Mahantesh; Krishnamoorthy, Sriram; Manzano Franco, Joseph B.; Vishnu, Abhinav; Hoisie, Adolfy

    2015-05-25

    Efficient utilization of high-performance computing (HPC) platforms is an important and complex problem. Execution models, abstract descriptions of the dynamic runtime behavior of the execution stack, have significant impact on the utilization of HPC systems. Using a computational chemistry kernel as a case study and a wide variety of execution models combined with load balancing techniques, we explore the impact of execution models on the utilization of an HPC system. We demonstrate a 50 percent improvement in performance by using work stealing relative to a more traditional static scheduling approach. We also use a novel semi-matching technique for load balancing that has comparable performance to a traditional hypergraph-based partitioning implementation, which is computationally expensive. Using this study, we found that execution model design choices and assumptions can limit critical optimizations such as global, dynamic load balancing and finding the correct balance between available work units and different system and runtime overheads. With the emergence of multi- and many-core architectures and the consequent growth in the complexity of HPC platforms, we believe that these lessons will be beneficial to researchers tuning diverse applications on modern HPC platforms, especially on emerging dynamic platforms with energy-induced performance variability.

  8. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry.

    PubMed

    Petraglia, Riccardo; Nicolaï, Adrien; Wodrich, Matthew D; Ceriotti, Michele; Corminboeuf, Clemence

    2016-01-01

    Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

  9. Development of an Undergraduate Course in the Use of Digital Computers With Chemistry Instrumentation.

    ERIC Educational Resources Information Center

    Wilkins, Charles L.

    Computer-assisted instruction (CAI) has proven useful in teaching chemistry instrumentation techniques to undergraduate students. The work completed at the time of this interim report has clearly shown that a general purpose laboratory computer system, equipped with suitable devices to allow direct data input from experiments, can be an effective…

  10. Using Free Computational Resources to Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

    ERIC Educational Resources Information Center

    Rodrigues, Ricardo P.; Andrade, Saulo F.; Mantoani, Susimaire P.; Eifler-Lima, Vera L.; Silva, Vinicius B.; Kawano, Daniel F.

    2015-01-01

    Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted "in silico" drug design…

  11. The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

    ERIC Educational Resources Information Center

    Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

    2008-01-01

    It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

  12. Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Sérgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

  13. Parallel Computation Chemistry Using Constraints: Final Report, LDRD 97-0301, Case 3504140000

    SciTech Connect

    Todd D. Plantenga

    1998-11-01

    Computer modeling to estimate material properties, design chem/bio sensors, and evaluate protein-protein interactions all require solving force field equations for molecular structures that contain tens of thousands of covalently connected atoms. Potential energy minimization is a key step in the calculation, but stiff covalent bonding forces make optimization difficult and expensive. This two-year LDRD developed two classes of advanced minimization algorithms that were specialized for chemistry applications and distributed computing machines. The project led to two successful algorithms that were implemented in three Sandia computational chemistry codes to support various users.

  14. Development and assessment of a chemistry-based computer video game as a learning tool

    NASA Astrophysics Data System (ADS)

    Martinez-Hernandez, Kermin Joel

    The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning experience through gameplay. The project consists of three areas: development, assessment, and implementation. However, the foci of this study were the development and assessment of the computer video game including possible learning outcomes and game design elements. A chemistry-based game using a mixed genre of a single player first-person game embedded with action-adventure and puzzle components was developed to determine if students' level of understanding of chemistry concepts change after gameplay intervention. Three phases have been completed to assess students' understanding of chemistry concepts prior and after gameplay intervention. Two main assessment instruments (pre/post open-ended content survey and individual semi-structured interviews) were used to assess student understanding of concepts. In addition, game design elements were evaluated for future development phases. Preliminary analyses of the interview data suggest that students were able to understand most of the chemistry challenges presented in the game and the game served as a review for previously learned concepts as well as a way to apply such previous knowledge. To guarantee a better understanding of the chemistry concepts, additions such as debriefing and feedback about the content presented in the game seem to be needed. The use of visuals in the game to represent chemical processes, game genre, and game idea appear to be the game design elements that students like the most about the current computer video game.

  15. The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

    NASA Astrophysics Data System (ADS)

    Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

    2008-10-01

    It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn electrochemistry. Students with different prior knowledge levels were found to use different approaches to solving problems with the use of computer simulations. In particular, the cases showed that students with a high level of prior knowledge tended to use the equations and formulas to accomplish the learning tasks and then use the computer simulations to confirm their predictions. Students with a low level of prior chemistry knowledge used the computer simulations as the main resources to accomplish their tasks. Considerations of individual differences and the integration of learning materials were suggested for further research on instructional use of computer simulations.

  16. Computers in Undergraduate Education: Mathematics, Physics, Statistics, and Chemistry.

    ERIC Educational Resources Information Center

    Lockard, J. David

    This is the report of a conference which was initiated by the National Science Foundation's Office of Computing Activities and which explored and summarized current thinking about the role of the computer for undergraduate curricula in the physical and mathematical sciences. The conference focused on deciding which goals of the existing…

  17. Suicidal chemistry: combined intoxication with carbon monoxide and formic acid.

    PubMed

    Bakovic, Marija; Nestic, Marina; Mayer, Davor

    2016-05-01

    Herein, we present a rare case of suicidal intoxication with carbon monoxide produced via reaction of formic and sulphuric acid with additional toxic effect of formic acid. The deceased was a 22-year-old men found dead in the bathroom locked from the inside. A bucket filled with liquid was found next to him, together with an almost empty canister labeled "formic acid" and another empty unlabeled canister. The postmortem examination revealed corrosive burns of the face, neck and chest, cherry-pink livor mortis, corrosive injury to the oropharyngeal area and trachea, subpleural petechiae, 100 mL of blood in stomach and superficial erosions of stomach mucosa. Toxicology analysis revealed 30% of carboxyhemoglobin in the femoral blood and the presence of the formic acid in various samples. Quantitative analysis of formic acid was performed by measuring methyl ester derivative of formic acid by using headspace gas chromatography with flame ionization detection. The highest concentration of formic acid was measured in the lungs (0.55 g/kg), gastric content (0.39 g/L), and blood (0.28 g/L). In addition, it was established that content of the unlabeled canister had a pH value of 0.79 and contained sulphuric ions. Morphological and toxicology findings suggested that the main route of exposure to formic acid was inhalation of vapors with a possible ingestion of only small amount of liquid acid. The cause of death was determined to be combined intoxication with carbon monoxide and formic acid. PMID:26041513

  18. Suicidal chemistry: combined intoxication with carbon monoxide and formic acid.

    PubMed

    Bakovic, Marija; Nestic, Marina; Mayer, Davor

    2016-05-01

    Herein, we present a rare case of suicidal intoxication with carbon monoxide produced via reaction of formic and sulphuric acid with additional toxic effect of formic acid. The deceased was a 22-year-old men found dead in the bathroom locked from the inside. A bucket filled with liquid was found next to him, together with an almost empty canister labeled "formic acid" and another empty unlabeled canister. The postmortem examination revealed corrosive burns of the face, neck and chest, cherry-pink livor mortis, corrosive injury to the oropharyngeal area and trachea, subpleural petechiae, 100 mL of blood in stomach and superficial erosions of stomach mucosa. Toxicology analysis revealed 30% of carboxyhemoglobin in the femoral blood and the presence of the formic acid in various samples. Quantitative analysis of formic acid was performed by measuring methyl ester derivative of formic acid by using headspace gas chromatography with flame ionization detection. The highest concentration of formic acid was measured in the lungs (0.55 g/kg), gastric content (0.39 g/L), and blood (0.28 g/L). In addition, it was established that content of the unlabeled canister had a pH value of 0.79 and contained sulphuric ions. Morphological and toxicology findings suggested that the main route of exposure to formic acid was inhalation of vapors with a possible ingestion of only small amount of liquid acid. The cause of death was determined to be combined intoxication with carbon monoxide and formic acid.

  19. Art, Meet Chemistry; Chemistry, Meet Art: Case Studies, Current Literature, and Instrumental Methods Combined to Create a Hands-On Experience for Nonmajors and Instrumental Analysis Students

    ERIC Educational Resources Information Center

    Nivens, Delana A.; Padgett, Clifford W.; Chase, Jeffery M.; Verges, Katie J.; Jamieson, Deborah S.

    2010-01-01

    Case studies and current literature are combined with spectroscopic analysis to provide a unique chemistry experience for art history students and to provide a unique inquiry-based laboratory experiment for analytical chemistry students. The XRF analysis method was used to demonstrate to nonscience majors (art history students) a powerful…

  20. CHEMEX; Understanding and Solving Problems in Chemistry. A Computer-Assisted Instruction Program for General Chemistry.

    ERIC Educational Resources Information Center

    Lower, Stephen K.

    A brief overview of CHEMEX--a problem-solving, tutorial style computer-assisted instructional course--is provided and sample problems are offered. In CHEMEX, students receive problems in advance and attempt to solve them before moving through the computer program, which assists them in overcoming difficulties and serves as a review mechanism.…

  1. Computer-based, Jeopardy™-like game in general chemistry for engineering majors

    NASA Astrophysics Data System (ADS)

    Ling, S. S.; Saffre, F.; Kadadha, M.; Gater, D. L.; Isakovic, A. F.

    2013-03-01

    We report on the design of Jeopardy™-like computer game for enhancement of learning of general chemistry for engineering majors. While we examine several parameters of student achievement and attitude, our primary concern is addressing the motivation of students, which tends to be low in a traditionally run chemistry lectures. The effect of the game-playing is tested by comparing paper-based game quiz, which constitutes a control group, and computer-based game quiz, constituting a treatment group. Computer-based game quizzes are Java™-based applications that students run once a week in the second part of the last lecture of the week. Overall effectiveness of the semester-long program is measured through pretest-postest conceptual testing of general chemistry. The objective of this research is to determine to what extent this ``gamification'' of the course delivery and course evaluation processes may be beneficial to the undergraduates' learning of science in general, and chemistry in particular. We present data addressing gender-specific difference in performance, as well as background (pre-college) level of general science and chemistry preparation. We outline the plan how to extend such approach to general physics courses and to modern science driven electives, and we offer live, in-lectures examples of our computer gaming experience. We acknowledge support from Khalifa University, Abu Dhabi

  2. Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

    PubMed

    Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

    2007-02-01

    Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

  3. Lee Pedersen's work in theoretical and computational chemistry and biochemistry.

    PubMed

    Pedersen, Lee G

    2011-02-26

    Nature at the lab level in biology and chemistry can be described by the application of quantum mechanics. In many cases, a reasonable approximation to quantum mechanics is classical mechanics realized through Newton's equations of motion. Dr. Pedersen began his career using quantum mechanics to describe the properties of small molecular complexes that could serve as models for biochemical systems. To describe large molecular systems required a drop-back to classical means and this led surprisingly to a major improvement in the classical treatment of electrostatics for all molecules, not just biological molecules. Recent work has involved the application of quantum mechanics for the putative active sites of enzymes to gain greater insight into the key steps in enzyme catalysis.

  4. The role of computational chemistry in the science and measurements of the atmosphere

    NASA Technical Reports Server (NTRS)

    Phillips, D. H.

    1978-01-01

    The role of computational chemistry in determining the stability, photochemistry, spectroscopic parameters, and parameters for estimating reaction rates of atmospheric constituents is discussed. Examples dealing with the photolysis cross sections of HOCl and (1 Delta g) O2 and with the stability of gaseous NH4Cl and asymmetric ClO3 are presented. It is concluded that computational chemistry can play an important role in the study of atmospheric constituents, particularly reactive and short-lived species which are difficult to investigate experimentally.

  5. Combination of organotrifluoroborates with photoredox catalysis marking a new phase in organic radical chemistry.

    PubMed

    Koike, Takashi; Akita, Munetaka

    2016-08-01

    Combination of organotrifluoroborates and visible-light-driven photoredox catalysis, both of which have attracted the attention of synthetic chemists, marks a new phase in the field of organic radical chemistry. We have developed photoredox-catalyzed radical reactions with organotrifluoroborates, which turn out to serve not only as a source of organic radicals but also as radical acceptors. The first part of this Perspective deals with the generation of organic radicals from organotrifluoroborates, and the latter part describes addition of the CF3 radical to alkenyltrifluoroborates. The good chemistry between organoborates and photoredox catalysis and its future will be discussed.

  6. A Computer Based Problem Solving Environment in Chemistry

    ERIC Educational Resources Information Center

    Bilgin, Ibrahim; Karakirik, Erol

    2005-01-01

    The purpose of this study was to introduce the Mole Solver, a computer based system that facilitates monitors and improves students' problem solving skills on mole concept. The system has three distinct modes that: (1) find step by step solutions to the word problems on the mole concept; (2) enable students to solve word problems on their own by…

  7. A Computer Based Problem Solving Environment in Chemistry

    ERIC Educational Resources Information Center

    Bilgin, Ibrahim; Karakirik, Erol

    2005-01-01

    The purpose of this study was to introduce the Mole Solver, a computer based system that facilitates monitors and improves the students' problems solving skills on mole concept. The system has three distinct modes that: i) finds step by step solutions to the word problems on the mole concept ii) enable students' to solve word problems on their own…

  8. Computer Programs for Chemistry Experiments I and II.

    ERIC Educational Resources Information Center

    Reynard, Dale C.

    This unit of instruction includes nine laboratory experiments. All of the experiments are from the D.C. Health Revision of the Chemical Education Materials Study (CHEMS) with one exception. Program six is the lab from the original version of the CHEMS program. Each program consists of three parts (1) the lab and computer hints, (2) the description…

  9. The Use of Computers to Aid Instruction in Beginning Chemistry

    ERIC Educational Resources Information Center

    Grandey, Robert C.

    1971-01-01

    Describes computer-aided lessons for determining chemical formulas from composition by weight, quantities from chemical equations, and balancing equations for oxidation-reduction reactions. Lessons were developed and used on the PLATO system at the University of Illinois. A brief analysis of student attitudes and of effectiveness of the programs…

  10. Spectroscopic and computational investigation of actinium coordination chemistry

    PubMed Central

    Ferrier, Maryline G.; Batista, Enrique R.; Berg, John M.; Birnbaum, Eva R.; Cross, Justin N.; Engle, Jonathan W.; La Pierre, Henry S.; Kozimor, Stosh A.; Lezama Pacheco, Juan S.; Stein, Benjamin W.; Stieber, S. Chantal E.; Wilson, Justin J.

    2016-01-01

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac–Cl and Ac–OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1– ligands (3.2±1.1) than AmIII (0.8±0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour. PMID:27531582

  11. Spectroscopic and computational investigation of actinium coordination chemistry.

    PubMed

    Ferrier, Maryline G; Batista, Enrique R; Berg, John M; Birnbaum, Eva R; Cross, Justin N; Engle, Jonathan W; La Pierre, Henry S; Kozimor, Stosh A; Lezama Pacheco, Juan S; Stein, Benjamin W; Stieber, S Chantal E; Wilson, Justin J

    2016-08-17

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, Ac(III) reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac-Cl and Ac-OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between Ac(III) and Am(III) in HCl solutions indicate Ac(III) coordinates more inner-sphere Cl(1-) ligands (3.2±1.1) than Am(III) (0.8±0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique Ac(III) chemical behaviour.

  12. Spectroscopic and computational investigation of actinium coordination chemistry.

    PubMed

    Ferrier, Maryline G; Batista, Enrique R; Berg, John M; Birnbaum, Eva R; Cross, Justin N; Engle, Jonathan W; La Pierre, Henry S; Kozimor, Stosh A; Lezama Pacheco, Juan S; Stein, Benjamin W; Stieber, S Chantal E; Wilson, Justin J

    2016-01-01

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, Ac(III) reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac-Cl and Ac-OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between Ac(III) and Am(III) in HCl solutions indicate Ac(III) coordinates more inner-sphere Cl(1-) ligands (3.2±1.1) than Am(III) (0.8±0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique Ac(III) chemical behaviour. PMID:27531582

  13. Spectroscopic and computational investigation of actinium coordination chemistry

    NASA Astrophysics Data System (ADS)

    Ferrier, Maryline G.; Batista, Enrique R.; Berg, John M.; Birnbaum, Eva R.; Cross, Justin N.; Engle, Jonathan W.; La Pierre, Henry S.; Kozimor, Stosh A.; Lezama Pacheco, Juan S.; Stein, Benjamin W.; Stieber, S. Chantal E.; Wilson, Justin J.

    2016-08-01

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac-Cl and Ac-OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1- ligands (3.2+/-1.1) than AmIII (0.8+/-0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour.

  14. Factors Affecting Energy Barriers for Pyramidal Inversion in Amines and Phosphines: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Montgomery, Craig D.

    2013-01-01

    An undergraduate exercise in computational chemistry that investigates the energy barrier for pyramidal inversion of amines and phosphines is presented. Semiempirical calculations (PM3) of the ground-state and transition-state energies for NR[superscript 1]R[superscript 2]R[superscript 3] and PR[superscript 1]R[superscript 2]R[superscript 3] allow…

  15. Project Longhorn: A Pilot Project in the Use of Batch Computing in High School Chemistry Teaching.

    ERIC Educational Resources Information Center

    Busboom, Sally Young

    1997-01-01

    Describes the use of batch-oriented computing as the basis for reintroducing homework problems as a teaching tool in beginning chemistry instruction. Stems from and expands upon a system used in a university setting that produces, delivers, grades, and keeps records for homework problems. (DDR)

  16. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    ERIC Educational Resources Information Center

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  17. Students' Cognitive Focus during a Chemistry Laboratory Exercise: Effects of a Computer-Simulated Prelab

    ERIC Educational Resources Information Center

    Winberg, T. Mikael; Berg, C. Anders R.

    2007-01-01

    To enhance the learning outcomes achieved by students, learners undertook a computer-simulated activity based on an acid-base titration prior to a university-level chemistry laboratory activity. Students were categorized with respect to their attitudes toward learning. During the laboratory exercise, questions that students asked their assistant…

  18. A Compilation of Postgraduate Theses Written in Turkey on Computer Assisted Instruction in Chemistry Education

    ERIC Educational Resources Information Center

    Bozdogan, Aykut Emre; Demirbas, Murat

    2014-01-01

    The purpose of the study conducted is to present in-depth information about the postgraduate theses written within the context of Computer Assisted Instruction in Chemistry Education in Turkey. The theses collected in National Thesis Centre of Turkish Council of Higher Education were examined. As a result of an examination, it was found that about…

  19. Annotated List of Chemistry Laboratory Experiments with Computer Access. Final Report.

    ERIC Educational Resources Information Center

    Bunce, S. C.; And Others

    Project Chemlab was designed to prepare an "Annotated List of Laboratory Experiments in Chemistry from the Journal of Chemical Education (1957-1979)" and to develop a computer file and program to search for specific types of experiments. Provided in this document are listings (photoreduced copies of printouts) of over 1500 entries classified into…

  20. A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry

    ERIC Educational Resources Information Center

    Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew

    2012-01-01

    In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…

  1. Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

    ERIC Educational Resources Information Center

    Simpson, Scott; Autschbach, Jochen; Zurek, Eva

    2013-01-01

    A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

  2. Computer Series, 106. KC? Discoverer. A Computer Program for Descriptive Inorganic Chemistry.

    ERIC Educational Resources Information Center

    Kotz, John C.

    1989-01-01

    Described is an interactive database of chemical information called "KC? Discoverer: Exploring the Periodic Table." An overview of the program and details of specific functions are given. The uses of this program in teaching undergraduate inorganic chemistry are stressed. (CW)

  3. Probing - and - Molecular Interactions via Irmpd Experiments and Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Hopkins, Scott; McMahon, Terry

    2015-06-01

    Experiments carried out at the CLIO Free Electron Facility have been used to probe a range of novel bonding motifs and dissociation dynamics in a variety of chemical systems. Among these are species which exhibit anion-pi interactions in complexes of halide ions with aromatic ring systems with electron withdrawing substituents; charge solvated and zwitterionic clusters of protonated methylamines with phenylalanines; hydrogen bonded dimers of nucleic acid analogues and Pd complexes potentially involving agnostic hydrogen bond interactions. Accompanying DFT computational work is used to assist in identifying the most probable structure(s) present in the IRMPD experiments.

  4. Recent developments in computer vision-based analytical chemistry: A tutorial review.

    PubMed

    Capitán-Vallvey, Luis Fermín; López-Ruiz, Nuria; Martínez-Olmos, Antonio; Erenas, Miguel M; Palma, Alberto J

    2015-10-29

    Chemical analysis based on colour changes recorded with imaging devices is gaining increasing interest. This is due to its several significant advantages, such as simplicity of use, and the fact that it is easily combinable with portable and widely distributed imaging devices, resulting in friendly analytical procedures in many areas that demand out-of-lab applications for in situ and real-time monitoring. This tutorial review covers computer vision-based analytical (CVAC) procedures and systems from 2005 to 2015, a period of time when 87.5% of the papers on this topic were published. The background regarding colour spaces and recent analytical system architectures of interest in analytical chemistry is presented in the form of a tutorial. Moreover, issues regarding images, such as the influence of illuminants, and the most relevant techniques for processing and analysing digital images are addressed. Some of the most relevant applications are then detailed, highlighting their main characteristics. Finally, our opinion about future perspectives is discussed.

  5. Constraints and Contributors Towards the Use of Computer Simulations in Manitoba Chemistry Classrooms: Content is Still King

    NASA Astrophysics Data System (ADS)

    Straub, Brian Frederick

    Manitoba Education Citizenship and Youth (MECY) recently redesigned Grade 11 and 12 Chemistry curricula in an effort to be responsive to new developments in chemistry education research. In order to support the teaching of the microscopic level of chemistry, the new curricula encourage the use of technology and computer simulations into specific outcomes to aid meaning making of abstract chemistry concepts by students. This study identifies constraints and contributing factors to the use of computer simulations to facilitate student meaning making in chemistry. A questionnaire survey and case study approach informed by Urie Bronfenbrenner's bio-ecological model was used to identify factors. The results of this survey show the chemistry teaching inventory of teachers has become more diversified. Although teachers are using technology as differentiated instruction, their pedagogical use of technology is primarily for content dissemination rather than utilizing the technology to assist students in a deep understanding of chemistry ideas.

  6. Effects of a test taking strategy on postsecondary computer assisted chemistry assessments

    NASA Astrophysics Data System (ADS)

    Manco, Sharon Ann

    Metacognitive test taking strategies have proven advantageous in improving content-based test scores in a wide variety of disciplines and age/grade levels using traditional paper-and-pencil tests. However, despite the increase in computer assisted assessment (CAA), little research has examined whether these test taking strategies are effective for computer assisted tests. Research was conducted to determine if learning a proven test taking strategy would improve the online quiz scores of six university students in an introductory chemistry course intended for science, technology, engineering and math majors. Participants completed six to ten chemistry quizzes prior to intervention---learning the test taking strategy---and four to eight chemistry quizzes after intervention. Results indicated that, while students learned the strategy, it had little effect on their online chemistry quiz scores. Additionally, at the end of the semester, participants completed a satisfaction survey indicating general satisfaction with having learned the test taking strategy and generalization to other courses and types of tests. Furthermore, results suggest that adaptations to the on-line delivery method of the quizzes and to the test taking strategies may improve the robustness of the effect. Due to the increased use of computer assisted assessment, additional research is warranted to determine appropriate test taking strategies for online tests.

  7. Registering the Amica electronic structure code in the extensible computational chemistry environment.

    PubMed

    Gdanitz, Robert J; Black, Gary D; Lansing, Carina S; Palmer, Bruce J; Schuchardt, Karen L

    2005-02-01

    We describe the integration and use of the Amica software package ("Atoms & Molecules In Chemical Accuracy") within the Extensible Computational Chemistry Environment (Ecce). Amica is capable of accurately solving the electronic Schrodinger equation of small atoms and molecules using terms that are linear in the interelectronic distances, r(12), on multireference level of theory, but it requires expert knowledge to configure and execute its algorithms. Ecce is a comprehensive suite of tools that support the computational chemistry research processes of computation setup, execution, and analysis through a convenient graphical user interface. Additionally, Ecce was architected with mechanisms to integrate alternative electronic structure codes. The successful integration of Amica within Ecce validates the architecture of the latter and brings the high-accuracy capabilities of Amica to a wider audience.

  8. Photocatalytic water splitting with acridine dyes: Guidelines from computational chemistry

    NASA Astrophysics Data System (ADS)

    Liu, Xiaojun; Karsili, Tolga N. V.; Sobolewski, Andrzej L.; Domcke, Wolfgang

    2016-01-01

    The photocatalytic splitting of water into Hrad and OHrad radicals in hydrogen-bonded chromophore-water complexes has been explored with computational methods for the chromophores acridine orange (AO) and benzacridine (BA). These dyes are strong absorbers within the range of the solar spectrum. It is shown that low-lying charge-transfer excited states exist in the hydrogen-bonded AOsbnd H2O and BAsbnd H2O complexes which drive the transfer of a proton from water to the chromophore, which results in AOHradsbnd OHrad or BAHradsbnd OHrad biradicals. The AOHrad and BAHrad radicals possess bright ππ∗ excited states with vertical excitation energies near 3.0 eV which are predissociated by a low-lying repulsive πσ∗ state. The conical intersections of the πσ∗ state with the ππ∗ excited states and the ground state provide a mechanism for the photodetachment of the H-atom by a second photon. Our results indicate that AO and BA are promising chromophores for water splitting with visible light.

  9. Lookup tables to compute high energy cosmic ray induced atmospheric ionization and changes in atmospheric chemistry

    SciTech Connect

    Atri, Dimitra; Melott, Adrian L.; Thomas, Brian C. E-mail: melott@ku.edu

    2010-05-01

    A variety of events such as gamma-ray bursts and supernovae may expose the Earth to an increased flux of high-energy cosmic rays, with potentially important effects on the biosphere. Existing atmospheric chemistry software does not have the capability of incorporating the effects of substantial cosmic ray flux above 10 GeV. An atmospheric code, the NASA-Goddard Space Flight Center two-dimensional (latitude, altitude) time-dependent atmospheric model (NGSFC), is used to study atmospheric chemistry changes. Using CORSIKA, we have created tables that can be used to compute high energy cosmic ray (10 GeV–1 PeV) induced atmospheric ionization and also, with the use of the NGSFC code, can be used to simulate the resulting atmospheric chemistry changes. We discuss the tables, their uses, weaknesses, and strengths.

  10. Microscopes and computers combined for analysis of chromosomes

    NASA Technical Reports Server (NTRS)

    Butler, J. W.; Butler, M. K.; Stroud, A. N.

    1969-01-01

    Scanning machine CHLOE, developed for photographic use, is combined with a digital computer to obtain quantitative and statistically significant data on chromosome shapes, distribution, density, and pairing. CHLOE permits data acquisition about a chromosome complement to be obtained two times faster than by manual pairing.

  11. Computational chemistry for graphene-based energy applications: progress and challenges

    NASA Astrophysics Data System (ADS)

    Hughes, Zak E.; Walsh, Tiffany R.

    2015-04-01

    Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

  12. Computational chemistry for graphene-based energy applications: progress and challenges.

    PubMed

    Hughes, Zak E; Walsh, Tiffany R

    2015-04-28

    Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future. PMID:25833794

  13. Integrating Free Computer Software in Chemistry and Biochemistry Instruction: An International Collaboration

    NASA Astrophysics Data System (ADS)

    Cedeño, David L.; Jones, Marjorie A.; Friesen, Jon A.; Wirtz, Mark W.; Ríos, Luz Amalia; Ocampo, Gonzalo Taborda

    2010-10-01

    At the Universidad de Caldas, Manizales, Colombia, we used their new computer facilities to introduce chemistry graduate students to biochemical database mining and quantum chemistry calculations using freeware. These hands-on workshops allowed the students a strong introduction to easily accessible software and how to use this software to begin to explore computer modeling. Each workshop was scheduled for 2 h and each included a tutorial exercise to familiarize the students with the main menus and features of the software. In addition, accompanying lectures and practical laboratory sections were provided. Both courses were taught in Spanish although the written instructions were in English. This was not a problem since these students have a comfort level with reading English. Student feedback following these workshops was highly enthusiastic and positive. This international collaborative will impact both the teaching and research goals for this cohort of graduate students.

  14. A numerical method for parameterization of atmospheric chemistry - Computation of tropospheric OH

    NASA Technical Reports Server (NTRS)

    Spivakovsky, C. M.; Wofsy, S. C.; Prather, M. J.

    1990-01-01

    An efficient and stable computational scheme for parameterization of atmospheric chemistry is described. The 24-hour-average concentration of OH is represented as a set of high-order polynomials in variables such as temperature, densities of H2O, CO, O3, and NO(t) (defined as NO + NO2 + NO3 + 2N2O5 + HNO2 + HNO4) as well as variables determining solar irradiance: cloud cover, density of the overhead ozone column, surface albedo, latitude, and solar declination. This parameterization of OH chemistry was used in the three-dimensional study of global distribution of CH3CCl3. The proposed computational scheme can be used for parameterization of rates of chemical production and loss or of any other output of a full chemical model.

  15. User's guide for vectorized code EQUIL for calculating equilibrium chemistry on Control Data STAR-100 computer

    NASA Technical Reports Server (NTRS)

    Kumar, A.; Graves, R. A., Jr.; Weilmuenster, K. J.

    1980-01-01

    A vectorized code, EQUIL, was developed for calculating the equilibrium chemistry of a reacting gas mixture on the Control Data STAR-100 computer. The code provides species mole fractions, mass fractions, and thermodynamic and transport properties of the mixture for given temperature, pressure, and elemental mass fractions. The code is set up for the electrons H, He, C, O, N system of elements. In all, 24 chemical species are included.

  16. Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology.

    PubMed

    González-Nilo, Fernando; Pérez-Acle, Tomás; Guínez-Molinos, Sergio; Geraldo, Daniela A; Sandoval, Claudia; Yévenes, Alejandro; Santos, Leonardo S; Laurie, V Felipe; Mendoza, Hegaly; Cachau, Raúl E

    2011-01-01

    After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.

  17. Drug Guru: a computer software program for drug design using medicinal chemistry rules.

    PubMed

    Stewart, Kent D; Shiroda, Melisa; James, Craig A

    2006-10-15

    Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.

  18. Water chemistry of a combined-cycle power plant's auxiliary equipment cooling system

    NASA Astrophysics Data System (ADS)

    Larin, B. M.; Korotkov, A. N.; Oparin, M. Yu.; Larin, A. B.

    2013-04-01

    Results from an analysis of methods aimed at reducing the corrosion rate of structural metal used in heat-transfer systems with water coolant are presented. Data from examination of the closed-circuit system for cooling the auxiliary mechanisms of a combined-cycle plant-based power unit and the results from adjustment of its water chemistry are given. A conclusion is drawn about the possibility of using a reagent prepared on the basis of sodium sulfite for reducing the corrosion rate when the loss of coolant is replenished with nondeaerated water.

  19. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

  20. Computational Materials Science and Chemistry: Accelerating Discovery and Innovation through Simulation-Based Engineering and Science

    SciTech Connect

    Crabtree, George; Glotzer, Sharon; McCurdy, Bill; Roberto, Jim

    2010-07-26

    This report is based on a SC Workshop on Computational Materials Science and Chemistry for Innovation on July 26-27, 2010, to assess the potential of state-of-the-art computer simulations to accelerate understanding and discovery in materials science and chemistry, with a focus on potential impacts in energy technologies and innovation. The urgent demand for new energy technologies has greatly exceeded the capabilities of today's materials and chemical processes. To convert sunlight to fuel, efficiently store energy, or enable a new generation of energy production and utilization technologies requires the development of new materials and processes of unprecedented functionality and performance. New materials and processes are critical pacing elements for progress in advanced energy systems and virtually all industrial technologies. Over the past two decades, the United States has developed and deployed the world's most powerful collection of tools for the synthesis, processing, characterization, and simulation and modeling of materials and chemical systems at the nanoscale, dimensions of a few atoms to a few hundred atoms across. These tools, which include world-leading x-ray and neutron sources, nanoscale science facilities, and high-performance computers, provide an unprecedented view of the atomic-scale structure and dynamics of materials and the molecular-scale basis of chemical processes. For the first time in history, we are able to synthesize, characterize, and model materials and chemical behavior at the length scale where this behavior is controlled. This ability is transformational for the discovery process and, as a result, confers a significant competitive advantage. Perhaps the most spectacular increase in capability has been demonstrated in high performance computing. Over the past decade, computational power has increased by a factor of a million due to advances in hardware and software. This rate of improvement, which shows no sign of abating, has

  1. Research and Teaching: Computational Methods in General Chemistry--Perceptions of Programming, Prior Experience, and Student Outcomes

    ERIC Educational Resources Information Center

    Wheeler, Lindsay B.; Chiu, Jennie L.; Grisham, Charles M.

    2016-01-01

    This article explores how integrating computational tools into a general chemistry laboratory course can influence student perceptions of programming and investigates relationships among student perceptions, prior experience, and student outcomes.

  2. Application of computer assisted combinatorial chemistry in antivirial, antimalarial and anticancer agents design

    NASA Astrophysics Data System (ADS)

    Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.

    Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.

  3. Managing the computational chemistry big data problem: the ioChem-BD platform.

    PubMed

    Álvarez-Moreno, M; de Graaf, C; López, N; Maseras, F; Poblet, J M; Bo, C

    2015-01-26

    We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media. PMID:25469626

  4. Combining the GRID with Cloud for Earth Science Computing

    NASA Astrophysics Data System (ADS)

    Mishin, Dmitry; Levchenko, Oleg; Groudnev, Andrei; Zhizhin, Mikhail

    2010-05-01

    Cloud computing is a new economic model of using large cluster computing resources which were earlier managed by GRID. Reusing existing GRID infrastructure gives an opportunity to combine the Cloud and GRID technologies on the same hardware and to provide GRID users with functionality for running high performance computing tasks inside virtual machines. In this case Cloud works "above" GRID, sharing computing power and utilizing unused processor time. We manage virtual machines with Eucalyptus elastic cloud and we use Torque system from gLite infrastructure for spreading Cloud jobs in GRID computing nodes to scale the parallel computing tasks on virtual machines created by elastic cloud. For this purpose we have added new types of tasks to the standard GRID task list: to run a virtual node and to run a job on a virtual node. This gives a possibility to seamlessly upscale the Cloud with the new tasks when needed and to shrink it when the tasks are completed. Using GRID components for managing the size of a virtual cloud simplifies building the billing system to charge the Cloud users for the processor time, disk space and outer traffic consumed. A list of Earth Science computing problems that can be solved by using the elastic Cloud include repetitive tasks of downloading, converting and storing in a database of large arrays of data (e.g. weather forecast); creating a pyramid of lower resolution images from a very large one for fast distributed browsing; processing and analyzing the large distributed amounts of data by running Earth Science numerical models.

  5. Optimizing qubit resources for quantum chemistry simulations in second quantization on a quantum computer

    NASA Astrophysics Data System (ADS)

    Moll, Nikolaj; Fuhrer, Andreas; Staar, Peter; Tavernelli, Ivano

    2016-07-01

    Quantum chemistry simulations on a quantum computer suffer from the overhead needed for encoding the Fermionic problem in a system of qubits. By exploiting the block diagonality of a Fermionic Hamiltonian, we show that the number of required qubits can be reduced while the number of terms in the Hamiltonian will increase. All operations for this reduction can be performed in operator space. The scheme is conceived as a pre-computational step that would be performed prior to the actual quantum simulation. We apply this scheme to reduce the number of qubits necessary to simulate both the Hamiltonian of the two-site Fermi-Hubbard model and the hydrogen molecule. Both quantum systems can then be simulated with a two-qubit quantum computer. Despite the increase in the number of Hamiltonian terms, the scheme still remains a useful tool to reduce the dimensionality of specific quantum systems for quantum simulators with a limited number of resources.

  6. Optimizing qubit resources for quantum chemistry simulations in second quantization on a quantum computer

    NASA Astrophysics Data System (ADS)

    Moll, Nikolaj; Fuhrer, Andreas; Staar, Peter; Tavernelli, Ivano

    2016-07-01

    Quantum chemistry simulations on a quantum computer suffer from the overhead needed for encoding the Fermionic problem in a system of qubits. By exploiting the block diagonality of a Fermionic Hamiltonian, we show that the number of required qubits can be reduced while the number of terms in the Hamiltonian will increase. All operations for this reduction can be performed in operator space. The scheme is conceived as a pre-computational step that would be performed prior to the actual quantum simulation. We apply this scheme to reduce the number of qubits necessary to simulate both the Hamiltonian of the two-site Fermi–Hubbard model and the hydrogen molecule. Both quantum systems can then be simulated with a two-qubit quantum computer. Despite the increase in the number of Hamiltonian terms, the scheme still remains a useful tool to reduce the dimensionality of specific quantum systems for quantum simulators with a limited number of resources.

  7. Combined effects of surface conditions, boundary layer dynamics and chemistry on diurnal SOA evolution

    NASA Astrophysics Data System (ADS)

    Janssen, R. H. H.; Vilà-Guerau de Arellano, J.; Ganzeveld, L. N.; Kabat, P.; Jimenez, J. L.; Farmer, D. K.; van Heerwaarden, C. C.; Mammarella, I.

    2012-08-01

    We study the combined effects of land surface conditions, atmospheric boundary layer dynamics and chemistry on the diurnal evolution of biogenic secondary organic aerosol in the atmospheric boundary layer, using a model that contains the essentials of all these components. First, we evaluate the model for a case study in Hyytiälä, Finland, and find that it is able to satisfactorily reproduce the observed dynamics and gas-phase chemistry. We show that the exchange of organic aerosol between the free troposphere and the boundary layer (entrainment) must be taken into account in order to explain the observed diurnal cycle in organic aerosol (OA) concentration. An examination of the budgets of organic aerosol and terpene concentrations show that the former is dominated by entrainment, while the latter is mainly driven by emission and chemical transformation. We systematically investigate the role of the land surface, which governs both the surface energy balance partitioning and terpene emissions, and the large-scale atmospheric process of vertical subsidence. Entrainment is especially important for the dilution of organic aerosol concentrations under conditions of dry soils and low terpene emissions. Subsidence suppresses boundary layer growth while enhancing entrainment. Therefore, it influences the relationship between organic aerosol and terpene concentrations. Our findings indicate that the diurnal evolution of secondary organic aerosols (SOA) in the boundary layer is the result of coupled effects of the land surface, dynamics of the atmospheric boundary layer, chemistry, and free troposphere conditions. This has potentially some consequences for the design of both field campaigns and large-scale modeling studies.

  8. The effects of computer animation on the particulate mental models of college chemistry students

    NASA Astrophysics Data System (ADS)

    Williamson, Vickie M.; Abraham, Michael R.

    Modern chemistry concepts have the particulate nature of matter at their core. Chemists explain most phenomena in terms of atomic and molecular models. The lack of understanding of chemistry concepts may be linked to the students' inability to build complete mental models that visualize particulate behavior. With computer animation technology, dynamic and three-dimensional presentations are possible. This study explores the effect of computer animations depicting the particulate nature of matter on college students' mental models of the chemical phenomena. A Particulate Nature of Matter Evaluation Test (PNMET) instrument was used to determine the nature of the students' visualizations and, therefore, their comprehension of the chemical concept studied. Animations were used in two treatment situations: (a) as a supplement in large-group lectures, and (b) as both the lecture supplement and an assigned individual activity in a computer laboratory. These two experimental treatments were compared to a control group. Both treatment groups received significantly higher conceptual understanding scores on the PNMET than did the control group. This increased understanding may be due to the superiority of the formation of more expertlike, dynamic mental models of particle behavior in these chemical processes.

  9. Post-16 Physics and Chemistry Uptake: Combining Large-Scale Secondary Analysis with In-Depth Qualitative Methods

    ERIC Educational Resources Information Center

    Hampden-Thompson, Gillian; Lubben, Fred; Bennett, Judith

    2011-01-01

    Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served…

  10. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  11. Energy-Efficient Computational Chemistry: Comparison of x86 and ARM Systems.

    PubMed

    Keipert, Kristopher; Mitra, Gaurav; Sunriyal, Vaibhav; Leang, Sarom S; Sosonkina, Masha; Rendell, Alistair P; Gordon, Mark S

    2015-11-10

    The computational efficiency and energy-to-solution of several applications using the GAMESS quantum chemistry suite of codes is evaluated for 32-bit and 64-bit ARM-based computers, and compared to an x86 machine. The x86 system completes all benchmark computations more quickly than either ARM system and is the best choice to minimize time to solution. The ARM64 and ARM32 computational performances are similar to each other for Hartree-Fock and density functional theory energy calculations. However, for memory-intensive second-order perturbation theory energy and gradient computations the lower ARM32 read/write memory bandwidth results in computation times as much as 86% longer than on the ARM64 system. The ARM32 system is more energy efficient than the x86 and ARM64 CPUs for all benchmarked methods, while the ARM64 CPU is more energy efficient than the x86 CPU for some core counts and molecular sizes.

  12. 4D sequential actuation: combining ionoprinting and redox chemistry in hydrogels

    NASA Astrophysics Data System (ADS)

    Baker, Anna B.; Wass, Duncan F.; Trask, Richard S.

    2016-10-01

    The programmable sequential actuation of two-dimensional hydrogel membranes into three-dimensional folded architectures has been achieved by combining ionoprinting and redox chemistry; this methodology permits the programmed evolution of complex architectures triggered through localized out-of-plane deformations. In our study we describe a soft actuator which utilizes ionoprinting of iron and vanadium, with the selective reduction of iron through a mild reducing agent, to achieve chemically controlled sequential folding. Through the optimization of solvent polarity and ionoprinting variables (voltage, duration and anode composition), we have shown how the actuation pathways, rate-of-movement and magnitude of angular rotation can be controlled for the design of a 4D sequential actuator.

  13. Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis.

    SciTech Connect

    Somorjai, Gabor A.; Li, Yimin

    2009-11-21

    Experimental discoveries followed by theoretical interpretations that pave the way of further advances by experimentalists is a developing pattern in modern surface chemistry and catalysis. The revolution of modern surface science started with the development of surface-sensitive techniques such as LEED, XPS, AES, ISS and SIMS, in which the close collaboration between experimentalists and theorists led to the quantitative determination of surface structure and composition. The experimental discovery of the chemical activity of surface defects and the trends in the reactivity of transitional metals followed by the explanations from the theoretical studies led to the molecular level understanding of active sites in catalysis. The molecular level knowledge, in turn, provided a guide for experiments to search for new generation of catalysts. These and many other examples of successes in experiment-and-theory-combined studies demonstrate the importance of the collaboration between experimentalists and theorists in the development of modern surface science.

  14. Investigation of hydrogen bonded molecular solids by diffraction, spectroscopy, and computational chemistry

    NASA Astrophysics Data System (ADS)

    Hudson, Matthew R.

    The nature of hydrogen-bonding interactions in the solid state is examined through the investigation of molecular crystals by incoherent inelastic neutron scattering (INS) spectroscopy, Raman spectroscopy, X-ray and neutron diffraction, and computational chemistry. The molecular solids studied range from small organic molecules to larger inorganic acid salts. Hydrogen bonding is the primary mode of interaction in the solid state for each of the systems studied. INS spectra were collected at 25 K for each molecular solid and the motions of the hydrogen atoms assigned. Raman spectra were collected at 78 and 298 K to aid in the molecular mode assignments of the INS spectra and to examine possible phase changes as a function of temperature. Neutron diffraction was employed, when possible, to accurately locate the hydrogen atom positions, and X-ray diffraction was performed to obtain accurate unit cell dimensions and to obtain initial characterizations of the samples. The diffraction structures served as the basis for solid-state density functional theory (DFT) calculations. DFT simulations were used to aid in the vibrational normal mode assignments, to investigate possible solid-phase transitions, and as a test of the limits of basis sets and the available DFT theory. Of the six molecular solids studied, several important observations were made: (1) the determination of a structural phase transition in L-alanine alaninium nitrate by both spectroscopic and theoretical methods, (2) the structure of picolinic acid was elucidated at 25 K and room-temperature by the combination of INS and theory, (3) glycine lithium sulfate was found to be a useful test of DFT to accurately optimize the structure and calculate the normal modes of a complex 3D network of hydrogen-bonding interactions, (4) nicotinic acid was found to be a useful test of one dimensional hydrogen-bonding interactions with pi-stacking interactions dominating the orthogonal directions, and (5) parabanic acid

  15. Computation and Experiment: A Powerful Combination to Understand and Predict Reactivities.

    PubMed

    Sperger, Theresa; Sanhueza, Italo A; Schoenebeck, Franziska

    2016-06-21

    Computational chemistry has become an established tool for the study of the origins of chemical phenomena and examination of molecular properties. Because of major advances in theory, hardware and software, calculations of molecular processes can nowadays be done with reasonable accuracy on a time-scale that is competitive or even faster than experiments. This overview will highlight broad applications of computational chemistry in the study of organic and organometallic reactivities, including catalytic (NHC-, Cu-, Pd-, Ni-catalyzed) and noncatalytic examples of relevance to organic synthesis. The selected examples showcase the ability of computational chemistry to rationalize and also predict reactivities of broad significance. A particular emphasis is placed on the synergistic interplay of computations and experiments. It is discussed how this approach allows one to (i) gain greater insight than the isolated techniques, (ii) inspire novel chemistry avenues, and (iii) assist in reaction development. Examples of successful rationalizations of reactivities are discussed, including the elucidation of mechanistic features (radical versus polar) and origins of stereoselectivity in NHC-catalyzed reactions as well as the rationalization of ligand effects on ligation states and selectivity in Pd- and Ni-catalyzed transformations. Beyond explaining, the synergistic interplay of computation and experiments is then discussed, showcasing the identification of the likely catalytically active species as a function of ligand, additive, and solvent in Pd-catalyzed cross-coupling reactions. These may vary between mono- or bisphosphine-bound or even anionic Pd complexes in polar media in the presence of coordinating additives. These fundamental studies also inspired avenues in catalysis via dinuclear Pd(I) cycles. Detailed mechanistic studies supporting the direct reactivity of Pd(I)-Pd(I) with aryl halides as well as applications of air-stable dinuclear Pd(I) catalysts are

  16. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions.

