Semiempirical and ab initio Calculations of Charged Species Used in the Physical Organic Chemistry Course.

ERIC Educational Resources Information Center

Gilliom, Richard D.

1989-01-01

Concentrates on the semiempirical methods MINDO/3, MNDO, and AMI available in the program AMPAC from the Quantum Chemistry Program Exchange at Indiana University. Uses charged ions in the teaching of computational chemistry. Finds that semiempirical methods are accurate enough for the general use of the bench chemist. (MVL)

The Computer Revolution and Physical Chemistry.

ERIC Educational Resources Information Center

O'Brien, James F.

1989-01-01

Describes laboratory-oriented software programs that are short, time-saving, eliminate computational errors, and not found in public domain courseware. Program availability for IBM and Apple microcomputers is included. (RT)

Computer Series, 29: Bits and Pieces, 10.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (available from authors) including molecular input to computer, programs for quantum chemistry, library orientation to technical literature, plotting potentiometric titration data, simulating oscilloscope curves, organic qualitative analysis with dynamic graphics, extended Huckel calculations, and calculator programs…

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.

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…

Practical application of computer programs for supersonic combustion

NASA Technical Reports Server (NTRS)

Groves, F. R., Jr.

1972-01-01

Experimental data were interpreted using two supersonic combustion computer programs. The P1 program is based on a conventional boundary layer treatment of the mixing of concentric gas streams and complete combustion chemistry. The H1 program is based on a modified boundary layer approach which accounts for radial pressure gradients in the flow and also incorporates a finite rate chemistry calculation. The objective of the investigation was to compare the experimental data with theoretical predictions of the two programs with special emphasis on the prediction of radial pressure gradients by the H1 program. A test of the H1 program was also desired through comparison with the experimental data and with the P1 program.

EnviroLand: A Simple Computer Program for Quantitative Stream Assessment.

ERIC Educational Resources Information Center

Dunnivant, Frank; Danowski, Dan; Timmens-Haroldson, Alice; Newman, Meredith

2002-01-01

Introduces the Enviroland computer program which features lab simulations of theoretical calculations for quantitative analysis and environmental chemistry, and fate and transport models. Uses the program to demonstrate the nature of linear and nonlinear equations. (Author/YDS)

Research in bioanalysis and separations at the University of Nebraska - Lincoln.

PubMed

Hage, David S; Dodds, Eric D; Du, Liangcheng; Powers, Robert

2011-05-01

The Chemistry Department at the University of Nebraska - Lincoln (UNL) is located in Hamilton Hall on the main campus of UNL in Lincoln, NE, USA. This department houses the primary graduate and research program in chemistry in the state of Nebraska. This program includes the traditional fields of analytical chemistry, biochemistry, inorganic chemistry, organic chemistry and physical chemistry. However, this program also contains a great deal of multidisciplinary research in fields that range from bioanalytical and biophysical chemistry to nanomaterials, energy research, catalysis and computational chemistry. Current research in bioanalytical and biophysical chemistry at UNL includes work with separation methods such as HPLC and CE, as well as with techniques such as MS and LC-MS, NMR spectroscopy, electrochemical biosensors, scanning probe microscopy and laser spectroscopy. This article will discuss several of these areas, with an emphasis being placed on research in bioanalytical separations, binding assays and related fields.

BASIC Simulation Programs; Volumes I and II. Biology, Earth Science, Chemistry.

ERIC Educational Resources Information Center

Digital Equipment Corp., Maynard, MA.

Computer programs which teach concepts and processes related to biology, earth science, and chemistry are presented. The seven biology problems deal with aspects of genetics, evolution and natural selection, gametogenesis, enzymes, photosynthesis, and the transport of material across a membrane. Four earth science problems concern climates, the…

Computer Series, 60: Bits and Pieces, 23.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1985-01-01

Describes: (1) an interactive computer simulation for a science fair display of chromatography inks; (2) analytical chemistry programs; (3) microcomputer-assisted drills in organic synthesis; (4) programs for conformation analysis of ethane and butane; (5) MOLPIX--a program for generating and displaying molecular structures; and (6) chemical…

Computer Series, 32.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Ten computer programs (available from authors) and a noncomputer calculation of the electron in one-dimensional, one-Bohr box are described, including programs for analytical chemistry, space group generation using Pascal, mass-spectral search system (Applesoft), microcomputer-simulated liquid chromatography, voltammetry/amperometric titrations,…

Computer Programs in Marine Science: Key to Oceanographic Records Documentation No. 5.

ERIC Educational Resources Information Center

Firestone, Mary A.

Presented are abstracts of 700 computer programs in marine science. The programs listed are categorized under a wide range of headings which include physical oceanography, chemistry, coastal and estuarine processes, biology, pollution, air-sea interaction and heat budget, navigation and charting, curve fitting, and applied mathematics. The…

CATS--Computer Assisted Teaching in Science.

ERIC Educational Resources Information Center

Barron, Marcelline A.

This document contains the listings for 46 computer programs which are designed to teach various concepts in chemistry and physics. Significant time was spent in writing programs in which students would input chemical and physical data from their laboratory experiments. No significant time was spent writing drill and practice programs other than…

"SimChemistry" as an Active Learning Tool in Chemical Education

ERIC Educational Resources Information Center

Bolton, Kim; Saalman, Elisabeth; Christie, Michael; Ingerman, Ake; Linder, Cedric

2008-01-01

The publicly available free computer program, "SimChemistry," was used as an active learning tool in the chemical engineering curriculum at the University College of Boras, Sweden. The activity involved students writing their own simulation programs on topics in the area of molecular structure and interactions. Evaluation of the learning…

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…

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…

75 FR 15675 - Professional Research Experience Program in Chemical Science and Technology Laboratory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... in physics, chemistry, mathematics, computer science, or engineering. Institutions should have a 4..., mathematics, computer science, or engineering with work experiences in laboratories or other settings...-0141-01] Professional Research Experience Program in Chemical Science and Technology Laboratory...

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…

Scientific Computing for Chemists: An Undergraduate Course in Simulations, Data Processing, and Visualization

ERIC Educational Resources Information Center

Weiss, Charles J.

2017-01-01

The Scientific Computing for Chemists course taught at Wabash College teaches chemistry students to use the Python programming language, Jupyter notebooks, and a number of common Python scientific libraries to process, analyze, and visualize data. Assuming no prior programming experience, the course introduces students to basic programming and…

Testing and Extending VSEPR with WebMO and MOPAC or GAMESS

ERIC Educational Resources Information Center

McNaught, Ian J.

2011-01-01

VSEPR is a topic that is commonly taught in undergraduate chemistry courses. The readily available Web-based program WebMO, in conjunction with the computational chemistry programs MOPAC and GAMESS, is used to quantitatively test a wide range of predictions of VSEPR. These predictions refer to the point group of the molecule, including the…

Qualitative Assessment of a 3D Simulation Program: Faculty, Students, and Bio-Organic Reaction Animations

ERIC Educational Resources Information Center

Günersel, Adalet B.; Fleming, Steven A.

2013-01-01

Research shows that computer-based simulations and animations are especially helpful in fields such as chemistry where concepts are abstract and cannot be directly observed. Bio-Organic Reaction Animations (BioORA) is a freely available 3D visualization software program developed to help students understand the chemistry of biomolecular events.…

Integration of Major Computer Program Packages into Experimental Courses: A Freshman Experience.

ERIC Educational Resources Information Center

Lipschitz, Irving

1981-01-01

Describes the use of the Gaussian 70 computer programs to carry out quantum chemical calculations, including single calculations, geometry, optimization, and potential surface scans. Includes a summary of student activities and benefits for students in an honors freshman chemistry course. (SK)

Equilibrium chemical reaction of supersonic hydrogen-air jets (the ALMA computer program)

NASA Technical Reports Server (NTRS)

Elghobashi, S.

1977-01-01

The ALMA (axi-symmetrical lateral momentum analyzer) program is concerned with the computation of two dimensional coaxial jets with large lateral pressure gradients. The jets may be free or confined, laminar or turbulent, reacting or non-reacting. Reaction chemistry is equilibrium.

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents biology, chemistry, physics, and health activities, experiments, demonstrations, and computer programs. Includes mechanism of stomatal opening, using aquatic plants to help demonstrate chemical buffering, microbial activity/contamination in milk samples, computer computation of fitness scores, reservoir project, complexes of transition…

Computer Series, 13: Bits and Pieces, 11.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (with ordering information) on various topics including, among others, modeling of thermodynamics and economics of solar energy, radioactive decay simulation, stoichiometry drill/tutorial (in Spanish), computer-generated safety quiz, medical chemistry computer game, medical biochemistry question bank, generation of…

Computer program determines chemical composition of physical system at equilibrium

NASA Technical Reports Server (NTRS)

Kwong, S. S.

1966-01-01

FORTRAN 4 digital computer program calculates equilibrium composition of complex, multiphase chemical systems. This is a free energy minimization method with solution of the problem reduced to mathematical operations, without concern for the chemistry involved. Also certain thermodynamic properties are determined as byproducts of the main calculations.

The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati

The Amber Biomolecular Simulation Programs

PubMed Central

CASE, DAVID A.; CHEATHAM, THOMAS E.; DARDEN, TOM; GOHLKE, HOLGER; LUO, RAY; MERZ, KENNETH M.; ONUFRIEV, ALEXEY; SIMMERLING, CARLOS; WANG, BING; WOODS, ROBERT J.

2006-01-01

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates. PMID:16200636

Investigating Impact Metrics for Performance for the US EPA National Center for Computational Toxicology (ACS Fall meeting)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...

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

ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING

EPA Science Inventory

The overall goal of the EPA-ORD NERL research program on Computational Toxicology (CompTox) is to provide the Agency with the tools of modern chemistry, biology, and computing to improve quantitative risk assessments and reduce uncertainties in the source-to-adverse outcome conti...

Delivering an Informational Hub for Data at the National Center for Computational Toxicology (ACS Spring Meeting) 7 of 7

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...

Use of Computer-Based Case Studies in a Problem-Solving Curriculum.

ERIC Educational Resources Information Center

Haworth, Ian S.; And Others

1997-01-01

Describes the use of three case studies, on computer, to enhance problem solving and critical thinking among doctoral pharmacy students in a physical chemistry course. Students are expected to use specific computer programs, spreadsheets, electronic mail, molecular graphics, word processing, online literature searching, and other computer-based…

The Use of Molecular Modeling Programs in Medicinal Chemistry Instruction.

ERIC Educational Resources Information Center

Harrold, Marc W.

1992-01-01

This paper describes and evaluates the use of a molecular modeling computer program (Alchemy II) in a pharmaceutical education program. Provided are the hardware requirements and basic program features as well as several examples of how this program and its features have been applied in the classroom. (GLR)

Reviews.

ERIC Educational Resources Information Center

Newland, Robert J.; And Others

1988-01-01

Reviews four organic chemistry computer programs and three books. Software includes: (1) NMR Simulator 7--for IBM or Macintosh, (2) Nucleic Acid Structure and Synthesis--for IBM, (3) Molecular Design Editor--for Apple II, and (4) Synthetic Adventure--for Apple II and IBM. Book topics include physical chemistry, polymer pioneers, and the basics of…

Report: NSF Instrumentation and Laboratory Improvement Grants in Chemistry

NASA Astrophysics Data System (ADS)

1997-01-01

The 1996 awards in chemistry under the Instrumentation and Laboratory Improvement Program (ILI) of the Division of Undergraduate Education (DUE) have been announced and are listed below. The ILI program provides matching funds in the range of 5,000 to 100,000 for purchasing equipment for laboratory improvement. Since the recipient institution must provide matching funds equaling or exceeding the NSF award, the supported projects range in cost from 10,000 to over 200,000. The 311 chemistry proposals requesting 13 million constituted 21% of the total number of proposals submitted to the ILI program. A total of 3.9 million was awarded in support of 110 projects in chemistry. The instruments requested most frequently were high field NMRs, GC/MS instruments, computers for data analysis, and FT-IRs; next most commonly requested were UV-vis spectrophotometers, followed by HPLCs, lasers, computers for molecular modeling, AAs, and GCs. In addition, one award was made this year in chemistry within the Leadership in Laboratory Development category. The next deadline for submission of ILI proposals is November 14, 1997. Guidelines for the preparation of proposals are found in the DUE Program Announcement (NSF 96-10), which may be obtained by calling (703) 306-1666 or by e-mail: undergrad@nsf.gov. Other information about DUE programs and activities and abstracts of the funded proposals can be found on the DUE Home Page at http://www.ehr.nsf.gov/EHR/DUE/start.htm. We thank Sandra D. Nelson, Science Education Analyst in DUE, for assistance in data gathering.

Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-01-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.

Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-11-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.

ESTIMATION OF PHYSIOCHEMICAL PROPERTIES OF ORGANIC COMPOUNDS BY SPARC

EPA Science Inventory

The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

Computer Series, 13.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1981-01-01

Provides short descriptions of chemists' applications of computers in instruction: an interactive instructional program for Instrumental-Qualitative Organic Analysis; question-and-answer exercises in organic chemistry; computerized organic nomenclature drills; integration of theoretical and descriptive materials; acid-base titration simulation;…

Quality assurance for health and environmental chemistry: 1990

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

Gautier, M.A.; Gladney, E.S.; Koski, N.L.

1991-10-01

This report documents the continuing quality assurance efforts of the Health and Environmental Chemistry Group (HSE-9) at the Los Alamos National Laboratory. The philosophy, methodology, computing resources, and laboratory information management system used by the quality assurance program to encompass the diversity of analytical chemistry practiced in the group are described. Included in the report are all quality assurance reference materials used, along with their certified or consensus concentrations, and all analytical chemistry quality assurance measurements made by HSE-9 during 1990.

Computer Series, 39.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1983-01-01

Describes use of Warnier-Orr program design method for preparing general chemistry tutorial on ideal gas calculations. This program (BASIC-PLUS) is available from the author. Also describes a multipurpose computerized class record system at the University of Toledo. (JN)

Programs as Polypeptides.

PubMed

Williams, Lance R

2016-01-01

Object-oriented combinator chemistry (OOCC) is an artificial chemistry with composition devices borrowed from object-oriented and functional programming languages. Actors in OOCC are embedded in space and subject to diffusion; since they are neither created nor destroyed, their mass is conserved. Actors use programs constructed from combinators to asynchronously update their own states and the states of other actors in their neighborhoods. The fact that programs and combinators are themselves reified as actors makes it possible to build programs that build programs from combinators of a few primitive types using asynchronous spatial processes that resemble chemistry as much as computation. To demonstrate this, OOCC is used to define a parallel, asynchronous, spatially distributed self-replicating system modeled in part on the living cell. Since interactions among its parts result in the construction of more of these same parts, the system is strongly constructive. The system's high normalized complexity is contrasted with that of a simple composome.

The Computer Bulletin Board. Modified Gran Plots of Very Weak Acids on a Spreadsheet.

ERIC Educational Resources Information Center

Chau, F. T.; And Others

1990-01-01

Presented are two applications of computer technology to chemistry instruction: the use of a spreadsheet program to analyze acid-base titration curves and the use of database software to catalog stockroom inventories. (CW)

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents 23 experiments, demonstrations, activities, and computer programs in biology, chemistry, and physics. Topics include lead in petrol, production of organic chemicals, reduction of water, enthalpy, X-ray diffraction model, nuclear magnetic resonance spectroscopy, computer simulation for additive mixing of colors, Archimedes Principle, and…

Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for chemistry education including "Osmosis and Diffusion" and "E.M.E. Titration Lab" for Apple II and "Simplex-V: An Interactive Computer Program for Experimental Optimization" for IBM PC. Summary ratings include ease of use, content, pedagogic value, student reaction, and…

EPAS TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS(S).

EPA Science Inventory

EPAs National Center for Computational Toxicology is developing methods that apply computational chemistry, high-throughput screening (HTS) and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

ESTIMATION OF PHYSICAL PROPERTIES AND CHEMICAL REACTIVITY PARAMETERS OF ORGANIC COMPOUNDS

EPA Science Inventory

The computer program SPARC (Sparc Performs Automated Reasoning in Chemistry)has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms ...

Computer Series, 102: Bits and Pieces, 40.

ERIC Educational Resources Information Center

Birk, James P., Ed.

1989-01-01

Discussed are seven computer programs: (1) a computer graphics experiment for organic chemistry laboratory; (2) a gel filtration simulation; (3) judging spelling correctness; (4) interfacing the TLC548 ADC; (5) a digitizing circuit for the Apple II game port; (6) a chemical information base; and (7) an IBM PC article database. (MVL)

Prospectus 2000

NASA Astrophysics Data System (ADS)

Holmes, Jon L.; Gettys, Nancy S.

2000-01-01

We begin 2000 with a message about our plans for JCE Software and what you will be seeing in this column as the year progresses. Floppy Disk --> CD-ROM Most software today is distributed on CD-ROM or by downloading from the Internet. Several new computers no longer include a floppy disk drive as "standard equipment". Today's software no longer fits on one or two floppies (the installation software alone can require two disks) and the cost of reproducing and distributing several disks is prohibitive. In short, distribution of software on floppy disks is no longer practical. Therefore, JCE Software will distribute all new software publications on CD-ROM rather than on disks. Regular Issues --> Collections Distribution of all our software on CD-ROM allows us to extend our concept of software collections that we started with the General Chemistry Collection. Such collections will contain all the previously published software that is still "in print" (i.e., is compatible with current operating systems and hardware) and any new programs that fall under the topic of the collection. Proposed topics in addition to General Chemistry currently include Advanced Chemistry, Instrument and Laboratory Simulations, and Spectroscopy. Eventually, all regular issues will be replaced by these collections, which will be updated annually or semiannually with new programs and updates to existing programs. Abstracts for all new programs will continue to appear in this column when a collection or its update is ready for publication. We will continue to offer special issues of single larger programs (e.g. Periodic Table Live!, Chemistry Comes Alive! volumes) on CD-ROM and video on videotape. Connect with Your Students outside Class JCE Software has always offered network licenses to allow instructors to make our software available to students in computer labs, but that model no longer fits the way many instructors and students work with computers. Many students (or their families) own a personal computer allowing them much more flexibility than a campus computer lab. Many instructors utilize the World Wide Web, creating HTML pages for students to use. JCE Software has options available to take advantage of both of these developments. Software Adoption To provide students who own computers access to JCE Software programs, consider adopting one or more of our CD-ROMs as you would a textbook. The General Chemistry Collection has been adopted by several general chemistry courses. We can arrange to bundle CDs with laboratory manuals or to be sold separately to students through the campus bookstore. The cost per CD can be quite low (as little as $5) when large numbers are ordered, making this a cost-effective method of allowing students access to the software they need whenever and wherever they desire. Web-Ready Publications Several JCE Software programs use HTML to present the material. Viewed with the ubiquitous Internet Browser, HTML is compatible with both Mac OS and Windows (as well most other current operating systems) and provides a flexible hypermedia interface that is familiar to an increasing number of instructors and students. HTML-based publications are also ready for use on local intranets, with appropriate licensing, and can be readily incorporated into other HTML-based materials. Already published in this format are: Chemistry Comes Alive!, Volumes 1 and 2 (Special Issues 18 and 21), Flying over Atoms (Special Issue 19), and Periodic Table Live! Second Edition (Special Issue 17). Solid State Resources Second Edition (Special Issue 12) and Chemistry Comes Alive!, Volume 3 (Special Issue 23) will be available soon. Other submissions being developed in HTML format include ChemPages Laboratory and Multimedia General Chemistry Problems. Contact the JCE Software office to learn about licensing alternatives that take advantage of the World Wide Web. Periodic Table Live! 2nd ed. is one of JCE Software's "Web-ready" publications. Publication Plans for 2000 We have several exciting new issues planned for publication in the coming year. Chemistry Comes Alive! The Chemistry Comes Alive! (CCA!) series continues with additional CD-ROMs for Mac OS and Windows. Each volume in this series contains video and animations of chemical reactions that can be easily incorporated into your own computer-based presentations. Our digital video now uses state-of-the-art compression that yields higher quality video with smaller file sizes and data rates more suited for WWW delivery. Video for Periodic Table Live! 2nd edition, Chemistry Comes Alive! Volumes 3, ChemPages Laboratory, and Multimedia General Chemistry Problems use this new format. We will be releasing updates of CCA! Volumes 1 and 2 to take advantage of this new technology. We are very pleased with the results and think you will be also. The reaction of aluminum with chlorine is included in Chemistry Comes Alive! Volume 3. ChemPages Laboratory ChemPages Laboratory, developed by the New Traditions Curriculum Project at the University of Wisconsin-Madison, is an HTML-based CD-ROM for Mac OS and Windows that contains lessons and tutorials to prepare introductory chemistry students to work in the laboratory. It includes text, photographs, computer graphics, animations, digital video, and voice narration to introduce students to the laboratory equipment and procedures. ChemPages Laboratory teaches introductory chemistry students about laboratory instruments, equipment, and procedures. Versatile Video Video demonstrating the "drinking bird" is included in the Chemistry Comes Alive! video collection. Video from this collection can be incorporated into many other projects. As an example, David Whisnant has used the drinking bird in his Multimedia General Chemistry Problems, where students view the video and are asked to explain why the bird bobs up and down. JCE Software anticipates publication of Multimedia General Chemistry Problems on CD-ROM for Mac OS and Windows in 2000. It will be "Web-ready". General Chemistry Collection, 4th Edition The General Chemistry Collection will be revised early in the summer and CDs will be shipped in time for fall adoptions. The 4th edition will include JCE Software publications for general chemistry published in 1999, as well as any programs for general chemistry accepted in 2000. Regular Issues We have had many recent submissions and submissions of work in progress. In 2000 we will work with the authors and our peer-reviewers to complete and publish these submissions individually or as part of a software collection on CD-ROM. An Invitation In collaboration with JCE Online we plan to make available in 2000 more support files for JCE Software. These will include not only troubleshooting tips and technical support notes, but also supporting information submitted by users such as lessons, specific assignments, and activities using JCE Software publications. All JCE Software users are invited to contribute to this area. Get in touch with JCE Software and let us know how you are using our materials so that we can share your ideas with others! Although the word software is in our name, many of our publications are not traditional software. We also publish video on videotape, videodisc, and CD-ROM and electronic documents (Mathcad and Mathematica, spreadsheet files and macros, HTML documents, and PowerPoint presentations). Most chemistry instructors who use a computer in their teaching have created or considered creating one or more of these for their classes. If you have an original computer presentation, electronic document, animation, video, or any other item that is not printed text it is probably an appropriate submission for JCE Software. By publishing your work in any branch of the Journal of Chemical Education, you will share your efforts with chemistry instructors and students all over the world and get professional recognition for your achievements. All JCE Software publications are Y2K compliant.

Journal of Chemical Education: Software.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Describes a chemistry software program that emulates a modern binary gradient HPLC system with reversed phase column behavior. Allows for solvent selection, adjustment of gradient program, column selection, detectory selection, handling of computer sample data, and sample preparation. (MVL)

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

PubMed

Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

2018-06-11

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

The importance of employing computational resources for the automation of drug discovery.

PubMed

Rosales-Hernández, Martha Cecilia; Correa-Basurto, José

2015-03-01

The application of computational tools to drug discovery helps researchers to design and evaluate new drugs swiftly with a reduce economic resources. To discover new potential drugs, computational chemistry incorporates automatization for obtaining biological data such as adsorption, distribution, metabolism, excretion and toxicity (ADMET), as well as drug mechanisms of action. This editorial looks at examples of these computational tools, including docking, molecular dynamics simulation, virtual screening, quantum chemistry, quantitative structural activity relationship, principal component analysis and drug screening workflow systems. The authors then provide their perspectives on the importance of these techniques for drug discovery. Computational tools help researchers to design and discover new drugs for the treatment of several human diseases without side effects, thus allowing for the evaluation of millions of compounds with a reduced cost in both time and economic resources. The problem is that operating each program is difficult; one is required to use several programs and understand each of the properties being tested. In the future, it is possible that a single computer and software program will be capable of evaluating the complete properties (mechanisms of action and ADMET properties) of ligands. It is also possible that after submitting one target, this computer-software will be capable of suggesting potential compounds along with ways to synthesize them, and presenting biological models for testing.

NASA's hypersonic fluid and thermal physics program (Aerothermodynamics)

NASA Technical Reports Server (NTRS)

Graves, R. A.; Hunt, J. L.

1985-01-01

This survey paper gives an overview of NASA's hypersonic fluid and thermal physics program (recently renamed aerothermodynamics). The purpose is to present the elements of, example results from, and rationale and projection for this program. The program is based on improving the fundamental understanding of aerodynamic and aerothermodynamic flow phenomena over hypersonic vehicles in the continuum, transitional, and rarefied flow regimes. Vehicle design capabilities, computational fluid dynamics, computational chemistry, turbulence modeling, aerothermal loads, orbiter flight data analysis, orbiter experiments, laser photodiagnostics, and facilities are discussed.

Computer Series, 115.

ERIC Educational Resources Information Center

Birk, James P., Ed.

1990-01-01

Reviewed are six computer programs which may be useful in teaching college level chemistry. Topics include dynamic data storage in FORTRAN, "KC?DISCOVERER," pH of acids and bases, calculating percent boundary surfaces for orbitals, and laboratory interfacing with PT Nomograph for the Macintosh. (CW)

The use of ARL trajectories for the evaluation of precipitation chemistry data

Treesearch

John M. Miller; James N. Galloway; Gene E. Likens

1976-01-01

One of the major problems in interpreting precipitation chemistry data is determining the possible source areas of the materials found in the precipitation. To investigate this problem, the trajectory program developed at Air Resources Laboratories (NOAA) was used to compute five-day backward air trajectories from Ithaca, New York.

Computations of non-reacting and reacting viscous blunt body flows, volume 2

NASA Technical Reports Server (NTRS)

Li, C. P.

1973-01-01

Computer programs for calculating the flow distribution in the nose region of a blunt body at arbitrary speed and altitude are discussed. The programs differ from each other in their ability to consider either thin shock or thick shock conditions and in the use of either ideal, equilibrium air, or nonequilibrium air chemistry. The application of the programs to analyzing the flow distribution around the nose of the shuttle orbiter during reentry is reported.

Media Exchange.

ERIC Educational Resources Information Center

Friedstein, Harriet G., Ed.

1982-01-01

Lists 13 producers/suppliers (including addresses) of computer programs in sciences, with brief comments related to chemistry. Also lists three periodicals and a book for pet microcomputer users. (JN)

Upwind MacCormack Euler solver with non-equilibrium chemistry

NASA Technical Reports Server (NTRS)

Sherer, Scott E.; Scott, James N.

1993-01-01

A computer code, designated UMPIRE, is currently under development to solve the Euler equations in two dimensions with non-equilibrium chemistry. UMPIRE employs an explicit MacCormack algorithm with dissipation introduced via Roe's flux-difference split upwind method. The code also has the capability to employ a point-implicit methodology for flows where stiffness is introduced through the chemical source term. A technique consisting of diagonal sweeps across the computational domain from each corner is presented, which is used to reduce storage and execution requirements. Results depicting one dimensional shock tube flow for both calorically perfect gas and thermally perfect, dissociating nitrogen are presented to verify current capabilities of the program. Also, computational results from a chemical reactor vessel with no fluid dynamic effects are presented to check the chemistry capability and to verify the point implicit strategy.

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

EPA Science Inventory

The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

Innovations

ERIC Educational Resources Information Center

Journal of College Science Teaching, 1972

1972-01-01

Listed are some new programs added in different institutions. Topics listed are oceanography, environmental education, interdisciplinary education, computer assisted instruction in chemistry laboratory, elementary education and FORTRAN IV for beginning students. (PS)

TOXCAST: A PROGRAM FOR PRIORTITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

Evaluating the potential of tens of thousands of chemicals for risk to human health and the environment is beyond the resource limits of the Environmental Protection Agency. The EPA's ToxCast program will explore alternative methods comprising computational chemistry, high-throug...

An Assessment of Research-Doctorate Programs in the United States: Mathematical & Physical Sciences.

ERIC Educational Resources Information Center

Jones, Lyle V., Ed.; And Others

The quality of doctoral-level chemistry (N=145), computer science (N=58), geoscience (N=91), mathematics (N=115), physics (N=123), and statistics/biostatistics (N=64) programs at United States universities was assessed, using 16 measures. These measures focused on variables related to: program size; characteristics of graduates; reputational…

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.

An Interactive Multimedia Software Program for Exploring Electrochemical Cells.

ERIC Educational Resources Information Center

Greenbowe, Thomas J.

1994-01-01

Describes computer-animated sequences and interactive multimedia instructional programs for use in introductory chemistry which allow students to explore electrochemical cells. The workbench section enables students to manipulate the experimental apparatus, chemicals, and instruments in order to design and build an experiment. The interactive…

Reduced Chemical Kinetic Mechanisms for Hydrocarbon Fuels

DTIC Science & Technology

2006-01-01

Technologies Reaction Engineering International 77 West 200 South, Suite # 210 Salt Lake City, UT 84101 3Professor Department of Mechanical ... Engineering University of California, Berkeley Berkeley, CA 94720 4Program Leader for Computational Chemistry Lawrence Livermore National Laboratory...species by the error introduced by assuming they are in quasi-steady state. The reduced mechanisms have been compared to detailed chemistry calculations

Energy and technology review

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

Quirk, W.J.; Canada, J.; de Vore, L.

1994-04-01

This issue highlights the Lawrence Livermore National Laboratory`s 1993 accomplishments in our mission areas and core programs: economic competitiveness, national security, energy, the environment, lasers, biology and biotechnology, engineering, physics, chemistry, materials science, computers and computing, and science and math education. Secondary topics include: nonproliferation, arms control, international security, environmental remediation, and waste management.

Data Aggregation, Curation and Modeling Approaches to Deliver Prediction Models to Support Computational Toxicology at the EPA (ACS Fall meeting)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program develops and utilizes QSAR modeling approaches across a broad range of applications. In terms of physical chemistry we have a particular interest in the prediction of basic physicochemical parameters ...

Ablation, Thermal Response, and Chemistry Program for Analysis of Thermal Protection Systems

NASA Technical Reports Server (NTRS)

Milos, Frank S.; Chen, Yih-Kanq

2010-01-01

In previous work, the authors documented the Multicomponent Ablation Thermochemistry (MAT) and Fully Implicit Ablation and Thermal response (FIAT) programs. In this work, key features from MAT and FIAT were combined to create the new Fully Implicit Ablation, Thermal response, and Chemistry (FIATC) program. FIATC is fully compatible with FIAT (version 2.5) but has expanded capabilities to compute the multispecies surface chemistry and ablation rate as part of the surface energy balance. This new methodology eliminates B' tables, provides blown species fractions as a function of time, and enables calculations that would otherwise be impractical (e.g. 4+ dimensional tables) such as pyrolysis and ablation with kinetic rates or unequal diffusion coefficients. Equations and solution procedures are presented, then representative calculations of equilibrium and finite-rate ablation in flight and ground-test environments are discussed.

Digital Simulation in Education.

ERIC Educational Resources Information Center

Braun, Ludwig

Simulation as a mode of computer use in instruction has been neglected by educators. This paper briefly explores the circumstances in which simulations are useful and presents several examples of simulation programs currently being used in high-school biology, chemistry, physics, and social studies classes. One program, STERIL, which simulates…

STAF: A Powerful and Sophisticated CAI System.

ERIC Educational Resources Information Center

Loach, Ken

1982-01-01

Describes the STAF (Science Teacher's Authoring Facility) computer-assisted instruction system developed at Leeds University (England), focusing on STAF language and major program features. Although programs for the system emphasize physical chemistry and organic spectroscopy, the system and language are general purpose and can be used in any…

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

Chemistry Research

NASA Technical Reports Server (NTRS)

1987-01-01

Philip Morris research center scientists use a computer program called CECTRP, for Chemical Equilibrium Composition and Transport Properties, to gain insight into the behavior of atoms as they progress along the reaction pathway. Use of the program lets the scientist accurately predict the behavior of a given molecule or group of molecules. Computer generated data must be checked by laboratory experiment, but the use of CECTRP saves the researchers hundreds of hours of laboratory time since experiments must run only to validate the computer's prediction. Philip Morris estimates that had CECTRP not been available, at least two man years would have been required to develop a program to perform similar free energy calculations.

Development and Application of Computational/In Vitro Toxicological Methods for Chemical Hazard Risk Reduction of New Materials for Advanced Weapon Systems

NASA Technical Reports Server (NTRS)

Frazier, John M.; Mattie, D. R.; Hussain, Saber; Pachter, Ruth; Boatz, Jerry; Hawkins, T. W.

2000-01-01

The development of quantitative structure-activity relationship (QSAR) is essential for reducing the chemical hazards of new weapon systems. The current collaboration between HEST (toxicology research and testing), MLPJ (computational chemistry) and PRS (computational chemistry, new propellant synthesis) is focusing R&D efforts on basic research goals that will rapidly transition to useful products for propellant development. Computational methods are being investigated that will assist in forecasting cellular toxicological end-points. Models developed from these chemical structure-toxicity relationships are useful for the prediction of the toxicological endpoints of new related compounds. Research is focusing on the evaluation tools to be used for the discovery of such relationships and the development of models of the mechanisms of action. Combinations of computational chemistry techniques, in vitro toxicity methods, and statistical correlations, will be employed to develop and explore potential predictive relationships; results for series of molecular systems that demonstrate the viability of this approach are reported. A number of hydrazine salts have been synthesized for evaluation. Computational chemistry methods are being used to elucidate the mechanism of action of these salts. Toxicity endpoints such as viability (LDH) and changes in enzyme activity (glutahoione peroxidase and catalase) are being experimentally measured as indicators of cellular damage. Extrapolation from computational/in vitro studies to human toxicity, is the ultimate goal. The product of this program will be a predictive tool to assist in the development of new, less toxic propellants.

Transpiration and film cooling boundary layer computer program. Volume 2: Computer program and user's manual

NASA Technical Reports Server (NTRS)

Gloss, R. J.

1971-01-01

A finite difference turbulent boundary layer computer program which allows for mass transfer wall cooling and equilibrium chemistry effects is presented. The program is capable of calculating laminar or turbulent boundary layer solutions for an arbitrary ideal gas or an equilibrium hydrogen oxygen system. Either two dimensional or axisymmetric geometric configurations may be considered. The equations are solved, in nondimension-alized physical coordinates, using the implicit Crank-Nicolson technique. The finite difference forms of the conservation of mass, momentum, total enthalpy and elements equations are linearized and uncoupled, thereby generating easily solvable tridiagonal sets of algebraic equations. A detailed description of the computer program, as well as a program user's manual is provided. Detailed descriptions of all boundary layer subroutines are included, as well as a section defining all program symbols of principal importance. Instructions are then given for preparing card input to the program and for interpreting the printed output. Finally, two sample cases are included to illustrate the use of the program.

Mammalian Toxicology Testing: Problem Definition Study, Personnel Plan.

DTIC Science & Technology

1981-03-01

Technician X X Biochemist X Biologist !Bookkeeper Cage Washer X Clinical Chemist Compound Preparation Technician X Computer Cooer X Computer ...Biologist 62 Bookkeeper 60 Cage rasher 33 Clinical Chemist 26 Comp. Prep. Technician 20 Computer Coder 31 Computer Programer 31 Electron Microscope Op...29,200 * Computer Programmer BS S SFByAe 900-2.0 18,400 - $24500 e Lab Tec-inician (Chemistry) BS 5 SF Say Area 16,600- 24.000 - 14.200- ’,0 * Animal

An efficient solver for large structured eigenvalue problems in relativistic quantum chemistry

NASA Astrophysics Data System (ADS)

Shiozaki, Toru

2017-01-01

We report an efficient program for computing the eigenvalues and symmetry-adapted eigenvectors of very large quaternionic (or Hermitian skew-Hamiltonian) matrices, using which structure-preserving diagonalisation of matrices of dimension N > 10, 000 is now routine on a single computer node. Such matrices appear frequently in relativistic quantum chemistry owing to the time-reversal symmetry. The implementation is based on a blocked version of the Paige-Van Loan algorithm, which allows us to use the Level 3 BLAS subroutines for most of the computations. Taking advantage of the symmetry, the program is faster by up to a factor of 2 than state-of-the-art implementations of complex Hermitian diagonalisation; diagonalising a 12, 800 × 12, 800 matrix took 42.8 (9.5) and 85.6 (12.6) minutes with 1 CPU core (16 CPU cores) using our symmetry-adapted solver and Intel Math Kernel Library's ZHEEV that is not structure-preserving, respectively. The source code is publicly available under the FreeBSD licence.

Students from Aurora Triumph in Competition of the Mind

Science.gov Websites

fast-paced questions about physics, math, biology, astronomy, chemistry, computers and the earth educational programs to help stimulate young people's interest in science and math. NR-00797

DEVELOPMENT OF EPA'S TOXCAST PROGRAM FOR PRIORITIZING THE TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS.

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS)and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1984

1984-01-01

Presents 28 activities, games, demonstrations, experiments, and computer programs for biology, chemistry, physics, and conservation education. Background information, laboratory procedures, equipment lists, and instructional strategies are included. Topics include nature conservation, chickens in school, human anatomy, nitrogen cycle, mechanism…

EDLAMP User’s Manual.

DTIC Science & Technology

1979-07-01

A computer program is described which can be used to analyze plasma chemistry effects on the performance of pulsed, electron-beam sustained, electric discharge lasers operating either in the open cycle or closed cycle mode. (Author)

Programming chemistry in DNA-addressable bioreactors

PubMed Central

Fellermann, Harold; Cardelli, Luca

2014-01-01

We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis. PMID:25121647

Parallel Performance of a Combustion Chemistry Simulation

DOE PAGES

Skinner, Gregg; Eigenmann, Rudolf

1995-01-01

We used a description of a combustion simulation's mathematical and computational methods to develop a version for parallel execution. The result was a reasonable performance improvement on small numbers of processors. We applied several important programming techniques, which we describe, in optimizing the application. This work has implications for programming languages, compiler design, and software engineering.

Duct flow nonuniformities for Space Shuttle Main Engine (SSME)

NASA Technical Reports Server (NTRS)

1987-01-01

A three-duct Space Shuttle Main Engine (SSME) Hot Gas Manifold geometry code was developed for use. The methodology of the program is described, recommendations on its implementation made, and an input guide, input deck listing, and a source code listing provided. The code listing is strewn with an abundance of comments to assist the user in following its development and logic. A working source deck will be provided. A thorough analysis was made of the proper boundary conditions and chemistry kinetics necessary for an accurate computational analysis of the flow environment in the SSME fuel side preburner chamber during the initial startup transient. Pertinent results were presented to facilitate incorporation of these findings into an appropriate CFD code. The computation must be a turbulent computation, since the flow field turbulent mixing will have a profound effect on the chemistry. Because of the additional equations demanded by the chemistry model it is recommended that for expediency a simple algebraic mixing length model be adopted. Performing this computation for all or selected time intervals of the startup time will require an abundance of computer CPU time regardless of the specific CFD code selected.

Delivering The Benefits of Chemical-Biological Integration in ...

EPA Pesticide Factsheets

Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy. Presentation at ACS TOXI session on Computational Chemistry and Toxicology in Chemical Discovery and Assessement (QSARs).

Advanced Chemistry Collection, 2nd Edition

NASA Astrophysics Data System (ADS)

2001-11-01

Software requirements are given in Table 3. Some programs have additional special requirements. Please see the individual program abstracts at JCE Online or the documentation included on the CD-ROM for more specific information. Table 3. General software requirements for the Advanced Chemistry Collection.

Literature Cited

1. General Chemistry Collection, 5th ed.; J. Chem. Educ. Software, 2001, SP16.
2. Advanced Chemistry Collection; J. Chem. Educ. Software, 2001, SP28.

Colorado Students Contend in Competition of the Mind

Science.gov Websites

-paced match of questions about physics, math, biology, astronomy, chemistry, computers and the earth one of its premier educational programs to help stimulate young people's interest in science and math

Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1984

1984-01-01

Presents 26 activities, experiments, demonstrations, games, and computer programs for biology, chemistry, and physics. Background information, laboratory procedures, equipment lists, and instructional strategies are given. Topics include eye measurements, nutrition, soil test tube rack, population dynamics, angular momentum, transition metals,…

Bringing Computers into College and University Teaching. Papers Presented at a Symposium Held under the Auspices of the Higher Education Research and Development Society of Australasia (Canberra, Australia, November 19, 1980).

ERIC Educational Resources Information Center

Miller, Allen H., Ed.; Ogilvie, John F., Ed.

The use of computers in higher education teaching programs is discussed in 16 papers and reports. Applications of computers in teaching particular subjects including prehistory and anthropology, mathematics, Hindi, plant science, chemistry, language, medicine, drawing, statistics, and engineering are discussed in 10 of the contributions. The other…

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.

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (S)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

THE TOXCAST PROGRAM FOR PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

The United States Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals...

Langley Aerospace Research Summer Scholars. Part 2

NASA Technical Reports Server (NTRS)

Schwan, Rafaela (Compiler)

1995-01-01

The Langley Aerospace Research Summer Scholars (LARSS) Program was established by Dr. Samuel E. Massenberg in 1986. The program has increased from 20 participants in 1986 to 114 participants in 1995. The program is LaRC-unique and is administered by Hampton University. The program was established for the benefit of undergraduate juniors and seniors and first-year graduate students who are pursuing degrees in aeronautical engineering, mechanical engineering, electrical engineering, material science, computer science, atmospheric science, astrophysics, physics, and chemistry. Two primary elements of the LARSS Program are: (1) a research project to be completed by each participant under the supervision of a researcher who will assume the role of a mentor for the summer, and (2) technical lectures by prominent engineers and scientists. Additional elements of this program include tours of LARC wind tunnels, computational facilities, and laboratories. Library and computer facilities will be available for use by the participants.

Technical Reports: Langley Aerospace Research Summer Scholars. Part 1

NASA Technical Reports Server (NTRS)

Schwan, Rafaela (Compiler)

1995-01-01

The Langley Aerospace Research Summer Scholars (LARSS) Program was established by Dr. Samuel E. Massenberg in 1986. The program has increased from 20 participants in 1986 to 114 participants in 1995. The program is LaRC-unique and is administered by Hampton University. The program was established for the benefit of undergraduate juniors and seniors and first-year graduate students who are pursuing degrees in aeronautical engineering, mechanical engineering, electrical engineering, material science, computer science, atmospheric science, astrophysics, physics, and chemistry. Two primary elements of the LARSS Program are: (1) a research project to be completed by each participant under the supervision of a researcher who will assume the role of a mentor for the summer, and (2) technical lectures by prominent engineers and scientists. Additional elements of this program include tours of LARC wind tunnels, computational facilities, and laboratories. Library and computer facilities will be available for use by the participants.