    PubMed

    Cheng, Gui-Juan; Zhang, Xinhao; Chung, Lung Wa; Xu, Liping; Wu, Yun-Dong

    2015-02-11

    Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

  17. Computational chemistry modeling and design of photoswitchable alignment materials for optically addressable liquid crystal devices

    NASA Astrophysics Data System (ADS)

    Marshall, K. L.; Sekera, E. R.; Xiao, K.

    2015-09-01

    Photoalignment technology based on optically switchable "command surfaces" has been receiving increasing interest for liquid crystal optics and photonics device applications. Azobenzene compounds in the form of low-molar-mass, watersoluble salts deposited either directly on the substrate surface or after dispersion in a polymer binder have been almost exclusively employed for these applications, and ongoing research in the area follows a largely empirical materials design and development approach. Recent computational chemistry advances now afford unprecedented opportunities to develop predictive capabilities that will lead to new photoswitchable alignment layer materials with low switching energies, enhanced bistability, write/erase fatigue resistance, and high laser-damage thresholds. In the work described here, computational methods based on the density functional theory and time-dependent density functional theory were employed to study the impact of molecular structure on optical switching properties in photoswitchable methacrylate and acrylamide polymers functionalized with azobenzene and spiropyran pendants.

  18. The Use of Modular Computer-Based Lessons in a Modification of the Classical Introductory Course in Organic Chemistry.

    ERIC Educational Resources Information Center

    Stotter, Philip L.; Culp, George H.

    An experimental course in organic chemistry utilized computer-assisted instructional (CAI) techniques. The CAI lessons provided tutorial drill and practice and simulated experiments and reactions. The Conversational Language for Instruction and Computing was used, along with a CDC 6400-6600 system; students scheduled and completed the lessons at…

  19. Chemical Equilibrium, Unit 2: Le Chatelier's Principle. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Jameson, A. Keith

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on Le Chatelier's principle includes objectives, prerequisites, pretest, instructions for executing the computer program, and…

  20. Heterogeneous processes at the intersection of chemistry and biology: A computational approach

    SciTech Connect

    Kuo, I W; Mundy, C J

    2008-02-11

    Heterogeneous processes hold the key to understanding many problems in biology and atmospheric science. In particular, recent experiments have shown that heterogeneous chemistry at the surface of sea-salt aerosols plays a large role in important atmospheric processes with far reaching implications towards understanding of the fate and transport of aerosolized chemical weapons (i.e. organophosphates such as sarin and VX). Unfortunately, the precise mechanistic details of the simplest surface enhanced chemical reactions remain unknown. Understanding heterogeneous processes also has implications in the biological sciences. Traditionally, it is accepted that enzymes catalyze reactions by stabilizing the transition state, thereby lowering the free energy barrier. However, recent findings have shown that a multitude of phenomena likely contribute to the efficiency of enzymes, such as coupled protein motion, quantum mechanical tunneling, or strong electrostatic binding. The objective of this project was to develop and validate a single computational framework based on first principles simulations using tera-scale computational resources to answer fundamental scientific questions about heterogeneous chemical processes relevant to atmospheric chemistry and biological sciences.

  1. Characterizing Molecular Structure by Combining Experimental Measurements with Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Lopez-Encarnacion, Juan M.

    2016-06-01

    In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21

  2. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

  3. Combined experiment and theory approach in surface chemistry: Stairway to heaven?

    NASA Astrophysics Data System (ADS)

    Exner, Kai S.; Heß, Franziska; Over, Herbert; Seitsonen, Ari Paavo

    2015-10-01

    In this perspective we discuss how an intimate interaction of experiments with theory is able to deepen our insight into the catalytic reaction system on the molecular level. This strategy is illustrated by discussing various examples from our own research of surface chemistry and model catalysis. The particular examples were carefully chosen to balance the specific strength of both approaches - theory and experiment - and emphasize the benefit of this combined approach. We start with the determination of complex surface structures, where diffraction techniques in combination with theory are clear-cut. The promoter action of alkali metals in heterogeneous catalysis is rationalized with theory and experiment for the case of CO coadsorption. Predictive power of theory is limited as demonstrated with the apparent activity of chlorinated TiO2(110) in the oxidation of HCl: Even if we know all elementary reaction steps of a catalytic reaction mechanism, the overall kinetics may remain elusive and require the application kinetic Monte Carlo simulations. Catalysts are not always stable under reaction conditions and may chemically transform as discussed for the CO oxidation reaction over ruthenium. Under oxidizing reaction conditions ruthenium transforms into RuO2, a process which is hardly understood on the molecular level. Lastly we focus on electrochemical reactions. Here theory is clearly ahead since spectroscopic methods are not available to resolve the processes at the electrode surface.

  4. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  5. User's Guide to Handlens - A Computer Program that Calculates the Chemistry of Minerals in Mixtures

    USGS Publications Warehouse

    Eberl, D.D.

    2008-01-01

    HandLens is a computer program, written in Excel macro language, that calculates the chemistry of minerals in mineral mixtures (for example, in rocks, soils and sediments) for related samples from inputs of quantitative mineralogy and chemistry. For best results, the related samples should contain minerals having the same chemical compositions; that is, the samples should differ only in the proportions of minerals present. This manual describes how to use the program, discusses the theory behind its operation, and presents test results of the program's accuracy. Required input for HandLens includes quantitative mineralogical data, obtained, for example, by RockJock analysis of X-ray diffraction (XRD) patterns, and quantitative chemical data, obtained, for example, by X-ray florescence (XRF) analysis of the same samples. Other quantitative data, such as sample depth, temperature, surface area, also can be entered. The minerals present in the samples are selected from a list, and the program is started. The results of the calculation include: (1) a table of linear coefficients of determination (r2's) which relate pairs of input data (for example, Si versus quartz weight percents); (2) a utility for plotting all input data, either as pairs of variables, or as sums of up to eight variables; (3) a table that presents the calculated chemical formulae for minerals in the samples; (4) a table that lists the calculated concentrations of major, minor, and trace elements in the various minerals; and (5) a table that presents chemical formulae for the minerals that have been corrected for possible systematic errors in the mineralogical and/or chemical analyses. In addition, the program contains a method for testing the assumption of constant chemistry of the minerals within a sample set.

  6. A Unique Master's Program in Combined Nuclear Technology and Nuclear Chemistry at Chalmers University of Technology, Sweden

    NASA Astrophysics Data System (ADS)

    Skarnemark, Gunnar; Allard, Stefan; Ekberg, Christian; Nordlund, Anders

    2009-08-01

    The need for engineers and scientists who can ensure safe and secure use of nuclear energy is large in Sweden and internationally. Chalmers University of Technology is therefore launching a new 2-year master's program in Nuclear Engineering, with start from the autumn of 2009. The program is open to Swedish and foreign students. The program starts with compulsory courses dealing with the basics of nuclear chemistry and physics, radiation protection, nuclear power and reactors, nuclear fuel supply, nuclear waste management and nuclear safety and security. There are also compulsory courses in nuclear industry applications and sustainable energy futures. The subsequent elective courses can be chosen freely but there is also a possibility to choose informal tracks that concentrate on nuclear chemistry or reactor technology and physics. The nuclear chemistry track comprises courses in e.g. chemistry of lanthanides, actinides and transactinides, solvent extraction, radioecology and radioanalytical chemistry and radiopharmaceuticals. The program is finished with a one semester thesis project. This is probably a unique master program in the sense of its combination of deep courses in both nuclear technology and nuclear chemistry.

  7. A Unique Master's Program in Combined Nuclear Technology and Nuclear Chemistry at Chalmers University of Technology, Sweden

    SciTech Connect

    Skarnemark, Gunnar; Allard, Stefan; Ekberg, Christian; Nordlund, Anders

    2009-08-19

    The need for engineers and scientists who can ensure safe and secure use of nuclear energy is large in Sweden and internationally. Chalmers University of Technology is therefore launching a new 2-year master's program in Nuclear Engineering, with start from the autumn of 2009. The program is open to Swedish and foreign students. The program starts with compulsory courses dealing with the basics of nuclear chemistry and physics, radiation protection, nuclear power and reactors, nuclear fuel supply, nuclear waste management and nuclear safety and security. There are also compulsory courses in nuclear industry applications and sustainable energy futures. The subsequent elective courses can be chosen freely but there is also a possibility to choose informal tracks that concentrate on nuclear chemistry or reactor technology and physics. The nuclear chemistry track comprises courses in e.g. chemistry of lanthanides, actinides and transactinides, solvent extraction, radioecology and radioanalytical chemistry and radiopharmaceuticals. The program is finished with a one semester thesis project. This is probably a unique master program in the sense of its combination of deep courses in both nuclear technology and nuclear chemistry.

  8. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    ERIC Educational Resources Information Center

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  9. A Combined Experimental/Computational Investigation of a Rocket Based Combined Cycle Inlet

    NASA Technical Reports Server (NTRS)

    Smart, Michael K.; Trexler, Carl A.; Goldman, Allen L.

    2001-01-01

    A rocket based combined cycle inlet geometry has undergone wind tunnel testing and computational analysis with Mach 4 flow at the inlet face. Performance parameters obtained from the wind tunnel tests were the mass capture, the maximum back-pressure, and the self-starting characteristics of the inlet. The CFD analysis supplied a confirmation of the mass capture, the inlet efficiency and the details of the flowfield structure. Physical parameters varied during the test program were cowl geometry, cowl position, body-side bleed magnitude and ingested boundary layer thickness. An optimum configuration was determined for the inlet as a result of this work.

  10. Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry.

    PubMed

    Ooms, F

    2000-02-01

    The development of new drugs with potential therapeutic applications is one of the most complex and difficult process in the pharmaceutical industry. Millions of dollars and man-hours are devoted to the discovery of new therapeutical agents. As, the activity of a drug is the result of a multitude of factors such as bioavailability, toxicity and metabolism, rational drug design has been utopias for centuries. Very recently, impressive technological advances in areas such as structural characterization of biomacromolecules, computer sciences and molecular biology have made rational drug design feasible. The aim of this review is to give an outline of studies in the field of medicinal chemistry in which molecular modeling has helped in the discovery process of new drugs. The emphasis will be on lead generation and optimization.

  11. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Thirteen ideas are presented that may be of use to chemistry teachers. Topics covered include vitamin C, industrial chemistry, electrical conductivity, electrolysis, alkali metals, vibration modes infra-red, dynamic equilibrium, and some new demonstrations in gaseous combinations. (PS)

  12. New Combined Laser Ablation Platform Determines Cell Wall Chemistry (Fact Sheet)

    SciTech Connect

    Not Available

    2011-09-01

    NREL has designed and developed a combined laser ablation/pulsed sample introduction/mass spectrometry platform that integrates pyrolysis and/or laser ablation with resonance-enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry. Using this apparatus, we can measure the cell wall chemical composition of untreated biomass materials. Understanding the chemical composition of untreated biomass is key to both the biochemical and thermochemical conversion of lignocellulosic biomass to biofuels. In the biochemical conversion process, the new technique provides a better understanding of the chemistry of lignin and will improve accessibility to plant sugars. In thermochemical conversion, the information provided by the new technique may help to reduce the formation of unwanted byproducts during gasification. NREL validated the ability of the system to detect pyrolysis products from plant materials using poplar, a potentially high-impact bioenergy feedstock. In the technique, biomass vapors are produced by laser ablation using the 3rd harmonic of an Nd:YAG laser (355 nm). The resulting vapors are entrained in a free jet expansion of helium, then skimmed and introduced into an ionization region. REMPI is used to ionize the vapors because it is highly sensitive for detecting lignin and aromatic metabolites. The laser ablation method was used to selectively volatilize specific plant tissues and detect lignin-based products from the vapors with enhanced sensitivity. This will allow the determination of lignin distribution in future biomass studies.

  13. Technetium chemistry in the fuel cycle: combining basic and applied studies.

    PubMed

    Poineau, Frederic; Mausolf, Edward; Jarvinen, Gordon D; Sattelberger, Alfred P; Czerwinski, Kenneth R

    2013-04-01

    Technetium is intimately linked with nuclear reactions. The ultraminute natural levels in the environment are due to the spontaneous fission of uranium isotopes. The discovery of technetium was born from accelerator reactions, and its use and presence in the modern world are directly due to nuclear reactors. While occupying a central location in the periodic table, the chemistry of technetium is poorly explored, especially when compared to its neighboring elements, i.e., molybdenum, ruthenium, and rhenium. This state of affairs, which is tied to the small number of laboratories equipped to work with the long-lived (99)Tc isotope, provides a remarkable opportunity to combine basic studies with applications for the nuclear fuel cycle. An example is given through examination of the technetium halide compounds. Binary metal halides represent some of the most fundamental of inorganic compounds. The synthesis of new technetium halides demonstrates trends with structure, coordination number, and speciation that can be utilized in the nuclear fuel cycle. Examples are provided for technetium-zirconium alloys as waste forms and the formation of reduced technetium species in separations. PMID:23153109

  14. Technetium chemistry in the fuel cycle: combining basic and applied studies.

    PubMed

    Poineau, Frederic; Mausolf, Edward; Jarvinen, Gordon D; Sattelberger, Alfred P; Czerwinski, Kenneth R

    2013-04-01

    Technetium is intimately linked with nuclear reactions. The ultraminute natural levels in the environment are due to the spontaneous fission of uranium isotopes. The discovery of technetium was born from accelerator reactions, and its use and presence in the modern world are directly due to nuclear reactors. While occupying a central location in the periodic table, the chemistry of technetium is poorly explored, especially when compared to its neighboring elements, i.e., molybdenum, ruthenium, and rhenium. This state of affairs, which is tied to the small number of laboratories equipped to work with the long-lived (99)Tc isotope, provides a remarkable opportunity to combine basic studies with applications for the nuclear fuel cycle. An example is given through examination of the technetium halide compounds. Binary metal halides represent some of the most fundamental of inorganic compounds. The synthesis of new technetium halides demonstrates trends with structure, coordination number, and speciation that can be utilized in the nuclear fuel cycle. Examples are provided for technetium-zirconium alloys as waste forms and the formation of reduced technetium species in separations.

  15. Bromine and heavy halide chemistry at the air/water and air/ice interfaces: a computational approach

    NASA Astrophysics Data System (ADS)

    Gladich, I.; Shepson, P. B.; Szleifer, I.; Carignano, M.

    2010-12-01

    The air-water and air-ice interfaces are critically important surfaces, with respect to the physical and chemical properties of the Earth's atmosphere. In particular chloride, bromide and iodide ions are strongly involved in the reactions occurring at aerosol surfaces that are hydrated and at the air-ice interface in the polar boundary layer. Unfortunately, experimental access to these interfaces are quite problematic and the computational approach, based on molecular dynamic simulations and quantum mechanic calculations, is an interesting alternative approach. In this work, molecular dynamic (MD) simulations are used to study the halide enhancements at the air-water interface in the case of a dilute mixture of iodide, bromide and chloride ions. The MD results show how the air- water halide enhancement is different in the case of mixtures from the case of binary solutions (i.e. anions plus counter-positive ions) and how the presence of these halides at the interfaces depends from their relative concentrations in solution. In detail, heavy halides are strongly enhanced at the interfaces even if they are minor constituents in the bulk. Furthermore the enhancement of the larger halide ions, like bromide, at the surface is greater if lighter halides, like chloride, are in greater excess in the bulk. The applications of this last result on some real system, like sea-water, and the importance of bromide ions in the polar chemistry of ozone depletion events suggest a combined approach, MD and quantum mechanism (QM) calculation, to investigate the ozonation reaction of bromide (Br-+O3 → BrO-+O2 ) in the ice-QLL and in bulk water. The study of the reaction constants suggests how the different environments can affect the kinetics of such reaction. These results can help to understand the complex chemistry occurring at the air-water interface of hydrated aerosol and at the air-ice interface in the polar boundary layer.

  16. The Combined Effects of Classroom Teaching and Learning Strategy Use on Students' Chemistry Self-Efficacy

    NASA Astrophysics Data System (ADS)

    Cheung, Derek

    2015-02-01

    For students to be successful in school chemistry, a strong sense of self-efficacy is essential. Chemistry self-efficacy can be defined as students' beliefs about the extent to which they are capable of performing specific chemistry tasks. According to Bandura (Psychol. Rev. 84:191-215, 1977), students acquire information about their level of self-efficacy from four sources: performance accomplishments, vicarious experiences, verbal persuasion, and physiological states. No published studies have investigated how instructional strategies in chemistry lessons can provide students with positive experiences with these four sources of self-efficacy information and how the instructional strategies promote students' chemistry self-efficacy. In this study, questionnaire items were constructed to measure student perceptions about instructional strategies, termed efficacy-enhancing teaching, which can provide positive experiences with the four sources of self-efficacy information. Structural equation modeling was then applied to test a hypothesized mediation model, positing that efficacy-enhancing teaching positively affects students' chemistry self-efficacy through their use of deep learning strategies such as metacognitive control strategies. A total of 590 chemistry students at nine secondary schools in Hong Kong participated in the survey. The mediation model provided a good fit to the student data. Efficacy-enhancing teaching had a direct effect on students' chemistry self-efficacy. Efficacy-enhancing teaching also directly affected students' use of deep learning strategies, which in turn affected students' chemistry self-efficacy. The implications of these findings for developing secondary school students' chemistry self-efficacy are discussed.

  17. Computational simulation of CV combination preferences in babbling

    PubMed Central

    Nam, Hosung; Goldstein, Louis M.; Giulivi, Sara; Levitt, Andrea G.; Whalen, D. H.

    2013-01-01

    There is a tendency for spoken consonant-vowel (CV) syllables, in babbling in particular, to show preferred combinations: labial consonants with central vowels, alveolars with front, and velars with back. This pattern was first described by MacNeilage and Davis, who found the evidence compatible with their “frame-then-content” (F/C) model. F/C postulates that CV syllables in babbling are produced with no control of the tongue (and therefore effectively random tongue positions) but systematic oscillation of the jaw. Articulatory Phonology (AP; Browman & Goldstein) predicts that CV preferences will depend on the degree of synergy of tongue movements for the C and V. We present computational modeling of both accounts using articulatory synthesis. Simulations found better correlations between patterns in babbling and the AP account than with the F/C model. These results indicate that the underlying assumptions of the F/C model are not supported and that the AP account provides a better and account with broader coverage by showing that articulatory synergies influence all CV syllables, not just the most common ones. PMID:24496111

  18. Interactive computer modeling of combustion chemistry and coalescence-dispersion modeling of turbulent combustion

    NASA Technical Reports Server (NTRS)

    Pratt, D. T.

    1984-01-01

    An interactive computer code for simulation of a high-intensity turbulent combustor as a single point inhomogeneous stirred reactor was developed from an existing batch processing computer code CDPSR. The interactive CDPSR code was used as a guide for interpretation and direction of DOE-sponsored companion experiments utilizing Xenon tracer with optical laser diagnostic techniques to experimentally determine the appropriate mixing frequency, and for validation of CDPSR as a mixing-chemistry model for a laboratory jet-stirred reactor. The coalescence-dispersion model for finite rate mixing was incorporated into an existing interactive code AVCO-MARK I, to enable simulation of a combustor as a modular array of stirred flow and plug flow elements, each having a prescribed finite mixing frequency, or axial distribution of mixing frequency, as appropriate. Further increase the speed and reliability of the batch kinetics integrator code CREKID was increased by rewriting in vectorized form for execution on a vector or parallel processor, and by incorporating numerical techniques which enhance execution speed by permitting specification of a very low accuracy tolerance.

  19. Solutions, Unit 2: Molarity, Molality, Concentration Conversions. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Bader, Morris

    Presented are the teacher's guide and student manual for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student module for this solution concentration unit includes objectives, prerequisites, pretest, discussion, and 20 problem sets. Included in the teacher's guide…

  20. Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling: Experiments for Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Bumpus, John A.; Lewis, Anne; Stotts, Corey; Cramer, Christopher J.

    2007-01-01

    Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of…

  1. Solutions, Unit 5: Colligative Properties of Solutions. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Bader, Morris

    Presented are the teacher's guide and student manual for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on the colligative properties of solutions includes objectives, prerequisites, pretest, discussion, and 20 problem sets. Included in…

  2. Computational Chemistry Methods for Predicting the Chiroptical Properties of Liquid Crystal Systems. II. Application to Chiral Azobenzenes

    SciTech Connect

    Marshall, K. L.; Noto, N.G.; Painter, G.; Tabiryan, N.

    2006-12-13

    Advances in computational chemistry hardware and software now make it possible to accurately model and predict physical properties (e.g., electronic spectra and chirality) in terms of hours or days instead of the weeks or months of intensive effort that were required only a few years ago.

  3. PREDICTING CHEMICAL REACTIVITY OF HUMIC SUBSTANCES FOR MINERALS AND XENOBIOTICS: USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY AND VIRTUAL REALITY

    EPA Science Inventory

    In this chapter we review the literature on scanning probe microscopy (SPM), virtual reality (VR), and computational chemistry and our earlier work dealing with modeling lignin, lignin-carbohydrate complexes (LCC), humic substances (HSs) and non-bonded organo-mineral interactions...

  4. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

    ERIC Educational Resources Information Center

    Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

  5. Using an Advanced Computational Laboratory Experiment to Extend and Deepen Physical Chemistry Students' Understanding of Atomic Structure

    ERIC Educational Resources Information Center

    Hoffman, Gary G.

    2015-01-01

    A computational laboratory experiment is described, which involves the advanced study of an atomic system. The students use concepts and techniques typically covered in a physical chemistry course but extend those concepts and techniques to more complex situations. The students get a chance to explore the study of atomic states and perform…

  6. Chemical Equilibrium, Unit 3: Chemical Equilibrium Calculations. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Jameson, Cynthia J.

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on chemical equilibrium calculations includes objectives, prerequisites, a discussion of the equilibrium constant (K), and ten…

  7. Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

    ERIC Educational Resources Information Center

    Springer, Michael T.

    2014-01-01

    Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

  8. Combining Chemistry and Music to Engage Student Interest: Using Songs to Accompany Selected Chemical Topics

    ERIC Educational Resources Information Center

    Last, Arthur M.

    2009-01-01

    The use of recorded music to add interest to a variety of lecture topics is described. Topics include the periodic table, the formation of ionic compounds, thermodynamics, carbohydrates, nuclear chemistry, and qualitative analysis. (Contains 1 note.)

  9. Toward computational cumulative biology by combining models of biological datasets.

    PubMed

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

  10. Toward Computational Cumulative Biology by Combining Models of Biological Datasets

    PubMed Central

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database. PMID:25427176

  11. The structural chemistry of metallocorroles: combined X-ray crystallography and quantum chemistry studies afford unique insights.

    PubMed

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine M; Ghosh, Abhik

    2012-08-21

    Although they share some superficial structural similarities with porphyrins, corroles, trianionic ligands with contracted cores, give rise to fundamentally different transition metal complexes in comparison with the dianionic porphyrins. Many metallocorroles are formally high-valent, although a good fraction of them are also noninnocent, with significant corrole radical character. These electronic-structural characteristics result in a variety of fascinating spectroscopic behavior, including highly characteristic, paramagnetically shifted NMR spectra and textbook cases of charge-transfer spectra. Although our early research on corroles focused on spectroscopy, we soon learned that the geometric structures of metallocorroles provide a fascinating window into their electronic-structural characteristics. Thus, we used X-ray structure determinations and quantum chemical studies, chiefly using DFT, to obtain a comprehensive understanding of metallocorrole geometric and electronic structures. This Account describes our studies of the structural chemistry of metallocorroles. At first blush, the planar or mildly domed structure of metallocorroles might appear somewhat uninteresting particularly when compared to metalloporphyrins. Metalloporphyrins, especially sterically hindered ones, are routinely ruffled or saddled, but the missing meso carbon apparently makes the corrole skeleton much more resistant to nonplanar distortions. Ruffling, where the pyrrole rings are alternately twisted about the M-N bonds, is energetically impossible for metallocorroles. Saddling is also uncommon; thus, a number of sterically hindered, fully substituted metallocorroles exhibit almost perfectly planar macrocycle cores. Against this backdrop, copper corroles stand out as an important exception. As a result of an energetically favorable Cu(d(x2-y2))-corrole(π) orbital interaction, copper corroles, even sterically unhindered ones, are inherently saddled. Sterically hindered substituents

  12. Final report summary of LDRD 02-LW-022''Quantum Vibrations in Molecules: A New Frontier in Computational Chemistry''

    SciTech Connect

    Glaesemann, K R

    2004-01-22

    With the trend towards needing information about chemistry at conditions significantly different from 298K and 1 atm., methods need to be developed to generate and interpret this data. This demand for information about chemistry at extreme conditions comes from many fields. The study of atmospheric chemistry requires knowledge of unusual species that are formed when molecules are exposed to ultraviolet radiation. Studying of energetic materials requires knowledge of the thermochemical and structural properties of a myriad of chemical species under a wide range of temperatures. Basic scientific understanding of the very nature of a chemical bond requires detailed information. Studying these problems computationally requires multiple capabilities. The methodology used must provide both high accuracy and computational efficiency. Studying extreme chemistry also suffers from all the challenges of studying chemistry under non-extreme conditions. Therefore, either a new method must be developed or an old method must be applied in an innovative way. The method we have chosen to use is path integral Monte Carlo (PIMC) for the nuclear degrees of freedom and ab initio electronic structure methods for the electronic degrees of freedom. PIMC and ab initio electronic structure are methods of treating the quantum nature of particles. These methods have been chosen, because an accurate treatment requires treating both the electrons and the nuclei as quantum particles. We developed new ''projected'' methods that reduce the computational demands. These methods along with PIMC in general are described in two Journal of Chemical Physics articles (UCRL-JC-144960 and UCRL-JC-147423). This methodology was implemented into a PIMC code developed as part of this LDRD. The code was parallelized in order to utilize the computational resources of LLNL.

  13. The use of computer-aided learning in chemistry laboratory instruction

    NASA Astrophysics Data System (ADS)

    Allred, Brian Robert Tracy

    This research involves developing and implementing computer software for chemistry laboratory instruction. The specific goal is to design the software and investigate whether it can be used to introduce concepts and laboratory procedures without a lecture format. This would allow students to conduct an experiment even though they may not have been introduced to the chemical concept in their lecture course. This would also allow for another type of interaction for those students who respond more positively to a visual approach to instruction. The first module developed was devoted to using computer software to help introduce students to the concepts related to thin-layer chromatography and setting up and running an experiment. This was achieved through the use of digitized pictures and digitized video clips along with written information. A review quiz was used to help reinforce the learned information. The second module was devoted to the concept of the "dry lab". This module presented students with relevant information regarding the chemical concepts and then showed them the outcome of mixing solutions. By these observations, they were to determine the composition of unknown solutions based on provided descriptions and comparison with their written observations. The third piece of the software designed was a computer game. This program followed the first two modules in providing information the students were to learn. The difference here, though, was incorporating a game scenario for students to use to help reinforce the learning. Students were then assessed to see how much information they retained after playing the game. In each of the three cases, a control group exposed to the traditional lecture format was used. Their results were compared to the experimental group using the computer modules. Based upon the findings, it can be concluded that using technology to aid in the instructional process is definitely of benefit and students were more successful in

  14. Combining human and computer interpretation capabilities to analyze ERTS imagery

    NASA Technical Reports Server (NTRS)

    Nichols, J. D.

    1973-01-01

    The human photointerpreter and the computer have complementary capabilities that are exploited in a computer-based data analysis system developed at the Forestry Remote Sensing Laboratory, University of California. This system is designed to optimize the process of extracting resource information from ERTS images. The human has the ability to quickly delineate gross differences in land classes, such as wildland, urban, and agriculture on appropriate ERTS images, and to further break these gross classes into meaningful subclasses. The computer, however, can more efficiently analyze point-by-point spectral information and localized textural information which can result in a much more detailed agricultural or wildland classification based on species composition and/or plant association. These human and computer capabilities have been integrated through the use of an inexpensive small scale computer dedicated to the interactive preprocessing of the human inputs and the display of raw ERTS images and computer classified images. The small computer is linked to a large scale computer system wherein the bulk of the statistical work and the automatic point-by-point classification is done.

  15. Computational chemistry insights in the REDOX Behaviour of Cr and W Fischer carbene complexes

    NASA Astrophysics Data System (ADS)

    Landman, Marile; Conradie, Jeanet; van Rooyen, Petrus H.

    2015-09-01

    An electrochemical study of a series of Fischer carbene complexes containing a hetero-aryl group showed that Cr and W carbenes exhibit different electrochemical behaviour. The Cr carbenes are oxidized in two one electron oxidation processes, namely Cr(0) to Cr(I) and Cr(I) to Cr(II). On the contrary, Fischer carbene complexes of tungsten are directly oxidized from W(0) to W(II). The first reduction process observed for both W- and Cr- carbenes, is a one electron process. A density functional theory (DFT) computational chemistry study of the electronic structure of the Cr- and W-carbenes, showed that the oxidation is metal based and the reduction is located on the carbene ligand. The DFT calculations further showed that the Cr(II) species is a triplet and the W(II) species a closed shell singlet. The DFT calculated energies of the HOMO and LUMO of the neutral carbenes relate linearly to the experimental oxidation and reduction potential, respectively. These mathematical relationships obtained can be used to predict experimentally measured potentials of related Fischer carbene complexes.

  16. Generation of naphthoquinone radical anions by electrospray ionization: solution, gas-phase, and computational chemistry studies.

    PubMed

    Vessecchi, Ricardo; Naal, Zeki; Lopes, José N C; Galembeck, Sérgio E; Lopes, Norberto P

    2011-06-01

    Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(•-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q+15](-) was described as being a reaction between the solvent system and the radical anion, Q(•-). The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses. PMID:21561138

  17. Combining Computational and Social Effort for Collaborative Problem Solving.

    PubMed

    Wagy, Mark D; Bongard, Josh C

    2015-01-01

    Rather than replacing human labor, there is growing evidence that networked computers create opportunities for collaborations of people and algorithms to solve problems beyond either of them. In this study, we demonstrate the conditions under which such synergy can arise. We show that, for a design task, three elements are sufficient: humans apply intuitions to the problem, algorithms automatically determine and report back on the quality of designs, and humans observe and innovate on others' designs to focus creative and computational effort on good designs. This study suggests how such collaborations should be composed for other domains, as well as how social and computational dynamics mutually influence one another during collaborative problem solving.

  18. Chemistry for Kids: Generating Carbon Dioxide in Elementary School Chemistry and Using a Computer To Write about It.

    ERIC Educational Resources Information Center

    Schlenker, Richard M.; Yoshida, Sarah

    This material describes an activity using vinegar and baking soda to generate carbon dioxide, and writing a report using the Appleworks word processing program for grades 3 to 8 students. Time requirement, relevant process skills, vocabulary, mathematics skills, computer skills, and materials are listed. Activity procedures including class…

  19. Combining high performance simulation, data acquisition, and graphics display computers

    NASA Technical Reports Server (NTRS)

    Hickman, Robert J.

    1989-01-01

    Issues involved in the continuing development of an advanced simulation complex are discussed. This approach provides the capability to perform the majority of tests on advanced systems, non-destructively. The controlled test environments can be replicated to examine the response of the systems under test to alternative treatments of the system control design, or test the function and qualification of specific hardware. Field tests verify that the elements simulated in the laboratories are sufficient. The digital computer is hosted by a Digital Equipment Corp. MicroVAX computer with an Aptec Computer Systems Model 24 I/O computer performing the communication function. An Applied Dynamics International AD100 performs the high speed simulation computing and an Evans and Sutherland PS350 performs on-line graphics display. A Scientific Computer Systems SCS40 acts as a high performance FORTRAN program processor to support the complex, by generating numerous large files from programs coded in FORTRAN that are required for the real time processing. Four programming languages are involved in the process, FORTRAN, ADSIM, ADRIO, and STAPLE. FORTRAN is employed on the MicroVAX host to initialize and terminate the simulation runs on the system. The generation of the data files on the SCS40 also is performed with FORTRAN programs. ADSIM and ADIRO are used to program the processing elements of the AD100 and its IOCP processor. STAPLE is used to program the Aptec DIP and DIA processors.

  20. Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations.

    PubMed

    Grimblat, Nicolas; Sarotti, Ariel M

    2016-08-22

    The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN-PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state-of-the-art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples. PMID:27405775

  1. Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations.

    PubMed

    Grimblat, Nicolas; Sarotti, Ariel M

    2016-08-22

    The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN-PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state-of-the-art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples.

  2. Combining Computational and Social Effort for Collaborative Problem Solving

    PubMed Central

    Wagy, Mark D.; Bongard, Josh C.

    2015-01-01

    Rather than replacing human labor, there is growing evidence that networked computers create opportunities for collaborations of people and algorithms to solve problems beyond either of them. In this study, we demonstrate the conditions under which such synergy can arise. We show that, for a design task, three elements are sufficient: humans apply intuitions to the problem, algorithms automatically determine and report back on the quality of designs, and humans observe and innovate on others’ designs to focus creative and computational effort on good designs. This study suggests how such collaborations should be composed for other domains, as well as how social and computational dynamics mutually influence one another during collaborative problem solving. PMID:26544199

  3. Combining Computational and Social Effort for Collaborative Problem Solving.

    PubMed

    Wagy, Mark D; Bongard, Josh C

    2015-01-01

    Rather than replacing human labor, there is growing evidence that networked computers create opportunities for collaborations of people and algorithms to solve problems beyond either of them. In this study, we demonstrate the conditions under which such synergy can arise. We show that, for a design task, three elements are sufficient: humans apply intuitions to the problem, algorithms automatically determine and report back on the quality of designs, and humans observe and innovate on others' designs to focus creative and computational effort on good designs. This study suggests how such collaborations should be composed for other domains, as well as how social and computational dynamics mutually influence one another during collaborative problem solving. PMID:26544199

  4. Formation rates, stability and reactivity of sulfuric acid - amine clusters predicted by computational chemistry

    NASA Astrophysics Data System (ADS)

    Kurtén, Theo; Ortega, Ismael; Kupiainen, Oona; Olenius, Tinja; Loukonen, Ville; Reiman, Heidi; McGrath, Matthew; Vehkamäki, Hanna

    2013-04-01

    Despite the importance of atmospheric particle formation for both climate and air quality, both experiments and non-empirical models using e.g. sulfuric acid, ammonia and water as condensing vapors have so far been unable to reproduce atmospheric observations using realistic trace gas concentrations. Recent experimental and theoretical evidence has shown that this mystery is likely resolved by amines. Combining first-principles evaporation rates for sulfuric acid - dimethylamine clusters with cluster kinetic modeling, we show that even sub-ppt concentrations of amines, together with atmospherically realistic concentrations of sulfuric acid, result in formation rates close to those observed in the atmosphere. Our simulated cluster formation rates are also close to, though somewhat larger than, those measured at the CLOUD experiment in CERN for both sulfuric acid - ammonia and sulfuric acid - dimethylamine systems. A sensitivity analysis indicates that the remaining discrepancy for the sulfuric acid - amine particle formation rates is likely caused by steric hindrances to cluster formation (due to alkyl groups of the amine molecules) rather than by significant errors in the evaporation rates. First-principles molecular dynamic and reaction kinetic modeling shed further light on the microscopic physics and chemistry of sulfuric acid - amine clusters. For example, while the number and type of hydrogen bonds in the clusters typically reach their equilibrium values on a picosecond timescale, and the overall bonding patterns predicted by traditional "static" quantum chemical calculations seem to be stable, the individual atoms participating in the hydrogen bonds continuously change at atmospherically realistic temperatures. From a chemical reactivity perspective, we have also discovered a surprising phenomenon: clustering with sulfuric acid molecules slightly increases the activation energy required for the abstraction of alkyl hydrogens from amine molecules. This implies

  5. Combining dynamical decoupling with fault-tolerant quantum computation

    SciTech Connect

    Ng, Hui Khoon; Preskill, John; Lidar, Daniel A.

    2011-07-15

    We study how dynamical decoupling (DD) pulse sequences can improve the reliability of quantum computers. We prove upper bounds on the accuracy of DD-protected quantum gates and derive sufficient conditions for DD-protected gates to outperform unprotected gates. Under suitable conditions, fault-tolerant quantum circuits constructed from DD-protected gates can tolerate stronger noise and have a lower overhead cost than fault-tolerant circuits constructed from unprotected gates. Our accuracy estimates depend on the dynamics of the bath that couples to the quantum computer and can be expressed either in terms of the operator norm of the bath's Hamiltonian or in terms of the power spectrum of bath correlations; we explain in particular how the performance of recursively generated concatenated pulse sequences can be analyzed from either viewpoint. Our results apply to Hamiltonian noise models with limited spatial correlations.

  6. New Mechanistic Insights on the Selectivity of Transition-Metal-Catalyzed Organic Reactions: The Role of Computational Chemistry.

    PubMed

    Zhang, Xinhao; Chung, Lung Wa; Wu, Yun-Dong

    2016-06-21

    With new advances in theoretical methods and increased computational power, applications of computational chemistry are becoming practical and routine in many fields of chemistry. In organic chemistry, computational chemistry plays an indispensable role in elucidating reaction mechanisms and the origins of various selectivities, such as chemo-, regio-, and stereoselectivities. Consequently, mechanistic understanding improves synthesis and assists in the rational design of new catalysts. In this Account, we present some of our recent works to illustrate how computational chemistry provides new mechanistic insights for improvement of the selectivities of several organic reactions. These examples include not only explanations for the existing experimental observations, but also predictions which were subsequently verified experimentally. This Account consists of three sections discuss three different kinds of selectivities. The first section discusses the regio- and stereoselectivities of hydrosilylations of alkynes, mainly catalyzed by [Cp*Ru(MeCN)3](+) or [CpRu(MeCN)3](+). Calculations suggest a new mechanism that involves a key ruthenacyclopropene intermediate. This mechanism not only explains the unusual Markovnikov regio-selectivity and anti-addition stereoselectivity observed by Trost and co-workers, but also motivated further experimental investigations. New intriguing experimental observations and further theoretical studies led to an extension of the reaction mechanism. The second section includes three cases of meta-selective C-H activation of aryl compounds. In the case of Cu-catalyzed selective meta-C-H activation of aniline, a new mechanism that involves a Cu(III)-Ar-mediated Heck-like transition state, in which the Ar group acts as an electrophile, was proposed. This mechanism predicted a higher reactivity for more electron-deficient Ar groups, which was supported by experiments. For two template-mediated, meta-selective C-H bond activations catalyzed by

  7. New Mechanistic Insights on the Selectivity of Transition-Metal-Catalyzed Organic Reactions: The Role of Computational Chemistry.

    PubMed

    Zhang, Xinhao; Chung, Lung Wa; Wu, Yun-Dong

    2016-06-21

    With new advances in theoretical methods and increased computational power, applications of computational chemistry are becoming practical and routine in many fields of chemistry. In organic chemistry, computational chemistry plays an indispensable role in elucidating reaction mechanisms and the origins of various selectivities, such as chemo-, regio-, and stereoselectivities. Consequently, mechanistic understanding improves synthesis and assists in the rational design of new catalysts. In this Account, we present some of our recent works to illustrate how computational chemistry provides new mechanistic insights for improvement of the selectivities of several organic reactions. These examples include not only explanations for the existing experimental observations, but also predictions which were subsequently verified experimentally. This Account consists of three sections discuss three different kinds of selectivities. The first section discusses the regio- and stereoselectivities of hydrosilylations of alkynes, mainly catalyzed by [Cp*Ru(MeCN)3](+) or [CpRu(MeCN)3](+). Calculations suggest a new mechanism that involves a key ruthenacyclopropene intermediate. This mechanism not only explains the unusual Markovnikov regio-selectivity and anti-addition stereoselectivity observed by Trost and co-workers, but also motivated further experimental investigations. New intriguing experimental observations and further theoretical studies led to an extension of the reaction mechanism. The second section includes three cases of meta-selective C-H activation of aryl compounds. In the case of Cu-catalyzed selective meta-C-H activation of aniline, a new mechanism that involves a Cu(III)-Ar-mediated Heck-like transition state, in which the Ar group acts as an electrophile, was proposed. This mechanism predicted a higher reactivity for more electron-deficient Ar groups, which was supported by experiments. For two template-mediated, meta-selective C-H bond activations catalyzed by

  8. Effects of Combined Hands-on Laboratory and Computer Modeling on Student Learning of Gas Laws: A Quasi-Experimental Study

    ERIC Educational Resources Information Center

    Liu, Xiufeng

    2006-01-01

    Based on current theories of chemistry learning, this study intends to test a hypothesis that computer modeling enhanced hands-on chemistry laboratories are more effective than hands-on laboratories or computer modeling laboratories alone in facilitating high school students' understanding of chemistry concepts. Thirty-three high school chemistry…

  9. Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples.

    PubMed

    van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A

    2011-01-11

    In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order computational chemistry methods, previously considered intractable. As the system sizes continue to increase, the computational chemistry domain continues to escalate this trend using parallel computing with programming models such as Message Passing Interface (MPI) and Partitioned Global Address Space (PGAS) programming models such as Global Arrays. The ever increasing scale of these supercomputers comes at a cost of reduced Mean Time Between Failures (MTBF), currently on the order of days and projected to be on the order of hours for upcoming extreme scale systems. While traditional disk-based check pointing methods are ubiquitous for storing intermediate solutions, they suffer from high overhead of writing and recovering from checkpoints. In practice, checkpointing itself often brings the system down. Clearly, methods beyond checkpointing are imperative to handling the aggravating issue of reducing MTBF. In this paper, we address this challenge by designing and implementing an efficient fault tolerant version of the Coupled Cluster (CC) method with NWChem, using in-memory data redundancy. We present the challenges associated with our design, including an efficient data storage model, maintenance of at least one consistent data copy, and the recovery process. Our performance evaluation without faults shows that the current design exhibits a small overhead. In the presence of a simulated fault, the proposed design incurs negligible overhead in comparison to the state of the art implementation without faults. PMID:26606219

  10. Anethole-Water a Combined Jet, Matrix, and Computational Study

    NASA Astrophysics Data System (ADS)

    Newby, Josh; Nesheiwat, Jackleen

    2016-06-01

    Anethole [(E)-1-methoxy-4-(1-propenyl)benzene] is a natural product molecule that is commonly recognized as the flavor component of anise, fennel, and licorice. Previously, we reported the jet-cooled, laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) spectra of anethole. In this work, several weak bands were observed and were tentatively assigned as van der Waals clusters of anethole with water. We have since confirmed this assignment and have conducted a more detailed study to determine the geometry of these clusters. Results from LIF, SVLF, and matrix isolation FTIR spectroscopy, as well as computational results will be presented in this talk. J. Phys. Chem. A, 2013, 117 (48), 12831-12841 Newly built system at Hobart and William Smith Colleges

  11. Zwitterionic polymer functionalization of polysulfone membrane with improved antifouling property and blood compatibility by combination of ATRP and click chemistry.