Evolution of computational chemistry, the "launch pad" to scientific computational models: The early days from a personal account, the present status from the TACC-2012 congress, and eventual future applications from the global simulation approach

NASA Astrophysics Data System (ADS)

Clementi, Enrico

2012-06-01

This is the introductory chapter to the AIP Proceedings volume "Theory and Applications of Computational Chemistry: The First Decade of the Second Millennium" where we discuss the evolution of "computational chemistry". Very early variational computational chemistry developments are reported in Sections 1 to 7, and 11, 12 by recalling some of the computational chemistry contributions by the author and his collaborators (from late 1950 to mid 1990); perturbation techniques are not considered in this already extended work. Present day's computational chemistry is partly considered in Sections 8 to 10 where more recent studies by the author and his collaborators are discussed, including the Hartree-Fock-Heitler-London method; a more general discussion on present day computational chemistry is presented in Section 14. The following chapters of this AIP volume provide a view of modern computational chemistry. Future computational chemistry developments can be extrapolated from the chapters of this AIP volume; further, in Sections 13 and 15 present an overall analysis on computational chemistry, obtained from the Global Simulation approach, by considering the evolution of scientific knowledge confronted with the opportunities offered by modern computers.

Virtually going green: The role of quantum computational chemistry in reducing pollution and toxicity in chemistry

NASA Astrophysics Data System (ADS)

Stevens, Jonathan

2017-07-01

Continuing advances in computational chemistry has permitted quantum mechanical calculation to assist in research in green chemistry and to contribute to the greening of chemical practice. Presented here are recent examples illustrating the contribution of computational quantum chemistry to green chemistry, including the possibility of using computation as a green alternative to experiments, but also illustrating contributions to greener catalysis and the search for greener solvents. Examples of applications of computation to ambitious projects for green synthetic chemistry using carbon dioxide are also presented.

Teaching Guide and Problem Supplement. A Publication of the Exemplary Project Problem Solving Computer Style 1969-1970.

ERIC Educational Resources Information Center

New Orleans Public Schools, LA.

Secondary school teachers incorporating the use of a computer in algebra, trigonometry, advanced mathematics, chemistry, or physics classes are the individuals for whom this book is intended. The content included in it is designed to aid the learning of programing techniques and basic scientific or mathematical principles, and to offer some…

A Case Study of the Introduction of RISC-based Computing and a Telecommunications Link to a Suburban High School.

ERIC Educational Resources Information Center

Hakerem, Gita; And Others

This study reports the efforts of the Water and Molecular Networks Project (WAMNet), a program in which high school chemistry students use computer simulations developed at Boston University (Massachusetts) to model the three-dimensional structure of molecules and the hydrogen bond network that holds water molecules together. This case study…

Case Study: The Use of a Hypercard Simulation to Aid in the Teaching of Laboratory Apparatus Operation.

ERIC Educational Resources Information Center

Waddick, John

1994-01-01

Compares the effect of a chemistry computer simulation, written by the author, with the effect of an instructor demonstration. The study indicates that in this particular situation the operation of a spectrophotometer can be effectively taught by computer simulation method. The program is written using HyperTalk, the HyperCard programming…

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.

Instrumental Analysis Chemistry Laboratory

ERIC Educational Resources Information Center

Munoz de la Pena, Arsenio; Gonzalez-Gomez, David; Munoz de la Pena, David; Gomez-Estern, Fabio; Sequedo, Manuel Sanchez

2013-01-01

designed for automating the collection and assessment of laboratory exercises is presented. This Web-based system has been extensively used in engineering courses such as control systems, mechanics, and computer programming. Goodle GMS allows the students to submit their results to a…

Numerical study of hydrogen-air supersonic combustion by using elliptic and parabolized equations

NASA Technical Reports Server (NTRS)

Chitsomboon, T.; Tiwari, S. N.

1986-01-01

The two-dimensional Navier-Stokes and species continuity equations are used to investigate supersonic chemically reacting flow problems which are related to scramjet-engine configurations. A global two-step finite-rate chemistry model is employed to represent the hydrogen-air combustion in the flow. An algebraic turbulent model is adopted for turbulent flow calculations. The explicit unsplit MacCormack finite-difference algorithm is used to develop a computer program suitable for a vector processing computer. The computer program developed is then used to integrate the system of the governing equations in time until convergence is attained. The chemistry source terms in the species continuity equations are evaluated implicitly to alleviate stiffness associated with fast chemical reactions. The problems solved by the elliptic code are re-investigated by using a set of two-dimensional parabolized Navier-Stokes and species equations. A linearized fully-coupled fully-implicit finite difference algorithm is used to develop a second computer code which solves the governing equations by marching in spce rather than time, resulting in a considerable saving in computer resources. Results obtained by using the parabolized formulation are compared with the results obtained by using the fully-elliptic equations. The comparisons indicate fairly good agreement of the results of the two formulations.

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…

Environmental research program. 1995 Annual report

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

Brown, N.J.

1996-06-01

The objective of the Environmental Research Program is to enhance the understanding of, and mitigate the effects of pollutants on health, ecological systems, global and regional climate, and air quality. The program is multidisciplinary and includes fundamental research and development in efficient and environmentally benign combustion, pollutant abatement and destruction, and novel methods of detection and analysis of criteria and noncriteria pollutants. This diverse group conducts investigations in combustion, atmospheric and marine processes, flue-gas chemistry, and ecological systems. Combustion chemistry research emphasizes modeling at microscopic and macroscopic scales. At the microscopic scale, functional sensitivity analysis is used to explore themore » nature of the potential-to-dynamics relationships for reacting systems. Rate coefficients are estimated using quantum dynamics and path integral approaches. At the macroscopic level, combustion processes are modelled using chemical mechanisms at the appropriate level of detail dictated by the requirements of predicting particular aspects of combustion behavior. Parallel computing has facilitated the efforts to use detailed chemistry in models of turbulent reacting flow to predict minor species concentrations.« less

The calculation of aquifer chemistry in hot-water geothermal systems

USGS Publications Warehouse

Truesdell, Alfred H.; Singers, Wendy

1974-01-01

The temperature and chemical conditions (pH, gas pressure, and ion activities) in a geothermal aquifer supplying a producing bore can be calculated from the enthalpy of the total fluid (liquid + vapor) produced and chemical analyses of water and steam separated and collected at known pressures. Alternatively, if a single water phase exists in the aquifer, the complete analysis (including gases) of a sample collected from the aquifer by a downhole sampler is sufficient to determine the aquifer chemistry without a measured value of the enthalpy. The assumptions made are that the fluid is produced from a single aquifer and is homogeneous in enthalpy and chemical composition. These calculations of aquifer chemistry involving large amounts of ancillary information and many iterations require computer methods. A computer program in PL-1 to perform these calculations is available from the National Technical Information Service as document PB-219 376.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Programming chemistry in DNA-addressable bioreactors.

PubMed

Fellermann, Harold; Cardelli, Luca

2014-10-06

We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Modeling the complete Otto cycle: Preliminary version. [computer programming

NASA Technical Reports Server (NTRS)

Zeleznik, F. J.; Mcbride, B. J.

1977-01-01

A description is given of the equations and the computer program being developed to model the complete Otto cycle. The program incorporates such important features as: (1) heat transfer, (2) finite combustion rates, (3) complete chemical kinetics in the burned gas, (4) exhaust gas recirculation, and (5) manifold vacuum or supercharging. Changes in thermodynamic, kinetic and transport data as well as model parameters can be made without reprogramming. Preliminary calculations indicate that: (1) chemistry and heat transfer significantly affect composition and performance, (2) there seems to be a strong interaction among model parameters, and (3) a number of cycles must be calculated in order to obtain steady-state conditions.

ToxCast: Using high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Applications of high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Predictive In Vitro Screening of Environmental Chemicals – The ToxCast Project

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Calculating Henry’s Constants of Charged Molecules Using SPARC

EPA Science Inventory

SPARC Performs Automated Reasoning in Chemistry is a computer program designed to model physical and chemical properties of molecules solely based on thier chemical structure. SPARC uses a toolbox of mechanistic perturbation models to model intermolecular interactions. SPARC has ...

EPA'S TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

PubMed Central

Caudill, Lester; Hill, April; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics. PMID:20810953

Impact of Interdisciplinary Undergraduate Research in mathematics and biology on the development of a new course integrating five STEM disciplines.

PubMed

Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was not only good science but also good science that motivated and informed course development. Here, we describe four recent undergraduate research projects involving students and faculty in biology, physics, mathematics, and computer science and how each contributed in significant ways to the conception and implementation of our new Integrated Quantitative Science course, a course for first-year students that integrates the material in the first course of the major in each of biology, chemistry, mathematics, computer science, and physics.

Computation of iodine species concentrations in water

NASA Technical Reports Server (NTRS)

Schultz, John R.; Mudgett, Paul D.; Flanagan, David T.; Sauer, Richard L.

1994-01-01

During an evaluation of the use of iodine as a water disinfectant and the development of methods for measuring various iodine species in water onboard Space Freedom, it became necessary to compute the concentration of the various species based on equilibrium principles alone. Of particular concern was the case when various amounts of iodine, iodide, strong acid, and strong base are added to water. Such solutions can be used to evaluate the performance of various monitoring methods being considered. The authors of this paper present an overview of aqueous iodine chemistry, a set of nonlinear equations which can be used to model the above case, and a computer program for solving this system of equations using the Newton-Raphson method. The program was validated by comparing results over a range of concentrations and pH values with those previously presented by Gottardi for a given pH. Use of this program indicated that there are multiple roots to many cases and selecting an appropriate initial guess is important. Comparison of program results with laboratory results for the case when only iodine is added to water indicates the program gives high pH values for the iodine concentrations normally used for water disinfection. Extending the model to include the effects of iodate formation results in the computer pH values being closer to those observed, but the model with iodate does not agree well for the case in which base is added in addition to iodine to raise the pH. Potential explanations include failure to obtain equilibrium conditions in the lab, inaccuracies in published values for the equilibrium constants, and inadequate model of iodine chemistry and/or the lack of adequate analytical methods for measuring the various iodine species in water.

Critical influence of finite rate chemistry and unmixedness on ignition and combustion of supersonic H2-air streams

NASA Technical Reports Server (NTRS)

Evans, J. S.; Schexnayder, C. J., Jr.

1979-01-01

Good agreement has been obtained between published profiles of composition and pitot pressure and the calculated results from a computer program in which finite rate chemistry was used. Significant differences are noted between results calculated using 7 species and 8 reactions and those calculated using 12 species and 25 reactions. Differences are also found between results in which the effect of unmixedness on reaction in turbulent flow is applied or is not applied.

A computer program for performance prediction of tripropellant rocket engines with tangential slot injection

NASA Technical Reports Server (NTRS)

Dang, Anthony; Nickerson, Gary R.

1987-01-01

For the development of a Heavy Lift Launch Vehicle (HLLV) several engines with different operating cycles and using LOX/Hydrocarbon propellants are presently being examined. Some concepts utilize hydrogen for thrust chamber wall cooling followed by a gas generator turbine drive cycle with subsequent dumping of H2/O2 combustion products into the nozzle downstream of the throat. In the Space Transportation Booster Engine (STBE) selection process the specific impulse will be one of the optimization criteria; however, the current performance prediction programs do not have the capability to include a third propellant in this process, nor to account for the effect of dumping the gas-generator product tangentially inside the nozzle. The purpose is to describe a computer program for accurately predicting the performance of such an engine. The code consists of two modules; one for the inviscid performance, and the other for the viscous loss. For the first module, the two-dimensional kinetics program (TDK) was modified to account for tripropellant chemistry, and for the effect of tangential slot injection. For the viscous loss, the Mass Addition Boundary Layer program (MABL) was modified to include the effects of the boundary layer-shear layer interaction, and tripropellant chemistry. Calculations were made for a real engine and compared with available data.

Systematic Changes in the Undergraduate Chemistry Curriculum Progam Award and Course and Curriculum Development Program Awards

NASA Astrophysics Data System (ADS)

1996-06-01

Eight awards in chemistry curriculum development for FY1996 have been announced. One award, to a consortium centered at the University of California-Los Angeles, represents the fifth award in the Systemic Changes in the Undergraduate Chemistry Curriculum program. Although no proposals will be accepted in this program for either planning or full grants for FY1997, it is anticipated that proposals will be accepted in June of 1997 for projects that would adapt and adopt materials developed by the five funded consortia: Molecular Science centered at the University of California-Los Angeles; ChemLinks centered at Beloit College; MolecularChem Consortium centered at the University of California-Berkeley; Workshop Chemistry centered at CUNY City College; and New Traditions centered at the University of Wisconsin-Madison. Seven awards have been made in the Course and Curriculum Development program. This ongoing program continues to accept proposals in chemistry as usual. Systemic Changes in the Undergraduate Chemistry Curriculum Program Award. Molecular Science. Orville L. Chapman University of California-Los Angeles DUE 9555605 FY96 725,000 FY97 575,000, FY98 575,000 FY99 275,000, FY00 275,000 The UCLA-CSUF-Community College Alliance (24 area community colleges that have worked together for more than 15 years) proposes a sweeping restructuring of the lower division chemistry curriculum and the auxiliary learning and assessment processes. In forming our new curriculum, we reject the positivist approach to science education in favor of a constructivist approach that emphasizes problem solving and exploratory learning. We make this change in order to focus on the developing key skills, traits, and abilities of our students. Our new curriculum, the Molecular Science Curriculum, cuts across departments and disciplines to embrace all activities that involve the study of atoms and molecules. In particular, environmental science, materials science, and molecular life science have important positions in the lower-division chemistry curriculum. The new curriculum reflects accurately current practice in research and the chemical industry where growth is occurring in these new fields. Today information-technology-based learning enables a practical approach to discovery learning, which educational theorists have long favored. Students can learn science by doing science. In particular, we will produce problem-based modular learning units that define the molecular science curriculum; data sets organized for exploratory learning; prepackaged molecular, mathematical, and schematic models illustrating important principles and phenomena; and a client/server system that manages education. Client/server technology enables individualized courses and frees students from rigid time constraints. The learning units will be used immediately by several of the community colleges in technology programs, such as those for science technicians and hazardous materials technicians at Mount San Antonio CC. New assessment vehicles including cumulative electronic portfolios of group and individual work provide new insight into student development and potential. The project also addresses the preparation of primary and secondary science teachers by involving them as active participants in the lower division courses of the molecular science curriculum. At both UCLA and CSUF, these students will gain experience with the modules, associated learning methods, and electronic delivery system. These experiences should result in teachers with a practical perspective on science teaching as well as the ability to utilize current technology to direct learning activities. The electronic delivery system will allow students at UCLA to work with the science education faculty at CSUF to obtain certification. Since 1990 two high schools (Aliso Niguel and Crossroads) have become members of the Alliance. These schools have the facilities to expose students, experienced teachers, and future teachers to both the content and learning methods of the molecular science curriculum. Course and Curriculum Development Program Awards. Studio General Chemistry with Full Merging of the Laboratory and Classroom Experiences. Thomas M. Apple Rensselaer Polytechnic Institute DUE 9555069 114,000 A workshop general chemistry class is being developed that includes experimental work during every meeting. Lab work is merged with classroom discussion. Students working in groups are challenged to link their macroscopic observations to chemical principles. The merger of thirty-minute, concept-based discovery labs with discussion and lateral development material provides a unique perspective of chemistry. In modernizing the general chemistry curriculum, fewer topics are treated and the more esoteric aspects of physical chemistry that are inappropriate for freshmen are eliminated. More time is allocated to materials chemistry, organic and biological chemistry, and environmental science. The course material is organized into modules or case-studies that contain material that is developed with the specific aim of showing the relevance of the material to problems to which the students already have been exposed. Societal relevance is built into every module of the syllabus by incorporating laboratories, discussion and "lateral development" problems for each topic. Dynamic Visualization in Chemistry. James P. Birk Arizona State University DUE 9555098 175,000 This project will produce real images of chemical and physical changes occurring at the microscopic and atomic levels. These images, from different instruments (optical, electron, and scanning probe microscopes), will be captured electronically (video tapes and CD ROMs) and used in conjunction with molecular modeling as instructional aids in introductory chemistry courses. The objective is to introduce students to the relationships between macroscopic changes in materials and the corresponding changes in the arrangements of their atoms and molecules. The graphic images will be combined with interactive benchtop demonstrations and computer animations to produce dynamic visual instructional components (dynamic visualization modules, DVMs) for introductory chemistry courses. The existing instrumentation and modeling facilities required for the project are currently in place. Once developed the DVMs will be tested with approximately 4000 general chemistry students at Arizona State University and the Maricopa Community College system. There is a goal of national dissemination by a commercial publisher once the DVMs have been tested in the local environment. An Introductory Course in Modeling Dynamic Chemical and Ecological Systems. Joseph E. Earley Georgetown University DUE 9554932 99,996 An introductory course in modeling of dynamic systems, with special emphasis on chemical and ecological problems, will be developed. The target student population will be first- and second-year social science and humanities students, but upper division students and interested science majors will not be excluded. Rather than placing emphasis on mathematical methods and techniques used in modeling, attention will be centered on salient aspects of complex-system behavior as illustrated by models constructed using the commercially available software-package STELLA II. Relatively straightforward models dealing with chemical reactions will be used to introduce fundamental features of complex-system dynamics. Problems of ecological and demographic interest, at moderate level of difficulty, will then be covered. The origin and behavior of "deterministic chaos" will be treated using examples from both chemistry and ecology. In the last third of the course, students will work in small groups (or individually) developing their own models, each related to a specific problem of current interest, preferably in fields of the students' major academic interest. Opportunity will be provided for some outstanding students to use less "user-friendly" software such as ODEPACK to deal with models involving "stiff" differential equations. The last exercise of the course will be a poster session, at which individuals and groups will present their project models to other members of the class and to guests. The main aims of the course will be to facilitate development of the students' insight with respect to types of functioning to be expected of complex networks of relationships, and therefore in important natural systems, and also to engender an appreciation of the power and limitations of modeling techniques. VizChem-Visualizing Chemistry. Leonard W. Fine Columbia University DUE 9555122 209,000 Multimedia computer modules suitable for undergraduate chemistry lecture and laboratory courses are being designed. The modules are both content and skills oriented, interdisciplinary and multidimensional, and take full advantage of the benefits of simulation, computation, and visualization. They are being designed and created as tools for the teacher and for the student and are primarily directed at general chemistry, organic chemistry, physical chemistry, inorganic chemistry, and materials science. Module topics will include the next version of IR Tutor and applicable and important spectroscopies and diagnostic devices such as electronic absorption (UV-vis) and electronic emission (fluorescence and phosphorescence); proton and carbon-13 nuclear magnetic resonance; atomic absorption; thermal analysis; topics in polymer chemistry and materials science; and PCR technology. Secondary objectives of the project include: a broadening of the chemistry curriculum beyond traditional disciplinary boundaries, new undergraduate courses, enhanced effectiveness of teaching assistants, an expanded role for postdoctoral students in undergraduate education, and improved performance by classes of students. Connecting Undergraduate/Analytical Courses to Modern Analytical Chemistry. Thomas R. Gilbert Northeastern University DUE 9554906 200,000 Application modules in the form of projects and active learning techniques to provide a strong foundation in the principles of chemical measurement and to pique the interest of both chemistry majors and nonmajors will be developed for use in introductory analytical courses. The modules will address an analytical problem drawn from current research in biological, environmental, or materials science. Students will be responsible for proposing and evaluating analytical protocols to solve the problems: they will conduct workshops and design their own laboratory experiments. A multidisciplinary Advisory Council will guide the PIs in problem selection and module development. A two-week faculty workshop will provide training in the use of these modules. A World Wide Web home page will be used to distribute information about the modules and will allow users to share experiences using them. Modules will ultimately be distributed by a commercial publisher. Process Workshops for General Chemistry. David M. Hanson SUNY at Stony Brook DUE 9555142 150,000 The process skills needed by students will be addressed by developing innovations in both content and methodology to replace recitation sessions associated with large lecture courses by process workshops, specifically for introductory chemistry courses. The novel format involves process skills, student participation, and active learning at the forefront. Students will work in cooperative-learning groups on lessons that involve discovery learning, critical thinking, problem solving, reporting, and assessment. Computer-based technology will be used to provide personalized quizzes, and the workshop lessons will be transported to a computer network, multi-media format. The objectives of this project are to develop teaching strategies that support a successful cooperative-learning environment, develop lessons that enhance the understanding of concepts and promote learning and problem solving through the use of higher order thinking skills, develop lessons incorporating interdisciplinary and real world perspectives, enhance learning with computer-driven technology, develop process skills in key areas, promote positive attitudes toward chemistry and science, help students develop confidence in their ability to learn and perform well, create a supportive social environment that will encourage students to involve themselves seriously and successfully in learning, and promote a culture where the university is a community of learners. The transformation of recitation sessions into workshops introduces the missing element in large lecture courses. The lectures structure information and make it available to the students, and the workshops complement that component by facilitating the construction of understanding, the application of knowledge, and the development of process skills. Such development is extremely significant because introductory chemistry courses involve large numbers of students early in their college careers. Among other things, summer teaching and authoring institutes will be held to excite the interest of others in this approach and to share ideas on the methodology, strategies, and lesson content. Forensic Science: An Interactive Multimedia Laboratory Program to Enhance Introductory Chemistry (Science) Courses. Lawrence J. Kaplan Williams College DUE 9554875 234,539 While major changes have taken place in all areas of the natural sciences, introductory instruction in both the lecture hall and the laboratory has not changed significantly in many years. The PI instituted innovative teaching techniques in an elementary chemistry course called "Chemistry and Crime: From Sherlock Holmes to Modern Forensic Science" for the nonscience major. The techniques used in the laboratory have received national attention and many colleagues have instituted similar innovations. However, many institutions do not have the resources to develop laboratory programs along these lines and, as times have changed, are increasingly concerned with exposing the students to situations now recognized as potentially dangerous. Since the PI has proven that forensics can be used to spark interest in science and since it is given that young people are intrigued by computer graphics, it was decided to use computer-animated simulations to allow extensive, intensive investigation of scientific evidence collected at simulated crime scenes and studied using simulated scientific instruments. These animated modules will enhance not only the laboratory program in the forensic science course but also the programs in introductory science courses for majors. The PI will guide the development of the computer-animated modules, develop the story board and oversee the computer interfacing and the integration of the components into the curriculum. The actual modules will be created by Engineering Animation, Inc. EAI, using their Vislab software, is one of the premier computer animation companies in the world. It is anticipated that implementing this innovative and creative approach, as part of an overall multimedia program including actual laboratory experience, will enhance science education by stimulating interest and engendering enthusiasm instead of promoting the stereotype that science is boring and hard.

Free Energy Minimization Calculation of Complex Chemical Equilibria. Reduction of Silicon Dioxide with Carbon at High Temperature.

ERIC Educational Resources Information Center

Wai, C. M.; Hutchinson, S. G.

1989-01-01

Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)

Applications of high throughput screening to identify profiles of biological activity relevant to carcinogenesis

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

ExpoCast: Exposure Science for Prioritization and Toxicity Testing (S)

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCast. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize limi...

ExpoCast: Exposure Science for Prioritization and Toxicity Testing

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCastTM. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize l...

Linear Scaling Density Functional Calculations with Gaussian Orbitals

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1999-01-01

Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.

Laboratory directed research and development. FY 1995 progress report

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

Vigil, J.; Prono, J.

1996-03-01

This document presents an overview of Laboratory Directed Research and Development Programs at Los Alamos. The nine technical disciplines in which research is described include materials, engineering and base technologies, plasma, fluids, and particle beams, chemistry, mathematics and computational science, atmic and molecular physics, geoscience, space science, and astrophysics, nuclear and particle physics, and biosciences. Brief descriptions are provided in the above programs.

The 1984 NASA/ASEE summer faculty fellowship program

NASA Technical Reports Server (NTRS)

Mcinnis, B. C.; Duke, M. B.; Crow, B.

1984-01-01

An overview is given of the program management and activities. Participants and research advisors are listed. Abstracts give describe and present results of research assignments performed by 31 fellows either at the Johnson Space Center, at the White Sands test Facility, or at the California Space Institute in La Jolla. Disciplines studied include engineering; biology/life sciences; Earth sciences; chemistry; mathematics/statistics/computer sciences; and physics/astronomy.

Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach

DTIC Science & Technology

2012-01-01

target representatives. Target profiles were then generated for a given query molecule by computing maximal shape/ chemistry overlap between the query...molecule and the drug sets assigned to each protein target. The overlap was computed using the program ROCS (Rapid Overlay of Chemical Structures ). We...approaches in off-target prediction has been reviewed.9,10 Many structure -based target fishing (SBTF) approaches, such as INVDOCK11 and Target Fishing Dock

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (Developing Predictive Bioactivity Signatures from ToxCasts HTS Data)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

Energy and technology review, July--August, 1990

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

Burnham, A.K.

1990-01-01

This report highlights various research programs conducted at the Lab to include: defense systems, laser research, fusion energy, biomedical and environmental sciences, engineering, physics, chemistry, materials science, and computational analysis. It also contains a statement on the state of the Lab and Laboratory Administration. (JEF)

JACOB: an enterprise framework for computational chemistry.

PubMed

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

2013-06-15

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: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

How to manage continuing education and retraining programs on optical physics and laser technology at a university: Moscow State experience

NASA Astrophysics Data System (ADS)

Zadkov, Victor N.; Koroteev, Nikolai I.

1995-10-01

An experience of managing the continuing education and retraining programs at the International Laser Center (ILC) of Moscow State University is discussed. The offered programs are in a wide range of areas, namely laser physics and technology, laser biophysics and biomedicine, laser chemistry, and computers in laser physics. The attendees who are presumably scientists, engineers, technical managers, and graduate students can join these programs through the annual ILC term (6 months), individual training and research programs (up to a year), annual ILC Laser Graduate School, graduate study, and post-docs program, which are reviewed in the paper. A curriculum that includes basic and specialized courses is described in detail. A brief description of the ILC Laser Teaching and Computer Labs that support all the educational courses is given as well.

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…

Daniel A. Ruddy, Ph.D. | NREL

Science.gov Websites

. "Experimental and Computational Investigation of Acetic Acid Deoxygenation over Oxophilic programmed reaction (TPRxn) at 200 to 500C. The right pane is a plot of experimental TPRxn data, collected Nanocrystal Films," The Journal of Physical Chemistry Letters (2013) "Non-aqueous Thermolytic Route

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)

Empirical Performance Model-Driven Data Layout Optimization and Library Call Selection for Tensor Contraction Expressions

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

Lu, Qingda; Gao, Xiaoyang; Krishnamoorthy, Sriram

Empirical optimizers like ATLAS have been very effective in optimizing computational kernels in libraries. The best choice of parameters such as tile size and degree of loop unrolling is determined by executing different versions of the computation. In contrast, optimizing compilers use a model-driven approach to program transformation. While the model-driven approach of optimizing compilers is generally orders of magnitude faster than ATLAS-like library generators, its effectiveness can be limited by the accuracy of the performance models used. In this paper, we describe an approach where a class of computations is modeled in terms of constituent operations that are empiricallymore » measured, thereby allowing modeling of the overall execution time. The performance model with empirically determined cost components is used to perform data layout optimization together with the selection of library calls and layout transformations in the context of the Tensor Contraction Engine, a compiler for a high-level domain-specific language for expressing computational models in quantum chemistry. The effectiveness of the approach is demonstrated through experimental measurements on representative computations from quantum chemistry.« less

Advances in analytical chemistry

NASA Technical Reports Server (NTRS)

Arendale, W. F.; Congo, Richard T.; Nielsen, Bruce J.

1991-01-01

Implementation of computer programs based on multivariate statistical algorithms makes possible obtaining reliable information from long data vectors that contain large amounts of extraneous information, for example, noise and/or analytes that we do not wish to control. Three examples are described. Each of these applications requires the use of techniques characteristic of modern analytical chemistry. The first example, using a quantitative or analytical model, describes the determination of the acid dissociation constant for 2,2'-pyridyl thiophene using archived data. The second example describes an investigation to determine the active biocidal species of iodine in aqueous solutions. The third example is taken from a research program directed toward advanced fiber-optic chemical sensors. The second and third examples require heuristic or empirical models.

Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields, volume 3

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1991-01-01

The computer programs developed to calculate the shock wave precursor and the method of using them are described. This method calculated the precursor flow field in a nitrogen gas including the effects of emission and absorption of radiation on the energy and composition of gas. The radiative transfer is calculated including the effects of absorption and emission through the line as well as the continuum process in the shock layer and through the continuum processes only in the precursor. The effects of local thermodynamic nonequilibrium in the shock layer and precursor regions are also included in the radiative transfer calculations. Three computer programs utilized by this computational scheme to calculate the precursor flow field solution for a given shock layer flow field are discussed.

Beyond [lambda][subscript max] Part 2: Predicting Molecular Color

ERIC Educational Resources Information Center

Williams, Darren L.; Flaherty, Thomas J.; Alnasleh, Bassam K.

2009-01-01

A concise roadmap for using computational chemistry programs (i.e., Gaussian 03W) to predict the color of a molecular species is presented. A color-predicting spreadsheet is available with the online material that uses transition wavelengths and peak-shape parameters to predict the visible absorbance spectrum, transmittance spectrum, chromaticity…

Microcomputer Calculation of Theoretical Pre-Exponential Factors for Bimolecular Reactions.

ERIC Educational Resources Information Center

Venugopalan, Mundiyath

1991-01-01

Described is the application of microcomputers to predict reaction rates based on theoretical atomic and molecular properties taught in undergraduate physical chemistry. Listed is the BASIC program which computes the partition functions for any specific bimolecular reactants. These functions are then used to calculate the pre-exponential factor of…

Application of Computers for Experiment Design, Data Acquisition, and Analysis in the Chemistry Laboratory

DTIC Science & Technology

1990-05-01

Obtain Thermistor Operating Characteristics ................................. 82 25. Ag+/Ci" Thermometric Titration ........................... 85 26...Experiment Program for Thermometric Titrations ............... 85 27. Appearance of the Spreadsheet in the Analysis Mode ............ 86 28...rate experiments, carbon dioxide exhalation monitoring, stream turbidity measurement, photosynthesis monitoring, pendulum timing, thermometric titrations

A Microcomputer-Based Data Acquisition System for Use in Undergraduate Laboratories.

ERIC Educational Resources Information Center

Johnson, Ray L.

1982-01-01

A laboratory computer system based on the Commodore PET 2001 is described including three applications for the undergraduate analytical chemistry laboratory: (1) recording a UV-visible absorption spectrum; (2) recording and use of calibration curves; and (3) recording potentiometric data. Lists of data acquisition programs described are available…

Project Solo; Newsletter Number Seven.

ERIC Educational Resources Information Center

Pittsburgh Univ., PA. Project Solo.

The current curriculum modules under development at Project Solo are listed. The modules are grouped under the subject matter that they are designed to teach--algebra II, biology, calculus, chemistry, computer science, 12th grade math, physics, social science. Special programs written for use on the Hewlett-Packard Plotter are listed that may be…

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

ERIC Educational Resources Information Center

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

2007-01-01

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

Multicore Challenges and Benefits for High Performance Scientific Computing

DOE PAGES

Nielsen, Ida M. B.; Janssen, Curtis L.

2008-01-01

Until recently, performance gains in processors were achieved largely by improvements in clock speeds and instruction level parallelism. Thus, applications could obtain performance increases with relatively minor changes by upgrading to the latest generation of computing hardware. Currently, however, processor performance improvements are realized by using multicore technology and hardware support for multiple threads within each core, and taking full advantage of this technology to improve the performance of applications requires exposure of extreme levels of software parallelism. We will here discuss the architecture of parallel computers constructed from many multicore chips as well as techniques for managing the complexitymore » of programming such computers, including the hybrid message-passing/multi-threading programming model. We will illustrate these ideas with a hybrid distributed memory matrix multiply and a quantum chemistry algorithm for energy computation using Møller–Plesset perturbation theory.« less

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.

Designing, programming, and optimizing a (small) quantum computer

NASA Astrophysics Data System (ADS)

Svore, Krysta

In 1982, Richard Feynman proposed to use a computer founded on the laws of quantum physics to simulate physical systems. In the more than thirty years since, quantum computers have shown promise to solve problems in number theory, chemistry, and materials science that would otherwise take longer than the lifetime of the universe to solve on an exascale classical machine. The practical realization of a quantum computer requires understanding and manipulating subtle quantum states while experimentally controlling quantum interference. It also requires an end-to-end software architecture for programming, optimizing, and implementing a quantum algorithm on the quantum device hardware. In this talk, we will introduce recent advances in connecting abstract theory to present-day real-world applications through software. We will highlight recent advancement of quantum algorithms and the challenges in ultimately performing a scalable solution on a quantum device.

A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

DOE PAGES

Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

2008-01-01

Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

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)

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…

Transpiration and film cooling boundary layer computer program. Volume 1: Numerical solutions of the turbulent boundary layer equations with equilibrium chemistry

NASA Technical Reports Server (NTRS)

Levine, J. N.

1971-01-01

A finite difference turbulent boundary layer computer program has been developed. The program is primarily oriented towards the calculation of boundary layer performance losses in rocket engines; however, the solution is general, and has much broader applicability. The effects of transpiration and film cooling as well as the effect of equilibrium chemical reactions (currently restricted to the H2-O2 system) can be calculated. The turbulent transport terms are evaluated using the phenomenological mixing length - eddy viscosity concept. The equations of motion are solved using the Crank-Nicolson implicit finite difference technique. The analysis and computer program have been checked out by solving a series of both laminar and turbulent test cases and comparing the results to data or other solutions. These comparisons have shown that the program is capable of producing very satisfactory results for a wide range of flows. Further refinements to the analysis and program, especially as applied to film cooling solutions, would be aided by the acquisition of a firm data base.

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

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

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less

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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transuranic Computational Chemistry.

PubMed

Kaltsoyannis, Nikolas

2018-02-26

Recent developments in the chemistry of the transuranic elements are surveyed, with particular emphasis on computational contributions. Examples are drawn from molecular coordination and organometallic chemistry, and from the study of extended solid systems. The role of the metal valence orbitals in covalent bonding is a particular focus, especially the consequences of the stabilization of the 5f orbitals as the actinide series is traversed. The fledgling chemistry of transuranic elements in the +II oxidation state is highlighted. Throughout, the symbiotic interplay of experimental and computational studies is emphasized; the extraordinary challenges of experimental transuranic chemistry afford computational chemistry a particularly valuable role at the frontier of the periodic table. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Problem-based learning on quantitative analytical chemistry course

NASA Astrophysics Data System (ADS)

Fitri, Noor

2017-12-01

This research applies problem-based learning method on chemical quantitative analytical chemistry, so called as "Analytical Chemistry II" course, especially related to essential oil analysis. The learning outcomes of this course include aspects of understanding of lectures, the skills of applying course materials, and the ability to identify, formulate and solve chemical analysis problems. The role of study groups is quite important in improving students' learning ability and in completing independent tasks and group tasks. Thus, students are not only aware of the basic concepts of Analytical Chemistry II, but also able to understand and apply analytical concepts that have been studied to solve given analytical chemistry problems, and have the attitude and ability to work together to solve the problems. Based on the learning outcome, it can be concluded that the problem-based learning method in Analytical Chemistry II course has been proven to improve students' knowledge, skill, ability and attitude. Students are not only skilled at solving problems in analytical chemistry especially in essential oil analysis in accordance with local genius of Chemistry Department, Universitas Islam Indonesia, but also have skilled work with computer program and able to understand material and problem in English.

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.

In-Service Chemistry Teachers Training: The Impact of Introducing Computer Technology on Teachers' Attitudes.

ERIC Educational Resources Information Center

Dori, Y. J.; Barnea, N.

A computer-assisted instruction (CAI) module on polymers was used to introduce chemistry teachers (n=64) to the variety of possibilities and benefits of using courseware in the current chemistry curriculum in Israel. From an analysis of a pre-and post-attitude questionnaire regarding the use of computers in chemistry teaching, it was concluded…

Report of the Eighth Biennial Conference on Chemical Education, University of Connecticut, Storrs, Connecticut, August 5-10, 1984.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1985

1985-01-01

Provides highlights of lectures, workshops, papers, and symposia presented at a conference which addressed such areas of chemical education as college/high school chemistry teaching; curriculum/curriculum development; safety; two-year programs; computers; toxicology and health hazards; problem-solving; writing skills development; textbooks;…

THE COMMUNITY RESOURCES POOL SEMINAR DESCRIPTIONS.

ERIC Educational Resources Information Center

SATURDAY MORNING SEMINARS FOR ELEMENTARY AND SECONDARY SCHOOL STUDENTS WERE CONDUCTED WITH PROFESSIONAL RESOURCE PERSONS AS TEACHERS. THE PROGRAM WAS VOLUNTARY. THREE 9-WEEK SEMINARS WERE CONDUCTED IN THE FALL. SUBJECTS STUDIED WERE MICROBIOLOGY AND ZOOLOGY (6TH GRADE), COMPUTER MATH (7TH AND 8TH GRADE), AND CHEMISTRY (GRADES 9-12). DURING THE…

Cumulative reports and publications through December 31, 1989

NASA Technical Reports Server (NTRS)

1990-01-01

A complete list of reports from the Institute for Computer Applications in Science and Engineering (ICASE) is presented. The major categories of the current ICASE research program are: numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; control and parameter identification problems, with emphasis on effectual numerical methods; computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, structural analysis, and chemistry; computer systems and software, especially vector and parallel computers, microcomputers, and data management. Since ICASE reports are intended to be preprints of articles that will appear in journals or conference proceedings, the published reference is included when it is available.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

PubMed

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

PubMed Central

2012-01-01

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

Program of research in severe storms

NASA Technical Reports Server (NTRS)

1979-01-01

Two modeling areas, the development of a mesoscale chemistry-meteorology interaction model, and the development of a combined urban chemical kinetics-transport model are examined. The problems associated with developing a three dimensional combined meteorological-chemical kinetics computer program package are defined. A similar three dimensional hydrostatic real time model which solves the fundamental Navier-Stokes equations for nonviscous flow is described. An urban air quality simulation model, developed to predict the temporal and spatial distribution of reactive and nonreactive gases in and around an urban area and to support a remote sensor evaluation program is reported.

Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

NASA Technical Reports Server (NTRS)

Nguyen, Howard; Willacy, Karen; Allen, Mark

2012-01-01

KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

Knowing when to give up: early-rejection stratagems in ligand docking

NASA Astrophysics Data System (ADS)

Skone, Gwyn; Voiculescu, Irina; Cameron, Stephen

2009-10-01

Virtual screening is an important resource in the drug discovery community, of which protein-ligand docking is a significant part. Much software has been developed for this purpose, largely by biochemists and those in related disciplines, who pursue ever more accurate representations of molecular interactions. The resulting tools, however, are very processor-intensive. This paper describes some initial results from a project to review computational chemistry techniques for docking from a non-chemistry standpoint. An abstract blueprint for protein-ligand docking using empirical scoring functions is suggested, and this is used to discuss potential improvements. By introducing computer science tactics such as lazy function evaluation, dramatic increases to throughput can and have been realized using a real-world docking program. Naturally, they can be extended to any system that approximately corresponds to the architecture outlined.

Cumulative Index to NASA Tech Briefs

NASA Technical Reports Server (NTRS)

1969-01-01

Tech Briefs are short announcements of new technology derived from the R&D activities of the National Aeronautics and Space Administration. This Index to NASA Tech Briefs lists the technological innovations derived from the U.S. space program and published during the period January through December 1968. A new five year cycle of cumulative indexes begins with this index. The main section is arranged in six categories: Electrical (Electronic); Physical Sciences (Energy Sources); Materials (Chemistry); Life Sciences; Mechanical; and Computer Programs.

Computational Nanotechnology Program

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1997-01-01

The objectives are: (1) development of methodological and computational tool for the quantum chemistry study of carbon nanostructures and (2) development of the fundamental understanding of the bonding, reactivity, and electronic structure of carbon nanostructures. Our calculations have continued to play a central role in understanding the outcome of the carbon nanotube macroscopic production experiment. The calculations on buckyonions offer the resolution of a long controversy between experiment and theory. Our new tight binding method offers increased speed for realistic simulations of large carbon nanostructures.

Silicon material task. Part 3: Low-cost silicon solar array project

NASA Technical Reports Server (NTRS)

Roques, R. A.; Coldwell, D. M.

1977-01-01

The feasibility of a process for carbon reduction of low impurity silica in a plasma heat source was investigated to produce low-cost solar-grade silicon. Theoretical aspects of the reaction chemistry were studied with the aid of a computer program using iterative free energy minimization. These calculations indicate a threshold temperature exists at 2400 K below which no silicon is formed. The computer simulation technique of molecular dynamics was used to study the quenching of product species.

Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

PubMed

Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

2012-04-01

A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations. Copyright © 2011 Elsevier Inc. All rights reserved.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

Massively parallel sparse matrix function calculations with NTPoly

NASA Astrophysics Data System (ADS)

Dawson, William; Nakajima, Takahito

2018-04-01

We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

NASA Astrophysics Data System (ADS)

Lahti, Paul M.; Motyka, Eric J.; Lancashire, Robert J.

2000-05-01

A straightforward procedure is described to combine computation of molecular vibrational modes using commonly available molecular modeling programs with visualization of the modes using advanced features of the MDL Information Systems Inc. Chime World Wide Web browser plug-in. Minor editing of experimental spectra that are stored in the JCAMP-DX format allows linkage of IR spectral frequency ranges to Chime molecular display windows. The spectra and animation files can be combined by Hypertext Markup Language programming to allow interactive linkage between experimental spectra and computationally generated vibrational displays. Both the spectra and the molecular displays can be interactively manipulated to allow the user maximum control of the objects being viewed. This procedure should be very valuable not only for aiding students through visual linkage of spectra and various vibrational animations, but also by assisting them in learning the advantages and limitations of computational chemistry by comparison to experiment.

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.

Practical use of a word processor in a histopathology laboratory.

PubMed Central

Briggs, J C; Ibrahim, N B; Mackintosh, I; Norris, D

1982-01-01

Some of the facilities available with a commercially purchased word processing program, linked to a DEC PDP 11/23 computer are described, together with an account of the practical histopathological use. The system is based on a share of the computer with a Clinical Chemistry Department. Development was time-consuming and required the constant availability of the Department of Physics. However, once working, considerable saving in secretarial time has resulted and a number of projects have been started which would not have been contemplated without the use of the word processor and its linked computer. Images PMID:7068906

Investigation of chemically-reacting supersonic internal flows

NASA Technical Reports Server (NTRS)

Chitsomboon, T.; Tiwari, S. N.

1985-01-01

This report covers work done on the research project Analysis and Computation of Internal Flow Field in a Scramjet Engine. The work is supported by the NASA Langley Research Center (Computational Methods Branch of the High-Speed Aerodynamics Division) through research grant NAG1-423. The governing equations of two-dimensional chemically-reacting flows are presented together with the global two-step chemistry model. The finite-difference algorithm used is illustrated and the method of circumventing the stiffness is discussed. The computer program developed is used to solve two model problems of a premixed chemically-reacting flow. The results obtained are physically reasonable.

chemf: A purely functional chemistry toolkit.

PubMed

Höck, Stefan; Riedl, Rainer

2012-12-20

Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project.

chemf: A purely functional chemistry toolkit

PubMed Central

2012-01-01

Background Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project. PMID:23253942

TOXCAST, A TOOL FOR CATEGORIZATION AND ...