    PubMed

    Xiang, Tao; Lu, Ting; Xie, Yi; Zhao, Wei-Feng; Sun, Shu-Dong; Zhao, Chang-Sheng

    2016-08-01

    The chemical compositions are very important for designing blood-contacting membranes with good antifouling property and blood compatibility. In this study, we propose a method combining ATRP and click chemistry to introduce zwitterionic polymer of poly(sulfobetaine methacrylate) (PSBMA), negatively charged polymers of poly(sodium methacrylate) (PNaMAA) and/or poly(sodium p-styrene sulfonate) (PNaSS), to improve the antifouling property and blood compatibility of polysulfone (PSf) membranes. Attenuated total reflectance-Fourier transform infrared spectra, X-ray photoelectron spectroscopy and water contact angle results confirmed the successful grafting of the functional polymers. The antifouling property and blood compatibility of the modified membranes were systematically investigated. The zwitterionic polymer (PSBMA) grafted membranes showed good resistance to protein adsorption and bacterial adhesion; the negatively charged polymer (PNaSS or PNaMAA) grafted membranes showed improved blood compatibility, especially the anticoagulant property. Moreover, the PSBMA/PNaMAA modified membrane showed both antifouling property and anticoagulant property, and exhibited a synergistic effect in inhibiting blood coagulation. The functionalization of membrane surfaces by a combination of ATRP and click chemistry is demonstrated as an effective route to improve the antifouling property and blood compatibility of membranes in blood-contact. PMID:27039977

  12. A Titanium-Organic Framework as an Exemplar of Combining the Chemistry of Metal- and Covalent-Organic Frameworks.

    PubMed

    Nguyen, Ha L; Gándara, Felipe; Furukawa, Hiroyasu; Doan, Tan L H; Cordova, Kyle E; Yaghi, Omar M

    2016-04-01

    A crystalline material with a two-dimensional structure, termed metal-organic framework-901 (MOF-901), was prepared using a strategy that combines the chemistry of MOFs and covalent-organic frameworks (COFs). This strategy involves in situ generation of an amine-functionalized titanium oxo cluster, Ti6O6(OCH3)6(AB)6 (AB = 4-aminobenzoate), which was linked with benzene-1,4-dialdehyde using imine condensation reactions, typical of COFs. The crystal structure of MOF-901 is composed of hexagonal porous layers that are likely stacked in staggered conformation (hxl topology). This MOF represents the first example of combining metal cluster chemistry with dynamic organic covalent bond formation to give a new crystalline, extended framework of titanium metal, which is rarely used in MOFs. The incorporation of Ti(IV) units made MOF-901 useful in the photocatalyzed polymerization of methyl methacrylate (MMA). The resulting polyMMA product was obtained with a high-number-average molar mass (26 850 g mol(-1)) and low polydispersity index (1.6), which in many respects are better than those achieved by the commercially available photocatalyst (P-25 TiO2). Additionally, the catalyst can be isolated, reused, and recycled with no loss in performance.

  13. Reveal protein dynamics by combining computer simulation and neutron scattering

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team

    2014-03-01

    Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.

  14. Human vision combines oriented filters to compute edges.

    PubMed

    Georgeson, M A

    1992-09-22

    The experiments examined the perceived spatial structure of plaid patterns, composed of two or three sinusoidal gratings of the same spatial frequency, superimposed at different orientations. Perceived structure corresponded well with the pattern of zero crossings in the output of a circular spatial filter applied to the image. This lends some support to Marr & Hildreth's (Proc. R. Soc. Lond. B 207, 187 (1980)) theory of edge detection as a model for human vision, but with a very different implementation. The perceived structure of two-component plaids was distorted by prior exposure to a masking or adapting grating, in a way that was perceptually equivalent to reducing the contrast of one of the plaid components. This was confirmed by finding that the plaid distortion could be nulled by increasing the contrast of the masked or adapted component. A corresponding reduction of perceived contrast for single gratings was observed after adaptation and in some masking conditions. I propose the outlines of a model for edge finding in human vision. The plaid components are processed through cortical, orientation-selective filters that are subject to attenuation by forward masking and adaptation. The outputs of these oriented filters are then linearly summed to emulate circular filtering, and zero crossings (zcs) in the combined output are used to determine edge locations. Masking or adapting to a grating attenuates some oriented filters more than others, and although this changes only the effective contrast of the components, it results in a geometric distortion at the zc level after different filters have been combined. The orientation of zcs may not correspond at all with the orientation of Fourier components, but they are correctly predicted by this two-stage model. The oriented filters are not 'orientation detectors', but are precursors to a more subtle stage that locates and represents spatial features.

  15. A Computer-Interfaced O2 Probe: Instrumentation for Undergraduate Chemistry Laboratories.

    ERIC Educational Resources Information Center

    Adamson, Gary E.; Nakhleh, Mary B.; Zimmerman, James R.

    1997-01-01

    Describes interfacing a hand-held oxygen probe with a microcomputer and suggests experiments for undergraduate chemistry courses that could facilitate student understanding of aquatic environmental processes which involve dissolved oxygen. Data can be analyzed through the program or exported into other software. Presents results of an experiment…

  16. Computational and Experimental Assessment of Benzene Cation Chemistry for the Measurement of Marine Derived Biogenic Volatile Organic Compounds with Chemical Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Zoerb, M.; Kim, M.; Zimmermann, K.; Bertram, T. H.

    2013-12-01

    Chemical ionization mass spectrometry (CIMS) is a highly selective and sensitive technique for the measurement of trace gases in the atmosphere. However, competing side reactions and dependence on relative humidity (RH) can make the transition from the laboratory to the field challenging. Effective implementation of chemical ionization requires a thorough knowledge of the elementary steps leading to ionization of the analyte. We have recently investigated benzene cations for the detection of marine derived biogenic volatile organic compounds (BVOCs), such isoprene and terpene compounds, from algal bloom events. Our experimental results indicate that benzene ion chemistry is an attractive candidate for field measurements, and the RH dependence is weak. To further understand the advantages and limitations of this approach, we have also used electronic structure theory calculations to compliment the experimental work. These theoretical methods can provide valuable insight into the physical chemistry of ion molecule reactions including thermodynamical information, the stability of ions to fragmentation, and potential sources of interference such as dehydration to form isobaric ions. The combined experimental and computational approach also allows validation of the theoretical methods and will provide useful information towards gaining predictive power for the selection of appropriate reagent ions for future experiments.

  17. Elucidating graphene - Ionic Liquid interfacial region: a combined experimental and computational study

    SciTech Connect

    Vijayakumar, M.; Schwenzer, Birgit; Shutthanandan, V.; Hu, Jian Z.; Liu, Jun; Aksay, Ilhan A.

    2014-01-10

    The interfacial region between graphene and an imidazolium based ionic liquid is studied using spectroscopic analysis and computational modelling. This combined approach reveals that the molecular level structure of the interfacial region is significantly influenced by functional group defects on the graphene surface.The combined experimental and computational study reveals that the molecular structure at interfacial region between graphene and imidazolium based ionic liquid is defined by the hydroxyl functional groups on the graphene surface

  18. Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics

    NASA Astrophysics Data System (ADS)

    Mitchell, Gabriel J.; Nelson, Daniel C.; Weitz, Joshua S.

    2010-12-01

    The number of microbial pathogens resistant to antibiotics continues to increase even as the rate of discovery and approval of new antibiotic therapeutics steadily decreases. Many researchers have begun to investigate the therapeutic potential of naturally occurring lytic enzymes as an alternative to traditional antibiotics. However, direct characterization of lytic enzymes using techniques based on synthetic substrates is often difficult because lytic enzymes bind to the complex superstructure of intact cell walls. Here we present a new standard for the analysis of lytic enzymes based on turbidity assays which allow us to probe the dynamics of lysis without preparing a synthetic substrate. The challenge in the analysis of these assays is to infer the microscopic details of lysis from macroscopic turbidity data. We propose a model of enzymatic lysis that integrates the chemistry responsible for bond cleavage with the physical mechanisms leading to cell wall failure. We then present a solution to an inverse problem in which we estimate reaction rate constants and the heterogeneous susceptibility to lysis among target cells. We validate our model given simulated and experimental turbidity assays. The ability to estimate reaction rate constants for lytic enzymes will facilitate their biochemical characterization and development as antimicrobial therapeutics.

  19. The combined effect of abandoned mines and agriculture on groundwater chemistry.

    PubMed

    Pauwels, Hélène; Pettenati, Marie; Greffié, Catherine

    2010-06-25

    Although it is well known that both mining and agriculture disturb groundwater quality, their mutual interactions are much less well documented, though agricultural activities may prevail once mining operations have ended. To study these potential interactions and their impacts on water chemistry, we monitored the chemical composition of groundwater at the outlet of a gold exploration gallery in an area of intensive agricultural activity along with an isotopic study of the groundwater, a reactive artificial tracer test that involved injecting H2O2 into the gallery, and geochemical modelling. The isotopic study revealed denitrification of the NO3-bearing groundwater that takes place through oxidation of the sulphide minerals associated with the gold deposit and leads to anomalous concentrations of some metals such as Zn, Co and Ni. It also contributes to liberating As into the groundwater, where the tracer test confirmed that As is sensitive to the redox conditions. The currently observed high arsenic concentrations in the groundwater are interpreted as resulting mainly from the former mining activities through a remobilization of As sorbed on or co-precipitated with the iron oxides that formed when the gallery was excavated. The geochemical modelling enabled us to calculate the respective role of each process involved in the As accumulation in the groundwater. It is also inferred that NO3 contamination from agricultural activities disturbs arsenic remobilization--by consuming available electron donors (e.g. organic matter), NO3 limits the reduction of iron oxides and consequently the release of arsenic.

  20. Cheminformatics and Computational Chemistry: A Powerful Combination for the Encoding of Process Science

    EPA Science Inventory

    The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural...

  1. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially the molecular shape is inferred from the crystal structures of m...

  2. Comprehensive mapping of protein N-glycosylation in human liver by combining hydrophilic interaction chromatography and hydrazide chemistry.

    PubMed

    Zhu, Jun; Sun, Zhen; Cheng, Kai; Chen, Rui; Ye, Mingliang; Xu, Bo; Sun, Deguang; Wang, Liming; Liu, Jing; Wang, Fangjun; Zou, Hanfa

    2014-03-01

    Although glycoproteomics is greatly developed in recent years, our knowledge about N-glycoproteome of human tissues is still very limited. In this study, we comprehensively mapped the N-glycosylation sites of human liver by combining click maltose-hydrophilic interaction chromatography (HILIC) and the improved hydrazide chemistry. The specificity could be as high as 90% for hydrazide chemistry and 80% for HILIC. Altogether, we identified 14,480 N-glycopeptides matched with N-!P-[S|T|C] sequence motif from human liver, corresponding to 2210 N-glycoproteins and 4783 N-glycosylation sites. These N-glycoproteins are widely involved into different types of biological processes, such as hepatic stellate cell activation and acute phase response of human liver, which all highly associate with the progression of liver diseases. Moreover, the exact N-glycosylation sites of some key-regulating proteins within different human liver physiological processes were also obtained, such as E-cadherin, transforming growth factor beta receptor and 29 members of G protein coupled receptors family.

  3. 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.

  4. One-pot peptide and protein conjugation: a combination of enzymatic transamidation and click chemistry.

    PubMed

    Rachel, N M; Pelletier, J N

    2016-02-11

    Enzymatic transamidation and copper-catalyzed azide-alkyne cycloaddition (CuAAC) were combined to yield covalently conjugated peptides and proteins. The addition of glutathione preserved enzymatic activity in the presence of copper. Tuning the reaction kinetics was key to success, providing up to 95% conversion. This one-pot reaction allowed for targeted fluorescent protein labeling. PMID:26741126

  5. Porous solids arising from synergistic and competing modes of assembly: combining coordination chemistry and covalent bond formation.

    PubMed

    Dutta, Ananya; Koh, Kyoungmoo; Wong-Foy, Antek G; Matzger, Adam J

    2015-03-23

    Design and synthesis of porous solids employing both reversible coordination chemistry and reversible covalent bond formation is described. The combination of two different linkage modes in a single material presents a link between two distinct classes of porous materials as exemplified by metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). This strategy, in addition to being a compelling material-discovery method, also offers a platform for developing a fundamental understanding of the factors influencing the competing modes of assembly. We also demonstrate that even temporary formation of reversible connections between components may be leveraged to make new phases thus offering design routes to polymorphic frameworks. Moreover, this approach has the striking potential of providing a rich landscape of structurally complex materials from commercially available or readily accessible feedstocks.

  6. Integration of Computational and Preparative Techniques to Demonstrate Physical Organic Concepts in Synthetic Organic Chemistry: An Example Using Diels-Alder Reaction

    ERIC Educational Resources Information Center

    Palmer, David R. J.

    2004-01-01

    The Diels-Alder reaction is used as an example for showing the integration of computational and preparative techniques, which help in demonstrating the physical organic concepts in synthetic organic chemistry. These experiments show that the students should not accept the computational results without questioning them and in many Diels-Alder…

  7. Conformer Hunting: An Open-Ended Computational Chemistry Exercise That Expresses Real-World Complexity and Student Forethought

    NASA Astrophysics Data System (ADS)

    Lipkowitz, Kenny B.; Robertson, Daniel

    2000-02-01

    A computational chemistry project suitable for both graduate and undergraduate classes has been developed, tested, and implemented successfully over the course of 10 years. In this project we ask students the following simple question: "Which conformer searching strategy in Spartan is the best?" To answer this question the students need to develop a working definition of what "best" means within the context of the project, design their own experiments that can address that question most suitably, carry out the calculations to derive a compelling answer, and then write their results in the form of a research paper. In addition to teaching students about potential energy surfaces, molecular modeling techniques, and stereochemistry, the pedagogical advantages of this computational chemistry exercise compared to others published in this Journal are that it (i) requires a significant amount of student forethought in addition to afterthought by forcing students to design their own experiments, (ii) demonstrates real-world levels of complexity by using molecules having multiple rotatable bonds, (iii) allows for student creativity that is missing in most other published exercises, (iv) focuses on writing in the curriculum.

  8. A novel UV degradation product of Ebastine: isolation and characterization using Q-TOF, NMR, IR and computational chemistry.

    PubMed

    Rapolu, Ravi; Pandey, Avadhesh Kumar; Raju, Ch Krishnam; Ghosh, Kaushik; Srinivas, Kolupula; Awasthi, Atul; Navalgund, Sameer G; Surendranath, Koduru V

    2015-03-25

    Forced degradation of Ebastine (1-(4-(1,1-dimethylethyl)phenyl)-4-(4-(diphenylmethoxy) piperidin-1-yl)butan-1-one) drug substance in ultraviolet light condition resulted into an unknown significant degradation product. This degradation product was analyzed using a newly developed reverse-phase HPLC, where it was eluted at 2.73 relative retention time to Ebastine peak. UV degradation product was isolated from reaction mass using preparative HPLC and its structure was elucidated using high resolution MS, multidimensional NMR and FTIR spectroscopic techniques. UV degradation product has been characterized as 2-(4-(benzhydryloxy)piperidin-1-yl)-1-(4-(tert-butyl)phenyl)-2-methylcyclopropanol. (1)H and (13)C NMR chemical shift values were generated using computational chemistry for possible two diastereomers (7R10S and 7R10R) and later 7R10R was confirmed (and its enantiomer) as final structure given it showed close agreement with experimental NMR data. Formation of UV degradation product as a recemic mixture was further verified by computational chemistry evaluation, chiral HPLC and polarimetery. To best of our knowledge, this is a novel degradation product which is not discussed at any form of publication yet. PMID:25679093

  9. The Combined Effects of Classroom Teaching and Learning Strategy Use on Students' Chemistry Self-Efficacy

    ERIC Educational Resources Information Center

    Cheung, Derek

    2015-01-01

    For students to be successful in school chemistry, a strong sense of self-efficacy is essential. Chemistry self-efficacy can be defined as students' beliefs about the extent to which they are capable of performing specific chemistry tasks. According to Bandura ("Psychol. Rev." 84:191-215, 1977), students acquire information about…

  10. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Waltemath, Dagmar; Bergmann, Frank T.; Chaouiya, Claudine; Czauderna, Tobias; Gleeson, Padraig; Goble, Carole; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Krebs, Olga; Le Novère, Nicolas; Mi, Huaiyu; Moraru, Ion I.; Myers, Chris J.; Nickerson, David; Olivier, Brett G.; Rodriguez, Nicolas; Schreiber, Falk; Smith, Lucian; Zhang, Fengkai; Bonnet, Eric

    2014-01-01

    The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.

  11. A diagonal implicit scheme for computing flows with finite-rate chemistry

    NASA Technical Reports Server (NTRS)

    Eberhardt, Scott; Imlay, Scott

    1990-01-01

    A new algorithm for solving steady, finite-rate chemistry, flow problems is presented. The new scheme eliminates the expense of inverting large block matrices that arise when species conservation equations are introduced. The source Jacobian matrix is replaced by a diagonal matrix which is tailored to account for the fastest reactions in the chemical system. A point-implicit procedure is discussed and then the algorithm is included into the LU-SGS scheme. Solutions are presented for hypervelocity reentry and Hydrogen-Oxygen combustion. For the LU-SGS scheme a CFL number in excess of 10,000 has been achieved.

  12. Calcite sealing in a fractured geothermal reservoir: Insights from combined EBSD and chemistry mapping

    NASA Astrophysics Data System (ADS)

    McNamara, David D.; Lister, Aaron; Prior, Dave J.

    2016-09-01

    Fractures play an important role as fluid flow pathways in geothermal resources hosted in indurated greywacke basement of the Taupo Volcanic Zone, New Zealand, including the Kawerau Geothermal Field. Over time, the permeability of such geothermal reservoirs can be degraded by fracture sealing as minerals deposit out of transported geothermal fluids. Calcite is one such fracture sealing mineral. This study, for the first time, utilises combined data from electron backscatter diffraction and chemical mapping to characterise calcite vein fill morphologies, and gain insight into the mechanisms of calcite fracture sealing in the Kawerau Geothermal Field. Two calcite sealing mechanisms are identified 1) asymmetrical syntaxial growth of calcite, inferred by the presence of single, twinned, calcite crystals spanning the entire fracture width, and 2) 3D, interlocking growth of bladed vein calcite into free space as determined from chemical and crystallographic orientation mapping. This study also identifies other potential uses of combined EBSD and chemical mapping to understand geothermal field evolution including, potentially informing on levels of fluid supersaturation from the study of calcite lattice distortion, and providing information on a reservoir's history of stress, strain, and deformation through investigation of calcite crystal deformation and twinning patterns.

  13. A Systematic Approach for Understanding Slater-Gaussian Functions in Computational Chemistry

    ERIC Educational Resources Information Center

    Stewart, Brianna; Hylton, Derrick J.; Ravi, Natarajan

    2013-01-01

    A systematic way to understand the intricacies of quantum mechanical computations done by a software package known as "Gaussian" is undertaken via an undergraduate research project. These computations involve the evaluation of key parameters in a fitting procedure to express a Slater-type orbital (STO) function in terms of the linear…

  14. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals

    NASA Astrophysics Data System (ADS)

    Garza, Alejandro J.; Sousa Alencar, Ana G.; Scuseria, Gustavo E.

    2015-12-01

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f0 actinyl series (UO22+, NpO23+, PuO24+), the isoelectronic NUN, and thorium (ThO, ThO2+) and nobelium (NoO, NoO2) oxides are studied.

  15. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals.

    PubMed

    Garza, Alejandro J; Sousa Alencar, Ana G; Scuseria, Gustavo E

    2015-12-28

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f(0) actinyl series (UO2(2+), NpO2(3+), PuO2(4+)), the isoelectronic NUN, and thorium (ThO, ThO(2+)) and nobelium (NoO, NoO2) oxides are studied.

  16. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals.

    PubMed

    Garza, Alejandro J; Sousa Alencar, Ana G; Scuseria, Gustavo E

    2015-12-28

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f(0) actinyl series (UO2(2+), NpO2(3+), PuO2(4+)), the isoelectronic NUN, and thorium (ThO, ThO(2+)) and nobelium (NoO, NoO2) oxides are studied. PMID:26723650

  17. The combined effect of surface chemistry and flow conditions on Staphylococcus epidermidis adhesion and ica operon expression.

    PubMed

    Foka, A; Katsikogianni, M G; Anastassiou, E D; Spiliopoulou, I; Missirlis, Y F

    2012-01-01

    The assessment of biomaterial susceptibility to infection relies mainly on the analysis of macroscopic bacterial responses to material interactions, usually under static conditions. However, new technologies permit a more profound understanding of the molecular basis of bacteria-biomaterial interactions. In this study, we combine both conventional phenotypic analysis - using confocal microscopy - and genotypic analysis - using the relative reverse transcription polymerase chain reaction (RT-PCR) - to examine the interaction of bacteria with OH- and CH3-terminated glass surfaces, under dynamic flow conditions. Bacterial adhesion, as well as slime production and biofilm formation, was much higher on the CH3-terminated than on the OH-terminated glass - for four Staphylococcus epidermidis strains. This was in agreement with the icaA and icaD gene expression results that showed increased expression for the bacteria adhering to the CH3-terminated substrate, especially under the higher shear rate. Therefore, the combined effect of the surface chemistry and shear significantly influence the adhesion and phenotype of interacting bacterial cells, while there are putative links between phenotypic responses to bacteria-material interactions and gene-expression profile alterations. This indicates that analysis of gene expression not only can greatly refine our knowledge of bacteria-material interactions, but also yield novel biomarkers for potential use in biocompatibility assessment. PMID:23160991

  18. Synthesis of Zwitterionic Polymer Particles via Combined Distillation Precipitation Polymerization and Click Chemistry for Highly Efficient Enrichment of Glycopeptide.

    PubMed

    Liu, Jianxi; Yang, Kaiguang; Shao, Wenya; Li, Senwu; Wu, Qi; Zhang, Shen; Qu, Yanyan; Zhang, Lihua; Zhang, Yukui

    2016-08-31

    Because of the low abundance of glycopeptide in natural biological samples, methods for efficient and selective enrichment of glycopeptides play a significant role in mass spectrometry (MS)-based glycoproteomics. In this study, a novel kind of zwitterionic hydrophilic interaction chromatography polymer particles, namely, poly(N,N-methylenebisacrylamide-co-methacrylic acid)@l-Cys (poly(MBAAm-co-MAA)@l-Cys), for the enrichment of glycopeptides was synthesized by a facile and efficient approach that combined distillation precipitation polymerization (DPP) and "thiol-ene" click reaction. In the DPP approach, residual vinyl groups explored outside the core with high density, then the functional ligand cysteine was immobilized onto the surface of core particles by highly efficient thiol-ene click reaction. Taking advantage of the unique structure of poly(MBAAm-co-MAA)@l-Cys, the resulting particles possess remarkable enrichment selectivity for glycopeptides from the tryptic digested human immunoglobulin G. The polymer particles were successfully employed for the analysis of human plasma, and 208 unique glycopeptides corresponding to 121 glycoproteins were reliably identified in triple independent nano-LC-MS/MS runs. The selectivity toward glycopeptides of these particles poly(MBAAm-co-MAA)@l-Cys is ∼2 times than that of the commercial beads. These results demonstrated that these particles had great potential for large-scale glycoproteomics research. Moreover, the strategy with the combination of DPP and thiol-ene click chemistry might be a facile method to produce functional polymer particles for bioenrichment application. PMID:27498760

  19. Crystals size and surface chemistry dependent phase diagram for nanocrystals of rutile and anatase: Experimental studies and computer modeling

    NASA Astrophysics Data System (ADS)

    Xu, H.; Barnard, A. S.

    2008-12-01

    It is well known that rutile is the thermodynamically stable phase of TiO2 under ambient conditions at the macroscale, and that anatase is the thermodynamically stable phase at the nanoscale. Both anatase and rutile have superior performance in a range of advanced photochemical applications. It is important for our understanding of the stability of nanostructures in different chemical and physical environments, because both rutile and anatase nanocrystals are used in different chemical and engineering environments. Using a size-, shape- and temperature-dependent thermodynamic model we have generated the first phase diagram for anatase and rutile nanocrystals by incorporating more experimentally relevant parameters (both the equilibrium shape and surface chemistry). Results from hydrothermal synthesis and DFT-based computer modeling show acidic environment favors rutile formation. The acidic solution also favors OH2-terminated surfaces of both anatase and rutile. The boundary between rutile an danatase ranges from ~ 10 nm to ~ 50 nm, depending on temperature and surface composition. The calculated phase map indicates that the equilibrium boundary between anatase and rutile nano-crystals is surface charge chemistry dependent, which relates to both their formation and post-synthesis environments.

  20. Computational chemistry: a useful (sometimes mandatory) tool in mass spectrometry studies.

    PubMed

    Alcamí, M; Mó, O; Yáñez, M

    2001-01-01

    In this review, we present a brief summary of the theoretical methods most frequently used in gas-phase ion chemistry. In subsequent sections, the performance of these methods is analyzed, paying attention to the reliability of geometries, vibrational frequencies, energies, and entropies. The possible pathologies of the different methods, in the form of instabilities of the wave function or spin contamination problems, are discussed. Several examples are presented to illustrate the usefulness of ab initio or density functional theory (DFT) methods to predict the existence of elusive molecules and/or to characterize non-conventional structures, and to rationalize the charge redistributions normally associated with ion-molecule interactions and which result in bond-weakening or bond-reinforcement effects. Finally, the role of non-classical structures in ion-molecule interactions is also illustrated with different examples.

  1. Structural Characteristics and Reactivity Relationships of Nitroaromatic and Nitramine Explosives – A Review of Our Computational Chemistry and Spectroscopic Research

    PubMed Central

    Qasim, Mohammad M.; Moore, Brett; Taylor, Lyssa; Honea, Patricia; Gorb, Leonid; Leszczynski, Jerzy

    2007-01-01

    Although much has been discovered, discussed and written as to problems of contamination by various military unique compounds, particularly by the nitrogen based energetics (NOCs), remaining problems dictate further evaluation of actual and potential risk to the environment by these energetics and their derivatives and metabolites through determination of their environmental impact—transport, fate and toxicity. This work comprises an effort to understand structural relationships and degradation mechanisms of current and emerging explosives, including nitroaromatic; cyclic and cage cyclic nitramine; and a nitrocubane. This review of our computational chemistry and spectroscopic research describes and compares competitive degradation mechanisms by free radical oxidative, reductive and alkali hydrolysis, relating them, when possible, to environmental risk.

  2. Providing full 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

    2013-04-16

    Methods, apparatus, and products are disclosed for providing full 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: receiving a network packet in a compute node, the network packet specifying a destination compute node; selecting, in dependence upon the destination compute node, at least one of the links for the compute node along which to forward the network packet toward the destination compute node; and forwarding the network packet along the selected link to the adjacent compute node connected to the compute node through the selected link.

  3. Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

    PubMed

    Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

    2014-11-01

    In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW).

  4. A Computational Approach to Understanding Aerosol Formation and Oxidant Chemistry in the Troposphere

    SciTech Connect

    Francisco, Joseph S.; Kathmann, Shawn M.; Schenter, Gregory K.; Dang, Liem X.; Xantheas, Sotiris S.; Garrett, Bruce C.; Du, Shiyu; Dixon, David A.; Bianco, Roberto; Wang, Shuzhi; Hynes, James T.; Morita, Akihiro; Peterson, Kirk A.

    2006-04-18

    An understanding of the mechanisms and kinetics of aerosol formation and ozone production in the troposphere is currently a high priority because these phenomena are recognized as two major effects of energy-related air pollution. Atmospheric aerosols are of concern because of their effect on visibility, climate, and human health. Equally important, aerosols can change the chemistry of the atmosphere, in dramatic fashion, by providing new chemical pathways (in the condensed phase) unavailable in the gas phase. The oxidation of volatile organic compounds (VOCs) and inorganic compounds (e.g., sulfuric acid, ammonia, nitric acid, ions, and mineral) can produce precursor molecules that act as nucleation seeds. The U.S. Department of Energy (DOE) Atmospheric Chemistry Program (ACP) has identified the need to evaluate the causes of variations in tropospheric aerosol chemical composition and concentrations, including determining the sources of aerosol particles and the fraction of such that are of primary and secondary origin. In particular, the ACP has called for a deeper understanding into aerosol formation because nucleation creates substantial concentrations of fresh particles that, via growth and coagulation, influence the Earth's radiation budget. Tropospheric ozone is also of concern primarily because of its impact on human health. Ozone levels are controlled by NOx and by VOCs in the lower troposphere. The VOCs can be either from natural emissions from such sources as vegetation and phytoplankton or from anthropogenic sources such as automobiles and oil-fueled power production plants. The major oxidant for VOCs in the atmosphere is the OH radical. With the increase in VOC emissions, there is rising concern regarding the available abundance of HOx species needed to initiate oxidation. Over the last five years, there have been four field studies aimed at initial measurements of HOx species (OH and HO? radicals). These measurements revealed HOx levels that are two to

  5. Computer Series, 82. The Application of Expert Systems in the General Chemistry Laboratory.

    ERIC Educational Resources Information Center

    Settle, Frank A., Jr.

    1987-01-01

    Describes the construction of expert computer systems using artificial intelligence technology and commercially available software, known as an expert system shell. Provides two applications; a simple one, the identification of seven white substances, and a more complicated one involving the qualitative analysis of six metal ions. (TW)

  6. Effect of Gender on Computer-Based Chemistry Problem Solving: Early Findings.

    ERIC Educational Resources Information Center

    Kumar, David D.; Helgeson, Stanley L.

    2000-01-01

    Studies the effect of gender on a computer-based approach to solving stoichiometric chemical equations. Implies that the feedback provided by the software might have had an effect on reducing the gender gap. However, upon closer examination, the results showed that the correctness means for males were higher than that for females, and the rate of…

  7. The Variation Theorem Applied to H-2+: A Simple Quantum Chemistry Computer Project

    ERIC Educational Resources Information Center

    Robiette, Alan G.

    1975-01-01

    Describes a student project which requires limited knowledge of Fortran and only minimal computing resources. The results illustrate such important principles of quantum mechanics as the variation theorem and the virial theorem. Presents sample calculations and the subprogram for energy calculations. (GS)

  8. The Effects of Study Tasks in a Computer-Based Chemistry Learning Environment

    ERIC Educational Resources Information Center

    Urhahne, Detlef; Nick, Sabine; Poepping, Anna Christin; Schulz , Sarah Jayne

    2013-01-01

    The present study examines the effects of different study tasks on the acquisition of knowledge about acids and bases in a computer-based learning environment. Three different task formats were selected to create three treatment conditions: learning with gap-fill and matching tasks, learning with multiple-choice tasks, and learning only from text…

  9. Computational medicinal chemistry in fragment-based drug discovery: what, how and when.

    PubMed

    Rabal, Obdulia; Urbano-Cuadrado, Manuel; Oyarzabal, Julen

    2011-01-01

    The use of fragment-based drug discovery (FBDD) has increased in the last decade due to the encouraging results obtained to date. In this scenario, computational approaches, together with experimental information, play an important role to guide and speed up the process. By default, FBDD is generally considered as a constructive approach. However, such additive behavior is not always present, therefore, simple fragment maturation will not always deliver the expected results. In this review, computational approaches utilized in FBDD are reported together with real case studies, where applicability domains are exemplified, in order to analyze them, and then, maximize their performance and reliability. Thus, a proper use of these computational tools can minimize misleading conclusions, keeping the credit on FBDD strategy, as well as achieve higher impact in the drug-discovery process. FBDD goes one step beyond a simple constructive approach. A broad set of computational tools: docking, R group quantitative structure-activity relationship, fragmentation tools, fragments management tools, patents analysis and fragment-hopping, for example, can be utilized in FBDD, providing a clear positive impact if they are utilized in the proper scenario - what, how and when. An initial assessment of additive/non-additive behavior is a critical point to define the most convenient approach for fragments elaboration. PMID:21428828

  10. Surface modification of carbon nanotubes via combination of mussel inspired chemistry and chain transfer free radical polymerization

    NASA Astrophysics Data System (ADS)

    Wan, Qing; Tian, Jianwen; Liu, Meiying; Zeng, Guangjian; Huang, Qiang; Wang, Ke; Zhang, Qingsong; Deng, Fengjie; Zhang, Xiaoyong; Wei, Yen

    2015-08-01

    In this work, a novel strategy for surface modification of carbon nanotubes (CNTs) was developed via combination of mussel inspired chemistry and chain transfer free radical polymerization. First, pristine CNTs were functionalized with polydopamine (PDA), which is formed via self-polymerization of dopamine in alkaline conditions. These PDA functionalized CNTs can be further reacted with amino-terminated polymers (named as PDMC), which was synthesized through chain transfer free radical polymerization using cysteamine hydrochloride as chain transfer agent and methacryloxyethyltrimethyl ammonium chloride as the monomer. PDMC perfectly conjugated with CNT-PDA was ascertained by a series of characterization techniques including transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS). The dispersibility of obtained CNT nanocomposites (named as CNT-PDA-PDMC) was further examined. Results showed that the dispersibility of CNT-PDA-PDMC in aqueous and organic solutions was obviously enhanced. Apart from PDMC, many other amino-terminated polymers can also be used to functionalization of CNTs via similar strategy. Therefore, the method described in this work should be a general strategy for fabrication various polymer nanocomposites.

  11. A City Parking Integration System Combined with Cloud Computing Technologies and Smart Mobile Devices

    ERIC Educational Resources Information Center

    Yeh, Her-Tyan; Chen, Bing-Chang; Wang, Bo-Xun

    2016-01-01

    The current study applied cloud computing technology and smart mobile devices combined with a streaming server for parking lots to plan a city parking integration system. It is also equipped with a parking search system, parking navigation system, parking reservation service, and car retrieval service. With this system, users can quickly find…

  12. Combining Self-Explaining with Computer Architecture Diagrams to Enhance the Learning of Assembly Language Programming

    ERIC Educational Resources Information Center

    Hung, Y.-C.

    2012-01-01

    This paper investigates the impact of combining self explaining (SE) with computer architecture diagrams to help novice students learn assembly language programming. Pre- and post-test scores for the experimental and control groups were compared and subjected to covariance (ANCOVA) statistical analysis. Results indicate that the SE-plus-diagram…

  13. Application of a bi-directional associative memory (BAM) network in computer assisted learning in chemistry.

    PubMed

    Chau, F T; Cheung, B; Tam, K Y; Li, L K

    1994-12-01

    A computer assisted learning software based on a bi-directional associative memory (BAM) network was developed. The software was implemented to assist students in associating the names of the elements in the periodic table with their chemical symbols. The use of the BAM facilitates the analysis and interpretation of students' responses. The software package can be modified easily as an educational tool for other disciplines. PMID:7812638

  14. Computational quantum chemistry for single Heisenberg spin couplings made simple: Just one spin flip required

    SciTech Connect

    Mayhall, Nicholas J.; Head-Gordon, Martin

    2014-10-07

    We highlight a simple strategy for computing the magnetic coupling constants, J, for a complex containing two multiradical centers. On the assumption that the system follows Heisenberg Hamiltonian physics, J is obtained from a spin-flip electronic structure calculation where only a single electron is excited (and spin-flipped), from the single reference with maximum S{sup ^}{sub z}, M, to the M − 1 manifold, regardless of the number of unpaired electrons, 2M, on the radical centers. In an active space picture involving 2M orbitals, only one β electron is required, together with only one α hole. While this observation is extremely simple, the reduction in the number of essential configurations from exponential in M to only linear provides dramatic computational benefits. This (M, M − 1) strategy for evaluating J is an unambiguous, spin-pure, wave function theory counterpart of the various projected broken symmetry density functional theory schemes, and likewise gives explicit energies for each possible spin-state that enable evaluation of properties. The approach is illustrated on five complexes with varying numbers of unpaired electrons, for which one spin-flip calculations are used to compute J. Some implications for further development of spin-flip methods are discussed.

  15. Contributions of computational chemistry and biophysical techniques to fragment-based drug discovery.

    PubMed

    Gozalbes, Rafael; Carbajo, Rodrigo J; Pineda-Lucena, Antonio

    2010-01-01

    In the last decade, fragment-based drug discovery (FBDD) has evolved from a novel approach in the search of new hits to a valuable alternative to the high-throughput screening (HTS) campaigns of many pharmaceutical companies. The increasing relevance of FBDD in the drug discovery universe has been concomitant with an implementation of the biophysical techniques used for the detection of weak inhibitors, e.g. NMR, X-ray crystallography or surface plasmon resonance (SPR). At the same time, computational approaches have also been progressively incorporated into the FBDD process and nowadays several computational tools are available. These stretch from the filtering of huge chemical databases in order to build fragment-focused libraries comprising compounds with adequate physicochemical properties, to more evolved models based on different in silico methods such as docking, pharmacophore modelling, QSAR and virtual screening. In this paper we will review the parallel evolution and complementarities of biophysical techniques and computational methods, providing some representative examples of drug discovery success stories by using FBDD.

  16. Testing the Potential for Computational Chemistry to Quantify Biophysical Properties of the Non-Proteinaceous Amino Acids

    NASA Astrophysics Data System (ADS)

    Lu, Yi; Freeland, Stephen

    2006-08-01

    Although most proteins of most living organisms are constructed from the same set of 20 amino acids, all indications are that this standard alphabet represents a mere subset of what was available to life during early evolution. However, we currently lack an appropriate quantitative framework with which to test the qualitative hypotheses that have been offered to date as explanations for nature's "choices." Specifically, although many indices have been developed to describe the 20 standard amino acids, few or no comparable data extend to prebiotically plausible alternatives because of the costly and time-consuming bench experiments that would be required. Computational chemistry (specifically quantitative structure property relationship methods) offers a potentially fast, cost-effective remedy for this knowledge gap by predicting such molecular properties in silico. Thus, we investigated the use of various freely accessible programs to predict three key amino acid properties (hydrophobicity, charge, and size). We assessed the accuracy of these predictions by comparisons with experimentally determined counterparts for appropriate test data sets. In light of these results, and factors of software accessibility and transparency, we suggest a method for further computational assessments of prebiotically plausible amino acids. The results serve as a starting point for future quantitative analysis of amino acid alphabet evolution.

  17. Accuracy of color prediction of anthraquinone dyes in methanol solution estimated from first principle quantum chemistry computations.

    PubMed

    Cysewski, Piotr; Jeliński, Tomasz

    2013-10-01

    The electronic spectrum of four different anthraquinones (1,2-dihydroxyanthraquinone, 1-aminoanthraquinone, 2-aminoanthraquinone and 1-amino-2-methylanthraquinone) in methanol solution was measured and used as reference data for theoretical color prediction. The visible part of the spectrum was modeled according to TD-DFT framework with a broad range of DFT functionals. The convoluted theoretical spectra were validated against experimental data by a direct color comparison in terms of CIE XYZ and CIE Lab tristimulus model color. It was found, that the 6-31G** basis set provides the most accurate color prediction and there is no need to extend the basis set since it does not improve the prediction of color. Although different functionals were found to give the most accurate color prediction for different anthraquinones, it is possible to apply the same DFT approach for the whole set of analyzed dyes. Especially three functionals seem to be valuable, namely mPW1LYP, B1LYP and PBE0 due to very similar spectra predictions. The major source of discrepancies between theoretical and experimental spectra comes from L values, representing the lightness, and the a parameter, depicting the position on green→magenta axis. Fortunately, the agreement between computed and observed blue→yellow axis (parameter b) is very precise in the case of studied anthraquinone dyes in methanol solution. Despite discussed shortcomings, color prediction from first principle quantum chemistry computations can lead to quite satisfactory results, expressed in terms of color space parameters.

  18. The Influence of Computer-Assisted Instruction on Students' Conceptual Understanding of Chemical Bonding and Attitude toward Chemistry: A Case for Turkey

    ERIC Educational Resources Information Center

    Ozmen, Haluk

    2008-01-01

    In this study, the effect of computer-assisted instruction on conceptual understanding of chemical bonding and attitude toward chemistry was investigated. The study employed a quasi-experimental design involving 11 grade students; 25 in an experimental and 25 in a control group. The Chemical Bonding Achievement Test (CBAT) consisting of 15…

  19. Students' Personality, Attitude, and Learning Style as Predictors of Performance in an Undergraduate Organic Chemistry Course Using Computer-Based Education.

    ERIC Educational Resources Information Center

    Kevin, Richard C.; Liberty, Paul G., Jr.

    Students enrolled in an organic chemistry course were given a diagnostic inventory according to the SCRAPE model. Information was obtained on 11 motivational personality variable and three attitudinal variables for students in both computer-based instruction and regular instruction sections. Descriptive statistics were obtained on each instrument…

  20. Chemical Equilibrium, Unit 4: Equilibria in Acid-Base Systems. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Settle, Frank A., Jr.

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this acid-base equilibria unit includes objectives, prerequisites, pretest, a discussion of equilibrium constants, and 20 problem sets.…

  1. Energy intensity of computer manufacturing: hybrid assessment combining process and economic input-output methods.

    PubMed

    Williams, Eric

    2004-11-15

    The total energy and fossil fuels used in producing a desktop computer with 17-in. CRT monitor are estimated at 6400 megajoules (MJ) and 260 kg, respectively. This indicates that computer manufacturing is energy intensive: the ratio of fossil fuel use to product weight is 11, an order of magnitude larger than the factor of 1-2 for many other manufactured goods. This high energy intensity of manufacturing, combined with rapid turnover in computers, results in an annual life cycle energy burden that is surprisingly high: about 2600 MJ per year, 1.3 times that of a refrigerator. In contrast with many home appliances, life cycle energy use of a computer is dominated by production (81%) as opposed to operation (19%). Extension of usable lifespan (e.g. by reselling or upgrading) is thus a promising approach to mitigating energy impacts as well as other environmental burdens associated with manufacturing and disposal.

  2. A Combined Geometric Approach for Computational Fluid Dynamics on Dynamic Grids

    NASA Technical Reports Server (NTRS)

    Slater, John W.

    1995-01-01

    A combined geometric approach for computational fluid dynamics is presented for the analysis of unsteady flow about mechanisms in which its components are in moderate relative motion. For a CFD analysis, the total dynamics problem involves the dynamics of the aspects of geometry modeling, grid generation, and flow modeling. The interrelationships between these three aspects allow for a more natural formulation of the problem and the sharing of information which can be advantageous to the computation of the dynamics. The approach is applied to planar geometries with the use of an efficient multi-block, structured grid generation method to compute unsteady, two-dimensional and axisymmetric flow. The applications presented include the computation of the unsteady, inviscid flow about a hinged-flap with flap deflections and a high-speed inlet with centerbody motion as part of the unstart / restart operation.

  3. Computational chemistry approach for the early detection of drug-induced idiosyncratic liver toxicity.

    PubMed

    Cruz-Monteagudo, Maykel; Cordeiro, M Natália D S; Borges, Fernanda

    2008-03-01

    Idiosyncratic drug toxicity (IDT), considered as a toxic host-dependent event, with an apparent lack of dose response relationship, is usually not predictable from early phases of clinical trials, representing a particularly confounding complication in drug development. Albeit a rare event (usually <1/5000), IDT is often life threatening and is one of the major reasons new drugs never reach the market or are withdrawn post marketing. Computational methodologies, like the computer-based approach proposed in the present study, can play an important role in addressing IDT in early drug discovery. We report for the first time a systematic evaluation of classification models to predict idiosyncratic hepatotoxicity based on linear discriminant analysis (LDA), artificial neural networks (ANN), and machine learning algorithms (OneR) in conjunction with a 3D molecular structure representation and feature selection methods. These modeling techniques (LDA, feature selection to prevent over-fitting and multicollinearity, ANN to capture nonlinear relationships in the data, as well as the simple OneR classifier) were found to produce QSTR models with satisfactory internal cross-validation statistics and predictivity on an external subset of chemicals. More specifically, the models reached values of accuracy/sensitivity/specificity over 84%/78%/90%, respectively in the training series along with predictivity values ranging from ca. 78 to 86% of correctly classified drugs. An LDA-based desirability analysis was carried out in order to select the levels of the predictor variables needed to trigger the more desirable drug, i.e. the drug with lower potential for idiosyncratic hepatotoxicity. Finally, two external test sets were used to evaluate the ability of the models in discriminating toxic from nontoxic structurally and pharmacologically related drugs and the ability of the best model (LDA) in detecting potential idiosyncratic hepatotoxic drugs, respectively. The computational

  4. Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

    PubMed

    Miller, Benjamin T; Singh, Rishi P; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R; Woodcock, H Lee

    2014-07-01

    This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. PMID:25057988

  5. Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

    PubMed Central

    Miller, Benjamin T.; Singh, Rishi P.; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S.; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R.; Woodcock, H. Lee

    2014-01-01

    This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. PMID:25057988

  6. Studying the Chemistry of Cationized Triacylglycerols Using Electrospray Ionization Mass Spectrometry and Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Grossert, J. Stuart; Herrera, Lisandra Cubero; Ramaley, Louis; Melanson, Jeremy E.