EPA Pesticide Factsheets

Across several EPA Program Offices (e.g., OPPTS, OW, OAR), there is a clear need to develop strategies and methods to screen large numbers of chemicals for potential toxicity, and to use the resulting information to prioritize the use of testing resources towards those entities and endpoints that present the greatest likelihood of risk to human health and the environment. This need could be addressed using the experience of the pharmaceutical industry in the use of advanced modern molecular biology and computational chemistry tools for the development of new drugs, with appropriate adjustment to the needs and desires of environmental toxicology. A conceptual approach named ToxCast has been developed to address the needs of EPA Program Offices in the area of prioritization and screening. Modern computational chemistry and molecular biology tools bring enabling technologies forward that can provide information about the physical and biological properties of large numbers of chemicals. The essence of the proposal is to conduct a demonstration project based upon a rich toxicological database (e.g., registered pesticides, or the chemicals tested in the NTP bioassay program), select a fairly large number (50-100 or more chemicals) representative of a number of differing structural classes and phenotypic outcomes (e.g., carcinogens, reproductive toxicants, neurotoxicants), and evaluate them across a broad spectrum of information domains that modern technology has pro

LECTURES ON PHYSICS, BIOPHYSICS, AND CHEMISTRY FOR HIGH SCHOOL SCIENCE TEACHERS GIVEN AT THE ERNEST O. LAWRENCE RADIATION LABORATORY, BERKELEY, CALIFORNIA, JUNE-AUGUST 1959

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

Calhoon, E.C.; Starring, P.W. eds.

1959-08-01

Lectures given at the Ernest 0. Lawrence Radiation Laboratory on physics, biophysics, and chemistry for high school science teachers are presented. Topics covered include a mathematics review, atomic physics, nuclear physics, solid-state physics, elementary particles, antiparticies, design of experiments, high-energy particle accelerators, survey of particle detectors, emulsion as a particle detector, counters used in high-energy physics, bubble chambers, computer programming, chromatography, the transuranium elements, health physics, photosynthesis, the chemistry and physics of virus, the biology of virus, lipoproteins and heart disease, origin and evolution of the solar system, the role of space satellites in gathering astronomical data, and radiation andmore » life in space. (M.C.G.)« less

Effect of non-equilibrium flow chemistry and surface catalysis on surface heating to AFE

NASA Technical Reports Server (NTRS)

Stewart, David A.; Henline, William D.; Chen, Yih-Kanq

1991-01-01

The effect of nonequilibrium flow chemistry on the surface temperature distribution over the forebody heat shield on the Aeroassisted Flight Experiment (AFE) vehicle was investigated using a reacting boundary-layer code. Computations were performed by using boundary-layer-edge properties determined from global iterations between the boundary-layer code and flow field solutions from a viscous shock layer (VSL) and a full Navier-Stokes solution. Surface temperature distribution over the AFE heat shield was calculated for two flight conditions during a nominal AFE trajectory. This study indicates that the surface temperature distribution is sensitive to the nonequilibrium chemistry in the shock layer. Heating distributions over the AFE forebody calculated using nonequilibrium edge properties were similar to values calculated using the VSL program.

VISCOUS CHARACTERICTICS ANALYSIS

NASA Technical Reports Server (NTRS)

Jenkins, R. V.

1994-01-01

Current investigations of the hydrogen-fueled supersonic combustion ramjet engine have delineated several technological problem areas. One area, the analysis of the injection, turbulent mixing, and combusiton of hydrogen, requires the accurate calculation of the supersonic combustion flow fields. This calculation has proven difficult because of an interesting phenomena which makes possible the transition from supersonic to subsonic flow in the combustion field, due to the temperature transitions which occur in the flow field. This computer program was developed to use viscous characteristics theory to analyze supersonic combustion flow fields with imbedded subsonic regions. Intended to be used as a practical design tool for two-dimensional and axisymmetric supersonic combustor development, this program has proven useful in the analysis of such problems as determining the flow field of a single underexpanded hydrogen jet, the internal flow of a gas sampling probe, the effects of fuel-injector strut shape, and the effects of changes in combustor configuration. Both combustion and diffusive effects can significantly alter the wave pattern in a supersonic field and generate significant pressure gradients in both the axial and radial directions. The induced pressure, in turn, substantially influences the ignition delay and reaction times as well as the velocity distribution. To accurately analyze the flow fields, the effects of finite rate chemistry, mixing, and wave propagation must be properly linked to one another. The viscous characteristics theory has been used in the past to describe flows that are purely supersonic; however, the interacting pressure effects in the combustor often allow for the development of shock waves and imbedded subsonic regions. Numerical investigation of these transonic situations has required the development of a new viscous characteristics procedure which is valid within the subsonic region and can be coupled with the standard viscous characteristics procedure in the supersonic region. The basic governing equations used are the 'viscous-inviscid' equations, similar to those employed in higher-order boundary layer analyses, with finite rate chemistry terms included. In addition, the Rankine-Hugoniot and Prandtl-Meyer relations are used to compute shock and expansion conditions. The program can handle up to 20 simultaneous shock waves. Chemistry terms are computed for a 7-species 8-mechanism hydrogen-air reaction scheme. The user input consists of a physical description of the combustor and flow determination parameters. Output includes detail flow parameter values at selected points within the flow field. This computer program is written in FORTRAN IV for batch execution and has been implemented on a CDC CYBER 175 with a central memory requirement of approximately 114K (octal) of 60 bit words. The program was developed in 1978.

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...

Transire, a Program for Generating Solid-State Interface Structures

DTIC Science & Technology

2017-09-14

function-based electron transport property calculator. Three test cases are presented to demonstrate the usage of Transire: the misorientation of the...graphene bilayer, the interface energy as a function of misorientation of copper grain boundaries, and electron transport transmission across the...gallium nitride/silicon carbide interface. 15. SUBJECT TERMS crystalline interface, electron transport, python, computational chemistry, grain boundary

JPL basic research review. [research and advanced development

NASA Technical Reports Server (NTRS)

1977-01-01

Current status, projected goals, and results of 49 research and advanced development programs at the Jet Propulsion Laboratory are reported in abstract form. Areas of investigation include: aerodynamics and fluid mechanics, applied mathematics and computer sciences, environment protection, materials science, propulsion, electric and solar power, guidance and navigation, communication and information sciences, general physics, and chemistry.

Credit by Examination at the University of Texas at Austin, 1985-1986.

ERIC Educational Resources Information Center

Mahoney, Susan S.

The University of Texas (UT) at Austin's credit by examination program is described. In 1985-86, credit by examination was offered in 55 subjects. Details were provided for each of 18 subject areas in which over 20 tests were administered: Biology; Chemistry; Chinese; Computer Science; Economics; Electrical Engineering; English; French; German;…

Biennial Conference on Chemical Education, Abstracts (11th, Atlanta, Georgia, August 5-9, 1990).

ERIC Educational Resources Information Center

Mellon, E. K.; Pulliam, E. J.

This publication includes more than 470 abstracts of papers scheduled to be presented at a chemical education conference. Topics of the papers include: (1) human impact on the environment; (2) technology; (3) forensic science; (4) paper chemistry; (5) computer interfacing, software, videodisc and graphics; (6) faculty enhancement programs; (7)…

NASA's supercomputing experience

NASA Technical Reports Server (NTRS)

Bailey, F. Ron

1990-01-01

A brief overview of NASA's recent experience in supercomputing is presented from two perspectives: early systems development and advanced supercomputing applications. NASA's role in supercomputing systems development is illustrated by discussion of activities carried out by the Numerical Aerodynamical Simulation Program. Current capabilities in advanced technology applications are illustrated with examples in turbulence physics, aerodynamics, aerothermodynamics, chemistry, and structural mechanics. Capabilities in science applications are illustrated by examples in astrophysics and atmospheric modeling. Future directions and NASA's new High Performance Computing Program are briefly discussed.

Computer modeling of photodegradation

NASA Technical Reports Server (NTRS)

Guillet, J.

1986-01-01

A computer program to simulate the photodegradation of materials exposed to terrestrial weathering environments is being developed. Input parameters would include the solar spectrum, the daily levels and variations of temperature and relative humidity, and materials such as EVA. A brief description of the program, its operating principles, and how it works was initially described. After that, the presentation focuses on the recent work of simulating aging in a normal, terrestrial day-night cycle. This is significant, as almost all accelerated aging schemes maintain a constant light illumination without a dark cycle, and this may be a critical factor not included in acceleration aging schemes. For outdoor aging, the computer model is indicating that the night dark cycle has a dramatic influence on the chemistry of photothermal degradation, and hints that a dark cycle may be needed in an accelerated aging scheme.

The ChemViz Project: Using a Supercomputer To Illustrate Abstract Concepts in Chemistry.

ERIC Educational Resources Information Center

Beckwith, E. Kenneth; Nelson, Christopher

1998-01-01

Describes the Chemistry Visualization (ChemViz) Project, a Web venture maintained by the University of Illinois National Center for Supercomputing Applications (NCSA) that enables high school students to use computational chemistry as a technique for understanding abstract concepts. Discusses the evolution of computational chemistry and provides a…

Extended Wordsearches in Chemistry

NASA Astrophysics Data System (ADS)

Cotton, Simon

1998-04-01

Students can be encouraged to develop their factual knowledge by use of puzzles. One strategy described here is the extended wordsearch, where the wordsearch element generates a number of words or phrases from which the answers to a series of questions are selected. The wordsearch can be generated with the aid of computer programs, though in order to make them suitable for students with dyslexia or other learning difficulties, a simpler form is more appropriate. These problems can be employed in a variety of contexts, for example, as topic tests and classroom end-of-lesson fillers. An example is provided in the area of calcium chemistry. Sources of suitable software are listed.

Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications

PubMed Central

Bajorath, Jurgen

2012-01-01

We have generated a number of  compound data sets and programs for different types of applications in pharmaceutical research. These data sets and programs were originally designed for our research projects and are made publicly available. Without consulting original literature sources, it is difficult to understand specific features of data sets and software tools, basic ideas underlying their design, and applicability domains. Currently, 30 different entries are available for download from our website. In this data article, we provide an overview of the data and tools we make available and designate the areas of research for which they should be useful. For selected data sets and methods/programs, detailed descriptions are given. This article should help interested readers to select data and tools for specific computational investigations. PMID:24358818

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…

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…

Microfluidics for High School Chemistry Students.

PubMed

Hemling, Melissa; Crooks, John A; Oliver, Piercen M; Brenner, Katie; Gilbertson, Jennifer; Lisensky, George C; Weibel, Douglas B

2014-01-14

We present a laboratory experiment that introduces high school chemistry students to microfluidics while teaching fundamental properties of acid-base chemistry. The procedure enables students to create microfluidic systems using nonspecialized equipment that is available in high school classrooms and reagents that are safe, inexpensive, and commercially available. The experiment is designed to ignite creativity and confidence about experimental design in a high school chemistry class. This experiment requires a computer program (e.g., PowerPoint), Shrinky Dink film, a readily available silicone polymer, weak acids, bases, and a colorimetric pH indicator. Over the span of five 45-min class periods, teams of students design and prepare devices in which two different pH solutions mix in a predictable way to create five different pH solutions. Initial device designs are instructive but rarely optimal. During two additional half-class periods, students have the opportunity to use their initial observations to redesign their microfluidic systems to optimize the outcome. The experiment exposes students to cutting-edge science and the design process, and solidifies introductory chemistry concepts including laminar flow, neutralization of weak acids-bases, and polymers.

Microfluidics for High School Chemistry Students

PubMed Central

Hemling, Melissa; Crooks, John A.; Oliver, Piercen M.; Brenner, Katie; Gilbertson, Jennifer; Lisensky, George C.; Weibel, Douglas B.

2014-01-01

We present a laboratory experiment that introduces high school chemistry students to microfluidics while teaching fundamental properties of acid–base chemistry. The procedure enables students to create microfluidic systems using nonspecialized equipment that is available in high school classrooms and reagents that are safe, inexpensive, and commercially available. The experiment is designed to ignite creativity and confidence about experimental design in a high school chemistry class. This experiment requires a computer program (e.g., PowerPoint), Shrinky Dink film, a readily available silicone polymer, weak acids, bases, and a colorimetric pH indicator. Over the span of five 45-min class periods, teams of students design and prepare devices in which two different pH solutions mix in a predictable way to create five different pH solutions. Initial device designs are instructive but rarely optimal. During two additional half-class periods, students have the opportunity to use their initial observations to redesign their microfluidic systems to optimize the outcome. The experiment exposes students to cutting-edge science and the design process, and solidifies introductory chemistry concepts including laminar flow, neutralization of weak acids–bases, and polymers. PMID:25584013

Computational thermochemistry: Automated generation of scale factors for vibrational frequencies calculated by electronic structure model chemistries

NASA Astrophysics Data System (ADS)

Yu, Haoyu S.; Fiedler, Lucas J.; Alecu, I. M.; Truhlar, Donald G.

2017-01-01

We present a Python program, FREQ, for calculating the optimal scale factors for calculating harmonic vibrational frequencies, fundamental vibrational frequencies, and zero-point vibrational energies from electronic structure calculations. The program utilizes a previously published scale factor optimization model (Alecu et al., 2010) to efficiently obtain all three scale factors from a set of computed vibrational harmonic frequencies. In order to obtain the three scale factors, the user only needs to provide zero-point energies of 15 or 6 selected molecules. If the user has access to the Gaussian 09 or Gaussian 03 program, we provide the option for the user to run the program by entering the keywords for a certain method and basis set in the Gaussian 09 or Gaussian 03 program. Four other Python programs, input.py, input6, pbs.py, and pbs6.py, are also provided for generating Gaussian 09 or Gaussian 03 input and PBS files. The program can also be used with data from any other electronic structure package. A manual of how to use this program is included in the code package.

Computations and interpretations: The growth of quantum chemistry, 1927-1967

NASA Astrophysics Data System (ADS)

Park, Buhm Soon

1999-10-01

This dissertation is a contribution to the historical study of scientific disciplines in the twentieth century. It seeks to examine the development of quantum chemistry during the four decades after its inception in 1927. This development was manifest in theories, tools, scientists, and institutions, all of which constituted the disciplinary identity of quantum chemistry. To characterize its identity, I deal with the origins of key ideas and concepts; the change of computational tools from desk calculators to digital computers; the formation of a network among research groups and individuals; and the institutionalization of annual meetings. The dissertation's thesis is three-fold. First, in the pre- World War II years, there were individual contributions to the development of theories in quantum chemistry, but the founding fathers worked in their disciplinary contexts of physics or chemistry with little interest in building a quantum chemistry community. Second, the introduction of electronic digital computers in the postwar years affected the resurgence of the ab initio approach-the attempt to solve the Schrödinger equation without recourse to empirical data-and also the emergence of a community of quantum chemists. But the use of computers did not give rise to a consensus over the aims, methods, or content of the discipline. Third, quantum chemistry exerted a significant influence upon the transformation of chemical education and research in general, thanks to ``chemical translators,'' who sought to explain the gist of quantum chemistry in a language that chemists could understand. In sum, quantum chemistry has been a discipline characterized by diverse traditions, and the whole of chemistry has been under the influence of computations and interpretations made by quantum chemists.

Impact of Interdisciplinary Undergraduate Research in Mathematics and Biology on the Development of a New Course Integrating Five STEM Disciplines

ERIC Educational Resources Information Center

Caudill, Lester; Hill, April; Hoke, Kathy; Lipan, Ovidiu

2010-01-01

Funded by innovative programs at the National Science Foundation and the Howard Hughes Medical Institute, University of Richmond faculty in biology, chemistry, mathematics, physics, and computer science teamed up to offer first- and second-year students the opportunity to contribute to vibrant, interdisciplinary research projects. The result was…

Simulation of the Dropping Mercury Electrode by Orthogonal Collocation.

DTIC Science & Technology

1982-08-18

Electro byOtoyI =111. - e 15,, "A’Al,.rt arp t2g? ____________ ;f f-1e of Navel Rehnar..h .905 Chemistry Program - Chemitry CO&e 41? Unkclass ified Pe . nI...transport to a dropping mercury electrode lomr.i. Accurate values for’ the concentration profiles and current are obtained with minimal computational effort...offered by COMPUTATIONAL ASP’ECTS KOutecky (14) which is corrected for spherical dittusion Results accurate to 0.4 0 of Koutecky’s calculated values I 08 n

Finite-rate chemistry effects upon convective and radiative heating of an atmospheric entry vehicle. [reentry aerothermochemistry

NASA Technical Reports Server (NTRS)

Guillermo, P.

1975-01-01

A mathematical model of the aerothermochemical environment along the stagnation line of a planetary return spacecraft using an ablative thermal protection system was developed and solved for conditions typical of atmospheric entry from planetary missions. The model, implemented as a FORTRAN 4 computer program, was designed to predict viscous, reactive and radiative coupled shock layer structure and the resulting body heating rates. The analysis includes flow field coupling with the ablator surface, binary diffusion, coupled line and continuum radiative and equilibrium or finite rate chemistry effects. The gas model used includes thermodynamic, transport, kinetic and radiative properties of air and ablation product species, including 19 chemical species and 16 chemical reactions. Specifically, the impact of nonequilibrium chemistry effects upon stagnation line shock layer structure and body heating rates was investigated.

Web-phreeq: a WWW instructional tool for modeling the distribution of chemical species in water

NASA Astrophysics Data System (ADS)

Saini-Eidukat, Bernhardt; Yahin, Andrew

1999-05-01

A WWW-based tool, WEB-PHREEQ, was developed for classroom teaching and for routine calculation of low temperature aqueous speciation. Accessible with any computer that has an internet-connected forms-capable WWW-browser, WEB-PHREEQ provides user interface and other support for modeling, creates a properly formatted input file, passes it to the public domain program PHREEQC and returns the output to the WWW browser. Users can calculate the equilibrium speciation of a solution over a range of temperatures or can react solid minerals or gases with a particular water and examine the resulting chemistry. WEB-PHREEQ is one of a number of interactive distributed-computing programs available on the WWW that are of interest to geoscientists.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.

Two-Year College Chemistry Conference Proceedings: Southern Regional Conference, (2nd, Little Rock, December 9, 1967); Eastern Regional Conference (1st, Philadelphia, February 2-3, 1968); and Annual Conference (8th, San Francisco, March 29-30, 1968).

ERIC Educational Resources Information Center

Chapman, Kenneth, Ed.

This report on three junior college chemistry conferences includes: (1) new and developing programs in 2-year college chemistry; (2) beginning chemistry offerings--repair of poor backgrounds in chemistry and math; (3) non-science major--chemistry program for non-science students; (4) first-year chemistry course: (a) programmed audio-tutorial…

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…

Graduate Education in Chemistry. The ACS Committee on Professional Training: Surveys of Programs and Participants.

ERIC Educational Resources Information Center

American Chemical Society, Washington, DC.

This document reports on graduate education in chemistry concerning the nature of graduate programs. Contents include: (1) "Graduate Education in Chemistry in the United States: A Snapshot from the Late Twentieth Century"; (2) "A Survey of Ph.D. Programs in Chemistry"; (4) "The Master's Degree in Chemistry"; (5) "A Survey of Ph.D. Recipients in…

Chemistry Outreach Project to High Schools Using a Mobile Chemistry Laboratory, ChemKits, and Teacher Workshops

ERIC Educational Resources Information Center

Long, Gary L.; Bailey, Carol A.; Bunn, Barbara B.; Slebodnick, Carla; Johnson, Michael R.; Derozier, Shad

2012-01-01

The Chemistry Outreach Program (ChOP) of Virginia Tech was a university-based outreach program that addressed the needs of high school chemistry classes in underfunded rural and inner-city school districts. The primary features of ChOP were a mobile chemistry laboratory (MCL), a shipping-based outreach program (ChemKits), and teacher workshops.…

Index to NASA Tech Briefs, 1974

NASA Technical Reports Server (NTRS)

1975-01-01

The following information was given for 1974: (1) abstracts of reports dealing with new technology derived from the research and development activities of NASA or the U.S. Atomic Energy Commission, arranged by subjects: electronics/electrical, electronics/electrical systems, physical sciences, materials/chemistry, life sciences, mechanics, machines, equipment and tools, fabrication technology, and computer programs, (2) indexes for the above documents: subject, personal author, originating center.

Ablation and radiation coupled viscous hypersonic shock layers, volume 1

NASA Technical Reports Server (NTRS)

Engel, C. D.

1971-01-01

The results for a stagnation-line analysis of the radiative heating of a phenolic-nylon ablator are presented. The analysis includes flow field coupling with the ablator surface, equilibrium chemistry, a step-function diffusion model and a coupled line and continuum radiation calculation. This report serves as the documentation, i e. users manual and operating instructions for the computer programs listed in the report.

A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

PubMed

Gonçalves, Cristina P; Mohallem, José R

2004-11-15

We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

Training the Future - Interns Harvesting & Testing Plant Experim

NASA Image and Video Library

2017-07-19

In the Space Life Sciences Laboratory at NASA's Kennedy Space Center in Florida, student interns such as Ayla Grandpre are joining agency scientists, contributing in the area of plant growth research for food production in space. Grandpre is majoring in computer science and chemistry at Rocky Mountain College in Billings, Montana. The agency attracts its future workforce through the NASA Internship, Fellowships and Scholarships, or NIFS, Program.