    2014-08-01

    Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na+). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na+, Li+, K+, Ag+, NH4 +). While most cations bind to oxygen, Ag+ binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M]+ was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS3). These lactones can account for all the major product ions in the MS3 spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

  7. A Case for Soft Error Detection and Correction in Computational Chemistry.

    PubMed

    van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A

    2013-09-10

    High performance computing platforms are expected to deliver 10(18) floating operations per second by the year 2022 through the deployment of millions of cores. Even if every core is highly reliable the sheer number of them will mean that the mean time between failures will become so short that most application runs will suffer at least one fault. In particular soft errors caused by intermittent incorrect behavior of the hardware are a concern as they lead to silent data corruption. In this paper we investigate the impact of soft errors on optimization algorithms using Hartree-Fock as a particular example. Optimization algorithms iteratively reduce the error in the initial guess to reach the intended solution. Therefore they may intuitively appear to be resilient to soft errors. Our results show that this is true for soft errors of small magnitudes but not for large errors. We suggest error detection and correction mechanisms for different classes of data structures. The results obtained with these mechanisms indicate that we can correct more than 95% of the soft errors at moderate increases in the computational cost.

  8. A Case for Soft Error Detection and Correction in Computational Chemistry

    SciTech Connect

    van Dam, Hubertus JJ; Vishnu, Abhinav; De Jong, Wibe A.

    2013-09-10

    High performance computing platforms are expected to deliver 10(18) floating operations per second by the year 2022 through the deployment of millions of cores. Even if every core is highly reliable the sheer number of the them will mean that the mean time between failures will become so short that most applications runs will suffer at least one fault. In particular soft errors caused by intermittent incorrect behavior of the hardware are a concern as they lead to silent data corruption. In this paper we investigate the impact of soft errors on optimization algorithms using Hartree-Fock as a particular example. Optimization algorithms iteratively reduce the error in the initial guess to reach the intended solution. Therefore they may intuitively appear to be resilient to soft errors. Our results show that this is true for soft errors of small magnitudes but not for large errors. We suggest error detection and correction mechanisms for different classes of data structures. The results obtained with these mechanisms indicate that we can correct more than 95% of the soft errors at moderate increases in the computational cost.

  9. Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

    PubMed

    Miller, Benjamin T; Singh, Rishi P; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R; Woodcock, H Lee

    2014-07-01

    This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

  10. Heat Transfer Computations of Internal Duct Flows With Combined Hydraulic and Thermal Developing Length

    NASA Technical Reports Server (NTRS)

    Wang, C. R.; Towne, C. E.; Hippensteele, S. A.; Poinsatte, P. E.

    1997-01-01

    This study investigated the Navier-Stokes computations of the surface heat transfer coefficients of a transition duct flow. A transition duct from an axisymmetric cross section to a non-axisymmetric cross section, is usually used to connect the turbine exit to the nozzle. As the gas turbine inlet temperature increases, the transition duct is subjected to the high temperature at the gas turbine exit. The transition duct flow has combined development of hydraulic and thermal entry length. The design of the transition duct required accurate surface heat transfer coefficients. The Navier-Stokes computational method could be used to predict the surface heat transfer coefficients of a transition duct flow. The Proteus three-dimensional Navier-Stokes numerical computational code was used in this study. The code was first studied for the computations of the turbulent developing flow properties within a circular duct and a square duct. The code was then used to compute the turbulent flow properties of a transition duct flow. The computational results of the surface pressure, the skin friction factor, and the surface heat transfer coefficient were described and compared with their values obtained from theoretical analyses or experiments. The comparison showed that the Navier-Stokes computation could predict approximately the surface heat transfer coefficients of a transition duct flow.

  11. Heats of formation of phosphorus compounds determined by current methods of computational quantum chemistry

    NASA Astrophysics Data System (ADS)

    Haworth, Naomi L.; Bacskay, George B.

    2002-12-01

    The heats of formation of a range of phosphorus containing molecules (P2, P4, PH, PH2, PH3, P2H2, P2H4, PO, PO2, PO3, P2O, P2O2, HPO, HPOH, H2POH, H3PO, HOPO, and HOPO2) have been determined by high level quantum chemical calculations. The equilibrium geometries and vibrational frequencies were computed via density functional theory, utilizing the B3LYP/6-31G(2df,p) functional and basis set. Atomization energies were obtained by the application of ab initio coupled cluster theory with single and double excitations from (spin)-restricted Hartree-Fock reference states with perturbative correction for triples [CCSD(T)], in conjunction with cc-pVnZ basis sets (n=T, Q, 5) which include an extra d function on the phosphorus atoms and diffuse functions on the oxygens, as recommended by Bauschlicher [J. Phys. Chem. A 103, 11126 (1999)]. The valence correlated atomization energies were extrapolated to the complete basis limit and corrected for core-valence (CV) correlation and scalar relativistic effects, as well as for basis set superposition errors (BSSE) in the CV terms. This methodology is effectively the same as the one adopted by Bauschlicher in his study of PO, PO2, PO3, HPO, HOPO, and HOPO2. Consequently, for these molecules the results of this work closely match Bauschlicher's computed values. The theoretical heats of formation, whose accuracy is estimated as ranging from ±1.0 to ±2.5 kcal mol-1, are consistent with the available experimental data. The current set of theoretical data represent a convenient benchmark, against which the results of other computational procedures, such as G3, G3X, and G3X2, can be compared. Despite the fact that G3X2 [which is an approximation to the quadratic CI procedure QCISD(T,Full)/G3Xlarge] is a formally higher level theory than G3X, the heats of formation obtained by these two methods are found to be of comparable accuracy. Both reproduce the benchmark heats of formation on the average to within ±2 kcal mol-1 and, for these

  12. Enhancing simulation of efficiency with analytical tools. [combining computer simulation and analytical techniques for cost reduction

    NASA Technical Reports Server (NTRS)

    Seltzer, S. M.

    1974-01-01

    Some means of combining both computer simulation and anlytical techniques are indicated in order to mutually enhance their efficiency as design tools and to motivate those involved in engineering design to consider using such combinations. While the idea is not new, heavy reliance on computers often seems to overshadow the potential utility of analytical tools. Although the example used is drawn from the area of dynamics and control, the principles espoused are applicable to other fields. In the example the parameter plane stability analysis technique is described briefly and extended beyond that reported in the literature to increase its utility (through a simple set of recursive formulas) and its applicability (through the portrayal of the effect of varying the sampling period of the computer). The numerical values that were rapidly selected by analysis were found to be correct for the hybrid computer simulation for which they were needed. This obviated the need for cut-and-try methods to choose the numerical values, thereby saving both time and computer utilization.

  13. Rapid Detection of Biological and Chemical Threat Agents Using Physical Chemistry, Active Detection, and Computational Analysis

    SciTech Connect

    Chung, Myung; Dong, Li; Fu, Rong; Liotta, Lance; Narayanan, Aarthi; Petricoin, Emanuel; Ross, Mark; Russo, Paul; Zhou, Weidong; Luchini, Alessandra; Manes, Nathan; Chertow, Jessica; Han, Suhua; Kidd, Jessica; Senina, Svetlana; Groves, Stephanie

    2007-01-01

    Basic technologies have been successfully developed within this project: rapid collection of aerosols and a rapid ultra-sensitive immunoassay technique. Water-soluble, humidity-resistant polyacrylamide nano-filters were shown to (1) capture aerosol particles as small as 20 nm, (2) work in humid air and (3) completely liberate their captured particles in an aqueous solution compatible with the immunoassay technique. The immunoassay technology developed within this project combines electrophoretic capture with magnetic bead detection. It allows detection of as few as 150-600 analyte molecules or viruses in only three minutes, something no other known method can duplicate. The technology can be used in a variety of applications where speed of analysis and/or extremely low detection limits are of great importance: in rapid analysis of donor blood for hepatitis, HIV and other blood-borne infections in emergency blood transfusions, in trace analysis of pollutants, or in search of biomarkers in biological fluids. Combined in a single device, the water-soluble filter and ultra-sensitive immunoassay technique may solve the problem of early warning type detection of aerosolized pathogens. These two technologies are protected with five patent applications and are ready for commercialization.

  14. [Computational fluid dynamics simulation of different impeller combinations in high viscosity fermentation and its application].

    PubMed

    Dong, Shuhao; Zhu, Ping; Xu, Xiaoying; Li, Sha; Jiang, Yongxiang; Xu, Hong

    2015-07-01

    Agitator is one of the essential factors to realize high efficient fermentation for high aerobic and viscous microorganisms, and the influence of different impeller combination on the fermentation process is very important. Welan gum is a microbial exopolysaccharide produced by Alcaligenes sp. under high aerobic and high viscos conditions. Computational fluid dynamics (CFD) numerical simulation was used for analyzing the distribution of velocity, shear rate and gas holdup in the welan fermentation reactor under six different impeller combinations. The best three combinations of impellers were applied to the fermentation of welan. By analyzing the fermentation performance, the MB-4-6 combination had better effect on dissolved oxygen and velocity. The content of welan was increased by 13%. Furthermore, the viscosity of production were also increased.

  15. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, teaching suggestions, and classroom materials/activities. These include: game for teaching ionic formulas; method for balancing equations; description of useful redox series; computer programs (with listings) for water electrolysis simulation and for determining chemical…

  16. Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy.

    PubMed

    Alves, Gelio; Yu, Yi-Kuo

    2011-01-01

    Given the expanding availability of scientific data and tools to analyze them, combining different assessments of the same piece of information has become increasingly important for social, biological, and even physical sciences. This task demands, to begin with, a method-independent standard, such as the P-value, that can be used to assess the reliability of a piece of information. Good's formula and Fisher's method combine independent P-values with respectively unequal and equal weights. Both approaches may be regarded as limiting instances of a general case of combining P-values from m groups; P-values within each group are weighted equally, while weight varies by group. When some of the weights become nearly degenerate, as cautioned by Good, numeric instability occurs in computation of the combined P-values. We deal explicitly with this difficulty by deriving a controlled expansion, in powers of differences in inverse weights, that provides both accurate statistics and stable numerics. We illustrate the utility of this systematic approach with a few examples. In addition, we also provide here an alternative derivation for the probability distribution function of the general case and show how the analytic formula obtained reduces to both Good's and Fisher's methods as special cases. A C++ program, which computes the combined P-values with equal numerical stability regardless of whether weights are (nearly) degenerate or not, is available for download at our group website http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads/CoinedPValues.html.

  17. Scaffolding a Complex Task of Experimental Design in Chemistry with a Computer Environment

    NASA Astrophysics Data System (ADS)

    Girault, Isabelle; d'Ham, Cédric

    2014-08-01

    When solving a scientific problem through experimentation, students may have the responsibility to design the experiment. When students work in a conventional condition, with paper and pencil, the designed procedures stay at a very general level. There is a need for additional scaffolds to help the students perform this complex task. We propose a computer environment (copex-chimie) with embedded scaffolds in order to help students to design an experimental procedure. A pre-structuring of the procedure where the students have to choose the actions of their procedure among pre-defined actions and specify the parameters forces the students to face the complexity of the design. However, this is not sufficient for them to succeed; they look for some feedback to improve their procedure and finally abandon their task. In another condition, the students were provided with individualized feedbacks on the errors detected in their procedures by an artificial tutor. These feedbacks proved to be necessary to accompany the students throughout their experimental design without being discouraged. With this kind of scaffold, students worked longer and succeeded better to the task than all the other students.

  18. To address accuracy and precision using methods from analytical chemistry and computational physics.

    PubMed

    Kozmutza, Cornelia; Picó, Yolanda

    2009-04-01

    In this work the pesticides were determined by liquid chromatography-mass spectrometry (LC-MS). In present study the occurrence of imidacloprid in 343 samples of oranges, tangerines, date plum, and watermelons from Valencian Community (Spain) has been investigated. The nine additional pesticides were chosen as they have been recommended for orchard treatment together with imidacloprid. The Mulliken population analysis has been applied to present the charge distribution in imidacloprid. Partitioned energy terms and the virial ratios have been calculated for certain molecules entering in interaction. A new technique based on the comparison of the decomposed total energy terms at various configurations is demonstrated in this work. The interaction ability could be established correctly in the studied case. An attempt is also made in this work to address accuracy and precision. These quantities are well-known in experimental measurements. In case precise theoretical description is achieved for the contributing monomers and also for the interacting complex structure some properties of this latter system can be predicted to quite a good accuracy. Based on simple hypothetical considerations we estimate the impact of applying computations on reducing the amount of analytical work.

  19. Using computational chemistry to understand proton transfer in Green Fluorescent Protein

    NASA Astrophysics Data System (ADS)

    Hoskin, Christa; Champion, Paul; Sage, Timothy; Benabbas, Abdelkrim; Demidov, Alexander; Salna, Bridget

    2012-02-01

    Green Fluorescent Protein has been studied experimentally by the scientific community for years yet frustratingly little is known about the underlying proton transfer process that produces the green fluorescence. We are trying to elucidate more about this process using Density Functional Theory to prepare and run various calculations on GFP that we compare with kinetics data, Raman and vibrational coherence spectra. I am building a model of wild type GFP that is realistically sized for our computational power, yet still contains key residues that might affect the proton transport process. I will compare my results to those of the E222D GFP mutant. This comparison will allow us to see any differences in energy and normal modes that give insights regarding the proton transfer process. For example, how does it depend on a variety of factors such as temperature, buffer, pH, mutations, etc.? We also plan to examine if the proton transfer propagates through the three donor-acceptor pairs of the ``proton wire'' consecutively versus the three protons on the wire transferring simultaneously. Finally, we will consider how quantum tunneling may be involved in the proton transfer.

  20. Emerging technology in surgical education: combining real-time augmented reality and wearable computing devices.

    PubMed

    Ponce, Brent A; Menendez, Mariano E; Oladeji, Lasun O; Fryberger, Charles T; Dantuluri, Phani K

    2014-11-01

    The authors describe the first surgical case adopting the combination of real-time augmented reality and wearable computing devices such as Google Glass (Google Inc, Mountain View, California). A 66-year-old man presented to their institution for a total shoulder replacement after 5 years of progressive right shoulder pain and decreased range of motion. Throughout the surgical procedure, Google Glass was integrated with the Virtual Interactive Presence and Augmented Reality system (University of Alabama at Birmingham, Birmingham, Alabama), enabling the local surgeon to interact with the remote surgeon within the local surgical field. Surgery was well tolerated by the patient and early surgical results were encouraging, with an improvement of shoulder pain and greater range of motion. The combination of real-time augmented reality and wearable computing devices such as Google Glass holds much promise in the field of surgery.

  1. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

    PubMed

    Poirot, Olivier; O'Toole, Eamonn; Notredame, Cedric

    2003-07-01

    This paper presents Tcoffee@igs, a new server provided to the community by Hewlet Packard computers and the Centre National de la Recherche Scientifique. This server is a web-based tool dedicated to the computation, the evaluation and the combination of multiple sequence alignments. It uses the latest version of the T-Coffee package. Given a set of unaligned sequences, the server returns an evaluated multiple sequence alignment and the associated phylogenetic tree. This server also makes it possible to evaluate the local reliability of an existing alignment and to combine several alternative multiple alignments into a single new one. Tcoffee@igs can be used for aligning protein, RNA or DNA sequences. Datasets of up to 100 sequences (2000 residues long) can be processed. The server and its documentation are available from: http://igs-server.cnrs-mrs.fr/Tcoffee/.

  2. Robert Boyle's chiral crystal chemistry: computational re-evaluation of enantioselective adsorption on quartz.

    PubMed

    Kahr, Bart; Chittenden, Brianne; Rohl, Andrew

    2006-02-01

    While searching for early examples of interactions of organic chromophores with minerals in the context of a systematic study of the process of dyeing crystals, we came across Robert Boyle's description of an experiment that may have been evidence of the enantioselective adsorption of a natural product, carminic acid (7-beta-D-glucopyranosyl-9,10-dihydro-3,5,6,8-tetrahydroxy-1-methyl-9,10-dioxo-2-anthracenecarboxylic acid), to the chiral surfaces of alpha-quartz, three centuries before such interactions became the subject of active chemical investigations. In order to determine whether Boyle did indeed observe enantioselective adsorption--albeit unbeknownst to him--we attempted to dye quartz with carminic acid according to his recipe. Quartz adsorbs carminic acid only because on heating it develops a network of microfissures that adsorb dye. This process depends on capillarity, not on specific non-covalent interactions; there is no evidence of enantioselectivity adsorption to heated crystals or enantioselective epitaxy to unheated crystals. These failures changed the focus of our inquiry: Why have almost all attempts to demonstrate the enantioselective adsorption of additives to quartz crystal surfaces been generally confounding and equivocal? In order to answer this question, we complement our experimental historical re-investigation with contemporary computational techniques for modeling crystal surface structure and the adsorption of additives. Minimizations of the energies associated with the adsorption of carminic acid to relaxed, hydrated d- and l-quartz {10(-)0} surfaces are analyzed in light of quartz's abysmal record as an enantioselective stationary phase.

  3. Robert Boyle's chiral crystal chemistry: computational re-evaluation of enantioselective adsorption on quartz.

    PubMed

    Kahr, Bart; Chittenden, Brianne; Rohl, Andrew

    2006-02-01

    While searching for early examples of interactions of organic chromophores with minerals in the context of a systematic study of the process of dyeing crystals, we came across Robert Boyle's description of an experiment that may have been evidence of the enantioselective adsorption of a natural product, carminic acid (7-beta-D-glucopyranosyl-9,10-dihydro-3,5,6,8-tetrahydroxy-1-methyl-9,10-dioxo-2-anthracenecarboxylic acid), to the chiral surfaces of alpha-quartz, three centuries before such interactions became the subject of active chemical investigations. In order to determine whether Boyle did indeed observe enantioselective adsorption--albeit unbeknownst to him--we attempted to dye quartz with carminic acid according to his recipe. Quartz adsorbs carminic acid only because on heating it develops a network of microfissures that adsorb dye. This process depends on capillarity, not on specific non-covalent interactions; there is no evidence of enantioselectivity adsorption to heated crystals or enantioselective epitaxy to unheated crystals. These failures changed the focus of our inquiry: Why have almost all attempts to demonstrate the enantioselective adsorption of additives to quartz crystal surfaces been generally confounding and equivocal? In order to answer this question, we complement our experimental historical re-investigation with contemporary computational techniques for modeling crystal surface structure and the adsorption of additives. Minimizations of the energies associated with the adsorption of carminic acid to relaxed, hydrated d- and l-quartz {10(-)0} surfaces are analyzed in light of quartz's abysmal record as an enantioselective stationary phase. PMID:16385623

  4. Computational Chemistry-Based Identification of Ultra-Low Temperature Water-Gas-Shift Catalysts

    SciTech Connect

    Manos Mavrikakis

    2008-08-31

    The current work seeks to identify novel, catalytically-active, stable, poison-resistant LWGS catalysts that retain the superior activity typical of conventional Cu catalysts but can be operated at similar or lower temperatures. A database for the Binding Energies (BEs) of the LWGS relevant species, namely CO, O and OH on the most-stable, close-packed facets of a set of 17 catalytically relevant transition metals was established. This BE data and a database of previously established segregation energies was utilized to predict the stability of bimetallic NSAs that could be synthesized by combinations of the 17 parent transition metals. NSAs that were potentially stable both in vacuo and under the influence of strong-binding WGS intermediates were then selected for adsorption studies. A set of 40 NSAs were identified that satisfied all three screener criteria and the binding energies of CO, O and OH were calculated on a set of 66, 43 and 79 NSA candidates respectively. Several NSAs were found that bound intermediates weaker than the monometallic catalysts and were thus potentially poison-resistant. Finally, kinetic studies were performed and resulted in the discovery of a specific NSA-based bimetallic catalyst Cu/Pt that is potentially a promising LWGS catalyst. This stable Cu/Pt subsurface alloy is expected to provide facile H{sub 2}O activation and remain relatively resistant from the poisoning by CO, S and formate intermediates.

  5. Navier-Stokes computations with finite-rate chemistry for LO2/LH2 rocket engine plume flow studies

    NASA Technical Reports Server (NTRS)

    Dougherty, N. Sam; Liu, Baw-Lin

    1991-01-01

    Computational fluid dynamics methods have been developed and applied to Space Shuttle Main Engine LO2/LH2 plume flow simulation/analysis of airloading and convective base heating effects on the vehicle at high flight velocities and altitudes. New methods are described which were applied to the simulation of a Return-to-Launch-Site abort where the vehicle would fly briefly at negative angles of attack into its own plume. A simplified two-perfect-gases-mixing approach is used where one gas is the plume and the other is air at 180-deg and 135-deg flight angle of attack. Related research has resulted in real gas multiple-plume interaction methods with finite-rate chemistry described herein which are applied to the same high-altitude-flight conditions of 0 deg angle of attack. Continuing research plans are to study Orbiter wake/plume flows at several Mach numbers and altitudes during ascent and then to merge this model with the Shuttle 'nose-to-tail' aerodynamic and SRB plume models for an overall 'nose-to-plume' capability. These new methods are also applicable to future launch vehicles using clustered-engine LO2/LH2 propulsion.

  6. Combined computational and experimental approach to improve the assessment of mitral regurgitation by echocardiography.

    PubMed

    Sonntag, Simon J; Li, Wei; Becker, Michael; Kaestner, Wiebke; Büsen, Martin R; Marx, Nikolaus; Merhof, Dorit; Steinseifer, Ulrich

    2014-05-01

    Mitral regurgitation (MR) is one of the most frequent valvular heart diseases. To assess MR severity, color Doppler imaging (CDI) is the clinical standard. However, inadequate reliability, poor reproducibility and heavy user-dependence are known limitations. A novel approach combining computational and experimental methods is currently under development aiming to improve the quantification. A flow chamber for a circulatory flow loop was developed. Three different orifices were used to mimic variations of MR. The flow field was recorded simultaneously by a 2D Doppler ultrasound transducer and Particle Image Velocimetry (PIV). Computational Fluid Dynamics (CFD) simulations were conducted using the same geometry and boundary conditions. The resulting computed velocity field was used to simulate synthetic Doppler signals. Comparison between PIV and CFD shows a high level of agreement. The simulated CDI exhibits the same characteristics as the recorded color Doppler images. The feasibility of the proposed combination of experimental and computational methods for the investigation of MR is shown and the numerical methods are successfully validated against the experiments. Furthermore, it is discussed how the approach can be used in the long run as a platform to improve the assessment of MR quantification.

  7. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  8. Computing the modal mass from the state space model in combined experimental-operational modal analysis

    NASA Astrophysics Data System (ADS)

    Cara, Javier

    2016-05-01

    Modal parameters comprise natural frequencies, damping ratios, modal vectors and modal masses. In a theoretic framework, these parameters are the basis for the solution of vibration problems using the theory of modal superposition. In practice, they can be computed from input-output vibration data: the usual procedure is to estimate a mathematical model from the data and then to compute the modal parameters from the estimated model. The most popular models for input-output data are based on the frequency response function, but in recent years the state space model in the time domain has become popular among researchers and practitioners of modal analysis with experimental data. In this work, the equations to compute the modal parameters from the state space model when input and output data are available (like in combined experimental-operational modal analysis) are derived in detail using invariants of the state space model: the equations needed to compute natural frequencies, damping ratios and modal vectors are well known in the operational modal analysis framework, but the equation needed to compute the modal masses has not generated much interest in technical literature. These equations are applied to both a numerical simulation and an experimental study in the last part of the work.

  9. Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic

    ERIC Educational Resources Information Center

    Jirat, Jiri; Cech, Petr; Znamenacek, Jiri; Simek, Miroslav; Skuta, Ctibor; Vanek, Tomas; Dibuszova, Eva; Nic, Miloslav; Svozil, Daniel

    2013-01-01

    Experience developing multidisciplinary bachelor's and master's curricula involving intertwined chemistry, informatics, and librarianship-editorship skills is described. The bachelor's curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chemical Technology…

  10. Identification of Unknown Chloride Salts Using a Combination of Qualitative Analysis and Titration with Silver Nitrate: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Maines, Laina L.; Bruch, Martha D.

    2012-01-01

    General chemistry students often have difficulty writing balanced equations and performing stoichiometry calculations for precipitation reactions, in part because of difficulty understanding the symbolic notation used to represent chemical reactions. We have developed a problem-based experiment to improve student learning of these concepts, and…

  11. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    ERIC Educational Resources Information Center

    Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

    2013-01-01

    In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

  12. Computational Chemistry Study of Accelerated Oxidation Mechanism of IGSCC of Structural Materials in LWR Environments and Theoretical Design of SCC Resistant Alloys

    SciTech Connect

    Ken Suzuki; Yo-ichi Takeda; Zhanpeng Lu; Tetsuo Shoji

    2004-07-01

    Computational chemistry has been used to investigate the mechanism of accelerated oxidation of IGSCC. It has been found that the iron atoms along the grain boundary were oxidized more easily than those at other sites. Moreover, success has been achieved in the examination of the effects of element additions to Fe-based alloys. The results indicated that the Ti, Mn, Sr, Y, Ce, and Hf could be used as such additional elements to obtain improvements in the SCC resistance. (authors)

  13. Computational Fluid Dynamic Modeling of Rocket Based Combined Cycle Engine Flowfields

    NASA Technical Reports Server (NTRS)

    Daines, Russell L.; Merkle, Charles L.

    1994-01-01

    Computational Fluid Dynamic techniques are used to study the flowfield of a fixed geometry Rocket Based Combined Cycle engine operating in rocket ejector mode. Heat addition resulting from the combustion of injected fuel causes the subsonic engine flow to choke and go supersonic in the slightly divergent combustor-mixer section. Reacting flow computations are undertaken to predict the characteristics of solutions where the heat addition is determined by the flowfield. Here, adaptive gridding is used to improve resolution in the shear layers. Results show that the sonic speed is reached in the unheated portions of the flow first, while the heated portions become supersonic later. Comparison with results from another code show reasonable agreement. The coupled solutions show that the character of the combustion-based thermal choking phenomenon can be controlled reasonably well such that there is opportunity to optimize the length and expansion ratio of the combustor-mixer.

  14. Three-dimensional computer-assisted simulation combining facial skeleton with facial morphology for orthognathic surgery.

    PubMed

    Chen, L H; Chen, W H

    1999-01-01

    The purpose of this study was to use a 3-dimensional (3D) computer-aided design (CAD) simulation system to plan surgical procedures and predict postoperative changes in orthognathic surgery patients. A computer-generated imaging model was developed by combining a 3D reconstructed cephalometric skeletal image and a laser-scanned facial surface image. Moreover, postoperative data were studied and linked to the simulator model for programming and executing simulated surgical procedures. Interactive editing capabilities allow surgeons to operate CAD surgical simulation, and predicted results can be presented graphically and numerically. The results indicate that the integration of 3D images and CAD techniques have a potential for simulating surgery and providing graphic information to patients in obtaining an informed consent.

  15. Determination of Radiative Heat Transfer Coefficient at High Temperatures Using a Combined Experimental-Computational Technique

    NASA Astrophysics Data System (ADS)

    Kočí, Václav; Kočí, Jan; Korecký, Tomáš; Maděra, Jiří; Černý, Robert Č.

    2015-04-01

    The radiative heat transfer coefficient at high temperatures is determined using a combination of experimental measurement and computational modeling. In the experimental part, cement mortar specimen is heated in a laboratory furnace to 600°C and the temperature field inside is recorded using built-in K-type thermocouples connected to a data logger. The measured temperatures are then used as input parameters in the three dimensional computational modeling whose objective is to find the best correlation between the measured and calculated data via four free parameters, namely the thermal conductivity of the specimen, effective thermal conductivity of thermal insulation, and heat transfer coefficients at normal and high temperatures. The optimization procedure which is performed using the genetic algorithms provides the value of the high-temperature radiative heat transfer coefficient of 3.64 W/(m2K).

  16. Combined positron emission tomography and computed tomography to visualize and quantify fluid flow in sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Fernø, M. A.; Gauteplass, J.; Hauge, L. P.; Abell, G. E.; Adamsen, T. C. H.; Graue, A.

    2015-09-01

    Here we show for the first time the combined positron emission tomography (PET) and computed tomography (CT) imaging of flow processes within porous rocks to quantify the development in local fluid saturations. The coupling between local rock structure and displacement fronts is demonstrated in exploratory experiments using this novel approach. We also compare quantification of 3-D temporal and spatial water saturations in two similar CO2 storage tests in sandstone imaged separately with PET and CT. The applicability of each visualization technique is evaluated for a range of displacement processes, and the favorable implementation of combining PET/CT for laboratory core analysis is discussed. We learn that the signal-to-noise ratio (SNR) is over an order of magnitude higher for PET compared with CT for the studied processes.

  17. Quantum science in secondary chemistry: Influence of teachers' beliefs and knowledge on the use of interactive computer models

    NASA Astrophysics Data System (ADS)

    Robblee, Karen M.

    Current science education reform efforts promote inquiry-based learning, a goal that requires appropriate tools and instructional approaches. This study investigated the influence of the beliefs and knowledge of four experienced secondary chemistry teachers in their use of new instructional software that generates models of atoms and molecules based on quantum mechanics. The software, which was developed through a National Science Foundation funded project, Quantum Science Across Disciplines (QSAD), was designed to promote inquiry learning. Qualitative research methods were used for this multiple case study. Data from surveys, interviews, and extended classroom observations revealed a close correlation between a teacher's model of the learner and his or her model of teaching. Combined models of learner and teacher had the greatest influence on their decisions about implementing QSAD software. Teachers who espoused a constructivist model of learning and related models of teaching used the software to promote student investigations and inductive approaches to learning. Other factors that appeared to support the use of inquiry methods included sufficient time for students to investigate phenomena, the extent of the teacher's pedagogical content knowledge, and the amount of training using QSAD software. The Views-On-Science-Technology-Society (VOSTS) instrument was used to compare the informants' beliefs about the epistemology of science to their classroom practices. Data related to the role of teachers' beliefs about scientific knowledge were inconclusive, and VOSTS results were inconsistent with the informants' stated beliefs. All four cases revealed that the teachers acted as agents of the school culture. In schools that promoted development of critical thinking, questioning, and self-direction in students, teachers were more likely to use a variety of instructional methods and emphasize construction of knowledge. These findings suggest that educational reform

  18. Exploring combinations of auditory and visual stimuli for gaze-independent brain-computer interfaces.

    PubMed

    An, Xingwei; Höhne, Johannes; Ming, Dong; Blankertz, Benjamin

    2014-01-01

    For Brain-Computer Interface (BCI) systems that are designed for users with severe impairments of the oculomotor system, an appropriate mode of presenting stimuli to the user is crucial. To investigate whether multi-sensory integration can be exploited in the gaze-independent event-related potentials (ERP) speller and to enhance BCI performance, we designed a visual-auditory speller. We investigate the possibility to enhance stimulus presentation by combining visual and auditory stimuli within gaze-independent spellers. In this study with N = 15 healthy users, two different ways of combining the two sensory modalities are proposed: simultaneous redundant streams (Combined-Speller) and interleaved independent streams (Parallel-Speller). Unimodal stimuli were applied as control conditions. The workload, ERP components, classification accuracy and resulting spelling speed were analyzed for each condition. The Combined-speller showed a lower workload than uni-modal paradigms, without the sacrifice of spelling performance. Besides, shorter latencies, lower amplitudes, as well as a shift of the temporal and spatial distribution of discriminative information were observed for Combined-speller. These results are important and are inspirations for future studies to search the reason for these differences. For the more innovative and demanding Parallel-Speller, where the auditory and visual domains are independent from each other, a proof of concept was obtained: fifteen users could spell online with a mean accuracy of 87.7% (chance level <3%) showing a competitive average speed of 1.65 symbols per minute. The fact that it requires only one selection period per symbol makes it a good candidate for a fast communication channel. It brings a new insight into the true multisensory stimuli paradigms. Novel approaches for combining two sensory modalities were designed here, which are valuable for the development of ERP-based BCI paradigms. PMID:25350547

  19. Exploring combinations of auditory and visual stimuli for gaze-independent brain-computer interfaces.

    PubMed

    An, Xingwei; Höhne, Johannes; Ming, Dong; Blankertz, Benjamin

    2014-01-01

    For Brain-Computer Interface (BCI) systems that are designed for users with severe impairments of the oculomotor system, an appropriate mode of presenting stimuli to the user is crucial. To investigate whether multi-sensory integration can be exploited in the gaze-independent event-related potentials (ERP) speller and to enhance BCI performance, we designed a visual-auditory speller. We investigate the possibility to enhance stimulus presentation by combining visual and auditory stimuli within gaze-independent spellers. In this study with N = 15 healthy users, two different ways of combining the two sensory modalities are proposed: simultaneous redundant streams (Combined-Speller) and interleaved independent streams (Parallel-Speller). Unimodal stimuli were applied as control conditions. The workload, ERP components, classification accuracy and resulting spelling speed were analyzed for each condition. The Combined-speller showed a lower workload than uni-modal paradigms, without the sacrifice of spelling performance. Besides, shorter latencies, lower amplitudes, as well as a shift of the temporal and spatial distribution of discriminative information were observed for Combined-speller. These results are important and are inspirations for future studies to search the reason for these differences. For the more innovative and demanding Parallel-Speller, where the auditory and visual domains are independent from each other, a proof of concept was obtained: fifteen users could spell online with a mean accuracy of 87.7% (chance level <3%) showing a competitive average speed of 1.65 symbols per minute. The fact that it requires only one selection period per symbol makes it a good candidate for a fast communication channel. It brings a new insight into the true multisensory stimuli paradigms. Novel approaches for combining two sensory modalities were designed here, which are valuable for the development of ERP-based BCI paradigms.

  20. Exploring Combinations of Auditory and Visual Stimuli for Gaze-Independent Brain-Computer Interfaces

    PubMed Central

    An, Xingwei; Höhne, Johannes; Ming, Dong; Blankertz, Benjamin

    2014-01-01

    For Brain-Computer Interface (BCI) systems that are designed for users with severe impairments of the oculomotor system, an appropriate mode of presenting stimuli to the user is crucial. To investigate whether multi-sensory integration can be exploited in the gaze-independent event-related potentials (ERP) speller and to enhance BCI performance, we designed a visual-auditory speller. We investigate the possibility to enhance stimulus presentation by combining visual and auditory stimuli within gaze-independent spellers. In this study with N = 15 healthy users, two different ways of combining the two sensory modalities are proposed: simultaneous redundant streams (Combined-Speller) and interleaved independent streams (Parallel-Speller). Unimodal stimuli were applied as control conditions. The workload, ERP components, classification accuracy and resulting spelling speed were analyzed for each condition. The Combined-speller showed a lower workload than uni-modal paradigms, without the sacrifice of spelling performance. Besides, shorter latencies, lower amplitudes, as well as a shift of the temporal and spatial distribution of discriminative information were observed for Combined-speller. These results are important and are inspirations for future studies to search the reason for these differences. For the more innovative and demanding Parallel-Speller, where the auditory and visual domains are independent from each other, a proof of concept was obtained: fifteen users could spell online with a mean accuracy of 87.7% (chance level <3%) showing a competitive average speed of 1.65 symbols per minute. The fact that it requires only one selection period per symbol makes it a good candidate for a fast communication channel. It brings a new insight into the true multisensory stimuli paradigms. Novel approaches for combining two sensory modalities were designed here, which are valuable for the development of ERP-based BCI paradigms. PMID:25350547

  1. Combined computational metabolite prediction and automated structure-based analysis of mass spectrometric data.

    PubMed

    Stranz, David D; Miao, Shichang; Campbell, Scott; Maydwell, George; Ekins, Sean

    2008-01-01

    ABSTRACT As high-throughput technologies have developed in the pharmaceutical industry, the demand for identification of possible metabolites using predominantly liquid chromatographic/mass spectrometry-mass spectrometry/mass spectrometry (LC/MS-MS/MS) for a large number of molecules in drug discovery has also increased. In parallel, computational technologies have also been developed to generate predictions for metabolites alongside methods to predict MS spectra and score the quality of the match with experimental spectra. The goal of the current study was to generate metabolite predictions from molecular structure with a software product, MetaDrug. In vitro microsomal incubations were used to ultimately produce MS data that could be used to verify the predictions with Apex, which is a new software tool that can predict the molecular ion spectrum and a fragmentation spectrum, automating the detailed examination of both MS and MS/MS spectra. For the test molecule imipramine used to illustrate the combined in vitro/in silico process proposed, MetaDrug predicts 16 metabolites. Following rat microsomal incubations with imipramine and analysis of the MS(n) data using the Apex software, strong evidence was found for imipramine and five metabolites and weaker evidence for five additional metabolites. This study suggests a new approach to streamline MS data analysis using a combination of predictive computational approaches with software capable of comparing the predicted metabolite output with empirical data when looking at drug metabolites.

  2. The description and validation of the computationally Efficient CH4-CO-OH (ECCOHv1.01) chemistry module for 3-D model applications

    NASA Astrophysics Data System (ADS)

    Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

    2016-02-01

    We present the Efficient CH4-CO-OH (ECCOH) chemistry module that allows for the simulation of the methane, carbon monoxide, and hydroxyl radical (CH4-CO-OH) system, within a chemistry climate model, carbon cycle model, or Earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO, and OH, and the concomitant impacts on climate. We implemented the ECCOH chemistry module in the NASA GEOS-5 atmospheric global circulation model (AGCM), performed multiple sensitivity simulations of the CH4-CO-OH system over 2 decades, and evaluated the model output with surface and satellite data sets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS-5 AGCM) with observations demonstrates the fidelity of the module for use in scientific research.

  3. Combining Brain–Computer Interfaces and Assistive Technologies: State-of-the-Art and Challenges

    PubMed Central

    Millán, J. d. R.; Rupp, R.; Müller-Putz, G. R.; Murray-Smith, R.; Giugliemma, C.; Tangermann, M.; Vidaurre, C.; Cincotti, F.; Kübler, A.; Leeb, R.; Neuper, C.; Müller, K.-R.; Mattia, D.

    2010-01-01

    In recent years, new research has brought the field of electroencephalogram (EEG)-based brain–computer interfacing (BCI) out of its infancy and into a phase of relative maturity through many demonstrated prototypes such as brain-controlled wheelchairs, keyboards, and computer games. With this proof-of-concept phase in the past, the time is now ripe to focus on the development of practical BCI technologies that can be brought out of the lab and into real-world applications. In particular, we focus on the prospect of improving the lives of countless disabled individuals through a combination of BCI technology with existing assistive technologies (AT). In pursuit of more practical BCIs for use outside of the lab, in this paper, we identify four application areas where disabled individuals could greatly benefit from advancements in BCI technology, namely, “Communication and Control”, “Motor Substitution”, “Entertainment”, and “Motor Recovery”. We review the current state of the art and possible future developments, while discussing the main research issues in these four areas. In particular, we expect the most progress in the development of technologies such as hybrid BCI architectures, user–machine adaptation algorithms, the exploitation of users’ mental states for BCI reliability and confidence measures, the incorporation of principles in human–computer interaction (HCI) to improve BCI usability, and the development of novel BCI technology including better EEG devices. PMID:20877434

  4. A review of combined experimental and computational procedures for assessing biopolymer structure–process–property relationships

    PubMed Central

    Gronau, Greta; Krishnaji, Sreevidhya T.; Kinahan, Michelle E.; Giesa, Tristan; Wong, Joyce Y.; Kaplan, David L.; Buehler, Markus J.

    2013-01-01

    Tailored biomaterials with tunable functional properties are desirable for many applications ranging from drug delivery to regenerative medicine. To improve the predictability of biopolymer materials functionality, multiple design parameters need to be considered, along with appropriate models. In this article we review the state of the art of synthesis and processing related to the design of biopolymers, with an emphasis on the integration of bottom-up computational modeling in the design process. We consider three prominent examples of well-studied biopolymer materials – elastin, silk, and collagen – and assess their hierarchical structure, intriguing functional properties and categorize existing approaches to study these materials. We find that an integrated design approach in which both experiments and computational modeling are used has rarely been applied for these materials due to difficulties in relating insights gained on different length- and time-scales. In this context, multiscale engineering offers a powerful means to accelerate the biomaterials design process for the development of tailored materials that suit the needs posed by the various applications. The combined use of experimental and computational tools has a very broad applicability not only in the field of biopolymers, but can be exploited to tailor the properties of other polymers and composite materials in general. PMID:22938765

  5. Using an innovative combination of quality-by-design and green analytical chemistry approaches for the development of a stability indicating UHPLC method in pharmaceutical products.

    PubMed

    Boussès, Christine; Ferey, Ludivine; Vedrines, Elodie; Gaudin, Karen

    2015-11-10

    An innovative combination of green chemistry and quality by design (QbD) approach is presented through the development of an UHPLC method for the analysis of the main degradation products of dextromethorphan hydrobromide. QbD strategy was integrated to the field of green analytical chemistry to improve method understanding while assuring quality and minimizing environmental impacts, and analyst exposure. This analytical method was thoroughly evaluated by applying risk assessment and multivariate analysis tools. After a scouting phase aimed at selecting a suitable stationary phase and an organic solvent in accordance with green chemistry principles, quality risk assessment tools were applied to determine the critical process parameters (CPPs). The effects of the CPPs on critical quality attributes (CQAs), i.e., resolutions, efficiencies, and solvent consumption were further evaluated by means of a screening design. A response surface methodology was then carried out to model CQAs as function of the selected CPPs and the optimal separation conditions were determined through a desirability analysis. Resulting contour plots enabled to establish the design space (DS) (method operable design region) where all CQAs fulfilled the requirements. An experimental validation of the DS proved that quality within the DS was guaranteed; therefore no more robustness study was required before the validation. Finally, this UHPLC method was validated using the concept of total error and was used to analyze a pharmaceutical drug product. PMID:26183807

  6. Combining metabolic engineering and biocompatible chemistry for high-yield production of homo-diacetyl and homo-(S,S)-2,3-butanediol.

    PubMed

    Liu, Jianming; Chan, Siu Hung Joshua; Brock-Nannestad, Theis; Chen, Jun; Lee, Sang Yup; Solem, Christian; Jensen, Peter Ruhdal

    2016-07-01

    Biocompatible chemistry is gaining increasing attention because of its potential within biotechnology for expanding the repertoire of biological transformations carried out by enzymes. Here we demonstrate how biocompatible chemistry can be used for synthesizing valuable compounds as well as for linking metabolic pathways to achieve redox balance and rescued growth. By comprehensive rerouting of metabolism, activation of respiration, and finally metal ion catalysis, we successfully managed to convert the homolactic bacterium Lactococcus lactis into a homo-diacetyl producer with high titer (95mM or 8.2g/L) and high yield (87% of the theoretical maximum). Subsequently, the pathway was extended to (S,S)-2,3-butanediol (S-BDO) through efficiently linking two metabolic pathways via chemical catalysis. This resulted in efficient homo-S-BDO production with a titer of 74mM (6.7g/L) S-BDO and a yield of 82%. The diacetyl and S-BDO production rates and yields obtained are the highest ever reported, demonstrating the promising combination of metabolic engineering and biocompatible chemistry as well as the great potential of L. lactis as a new production platform. PMID:26969254

  7. Using an innovative combination of quality-by-design and green analytical chemistry approaches for the development of a stability indicating UHPLC method in pharmaceutical products.

    PubMed

    Boussès, Christine; Ferey, Ludivine; Vedrines, Elodie; Gaudin, Karen

    2015-11-10

    An innovative combination of green chemistry and quality by design (QbD) approach is presented through the development of an UHPLC method for the analysis of the main degradation products of dextromethorphan hydrobromide. QbD strategy was integrated to the field of green analytical chemistry to improve method understanding while assuring quality and minimizing environmental impacts, and analyst exposure. This analytical method was thoroughly evaluated by applying risk assessment and multivariate analysis tools. After a scouting phase aimed at selecting a suitable stationary phase and an organic solvent in accordance with green chemistry principles, quality risk assessment tools were applied to determine the critical process parameters (CPPs). The effects of the CPPs on critical quality attributes (CQAs), i.e., resolutions, efficiencies, and solvent consumption were further evaluated by means of a screening design. A response surface methodology was then carried out to model CQAs as function of the selected CPPs and the optimal separation conditions were determined through a desirability analysis. Resulting contour plots enabled to establish the design space (DS) (method operable design region) where all CQAs fulfilled the requirements. An experimental validation of the DS proved that quality within the DS was guaranteed; therefore no more robustness study was required before the validation. Finally, this UHPLC method was validated using the concept of total error and was used to analyze a pharmaceutical drug product.

  8. Combining metabolic engineering and biocompatible chemistry for high-yield production of homo-diacetyl and homo-(S,S)-2,3-butanediol.

    PubMed

    Liu, Jianming; Chan, Siu Hung Joshua; Brock-Nannestad, Theis; Chen, Jun; Lee, Sang Yup; Solem, Christian; Jensen, Peter Ruhdal

    2016-07-01

    Biocompatible chemistry is gaining increasing attention because of its potential within biotechnology for expanding the repertoire of biological transformations carried out by enzymes. Here we demonstrate how biocompatible chemistry can be used for synthesizing valuable compounds as well as for linking metabolic pathways to achieve redox balance and rescued growth. By comprehensive rerouting of metabolism, activation of respiration, and finally metal ion catalysis, we successfully managed to convert the homolactic bacterium Lactococcus lactis into a homo-diacetyl producer with high titer (95mM or 8.2g/L) and high yield (87% of the theoretical maximum). Subsequently, the pathway was extended to (S,S)-2,3-butanediol (S-BDO) through efficiently linking two metabolic pathways via chemical catalysis. This resulted in efficient homo-S-BDO production with a titer of 74mM (6.7g/L) S-BDO and a yield of 82%. The diacetyl and S-BDO production rates and yields obtained are the highest ever reported, demonstrating the promising combination of metabolic engineering and biocompatible chemistry as well as the great potential of L. lactis as a new production platform.

  9. Computational chemistry study of the environmentally important acid-catalyzed hydrolysis of atrazine and related 2-chloro-s-triazines.

    PubMed

    Sawunyama, Phillip; Bailey, George W

    2002-08-01

    Many chlorine-containing pesticides, for example 2-chloro-s-triazines, are of great concern both environmentally and toxicologically. As a result, ascertaining or predicting the fate and transport of these compounds in soils and water is of current interest. Transformation pathways for 2-chloro-s-triazines in the environment include dealkylation, dechlorination (hydrolysis), and ring cleavage. This study explored the feasibility of using computational chemistry, specifically the hybrid density functional theory method, B3LYP, to predict hydrolysis trends of atrazine (2-chloro-N4-ethyl-N6-isopropyl-1,3,5-triazine-2,4-diamine) and related 2-chloro-s-triazines to the corresponding 2-hydroxy-s-triazines. Gas-phase energetics are described on the basis of calculations performed at the B3LYP/6-311++G(d,p)//B3LYP/6-31G* level of theory. Calculated free energies of hydrolysis (delta h G298) are nearly the same for simazine (2-chloro-N4,N6-diethyl-1,3,5-triazine-2,4-diamine), atrazine, and propazine (2-chloro-N4,N6-di-isopropyl-1,3,5-triazine-2,4-diamine), suggesting that hydrolysis is not significantly affected by the side-chain amine-nitrogen alkyl substituents. High-energy barriers also suggest that the reactions are not likely to be observed in the gas phase. Aqueous solvation effects were examined by means of self-consistent reaction field methods (SCRF). Molecular structures were optimized at the B3LYP/6-31G* level using the Onsager model, and solvation energies were calculated at the B3LYP/6-311++G(d,p) level using the isodensity surface polarizable continuum model (IPCM). Although the extent of solvent stabilization was greater for cationic species than neutral ones, the full extent of solvation is underestimated, especially for the transition state structures. As a consequence, the calculated hydrolysis barrier for protonated atrazine is exaggerated compared with the experimentally determined one. Overall, the hydrolysis reactions follow a concerted nucleophilic

  10. Computational Analysis for Rocket-Based Combined-Cycle Systems During Rocket-Only Operation

    NASA Technical Reports Server (NTRS)

    Steffen, C. J., Jr.; Smith, T. D.; Yungster, S.; Keller, D. J.

    2000-01-01

    A series of Reynolds-averaged Navier-Stokes calculations were employed to study the performance of rocket-based combined-cycle systems operating in an all-rocket mode. This parametric series of calculations were executed within a statistical framework, commonly known as design of experiments. The parametric design space included four geometric and two flowfield variables set at three levels each, for a total of 729 possible combinations. A D-optimal design strategy was selected. It required that only 36 separate computational fluid dynamics (CFD) solutions be performed to develop a full response surface model, which quantified the linear, bilinear, and curvilinear effects of the six experimental variables. The axisymmetric, Reynolds-averaged Navier-Stokes simulations were executed with the NPARC v3.0 code. The response used in the statistical analysis was created from Isp efficiency data integrated from the 36 CFD simulations. The influence of turbulence modeling was analyzed by using both one- and two-equation models. Careful attention was also given to quantify the influence of mesh dependence, iterative convergence, and artificial viscosity upon the resulting statistical model. Thirteen statistically significant effects were observed to have an influence on rocket-based combined-cycle nozzle performance. It was apparent that the free-expansion process, directly downstream of the rocket nozzle, can influence the Isp efficiency. Numerical schlieren images and particle traces have been used to further understand the physical phenomena behind several of the statistically significant results.

  11. Subject combination and electrode selection in cooperative brain-computer interface based on event related potentials.

    PubMed

    Cecotti, Hubert; Rivet, Bertrand

    2014-01-01

    New paradigms are required in Brain-Computer Interface (BCI) systems for the needs and expectations of healthy people. To solve this issue, we explore the emerging field of cooperative BCIs, which involves several users in a single BCI system. Contrary to classical BCIs that are dependent on the unique subject's will, cooperative BCIs are used for problem solving tasks where several people shall be engaged by sharing a common goal. Similarly as combining trials over time improves performance, combining trials across subjects can significantly improve performance compared with when only a single user is involved. Yet, cooperative BCIs may only be used in particular settings, and new paradigms must be proposed to efficiently use this approach. The possible benefits of using several subjects are addressed, and compared with current single-subject BCI paradigms. To show the advantages of a cooperative BCI, we evaluate the performance of combining decisions across subjects with data from an event-related potentials (ERP) based experiment where each subject observed the same sequence of visual stimuli. Furthermore, we show that it is possible to achieve a mean AUC superior to 0.95 with 10 subjects and 3 electrodes on each subject, or with 4 subjects and 6 electrodes on each subject. Several emerging challenges and possible applications are proposed to highlight how cooperative BCIs could be efficiently used with current technologies and leverage BCI applications. PMID:24961765

  12. Computer simulation of combine harvesting and handling of sugar cane in Barbados

    SciTech Connect

    Harvey, W.O.

    1983-01-01

    The broad objective of this study was to improve the efficiency of combine harvesting of sugar cane in Barbados. The harvesting process was broken down into two subsystems: a field subsystem and a factory yard subsystem. Two computer simulation models structured in GASP IV simulation language, were developed to model the operations involved in these systems. Model FIELDOP simulated the activities involved in the harvesting and loading of cane in the field, and in its transportation to the factory for processing. Model FACYARD simulated the weighing and unloading activities performed on cane transport units at the factory. Output from the models included utilization factors for the various component machines, daily cane delivery from the field system, and daily amounts of cane handled by the factory yard system. This output was fed into a cost program which calculated unit harvesting costs and total annual cane delivery for the equipment combinations simulated. Results indicated that a second scale at the factory can reduce the factory residence time of transport units by 88%, increase combine harvester utilization efficiency by 50-60%, increase daily cane receipts at the factory by more than 30%, and eliminate milling lost time due to lack of cane. The economic analysis demonstrated that harvesting cost per tonne can be significantly reduced.

  13. Subject Combination and Electrode Selection in Cooperative Brain-Computer Interface Based on Event Related Potentials

    PubMed Central

    Cecotti, Hubert; Rivet, Bertrand

    2014-01-01

    New paradigms are required in Brain-Computer Interface (BCI) systems for the needs and expectations of healthy people. To solve this issue, we explore the emerging field of cooperative BCIs, which involves several users in a single BCI system. Contrary to classical BCIs that are dependent on the unique subject’s will, cooperative BCIs are used for problem solving tasks where several people shall be engaged by sharing a common goal. Similarly as combining trials over time improves performance, combining trials across subjects can significantly improve performance compared with when only a single user is involved. Yet, cooperative BCIs may only be used in particular settings, and new paradigms must be proposed to efficiently use this approach. The possible benefits of using several subjects are addressed, and compared with current single-subject BCI paradigms. To show the advantages of a cooperative BCI, we evaluate the performance of combining decisions across subjects with data from an event-related potentials (ERP) based experiment where each subject observed the same sequence of visual stimuli. Furthermore, we show that it is possible to achieve a mean AUC superior to 0.95 with 10 subjects and 3 electrodes on each subject, or with 4 subjects and 6 electrodes on each subject. Several emerging challenges and possible applications are proposed to highlight how cooperative BCIs could be efficiently used with current technologies and leverage BCI applications. PMID:24961765

  14. Evaluation of control strategies for different smart window combinations using computer simulations

    SciTech Connect

    Jonsson, Andreas; Roos, Arne

    2010-01-15

    Several studies have shown that the use of switchable windows could lower the energy consumption of buildings. Since the main function of windows is to provide daylight and visual contact with the external world, high visible transmittance is needed. From an energy perspective it is always best to have the windows in their low-transparent state whenever there are cooling needs, but this is generally not preferable from a daylight and visual contact point of view. Therefore a control system, which can be based on user presence, is needed in connection with switchable windows. In this study the heating and cooling needs of the building, using different control mechanisms were evaluated. This was done for different locations and for different combinations of switchable windows, using electrochromic glazing in combination with either low-e or solar control glazing. Four control mechanisms were investigated; one that only optimizes the window to lower the need for heating and cooling, one that assumes that the office is in use during the daytime, one based on user presence and one limiting the perpendicular component of the incident solar irradiation to avoid glare and too strong daylight. The control mechanisms were compared using computer simulations. A simplified approach based on the balance temperature concept was used instead of performing complete building simulations. The results show that an occupancy-based control system is clearly beneficial and also that the best way to combine the panes in the switchable window differs depending on the balance temperature of the building and on the climate. It is also shown that it can be beneficial to have different window combinations for different orientations. (author)

  15. A combined computational and structural model of the full-length human prolactin receptor

    NASA Astrophysics Data System (ADS)

    Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

    2016-05-01

    The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg.

  16. Obtaining a linear combination of the principal components of a matrix on quantum computers

    NASA Astrophysics Data System (ADS)

    Daskin, Ammar

    2016-10-01

    Principal component analysis is a multivariate statistical method frequently used in science and engineering to reduce the dimension of a problem or extract the most significant features from a dataset. In this paper, using a similar notion to the quantum counting, we show how to apply the amplitude amplification together with the phase estimation algorithm to an operator in order to procure the eigenvectors of the operator associated to the eigenvalues defined in the range [ a, b] , where a and b are real and 0 ≤ a ≤ b ≤ 1. This makes possible to obtain a combination of the eigenvectors associated with the largest eigenvalues and so can be used to do principal component analysis on quantum computers.

  17. Rational modification of estrogen receptor by combination of computational and experimental analysis.

    PubMed

    Ferrero, Valentina Elisabetta Viviana; Pedotti, Mattia; Chiadò, Alessandro; Simonelli, Luca; Calzolai, Luigi; Varani, Luca; Lettieri, Teresa

    2014-01-01

    In this manuscript, we modulate the binding properties of estrogen receptor protein by rationally modifying the amino acid composition of its ligand binding domain. By combining sequence alignment and structural analysis of known estrogen receptor-ligand complexes with computational analysis, we were able to predict estrogen receptor mutants with altered binding properties. These predictions were experimentally confirmed by producing single point variants with up to an order of magnitude increased binding affinity towards some estrogen disrupting chemicals and reaching an half maximal inhibitory concentration (IC50) value of 2 nM for the 17α-ethinylestradiol ligand. Due to increased affinity and stability, utilizing such mutated estrogen receptor instead of the wild type as bio-recognition element would be beneficial in an assay or biosensor.

  18. A combined computational and structural model of the full-length human prolactin receptor

    PubMed Central

    Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

    2016-01-01

    The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg. PMID:27174498

  19. Obtaining a linear combination of the principal components of a matrix on quantum computers

    NASA Astrophysics Data System (ADS)

    Daskin, Ammar

    2016-07-01

    Principal component analysis is a multivariate statistical method frequently used in science and engineering to reduce the dimension of a problem or extract the most significant features from a dataset. In this paper, using a similar notion to the quantum counting, we show how to apply the amplitude amplification together with the phase estimation algorithm to an operator in order to procure the eigenvectors of the operator associated to the eigenvalues defined in the range [ a, b] , where a and b are real and 0 ≤ a ≤ b ≤ 1 . This makes possible to obtain a combination of the eigenvectors associated with the largest eigenvalues and so can be used to do principal component analysis on quantum computers.

  20. Dispatching packets on a global combining network of a parallel computer

    DOEpatents

    Almasi, Gheorghe; Archer, Charles J.

    2011-07-19

    Methods, apparatus, and products are disclosed for dispatching packets on a global combining network of a parallel computer comprising a plurality of nodes connected for data communications using the network capable of performing collective operations and point to point operations that include: receiving, by an origin system messaging module on an origin node from an origin application messaging module on the origin node, a storage identifier and an operation identifier, the storage identifier specifying storage containing an application message for transmission to a target node, and the operation identifier specifying a message passing operation; packetizing, by the origin system messaging module, the application message into network packets for transmission to the target node, each network packet specifying the operation identifier and an operation type for the message passing operation specified by the operation identifier; and transmitting, by the origin system messaging module, the network packets to the target node.

  1. Rational modification of estrogen receptor by combination of computational and experimental analysis.

    PubMed

    Ferrero, Valentina Elisabetta Viviana; Pedotti, Mattia; Chiadò, Alessandro; Simonelli, Luca; Calzolai, Luigi; Varani, Luca; Lettieri, Teresa

    2014-01-01

    In this manuscript, we modulate the binding properties of estrogen receptor protein by rationally modifying the amino acid composition of its ligand binding domain. By combining sequence alignment and structural analysis of known estrogen receptor-ligand complexes with computational analysis, we were able to predict estrogen receptor mutants with altered binding properties. These predictions were experimentally confirmed by producing single point variants with up to an order of magnitude increased binding affinity towards some estrogen disrupting chemicals and reaching an half maximal inhibitory concentration (IC50) value of 2 nM for the 17α-ethinylestradiol ligand. Due to increased affinity and stability, utilizing such mutated estrogen receptor instead of the wild type as bio-recognition element would be beneficial in an assay or biosensor. PMID:25075862

  2. Dynamic Inlet Distortion Prediction with a Combined Computational Fluid Dynamics and Distortion Synthesis Approach

    NASA Technical Reports Server (NTRS)

    Norby, W. P.; Ladd, J. A.; Yuhas, A. J.

    1996-01-01

    A procedure has been developed for predicting peak dynamic inlet distortion. This procedure combines Computational Fluid Dynamics (CFD) and distortion synthesis analysis to obtain a prediction of peak dynamic distortion intensity and the associated instantaneous total pressure pattern. A prediction of the steady state total pressure pattern at the Aerodynamic Interface Plane is first obtained using an appropriate CFD flow solver. A corresponding inlet turbulence pattern is obtained from the CFD solution via a correlation linking root mean square (RMS) inlet turbulence to a formulation of several CFD parameters representative of flow turbulence intensity. This correlation was derived using flight data obtained from the NASA High Alpha Research Vehicle flight test program and several CFD solutions at conditions matching the flight test data. A distortion synthesis analysis is then performed on the predicted steady state total pressure and RMS turbulence patterns to yield a predicted value of dynamic distortion intensity and the associated instantaneous total pressure pattern.

  3. On a 3-D singularity element for computation of combined mode stress intensities

    NASA Technical Reports Server (NTRS)

    Atluri, S. N.; Kathiresan, K.

    1976-01-01

    A special three-dimensional singularity element is developed for the computation of combined modes 1, 2, and 3 stress intensity factors, which vary along an arbitrarily curved crack front in three dimensional linear elastic fracture problems. The finite element method is based on a displacement-hybrid finite element model, based on a modified variational principle of potential energy, with arbitrary element interior displacements, interelement boundary displacements, and element boundary tractions as variables. The special crack-front element used in this analysis contains the square root singularity in strains and stresses, where the stress-intensity factors K(1), K(2), and K(3) are quadratically variable along the crack front and are solved directly along with the unknown nodal displacements.

  4. A combined computational and structural model of the full-length human prolactin receptor.

    PubMed

    Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W; Hopper, Jonathan T S; Robinson, Carol V; Olsen, Johan G; Lindorff-Larsen, Kresten; Kragelund, Birthe B

    2016-01-01

    The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg.

  5. Acidity of the amidoxime functional group in aqueous solution. A combined experimental and computational study

    DOE PAGES

    Mehio, Nada; Lashely, Mark A.; Nugent, Joseph W.; Tucker, Lyndsay; Correia, Bruna; Do-Thanh, Chi-Linh; Dai, Sheng; Hancock, Robert D.; Bryantsev, Vyacheslav S.

    2015-01-26

    Poly(acrylamidoxime) adsorbents are often invoked in discussions of mining uranium from seawater. It has been demonstrated repeatedly in the literature that the success of these materials is due to the amidoxime functional group. While the amidoxime-uranyl chelation mode has been established, a number of essential binding constants remain unclear. This is largely due to the wide range of conflicting pKa values that have been reported for the amidoxime functional group in the literature. To resolve this existing controversy we investigated the pKa values of the amidoxime functional group using a combination of experimental and computational methods. Experimentally, we used spectroscopicmore » titrations to measure the pKa values of representative amidoximes, acetamidoxime and benzamidoxime. Computationally, we report on the performance of several protocols for predicting the pKa values of aqueous oxoacids. Calculations carried out at the MP2 or M06-2X levels of theory combined with solvent effects calculated using the SMD model provide the best overall performance with a mean absolute error of 0.33 pKa units and 0.35 pKa units, respectively, and a root mean square deviation of 0.46 pKa units and 0.45 pKa units, respectively. Finally, we employ our two best methods to predict the pKa values of promising, uncharacterized amidoxime ligands. Hence, our study provides a convenient means for screening suitable amidoxime monomers for future generations of poly(acrylamidoxime) adsorbents used to mine uranium from seawater.« less

  6. Acidity of the amidoxime functional group in aqueous solution. A combined experimental and computational study

    SciTech Connect

    Mehio, Nada; Lashely, Mark A.; Nugent, Joseph W.; Tucker, Lyndsay; Correia, Bruna; Do-Thanh, Chi-Linh; Dai, Sheng; Hancock, Robert D.; Bryantsev, Vyacheslav S.

    2015-01-26

    Poly(acrylamidoxime) adsorbents are often invoked in discussions of mining uranium from seawater. It has been demonstrated repeatedly in the literature that the success of these materials is due to the amidoxime functional group. While the amidoxime-uranyl chelation mode has been established, a number of essential binding constants remain unclear. This is largely due to the wide range of conflicting pKa values that have been reported for the amidoxime functional group in the literature. To resolve this existing controversy we investigated the pKa values of the amidoxime functional group using a combination of experimental and computational methods. Experimentally, we used spectroscopic titrations to measure the pKa values of representative amidoximes, acetamidoxime and benzamidoxime. Computationally, we report on the performance of several protocols for predicting the pKa values of aqueous oxoacids. Calculations carried out at the MP2 or M06-2X levels of theory combined with solvent effects calculated using the SMD model provide the best overall performance with a mean absolute error of 0.33 pKa units and 0.35 pKa units, respectively, and a root mean square deviation of 0.46 pKa units and 0.45 pKa units, respectively. Finally, we employ our two best methods to predict the pKa values of promising, uncharacterized amidoxime ligands. Hence, our study provides a convenient means for screening suitable amidoxime monomers for future generations of poly(acrylamidoxime) adsorbents used to mine uranium from seawater.

  7. Computational modeling of epileptiform activities in medial temporal lobe epilepsy combined with in vitro experiments.

    PubMed

    Ahn, Sora; Jun, Sang Beom; Lee, Hyang Woon; Lee, Seungjun

    2016-10-01

    In this paper, we propose a comprehensive computational model that is able to reproduce three epileptiform activities. The model targets a hippocampal formation that is known to be an important lesion in medial temporal lobe epilepsy. It consists of four sub-networks consisting of excitatory and inhibitory neurons and well-known signal pathways, with consideration of propagation delay. The three epileptiform activities involve fast and slow interictal discharge and ictal discharge, and those activities can be induced in vitro by application of 4-Aminopyridine in entorhinal cortex combined hippocampal slices. We model the three epileptiform activities upon previously reported biological mechanisms and verify the simulation results by comparing them with in vitro experimental data obtained using a microelectrode array. We use the results of Granger causality analysis of recorded data to set input gains of signal pathways in the model, so that the compatibility between the computational and experimental models can be improved. The proposed model can be expanded to evaluate the suppression effect of epileptiform activities due to new treatment methods. PMID:27416961

  8. Type-2 fuzzy set extension of DEMATEL method combined with perceptual computing for decision making

    NASA Astrophysics Data System (ADS)

    Hosseini, Mitra Bokaei; Tarokh, Mohammad Jafar

    2013-05-01

    Most decision making methods used to evaluate a system or demonstrate the weak and strength points are based on fuzzy sets and evaluate the criteria with words that are modeled with fuzzy sets. The ambiguity and vagueness of the words and different perceptions of a word are not considered in these methods. For this reason, the decision making methods that consider the perceptions of decision makers are desirable. Perceptual computing is a subjective judgment method that considers that words mean different things to different people. This method models words with interval type-2 fuzzy sets that consider the uncertainty of the words. Also, there are interrelations and dependency between the decision making criteria in the real world; therefore, using decision making methods that cannot consider these relations is not feasible in some situations. The Decision-Making Trail and Evaluation Laboratory (DEMATEL) method considers the interrelations between decision making criteria. The current study used the combination of DEMATEL and perceptual computing in order to improve the decision making methods. For this reason, the fuzzy DEMATEL method was extended into type-2 fuzzy sets in order to obtain the weights of dependent criteria based on the words. The application of the proposed method is presented for knowledge management evaluation criteria.

  9. Boolean Combinations of Implicit Functions for Model Clipping in Computer-Assisted Surgical Planning

    PubMed Central

    2016-01-01

    This paper proposes an interactive method of model clipping for computer-assisted surgical planning. The model is separated by a data filter that is defined by the implicit function of the clipping path. Being interactive to surgeons, the clipping path that is composed of the plane widgets can be manually repositioned along the desirable presurgical path, which means that surgeons can produce any accurate shape of the clipped model. The implicit function is acquired through a recursive algorithm based on the Boolean combinations (including Boolean union and Boolean intersection) of a series of plane widgets’ implicit functions. The algorithm is evaluated as highly efficient because the best time performance of the algorithm is linear, which applies to most of the cases in the computer-assisted surgical planning. Based on the above stated algorithm, a user-friendly module named SmartModelClip is developed on the basis of Slicer platform and VTK. A number of arbitrary clipping paths have been tested. Experimental results of presurgical planning for three types of Le Fort fractures and for tumor removal demonstrate the high reliability and efficiency of our recursive algorithm and robustness of the module. PMID:26751685

  10. Boolean Combinations of Implicit Functions for Model Clipping in Computer-Assisted Surgical Planning.

    PubMed

    Zhan, Qiqin; Chen, Xiaojun

    2016-01-01

    This paper proposes an interactive method of model clipping for computer-assisted surgical planning. The model is separated by a data filter that is defined by the implicit function of the clipping path. Being interactive to surgeons, the clipping path that is composed of the plane widgets can be manually repositioned along the desirable presurgical path, which means that surgeons can produce any accurate shape of the clipped model. The implicit function is acquired through a recursive algorithm based on the Boolean combinations (including Boolean union and Boolean intersection) of a series of plane widgets' implicit functions. The algorithm is evaluated as highly efficient because the best time performance of the algorithm is linear, which applies to most of the cases in the computer-assisted surgical planning. Based on the above stated algorithm, a user-friendly module named SmartModelClip is developed on the basis of Slicer platform and VTK. A number of arbitrary clipping paths have been tested. Experimental results of presurgical planning for three types of Le Fort fractures and for tumor removal demonstrate the high reliability and efficiency of our recursive algorithm and robustness of the module.

  11. Increasing chemical space coverage by combining empirical and computational fragment screens.

    PubMed

    Barelier, Sarah; Eidam, Oliv; Fish, Inbar; Hollander, Johan; Figaroa, Francis; Nachane, Ruta; Irwin, John J; Shoichet, Brian K; Siegal, Gregg

    2014-07-18

    Most libraries for fragment-based drug discovery are restricted to 1,000-10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources. PMID:24807704

  12. Combined micro computed tomography and histology study of bone augmentation and distraction osteogenesis

    NASA Astrophysics Data System (ADS)

    Ilgenstein, Bernd; Deyhle, Hans; Jaquiery, Claude; Kunz, Christoph; Stalder, Anja; Stübinger, Stefan; Jundt, Gernot; Beckmann, Felix; Müller, Bert; Hieber, Simone E.

    2012-10-01

    Bone augmentation is a vital part of surgical interventions of the oral and maxillofacial area including dental implantology. Prior to implant placement, sufficient bone volume is needed to reduce the risk of peri-implantitis. While augmentation using harvested autologous bone is still considered as gold standard, many surgeons prefer bone substitutes to reduce operation time and to avoid donor site morbidity. To assess the osteogenic efficacy of commercially available augmentation materials we analyzed drill cores extracted before implant insertion. In younger patients, distraction osteogenesis is successfully applied to correct craniofacial deformities through targeted bone formation. To study the influence of mesenchymal stem cells on bone regeneration during distraction osteogenesis, human mesenchymal stem cells were injected into the distraction gap of nude rat mandibles immediately after osteotomy. The distraction was performed over eleven days to reach a distraction gap of 6 mm. Both the rat mandibles and the drill cores were scanned using synchrotron radiation-based micro computed tomography. The three-dimensional data were manually registered and compared with corresponding two-dimensional histological sections to assess bone regeneration and its morphology. The analysis of the rat mandibles indicates that bone formation is enhanced by mesenchymal stem cells injected before distraction. The bone substitutes yielded a wide range of bone volume and degree of resorption. The volume fraction of the newly formed bone was determined to 34.4% in the computed tomography dataset for the augmentation material Geistlich Bio-Oss®. The combination of computed tomography and histology allowed a complementary assessment for both bone augmentation and distraction osteogenesis.

  13. 5 CFR 591.221 - How does OPM compute the consumer expenditure weights it uses to combine price indexes?

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... expenditure weights it uses to combine price indexes? 591.221 Section 591.221 Administrative Personnel OFFICE... the consumer expenditure weights it uses to combine price indexes? OPM uses the following ten-step... aggregation. (f) Step 6. OPM computes a set of ratios by dividing each expenditure share of the...

  14. 5 CFR 591.221 - How does OPM compute the consumer expenditure weights it uses to combine price indexes?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... the consumer expenditure weights it uses to combine price indexes? OPM uses the following ten-step... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false How does OPM compute the consumer expenditure weights it uses to combine price indexes? 591.221 Section 591.221 Administrative Personnel...

  15. COMPUTATIONAL CHEMISTRY METHOD FOR PREDICTING VAPOR PRESSURES AND ACTIVITY COEFFICIENTS OF POLAR ORGANIC OXYGENATES IN PM2.5

    EPA Science Inventory

    Parameterizations of interactions of polar multifunctional organic oxygenates in PM2.5 must be included in aerosol chemistry models for evaluating control strategies for reducing ambient concentrations of PM2.5 compounds. Vapor pressures and activity coefficients of these compo...

  16. A Study of the Relationship between Reading, Computational, and Critical Thinking Skills and Academic Success in Fundamentals of Chemistry.

    ERIC Educational Resources Information Center

    Hurov, Janet Torrisi

    In spring 1987, a study was conducted at St. Louis Community College at Florissant Valley (Missouri) to identify the basic skills necessary for the successful completion of the course, "Fundamentals of Chemistry." The study evaluated the relationship between performance on the Nelson-Denny Reading Test (NDRT), the Numerical Reasoning subtest of…

  17. Computational assessment of combinations of gait modifications for knee osteoarthritis rehabilitation.

    PubMed

    Fregly, Benjamin J

    2008-08-01

    Gait modification is a noninvasive strategy for reducing the external knee adduction torque in patients with medial compartment knee osteoarthritis. Recently, a novel "medial thrust" gait pattern characterized by knee medialization during stance phase has been shown to reduce both adduction torque peaks significantly. While changes in footpath (i.e., toe out angle and stance width) also affect the adduction torque peaks, the extent to which footpath changes may alter the effectiveness of medial thrust gait is unknown. This study used a validated patient-specific computational model to investigate this issue. A dynamic optimization framework that accurately predicted adduction torque changes caused by knee medialization or footpath alteration for a specific patient was modified to predict the simultaneous effect of both factors. Medial thrust gait optimizations were then performed for the same patient using imposed footpath alterations consisting of all possible combinations of three toe out angles (nominal +/- 15 degrees) and three stance widths (nominal +/- 50 mm). Overall, predicted adduction torque reductions produced by medial thrust gait were relatively insensitive to footpath alterations. The 32%-34% reduction in both peaks achieved with the nominal footpath was augmented by at most 9% and reduced by at most 3% for the altered footpaths. When combined with knee medialization, footpath alterations would likely have only a secondary effect on knee adduction torque reductions for this particular patient.

  18. Combining Geometric and Probabilistic Reasoning for Computer-based Penetrating-Trauma Assessment

    PubMed Central

    Ogunyemi, Omolola I.; Clarke, John R.; Ash, Nachman; Webber, Bonnie L.

    2002-01-01

    Objective: To ascertain whether three-dimensional geometric and probabilistic reasoning methods can be successfully combined for computer-based assessment of conditions arising from ballistic penetrating trauma to the chest and abdomen. Design: The authors created a computer system (TraumaSCAN) that integrates three-dimensional geometric reasoning about anatomic likelihood of injury with probabilistic reasoning about injury consequences using Bayesian networks. Preliminary evaluation of TraumaSCAN was performed via a retrospective study testing performance of the system on data from 26 cases of actual gunshot wounds. Measurements: Areas under the receiver operating characteristics (ROC) curve were calculated for each condition modeled in TraumaSCAN that was present in the 26 cases. The comprehensiveness and relevance of the TraumaSCAN diagnosis for the 26 cases were used to assess the overall performance of the system. To test the ability of TraumaSCAN to handle limited findings, these measurements were calculated both with and without input of observed findings into the Bayesian network. Results: For the 11 conditions assessed, the worst area under the ROC curve with no observed findings input into the Bayesian network was 0.542 (95% CI, 0.146–0.937), the median was 0.883 (95% CI, 0.713–1.000), and the best was 1.00 (95% CI, 1.000–1.000). The worst area under the ROC curve with all observed findings input into the Bayesian network was 0.835 (95% CI, 0.602–1.000), the median was 0.941 (95% CI, 0.827–1.000), and the best was 0.992 (95% CI, 0.965–1.000). A comparison of the areas under the curve obtained with and without input of observed findings into the Bayesian network showed that there were significant differences for 2 of the 11 conditions assessed. Conclusion: A computer-based method that combines geometric and probabilistic reasoning shows promise as a tool for assessing ballistic penetrating trauma to the chest and abdomen. PMID:11971888

  19. Mass Spectrometric Analysis of the Cell Surface N-Glycoproteome by Combining Metabolic Labeling and Click Chemistry

    NASA Astrophysics Data System (ADS)

    Smeekens, Johanna M.; Chen, Weixuan; Wu, Ronghu

    2015-04-01

    Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide- N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

  20. Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry.

    PubMed

    Smeekens, Johanna M; Chen, Weixuan; Wu, Ronghu

    2015-04-01

    Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide-N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

  1. High-resolution combined global gravity field modelling: Solving large kite systems using distributed computational algorithms

    NASA Astrophysics Data System (ADS)

    Zingerle, Philipp; Fecher, Thomas; Pail, Roland; Gruber, Thomas

    2016-04-01

    One of the major obstacles in modern global gravity field modelling is the seamless combination of lower degree inhomogeneous gravity field observations (e.g. data from satellite missions) with (very) high degree homogeneous information (e.g. gridded and reduced gravity anomalies, beyond d/o 1000). Actual approaches mostly combine such data only on the basis of the coefficients, meaning that previously for both observation classes (resp. models) a spherical harmonic analysis is done independently, solving dense normal equations (NEQ) for the inhomogeneous model and block-diagonal NEQs for the homogeneous. Obviously those methods are unable to identify or eliminate effects as spectral leakage due to band limitations of the models and non-orthogonality of the spherical harmonic base functions. To antagonize such problems a combination of both models on NEQ-basis is desirable. Theoretically this can be achieved using NEQ-stacking. Because of the higher maximum degree of the homogeneous model a reordering of the coefficient is needed which leads inevitably to the destruction of the block diagonal structure of the appropriate NEQ-matrix and therefore also to the destruction of simple sparsity. Hence, a special coefficient ordering is needed to create some new favorable sparsity pattern leading to a later efficient computational solving method. Such pattern can be found in the so called kite-structure (Bosch, 1993), achieving when applying the kite-ordering to the stacked NEQ-matrix. In a first step it is shown what is needed to attain the kite-(NEQ)system, how to solve it efficiently and also how to calculate the appropriate variance information from it. Further, because of the massive computational workload when operating on large kite-systems (theoretically possible up to about max. d/o 100.000), the main emphasis is put on to the presentation of special distributed algorithms which may solve those systems parallel on an indeterminate number of processes and are

  2. Computational Fluid Dynamics Analysis Method Developed for Rocket-Based Combined Cycle Engine Inlet

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Renewed interest in hypersonic propulsion systems has led to research programs investigating combined cycle engines that are designed to operate efficiently across the flight regime. The Rocket-Based Combined Cycle Engine is a propulsion system under development at the NASA Lewis Research Center. This engine integrates a high specific impulse, low thrust-to-weight, airbreathing engine with a low-impulse, high thrust-to-weight rocket. From takeoff to Mach 2.5, the engine operates as an air-augmented rocket. At Mach 2.5, the engine becomes a dual-mode ramjet; and beyond Mach 8, the rocket is turned back on. One Rocket-Based Combined Cycle Engine variation known as the "Strut-Jet" concept is being investigated jointly by NASA Lewis, the U.S. Air Force, Gencorp Aerojet, General Applied Science Labs (GASL), and Lockheed Martin Corporation. Work thus far has included wind tunnel experiments and computational fluid dynamics (CFD) investigations with the NPARC code. The CFD method was initiated by modeling the geometry of the Strut-Jet with the GRIDGEN structured grid generator. Grids representing a subscale inlet model and the full-scale demonstrator geometry were constructed. These grids modeled one-half of the symmetric inlet flow path, including the precompression plate, diverter, center duct, side duct, and combustor. After the grid generation, full Navier-Stokes flow simulations were conducted with the NPARC Navier-Stokes code. The Chien low-Reynolds-number k-e turbulence model was employed to simulate the high-speed turbulent flow. Finally, the CFD solutions were postprocessed with a Fortran code. This code provided wall static pressure distributions, pitot pressure distributions, mass flow rates, and internal drag. These results were compared with experimental data from a subscale inlet test for code validation; then they were used to help evaluate the demonstrator engine net thrust.

  3. Developing advanced X-ray scattering methods combined with crystallography and computation.

    PubMed

    Perry, J Jefferson P; Tainer, John A

    2013-03-01

    The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered

  4. Developing advanced x-ray scattering methods combined with crystallography and computation

    PubMed Central

    Perry, J. Jefferson P.; Tainer, John A.

    2013-01-01

    The extensive use of small angle x-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered

  5. Heterogeneous Chemistry of Individual Mineral Dust Particles with Nitric Acid. A Combined CCSEM/EDX, ESEM AND ICP-MS Study

    SciTech Connect

    Laskin, Alexander; Wietsma, Thomas W.; Krueger, Brenda J.; Grassian, Vicki H.

    2005-05-26

    The heterogeneous chemistry of individual dust particles from four authentic dust samples with gas-phase nitric acid was investigated in this study. Morphology and compositional changes of individual particles as they react with nitric acid were observed using conventional scanning electron microscopy with energy dispersive analysis of X-rays (SEM/EDX) and computer controlled SEM/EDX. Environmental Scanning Electron Microscopy (ESEM) was utilized to investigate the hygroscopic behavior of mineral dust particles reacted with nitric acid. Differences in the reactivity of mineral dust particles from these four different dust source regions with nitric acid were observed. Mineral dust from source regions containing high levels of calcium, namely China loess dust and Saudi coastal dust, were found to react to the greatest extent.

  6. Mathematical Modeling of Complex Reaction Systems for Computer-Aided Control and its Illustration on Atmospheric Chemistry

    NASA Astrophysics Data System (ADS)

    Amiryan, A.

    2015-12-01

    Modeling of sequential process has its own importance in Atmospheric Chemistry. Numerical calculations which allow to predict separate stages and components of chemical reaction make possible the reaction management, such is the new and perspective direction in chemical researches. Chemical processes basically pass multiple simple stages where various atoms and radicals participate. The complex chain of chemical reactionary systems complicates their research and the research is impossible without new methods of mathematical simulation and high technologies which allow not only to explain results of experiments but also to predict dynamics of processes. A new program package is suggested for solving research problems of chemical kinetics. The program is tested on different illustrative examples on Atmospheric Chemistry and installed in various scientific and educational institutions.

  7. Computer-aided texture analysis combined with experts' knowledge: Improving endoscopic celiac disease diagnosis

    PubMed Central

    Gadermayr, Michael; Kogler, Hubert; Karla, Maximilian; Merhof, Dorit; Uhl, Andreas; Vécsei, Andreas

    2016-01-01

    AIM To further improve the endoscopic detection of intestinal mucosa alterations due to celiac disease (CD). METHODS We assessed a hybrid approach based on the integration of expert knowledge into the computer-based classification pipeline. A total of 2835 endoscopic images from the duodenum were recorded in 290 children using the modified immersion technique (MIT). These children underwent routine upper endoscopy for suspected CD or non-celiac upper abdominal symptoms between August 2008 and December 2014. Blinded to the clinical data and biopsy results, three medical experts visually classified each image as normal mucosa (Marsh-0) or villous atrophy (Marsh-3). The experts’ decisions were further integrated into state-of-the-art texture recognition systems. Using the biopsy results as the reference standard, the classification accuracies of this hybrid approach were compared to the experts’ diagnoses in 27 different settings. RESULTS Compared to the experts’ diagnoses, in 24 of 27 classification settings (consisting of three imaging modalities, three endoscopists and three classification approaches), the best overall classification accuracies were obtained with the new hybrid approach. In 17 of 24 classification settings, the improvements achieved with the hybrid approach were statistically significant (P < 0.05). Using the hybrid approach classification accuracies between 94% and 100% were obtained. Whereas the improvements are only moderate in the case of the most experienced expert, the results of the less experienced expert could be improved significantly in 17 out of 18 classification settings. Furthermore, the lowest classification accuracy, based on the combination of one database and one specific expert, could be improved from 80% to 95% (P < 0.001). CONCLUSION The overall classification performance of medical experts, especially less experienced experts, can be boosted significantly by integrating expert knowledge into computer-aided diagnosis

  8. Extending peripersonal space representation without tool-use: evidence from a combined behavioral-computational approach.

    PubMed

    Serino, Andrea; Canzoneri, Elisa; Marzolla, Marilena; di Pellegrino, Giuseppe; Magosso, Elisa

    2015-01-01

    Stimuli from different sensory modalities occurring on or close to the body are integrated in a multisensory representation of the space surrounding the body, i.e., peripersonal space (PPS). PPS dynamically modifies depending on experience, e.g., it extends after using a tool to reach far objects. However, the neural mechanism underlying PPS plasticity after tool use is largely unknown. Here we use a combined computational-behavioral approach to propose and test a possible mechanism accounting for PPS extension. We first present a neural network model simulating audio-tactile representation in the PPS around one hand. Simulation experiments showed that our model reproduced the main property of PPS neurons, i.e., selective multisensory response for stimuli occurring close to the hand. We used the neural network model to simulate the effects of a tool-use training. In terms of sensory inputs, tool use was conceptualized as a concurrent tactile stimulation from the hand, due to holding the tool, and an auditory stimulation from the far space, due to tool-mediated action. Results showed that after exposure to those inputs, PPS neurons responded also to multisensory stimuli far from the hand. The model thus suggests that synchronous pairing of tactile hand stimulation and auditory stimulation from the far space is sufficient to extend PPS, such as after tool-use. Such prediction was confirmed by a behavioral experiment, where we used an audio-tactile interaction paradigm to measure the boundaries of PPS representation. We found that PPS extended after synchronous tactile-hand stimulation and auditory-far stimulation in a group of healthy volunteers. Control experiments both in simulation and behavioral settings showed that the same amount of tactile and auditory inputs administered out of synchrony did not change PPS representation. We conclude by proposing a simple, biological-plausible model to explain plasticity in PPS representation after tool-use, which is

  9. Extending peripersonal space representation without tool-use: evidence from a combined behavioral-computational approach

    PubMed Central

    Serino, Andrea; Canzoneri, Elisa; Marzolla, Marilena; di Pellegrino, Giuseppe; Magosso, Elisa

    2015-01-01

    Stimuli from different sensory modalities occurring on or close to the body are integrated in a multisensory representation of the space surrounding the body, i.e., peripersonal space (PPS). PPS dynamically modifies depending on experience, e.g., it extends after using a tool to reach far objects. However, the neural mechanism underlying PPS plasticity after tool use is largely unknown. Here we use a combined computational-behavioral approach to propose and test a possible mechanism accounting for PPS extension. We first present a neural network model simulating audio-tactile representation in the PPS around one hand. Simulation experiments showed that our model reproduced the main property of PPS neurons, i.e., selective multisensory response for stimuli occurring close to the hand. We used the neural network model to simulate the effects of a tool-use training. In terms of sensory inputs, tool use was conceptualized as a concurrent tactile stimulation from the hand, due to holding the tool, and an auditory stimulation from the far space, due to tool-mediated action. Results showed that after exposure to those inputs, PPS neurons responded also to multisensory stimuli far from the hand. The model thus suggests that synchronous pairing of tactile hand stimulation and auditory stimulation from the far space is sufficient to extend PPS, such as after tool-use. Such prediction was confirmed by a behavioral experiment, where we used an audio-tactile interaction paradigm to measure the boundaries of PPS representation. We found that PPS extended after synchronous tactile-hand stimulation and auditory-far stimulation in a group of healthy volunteers. Control experiments both in simulation and behavioral settings showed that the same amount of tactile and auditory inputs administered out of synchrony did not change PPS representation. We conclude by proposing a simple, biological-plausible model to explain plasticity in PPS representation after tool-use, which is

  10. Computer-aided texture analysis combined with experts' knowledge: Improving endoscopic celiac disease diagnosis

    PubMed Central

    Gadermayr, Michael; Kogler, Hubert; Karla, Maximilian; Merhof, Dorit; Uhl, Andreas; Vécsei, Andreas

    2016-01-01

    AIM To further improve the endoscopic detection of intestinal mucosa alterations due to celiac disease (CD). METHODS We assessed a hybrid approach based on the integration of expert knowledge into the computer-based classification pipeline. A total of 2835 endoscopic images from the duodenum were recorded in 290 children using the modified immersion technique (MIT). These children underwent routine upper endoscopy for suspected CD or non-celiac upper abdominal symptoms between August 2008 and December 2014. Blinded to the clinical data and biopsy results, three medical experts visually classified each image as normal mucosa (Marsh-0) or villous atrophy (Marsh-3). The experts’ decisions were further integrated into state-of-the-art texture recognition systems. Using the biopsy results as the reference standard, the classification accuracies of this hybrid approach were compared to the experts’ diagnoses in 27 different settings. RESULTS Compared to the experts’ diagnoses, in 24 of 27 classification settings (consisting of three imaging modalities, three endoscopists and three classification approaches), the best overall classification accuracies were obtained with the new hybrid approach. In 17 of 24 classification settings, the improvements achieved with the hybrid approach were statistically significant (P < 0.05). Using the hybrid approach classification accuracies between 94% and 100% were obtained. Whereas the improvements are only moderate in the case of the most experienced expert, the results of the less experienced expert could be improved significantly in 17 out of 18 classification settings. Furthermore, the lowest classification accuracy, based on the combination of one database and one specific expert, could be improved from 80% to 95% (P < 0.001). CONCLUSION The overall classification performance of medical experts, especially less experienced experts, can be boosted significantly by integrating expert knowledge into computer-aided diagnosis

  11. Advanced fuel chemistry for advanced engines.

    SciTech Connect

    Taatjes, Craig A.; Jusinski, Leonard E.; Zador, Judit; Fernandes, Ravi X.; Miller, James A.

    2009-09-01

    Autoignition chemistry is central to predictive modeling of many advanced engine designs that combine high efficiency and low inherent pollutant emissions. This chemistry, and especially its pressure dependence, is poorly known for fuels derived from heavy petroleum and for biofuels, both of which are becoming increasingly prominent in the nation's fuel stream. We have investigated the pressure dependence of key ignition reactions for a series of molecules representative of non-traditional and alternative fuels. These investigations combined experimental characterization of hydroxyl radical production in well-controlled photolytically initiated oxidation and a hybrid modeling strategy that linked detailed quantum chemistry and computational kinetics of critical reactions with rate-equation models of the global chemical system. Comprehensive mechanisms for autoignition generally ignore the pressure dependence of branching fractions in the important alkyl + O{sub 2} reaction systems; however we have demonstrated that pressure-dependent 'formally direct' pathways persist at in-cylinder pressures.