Development of a Computational Chemical Vapor Deposition Model: Applications to Indium Nitride and Dicyanovinylaniline

NASA Technical Reports Server (NTRS)

Cardelino, Carlos

1999-01-01

A computational chemical vapor deposition (CVD) model is presented, that couples chemical reaction mechanisms with fluid dynamic simulations for vapor deposition experiments. The chemical properties of the systems under investigation are evaluated using quantum, molecular and statistical mechanics models. The fluid dynamic computations are performed using the CFD-ACE program, which can simulate multispecies transport, heat and mass transfer, gas phase chemistry, chemistry of adsorbed species, pulsed reactant flow and variable gravity conditions. Two experimental setups are being studied, in order to fabricate films of: (a) indium nitride (InN) from the gas or surface phase reaction of trimethylindium and ammonia; and (b) 4-(1,1)dicyanovinyl-dimethylaminoaniline (DCVA) by vapor deposition. Modeling of these setups requires knowledge of three groups of properties: thermodynamic properties (heat capacity), transport properties (diffusion, viscosity, and thermal conductivity), and kinetic properties (rate constants for all possible elementary chemical reactions). These properties are evaluated using computational methods whenever experimental data is not available for the species or for the elementary reactions. The chemical vapor deposition model is applied to InN and DCVA. Several possible InN mechanisms are proposed and analyzed. The CVD model simulations of InN show that the deposition rate of InN is more efficient when pulsing chemistry is used under conditions of high pressure and microgravity. An analysis of the chemical properties of DCVA show that DCVA dimers may form under certain conditions of physical vapor transport. CVD simulations of the DCVA system suggest that deposition of the DCVA dimer may play a small role in the film and crystal growth processes.

42 CFR 493.931 - Routine chemistry.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Routine chemistry. 493.931 Section 493.931 Public... Proficiency Testing Programs by Specialty and Subspecialty § 493.931 Routine chemistry. (a) Program content and frequency of challenge. To be approved for proficiency testing for routine chemistry, a program...

42 CFR 493.931 - Routine chemistry.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Routine chemistry. 493.931 Section 493.931 Public... Proficiency Testing Programs by Specialty and Subspecialty § 493.931 Routine chemistry. (a) Program content and frequency of challenge. To be approved for proficiency testing for routine chemistry, a program...

42 CFR 493.931 - Routine chemistry.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Routine chemistry. 493.931 Section 493.931 Public... Proficiency Testing Programs by Specialty and Subspecialty § 493.931 Routine chemistry. (a) Program content and frequency of challenge. To be approved for proficiency testing for routine chemistry, a program...

42 CFR 493.931 - Routine chemistry.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Routine chemistry. 493.931 Section 493.931 Public... Proficiency Testing Programs by Specialty and Subspecialty § 493.931 Routine chemistry. (a) Program content and frequency of challenge. To be approved for proficiency testing for routine chemistry, a program...

42 CFR 493.931 - Routine chemistry.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Routine chemistry. 493.931 Section 493.931 Public... Proficiency Testing Programs by Specialty and Subspecialty § 493.931 Routine chemistry. (a) Program content and frequency of challenge. To be approved for proficiency testing for routine chemistry, a program...

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications

PubMed Central

D’Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

2015-01-01

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004–2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average. PMID:26191337

Integrative Biological Chemistry Program Includes The Use Of Informatics Tools, GIS And SAS Software Applications.

PubMed

D'Souza, Malcolm J; Kashmar, Richard J; Hurst, Kent; Fiedler, Frank; Gross, Catherine E; Deol, Jasbir K; Wilson, Alora

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning courses using instrumentation, data-collection, data-storage, statistical-modeling analysis, visualization, and computational techniques. In this revised curriculum, students begin with a traditional set of biology, chemistry, physics, and mathematics major core-requirements, a geographic information systems (GIS) course, a choice of an instrumental analysis course or a statistical analysis systems (SAS) programming course, and then, students can add major-electives that further add depth and value to their future post-graduate specialty areas. Open-sourced georeferenced census, health and health disparity data were coupled with GIS and SAS tools, in a public health surveillance system project, based on US county zip-codes, to develop use-cases for chronic adult obesity where income, poverty status, health insurance coverage, education, and age were categorical variables. Across the 48 contiguous states, obesity rates are found to be directly proportional to high poverty and inversely proportional to median income and educational achievement. For the State of Delaware, age and educational attainment were found to be limiting obesity risk-factors in its adult population. Furthermore, the 2004-2010 obesity trends showed that for two of the less densely populated Delaware counties; Sussex and Kent, the rates of adult obesity were found to be progressing at much higher proportions when compared to the national average.

STAIRSTEP -- a research-oriented program for undergraduate students at Lamar University

NASA Astrophysics Data System (ADS)

Bahrim, Cristian

2011-03-01

The relative low number of undergraduate STEM students in many science disciplines, and in particular in physics, represents a major concern for our faculty and the administration at Lamar University. Therefore, a collaborative effort between several science programs, including computer science, chemistry, geology, mathematics and physics was set up with the goal of increasing the number of science majors and to minimize the retention rate. Lamar's Student Advancing through Involvement in Research Student Talent Expansion Program (STAIRSTEP) is a NSF-DUE sponsored program designed to motivate STEM students to graduate with a science degree from one of these five disciplines by involving them in state-of-the-art research projects and various outreach activities organized on-campus or in road shows at the secondary and high schools. The physics program offers hands-on experience in optics, such as computer-based experiments for studying the diffraction and interference of light incident on nettings or electronic wave packets incident on crystals, with applications in optical imaging, electron microscopy, and crystallography. The impact of the various activities done in STAIRSTEP on our Physics Program will be discussed.

In This Issue

NASA Astrophysics Data System (ADS)

1996-02-01

Computational Chemistry for the Masses Not long ago, chemical computation was considered a specialty area requiring extensive computer knowledge, power, and time. Over the past decade, however, it has changed from the arcane pursuit of a few advanced university researchers in the area of physical chemistry to a familiar tool used by a wide range of chemists. Nevertheless, it has required its practitioners to have extensive knowledge of computer programming and a thorough understanding of theoretical chemical concepts and as a result usually was reserved for the graduate curriculum. Now a further metamorphosis is in progress, as computational chemistry moves into the undergraduate curriculum, often using off-the-shelf software--commercial packages or adaptations of them that are readily shared by their creators. As we put this issue together, we realized that many of the articles involved sophisticated computations that would not have been possible a few years ago in the courses described. Further, the hard and software used was widely available at a reasonable cost. Some of the articles focus on the teaching of computational methods and others simply incorporate it as a facet in their overall strategy; however, taken together, they reflect a strong trend to utilize a diverse set of readily available methods and products in the undergraduate curriculum. The most familiar recent use of computational chemistry is the computer design of molecules in organic, medicinal, and biochemistry. However, computational chemistry is useful for inorganic chemists as well and is now migrating to undergraduate courses. Lipkowitz, Pearl, Robertson, and Schultz (page 105) make a strong case for its inclusion and present a two-week component they have developed for their senior-level laboratory course. Comba and Zimmer (page 108) offer a review of inorganic molecular mechanics calculations, which is designed for the novice and includes the basic equations, their application to inorganic molecules, and a discussion of the how to evaluate the reliability of the results. A computational experiment has been specifically designed for the undergraduate laboratory by Bakalbassis, Stiakaki, Tsipis, and Tsipis (page 111). The students use an atom-superposition and electron-delocalization molecular orbital model to predict the structural, spectroscopic, and energetic properties of highly ionic metal-containing systems. The exercise introduces students to the value of computational experiments as an alternative to wet-lab work and teaches enough quantum theory to make them comfortable with current literature. For teachers of organic chemistry, Delaware and Fountain (page 116) analyze how models can actually hinder learning in the introductory course if presented passively and describe how to use computer visualizations of reactions in an active, cooperative learning mode. They argue that these computational exercises need to be embedded in a carefully planned learning system to be effective. In similar fashion, Sauers (page 114) finds that a computer-assisted molecular modeling experiment is an effective way of making the concept of "steric interactions" more accessible. The theoretical number of isomers and derivatives of organic compounds is another concept difficult to visualize, and the calculations that would used for enumeration are complex enough that they are not usually brought into the undergraduate curriculum. However, Novak (page 120) demonstrates that widely available PC software, such as Mathematica, can be used by undergraduates along with the Polya enumeration method to enumerate derivatives and see the connection between these numbers and the symmetry of the parent molecule. A different use of computational software in biochemistry than the usual computer-assisted design of molecules is the main focus of a Computer Series article by Letkeman (page 165), who models the complex interactions of metal ions in human blood serum.

Chemistry 200, 300 Interim Guide.

ERIC Educational Resources Information Center

Manitoba Dept. of Education, Winnipeg.

This guide, developed for the chemistry 200, 300 program in Manitoba, is designed to articulate with previous science courses, provide concepts, processes, and skills which will enable students to continue in chemistry-related areas, and relate chemistry to practical applications in everyday life. It includes a program overview (with program goals…

What Chemists (or Chemistry Students) Need to Know about Computing.

ERIC Educational Resources Information Center

Swift, Mary L.; Zielinski, Theresa Julia

1995-01-01

Presents key points of an on-line conference discussion and integrates them with information from the literature. Key points included: computer as a tool for learning, study, research, and communication; hardware, software, computing concepts, and other teaching concerns; and the appropriate place for chemistry computer-usage instruction. (45…

An Educational Approach to Computationally Modeling Dynamical Systems

ERIC Educational Resources Information Center

Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl

2009-01-01

Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…

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…

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…

Conformational Analysis of Drug Molecules: A Practical Exercise in the Medicinal Chemistry Course

ERIC Educational Resources Information Center

Yuriev, Elizabeth; Chalmers, David; Capuano, Ben

2009-01-01

Medicinal chemistry is a specialized, scientific discipline. Computational chemistry and structure-based drug design constitute important themes in the education of medicinal chemists. This problem-based task is associated with structure-based drug design lectures. It requires students to use computational techniques to investigate conformational…

Physics through the 1990s: Scientific interfaces and technological applications

NASA Technical Reports Server (NTRS)

1986-01-01

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

Organic Chemistry in Action! What Is the Reaction?

ERIC Educational Resources Information Center

O'Dwyer, Anne; Childs, Peter

2015-01-01

The "Organic Chemistry in Action!" ("OCIA!") program is a set of teaching resources designed to facilitate the teaching and learning of introductory level organic chemistry. The "OCIA!" program was developed in collaboration with practicing and experienced chemistry teachers, using findings from Chemistry Education…

Computational Fluid Dynamics Program at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Holst, Terry L.

1989-01-01

The Computational Fluid Dynamics (CFD) Program at NASA Ames Research Center is reviewed and discussed. The technical elements of the CFD Program are listed and briefly discussed. These elements include algorithm research, research and pilot code development, scientific visualization, advanced surface representation, volume grid generation, and numerical optimization. Next, the discipline of CFD is briefly discussed and related to other areas of research at NASA Ames including experimental fluid dynamics, computer science research, computational chemistry, and numerical aerodynamic simulation. These areas combine with CFD to form a larger area of research, which might collectively be called computational technology. The ultimate goal of computational technology research at NASA Ames is to increase the physical understanding of the world in which we live, solve problems of national importance, and increase the technical capabilities of the aerospace community. Next, the major programs at NASA Ames that either use CFD technology or perform research in CFD are listed and discussed. Briefly, this list includes turbulent/transition physics and modeling, high-speed real gas flows, interdisciplinary research, turbomachinery demonstration computations, complete aircraft aerodynamics, rotorcraft applications, powered lift flows, high alpha flows, multiple body aerodynamics, and incompressible flow applications. Some of the individual problems actively being worked in each of these areas is listed to help define the breadth or extent of CFD involvement in each of these major programs. State-of-the-art examples of various CFD applications are presented to highlight most of these areas. The main emphasis of this portion of the presentation is on examples which will not otherwise be treated at this conference by the individual presentations. Finally, a list of principal current limitations and expected future directions is given.

Computer-aided drug discovery research at a global contract research organization

NASA Astrophysics Data System (ADS)

Kitchen, Douglas B.

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.

Computer-aided drug discovery research at a global contract research organization.

PubMed

Kitchen, Douglas B

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.

Follow up: Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer.

PubMed

Hu, Ye; Bajorath, Jürgen

2014-01-01

In 2012, we reported 30 compound data sets and/or programs developed in our laboratory in a data article and made them freely available to the scientific community to support chemoinformatics and computational medicinal chemistry applications. These data sets and computational tools were provided for download from our website. Since publication of this data article, we have generated 13 new data sets with which we further extend our collection of publicly available data and tools. Due to changes in web servers and website architectures, data accessibility has recently been limited at times. Therefore, we have also transferred our data sets and tools to a public repository to ensure full and stable accessibility. To aid in data selection, we have classified the data sets according to scientific subject areas. Herein, we describe new data sets, introduce the data organization scheme, summarize the database content and provide detailed access information in ZENODO (doi: 10.5281/zenodo.8451 and doi:10.5281/zenodo.8455).

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…

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…

Brookhaven highlights. Report on research, October 1, 1992--September 30, 1993

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

Rowe, M.S.; Belford, M.; Cohen, A.

This report highlights the research activities of Brookhaven National Laboratory during the period dating from October 1, 1992 through September 30, 1993. There are contributions to the report from different programs and departments within the laboratory. These include technology transfer, RHIC, Alternating Gradient Synchrotron, physics, biology, national synchrotron light source, applied science, medical science, advanced technology, chemistry, reactor physics, safety and environmental protection, instrumentation, and computing and communications.

Summer Course Promotes Polymer Chemistry for Small Colleges.

ERIC Educational Resources Information Center

Stinson, Stephen

1989-01-01

Describes a three-week summer program teaching selected chemistry faculty how to incorporate polymer chemistry into chemistry courses. In addition to lectures, the program conducted many experiments and provided a trip to industry laboratories. (YP)

Computational Science at the Argonne Leadership Computing Facility

NASA Astrophysics Data System (ADS)

Romero, Nichols

2014-03-01

The goal of the Argonne Leadership Computing Facility (ALCF) is to extend the frontiers of science by solving problems that require innovative approaches and the largest-scale computing systems. ALCF's most powerful computer - Mira, an IBM Blue Gene/Q system - has nearly one million cores. How does one program such systems? What software tools are available? Which scientific and engineering applications are able to utilize such levels of parallelism? This talk will address these questions and describe a sampling of projects that are using ALCF systems in their research, including ones in nanoscience, materials science, and chemistry. Finally, the ways to gain access to ALCF resources will be presented. This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357.

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.

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

2014-01-07

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.

From transistor to trapped-ion computers for quantum chemistry

PubMed Central

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

Student science enrichment training program

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

Sandhu, S.S.

1994-08-01

This is a report on the Student Science Enrichment Training Program, with special emphasis on chemical and computer science fields. The residential summer session was held at the campus of Claflin College, Orangeburg, SC, for six weeks during 1993 summer, to run concomitantly with the college`s summer school. Fifty participants selected for this program, included high school sophomores, juniors and seniors. The students came from rural South Carolina and adjoining states which, presently, have limited science and computer science facilities. The program focused on high ability minority students, with high potential for science engineering and mathematical careers. The major objectivemore » was to increase the pool of well qualified college entering minority students who would elect to go into science, engineering and mathematical careers. The Division of Natural Sciences and Mathematics and engineering at Claflin College received major benefits from this program as it helped them to expand the Departments of Chemistry, Engineering, Mathematics and Computer Science as a result of additional enrollment. It also established an expanded pool of well qualified minority science and mathematics graduates, which were recruited by the federal agencies and private corporations, visiting Claflin College Campus. Department of Energy`s relationship with Claflin College increased the public awareness of energy related job opportunities in the public and private sectors.« less

Student science enrichment training program. Progress report, June 1, 1991--May 31, 1992

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

Sandhu, S.S.

1992-04-21

Historically Black Colleges and Universities wing of the United States Department of Energy (DOE) provided funds to Claflin College, Orangeburg, S.C. To conduct a student Science Enrichment Training Program for a period of six weeks during 1991 summer. Thirty participants were selected from a pool of applicants, generated by the High School Seniors and Juniors and the Freshmen class of 1990-1991 at Claflin College. The program primarily focused on high ability students, with potential for Science, Mathematics and Engineering Careers. The major objectives of the program were W to increase the pool of well qualified college entering minority students whomore » will elect to go in Physical Sciences and Engineering and (II) to increase the enrollment in Chemistry and Preprofessional-Pre-Med, Pre-Dent, etc.-majors at Claflin College by including the Claflin students to participate in summer academic program. The summer academic program consisted of Chemistry and Computer Science training. The program placed emphasis upon laboratory experience and research. Visits to Scientific and Industrial laboratories were arranged. Guest speakers which were drawn from academia, industry and several federal agencies, addressed the participants on the future role of Science in the industrial growth of United States of America. The guest speakers also acted as role models for the participants. Several videos and films, emphasizing the role of Science in human life, were also screened.« less

Prospectus 1999

NASA Astrophysics Data System (ADS)

Holmes, Jon L.; Gettys, Nancy S.

1999-01-01

We begin 1999 with a message to all Journal subscribers about our plans for JCE Software and what you will be seeing in this column as the year progresses. Series News JCE Software will continue to publish individual programs, one to an issue as they become ready for distribution. The old Series B, C, and D designations no longer exist. Regular Issue numbers for 1999 will start with 99, and end with M for Mac OS, W for Windows, or MW for programs that will run under both the Mac OS and Windows. Windows programs will be compatible with Windows 95/98 and may or may not be compatible with Windows 3.1. Special Issues, such as CD-ROMs and videotapes will continue to be designated with SP followed by a number. Publication Plans for 1999 Periodic Table Live! Second Edition Periodic Table Live! Second Edition is a new version of one of JCE Software's most popular publications. The best features of Illustrated Periodic Table (1) for Windows and Chemistry Navigator (2) for Mac OS are combined in a new HTML-based, multimedia presentation format. Together with the video from Periodic Table Videodisc (3), digitized to take advantage of new features available in QuickTime 3 (4), the new Periodic Table Live! will be easy to use with complete features available to both Windows and Mac OS user. Chemistry Comes Alive! The Chemistry Comes Alive! (CCA!) series continues in 1999 with CD-ROMs for Mac OS and Windows. Like the first two volumes (5,6), new CDs will contain video and animations of chemical reactions, including clips from our videodiscs ChemDemos (7), ChemDemos II (8), and Titration Techniques (9). Other clips are new, available for the first time in Chemistry Comes Alive! New CCA! CDs will be made available in two varieties for individual users, one to take advantage of the high-quality video that can be displayed by new, faster computers, and another that will play well on older, slower models. In addition, a third variation for network licensing will include video optimized for delivery via the World Wide Web. If all goes according to plan, two new CCA! volumes will be announced in 1999, and CCA! 1 and CCA! 2 will be updated to take advantage of the latest digital video technology. Chem Pages Chem Pages, Laboratory Techniques, was developed by the New Traditions Curriculum Project at the University of Wisconsin-Madison. It is an HTML-based CD-ROM for Mac OS and Windows that contains lessons and tutorials to prepare introductory chemistry students to work in the laboratory. It includes text, photographs, computer graphics, animations, digital video, and voice narration to introduce students to the laboratory equipment and procedures. Regular Issues Programs that have been accepted for publication as Regular Issues in 1999 include a gas chromatography simulation for Windows 95 by Bruce Armitage, a collection of lessons on torsional rotation for organic chemistry students by Ronald Starkey, and a tutorial on pericyclic reactions, also for organic chemistry, by Albert Lee, C. T. So, and C. L. Chan. We have had many recent submissions and submissions of work in progress. In 1999 we will work with the authors and our peer-reviewers to complete and publish these submissions. Submissions include Multimedia Problems for General Chemistry by David Whisnant, lessons on point groups and crystallography by Margaret Kastner, et al., a mass spectrum simulator by Stephen W. Bigger and Robert A. Craig, a tutorial for introductory chemistry on determining the pH of very dilute acid and base solutions by Paul Mihas and George Papageorgiou, and many others. Also under development by the JCE Software staff are The General Chemistry Collection (instructor's edition) CD-ROM along with an updated student edition. An Invitation In collaboration with JCE Online we plan to make available in 1999 support files for JCE Software. These will include not only troubleshooting tips and technical support notes, but also supporting information such as lessons, specific assignments, and activities using JCE Software publications submitted by users. All JCE Software users are invited to contribute to this area. Get in touch with JCE Software and let us know how you are using our materials so that we can share your ideas with others! Although the word software is in our name, many of our publications are not traditional software. We also publish video on videotape, videodisc, and CD-ROM and electronic documents (Mathcad and Mathematica, spreadsheet files and macros, HTML documents, and PowerPoint presentations). Most chemistry instructors who use a computer in their teaching have created or considered creating one or more of these for their classes. If you have an original computer presentation, electronic document, animation, video, or any other item that is not printed text it is probably an appropriate submission for JCE Software. By publishing your work in any branch of the Journal of Chemical Education, you will share your efforts with chemistry instructors and students all over the world and get professional recognition for your achievements. Literature Cited 1. Schatz, P. F.; Moore, J. W.; Holmes, J. L. Illustrated Periodic Table; J. Chem. Educ. Software 1995, 2D2. 2. Kotz. J. C.; Young, S. Chemistry Navigator; J. Chem. Educ. Software 1995, 6C2. 3. Banks, A. Periodic Table Videodisc, 2nd ed.; J. Chem. Educ. Software 1996, SP1. 4. QuickTime 3.0, Apple Computer, Inc.: 1 Infinite Loop, Cupertino, CA 95014-2084. 5. Jacobsen, J. J.; Moore, J. W. Chemistry Comes Alive!, Volume 1; J. Chem. Educ. Software 1997, SP 18. 6. Jacobsen, J. J.; Moore, J. W. Chemistry Comes Alive!, Volume 2; Chem. Educ. Software 1998, SP 21. 7. Moore, J. W.; Jacobsen, J. J.; Hunsberger, L. R.; Gammon, S. D.; Jetzer, K. H.; Zimmerman, J. ChemDemos Videodisc; J. Chem. Educ. Software 1994, SP 8. 8. Moore, J. W.; Jacobsen, J. J.; Jetzer, K. H.; Gilbert, G.; Mattes, F.; Phillips, D.; Lisensky, G.; Zweerink, G. ChemDemos II; J. Chem. Educ. Software 1996, SP 14. 9. Jacobsen, J. J.; Jetzer, K. H.; Patani, N.; Zimmerman, J. Titration Techniques Videodisc; J. Chem. Educ. Software 1995, SP 9. JCE Software CD-ROMs In addition to more than 100 traditional computer programs and videodiscs, JCE Software has published nine CD-ROMs and four videotapes. Recently published CDs now available include:

• JCE CD 98
• Solid State Resources, 2nd Edition
• General Chemistry Collection, 2nd Edition (Student Edition)
• Chemistry Comes Alive!, Volumes 1 and 2
• Flying over Atoms

Towards validated chemistry at extreme conditions: reactive MD simulations of shocked Polyvinyl Nitrate and Nitromethane

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

A detailed atomistic-level understanding of the ultrafast chemistry of detonation processes of high energy materials is crucial to understand their performance and safety. Recent advances in laser shocks and ultra-fast spectroscopy is yielding the first direct experimental evidence of chemistry at extreme conditions. At the same time, reactive molecular dynamics (MD) in current high-performance computing platforms enable an atomic description of shock-induced chemistry with length and timescales approaching those of experiments. We use MD simulations with the reactive force field ReaxFF to investigate the shock-induced chemical decomposition mechanisms of polyvinyl nitrate (PVN) and nitromethane (NM). The effect of shock pressure on chemical reaction mechanisms and kinetics of both the materials are investigated. For direct comparison of our simulation results with experimentally derived IR absorption data, we performed spectral analysis using atomistic velocity at various shock conditions. The combination of reactive MD simulations and ultrafast spectroscopy enables both the validation of ReaxFF at extreme conditions and contributes to the interpretation of the experimental data relating changes in spectral features to atomic processes. Office of Naval Research MURI program.