  12. A combination strategy based brain-computer interface for two-dimensional movement control

    NASA Astrophysics Data System (ADS)

    Xia, Bin; Maysam, Oladazimi; Veser, Sandra; Cao, Lei; Li, Jie; Jia, Jie; Xie, Hong; Birbaumer, Niels

    2015-08-01

    Objective. Two-dimensional (2D) movement control is an important issue in brain-computer interfaces (BCIs) research because being able to move, for example, a cursor with the brain will enable patients with motor disabilities to control their environment. However, it is still a challenge to continuously control 2D movement with a non-invasive BCI system. In this paper, we developed a 2D cursor control with motor imagery BCI tasks allowing users to move a cursor to any position by using a combination strategy. With this strategy, a user can combine multiple motor imagery tasks, alternatively or simultaneously, to control 2D movements. Approach. After a training session, six participants took part in the first control strategy experiment (the center-out experiment) to verify the effectiveness of the cursor control. Three of the six participants performed an additional experiment, in which they were required to move the cursor to hit five targets in a given sequence. Main results. The average hit rate was more than 95.6% and the trajectories were close to the shortest path. The average hit rate was more than 95.6% and the trajectories were close to the shortest path in the center-out experiment. In the additional experiment, three participants achieved a 100% hit rate with a short trajectory. Significance. The results demonstrated that users were able to effectively control the 2D movement using the proposed strategy. The present system may be used as a tool to interact with the external world.

  13. Teachers and Students' Conceptions of Computer-Based Models in the Context of High School Chemistry: Elicitations at the Pre-intervention Stage

    NASA Astrophysics Data System (ADS)

    Waight, Noemi; Gillmeister, Kristina

    2014-04-01

    This study examined teachers' and students' initial conceptions of computer-based models—Flash and NetLogo models—and documented how teachers and students reconciled notions of multiple representations featuring macroscopic, submicroscopic and symbolic representations prior to actual intervention in eight high school chemistry classrooms. Individual in-depth interviews were conducted with 32 students and 6 teachers. Findings revealed an interplay of complex factors that functioned as opportunities and obstacles in the implementation of technologies in science classrooms. Students revealed preferences for the Flash models as opposed to the open-ended NetLogo models. Altogether, due to lack of content and modeling background knowledge, students experienced difficulties articulating coherent and blended understandings of multiple representations. Concurrently, while the aesthetic and interactive features of the models were of great value, they did not sustain students' initial curiosity and opportunities to improve understandings about chemistry phenomena. Most teachers recognized direct alignment of the Flash model with their existing curriculum; however, the benefits were relegated to existing procedural and passive classroom practices. The findings have implications for pedagogical approaches that address the implementation of computer-based models, function of models, models as multiple representations and the role of background knowledge and cognitive load, and the role of teacher vision and classroom practices.

  14. Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology.

    PubMed

    van der Kamp, Marc W; Mulholland, Adrian J

    2013-04-23

    Computational enzymology is a rapidly maturing field that is increasingly integral to understanding mechanisms of enzyme-catalyzed reactions and their practical applications. Combined quantum mechanics/molecular mechanics (QM/MM) methods are important in this field. By treating the reacting species with a quantum mechanical method (i.e., a method that calculates the electronic structure of the active site) and including the enzyme environment with simpler molecular mechanical methods, enzyme reactions can be modeled. Here, we review QM/MM methods and their application to enzyme-catalyzed reactions to investigate fundamental and practical problems in enzymology. A range of QM/MM methods is available, from cheaper and more approximate methods, which can be used for molecular dynamics simulations, to highly accurate electronic structure methods. We discuss how modeling of reactions using such methods can provide detailed insight into enzyme mechanisms and illustrate this by reviewing some recent applications. We outline some practical considerations for such simulations. Further, we highlight applications that show how QM/MM methods can contribute to the practical development and application of enzymology, e.g., in the interpretation and prediction of the effects of mutagenesis and in drug and catalyst design.

  15. A combined computational and experimental investigation of Mg doped α-Fe2O3.

    PubMed

    Kosa, Monica; Barad, Hannah Noa; Singh, Vijay; Keller, David A; Shimanovich, Klimentiy; Rühle, Sven; Anderson, Assaf Y; Zaban, Arie; Major, Dan Thomas

    2016-01-14

    In the current work, pristine α-Fe2O3 metal oxide was doped with Mg in an attempt to modulate its electronic properties. To this end, we employed an experimental high throughput strategy, including scanning XRD and optical spectroscopy, which were complimented by atomistic density functional theory (DFT) calculations. The combined study reveals that at Mg/Fe atomic ratios up to ∼1/3, the bandgaps of the hematite-Mg composite materials are similar to that of the pure material. The observed bandgaps are rationalized by electronic band structure and density of states calculations. Additional rationale for the similar bandgaps in pure and doped hematite is provided by topological Bader charge analyses, which indicate that the Mg and Fe ions in the hematite matrix have similar partial atomic charges. Nonetheless, the small charge density difference between the Mg and Fe ions induces a slight spin polarization on both oxygen and Fe ions, resulting in changes in the band edges. Further charge density analyses, using charge density maps and chemical-bonding analyses with the crystal orbital Hamiltonian population scheme, indicate that Mg forms ionic bonds with the neighboring oxygen atoms. This change from iron-oxygen covalent bonds to a more ionic nature for magnesium-oxygen bonds is probably responsible for the reduction observed in the computed bulk modulus of α-Mg(0.17)Fe(1.83)O3 (193 GPa) compared to α-Fe2O3 (202 GPa). PMID:26625981

  16. Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches.

    PubMed

    Xanthopoulos, Dimitrios; Kritsi, Eftichia; Supuran, Claudiu T; Papadopoulos, Manthos G; Leonis, Georgios; Zoumpoulakis, Panagiotis

    2016-08-01

    A combination of computational techniques and inhibition assay experiments was employed to identify hit compounds from commercial libraries with enhanced inhibitory potency against HIV type 1 aspartic protease (HIV PR). Extensive virtual screening with the aid of reliable pharmacophore models yielded five candidate protease inhibitors. Subsequent molecular dynamics and molecular mechanics Poisson-Boltzmann surface area free-energy calculations for the five ligand-HIV PR complexes suggested a high stability of the systems through hydrogen-bond interactions between the ligands and the protease's flaps (Ile50/50'), as well as interactions with residues of the active site (Asp25/25'/29/29'/30/30'). Binding-energy calculations for the three most promising compounds yielded values between -5 and -10 kcal mol(-1) and suggested that van der Waals interactions contribute most favorably to the total energy. The predicted binding-energy values were verified by in vitro inhibition assays, which showed promising results in the high nanomolar range. These results provide structural considerations that may guide further hit-to-lead optimization toward improved anti-HIV drugs. PMID:27411556

  17. Clinical experience with the first combined positron emission tomography/computed tomography scanner in Australia.

    PubMed

    Lau, W F Eddie; Binns, David S; Ware, Robert E; Ramdave, Shakher; Cachin, Florent; Pitman, Alexander G; Hicks, Rodney J

    2005-02-21

    Metabolic imaging with fluorine-18-fluorodeoxyglucose positron emission tomography (FDG-PET) is increasing rapidly worldwide because of superior accuracy compared with conventional non-invasive techniques used for evaluating cancer. Limited anatomical information from FDG-PET images alone dictates that complementary use with structural imaging is required to optimise benefit. Recently, combined positron emission tomography/computed tomography (PET/CT) scanners have overtaken standalone PET scanners as the most commonly purchased PET devices. We describe our experience of over 5500 scans performed since the first PET/CT scanner in Australia was commissioned at the Peter MacCallum Cancer Centre (PMCC), Melbourne, in January 2002. Clinical indications for PET/CT scans performed at PMCC largely reflect current Medicare reimbursement policy. Advantages of PET/CT include greater patient comfort and higher throughput, greater diagnostic certainty and accuracy, improved biopsy methods, and better treatment planning. We believe PET/CT will underpin more effective and efficient imaging paradigms for many common tumours, and lead to a decrease in imaging costs. PMID:15720173

  18. Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis

    PubMed Central

    Taffi, Marianna; Paoletti, Nicola; Angione, Claudio; Pucciarelli, Sandra; Marini, Mauro; Liò, Pietro

    2014-01-01

    The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains. In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs) in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746) with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links. The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs. PMID:25309577

  19. Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II

    NASA Astrophysics Data System (ADS)

    Wang, Qian; Christiansen, Alexander; Samiotakis, Antonios; Wittung-Stafshede, Pernilla; Cheung, Margaret S.

    2011-11-01

    Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature Tb and chemical denaturation at another temperature Tu using the stability change of a protein (ΔG). For this, we related the dependence of ΔG on temperature, in the Gibbs-Helmholtz equation, to that of ΔG on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (Tu) and the aqueous (Tb) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, Tb, and the temperature of the same structural ensemble at a specific urea concentration, Tu. The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.

  20. A combined computational and experimental investigation of Mg doped α-Fe2O3.

    PubMed

    Kosa, Monica; Barad, Hannah Noa; Singh, Vijay; Keller, David A; Shimanovich, Klimentiy; Rühle, Sven; Anderson, Assaf Y; Zaban, Arie; Major, Dan Thomas

    2016-01-14

    In the current work, pristine α-Fe2O3 metal oxide was doped with Mg in an attempt to modulate its electronic properties. To this end, we employed an experimental high throughput strategy, including scanning XRD and optical spectroscopy, which were complimented by atomistic density functional theory (DFT) calculations. The combined study reveals that at Mg/Fe atomic ratios up to ∼1/3, the bandgaps of the hematite-Mg composite materials are similar to that of the pure material. The observed bandgaps are rationalized by electronic band structure and density of states calculations. Additional rationale for the similar bandgaps in pure and doped hematite is provided by topological Bader charge analyses, which indicate that the Mg and Fe ions in the hematite matrix have similar partial atomic charges. Nonetheless, the small charge density difference between the Mg and Fe ions induces a slight spin polarization on both oxygen and Fe ions, resulting in changes in the band edges. Further charge density analyses, using charge density maps and chemical-bonding analyses with the crystal orbital Hamiltonian population scheme, indicate that Mg forms ionic bonds with the neighboring oxygen atoms. This change from iron-oxygen covalent bonds to a more ionic nature for magnesium-oxygen bonds is probably responsible for the reduction observed in the computed bulk modulus of α-Mg(0.17)Fe(1.83)O3 (193 GPa) compared to α-Fe2O3 (202 GPa).

  1. Discovery of HIV Type 1 Aspartic Protease Hit Compounds through Combined Computational Approaches.

    PubMed

    Xanthopoulos, Dimitrios; Kritsi, Eftichia; Supuran, Claudiu T; Papadopoulos, Manthos G; Leonis, Georgios; Zoumpoulakis, Panagiotis

    2016-08-01

    A combination of computational techniques and inhibition assay experiments was employed to identify hit compounds from commercial libraries with enhanced inhibitory potency against HIV type 1 aspartic protease (HIV PR). Extensive virtual screening with the aid of reliable pharmacophore models yielded five candidate protease inhibitors. Subsequent molecular dynamics and molecular mechanics Poisson-Boltzmann surface area free-energy calculations for the five ligand-HIV PR complexes suggested a high stability of the systems through hydrogen-bond interactions between the ligands and the protease's flaps (Ile50/50'), as well as interactions with residues of the active site (Asp25/25'/29/29'/30/30'). Binding-energy calculations for the three most promising compounds yielded values between -5 and -10 kcal mol(-1) and suggested that van der Waals interactions contribute most favorably to the total energy. The predicted binding-energy values were verified by in vitro inhibition assays, which showed promising results in the high nanomolar range. These results provide structural considerations that may guide further hit-to-lead optimization toward improved anti-HIV drugs.

  2. Spectroscopic Properties of Anisole at the Air-Ice Interface: A Combined Experimental-Computational Approach.

    PubMed

    Malongwe, Joseph K'Ekuboni; Nachtigallová, Dana; Corrochano, Pablo; Klán, Petr

    2016-06-14

    A combined experimental and computational approach was used to investigate the spectroscopic properties of anisole in aqueous solutions and at the ice-air interface in the temperature range of 77-298 K. The absorption, diffuse reflectance, and emission spectra of ice samples containing anisole prepared by different techniques, such as slow freezing (frozen aqueous solutions), shock freezing (ice grains), or anisole vapor deposition on ice grains, were measured to evaluate changes in the contaminated ice matrix that occur at different temperatures. It was found that the position of the lowest absorption band of anisole and its tail shift bathochromically by ∼4 nm in frozen samples compared to liquid aqueous solutions. On the other hand, the emission spectra of aqueous anisole solutions were found to fundamentally change upon freezing. While one emission band (∼290 nm) was observed under all circumstances, the second band at ∼350 nm, assigned to an anisole excimer, appeared only at certain temperatures (150-250 K). Its disappearance at lower temperatures is attributed to the formation of crystalline anisole on the ice surface. DFT and ADC(2) calculations were used to interpret the absorption and emission spectra of anisole monomer and dimer associates. Various stable arrangements of the anisole associates were found at the disordered water-air interface in the ground and excited states, but only those with a substantial overlap of the aromatic rings are manifested by the emission band at ∼350 nm. PMID:27243785

  3. Computational analysis of a rarefied hypersonic flow over combined gap/step geometries

    NASA Astrophysics Data System (ADS)

    Leite, P. H. M.; Santos, W. F. N.

    2015-06-01

    This work describes a computational analysis of a hypersonic flow over a combined gap/step configuration at zero degree angle of attack, in chemical equilibrium and thermal nonequilibrium. Effects on the flowfield structure due to changes on the step frontal-face height have been investigated by employing the Direct Simulation Monte Carlo (DSMC) method. The work focuses the attention of designers of hypersonic configurations on the fundamental parameter of surface discontinuity, which can have an important impact on even initial designs. The results highlight the sensitivity of the primary flowfield properties, velocity, density, pressure, and temperature due to changes on the step frontal-face height. The analysis showed that the upstream disturbance in the gap/step configuration increased with increasing the frontal-face height. In addition, it was observed that the separation region for the gap/step configuration increased with increasing the step frontal-face height. It was found that density and pressure for the gap/step configuration dramatically increased inside the gap as compared to those observed for the gap configuration, i. e., a gap without a step.

  4. Atomic-Scale Design of Iron Fischer-Tropsch Catalysts: A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

    SciTech Connect

    Manos Mavrikakis; James A. Dumesic; Rahul P. Nabar

    2006-09-29

    Work continued on the development of a microkinetic model of Fischer-Tropsch synthesis (FTS) on supported and unsupported Fe catalysts. The following aspects of the FT mechanism on unsupported iron catalysts were investigated on during this third year: (1) the collection of rate data in a Berty CSTR reactor based on sequential design of experiments; (2) CO adsorption and CO-TPD for obtaining the heat of adsorption of CO on polycrystalline iron; and (3) isothermal hydrogenation (IH) after Fischer Tropsch reaction to identify and quantify surface carbonaceous species. Rates of C{sub 2+} formation on unsupported iron catalysts at 220 C and 20 atm correlated well to a Langmuir-Hinshelwood type expression, derived assuming carbon hydrogenation to CH and OH recombination to water to be rate-determining steps. From desorption of molecularly adsorbed CO at different temperatures the heat of adsorption of CO on polycrystalline iron was determined to be 100 kJ/mol. Amounts and types of carbonaceous species formed after FT reaction for 5-10 minutes at 150, 175, 200 and 285 C vary significantly with temperature. Mr. Brian Critchfield completed his M.S. thesis work on a statistically designed study of the kinetics of FTS on 20% Fe/alumina. Preparation of a paper describing this work is in progress. Results of these studies were reported at the Annual Meeting of the Western States Catalysis and at the San Francisco AIChE meeting. In the coming period, studies will focus on quantitative determination of the rates of kinetically-relevant elementary steps on unsupported Fe catalysts with/without K and Pt promoters by SSITKA method. This study will help us to (1) understand effects of promoter and support on elementary kinetic parameters and (2) build a microkinetics model for FTS on iron. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on models of defected Fe surfaces, most significantly the stepped Fe(211) surface. Binding Energies (BE's), preferred adsorption sites and geometries of all the FTS relevant stable species and intermediates were evaluated. Each elementary step of our reaction model was fully characterized with respect to its thermochemistry and comparisons between the stepped Fe(211) facet and the most-stable Fe(110) facet were established. In most cases the BE's on Fe(211) reflected the trends observed earlier on Fe(110), yet there were significant variations imposed on the underlying trends. Vibrational frequencies were evaluated for the preferred adsorption configurations of each species with the aim of evaluating the entropy-changes and preexponential factors for each elementary step. Kinetic studies were performed for the early steps of FTS (up to CH{sub 4} formation) and CO dissociation. This involved evaluation of the Minimum Energy Pathway (MEP) and activation energy barrier for the steps involved. We concluded that Fe(211) would allow for far more facile CO dissociation in comparison to other Fe catalysts studied so far, but the other FTS steps studied remained mostly unchanged.

  5. Combination of artificial intelligence and procedural language programs in a computer application system supporting nuclear reactor operations

    SciTech Connect

    Town, G.G.; Stratton, R.C.

    1985-01-01

    A computer application system is described which provides nuclear reactor power plant operators with an improved decision support system. This system combines traditional computer applications such as graphics display with artificial intelligence methodologies such as reasoning and diagnosis so as to improve plant operability. This paper discusses the issues, and a solution, involved with the system integration of applications developed using traditional and artificial intelligence languages.

  6. A computationally-efficient, semi-implicit, iterative method for the time-integration of reacting flows with stiff chemistry

    NASA Astrophysics Data System (ADS)

    Savard, B.; Xuan, Y.; Bobbitt, B.; Blanquart, G.

    2015-08-01

    A semi-implicit preconditioned iterative method is proposed for the time-integration of the stiff chemistry in simulations of unsteady reacting flows, such as turbulent flames, using detailed chemical kinetic mechanisms. Emphasis is placed on the simultaneous treatment of convection, diffusion, and chemistry, without using operator splitting techniques. The preconditioner corresponds to an approximation of the diagonal of the chemical Jacobian. Upon convergence of the sub-iterations, the fully-implicit, second-order time-accurate, Crank-Nicolson formulation is recovered. Performance of the proposed method is tested theoretically and numerically on one-dimensional laminar and three-dimensional high Karlovitz turbulent premixed n-heptane/air flames. The species lifetimes contained in the diagonal preconditioner are found to capture all critical small chemical timescales, such that the largest stable time step size for the simulation of the turbulent flame with the proposed method is limited by the convective CFL, rather than chemistry. The theoretical and numerical stability limits are in good agreement and are independent of the number of sub-iterations. The results indicate that the overall procedure is second-order accurate in time, free of lagging errors, and the cost per iteration is similar to that of an explicit time integration. The theoretical analysis is extended to a wide range of flames (premixed and non-premixed), unburnt conditions, fuels, and chemical mechanisms. In all cases, the proposed method is found (theoretically) to be stable and to provide good convergence rate for the sub-iterations up to a time step size larger than 1 μs. This makes the proposed method ideal for the simulation of turbulent flames.

  7. Coil combination for receive array spectroscopy: Are data‐driven methods superior to methods using computed field maps?

    PubMed Central

    Robson, Matthew D.

    2015-01-01

    Purpose Combining spectra from receive arrays, particularly X‐nuclear spectra with low signal‐to‐noise ratios (SNRs), is challenging. We test whether data‐driven combination methods are better than using computed coil sensitivities. Theory Several combination algorithms are recast into the notation of Roemer's classic formula, showing that they differ primarily in their estimation of coil receive sensitivities. This viewpoint reveals two extensions of the whitened singular‐value decomposition (WSVD) algorithm, using temporal or temporal + spatial apodization to improve the coil sensitivities, and thus the combined spectral SNR. Methods Radiofrequency fields from an array were simulated and used to make synthetic spectra. These were combined with 10 algorithms. The combined spectra were then assessed in terms of their SNR. Validation used phantoms and cardiac 31P spectra from five subjects at 3T. Results Combined spectral SNRs from simulations, phantoms, and humans showed the same trends. In phantoms, the combined SNR using computed coil sensitivities was lower than with WSVD combination whenever the WSVD SNR was >14 (or >11 with temporal apodization, or >9 with temporal + spatial apodization). These new apodized WSVD methods gave higher SNRs than other data‐driven methods. Conclusion In the human torso, at frequencies ≥49 MHz, data‐driven combination is preferable to using computed coil sensitivities. Magn Reson, 2015. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Magn Reson Med 75:473–487, 2016. © 2015 The Authors. Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic

  8. Experimental and computational investigation of acetic acid deoxygenation over oxophilic molybdenum carbide: Surface chemistry and active site identity

    DOE PAGES

    Schaidle, Joshua A.; Blackburn, Jeffrey; Farberow, Carrie A.; Nash, Connor; Steirer, K. Xerxes; Clark, Jared; Robichaud, David J.; Ruddy, Daniel A.

    2016-01-21

    Ex situ catalytic fast pyrolysis (CFP) is a promising route for producing fungible biofuels; however, this process requires bifunctional catalysts that favor C–O bond cleavage, activate hydrogen at near atmospheric pressure and high temperature (350–500 °C), and are stable under high-steam, low hydrogen-to-carbon environments. Recently, early transition-metal carbides have been reported to selectively cleave C–O bonds of alcohols, aldehydes, and oxygenated aromatics, yet there is limited understanding of the metal carbide surface chemistry under reaction conditions and the identity of the active sites for deoxygenation. In this study, we evaluated molybdenum carbide (Mo2C) for the deoxygenation of acetic acid, anmore » abundant component of biomass pyrolysis vapors, under ex situ CFP conditions, and we probed the Mo2C surface chemistry, identity of the active sites, and deoxygenation pathways using in situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations.« less

  9. On the spectral combination of satellite gravity model, terrestrial and airborne gravity data for local gravimetric geoid computation

    NASA Astrophysics Data System (ADS)

    Jiang, Tao; Wang, Yan Ming

    2016-07-01

    One of the challenges for geoid determination is the combination of heterogeneous gravity data. Because of the distinctive spectral content of different data sets, spectral combination is a suitable candidate for its solution. The key to have a successful combination is to determine the proper spectral weights, or the error degree variances of each data set. In this paper, the error degree variances of terrestrial and airborne gravity data at low degrees are estimated by the aid of a satellite gravity model using harmonic analysis. For higher degrees, the error covariances are estimated from local gravity data first, and then used to compute the error degree variances. The white and colored noise models are also used to estimate the error degree variances of local gravity data for comparisons. Based on the error degree variances, the spectral weights of satellite gravity models, terrestrial and airborne gravity data are determined and applied for geoid computation in Texas area. The computed gravimetric geoid models are tested against an independent, highly accurate geoid profile of the Geoid Slope Validation Survey 2011 (GSVS11). The geoid computed by combining satellite gravity model GOCO03S and terrestrial (land and DTU13 altimetric) gravity data agrees with GSVS11 to ±1.1 cm in terms of standard deviation along a line of 325 km. After incorporating the airborne gravity data collected at 11 km altitude, the standard deviation is reduced to ±0.8 cm. Numerical tests demonstrate the feasibility of spectral combination in geoid computation and the contribution of airborne gravity in an area of high quality terrestrial gravity data. Using the GSVS11 data and the spectral combination, the degree of correctness of the error spectra and the quality of satellite gravity models can also be revealed.

  10. Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

    SciTech Connect

    Pierce, Eric M; Bacon, Diana

    2011-01-01

    The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic time-scales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models are validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test-B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year long PUF experiment was conducted with the subsurface transport over reactive multi-phases code. Results show that parameterization of the computer model by combining direct bench-scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year long test duration, the rate decreased from 0.2 to 0.01 g/(m2 d) base on B release. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by 4 orders of magnitude) and suggest the gel-layer properties are less protective under these dynamic conditions.

  11. Combined Experimental and Computational Approach to Predict the Glass-Water Reaction

    SciTech Connect

    Pierce, Eric M.; Bacon, Diana H.

    2011-10-01

    The use of mineral and glass dissolution rates measured in laboratory experiments to predict the weathering of primary minerals and volcanic and nuclear waste glasses in field studies requires the construction of rate models that accurately describe the weathering process over geologic timescales. Additionally, the need to model the long-term behavior of nuclear waste glass for the purpose of estimating radionuclide release rates requires that rate models be validated with long-term experiments. Several long-term test methods have been developed to accelerate the glass-water reaction [drip test, vapor hydration test, product consistency test B, and pressurized unsaturated flow (PUF)], thereby reducing the duration required to evaluate long-term performance. Currently, the PUF test is the only method that mimics the unsaturated hydraulic properties expected in a subsurface disposal facility and simultaneously monitors the glass-water reaction. PUF tests are being conducted to accelerate the weathering of glass and validate the model parameters being used to predict long-term glass behavior. A one-dimensional reactive chemical transport simulation of glass dissolution and secondary phase formation during a 1.5-year-long PUF experiment was conducted with the Subsurface Transport Over Reactive Multiphases (STORM) code. Results show that parameterization of the computer model by combining direct bench scale laboratory measurements and thermodynamic data provides an integrated approach to predicting glass behavior over the length of the experiment. Over the 1.5-year-long test duration, the rate decreased from 0.2 to 0.01 g/(m2 day) based on B release for low-activity waste glass LAWA44. The observed decrease is approximately two orders of magnitude higher than the decrease observed under static conditions with the SON68 glass (estimated to be a decrease by four orders of magnitude) and suggests that the gel-layer properties are less protective under these dynamic

  12. Combining Computational Methods for Hit to Lead Optimization in Mycobacterium tuberculosis Drug Discovery

    PubMed Central

    Ekins, Sean; Freundlich, Joel S.; Hobrath, Judith V.; White, E. Lucile; Reynolds, Robert C

    2013-01-01

    Purpose Tuberculosis treatments need to be shorter and overcome drug resistance. Our previous large scale phenotypic high-throughput screening against Mycobacterium tuberculosis (Mtb) has identified 737 active compounds and thousands that are inactive. We have used this data for building computational models as an approach to minimize the number of compounds tested. Methods A cheminformatics clustering approach followed by Bayesian machine learning models (based on publicly available Mtb screening data) was used to illustrate that application of these models for screening set selections can enrich the hit rate. Results In order to explore chemical diversity around active cluster scaffolds of the dose-response hits obtained from our previous Mtb screens a set of 1924 commercially available molecules have been selected and evaluated for antitubercular activity and cytotoxicity using Vero, THP-1 and HepG2 cell lines with 4.3%, 4.2% and 2.7% hit rates, respectively. We demonstrate that models incorporating antitubercular and cytotoxicity data in Vero cells can significantly enrich the selection of non-toxic actives compared to random selection. Across all cell lines, the Molecular Libraries Small Molecule Repository (MLSMR) and cytotoxicity model identified ~10% of the hits in the top 1% screened (>10 fold enrichment). We also showed that seven out of nine Mtb active compounds from different academic published studies and eight out of eleven Mtb active compounds from a pharmaceutical screen (GSK) would have been identified by these Bayesian models. Conclusion Combining clustering and Bayesian models represents a useful strategy for compound prioritization and hit-to lead optimization of antitubercular agents. PMID:24132686

  13. Is there something special with probabilities?--insight vs. computational ability in multiple risk combination.

    PubMed

    Juslin, Peter; Lindskog, Marcus; Mayerhofer, Bastian

    2015-03-01

    While a wealth of evidence suggests that humans tend to rely on additive cue combination to make controlled judgments, many of the normative rules for probability combination require multiplicative combination. In this article, the authors combine the experimental paradigms on probability reasoning and multiple-cue judgment to allow a comparison between formally identical tasks that involve probability vs. other task contents. The purpose was to investigate if people have cognitive algorithms for the combination, specifically, of probability, affording multiplicative combination in the context of probability. Three experiments suggest that, although people show some signs of a qualitative understanding of the combination rules that are specific to probability, in all but the simplest cases they lack the cognitive algorithms needed for multiplication, but instead use a variety of additive heuristics to approximate the normative combination. Although these heuristics are surprisingly accurate, normative combination is not consistently achieved until the problems are framed in an additive way.

  14. Is there something special with probabilities?--insight vs. computational ability in multiple risk combination.

    PubMed

    Juslin, Peter; Lindskog, Marcus; Mayerhofer, Bastian

    2015-03-01

    While a wealth of evidence suggests that humans tend to rely on additive cue combination to make controlled judgments, many of the normative rules for probability combination require multiplicative combination. In this article, the authors combine the experimental paradigms on probability reasoning and multiple-cue judgment to allow a comparison between formally identical tasks that involve probability vs. other task contents. The purpose was to investigate if people have cognitive algorithms for the combination, specifically, of probability, affording multiplicative combination in the context of probability. Three experiments suggest that, although people show some signs of a qualitative understanding of the combination rules that are specific to probability, in all but the simplest cases they lack the cognitive algorithms needed for multiplication, but instead use a variety of additive heuristics to approximate the normative combination. Although these heuristics are surprisingly accurate, normative combination is not consistently achieved until the problems are framed in an additive way. PMID:25514208

  15. T and D-Bench--Innovative Combined Support for Education and Research in Computer Architecture and Embedded Systems

    ERIC Educational Resources Information Center

    Soares, S. N.; Wagner, F. R.

    2011-01-01

    Teaching and Design Workbench (T&D-Bench) is a framework aimed at education and research in the areas of computer architecture and embedded systems. It includes a set of features not found in other educational environments. This set of features is the result of an original combination of design requirements for T&D-Bench: that the framework should…

  16. Selective Catalytic Synthesis Using the Combination of Carbon Dioxide and Hydrogen: Catalytic Chess at the Interface of Energy and Chemistry.

    PubMed

    Klankermayer, Jürgen; Wesselbaum, Sebastian; Beydoun, Kassem; Leitner, Walter

    2016-06-20

    The present Review highlights the challenges and opportunities when using the combination CO2 /H2 as a C1 synthon in catalytic reactions and processes. The transformations are classified according to the reduction level and the bond-forming processes, covering the value chain from high volume basic chemicals to complex molecules, including biologically active substances. Whereas some of these concepts can facilitate the transition of the energy system by harvesting renewable energy into chemical products, others provide options to reduce the environmental impact of chemical production already in today's petrochemical-based industry. Interdisciplinary fundamental research from chemists and chemical engineers can make important contributions to sustainable development at the interface of the energetic and chemical value chain. The present Review invites the reader to enjoy this exciting area of "catalytic chess" and maybe even to start playing some games in her or his laboratory. PMID:27237963

  17. Selective Catalytic Synthesis Using the Combination of Carbon Dioxide and Hydrogen: Catalytic Chess at the Interface of Energy and Chemistry.

    PubMed

    Klankermayer, Jürgen; Wesselbaum, Sebastian; Beydoun, Kassem; Leitner, Walter

    2016-06-20

    The present Review highlights the challenges and opportunities when using the combination CO2 /H2 as a C1 synthon in catalytic reactions and processes. The transformations are classified according to the reduction level and the bond-forming processes, covering the value chain from high volume basic chemicals to complex molecules, including biologically active substances. Whereas some of these concepts can facilitate the transition of the energy system by harvesting renewable energy into chemical products, others provide options to reduce the environmental impact of chemical production already in today's petrochemical-based industry. Interdisciplinary fundamental research from chemists and chemical engineers can make important contributions to sustainable development at the interface of the energetic and chemical value chain. The present Review invites the reader to enjoy this exciting area of "catalytic chess" and maybe even to start playing some games in her or his laboratory.

  18. Dual-Modality Imaging of the Human Finger Joint Systems by Using Combined Multispectral Photoacoustic Computed Tomography and Ultrasound Computed Tomography

    PubMed Central

    Liu, Yubin; Wang, Yating

    2016-01-01

    We developed a homemade dual-modality imaging system that combines multispectral photoacoustic computed tomography and ultrasound computed tomography for reconstructing the structural and functional information of human finger joint systems. The fused multispectral photoacoustic-ultrasound computed tomography (MPAUCT) system was examined by the phantom and in vivo experimental tests. The imaging results indicate that the hard tissues such as the bones and the soft tissues including the blood vessels, the tendon, the skins, and the subcutaneous tissues in the finger joints systems can be effectively recovered by using our multimodality MPAUCT system. The developed MPAUCT system is able to provide us with more comprehensive information of the human finger joints, which shows its potential for characterization and diagnosis of bone or joint diseases. PMID:27774453

  19. Computer-aided design provisionalization and implant insertion combined with optical scanning of plaster casts and computed tomography data

    PubMed Central

    Hara, Shingo; Mitsugi, Masaharu; Kanno, Takahiro; Tatemoto, Yukihiro

    2014-01-01

    The conventional implant prosthesis planning process currently involves confirmation of two-dimensional anatomical findings or the quantity and quality of bones using panoramic X-ray images. The introduction of computed tomography (CT) into the field has enabled the previously impossible confirmation of three-dimensional findings, making implant planning in precise locations possible. However, artifacts caused by the presence of metal prostheses can become problematic and can result in obstacles to diagnosis and implant planning. The most updated version of SimPlant® Pro has made it possible to integrate plaster cast images with CT data using optical scanning. Using this function, the obstacles created by metal prostheses are eliminated, facilitating implant planning at the actual intraoral location. Furthermore, a SurgiGuide® based on individual patient information can be created on plaster casts, resulting in easier and more precise implant insertion. PMID:24987602

  20. Theoretical Chemistry Comes Alive: Full Partner with Experiment.

    ERIC Educational Resources Information Center

    Goddard, William A., III

    1985-01-01

    The expected thrust for theoretical chemistry in the next decade will be to combine knowledge of fundamental chemical steps/interactions with advances in chemical dynamics, irreversible statistical mechanics, and computer technology to produce simulations of chemical systems with reaction site competition. A sample simulation (using the enzyme…

  1. A Web-Based Data Architecture for Problem-Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment

    SciTech Connect

    Schuchardt, Karen L. ); Myers, James D. ); Stephan, Eric G. )

    2001-12-01

    Next-generation problem-solving environments (PSEs) promise significant advances over those now available. They will span scientific disciplines and incorporate collaboration capabilities. They will host feature-detection and other agents, allow data mining and pedigree tracking, and provide access from a wide range of devices. Fundamental changes in PSE architecture are required to realize these and other PSE goals. This paper focuses specifically on issues related to data management and recommends an approach based on open, metadata-driven repositories with loosely defined, dynamic schemas. Benefits of this approach are discussed, and the redesign of the Extensible Computational Chemistry Environment's (Ecce) data storage architecture to use such a repository is described, based on the distributed authoring and versioning (DAV) standard. The suitability of DAV for scientific data, the mapping of the Ecce schema to DAV, and promising initial results are presented.

  2. Combined Quantum Chemistry and Photoelectron Spectroscopy Study of the Electronic Structure and Reduction Potentials of Rubredoxin Redox Site Analogues

    SciTech Connect

    Niu, Shuqiang; Wang, Xue B.; Nichols, J. A.; Wang, Lai S.; Ichiye, Toshiko

    2003-04-24

    Iron-sulfur proteins are an important class of electron carriers in a wide variety of biological reactions. Determining the intrinsic contribution of the metal site to the redox potential is crucial in understanding how the protein environment influences the overall redox properties of the Fe-S proteins. Here we combine density functional theory and coupled cluster methods with photodetachment spectroscopy to study the electronic structures and gas-phase redox potentials of the [Fe(SCH3)(4)](2-/-/0) and [Fe(SCH3)(3)](-/0) analogues of the rubredoxin redox site. The calculations show that oxidations of [Fe(SCH3)(4)](2-) and [Fe(SCH3)(4)](-) involve mainly the Fe 3d and S 3p orbitals, respectively. The calculated adiabatic and vertical detachment energies are in good agreement with the experiment for [Fe(SCH3)(3)](-) and [Fe(SCH3)(4)](-). The current results further confirm the "inverted level scheme" for the high-spin [1Fe] systems. The redox couple, [Fe(SCH3)(4)](- /2), which is the one found in rubredoxin, but cannot be accessed experimentally in the gas phase, was investigated using a thermodynamic cycle that relates it to the [Fe(SCH3)(3)](-/0) couple and the ligand association reaction, [Fe(SCH3)(3)](0/-) + SCH3- --> [Fe(SCH3)(4)](-/2-). The calculated reduction energy of [Fe(SCH3)(4)](-) (1.7 eV) compares well with the value (1.6 eV) estimated from the calculated bond energies and the experimental detachment energy of [Fe(SCH3)(3)](-). Thus, this thermodynamic cycle method can be used to estimate metal-ligand bonding energies and determine intrinsic reduction potentials from photodetachment experiments when the reduced forms are not stable in the gas phase.

  3. A computational chemistry perspective on the current status and future direction of hepatitis B antiviral drug discovery.

    PubMed

    Morgnanesi, Dante; Heinrichs, Eric J; Mele, Anthony R; Wilkinson, Sean; Zhou, Suzanne; Kulp, John L

    2015-11-01

    Computational chemical biology, applied to research on hepatitis B virus (HBV), has two major branches: bioinformatics (statistical models) and first-principle methods (molecular physics). While bioinformatics focuses on statistical tools and biological databases, molecular physics uses mathematics and chemical theory to study the interactions of biomolecules. Three computational techniques most commonly used in HBV research are homology modeling, molecular docking, and molecular dynamics. Homology modeling is a computational simulation to predict protein structure and has been used to construct conformers of the viral polymerase (reverse transcriptase domain and RNase H domain) and the HBV X protein. Molecular docking is used to predict the most likely orientation of a ligand when it is bound to a protein, as well as determining an energy score of the docked conformation. Molecular dynamics is a simulation that analyzes biomolecule motions and determines conformation and stability patterns. All of these modeling techniques have aided in the understanding of resistance mutations on HBV non-nucleos(t)ide reverse-transcriptase inhibitor binding. Finally, bioinformatics can be used to study the DNA and RNA protein sequences of viruses to both analyze drug resistance and to genotype the viral genomes. Overall, with these techniques, and others, computational chemical biology is becoming more and more necessary in hepatitis B research. This article forms part of a symposium in Antiviral Research on "An unfinished story: from the discovery of the Australia antigen to the development of new curative therapies for hepatitis B."

  4. Density Functional Computations and Mass Spectrometric Measurements. Can this Coupling Enlarge the Knowledge of Gas-Phase Chemistry?

    NASA Astrophysics Data System (ADS)

    Marino, T.; Russo, N.; Sicilia, E.; Toscano, M.; Mineva, T.

    A series of gas-phase properties of the systems has been investigated by using different exchange-correlation potentials and basis sets of increasing size in the framework of Density Functional theory with the aim to determine a strategy able to give reliable results with reasonable computational efforts.

  5. Structural and Thermodynamic Properties of the Argon Dimer: A Computational Chemistry Exercise in Quantum and Statistical Mechanics

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2010-01-01

    Using readily available computational applications and resources, students can construct a high-level ab initio potential energy surface (PES) for the argon dimer. From this information, they can obtain detailed molecular constants of the dimer, including its dissociation energy, which compare well with experimental determinations. Using both…

  6. A combined direct/inverse three-dimensional transonic wing design method for vector computers

    NASA Technical Reports Server (NTRS)

    Weed, R. A.; Carlson, L. A.; Anderson, W. K.

    1984-01-01

    A three-dimensional transonic-wing design algorithm for vector computers is developed, and the results of sample computations are presented graphically. The method incorporates the direct/inverse scheme of Carlson (1975), a Cartesian grid system with boundary conditions applied at a mean plane, and a potential-flow solver based on the conservative form of the full potential equation and using the ZEBRA II vectorizable solution algorithm of South et al. (1980). The accuracy and consistency of the method with regard to direct and inverse analysis and trailing-edge closure are verified in the test computations.

  7. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  8. Integrating a Single Tablet PC in Chemistry, Engineering, and Physics Courses

    ERIC Educational Resources Information Center

    Rogers, James W.; Cox, James R.

    2008-01-01

    A tablet PC is a versatile computer that combines the computing power of a notebook with the pen functionality of a PDA (Cox and Rogers 2005b). The authors adopted tablet PC technology in order to improve the process and product of the lecture format in their chemistry, engineering, and physics courses. In this high-tech model, a single tablet PC…

  9. Computer Aided Design of Ka-Band Waveguide Power Combining Architectures for Interplanetary Spacecraft

    NASA Technical Reports Server (NTRS)

    Vaden, Karl R.

    2006-01-01

    Communication systems for future NASA interplanetary spacecraft require transmitter power ranging from several hundred watts to kilowatts. Several hybrid junctions are considered as elements within a corporate combining architecture for high power Ka-band space traveling-wave tube amplifiers (TWTAs). This report presents the simulated transmission characteristics of several hybrid junctions designed for a low loss, high power waveguide based power combiner.

  10. Carbon dioxide splitting in a dielectric barrier discharge plasma: a combined experimental and computational study.

    PubMed

    Aerts, Robby; Somers, Wesley; Bogaerts, Annemie

    2015-02-01

    Plasma technology is gaining increasing interest for the splitting of CO2 into CO and O2 . We have performed experiments to study this process in a dielectric barrier discharge (DBD) plasma with a wide range of parameters. The frequency and dielectric material did not affect the CO2 conversion and energy efficiency, but the discharge gap can have a considerable effect. The specific energy input has the most important effect on the CO2 conversion and energy efficiency. We have also presented a plasma chemistry model for CO2 splitting, which shows reasonable agreement with the experimental conversion and energy efficiency. This model is used to elucidate the critical reactions that are mostly responsible for the CO2 conversion. Finally, we have compared our results with other CO2 splitting techniques and we identified the limitations as well as the benefits and future possibilities in terms of modifications of DBD plasmas for greenhouse gas conversion in general.

  11. Carbon dioxide splitting in a dielectric barrier discharge plasma: a combined experimental and computational study.

    PubMed

    Aerts, Robby; Somers, Wesley; Bogaerts, Annemie

    2015-02-01

    Plasma technology is gaining increasing interest for the splitting of CO2 into CO and O2 . We have performed experiments to study this process in a dielectric barrier discharge (DBD) plasma with a wide range of parameters. The frequency and dielectric material did not affect the CO2 conversion and energy efficiency, but the discharge gap can have a considerable effect. The specific energy input has the most important effect on the CO2 conversion and energy efficiency. We have also presented a plasma chemistry model for CO2 splitting, which shows reasonable agreement with the experimental conversion and energy efficiency. This model is used to elucidate the critical reactions that are mostly responsible for the CO2 conversion. Finally, we have compared our results with other CO2 splitting techniques and we identified the limitations as well as the benefits and future possibilities in terms of modifications of DBD plasmas for greenhouse gas conversion in general. PMID:25641832

  12. Northwestern University Initiative for Teaching NanoSciences (NUITNS): An Approach for Teaching Computational Chemistry to Engineering Undergraduate Students

    ERIC Educational Resources Information Center

    Simeon, Tomekia; Aikens, Christine M.; Tejerina, Baudilio; Schatz, George C.

    2011-01-01

    The Northwestern University Initiative for Teaching Nanosciences (NUITNS) at nanohub.org Web site combines several tools for doing electronic structure calculations and analyzing and displaying the results into a coordinated package. In this article, we describe this package and show how it can be used as part of an upper-level quantum chemistry…

  13. Teacher Conceptions and Approaches Associated with an Immersive Instructional Implementation of Computer-Based Models and Assessment in a Secondary Chemistry Classroom

    NASA Astrophysics Data System (ADS)

    Waight, Noemi; Liu, Xiufeng; Gregorius, Roberto Ma.; Smith, Erica; Park, Mihwa

    2014-02-01

    This paper reports on a case study of an immersive and integrated multi-instructional approach (namely computer-based model introduction and connection with content; facilitation of individual student exploration guided by exploratory worksheet; use of associated differentiated labs and use of model-based assessments) in the implementation of coupled computer-based models and assessment in a high-school chemistry classroom. Data collection included in-depth teacher interviews, classroom observations, student interviews and researcher notes. Teacher conceptions highlighted the role of models as tools; the benefits of abstract portrayal via visualizations; appropriate enactment of model implementation; concerns with student learning and issues with time. The case study revealed numerous challenges reconciling macro, submicro and symbolic phenomena with the NetLogo model. Nonetheless, the effort exhibited by the teacher provided a platform to support the evolution of practice over time. Students' reactions reflected a continuum of confusion and benefits which were directly related to their background knowledge and experiences with instructional modes. The findings have implications for the role of teacher knowledge of models, the modeling process and pedagogical content knowledge; the continuum of student knowledge as novice users and the role of visual literacy in model decoding, comprehension and translation.

  14. Assessing Changes in High School Students' Conceptual Understanding through Concept Maps before and after the Computer-Based Predict-Observe-Explain (CB-POE) Tasks on Acid-Base Chemistry at the Secondary Level

    ERIC Educational Resources Information Center

    Yaman, Fatma; Ayas, Alipasa

    2015-01-01

    Although concept maps have been used as alternative assessment methods in education, there has been an ongoing debate on how to evaluate students' concept maps. This study discusses how to evaluate students' concept maps as an assessment tool before and after 15 computer-based Predict-Observe-Explain (CB-POE) tasks related to acid-base chemistry.…

  15. A Combined Experimental and Computational Study on the Stability of Nanofluids Containing Metal Organic Frameworks.

    PubMed

    Annapureddy, Harsha V R; Nune, Satish K; Motkuri, Radha Kishan; McGrail, B Peter; Dang, Liem X

    2015-07-23

    Computational studies on nanofluids composed of metal organic frameworks were performed using molecular modeling techniques. Grand Canonical Monte Carlo simulations were used to study the adsorption behavior of 1,1,1,3,3-pentafluoropropane (R-245fa) in a MIL-101 metal organic frameworks at various temperatures. To understand the stability of the nanofluid composed of MIL-101 particles, we performed molecular dynamics simulations to compute potentials of mean force between hypothetical MIL-101 fragments terminated with two different kinds of modulators in R-245fa and water. Our computed potentials of mean force results indicate that the metal organic frameworks particles tend to disperse better in water than in R-245fa. The reasons for this difference in dispersion were analyzed and are discussed in the paper. Our results agree with experimental results indicating that the potential models employed and modeling approaches provide good descriptions of molecular interactions and the reliabilities. PMID:25569021

  16. A Combined Experimental and Computational Study on the Stability of Nanofluids Containing Metal Organic Frameworks.

    PubMed

    Annapureddy, Harsha V R; Nune, Satish K; Motkuri, Radha Kishan; McGrail, B Peter; Dang, Liem X

    2015-07-23

    Computational studies on nanofluids composed of metal organic frameworks were performed using molecular modeling techniques. Grand Canonical Monte Carlo simulations were used to study the adsorption behavior of 1,1,1,3,3-pentafluoropropane (R-245fa) in a MIL-101 metal organic frameworks at various temperatures. To understand the stability of the nanofluid composed of MIL-101 particles, we performed molecular dynamics simulations to compute potentials of mean force between hypothetical MIL-101 fragments terminated with two different kinds of modulators in R-245fa and water. Our computed potentials of mean force results indicate that the metal organic frameworks particles tend to disperse better in water than in R-245fa. The reasons for this difference in dispersion were analyzed and are discussed in the paper. Our results agree with experimental results indicating that the potential models employed and modeling approaches provide good descriptions of molecular interactions and the reliabilities.

  17. Strategies and tactics for optimizing the Hit-to-Lead process and beyond--a computational chemistry perspective.

    PubMed

    Manly, Charles J; Chandrasekhar, Jayaraman; Ochterski, Joseph W; Hammer, Jack D; Warfield, Benjamin B

    2008-02-01

    The Hit-to-Lead-to-Candidate process continues to evolve rapidly, and while technological advances offer much potential, the reality often pales to the promise. Conversely, strategies and tactics implementing existing technologies may result in more benefit in the end. This article focuses on some of the thinking and approaches that may improve the efficiency and effectiveness of the beginnings of the drug discovery path. From the perspective of computational chemists, different types of strategy and philosophy of approach will be treated including: considerations of early lead choices, strategies for improving poor leads, multivariate optimization, opportunities for informatics, and engineering good decisions.

  18. Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

    NASA Astrophysics Data System (ADS)

    Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

    2010-03-01

    Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species

  19. Combined experimental and computational study of the thermochemistry of the fluoroaniline isomers.

    PubMed

    Ribeiro da Silva, Manuel A V; Ferreira, Ana I M C L; Gomes, José R B

    2007-03-01

    The standard (p degrees = 0.1 MPa) molar enthalpies of formation in the condensed phase of all the fluoroanilines, with the exception of the 2,3,5-trifluoroaniline compound, were derived from the standard molar energies of combustion in oxygen at T = 298.15 K, measured by rotating bomb combustion calorimetry. Calvet high-temperature vacuum sublimation experiments were performed to measure their enthalpies of vaporization or sublimation. These experiments allowed the determination of the standard molar enthalpies of formation in the gaseous phase and at T = 298.15 K. These values are also compared with estimates based on G3MP2B3 and BP86/6-31+G(d) computations, which have been extended also to the fluoroaniline that was not studied experimentally. The results are in close agreement with a mean deviation of approximately 3 kJ.mol-1. The largest difference between experimental and G3MP2B3 values is found for the pentafluoroaniline (-7.0 kJ.mol-1). For the three monofluoroanilines, the composite approach has been used also to compute gas-phase acidities, electron and proton affinities, ionization enthalpies and N-H bond dissociation enthalpies. The computed values compare well with available experimental results supporting the new computed data. PMID:17279791

  20. Can Computer-Assisted Discovery Learning Foster First Graders' Fluency with the Most Basic Addition Combinations?

    ERIC Educational Resources Information Center

    Baroody, Arthur J.; Eiland, Michael D.; Purpura, David J.; Reid, Erin E.

    2013-01-01

    In a 9-month training experiment, 64 first graders with a risk factor were randomly assigned to computer-assisted structured discovery of the add-1 rule (e.g., the sum of 7 + 1 is the number after "seven" when we count), unstructured discovery learning of this regularity, or an active-control group. Planned contrasts revealed that the add-1…

  1. Children's Writing Processes when Using Computers: Insights Based on Combining Analyses of Product and Process

    ERIC Educational Resources Information Center

    Gnach, Aleksandra; Wiesner, Esther; Bertschi-Kaufmann, Andrea; Perrin, Daniel

    2007-01-01

    Children and young people are increasingly performing a variety of writing tasks using computers, with word processing programs thus becoming their natural writing environment. The development of keystroke logging programs enables us to track the process of writing, without changing the writing environment for the writers. In the myMoment schools…

  2. The Benefits of Combining Computer Technology and Traditional Teaching Methods in Large Enrollment Geoscience Classes.

    ERIC Educational Resources Information Center

    Durbin, James M.

    2002-01-01

    Examines data collected from large enrollment, entry level Geoscience courses over a span of seven semesters and investigates the use of computers as a presentation tool and the incorporation of the Internet as a means to give students increased exposure to course content, increased exam scores, and knowledge of Earth Sciences. Includes 13…

  3. An Exploratory Framework for Combining CFD Analysis and Evolutionary Optimization into a Single Integrated Computational Environment

    SciTech Connect

    McCorkle, Douglas S.; Bryden, Kenneth M.

    2011-01-01

    Several recent reports and workshops have identified integrated computational engineering as an emerging technology with the potential to transform engineering design. The goal is to integrate geometric models, analyses, simulations, optimization and decision-making tools, and all other aspects of the engineering process into a shared, interactive computer-generated environment that facilitates multidisciplinary and collaborative engineering. While integrated computational engineering environments can be constructed from scratch with high-level programming languages, the complexity of these proposed environments makes this type of approach prohibitively slow and expensive. Rather, a high-level software framework is needed to provide the user with the capability to construct an application in an intuitive manner using existing models and engineering tools with minimal programming. In this paper, we present an exploratory open source software framework that can be used to integrate the geometric models, computational fluid dynamics (CFD), and optimization tools needed for shape optimization of complex systems. This framework is demonstrated using the multiphase flow analysis of a complete coal transport system for an 800 MW pulverized coal power station. The framework uses engineering objects and three-dimensional visualization to enable the user to interactively design and optimize the performance of the coal transport system.

  4. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Describes experiments, demonstrations, activities and ideas relating to various fields of chemistry to be used in chemistry courses of secondary schools. Three experiments concerning differential thermal analysis are among these notes presented. (HM)

  5. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)

  6. Colour Chemistry

    ERIC Educational Resources Information Center

    Griffiths, J.; Rattee, I. D.

    1973-01-01

    Discusses the course offerings in pure color chemistry at two universities and the three main aspects of study: dyestuff chemistry, color measurement, and color application. Indicates that there exists a constant challenge to ingenuity in the subject discipline. (CC)

  7. Delay-based reservoir computing: noise effects in a combined analog and digital implementation.

    PubMed

    Soriano, Miguel C; Ortín, Silvia; Keuninckx, Lars; Appeltant, Lennert; Danckaert, Jan; Pesquera, Luis; van der Sande, Guy

    2015-02-01

    Reservoir computing is a paradigm in machine learning whose processing capabilities rely on the dynamical behavior of recurrent neural networks. We present a mixed analog and digital implementation of this concept with a nonlinear analog electronic circuit as a main computational unit. In our approach, the reservoir network can be replaced by a single nonlinear element with delay via time-multiplexing. We analyze the influence of noise on the performance of the system for two benchmark tasks: 1) a classification problem and 2) a chaotic time-series prediction task. Special attention is given to the role of quantization noise, which is studied by varying the resolution in the conversion interface between the analog and digital worlds. PMID:25608295

  8. Combined experimental and computational investigation of sterile air flows in surgical environments

    NASA Astrophysics Data System (ADS)

    McNeill, James; Hertzberg, Jean; Zhai, Zhiqiang

    2010-11-01

    Surgical environments in hospitals utilize downward, low-turbulence, sterile air flow across the patient to inhibit transmission of infectious diseases to the surgical site. Full-scale laboratory experiments using particle image velocimetry were conducted to investigate the air distribution above the patient area. Computational fluid dynamics models were developed to further investigate the air distribution within the operating room in order to determine the impact of ventilation design of airborne infectious disease pathways. Both Reynolds-averaged Navier-Stokes equations and large eddy simulation techniques are currently being used in the computational modeling to study the effect of turbulence modeling on the indoor air distribution. CFD models are being calibrated based on the experimental data and will be used to study the probability of infectious particles entering the sterile region of the room.

  9. Delay-based reservoir computing: noise effects in a combined analog and digital implementation.

    PubMed

    Soriano, Miguel C; Ortín, Silvia; Keuninckx, Lars; Appeltant, Lennert; Danckaert, Jan; Pesquera, Luis; van der Sande, Guy

    2015-02-01

    Reservoir computing is a paradigm in machine learning whose processing capabilities rely on the dynamical behavior of recurrent neural networks. We present a mixed analog and digital implementation of this concept with a nonlinear analog electronic circuit as a main computational unit. In our approach, the reservoir network can be replaced by a single nonlinear element with delay via time-multiplexing. We analyze the influence of noise on the performance of the system for two benchmark tasks: 1) a classification problem and 2) a chaotic time-series prediction task. Special attention is given to the role of quantization noise, which is studied by varying the resolution in the conversion interface between the analog and digital worlds.

  10. Objective Definition of Rosette Shape Variation Using a Combined Computer Vision and Data Mining Approach

    PubMed Central

    Camargo, Anyela; Papadopoulou, Dimitra; Spyropoulou, Zoi; Vlachonasios, Konstantinos; Doonan, John H.; Gay, Alan P.

    2014-01-01

    Computer-vision based measurements of phenotypic variation have implications for crop improvement and food security because they are intrinsically objective. It should be possible therefore to use such approaches to select robust genotypes. However, plants are morphologically complex and identification of meaningful traits from automatically acquired image data is not straightforward. Bespoke algorithms can be designed to capture and/or quantitate specific features but this approach is inflexible and is not generally applicable to a wide range of traits. In this paper, we have used industry-standard computer vision techniques to extract a wide range of features from images of genetically diverse Arabidopsis rosettes growing under non-stimulated conditions, and then used statistical analysis to identify those features that provide good discrimination between ecotypes. This analysis indicates that almost all the observed shape variation can be described by 5 principal components. We describe an easily implemented pipeline including image segmentation, feature extraction and statistical analysis. This pipeline provides a cost-effective and inherently scalable method to parameterise and analyse variation in rosette shape. The acquisition of images does not require any specialised equipment and the computer routines for image processing and data analysis have been implemented using open source software. Source code for data analysis is written using the R package. The equations to calculate image descriptors have been also provided. PMID:24804972

  11. A Combined Experimental and Computational Study on the Stability of Nanofluids Containing Metal Organic Frameworks

    SciTech Connect

    Annapureddy, Harsha Vardhan Reddy; Nune, Satish K.; Motkuri, Radha K.; McGrail, B. Peter; Dang, Liem X.

    2015-01-08

    Computational studies on nanofluids composed of metal organic frameworks (MOFs) were performed using molecular modeling techniques. Grand Canonical Monte Carlo (GCMC) simulations were used to study adsorption behavior of 1,1,1,3,3-pentafluoropropane (R-245fa) in a MIL-101 MOF at various temperatures. To understand the stability of the nanofluid composed of MIL-101 particles, we performed molecular dynamics simulations to compute potentials of mean force between hypothetical MIL-101 fragments terminated with two different kinds of modulators in R-245fa and water. Our computed potentials of mean force results indicate that the MOF particles tend to disperse better in water than in R-245fa. The reasons for this observation were analyzed and discussed. Our results agree with experimental results indicating that the employed potential models and modeling approaches provide good description of molecular interactions and the reliabilities. Work performed by LXD was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Work performed by HVRA, SKN, RKM, and PBM was supported by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.

  12. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and experiments for chemistry. Topics include superheavy elements, polarizing power and chemistry of alkali metals, particulate carbon from combustion, tips for the chemistry laboratory, interesting/colorful experiments, behavior of bismuth (III) iodine, and…

  13. Computer-Based Simulation Systems and Role-Playing: An Effective Combination for Fostering Conditional Knowledge.

    ERIC Educational Resources Information Center

    Shlechter, Theodore M.; And Others

    1992-01-01

    Examines the effectiveness of SIMNET (Simulation Networking), a virtual reality training simulation system, combined with a program of role-playing activities for helping Army classes to master the conditional knowledge needed for successful field performance. The value of active forms of learning for promoting higher order cognitive thinking is…

  14. Interdisciplinary Educational Collaborations: Chemistry and Computer Science 967 Ronald S. Haines, Daniel T. Woo, Benjamin T. Hudson, Joji C. Mori, Evey S. M. Ngan, and Wing-Yee Pak

    NASA Astrophysics Data System (ADS)

    Goedhart, Martin J.

    2007-06-01

    While chemists are usually aware of the possibilities of interdisciplinary collaboration in chemical research they may be less aware of the possibilities of such collaboration in education. This article documents an ongoing collaboration between a chemist and computer scientist to co-supervise computer science students engaged in developing software for chemical education, highlights the benefits to both the chemistry and computer science students, notes some unexpected outcomes, and provides guidance to those planning such collaborations. The experiences described in this work should motivate chemistry educators to approach their colleagues in other disciplines with proposals for joint research projects. The collaboration described here initially resulted in the development of student-friendly software for operating a spectrophotometer. Recent co-supervised students have begun developing other software for chemical education.

  15. N-glycoproteome Analysis of the Secretome of Human Metastatic Hepatocellular Carcinoma Cell Lines Combining Hydrazide Chemistry, HILIC Enrichment and Mass Spectrometry

    PubMed Central

    Li, Xianyu; Jiang, Jing; Zhao, Xinyuan; Wang, Jifeng; Han, Huanhuan; Zhao, Yan; Peng, Bo; Zhong, Rugang; Ying, Wantao; Qian, Xiaohong

    2013-01-01

    Cancer cell metastasis is a major cause of cancer death. Unfortunately, the underlying molecular mechanisms remain unknown, which results in the lack of efficient diagnosis, therapy and prevention approaches. Nevertheless, the dysregulation of the cancer cell secretome is known to play key roles in tumor transformation and progression. The majority of proteins in the secretome are secretory proteins and membrane-released proteins, and, mostly, the glycosylated proteins. Until recently, few studies have explored protein N-glycosylation changes in the secretome, although protein glycosylation has received increasing attention in the study of tumor development processes. Here, the N-glycoproteins in the secretome of two human hepatocellular carcinoma (HCC) cell lines with low (MHCC97L) or high (HCCLM3) metastatic potential were investigated with a in-depth characterization of the N-glycosites by combining two general glycopeptide enrichment approaches, hydrazide chemistry and zwitterionic hydrophilic interaction chromatography (zic-HILIC), with mass spectrometry analysis. A total of 1,213 unique N-glycosites from 611 N-glycoproteins were confidently identified. These N-glycoproteins were primarily localized to the extracellular space and plasma membrane, supporting the important role of N-glycosylation in the secretory pathway. Coupling label-free quantification with a hierarchical clustering strategy, we determined the differential regulation of several N-glycoproteins that are related to metastasis, among which AFP, DKK1, FN1, CD151 and TGFβ2 were up-regulated in HCCLM3 cells. The inclusion of the well-known metastasis-related proteins AFP and DKK1 in this list provides solid supports for our study. Further western blotting experiments detecting FN1 and FAT1 confirmed our discovery. The glycoproteome strategy in this study provides an effective means to explore potential cancer biomarkers. PMID:24324730

  16. Synthetic scope, computational chemistry and mechanism of a base induced 5-endo cyclization of benzyl alkynyl sulfides

    PubMed Central

    Motto, John M.; Castillo, Álvaro; Montemayer, Laura K.; Sheepwash, Erin E.

    2011-01-01

    We present an experimental and computational study of the reaction of aryl substituted benzyl 1-alkynyl sulfides with potassium alkoxide in acetonitrile, which produces 2-aryl 2,3-dihydrothiophenes in poor to good yields. The cyclization is most efficient with electron withdrawing groups on the aromatic ring. Evidence indicates there is rapid exchange of protons and tautomerism of the alkynyl unit prior to cyclization. Theoretical calculations were also conducted to help rationalize the base induced 5-endo cyclization of benzyl 1-propynyl sulfide (1a). The potential energy surface was calculated for the formation of 2,3-dihydrothiophene in a reaction of benzyl 1-propynyl sulfide (1a) with potassium methoxide. Geometries were optimized with CAM-B3LYP/6-311+G(d,p) in acetonitrile with the CPCM solvent model. It is significant that the benzyl propa-1,2-dien-1-yl sulfane (6) possessed a lower benzylic proton affinity than the benzyl prop-2-yn-1-yl sulfane (8) thus favoring the base induced reaction of the former. From benzyl(propa-1,2-dien-1-yl sulfane (6), 2,3-dihydrothiophene can be formed via a conjugate base that undergoes 5-endo-trig cyclization followed by a protonation step. PMID:21442022

  17. Monitoring of facial stress during space flight: Optical computer recognition combining discriminative and generative methods

    NASA Astrophysics Data System (ADS)

    Dinges, David F.; Venkataraman, Sundara; McGlinchey, Eleanor L.; Metaxas, Dimitris N.

    2007-02-01

    Astronauts are required to perform mission-critical tasks at a high level of functional capability throughout spaceflight. Stressors can compromise their ability to do so, making early objective detection of neurobehavioral problems in spaceflight a priority. Computer optical approaches offer a completely unobtrusive way to detect distress during critical operations in space flight. A methodology was developed and a study completed to determine whether optical computer recognition algorithms could be used to discriminate facial expressions during stress induced by performance demands. Stress recognition from a facial image sequence is a subject that has not received much attention although it is an important problem for many applications beyond space flight (security, human-computer interaction, etc.). This paper proposes a comprehensive method to detect stress from facial image sequences by using a model-based tracker. The image sequences were captured as subjects underwent a battery of psychological tests under high- and low-stress conditions. A cue integration-based tracking system accurately captured the rigid and non-rigid parameters of different parts of the face (eyebrows, lips). The labeled sequences were used to train the recognition system, which consisted of generative (hidden Markov model) and discriminative (support vector machine) parts that yield results superior to using either approach individually. The current optical algorithm methods performed at a 68% accuracy rate in an experimental study of 60 healthy adults undergoing periods of high-stress versus low-stress performance demands. Accuracy and practical feasibility of the technique is being improved further with automatic multi-resolution selection for the discretization of the mask, and automated face detection and mask initialization algorithms.

  18. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  19. Forensic Chemistry

    NASA Astrophysics Data System (ADS)

    Bell, Suzanne

    2009-07-01

    Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.

  20. Inter-staple Dithiol Crosslinking in Au25(SR)18 Nanomolecules: A Combined Mass Spectrometric and Computational Study

    SciTech Connect

    Dass, Amala; Jiang, Deen; Jupally, Vijay; Kota, Rajesh; Mattern, Daniell; Tschumper, Gregory; Van Dornshuld, Eric

    2011-01-01

    A systematic study of cross-linking chemistry of the Au{sub 25}(SR){sub 18} nanomolecule by dithiols of varying chain length, HS-(CH{sub 2}){sub n}-SH where n = 2, 3, 4, 5, and 6, is presented here. Monothiolated Au{sub 25} has six [RSAuSRAuSR] staple motifs on its surface, and MALDI mass spectrometry data of the ligand exchanged clusters show that propane (C3) and butane (C4) dithiols have ideal chain lengths for interstaple cross-linking and that up to six C3 or C4 dithiols can be facilely exchanged onto the cluster surface. Propanedithiol predominately exchanges with two monothiols at a time, making cross-linking bridges, while butanedithiol can exchange with either one or two monothiols at a time. The extent of cross-linking can be controlled by the Au{sub 25}(SR){sub 18} to dithiol ratio, the reaction time of ligand exchange, or the addition of a hydrophobic tail to the dithiol. MALDI MS suggests that during ethane (C2) dithiol exchange, two ethanedithiols become connected by a disulfide bond; this result is supported by density functional theory (DFT) prediction of the optimal chain length for the intrastaple coupling. Both optical absorption spectroscopy and DFT computations show that the electronic structure of the Au{sub 25} nanomolecule retains its main features after exchange of up to eight monothiol ligands.

  1. A model for combined targeting and tracking tasks in computer applications.

    PubMed

    Senanayake, Ransalu; Hoffmann, Errol R; Goonetilleke, Ravindra S

    2013-11-01

    Current models for targeted-tracking are discussed and shown to be inadequate as a means of understanding the combined task of tracking, as in the Drury's paradigm, and having a final target to be aimed at, as in the Fitts' paradigm. It is shown that the task has to be split into components that are, in general, performed sequentially and have a movement time component dependent on the difficulty of the individual component of the task. In some cases, the task time may be controlled by the Fitts' task difficulty, and in others, it may be dominated by the Drury's task difficulty. Based on an experiment carried out that captured movement time in combinations of visually controlled and ballistic movements, a model for movement time in targeted-tracking was developed. PMID:24081679

  2. A model for combined targeting and tracking tasks in computer applications.

    PubMed

    Senanayake, Ransalu; Hoffmann, Errol R; Goonetilleke, Ravindra S

    2013-11-01

    Current models for targeted-tracking are discussed and shown to be inadequate as a means of understanding the combined task of tracking, as in the Drury's paradigm, and having a final target to be aimed at, as in the Fitts' paradigm. It is shown that the task has to be split into components that are, in general, performed sequentially and have a movement time component dependent on the difficulty of the individual component of the task. In some cases, the task time may be controlled by the Fitts' task difficulty, and in others, it may be dominated by the Drury's task difficulty. Based on an experiment carried out that captured movement time in combinations of visually controlled and ballistic movements, a model for movement time in targeted-tracking was developed.

  3. An automated tuberculosis screening strategy combining X-ray-based computer-aided detection and clinical information

    PubMed Central

    Melendez, Jaime; Sánchez, Clara I.; Philipsen, Rick H. H. M.; Maduskar, Pragnya; Dawson, Rodney; Theron, Grant; Dheda, Keertan; van Ginneken, Bram

    2016-01-01

    Lack of human resources and radiological interpretation expertise impair tuberculosis (TB) screening programmes in TB-endemic countries. Computer-aided detection (CAD) constitutes a viable alternative for chest radiograph (CXR) reading. However, no automated techniques that exploit the additional clinical information typically available during screening exist. To address this issue and optimally exploit this information, a machine learning-based combination framework is introduced. We have evaluated this framework on a database containing 392 patient records from suspected TB subjects prospectively recruited in Cape Town, South Africa. Each record comprised a CAD score, automatically computed from a CXR, and 12 clinical features. Comparisons with strategies relying on either CAD scores or clinical information alone were performed. Our results indicate that the combination framework outperforms the individual strategies in terms of the area under the receiving operating characteristic curve (0.84 versus 0.78 and 0.72), specificity at 95% sensitivity (49% versus 24% and 31%) and negative predictive value (98% versus 95% and 96%). Thus, it is believed that combining CAD and clinical information to estimate the risk of active disease is a promising tool for TB screening. PMID:27126741

  4. The Mark III Hypercube-Ensemble Computers

    NASA Technical Reports Server (NTRS)

    Peterson, John C.; Tuazon, Jesus O.; Lieberman, Don; Pniel, Moshe

    1988-01-01

    Mark III Hypercube concept applied in development of series of increasingly powerful computers. Processor of each node of Mark III Hypercube ensemble is specialized computer containing three subprocessors and shared main memory. Solves problem quickly by simultaneously processing part of problem at each such node and passing combined results to host computer. Disciplines benefitting from speed and memory capacity include astrophysics, geophysics, chemistry, weather, high-energy physics, applied mechanics, image processing, oil exploration, aircraft design, and microcircuit design.

  5. Computational Model of Primary Visual Cortex Combining Visual Attention for Action Recognition.

    PubMed

    Shu, Na; Gao, Zhiyong; Chen, Xiangan; Liu, Haihua

    2015-01-01

    Humans can easily understand other people's actions through visual systems, while computers cannot. Therefore, a new bio-inspired computational model is proposed in this paper aiming for automatic action recognition. The model focuses on dynamic properties of neurons and neural networks in the primary visual cortex (V1), and simulates the procedure of information processing in V1, which consists of visual perception, visual attention and representation of human action. In our model, a family of the three-dimensional spatial-temporal correlative Gabor filters is used to model the dynamic properties of the classical receptive field of V1 simple cell tuned to different speeds and orientations in time for detection of spatiotemporal information from video sequences. Based on the inhibitory effect of stimuli outside the classical receptive field caused by lateral connections of spiking neuron networks in V1, we propose surround suppressive operator to further process spatiotemporal information. Visual attention model based on perceptual grouping is integrated into our model to filter and group different regions. Moreover, in order to represent the human action, we consider the characteristic of the neural code: mean motion map based on analysis of spike trains generated by spiking neurons. The experimental evaluation on some publicly available action datasets and comparison with the state-of-the-art approaches demonstrate the superior performance of the proposed model. PMID:26132270

  6. Computational Model of Primary Visual Cortex Combining Visual Attention for Action Recognition

    PubMed Central

    Shu, Na; Gao, Zhiyong; Chen, Xiangan; Liu, Haihua

    2015-01-01

    Humans can easily understand other people’s actions through visual systems, while computers cannot. Therefore, a new bio-inspired computational model is proposed in this paper aiming for automatic action recognition. The model focuses on dynamic properties of neurons and neural networks in the primary visual cortex (V1), and simulates the procedure of information processing in V1, which consists of visual perception, visual attention and representation of human action. In our model, a family of the three-dimensional spatial-temporal correlative Gabor filters is used to model the dynamic properties of the classical receptive field of V1 simple cell tuned to different speeds and orientations in time for detection of spatiotemporal information from video sequences. Based on the inhibitory effect of stimuli outside the classical receptive field caused by lateral connections of spiking neuron networks in V1, we propose surround suppressive operator to further process spatiotemporal information. Visual attention model based on perceptual grouping is integrated into our model to filter and group different regions. Moreover, in order to represent the human action, we consider the characteristic of the neural code: mean motion map based on analysis of spike trains generated by spiking neurons. The experimental evaluation on some publicly available action datasets and comparison with the state-of-the-art approaches demonstrate the superior performance of the proposed model. PMID:26132270

  7. O2: A novel combined online and offline computing system for the ALICE Experiment after 2018

    NASA Astrophysics Data System (ADS)

    Ananya; Alarcon Do Passo Suaide, A.; Alves Garcia Prado, C.; Alt, T.; Aphecetche, L.; Agrawal, N.; Avasthi, A.; Bach, M.; Bala, R.; Barnafoldi, G.; Bhasin, A.; Belikov, J.; Bellini, F.; Betev, L.; Breitner, T.; Buncic, P.; Carena, F.; Carena, W.; Chapeland, S.; Chibante Barroso, V.; Cliff, F.; Costa, F.; Cunqueiro Mendez, L.; Dash, S.; Delort, C.; Denes, E.; Divia, R.; Doenigus, B.; Engel, H.; Eschweiler, D.; Fuchs, U.; Gheata, A.; Gheata, M.; Gomez Ramirez, A.; Gorbunov, S.; Graczykowski, L.; Grigoras, A.; Grigoras, C.; Grigore, A.; Grosso, R.; Guernane, R.; Gupta, A.; Hrivnacova, I.; Hristov, P.; Ionita, C.; Ivanov, M.; Janik, M.; Kalcher, S.; Kassalias, N.; Kebschull, U.; Khandelwal, R.; Kushpil, S.; Kisel, I.; Kiss, T.; Kollegger, T.; Kowalski, M.; Kretz, M.; Kulakov, I.; Lafage, V.; Lara, C.; Legrand, I.; Lindenstruth, V.; Maevskaya, A.; Malzacher, P.; Morsch, A.; Nandi, B.; Niculescu, M.; Pillot, P.; Planinic, M.; Pluta, J.; Poljak, N.; Rajput, S.; Read, K.; Ribon, A.; Rohr, D.; Rubin, G.; Shahoyan, R.; Sharma, A.; Simonetti, G.; Smorholm, O.; Soós, C.; Szymanski, M.; Telesca, A.; Thaeder, J.; Udupa, A.; Vande Vyvre, P.; Vennedey, F.; von Haller, B.; Wenzel, S.; Zampolli, C.; Zyzak, M.; Alice Collaboration

    2014-06-01

    ALICE (A Large Ion Collider Experiment) is a detector dedicated to the studies with heavy ion collisions exploring the physics of strongly interacting nuclear matter and the quark-gluon plasma at the CERN LHC (Large Hadron Collider). After the second long shutdown of the LHC, the ALICE Experiment will be upgraded to make high precision measurements of rare probes at low pT, which cannot be selected with a trigger, and therefore require a very large sample of events recorded on tape. The online computing system will be completely redesigned to address the major challenge of sampling the full 50 kHz Pb-Pb interaction rate increasing the present limit by a factor of 100. This upgrade will also include the continuous un-triggered read-out of two detectors: ITS (Inner Tracking System) and TPC (Time Projection Chamber)) producing a sustained throughput of 1 TB/s. This unprecedented data rate will be reduced by adopting an entirely new strategy where calibration and reconstruction are performed online, and only the reconstruction results are stored while the raw data are discarded. This system, already demonstrated in production on the TPC data since 2011, will be optimized for the online usage of reconstruction algorithms. This implies much tighter coupling between online and offline computing systems. An R&D program has been set up to meet this huge challenge. The object of this paper is to present this program and its first results.

  8. Combining computational models, semantic annotations and simulation experiments in a graph database

    PubMed Central

    Henkel, Ron; Wolkenhauer, Olaf; Waltemath, Dagmar

    2015-01-01

    Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models’ structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/ PMID:25754863

  9. Crossing Levels and Representations: The Connected Chemistry (CC1) Curriculum

    ERIC Educational Resources Information Center

    Levy, Sharona T.; Wilensky, Uri

    2009-01-01

    Connected Chemistry (named CC1 to denote Connected Chemistry Chapter 1) is a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry. It views chemistry from an "emergent" perspective, how macroscopic phenomena result from the interaction of many submicroscopic particles. Connected Chemistry employs…

  10. Response Surface Modeling of Combined-Cycle Propulsion Components using Computational Fluid Dynamics

    NASA Technical Reports Server (NTRS)

    Steffen, C. J., Jr.

    2002-01-01

    Three examples of response surface modeling with CFD are presented for combined cycle propulsion components. The examples include a mixed-compression-inlet during hypersonic flight, a hydrogen-fueled scramjet combustor during hypersonic flight, and a ducted-rocket nozzle during all-rocket flight. Three different experimental strategies were examined, including full factorial, fractionated central-composite, and D-optimal with embedded Plackett-Burman designs. The response variables have been confined to integral data extracted from multidimensional CFD results. Careful attention to uncertainty assessment and modeling bias has been addressed. The importance of automating experimental setup and effectively communicating statistical results are emphasized.

  11. Novel diode-based laser system for combined transcutaneous monitoring and computer-controlled intermittent treatment of jaundiced neonates

    NASA Astrophysics Data System (ADS)

    Hamza, Mostafa; El-Ahl, Mohammad H. S.; Hamza, Ahmad M.

    2001-06-01

    The high efficacy of laser phototherapy combined with transcutaneous monitoring of serum bilirubin provides optimum safety for jaundiced infants from the risk of bilirubin encephalopathy. In this paper the authors introduce the design and operating principles of a new laser system that can provide simultaneous monitoring and treatment of several jaundiced babies at one time. The new system incorporates diode-based laser sources oscillating at selected wavelengths to achieve both transcutaneous differential absorption measurements of bilirubin concentration in addition to the computer controlled intermittent laser therapy through a network of optical fibers. The detailed description and operating characteristics of this system are presented.

  12. Inlet Development for a Rocket Based Combined Cycle, Single Stage to Orbit Vehicle Using Computational Fluid Dynamics

    NASA Technical Reports Server (NTRS)

    DeBonis, J. R.; Trefny, C. J.; Steffen, C. J., Jr.

    1999-01-01

    Design and analysis of the inlet for a rocket based combined cycle engine is discussed. Computational fluid dynamics was used in both the design and subsequent analysis. Reynolds averaged Navier-Stokes simulations were performed using both perfect gas and real gas assumptions. An inlet design that operates over the required Mach number range from 0 to 12 was produced. Performance data for cycle analysis was post processed using a stream thrust averaging technique. A detailed performance database for cycle analysis is presented. The effect ot vehicle forebody compression on air capture is also examined.

  13. A computer-based training system combining virtual reality and multimedia

    NASA Technical Reports Server (NTRS)

    Stansfield, Sharon A.

    1993-01-01

    Training new users of complex machines is often an expensive and time-consuming process. This is particularly true for special purpose systems, such as those frequently encountered in DOE applications. This paper presents a computer-based training system intended as a partial solution to this problem. The system extends the basic virtual reality (VR) training paradigm by adding a multimedia component which may be accessed during interaction with the virtual environment. The 3D model used to create the virtual reality is also used as the primary navigation tool through the associated multimedia. This method exploits the natural mapping between a virtual world and the real world that it represents to provide a more intuitive way for the student to interact with all forms of information about the system.

  14. Improved Wind Turbine Drivetrain Reliability using a Combined Experimental, Computational, and Analytical Approach (Presentation)

    SciTech Connect

    Guo, Yi; Bergua, R.; van Dam, J.; Jove, J.; Campbell, J.

    2014-08-01

    Nontorque loads induced by the wind turbine rotor overhang weight and aerodynamic forces can greatly affect drivetrain loads and responses. If not addressed properly, these loads can result in a decrease in gearbox component life. This work uses analytical modeling, computational modeling, and experimental data to evaluate a unique drivetrain design that minimize the effects of nontorque loads on gearbox reliability: the Pure Torque drivetrain developed by Alstom. The drivetrain has a hub-support configuration that transmits nontorque loads directly into the tower rather than through the gearbox as in other design approaches. An analytical model of Alstom's Pure Torque drivetrain provides insight into the relationships among turbine component weights, aerodynamic forces, and the resulting drivetrain loads. Main shaft bending loads are orders of magnitude lower than the rated torque and are hardly affected by wind speed and turbine operations.

  15. Structures, Electronics, and Reactivity of Strained Phosphazane Cages: A Combined Experimental and Computational Study.

    PubMed

    Roth, Torsten; Vasilenko, Vladislav; Wadepohl, Hubert; Wright, Dominic S; Gade, Lutz H

    2015-08-01

    A series of formamidine-bridged P2N2 cages have been prepared. Upon deprotonation, these compounds serve as valuable precursors to hybrid N-heterocyclic carbene ligands, whereas direct metalation gives rearranged dimetallic complexes as a result of cleavage of the formamidine bridge. The latter metal complexes contain an intact cyclophosphazane moiety that coordinates two distinct metal centers in a monodentate and a chelating fashion. A computational study has been carried out to elucidate the bonding within the P2N2 framework as well as the reactivity patterns. Natural bond orbital analysis indicates that the cage motif is poorly described by localized Lewis structures and that negative hyperconjugation effects govern the stability of the bicyclic framework. The donor capacity of the cyclophosphazane unit was assessed by inspection of the frontier molecular orbitals, highlighting the fact that π-back-donation from the metal fragments is crucial for effective metal-ligand binding. PMID:26181231

  16. A computer-based training system combining virtual reality and multimedia

    SciTech Connect

    Stansfield, S.A.

    1993-04-28

    Training new users of complex machines is often an expensive and time-consuming process. This is particularly true for special purpose systems, such as those frequently encountered in DOE applications. This paper presents a computer-based training system intended as a partial solution to this problem. The system extends the basic virtual reality (VR) training paradigm by adding a multimedia component which may be accessed during interaction with the virtual environment: The 3D model used to create the virtual reality is also used as the primary navigation tool through the associated multimedia. This method exploits the natural mapping between a virtual world and the real world that it represents to provide a more intuitive way for the student to interact with all forms of information about the system.

  17. Combined bending and thermal fatigue of high-temperature metal-matrix composites - Computational simulation

    NASA Technical Reports Server (NTRS)

    Gotsis, Pascal K.; Chamis, Christos C.

    1992-01-01

    The nonlinear behavior of a high-temperature metal-matrix composite (HT-MMC) was simulated by using the metal matrix composite analyzer (METCAN) computer code. The simulation started with the fabrication process, proceeded to thermomechanical cyclic loading, and ended with the application of a monotonic load. Classical laminate theory and composite micromechanics and macromechanics are used in METCAN, along with a multifactor interaction model for the constituents behavior. The simulation of the stress-strain behavior from the macromechanical and the micromechanical points of view, as well as the initiation and final failure of the constituents and the plies in the composite, were examined in detail. It was shown that, when the fibers and the matrix were perfectly bonded, the fracture started in the matrix and then propagated with increasing load to the fibers. After the fibers fractured, the composite lost its capacity to carry additional load and fractured.

  18. A Combined Experimental and Computational Study on Selected Physical Properties of Aminosilicones

    SciTech Connect

    Perry, RJ; Genovese, SE; Farnum, RL; Spiry, I; Perry, TM; O'Brien, MJ; Xie, HB; Chen, DL; Enick, RM; Johnson, JK; Alshahrani, SS

    2014-01-29

    A number of physical properties of aminosilicones have been determined experimentally and predicted computationally. It was found that COSMO-RS predicted the densities of the materials under study to within about 4% of the experimentally determined values. Vapor pressure measurements were performed, and all of the aminosilicones of interest were found to be significantly less volatile than the benchmark MEA material. COSMO-RS was reasonably accurate for predicting the vapor pressures for aminosilicones that were thermally stable. The heat capacities of all aminosilicones tested were between 2.0 and 2.3 J/(g.degrees C); again substantially lower than a benchmark 30% aqueous MEA solution. Surface energies for the aminosilicones were found to be 23.3-28.3 dyne/cm and were accurately predicted using the parachor method.

  19. Combined thermal and bending fatigue of high-temperature metal-matrix composites: Computational simulation

    NASA Technical Reports Server (NTRS)

    Gotsis, Pascal K.

    1991-01-01

    The nonlinear behavior of a high-temperature metal-matrix composite (HT-MMC) was simulated by using the metal matrix composite analyzer (METCAN) computer code. The simulation started with the fabrication process, proceeded to thermomechanical cyclic loading, and ended with the application of a monotonic load. Classical laminate theory and composite micromechanics and macromechanics are used in METCAN, along with a multifactor interaction model for the constituents behavior. The simulation of the stress-strain behavior from the macromechanical and the micromechanical points of view, as well as the initiation and final failure of the constituents and the plies in the composite, were examined in detail. It was shown that, when the fibers and the matrix were perfectly bonded, the fracture started in the matrix and then propagated with increasing load to the fibers. After the fibers fractured, the composite lost its capacity to carry additional load and fractured.

  20. Improving Wind Turbine Drivetrain Reliability Using a Combined Experimental, Computational, and Analytical Approach

    SciTech Connect

    Guo, Y.; van Dam, J.; Bergua, R.; Jove, J.; Campbell, J.

    2015-03-01

    Nontorque loads induced by the wind turbine rotor overhang weight and aerodynamic forces can greatly affect drivetrain loads and responses. If not addressed properly, these loads can result in a decrease in gearbox component life. This work uses analytical modeling, computational modeling, and experimental data to evaluate a unique drivetrain design that minimizes the effects of nontorque loads on gearbox reliability: the Pure Torque(R) drivetrain developed by Alstom. The drivetrain has a hub-support configuration that transmits nontorque loads directly into the tower rather than through the gearbox as in other design approaches. An analytical model of Alstom's Pure Torque drivetrain provides insight into the relationships among turbine component weights, aerodynamic forces, and the resulting drivetrain loads. Main shaft bending loads are orders of magnitude lower than the rated torque and are hardly affected by wind conditions and turbine operations.

  1. Long term pH-static experiments in combination with computer modelling

    SciTech Connect

    Baeverman, C.; Neretnieks, I.

    1996-12-31

    Large quantities of MSWI bottom ash are produced in the world today, and has to be taken care of. According to the physical properties of the ash it can be used, instead of gravel, as filling material in, for example, road construction. For environmental reasons this is acceptable only if the leaching from the construction does not affect the surroundings. In Sweden the bottom ash has so far been placed in landfills and even there the environmental impact has to be minimized. Long term pH-static experiments have been performed on municipal solid waste (MSWI) bottom ash between pH 6 and 9.25. Most of the reactions take place within the first 50 days of the experiment. The experiments resulted in a pH titration curve that can be used for determining the pH buffering capacity at different pH levels. The curve is used to assess the different pK{sub a}-values of the ash. These can be used to identify the main pH buffering minerals in the ash as the pK{sub a}-values are mineral specific. The buffering capacity at the different pK{sub a}-values gives the amount of the mineral present in the ash. The information obtained by the pH-static experiments can be used for long time computer simulations with geochemical transport programs. Both laboratory experiments and computer simulations have shown that the pH buffering capacity is the key variable that controls the leaching of many metals e.g. copper. Simulations have shown that the copper in a pile of ash can be accumulated at a pH front, where the pH changes rapidly because the buffering capacity is depleted, and later leached all at the same time with very high concentration.

  2. The effects of computer-assisted instruction on number combination skill in at-risk first graders.

    PubMed

    Fuchs, Lynn S; Fuchs, Douglas; Hamlet, Carol L; Powell, Sarah R; Capizzi, Andrea M; Seethaler, Pamela M

    2006-01-01

    The purpose of this pilot study was to assess the potential for computer-assisted instruction (CAI) to enhance number combination skill among children with concurrent risk for math disability and reading disability. A secondary purpose was to examine the effects of CAI on spelling. At-risk students were assigned randomly to math or spelling CAI, which they received in 50 sessions over 18 weeks. Acquisition and transfer effects were assessed. The results indicated that math CAI was effective in promoting addition but not subtraction number combination skill and that transfer to arithmetic story problems did not occur. Spelling CAI effects were reliable on acquisition and transfer spelling measures, with small to moderate effect sizes on transfer to reading measures. These results provide the basis for additional work with larger samples. PMID:17004677

  3. Positioning accuracy of cone-beam computed tomography in combination with a HexaPOD robot treatment table

    SciTech Connect

    Meyer, Juergen . E-mail: juergen.meyer@canterbury.ac.nz; Wilbert, Juergen; Baier, Kurt; Guckenberger, Matthias; Richter, Anne; Sauer, Otto; Flentje, Michael

    2007-03-15

    Purpose: To scrutinize the positioning accuracy and reproducibility of a commercial hexapod robot treatment table (HRTT) in combination with a commercial cone-beam computed tomography system for image-guided radiotherapy (IGRT). Methods and Materials: The mechanical stability of the X-ray volume imaging (XVI) system was tested in terms of reproducibility and with a focus on the moveable parts, i.e., the influence of kV panel and the source arm on the reproducibility and accuracy of both bone and gray value registration using a head-and-neck phantom. In consecutive measurements the accuracy of the HRTT for translational, rotational, and a combination of translational and rotational corrections was investigated. The operational range of the HRTT was also determined and analyzed. Results: The system performance of the XVI system alone was very stable with mean translational and rotational errors of below 0.2 mm and below 0.2{sup o}, respectively. The mean positioning accuracy of the HRTT in combination with the XVI system summarized over all measurements was below 0.3 mm and below 0.3{sup o} for translational and rotational corrections, respectively. The gray value match was more accurate than the bone match. Conclusion: The XVI image acquisition and registration procedure were highly reproducible. Both translational and rotational positioning errors can be corrected very precisely with the HRTT. The HRTT is therefore well suited to complement cone-beam computed tomography to take full advantage of position correction in six degrees of freedom for IGRT. The combination of XVI and the HRTT has the potential to improve the accuracy of high-precision treatments.