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.

Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

ERIC Educational Resources Information Center

Singh, Gurmukh

2012-01-01

The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…

1999 LDRD Laboratory Directed Research and Development

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

Rita Spencer; Kyle Wheeler

This is the FY 1999 Progress Report for the Laboratory Directed Research and Development (LDRD) Program at Los Alamos National Laboratory. It gives an overview of the LDRD Program, summarizes work done on individual research projects, relates the projects to major Laboratory program sponsors, and provides an index to the principal investigators. Project summaries are grouped by their LDRD component: Competency Development, Program Development, and Individual Projects. Within each component, they are further grouped into nine technical categories: (1) materials science, (2) chemistry, (3) mathematics and computational science, (4) atomic, molecular, optical, and plasma physics, fluids, and particle beams, (5)more » engineering science, (6) instrumentation and diagnostics, (7) geoscience, space science, and astrophysics, (8) nuclear and particle physics, and (9) bioscience.« less

Laboratory Directed Research and Development FY 1998 Progress Report

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

John Vigil; Kyle Wheeler

This is the FY 1998 Progress Report for the Laboratory Directed Research and Development (LDRD) Program at Los Alamos National Laboratory. It gives an overview of the LDRD Program, summarizes work done on individual research projects, relates the projects to major Laboratory program sponsors, and provides an index to the principle investigators. Project summaries are grouped by their LDRD component: Competency Development, Program Development, and Individual Projects. Within each component, they are further grouped into nine technical categories: (1) materials science, (2) chemistry, (3) mathematics and computational science, (4) atomic, molecular, optical, and plasma physics, fluids, and particle beams, (5)more » engineering science, (6) instrumentation and diagnostics, (7) geoscience, space science, and astrophysics, (8) nuclear and particle physics, and (9) bioscience.« less

Laboratory directed research and development: FY 1997 progress report

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

Vigil, J.; Prono, J.

1998-05-01

This is the FY 1997 Progress Report for the Laboratory Directed Research and Development (LDRD) program at Los Alamos National Laboratory. It gives an overview of the LDRD program, summarizes work done on individual research projects, relates the projects to major Laboratory program sponsors, and provides an index to the principal investigators. Project summaries are grouped by their LDRD component: Competency Development, Program Development, and Individual Projects. Within each component, they are further grouped into nine technical categories: (1) materials science, (2) chemistry, (3) mathematics and computational science, (4) atomic and molecular physics and plasmas, fluids, and particle beams, (5)more » engineering science, (6) instrumentation and diagnostics, (7) geoscience, space science, and astrophysics, (8) nuclear and particle physics, and (9) bioscience.« less

Ambarish Nag | NREL

Science.gov Websites

|Mathematical biology Education Ph.D., Computational Chemistry, University of Chicago M.S., Chemistry , University of Chicago M.S., (2-Year) Chemistry, Indian Institute of Technology, Kanpur, India B.S., Chemistry

CDAC Student Report: Summary of LLNL Internship

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

Herriman, Jane E.

Multiple objectives motivated me to apply for an internship at LLNL: I wanted to experience the work environment at a national lab, to learn about research and job opportunities at LLNL in particular, and to gain greater experience with code development, particularly within the realm of high performance computing (HPC). This summer I was selected to participate in LLNL's Computational Chemistry and Material Science Summer Institute (CCMS). CCMS is a 10 week program hosted by the Quantum Simulations group leader, Dr. Eric Schwegler. CCMS connects graduate students to mentors at LLNL involved in similar re- search and provides weekly seminarsmore » on a broad array of topics from within chemistry and materials science. Dr. Xavier Andrade and Dr. Erik Draeger served as my co-mentors over the summer, and Dr. Andrade continues to mentor me now that CCMS has concluded. Dr. Andrade is a member of the Quantum Simulations group within the Physical and Life Sciences at LLNL, and Dr. Draeger leads the HPC group within the Center for Applied Scientific Computing (CASC). The two have worked together to develop Qb@ll, an open-source first principles molecular dynamics code that was the platform for my summer research project.« less

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

The journey from forensic to predictive materials science using density functional theory

DOE PAGES

Schultz, Peter A.

2017-09-12

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

The journey from forensic to predictive materials science using density functional theory

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

Schultz, Peter A.

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.

Software Integration in Multi-scale Simulations: the PUPIL System

NASA Astrophysics Data System (ADS)

Torras, J.; Deumens, E.; Trickey, S. B.

2006-10-01

The state of the art for computational tools in both computational chemistry and computational materials physics includes many algorithms and functionalities which are implemented again and again. Several projects aim to reduce, eliminate, or avoid this problem. Most such efforts seem to be focused within a particular specialty, either quantum chemistry or materials physics. Multi-scale simulations, by their very nature however, cannot respect that specialization. In simulation of fracture, for example, the energy gradients that drive the molecular dynamics (MD) come from a quantum mechanical treatment that most often derives from quantum chemistry. That “QM” region is linked to a surrounding “CM” region in which potentials yield the forces. The approach therefore requires the integration or at least inter-operation of quantum chemistry and materials physics algorithms. The same problem occurs in “QM/MM” simulations in computational biology. The challenge grows if pattern recognition or other analysis codes of some kind must be used as well. The most common mode of inter-operation is user intervention: codes are modified as needed and data files are managed “by hand” by the user (interactively and via shell scripts). User intervention is however inefficient by nature, difficult to transfer to the community, and prone to error. Some progress (e.g Sethna’s work at Cornell [C.R. Myers et al., Mat. Res. Soc. Symp. Proc., 538(1999) 509, C.-S. Chen et al., Poster presented at the Material Research Society Meeting (2000)]) has been made on using Python scripts to achieve a more efficient level of interoperation. In this communication we present an alternative approach to merging current working packages without the necessity of major recoding and with only a relatively light wrapper interface. The scheme supports communication among the different components required for a given multi-scale calculation and access to the functionalities of those components for the potential user. A general main program allows the management of every package with a special communication protocol between their interfaces following the directives introduced by the user which are stored in an XML structured file. The initial prototype of the PUPIL (Program for User Packages Interfacing and Linking) system has been done using Java as a fast, easy prototyping object oriented (OO) language. In order to test it, we have applied this prototype to a previously studied problem, the fracture of a silica nanorod. We did so joining two different packages to do a QM/MD calculation. The results show the potential for this software system to do different kind of simulations and its simplicity of maintenance.

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…

Quantum chemistry simulation on quantum computers: theories and experiments.

PubMed

Lu, Dawei; Xu, Boruo; Xu, Nanyang; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

2012-07-14

It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

Computational chemistry at Janssen

NASA Astrophysics Data System (ADS)

van Vlijmen, Herman; Desjarlais, Renee L.; Mirzadegan, Tara

2017-03-01

Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.

GeoChange Global Change Data

USGS Publications Warehouse

,

1997-01-01

GeoChange is an online data system providing access to research results and data generated by the U.S. Geological Survey's Global Change Research Program. Researchers in this program study climate history and the causes of climatic variations, as well as providing baseline data sets on contemporary atmospheric chemistry, high-resolution meteorology, and dust deposition. Research results are packaged as data sets, groups of digital files containing scientific observations, documentation, and interpretation. The data sets are arranged in a consistent manner using standard file formats so that users of a variety of computer systems can access and use them.

ACS-Hach Programs: Supporting Excellence in High School Chemistry Teaching

NASA Astrophysics Data System (ADS)

Taylor, Terri

2009-05-01

In January 2009, the ACS received a gift of approximately $33 million from the Hach Scientific Foundation, the largest gift in the society's 133-year history. The foundation's programs will be continued by the ACS and will complement pre-existing ACS resources that support high school chemistry teaching. Three activities serve as the pillars of the ACS-Hach programs—the High School Chemistry Grant Program, the Second Career Teacher Scholarship Program, and the Land Grant University Scholars Program. Collectively, the ACS-Hach programs support high school chemistry teaching and learning by responding to the needs of both in-service and pre-service secondary teachers. The goals of each of the ACS-Hach programs align well with the ACS Mission—to advance the broader chemistry enterprise and its practitioners for the benefit of Earth and its people.

Application of computational fluid dynamics to the design of the Space Transportation Main Engine subscale nozzle

NASA Technical Reports Server (NTRS)

Garrett, J. L.; Syed, S. A.

1992-01-01

CFD analyses of the Space Transportation Main Engine film/dump cooled subscale nozzle are presented, with an emphasis on the timely impact of CFD in the design of the subscale nozzle secondary coolant system. Calculations were performed with the Generalized Aerodynamic Simulation Program (GASP), using a Baldwin-Lomas Turbulence model, and finite rate hydrogen-oxygen chemistry. Design iterations for both the secondary coolant cavity passage and the secondary coolant lip are presented. In addition, validation of the GASP chemistry and turbulence models by comparison with data and other CFD codes are presented for a hypersonic laminar separation corner, a backward facing step, and a 2D scramjet nozzle with hydrogen-oxygen kinetics.

Using Games To Teach Chemistry: An Annotated Bibliography

NASA Astrophysics Data System (ADS)

Russell, Jeanne V.

1999-04-01

A list of published or marketed games based on a chemistry motif is presented. Each game is listed according to its level, subject matter, and title. A bibliographic notation and a short description are given for each game. For Introductory/High School/General Chemistry, 45 games are listed under the subjects General Knowledge; Elements & Atomic Structure (not Symbols); Nomenclature, Formulas, & Equation Writing; Chemical Reactions: Solutions & Solubilities; and Other Subjects. Seventeen games are listed under Organic Chemistry and 4 games under Other Chemistry Games. Computer games designed for outdated computers (PDP-11, TRS-80, and Apple II) are not included.

Computers in Science: Thinking Outside the Discipline.

ERIC Educational Resources Information Center

Hamilton, Todd M.

2003-01-01

Describes the Computers in Science course which integrates computer-related techniques into the science disciplines of chemistry, physics, biology, and Earth science. Uses a team teaching approach and teaches students how to solve chemistry problems with spreadsheets, identify minerals with X-rays, and chemical and force analysis. (Contains 14…

Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

ERIC Educational Resources Information Center

Aksela, Maija; Lundell, Jan

2008-01-01

Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…

The winding road to being a code monkey

NASA Astrophysics Data System (ADS)

Sarahan, Michael

2017-09-01

I am now a software engineer at a company that provides data analytics services, and helps support the open source data science community. I have been a computer nerd for a very long time, but it was my CEU experience at Texas A&M with Sherry Yennello (2003-2005) that helped me put my nerd skills to productive use. My project then was simulation of pulse shape discrimination electronics, and it was an excellent introduction to core computational concerns, such as digitization: when you see a line on the screen, that's not really how the computer sees it. I wandered in graduate school through a chemistry program into using electron microscopes. My programming interest got me into image and signal processing, which led naturally to jobs in analyzing data, and also in acquiring data. Throughout, it was always difficult just to make software work. I got pretty good at making it work. That's what I do for a living now - package software so that it is easy for other people to do great science with.

Cometary MHD and chemistry

NASA Technical Reports Server (NTRS)

Wegmann, R.; Schmidt, H. U.; Huebner, W. F.; Boice, D. C.

1987-01-01

An MHD and chemical comet-coma model was developed, applying the computer program of Huebner (1985) for the detailed chemical evolution of a spherically expanding coma and the program of Schmidt and Wegman (1982) and Wegman (1987) for the MHD flow of plasma and magnetic field in a comet to the Giotto-mission data on the ion abundances measured by the HIS ion mass spectrometer. The physics and chemistry of the coma are modeled in great detail, including photoprocesses, gas-phase chemical kinetics, energy balance with a separate electron temperature, multifluid hydrodynamics with a transition to free molecular flow, fast-streaming atomic and molecular hydrogen, counter and cross streaming of the ionized species relative to the neutral species in the coma-solar wind interaction region with momentum exchange by elastic collisions, mass-loading through ion pick-up, and Lorentz forces of the advected magnetic field. The results, both inside and outside of the contact surface, are discussed and compared with the relevant HIS ion mass spectra.

Case Studies in Systems Chemistry. Final Report. [Includes Complete Case Study, Carboxylic Acid Equilibria

ERIC Educational Resources Information Center

Fleck, George

This publication was produced as a teaching tool for college chemistry. The book is a text for a computer-based unit on the chemistry of acid-base titrations, and is designed for use with FORTRAN or BASIC computer systems, and with a programmable electronic calculator, in a variety of educational settings. The text attempts to present computer…

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…

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…

Reaction of formaldehyde at the ortho- and para-positions of phenol: exploration of mechanisms using computational chemistry.

Treesearch

Anthony H. Conner; Melissa S. Reeves

2001-01-01

Computational chemistry methods can be used to explore the theoretical chemistry behind reactive systems, to compare the relative chemical reactivity of different systems, and, by extension, to predict the reactivity of new systems. Ongoing research has focused on the reactivity of a wide variety of phenolic compounds with formaldehyde using semi-empirical and ab...

Workshop report on large-scale matrix diagonalization methods in chemistry theory institute

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

Bischof, C.H.; Shepard, R.L.; Huss-Lederman, S.

The Large-Scale Matrix Diagonalization Methods in Chemistry theory institute brought together 41 computational chemists and numerical analysts. The goal was to understand the needs of the computational chemistry community in problems that utilize matrix diagonalization techniques. This was accomplished by reviewing the current state of the art and looking toward future directions in matrix diagonalization techniques. This institute occurred about 20 years after a related meeting of similar size. During those 20 years the Davidson method continued to dominate the problem of finding a few extremal eigenvalues for many computational chemistry problems. Work on non-diagonally dominant and non-Hermitian problems asmore » well as parallel computing has also brought new methods to bear. The changes and similarities in problems and methods over the past two decades offered an interesting viewpoint for the success in this area. One important area covered by the talks was overviews of the source and nature of the chemistry problems. The numerical analysts were uniformly grateful for the efforts to convey a better understanding of the problems and issues faced in computational chemistry. An important outcome was an understanding of the wide range of eigenproblems encountered in computational chemistry. The workshop covered problems involving self- consistent-field (SCF), configuration interaction (CI), intramolecular vibrational relaxation (IVR), and scattering problems. In atomic structure calculations using the Hartree-Fock method (SCF), the symmetric matrices can range from order hundreds to thousands. These matrices often include large clusters of eigenvalues which can be as much as 25% of the spectrum. However, if Cl methods are also used, the matrix size can be between 10{sup 4} and 10{sup 9} where only one or a few extremal eigenvalues and eigenvectors are needed. Working with very large matrices has lead to the development of« less

Making Connections: Learning and Teaching Chemistry in Context

ERIC Educational Resources Information Center

King, Donna; Bellocchi, Alberto; Ritchie, Stephen M.

2008-01-01

Even though several studies have reported positive attitudinal outcomes from context-based chemistry programs, methodological obstacles have prevented researchers from comparing satisfactorily the chemistry-learning outcomes between students who experience a context-based program with those who experience a content-driven program. In this…

The production of nitric oxide in the troposphere as a result of solid-rocket-motor afterburning

NASA Technical Reports Server (NTRS)

Stewart, R. B.; Gomberg, R. I.

1976-01-01

As part of an ongoing assessment of the environmental effects of solid-rocket-motor operations in the troposphere, estimates were made of the nitric oxide produced in the troposphere by the space shuttle and Titan 3-C boosters. Calculations were made with the low-altitude plume computer program and included the effects of coupled finite-rate chemistry and turbulent mixing. A recent measurement of nitric oxide taken in the effluent cloud of a Titan 3-C booster is compared with calculations made with this computer code. The various chemical reactions of the exhaust gases are listed in tabular form.

A Comparison of Secondary Chemistry Courses and Chemistry Teacher Preparation Programs in Iowa and Saint Petersburg, Russia

NASA Astrophysics Data System (ADS)

Sanger, Michael J.; Brincks, Erik L.; Phelps, Amy J.; Pak, Maria S.; Lyovkin, Antony N.

2001-09-01

This paper, which is a result of the collaboration between the University of Northern Iowa (UNI) in Cedar Falls, Iowa, and Herzen State Pedagogical University of Russia in Saint Petersburg, compares the 7-12 chemistry courses in Iowa and Saint Petersburg and the chemistry teacher preparation programs at UNI and Herzen. Differences in the 7-12 chemistry courses include curriculum design (spiral versus layer cake), students' extracurricular activities, and access to technology in the classroom. Differences in the chemistry teacher preparation programs include the number of methods and chemistry content courses required, the number of chemistry teaching majors, the proportion of teaching majors enrolled in the different natural science programs, and the typical minors and endorsements received by these majors. Although we noted many differences in chemistry instruction between Iowa and Saint Petersburg, the secondary and college instructors still face many similar issues, which include overcoming student chemophobia, improving students' algorithmic and problem-solving skills, improving students' conceptual understanding at the particulate level, and dealing with shortages in qualified secondary science teachers.

American Chemical Society. 23rd Great Lakes Regional Meeting. Program and abstracts

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

Not Available

1990-01-01

The technical program includes some 250 papers in 38 sessions, featuring 16 symposia with 99 invited speakers. Program highlights include a plenary lecture, The Origin and Consequences of Scientific Illiteracy, by Jon D. Miller. Sessions for general technical papers are scheduled in the following categories: analytical chemistry; biochemistry; inorganic chemistry; organic chemistry; and physical chemistry. Papers have been processed for inclusion on the data base.

Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

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

Bertoni, Colleen

Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactionsmore » methods, analytic gradients, and taking advantage of new hardware.« less

AutoClickChem: click chemistry in silico.

PubMed

Durrant, Jacob D; McCammon, J Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in "big pharma." High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu.

AutoClickChem: Click Chemistry in Silico

PubMed Central

Durrant, Jacob D.; McCammon, J. Andrew

2012-01-01

Academic researchers and many in industry often lack the financial resources available to scientists working in “big pharma.” High costs include those associated with high-throughput screening and chemical synthesis. In order to address these challenges, many researchers have in part turned to alternate methodologies. Virtual screening, for example, often substitutes for high-throughput screening, and click chemistry ensures that chemical synthesis is fast, cheap, and comparatively easy. Though both in silico screening and click chemistry seek to make drug discovery more feasible, it is not yet routine to couple these two methodologies. We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. AutoClickChem can be used to produce large combinatorial libraries of compound models for use in virtual screens. As the compounds of these libraries are constructed according to the reactions of click chemistry, they can be easily synthesized for subsequent testing in biochemical assays. Additionally, in silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization. AutoClickChem is based on the pymolecule toolbox, a framework that may facilitate the development of future python-based programs that require the manipulation of molecular models. Both the pymolecule toolbox and AutoClickChem are released under the GNU General Public License version 3 and are available for download from http://autoclickchem.ucsd.edu. PMID:22438795

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.

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.

Understanding the many-body expansion for large systems. I. Precision considerations

NASA Astrophysics Data System (ADS)

Richard, Ryan M.; Lao, Ka Un; Herbert, John M.

2014-07-01

Electronic structure methods based on low-order "n-body" expansions are an increasingly popular means to defeat the highly nonlinear scaling of ab initio quantum chemistry calculations, taking advantage of the inherently distributable nature of the numerous subsystem calculations. Here, we examine how the finite precision of these subsystem calculations manifests in applications to large systems, in this case, a sequence of water clusters ranging in size up to (H_2O)_{47}. Using two different computer implementations of the n-body expansion, one fully integrated into a quantum chemistry program and the other written as a separate driver routine for the same program, we examine the reproducibility of total binding energies as a function of cluster size. The combinatorial nature of the n-body expansion amplifies subtle differences between the two implementations, especially for n ⩾ 4, leading to total energies that differ by as much as several kcal/mol between two implementations of what is ostensibly the same method. This behavior can be understood based on a propagation-of-errors analysis applied to a closed-form expression for the n-body expansion, which is derived here for the first time. Discrepancies between the two implementations arise primarily from the Coulomb self-energy correction that is required when electrostatic embedding charges are implemented by means of an external driver program. For reliable results in large systems, our analysis suggests that script- or driver-based implementations should read binary output files from an electronic structure program, in full double precision, or better yet be fully integrated in a way that avoids the need to compute the aforementioned self-energy. Moreover, four-body and higher-order expansions may be too sensitive to numerical thresholds to be of practical use in large systems.