  4. Evaluation of various mental task combinations for near-infrared spectroscopy-based brain-computer interfaces

    NASA Astrophysics Data System (ADS)

    Hwang, Han-Jeong; Lim, Jeong-Hwan; Kim, Do-Won; Im, Chang-Hwan

    2014-07-01

    A number of recent studies have demonstrated that near-infrared spectroscopy (NIRS) is a promising neuroimaging modality for brain-computer interfaces (BCIs). So far, most NIRS-based BCI studies have focused on enhancing the accuracy of the classification of different mental tasks. In the present study, we evaluated the performances of a variety of mental task combinations in order to determine the mental task pairs that are best suited for customized NIRS-based BCIs. To this end, we recorded event-related hemodynamic responses while seven participants performed eight different mental tasks. Classification accuracies were then estimated for all possible pairs of the eight mental tasks (C=28). Based on this analysis, mental task combinations with relatively high classification accuracies frequently included the following three mental tasks: "mental multiplication," "mental rotation," and "right-hand motor imagery." Specifically, mental task combinations consisting of two of these three mental tasks showed the highest mean classification accuracies. It is expected that our results will be a useful reference to reduce the time needed for preliminary tests when discovering individual-specific mental task combinations.

  5. Evaluation of various mental task combinations for near-infrared spectroscopy-based brain-computer interfaces.

    PubMed

    Hwang, Han-Jeong; Lim, Jeong-Hwan; Kim, Do-Won; Im, Chang-Hwan

    2014-01-01

    A number of recent studies have demonstrated that near-infrared spectroscopy (NIRS) is a promisingneuroimaging modality for brain-computer interfaces (BCIs). So far, most NIRS-based BCI studies have focusedon enhancing the accuracy of the classification of different mental tasks. In the present study, we evaluated theperformances of a variety of mental task combinations in order to determine the mental task pairs that are bestsuited for customized NIRS-based BCIs. To this end, we recorded event-related hemodynamic responses whileseven participants performed eight different mental tasks. Classification accuracies were then estimated for allpossible pairs of the eight mental tasks (8C2 = 28). Based on this analysis, mental task combinations with relatively high classification accuracies frequently included the following three mental tasks: “mental multiplication,” “mental rotation,” and “right-hand motor imagery.” Specifically, mental task combinations consisting of two of these three mental tasks showed the highest mean classification accuracies. It is expected that our results will be a useful reference to reduce the time needed for preliminary tests when discovering individual-specific mental task combinations.

  6. Opening of an icosahedral boron framework: A combined infrared spectroscopic and computational study

    NASA Astrophysics Data System (ADS)

    Fagiani, Matias R.; Liu Zeonjuk, L.; Esser, Tim K.; Gabel, Detlef; Heine, Thomas; Asmis, Knut R.; Warneke, Jonas

    2015-04-01

    The opening of an icosahderal boron cage in the periodinated closo-dodecaborate B12I122- upon deiodination is studied using cryogenic ion trap vibrational spectroscopy combined with electronic structure calculations. Comparison of simulated vibrational spectra to the infrared photodissociation spectra of messenger-tagged B12I122- and B12In- (n = 7-9) formed by skimmer collision induced dissociation shows that the larger clusters absorb exclusively below 975 cm-1 and hence exhibit quasi-icosahedral B12-cage structures, while the higher energy absorptions in-between 1000 and 1300 cm-1 observed for n = 7 can only be recovered by considering a breakup of the icosahedral cage upon deiodination from n = 8 to n = 7.

  7. Combined experimental and computational study of high-pressure behavior of triphenylene.

    PubMed

    Zhao, Xiao-Miao; Zhong, Guo-Hua; Zhang, Jiang; Huang, Qiao-Wei; Goncharov, Alexander F; Lin, Hai-Qing; Chen, Xiao-Jia

    2016-01-01

    We have performed measurements of Raman scattering, synchrotron x-ray diffraction, and visible transmission spectroscopy combined with density functional theory calculations to study the pressure effect on solid triphenylene. The spectroscopic results demonstrate substantial change of the molecular configuration at 1.4 GPa from the abrupt change of splitting, disappearance, and appearance of some modes. The structure of triphenylene is found be to stable at high pressures without any evidence of structural transition from the x-ray diffraction patterns. The obtained lattice parameters show a good agreement between experiments and calculations. The obtained band gap systematically decreases with increasing pressure. With the application of pressure, the molecular planes become more and more parallel relative to each other. The theoretical calculations indicate that this organic compound becomes metallic at 180 GPa, fueling the hope for the possible realization of superconductivity at high pressure. PMID:27161429

  8. Bioinspired Tungsten Dithiolene Catalysts for Hydrogen Evolution: A Combined Electrochemical, Photochemical, and Computational Study.

    PubMed

    Gomez-Mingot, Maria; Porcher, Jean-Philippe; Todorova, Tanya K; Fogeron, Thibault; Mellot-Draznieks, Caroline; Li, Yun; Fontecave, Marc

    2015-10-29

    Bis(dithiolene)tungsten complexes, W(VI)O2 (L = dithiolene)2 and W(IV)O (L = dithiolene)2, which mimic the active site of formate dehydrogenases, have been characterized by cyclic voltammetry and controlled potential electrolysis in acetonitrile. They are shown to be able to catalyze the electroreduction of protons into hydrogen in acidic organic media, with good Faradaic yields (75-95%) and good activity (rate constants of 100 s(-1)), with relatively high overpotentials (700 mV). They also catalyze proton reduction into hydrogen upon visible light irradiation, in combination with [Ru(bipyridine)3](2+) as a photosensitizer and ascorbic acid as a sacrificial electron donor. On the basis of detailed DFT calculations, a reaction mechanism is proposed in which the starting W(VI)O2 (L = dithiolene)2 complex acts as a precatalyst and hydrogen is further formed from a key reduced W-hydroxo-hydride intermediate.

  9. Combined experimental and computational study of high-pressure behavior of triphenylene

    PubMed Central

    Zhao, Xiao-Miao; Zhong, Guo-Hua; Zhang, Jiang; Huang, Qiao-Wei; Goncharov, Alexander F.; Lin, Hai-Qing; Chen, Xiao-Jia

    2016-01-01

    We have performed measurements of Raman scattering, synchrotron x-ray diffraction, and visible transmission spectroscopy combined with density functional theory calculations to study the pressure effect on solid triphenylene. The spectroscopic results demonstrate substantial change of the molecular configuration at 1.4 GPa from the abrupt change of splitting, disappearance, and appearance of some modes. The structure of triphenylene is found be to stable at high pressures without any evidence of structural transition from the x-ray diffraction patterns. The obtained lattice parameters show a good agreement between experiments and calculations. The obtained band gap systematically decreases with increasing pressure. With the application of pressure, the molecular planes become more and more parallel relative to each other. The theoretical calculations indicate that this organic compound becomes metallic at 180 GPa, fueling the hope for the possible realization of superconductivity at high pressure. PMID:27161429

  10. A Combined Experimental and Computational Investigation on Spectroscopic and Photophysical Properties of a Coumarinyl Chalcone.

    PubMed

    Al-Sehemi, Abdullah G; Pannipara, Mehboobali; Kalam, Abul; Asiri, Abdullah M

    2016-07-01

    Here, we synthesized a new coumarinyl chalcone derivative 3-[3-(3-Methyl-thiophen-2-yl)-acryloyl]-chromen-2-one (MTC) by simple and proficient method. A comprehensive study on the photophysics of a coumarinyl chalcone derivative having pi-conjugated potential chromophore system 3-[3-(3-Methyl-thiophen-2-yl)-acryloyl]-chromen-2-one (MTC) has been carried out spectroscopically. The electronic absorption and emission characteristic of MTC were studied in different protic and aprotic solvents using absorption and steady-state fluorescence techniques. The spectral behavior of this compound is found to be extremely sensitive to the polarity and hydrogen bonding nature of the solvent. The compound shows very strong solvent polarity dependent changes in their photophysical characteristics, namely, remarkable red shift in the emission spectra with increasing solvent polarity, change in Stokes shift, significant reduction in the fluorescence quantum yield; indicating that the fluorescence states of these compounds are of intramolecular charge transfer (ICT) character. The solvent effect on the photophysical parameters such as singlet absorption, molar absorptivity, oscillator strength, dipole moment, fluorescence spectra, and fluorescence quantum yield of the compound has been investigated in detail. The difference between the excited and ground state dipole moments (Δμ) were estimated from solvatochromic methods using Lippert-Mataga and Reichardt's correlations. The prepared compound was also studied by density functional theory (DFT) and time-dependent density functional theory (TDDFT). The results revealed that it could be easily reproduce by computational means. PMID:27307021

  11. Combined kinetic studies and computational analysis on kojic acid analogous as tyrosinase inhibitors.

    PubMed

    Lima, Carlyle Ribeiro; Silva, José Rogério A; de Tássia Carvalho Cardoso, Erica; Silva, Edilene O; Lameira, Jerônimo; do Nascimento, José Luiz Martins; do Socorro Barros Brasil, Davi; Alves, Cláudio N

    2014-01-01

    Tyrosinase is a key enzyme in melanin synthesis and widely distributed in plants and animals tissues. In mammals, this enzyme is related to pigment production, involved in wound healing, primary immune response and it can also contribute to catecholamines synthesis in the brain. Consequently, tyrosinase enzyme represents an attractive and selective target in the field of the medicine, cosmetics and bio-insecticides. In this paper, experimental kinetics and computational analysis were used to study the inhibition of tyrosinase by analogous of Kojic acid. The main interactions occurring between inhibitors-tyrosinase complexes and the influence of divalent cation (Cu2+) in enzymatic inhibition were investigated by using molecular docking, molecular dynamic simulations and electrostatic binding free energy by using the Linear Interaction Energy (LIE) method. The results showed that the electrostatic binding free energy are correlated with values of constant inhibition (r2 = 0.97).Thus, the model obtained here could contribute to future studies of this important system and, therefore, eventually facilitate development of tyrosinase inhibitors. PMID:25004069

  12. Study of injuries combining computer simulation in motorcycle-car collision accidents.

    PubMed

    Guo, Lei; Jin, Xian-Long; Zhang, Xiao-Yun; Shen, Jie; Chen, Yi-Jiu; Chen, Jian-Guo

    2008-05-20

    This paper presents the approach of computer simulation to clarify the questions faced by forensic experts about what causes the various injuries characteristic of two motorcycle victims, including the motorcycle driver and the back seat occupant on the motorcycle, and how to exactly confirm which one of them is the motorcycle driver. Two typical motorcycle-car accident cases were reconstructed to analyze the movement and the load of both the motorcycle driver and the back seat occupant in the collision course. In case one, the back seat occupant suffered fatal head injuries when he fell on the ground after being thrown higher than the motorcycle driver over the top of the car. In case two, the compressive force loaded by the right tibia of the back seat occupant was larger and more durative compared with the motorcycle driver; the back seat occupant suffered a bursting fracture injury of his right tibia. These results might be useful for forensic experts in dealing with similar motorcycle-car collision accidents in the future.

  13. Osteogenesis effect of guided bone regeneration combined with alveolar cleft grafting: assessment by cone beam computed tomography.

    PubMed

    Xiao, W-L; Zhang, D-Z; Chen, X-J; Yuan, C; Xue, L-F

    2016-06-01

    Cone beam computed tomography (CBCT) allows for a significantly lower radiation dose than conventional computed tomography (CT) scans and provides accurate images of the alveolar cleft area. The osteogenic effect of guided bone regeneration (GBR) vs. conventional alveolar bone grafting alone for alveolar cleft defects was evaluated in this study. Sixty alveolar cleft patients were divided randomly into two groups. One group underwent GBR using acellular dermal matrix film combined with alveolar bone grafting using iliac crest bone grafts (GBR group), while the other group underwent alveolar bone grafting only (non-GBR group). CBCT images were obtained at 1 week and at 3 months following the procedure. Using Simplant 11.04 software, the bone resorption rate was calculated and compared between the two groups. The bone resorption rate from 1 week to 3 months following bone grafting without the GBR technique was 36.50±5.04%, whereas the bone resorption rate using the GBR technique was 31.69±5.50% (P=0.017). The application of autogenous iliac bone combined with the GBR technique for alveolar bone grafting of alveolar cleft patients can reduce bone resorption and result in better osteogenesis.

  14. Osteogenesis effect of guided bone regeneration combined with alveolar cleft grafting: assessment by cone beam computed tomography.

    PubMed

    Xiao, W-L; Zhang, D-Z; Chen, X-J; Yuan, C; Xue, L-F

    2016-06-01

    Cone beam computed tomography (CBCT) allows for a significantly lower radiation dose than conventional computed tomography (CT) scans and provides accurate images of the alveolar cleft area. The osteogenic effect of guided bone regeneration (GBR) vs. conventional alveolar bone grafting alone for alveolar cleft defects was evaluated in this study. Sixty alveolar cleft patients were divided randomly into two groups. One group underwent GBR using acellular dermal matrix film combined with alveolar bone grafting using iliac crest bone grafts (GBR group), while the other group underwent alveolar bone grafting only (non-GBR group). CBCT images were obtained at 1 week and at 3 months following the procedure. Using Simplant 11.04 software, the bone resorption rate was calculated and compared between the two groups. The bone resorption rate from 1 week to 3 months following bone grafting without the GBR technique was 36.50±5.04%, whereas the bone resorption rate using the GBR technique was 31.69±5.50% (P=0.017). The application of autogenous iliac bone combined with the GBR technique for alveolar bone grafting of alveolar cleft patients can reduce bone resorption and result in better osteogenesis. PMID:26876144

  15. Predicting transient particle transport in enclosed environments with the combined computational fluid dynamics and Markov chain method.

    PubMed

    Chen, C; Lin, C-H; Long, Z; Chen, Q

    2014-02-01

    To quickly obtain information about airborne infectious disease transmission in enclosed environments is critical in reducing the infection risk to the occupants. This study developed a combined computational fluid dynamics (CFD) and Markov chain method for quickly predicting transient particle transport in enclosed environments. The method first calculated a transition probability matrix using CFD simulations. Next, the Markov chain technique was applied to calculate the transient particle concentration distributions. This investigation used three cases, particle transport in an isothermal clean room, an office with an underfloor air distribution system, and the first-class cabin of an MD-82 airliner, to validate the combined CFD and Markov chain method. The general trends of the particle concentrations vs. time predicted by the Markov chain method agreed with the CFD simulations for these cases. The proposed Markov chain method can provide faster-than-real-time information about particle transport in enclosed environments. Furthermore, for a fixed airflow field, when the source location is changed, the Markov chain method can be used to avoid recalculation of the particle transport equation and thus reduce computing costs. PMID:23789964

  16. Interaction between transition metals and phenylalanine: a combined experimental and computational study.

    PubMed

    Elius Hossain, Md; Mahmudul Hasan, Md; Halim, M E; Ehsan, M Q; Halim, Mohammad A

    2015-03-01

    Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M=Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

  17. Steroid Hydroxylation by Basidiomycete Peroxygenases: a Combined Experimental and Computational Study

    PubMed Central

    Babot, Esteban D.; del Río, José C.; Cañellas, Marina; Sancho, Ferran; Lucas, Fátima; Guallar, Víctor; Kalum, Lisbeth; Lund, Henrik; Gröbe, Glenn; Scheibner, Katrin; Ullrich, René; Hofrichter, Martin; Martínez, Angel T.

    2015-01-01

    The goal of this study is the selective oxyfunctionalization of steroids under mild and environmentally friendly conditions using fungal enzymes. With this purpose, peroxygenases from three basidiomycete species were tested for the hydroxylation of a variety of steroidal compounds, using H2O2 as the only cosubstrate. Two of them are wild-type enzymes from Agrocybe aegerita and Marasmius rotula, and the third one is a recombinant enzyme from Coprinopsis cinerea. The enzymatic reactions on free and esterified sterols, steroid hydrocarbons, and ketones were monitored by gas chromatography, and the products were identified by mass spectrometry. Hydroxylation at the side chain over the steroidal rings was preferred, with the 25-hydroxyderivatives predominating. Interestingly, antiviral and other biological activities of 25-hydroxycholesterol have been reported recently (M. Blanc et al., Immunity 38:106–118, 2013, http://dx.doi.org/10.1016/j.immuni.2012.11.004). However, hydroxylation in the ring moiety and terminal hydroxylation at the side chain also was observed in some steroids, the former favored by the absence of oxygenated groups at C-3 and by the presence of conjugated double bonds in the rings. To understand the yield and selectivity differences between the different steroids, a computational study was performed using Protein Energy Landscape Exploration (PELE) software for dynamic ligand diffusion. These simulations showed that the active-site geometry and hydrophobicity favors the entrance of the steroid side chain, while the entrance of the ring is energetically penalized. Also, a direct correlation between the conversion rate and the side chain entrance ratio could be established that explains the various reaction yields observed. PMID:25862224

  18. Interaction between transition metals and phenylalanine: A combined experimental and computational study

    NASA Astrophysics Data System (ADS)

    Elius Hossain, Md.; Mahmudul Hasan, Md.; Halim, M. E.; Ehsan, M. Q.; Halim, Mohammad A.

    2015-03-01

    Some transition metal complexes of phenylalanine of general formula [M(C9H10NO2)2]; where M = Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) are prepared in aqueous medium and characterized by spectroscopic, thermo-gravimetric (TG) and magnetic susceptibility analysis. Density functional theory (DFT) has been employed calculating the equilibrium geometries and vibrational frequencies of those complexes at B3LYP level of theory using 6-31G(d) and SDD basis sets. In addition, frontier molecular orbital and time-dependent density functional theory (TD-DFT) calculations are performed with CAM-B3LYP/6-31+G(d,p) and B3LYP/SDD level of theories. Thermo-gravimetric analysis confirms the composition of the complexes by comparing the experimental and calculated data for C, H, N and metals. Experimental and computed IR results predict a significant change in vibrational frequencies of metal-phenylalanine complexes compared to free ligand. DFT calculation confirms that Mn, Co, Ni and Cu complexes form square planar structure whereas Zn adopts distorted tetrahedral geometry. The metal-oxygen bonds in the optimized geometry of all complexes are shorter compared to the metal-nitrogen bonds which is consistent with a previous study. Cation-binding energy, enthalpy and Gibbs free energy indicates that these complexes are thermodynamically stable. UV-vis and TD-DFT studies reveal that these complexes demonstrate representative metal-to-ligand charge transfer (MLCT) and d-d transitions bands. TG analysis and IR spectra of the metal complexes strongly support the absence of water in crystallization. Magnetic susceptibility data of the complexes exhibits that all except Zn(II) complex are high spin paramagnetic.

  19. A combined experiment/computational study of flow in turbine blade cooling passage

    NASA Astrophysics Data System (ADS)

    Tse, D. G. N.; Kreskovsky, J. P.; Shamroth, S. J.; McGrath, D. B.

    1994-05-01

    Laser velocimetry was utilized to map the velocity field in a serpentine turbine blade cooling passage at Reynolds and Rotation numbers of up to 25.000 and 0.48. These results were used to assess the combined influence of passage curvature and Coriolis force on the secondary velocity field generated. A Navier-Stokes code (NASTAR) was validated against incompressible test data and then used to simulate the effect of buoyancy. The measurements show a net convection from the low pressure surface to high pressure surface. The interaction of the secondary flows induced by the turns and rotation produces swirl at the turns, which persisted beyond 2 hydraulic diameters downstream of the turns. The incompressible flow field predictions agree well with the measured velocities. With radially outward flow, the buoyancy force causes a further increase in velocity on the high pressure surface and a reduction on the low pressure surface. The results were analyzed in relation to the heat transfer measurements of Wagner et al. (1991). Predicted heat transfer is enhanced on the high pressure surfaces and in turns. The incompressible flow simulation underpredicts heat transfer in these locations. Improvements observed in compressible flow simulation indicate that the buoyancy force may be important.

  20. Combined experimental and computational NMR study of crystalline and amorphous zeolitic imidazolate frameworks.

    PubMed

    Baxter, Emma F; Bennett, Thomas D; Mellot-Draznieks, Caroline; Gervais, Christel; Blanc, Frédéric; Cheetham, Anthony K

    2015-10-14

    Zeolitic imidazolate frameworks (ZIFs) have attracted great interest in recent years due to their high chemical and thermal stability with promising applications in gas storage and separations. We investigate the structures of three different crystalline ZIFs - ZIF-4, ZIF-8, ZIF-zni - and their amorphous counterparts using high field (13)C and (15)N CP MAS NMR. The high field (20 T) allows for the observation of all crystallographically independent carbon and nitrogen atoms in the crystalline ZIFs. Combining our experimental results with density functional theory calculations enabled the assignment of all chemical shifts. The crystalline spectra reveal the potential of high field NMR to distinguish between two ZIF polymorphs, ZIF-4 and ZIF-zni, with identical [Zn(C3H3N2)2] chemical compositions. (13)C and (15)N CP MAS NMR data obtained for the amorphous ZIFs clearly showed signal broadening upon amorphization, confirming the retention of chemical composition and the structural similarity of amorphous ZIF-4 and ZIF-zni. In the case of amorphous ZIF-8, we present evidence for the partial de-coordination of the 2-methyl imidazole linker.

  1. Combined experimental and computational NMR study of crystalline and amorphous zeolitic imidazolate frameworks.

    PubMed

    Baxter, Emma F; Bennett, Thomas D; Mellot-Draznieks, Caroline; Gervais, Christel; Blanc, Frédéric; Cheetham, Anthony K

    2015-10-14

    Zeolitic imidazolate frameworks (ZIFs) have attracted great interest in recent years due to their high chemical and thermal stability with promising applications in gas storage and separations. We investigate the structures of three different crystalline ZIFs - ZIF-4, ZIF-8, ZIF-zni - and their amorphous counterparts using high field (13)C and (15)N CP MAS NMR. The high field (20 T) allows for the observation of all crystallographically independent carbon and nitrogen atoms in the crystalline ZIFs. Combining our experimental results with density functional theory calculations enabled the assignment of all chemical shifts. The crystalline spectra reveal the potential of high field NMR to distinguish between two ZIF polymorphs, ZIF-4 and ZIF-zni, with identical [Zn(C3H3N2)2] chemical compositions. (13)C and (15)N CP MAS NMR data obtained for the amorphous ZIFs clearly showed signal broadening upon amorphization, confirming the retention of chemical composition and the structural similarity of amorphous ZIF-4 and ZIF-zni. In the case of amorphous ZIF-8, we present evidence for the partial de-coordination of the 2-methyl imidazole linker. PMID:26351979

  2. Implementation of combined SVM-algorithm and computer-aided perception feedback for pulmonary nodule detection

    NASA Astrophysics Data System (ADS)

    Pietrzyk, Mariusz W.; Rannou, Didier; Brennan, Patrick C.

    2012-02-01

    This pilot study examines the effect of a novel decision support system in medical image interpretation. This system is based on combining image spatial frequency properties and eye-tracking data in order to recognize over and under calling errors. Thus, before it can be implemented as a detection aided schema, training is required during which SVMbased algorithm learns to recognize FP from all reported outcomes, and, FN from all unreported prolonged dwelled regions. Eight radiologists inspected 50 PA chest radiographs with the specific task of identifying lung nodules. Twentyfive cases contained CT proven subtle malignant lesions (5-20mm), but prevalence was not known by the subjects, who took part in two sequential reading sessions, the second, without and with support system feedback. MCMR ROC DBM and JAFROC analyses were conducted and demonstrated significantly higher scores following feedback with p values of 0.04, and 0.03 respectively, highlighting significant improvements in radiology performance once feedback was used. This positive effect on radiologists' performance might have important implications for future CAD-system development.

  3. A Combined Experimental/Computational Study of Flow in Turbine Blade Cooling Passage

    NASA Technical Reports Server (NTRS)

    Tse, D. G. N.; Kreskovsky, J. P.; Shamroth, S. J.; Mcgrath, D. B.

    1994-01-01

    Laser velocimetry was utilized to map the velocity field in a serpentine turbine blade cooling passage at Reynolds and Rotation numbers of up to 25.000 and 0.48. These results were used to assess the combined influence of passage curvature and Coriolis force on the secondary velocity field generated. A Navier-Stokes code (NASTAR) was validated against incompressible test data and then used to simulate the effect of buoyancy. The measurements show a net convection from the low pressure surface to high pressure surface. The interaction of the secondary flows induced by the turns and rotation produces swirl at the turns, which persisted beyond 2 hydraulic diameters downstream of the turns. The incompressible flow field predictions agree well with the measured velocities. With radially outward flow, the buoyancy force causes a further increase in velocity on the high pressure surface and a reduction on the low pressure surface. The results were analyzed in relation to the heat transfer measurements of Wagner et al. (1991). Predicted heat transfer is enhanced on the high pressure surfaces and in turns. The incompressible flow simulation underpredicts heat transfer in these locations. Improvements observed in compressible flow simulation indicate that the buoyancy force may be important.

  4. Array processors in chemistry

    SciTech Connect

    Ostlund, N.S.

    1980-01-01

    The field of attached scientific processors (''array processors'') is surveyed, and an attempt is made to indicate their present and possible future use in computational chemistry. The current commercial products from Floating Point Systems, Inc., Datawest Corporation, and CSP, Inc. are discussed.

  5. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new chemistry expermiments are described. Broad areas covered include atomic structure, solubility, gaseous diffusion, endothermic reactions, alcohols, equilibrium, atomic volumes, and some improvised apparatus. (PS)

  6. Feasibility studies on explosive detection and homeland security applications using a neutron and x-ray combined computed tomography system

    NASA Astrophysics Data System (ADS)

    Sinha, V.; Srivastava, A.; Lee, H. K.; Liu, X.

    2013-05-01

    The successful creation and operation of a neutron and X-ray combined computed tomography (NXCT) system has been demonstrated by researchers at the Missouri University of Science and Technology. The NXCT system has numerous applications in the field of material characterization and object identification in materials with a mixture of atomic numbers represented. Presently, the feasibility studies have been performed for explosive detection and homeland security applications, particularly in concealed material detection and determination of the light atomic number materials. These materials cannot be detected using traditional X-ray imaging. The new system has the capability to provide complete structural and compositional information due to the complementary nature of X-ray and neutron interactions with materials. The design of the NXCT system facilitates simultaneous and instantaneous imaging operation, promising enhanced detection capabilities of explosive materials, low atomic number materials and illicit materials for homeland security applications. In addition, a sample positioning system allowing the user to remotely and automatically manipulate the sample makes the system viable for commercial applications. Several explosives and weapon simulants have been imaged and the results are provided. The fusion algorithms which combine the data from the neutron and X-ray imaging produce superior images. This paper is a compete overview of the NXCT system for feasibility studies of explosive detection and homeland security applications. The design of the system, operation, algorithm development, and detection schemes are provided. This is the first combined neutron and X-ray computed tomography system in operation. Furthermore, the method of fusing neutron and X-ray images together is a new approach which provides high contrast images of the desired object. The system could serve as a standardized tool in nondestructive testing of many applications, especially in

  7. A Combined Experimental and Computational Approach to Subject-Specific Analysis of Knee Joint Laxity.

    PubMed

    Harris, Michael D; Cyr, Adam J; Ali, Azhar A; Fitzpatrick, Clare K; Rullkoetter, Paul J; Maletsky, Lorin P; Shelburne, Kevin B

    2016-08-01

    Modeling complex knee biomechanics is a continual challenge, which has resulted in many models of varying levels of quality, complexity, and validation. Beyond modeling healthy knees, accurately mimicking pathologic knee mechanics, such as after cruciate rupture or meniscectomy, is difficult. Experimental tests of knee laxity can provide important information about ligament engagement and overall contributions to knee stability for development of subject-specific models to accurately simulate knee motion and loading. Our objective was to provide combined experimental tests and finite-element (FE) models of natural knee laxity that are subject-specific, have one-to-one experiment to model calibration, simulate ligament engagement in agreement with literature, and are adaptable for a variety of biomechanical investigations (e.g., cartilage contact, ligament strain, in vivo kinematics). Calibration involved perturbing ligament stiffness, initial ligament strain, and attachment location until model-predicted kinematics and ligament engagement matched experimental reports. Errors between model-predicted and experimental kinematics averaged <2 deg during varus-valgus (VV) rotations, <6 deg during internal-external (IE) rotations, and <3 mm of translation during anterior-posterior (AP) displacements. Engagement of the individual ligaments agreed with literature descriptions. These results demonstrate the ability of our constraint models to be customized for multiple individuals and simultaneously call attention to the need to verify that ligament engagement is in good general agreement with literature. To facilitate further investigations of subject-specific or population based knee joint biomechanics, data collected during the experimental and modeling phases of this study are available for download by the research community. PMID:27306137

  8. A Combined Experimental and Computational Approach to Subject-Specific Analysis of Knee Joint Laxity.

    PubMed

    Harris, Michael D; Cyr, Adam J; Ali, Azhar A; Fitzpatrick, Clare K; Rullkoetter, Paul J; Maletsky, Lorin P; Shelburne, Kevin B

    2016-08-01

    Modeling complex knee biomechanics is a continual challenge, which has resulted in many models of varying levels of quality, complexity, and validation. Beyond modeling healthy knees, accurately mimicking pathologic knee mechanics, such as after cruciate rupture or meniscectomy, is difficult. Experimental tests of knee laxity can provide important information about ligament engagement and overall contributions to knee stability for development of subject-specific models to accurately simulate knee motion and loading. Our objective was to provide combined experimental tests and finite-element (FE) models of natural knee laxity that are subject-specific, have one-to-one experiment to model calibration, simulate ligament engagement in agreement with literature, and are adaptable for a variety of biomechanical investigations (e.g., cartilage contact, ligament strain, in vivo kinematics). Calibration involved perturbing ligament stiffness, initial ligament strain, and attachment location until model-predicted kinematics and ligament engagement matched experimental reports. Errors between model-predicted and experimental kinematics averaged <2 deg during varus-valgus (VV) rotations, <6 deg during internal-external (IE) rotations, and <3 mm of translation during anterior-posterior (AP) displacements. Engagement of the individual ligaments agreed with literature descriptions. These results demonstrate the ability of our constraint models to be customized for multiple individuals and simultaneously call attention to the need to verify that ligament engagement is in good general agreement with literature. To facilitate further investigations of subject-specific or population based knee joint biomechanics, data collected during the experimental and modeling phases of this study are available for download by the research community.

  9. Investigating the role of combined acoustic-visual feedback in one-dimensional synchronous brain computer interfaces, a preliminary study

    PubMed Central

    Gargiulo, Gaetano D; Mohamed, Armin; McEwan, Alistair L; Bifulco, Paolo; Cesarelli, Mario; Jin, Craig T; Ruffo, Mariano; Tapson, Jonathan; van Schaik, André

    2012-01-01

    Feedback plays an important role when learning to use a brain computer interface (BCI), particularly in the case of synchronous feedback that relies on the interaction subject. In this preliminary study, we investigate the role of combined auditory-visual feedback during synchronous μ rhythm-based BCI sessions to help the subject to remain focused on the selected imaginary task. This new combined feedback, now integrated within the general purpose BCI2000 software, has been tested on eight untrained and three trained subjects during a monodimensional left-right control task. In order to reduce the setup burden and maximize subject comfort, an electroencephalographic device suitable for dry electrodes that required no skin preparation was used. Quality and index of improvement was evaluated based on a personal self-assessment questionnaire from each subject and quantitative data based on subject performance. Results for this preliminary study show that the combined feedback was well tolerated by the subjects and improved performance in 75% of the naïve subjects compared with visual feedback alone. PMID:23152713

  10. Investigating the role of combined acoustic-visual feedback in one-dimensional synchronous brain computer interfaces, a preliminary study.

    PubMed

    Gargiulo, Gaetano D; Mohamed, Armin; McEwan, Alistair L; Bifulco, Paolo; Cesarelli, Mario; Jin, Craig T; Ruffo, Mariano; Tapson, Jonathan; van Schaik, André

    2012-01-01

    Feedback plays an important role when learning to use a brain computer interface (BCI), particularly in the case of synchronous feedback that relies on the interaction subject. In this preliminary study, we investigate the role of combined auditory-visual feedback during synchronous μ rhythm-based BCI sessions to help the subject to remain focused on the selected imaginary task. This new combined feedback, now integrated within the general purpose BCI2000 software, has been tested on eight untrained and three trained subjects during a monodimensional left-right control task. In order to reduce the setup burden and maximize subject comfort, an electroencephalographic device suitable for dry electrodes that required no skin preparation was used. Quality and index of improvement was evaluated based on a personal self-assessment questionnaire from each subject and quantitative data based on subject performance. Results for this preliminary study show that the combined feedback was well tolerated by the subjects and improved performance in 75% of the naïve subjects compared with visual feedback alone.

  11. Computer-aided classification of Alzheimer's disease based on support vector machine with combination of cerebral image features in MRI

    NASA Astrophysics Data System (ADS)

    Jongkreangkrai, C.; Vichianin, Y.; Tocharoenchai, C.; Arimura, H.; Alzheimer's Disease Neuroimaging Initiative

    2016-03-01

    Several studies have differentiated Alzheimer's disease (AD) using cerebral image features derived from MR brain images. In this study, we were interested in combining hippocampus and amygdala volumes and entorhinal cortex thickness to improve the performance of AD differentiation. Thus, our objective was to investigate the useful features obtained from MRI for classification of AD patients using support vector machine (SVM). T1-weighted MR brain images of 100 AD patients and 100 normal subjects were processed using FreeSurfer software to measure hippocampus and amygdala volumes and entorhinal cortex thicknesses in both brain hemispheres. Relative volumes of hippocampus and amygdala were calculated to correct variation in individual head size. SVM was employed with five combinations of features (H: hippocampus relative volumes, A: amygdala relative volumes, E: entorhinal cortex thicknesses, HA: hippocampus and amygdala relative volumes and ALL: all features). Receiver operating characteristic (ROC) analysis was used to evaluate the method. AUC values of five combinations were 0.8575 (H), 0.8374 (A), 0.8422 (E), 0.8631 (HA) and 0.8906 (ALL). Although “ALL” provided the highest AUC, there were no statistically significant differences among them except for “A” feature. Our results showed that all suggested features may be feasible for computer-aided classification of AD patients.

  12. [Techniques of mediation. Chemistry as a combination of work, teaching and research: the case of J. F. A. Göttling].

    PubMed

    Frercks, Jan

    2008-01-01

    Atypical career of a chemist in Germany around 1800 consisted of being trained as an apothecary, followed by an occupation as a professor at a university or another institution of higher education. These conditions deeply influenced the concept and the practice of chemistry as a science. Johann Friedrich August Göttling is an intriguing example for merging education and daily duties of teaching with the self-image of a scientific chemist. He linked chemical teaching, work, and research by using different hybrid media, such as the Almanach oder Taschenbuch für Scheidekünstler und Apotheker, a stove specifically designed for the narrow student's room, portable laboratories, a pharmaceutical boarding school and textbooks. This allowed him to practice three different forms of chemistry as a science. A "socio-epistemological diagram" of German chemistry around 1800 shows that these forms neatly corresponded to the then predominant three-level epistemology. In particular, the concept of a chemical fact served to link pharmaceutical practice with teaching practice, while granting only the chemistry done by professors the status of a science. PMID:19244834

  13. Combining Human Computing and Machine Learning to Make Sense of Big (Aerial) Data for Disaster Response.

    PubMed

    Ofli, Ferda; Meier, Patrick; Imran, Muhammad; Castillo, Carlos; Tuia, Devis; Rey, Nicolas; Briant, Julien; Millet, Pauline; Reinhard, Friedrich; Parkan, Matthew; Joost, Stéphane

    2016-03-01

    results suggest that the platform we have developed to combine crowdsourcing and machine learning to make sense of large volumes of aerial images can be used for disaster response.

  14. Protein thermal stability enhancement by designing salt bridges: a combined computational and experimental study.

    PubMed

    Lee, Chi-Wen; Wang, Hsiu-Jung; Hwang, Jenn-Kang; Tseng, Ching-Ping

    2014-01-01

    Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures. These salt bridges were first categorized based on pairing residues, secondary structure locations, and Cα-Cα distances. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number, relative solvent accessibility, and conservation prescreening to determine the residues appropriate for the thermal adaptive design of salt bridges. According to our method, eight putative salt-bridges were designed on a mesophilic β-glucosidase and 24 variants were constructed to verify the predictions. Six putative salt-bridges leaded to the increase of the enzyme thermal stability. A significant increase in melting temperature of 8.8, 4.8, 3.7, 1.3, 1.2, and 0.7°C of the putative salt-bridges N437K-D49, E96R-D28, E96K-D28, S440K-E70, T231K-D388, and Q277E-D282 was detected, respectively. Reversing the polarity of T231K-D388 to T231D-D388K resulted in a further increase in melting temperatures by 3.6°C, which may be caused by the transformation of an intra-subunit electrostatic interaction into an inter-subunit one depending on the local environment. The combination of the thermostable variants (N437K, E96R, T231D and D388K) generated a melting temperature increase of 15.7°C. Thus, this study demonstrated a novel

  15. Combining Human Computing and Machine Learning to Make Sense of Big (Aerial) Data for Disaster Response.

    PubMed

    Ofli, Ferda; Meier, Patrick; Imran, Muhammad; Castillo, Carlos; Tuia, Devis; Rey, Nicolas; Briant, Julien; Millet, Pauline; Reinhard, Friedrich; Parkan, Matthew; Joost, Stéphane

    2016-03-01

    results suggest that the platform we have developed to combine crowdsourcing and machine learning to make sense of large volumes of aerial images can be used for disaster response. PMID:27441584

  16. Protein Thermal Stability Enhancement by Designing Salt Bridges: A Combined Computational and Experimental Study

    PubMed Central

    Hwang, Jenn-Kang; Tseng, Ching-Ping

    2014-01-01

    Protein thermal stability is an important factor considered in medical and industrial applications. Many structural characteristics related to protein thermal stability have been elucidated, and increasing salt bridges is considered as one of the most efficient strategies to increase protein thermal stability. However, the accurate simulation of salt bridges remains difficult. In this study, a novel method for salt-bridge design was proposed based on the statistical analysis of 10,556 surface salt bridges on 6,493 X-ray protein structures. These salt bridges were first categorized based on pairing residues, secondary structure locations, and Cα–Cα distances. Pairing preferences generalized from statistical analysis were used to construct a salt-bridge pair index and utilized in a weighted electrostatic attraction model to find the effective pairings for designing salt bridges. The model was also coupled with B-factor, weighted contact number, relative solvent accessibility, and conservation prescreening to determine the residues appropriate for the thermal adaptive design of salt bridges. According to our method, eight putative salt-bridges were designed on a mesophilic β-glucosidase and 24 variants were constructed to verify the predictions. Six putative salt-bridges leaded to the increase of the enzyme thermal stability. A significant increase in melting temperature of 8.8, 4.8, 3.7, 1.3, 1.2, and 0.7°C of the putative salt-bridges N437K–D49, E96R–D28, E96K–D28, S440K–E70, T231K–D388, and Q277E–D282 was detected, respectively. Reversing the polarity of T231K–D388 to T231D–D388K resulted in a further increase in melting temperatures by 3.6°C, which may be caused by the transformation of an intra-subunit electrostatic interaction into an inter-subunit one depending on the local environment. The combination of the thermostable variants (N437K, E96R, T231D and D388K) generated a melting temperature increase of 15.7°C. Thus, this study

  17. Computational solution of chemistry problems

    NASA Technical Reports Server (NTRS)

    Ake, Robert L.

    1989-01-01

    AB initio quantum chemical techniques have been used to investigate weakly bound complexes of H2O and SO2. An energy gradient program was used to locate stable structures for the H2O, SO2 complexes, and SCF calculations were carried out to determine the binding energies of complexes with multiple water molecules. A 4-31G basis set was used for most potential energy searches. More accurate basis sets including a generally contracted basis set with d orbitals on the sulfur were used for geometry and binding energy verification. For single water complexes, five different stable geometries were located with binding energies between 4 and 11 Kcal mol(-1), suggesting a binding shell for H2O around SO2 and a mechanism for the formation of an SO2-containing water droplet. Calculations on one of the complexes utilizing a larger double zeta basis and d functions on the sulfur atom lead to adjusted binding energies in the range 3 to 8 Kcal mol(-1). Very little charge transfer between SO2 and H2O was present. Addition of more than one H2O was found to be energetically favorable although the addition of the fourth water in certain geometries did not increase the stability of the complex. An alternative mechanism for the tropospheric gas phase production of acid rain is suggested.

  18. Combining computer game-based behavioural experiments with high-density EEG and infrared gaze tracking.

    PubMed

    Yoder, Keith J; Belmonte, Matthew K

    2010-01-01

    inhibition, a psychophysical motion coherence threshold task, the Embedded Figures Test (Witkin, 1950, 1954) and a theory-of-mind (Wimmer & Perner, 1983) task. The game software automatically registers game stimuli and subjects' actions and responses in a log file, and sends event codes to synchronise with physiological data recorders. Thus the game can be combined with physiological measures such as EEG or fMRI, and with moment-to-moment tracking of gaze. Gaze tracking can verify subjects' compliance with behavioural tasks (e.g. fixation) and overt attention to experimental stimuli, and also physiological arousal as reflected in pupil dilation (Bradley et al., 2008). At great enough sampling frequencies, gaze tracking may also help assess covert attention as reflected in microsaccades - eye movements that are too small to foveate a new object, but are as rapid in onset and have the same relationship between angular distance and peak velocity as do saccades that traverse greater distances. The distribution of directions of microsaccades correlates with the (otherwise) covert direction of attention (Hafed & Clark, 2002). PMID:21206465

  19. Combining Computer Game-Based Behavioural Experiments With High-Density EEG and Infrared Gaze Tracking

    PubMed Central

    Yoder, Keith J.; Belmonte, Matthew K.

    2010-01-01

    inhibition, a psychophysical motion coherence threshold task, the Embedded Figures Test (Witkin, 1950, 1954) and a theory-of-mind (Wimmer & Perner, 1983) task. The game software automatically registers game stimuli and subjects' actions and responses in a log file, and sends event codes to synchronise with physiological data recorders. Thus the game can be combined with physiological measures such as EEG or fMRI, and with moment-to-moment tracking of gaze. Gaze tracking can verify subjects' compliance with behavioural tasks (e.g. fixation) and overt attention to experimental stimuli, and also physiological arousal as reflected in pupil dilation (Bradley et al., 2008). At great enough sampling frequencies, gaze tracking may also help assess covert attention as reflected in microsaccades - eye movements that are too small to foveate a new object, but are as rapid in onset and have the same relationship between angular distance and peak velocity as do saccades that traverse greater distances. The distribution of directions of microsaccades correlates with the (otherwise) covert direction of attention (Hafed & Clark, 2002). PMID:21206465

  20. A new method for combining live action and computer graphics in stereoscopic 3D

    NASA Astrophysics Data System (ADS)

    Rupkalvis, John A.; Gillen, Ron

    2008-02-01

    A primary requirement when elements are to be combined stereoscopically, is that homologous points in each eye view of each element have identical parallax separation at any point of interaction. If this is not done, the image parts on one element will appear to be at a different distance from the corresponding or associated parts on the other element. This results in a visual discontinuity that appears very unnatural. For example, if a live actor were to appear to "shake hands" with a cartoon character, a very natural appearing juncture may appear to be the case when seen in 2-D, but their hands may appear to miss when seen in 3-D. Previous efforts to compensate, or correct these errors have involved painstaking time-consuming trial-and-error tests. In the area of pure animation, efforts to make cartoon characters appear more realistic were developed. A "motion tracking" technique was developed. This involves an actor wearing a special suit with indicator marks at various points on their body. The actor walks through the scene, then the animator tracks the points using motion capture software. Because live action and CG elements can interact or change at several different points and levels within a scene, additional requirements must also be addressed. "Occlusions" occur when one object passes in front of another. A particular tracking point may appear in one eye-view, and not the other. When Z-axis differentials are to be considered in the live action as well as the CG elements, and both are to interact with each other, both eye-views must be tracked, especially at points of occlusion. A new approach would be to generate a three dimensional grid, within which the action is to take place. This grid can be projected, onto the stage where the live action part is to take place. When differential occlusions occur, the grid may be seen and CG elements plotted in reference to it. Because of the capability of precisely locating points in a digital image, a pixel