Understanding the many-body expansion for large systems. I. Precision considerations

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

Richard, Ryan M.; Lao, Ka Un; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu

2014-07-07

Electronic structure methods based on low-order “n-body” expansions are an increasingly popular means to defeat the highly nonlinear scaling of ab initio quantum chemistry calculations, taking advantage of the inherently distributable nature of the numerous subsystem calculations. Here, we examine how the finite precision of these subsystem calculations manifests in applications to large systems, in this case, a sequence of water clusters ranging in size up to (H{sub 2}O){sub 47}. Using two different computer implementations of the n-body expansion, one fully integrated into a quantum chemistry program and the other written as a separate driver routine for the same program,more » we examine the reproducibility of total binding energies as a function of cluster size. The combinatorial nature of the n-body expansion amplifies subtle differences between the two implementations, especially for n ⩾ 4, leading to total energies that differ by as much as several kcal/mol between two implementations of what is ostensibly the same method. This behavior can be understood based on a propagation-of-errors analysis applied to a closed-form expression for the n-body expansion, which is derived here for the first time. Discrepancies between the two implementations arise primarily from the Coulomb self-energy correction that is required when electrostatic embedding charges are implemented by means of an external driver program. For reliable results in large systems, our analysis suggests that script- or driver-based implementations should read binary output files from an electronic structure program, in full double precision, or better yet be fully integrated in a way that avoids the need to compute the aforementioned self-energy. Moreover, four-body and higher-order expansions may be too sensitive to numerical thresholds to be of practical use in large systems.« less

The Development of Computational Thinking in a High School Chemistry Course

ERIC Educational Resources Information Center

Matsumoto, Paul S.; Cao, Jiankang

2017-01-01

Computational thinking is a component of the Science and Engineering Practices in the Next Generation Science Standards, which were adopted by some states. We describe the activities in a high school chemistry course that may develop students' computational thinking skills by primarily using Excel, a widely available spreadsheet software. These…

Proceedings: Conference on Computers in Chemical Education and Research, Dekalb, Illinois, 19-23 July 1971.

ERIC Educational Resources Information Center

1971

Computers have effected a comprehensive transformation of chemistry. Computers have greatly enhanced the chemist's ability to do model building, simulations, data refinement and reduction, analysis of data in terms of models, on-line data logging, automated control of experiments, quantum chemistry and statistical and mechanical calculations, and…

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…

42 CFR 493.929 - Chemistry.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 5 2010-10-01 2010-10-01 false Chemistry. 493.929 Section 493.929 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.929 Chemistry. The subspecialties under the specialty of chemistry for which a proficiency testing program may offer proficiency testing are routine...

42 CFR 493.929 - Chemistry.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 42 Public Health 5 2012-10-01 2012-10-01 false Chemistry. 493.929 Section 493.929 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.929 Chemistry. The subspecialties under the specialty of chemistry for which a proficiency testing program may offer proficiency testing are routine...

42 CFR 493.929 - Chemistry.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 42 Public Health 5 2014-10-01 2014-10-01 false Chemistry. 493.929 Section 493.929 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.929 Chemistry. The subspecialties under the specialty of chemistry for which a proficiency testing program may offer proficiency testing are routine...

42 CFR 493.929 - Chemistry.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 42 Public Health 5 2013-10-01 2013-10-01 false Chemistry. 493.929 Section 493.929 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.929 Chemistry. The subspecialties under the specialty of chemistry for which a proficiency testing program may offer proficiency testing are routine...

42 CFR 493.929 - Chemistry.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 42 Public Health 5 2011-10-01 2011-10-01 false Chemistry. 493.929 Section 493.929 Public Health... Proficiency Testing Programs by Specialty and Subspecialty § 493.929 Chemistry. The subspecialties under the specialty of chemistry for which a proficiency testing program may offer proficiency testing are routine...

Designing a Software Tool for Fuzzy Logic Programming

NASA Astrophysics Data System (ADS)

Abietar, José M.; Morcillo, Pedro J.; Moreno, Ginés

2007-12-01

Fuzzy Logic Programming is an interesting and still growing research area that agglutinates the efforts for introducing fuzzy logic into logic programming (LP), in order to incorporate more expressive resources on such languages for dealing with uncertainty and approximated reasoning. The multi-adjoint logic programming approach is a recent and extremely flexible fuzzy logic paradigm for which, unfortunately, we have not found practical tools implemented so far. In this work, we describe a prototype system which is able to directly translate fuzzy logic programs into Prolog code in order to safely execute these residual programs inside any standard Prolog interpreter in a completely transparent way for the final user. We think that the development of such fuzzy languages and programing tools might play an important role in the design of advanced software applications for computational physics, chemistry, mathematics, medicine, industrial control and so on.

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.

Teacher's Guide to SERAPHIM Software I. Chemistry: Experimental Foundations.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the first in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Chemistry: Experimental Foundations." Program suggestions are…

European TV Brings Chemistry into the Home

ERIC Educational Resources Information Center

O'Sullivan, Dermot A.

1975-01-01

Describes television programs broadcast in the Netherlands and West Germany which explain what chemistry is all about. Both programs, planned under the direction of trained chemists, comprise 13 half-hour presentations and include segments on energy, polymers, chemical processes, the chemistry of life, atomic and molecular chemistry, and chemistry…

75 FR 3942 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-25

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance..., Proposal Review Panel for Chemistry, 1191. Dates & Times: February 23, 2010; 8:30 a.m.-4:30 p.m. February... Brittain, Program Director, Chemistry Centers Program, Division of Materials Research, Room 1055, National...

Users' instructions for the NASA/MSFC cloud-rise preprocessor program, version 6, and the NASA/MSFC multilayer diffusion program, version 6: Research version for Univac 1108 system

NASA Technical Reports Server (NTRS)

Bjorklund, J. R.

1978-01-01

The cloud-rise preprocessor and multilayer diffusion computer programs were used by NASA in predicting concentrations and dosages downwind from normal and abnormal launches of rocket vehicles. These programs incorporated: (1) the latest data for the heat content and chemistry of rocket exhaust clouds; (2) provision for the automated calculation of surface water pH due to deposition of HCl from precipitation scavenging; (3) provision for automated calculation of concentration and dosage parameters at any level within the vertical grounds for which meteorological inputs have been specified; and (4) provision for execution of multiple cases of meteorological data. Procedures used to automatically calculate wind direction shear in a layer were updated.

Molecular simulation workflows as parallel algorithms: the execution engine of Copernicus, a distributed high-performance computing platform.

PubMed

Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik

2015-06-09

Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

Development and Formative Evaluation of Computer Simulated College Chemistry Experiments.

ERIC Educational Resources Information Center

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

1978-01-01

This article describes the design, preparation, and initial evaluation of a set of computer-simulated chemistry experiments. The experiments entailed the use of an atomic emission spectroscope and a single-beam visible absorption spectrophometer. (Author/IRT)

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…

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…

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…

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…

Brookhaven highlights for fiscal year 1991, October 1, 1990--September 30, 1991

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

Rowe, M.S.; Cohen, A.; Greenberg, D.

1991-12-31

This report highlights Brookhaven National Laboratory`s activities for fiscal year 1991. Topics from the four research divisions: Computing and Communications, Instrumentation, Reactors, and Safety and Environmental Protection are presented. The research programs at Brookhaven are diverse, as is reflected by the nine different scientific departments: Accelerator Development, Alternating Gradient Synchrotron, Applied Science, Biology, Chemistry, Medical, National Synchrotron Light Source, Nuclear Energy, and Physics. Administrative and managerial information about Brookhaven are also disclosed. (GHH)

Brookhaven highlights for fiscal year 1991, October 1, 1990--September 30, 1991

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

Rowe, M.S.; Cohen, A.; Greenberg, D.

1991-01-01

This report highlights Brookhaven National Laboratory's activities for fiscal year 1991. Topics from the four research divisions: Computing and Communications, Instrumentation, Reactors, and Safety and Environmental Protection are presented. The research programs at Brookhaven are diverse, as is reflected by the nine different scientific departments: Accelerator Development, Alternating Gradient Synchrotron, Applied Science, Biology, Chemistry, Medical, National Synchrotron Light Source, Nuclear Energy, and Physics. Administrative and managerial information about Brookhaven are also disclosed. (GHH)

Simulating the Physical World

NASA Astrophysics Data System (ADS)

Berendsen, Herman J. C.

2004-06-01

The simulation of physical systems requires a simplified, hierarchical approach which models each level from the atomistic to the macroscopic scale. From quantum mechanics to fluid dynamics, this book systematically treats the broad scope of computer modeling and simulations, describing the fundamental theory behind each level of approximation. Berendsen evaluates each stage in relation to its applications giving the reader insight into the possibilities and limitations of the models. Practical guidance for applications and sample programs in Python are provided. With a strong emphasis on molecular models in chemistry and biochemistry, this book will be suitable for advanced undergraduate and graduate courses on molecular modeling and simulation within physics, biophysics, physical chemistry and materials science. It will also be a useful reference to all those working in the field. Additional resources for this title including solutions for instructors and programs are available online at www.cambridge.org/9780521835275. The first book to cover the wide range of modeling and simulations, from atomistic to the macroscopic scale, in a systematic fashion Providing a wealth of background material, it does not assume advanced knowledge and is eminently suitable for course use Contains practical examples and sample programs in Python

Teacher's Guide to SERAPHIM Software III. Modern Chemistry.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the third in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Modern Chemistry." Program suggestions are arranged in the same…

Teacher's Guide to SERAPHIM Software IV Chemistry: A Modern Course.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the fourth in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Chemistry: A Modern Course." Program suggestions are arranged…

Teacher's Guide to SERAPHIM Software VI. Chemistry: The Study of Matter.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the sixth in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Chemistry: The Study of Matter." Program suggestions are…

Independent Study in High School Chemistry: A Progress Report.

ERIC Educational Resources Information Center

DeRose, James V.

This is a progress report of an independent study program in chemistry at a senior high school. Currently in its fourth year of operation, the program is designed to provide students with individualized, self-paced instruction in college-preparatory chemistry. The author discusses the rationale for the program, the initial phases, the problems…

A Transition Program for Underprepared Students in General Chemistry: Diagnosis, Implementation, and Evaluation

ERIC Educational Resources Information Center

Shields, Shawn P.; Hogrebe, Mark C.; Spees, William M.; Handlin, Larry B.; Noelken, Greg P.; Riley, Julie M.; Frey, Regina F.

2012-01-01

We developed an online exam to diagnose students who are underprepared for college-level general chemistry and implemented a program to support them during the general chemistry sequence. This transition program consists of extended-length recitations, peer-led team-learning (PLTL) study groups, and peer-mentoring groups. We evaluated this…

Teacher's Guide to SERAPHIM Software V. Chemistry: The Central Science.

ERIC Educational Resources Information Center

Bogner, Donna J.

Designed to assist chemistry teachers in selecting appropriate software programs, this publication is the fifth in a series of six teacher's guides from Project SERAPHIM, a program sponsored by the National Science Foundation. This guide is keyed to the chapters of the text "Chemistry: The Central Science." Program suggestions are…

Recent advances at NASA in calculating the electronic spectra of diatomic molecules

NASA Technical Reports Server (NTRS)

Whiting, Ellis E.; Paterson, John A.

1988-01-01

Advanced entry vehicles, such as the proposed Aero-assisted Orbital Transfer Vehicle, provide new and challenging problems for spectroscopy. Large portions of the flow field about such vehicles will be characterized by chemical and thermal nonequilibrium. Only by considering the actual overlap of the atomic and rotational lines emitted by the species present can the impact of radiative transport within the flow field be assessed correctly. To help make such an assessment, a new computer program is described that can generate high-resolution, line-by-line spectra for any spin-allowed transitions in diatomic molecules. The program includes the matrix elements for the rotational energy and distortion to the fourth order; the spin-orbit, spin-spin, and spin-rotation interactions to first order; and the lambda splitting by a perturbation calculation. An overview of the Computational Chemistry Branch at Ames Research Center is also presented.

ECUT: Energy Conversion and Utilization Technologies program. Heterogeneous catalysis modeling program concept

NASA Technical Reports Server (NTRS)

Voecks, G. E.

1983-01-01

Insufficient theoretical definition of heterogeneous catalysts is the major difficulty confronting industrial suppliers who seek catalyst systems which are more active, selective, and stable than those currently available. In contrast, progress was made in tailoring homogeneous catalysts to specific reactions because more is known about the reaction intermediates promoted and/or stabilized by these catalysts during the course of reaction. However, modeling heterogeneous catalysts on a microscopic scale requires compiling and verifying complex information on reaction intermediates and pathways. This can be achieved by adapting homogeneous catalyzed reaction intermediate species, applying theoretical quantum chemistry and computer technology, and developing a better understanding of heterogeneous catalyst system environments. Research in microscopic reaction modeling is now at a stage where computer modeling, supported by physical experimental verification, could provide information about the dynamics of the reactions that will lead to designing supported catalysts with improved selectivity and stability.

Analysis of Water-Quality Trends for Selected Streams in the Water Chemistry Monitoring Program, Michigan, 1998-2005

USGS Publications Warehouse

Hoard, C.J.; Fuller, Lori M.; Fogarty, Lisa R.

2009-01-01

In 1998, the Michigan Department of Environmental Quality and the U.S. Geological Survey began a long-term monitoring program to evaluate the water quality of most watersheds in Michigan. Major goals of this Water-Chemistry Monitoring Program were to identify streams exceeding or not meeting State or Federal water-quality standards and to assess if constituent concentrations reflecting water quality in these streams were increasing or decreasing over time. As part of this program, water-quality data collected from 1998 to 2005 were analyzed to identify potential trends. Sixteen water-quality constituents were analyzed at 31 sites across Michigan, 28 of which had sufficient data to analyze for trends. Trend analysis on the various water-quality data was done using the uncensored Seasonal Kendall test within the computer program ESTREND. The most prevalent trend detected throughout the state was for chloride. Chloride trends were detected at 8 of the 28 sites; trends at 7 sites were increasing and the trend at 1 site was decreasing. Although no trends were detected for various nitrogen species or phosphorus, these constituents were detected at levels greater than the U.S. Environmental Protection Agency recommendations for nutrients in water. The results of the trend analysis will help to establish a baseline to evaluate future changes in water quality in Michigan streams.

COAChing Women to Succeed in Academic Careers in the Chemical Sciences

NASA Astrophysics Data System (ADS)

Richmond, Geraldine L.

2005-03-01

COAChing (Committee on the Advancement of Women Chemists) was formed in 1998 by a group of senior women chemists to address issues related to the documented disparity in hiring, promotion, and advancement of women faculty in academic chemistry departments in the United States. Several national programs have been launched by COACh that are already showing a high degree of impact on the lives and careers of many women chemists in the academic arena. As word of the effectiveness of these programs has spread, other science disciplines (including physics, biology, mathematics, and computer science) have adopted COACh programs with similar goals in mind. This article describes several opportunities that COACh is providing to help increase the number and success of women scientists in academia.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes

NASA Astrophysics Data System (ADS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-05-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes. [predicting afterbody drag

NASA Technical Reports Server (NTRS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-01-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

[Advancements of computer chemistry in separation of Chinese medicine].

PubMed

Li, Lingjuan; Hong, Hong; Xu, Xuesong; Guo, Liwei

2011-12-01

Separating technique of Chinese medicine is not only a key technique in the field of Chinese medicine' s research and development, but also a significant step in the modernization of Chinese medicinal preparation. Computer chemistry can build model and look for the regulations from Chinese medicine system which is full of complicated data. This paper analyzed the applicability, key technology, basic mode and common algorithm of computer chemistry applied in the separation of Chinese medicine, introduced the mathematic mode and the setting methods of Extraction kinetics, investigated several problems which based on traditional Chinese medicine membrane procession, and forecasted the application prospect.

Protein Engineering: Development of a Metal Ion Dependent Switch

DTIC Science & Technology

2017-05-22

Society of Chemistry Royal Society of Chemistry Biochemistry PNAS Escherichia coli Journal of Biotechnology Biochemistry Nature Protocols Journal of...Molecular Biology Biochemistry Royal Society of Chemistry Proteins: Structure, Function, and Bioinformatics Journal of Molecular Biology Biophysical...Biophysical Journal Protein Science Journal of Computational Chemistry Current Opinion in Chemical Biology Royal Society of Chemistry

Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

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

Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NO x reduction. Furthermore, wemore » then discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

DOE PAGES

Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

2015-06-05

Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NO x reduction. Furthermore, wemore » then discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

AceDRG: a stereochemical description generator for ligands

PubMed Central

Emsley, Paul; Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas

2017-01-01

The program AceDRG is designed for the derivation of stereochemical information about small molecules. It uses local chemical and topological environment-based atom typing to derive and organize bond lengths and angles from a small-molecule database: the Crystallography Open Database (COD). Information about the hybridization states of atoms, whether they belong to small rings (up to seven-membered rings), ring aromaticity and nearest-neighbour information is encoded in the atom types. All atoms from the COD have been classified according to the generated atom types. All bonds and angles have also been classified according to the atom types and, in a certain sense, bond types. Derived data are tabulated in a machine-readable form that is freely available from CCP4. AceDRG can also generate stereochemical information, provided that the basic bonding pattern of a ligand is known. The basic bonding pattern is perceived from one of the computational chemistry file formats, including SMILES, mmCIF, SDF MOL and SYBYL MOL2 files. Using the bonding chemistry, atom types, and bond and angle tables generated from the COD, AceDRG derives the ‘ideal’ bond lengths, angles, plane groups, aromatic rings and chirality information, and writes them to an mmCIF file that can be used by the refinement program REFMAC5 and the model-building program Coot. Other refinement and model-building programs such as PHENIX and BUSTER can also use these files. AceDRG also generates one or more coordinate sets corresponding to the most favourable conformation(s) of a given ligand. AceDRG employs RDKit for chemistry perception and for initial conformation generation, as well as for the interpretation of SMILES strings, SDF MOL and SYBYL MOL2 files. PMID:28177307

Using NASA and the Space Program to Help High School and College Students Learn Chemistry.

ERIC Educational Resources Information Center

Kelter, Paul B.; And Others

1987-01-01

Discusses some of the chemical concepts that the United States Space Program illustrates. Describes ways to use the space program to motivate students to learn chemistry and its relationship to the world. Provides examples of classroom applications to environmental chemistry and biochemistry in studying the operation of the space shuttle. (TW)

BCTC for Windows: Abstract of Issue 9903W

NASA Astrophysics Data System (ADS)

Whisnant, David M.; McCormick, James A.

1999-05-01

BCTC for Windows was originally published by JCE Software in 1992 (1) in Series B for PC-compatible (MS-DOS) computers. JCE Software is now re-releasing BCTC for Windows as issue 9903W to make it more accessible to Windows users-especially those running Windows 95 and Windows 98-while we continue to phase out Series B (DOS) issues. Aside from a new Windows-compatible installation program, BCTC is unchanged. BCTC is an environmental simulation modeled after the dioxin controversy (2). In the simulation, students are involved in the investigation of a suspected carcinogen called BCTC, which has been found in a river below a chemical plant and above the water supply of a nearby city. The students have the options of taking water samples, analyzing the water (for BCTC, oxygen, metals, and pesticides), determining LD50s in an animal lab, visiting a library, making economic analyses, and conferring with colleagues, all using the computer. In the Classroom BCTC gives students experience with science in the context of a larger social and political problem. It can serve as the basis for a scientific report, class discussion, or a role-playing exercise (3). Because it requires no previous laboratory experience, this simulation can be used by students in middle and high school science classes, or in college courses for non-science majors. It also has been used in introductory chemistry courses for science majors. One of the intentions of BCTC is to involve students in an exercise (2) that closely approximates what scientists do. The realistic pictures, many of them captured with a video camera, create an atmosphere that furthers this goal. BCTC also reflects the comments of teachers who have used the program (4) and accounts of dioxin research (5). Screen from BCTC showing location of the entry of the effluent in the river, the city, and the city water supply.

Using Tutte polynomials to analyze the structure of the benzodiazepines

NASA Astrophysics Data System (ADS)

Cadavid Muñoz, Juan José

2014-05-01

Graph theory in general and Tutte polynomials in particular, are implemented for analyzing the chemical structure of the benzodiazepines. Similarity analysis are used with the Tutte polynomials for finding other molecules that are similar to the benzodiazepines and therefore that might show similar psycho-active actions for medical purpose, in order to evade the drawbacks associated to the benzodiazepines based medicine. For each type of benzodiazepines, Tutte polynomials are computed and some numeric characteristics are obtained, such as the number of spanning trees and the number of spanning forests. Computations are done using the computer algebra Maple's GraphTheory package. The obtained analytical results are of great importance in pharmaceutical engineering. As a future research line, the usage of the chemistry computational program named Spartan, will be used to extent and compare it with the obtained results from the Tutte polynomials of benzodiazepines.

Strategies for Fostering Synergy between Neuroscience Programs and Chemistry Departments

PubMed Central

Ulness, Darin J.; Mach, Julie R.

2011-01-01

The successful model of the Neuroscience Program at Concordia College is used as a source of illustrative examples in a presentation of strategies to foster synergy between neuroscience programs and chemistry departments. Chemistry is an increasing voice in the dialog of modern neuroscience. To be well-prepared to engage in this dialog, students must have strong chemistry training and be comfortable applying it to situations in neuroscience. The strategies presented here are designed to stimulate thought and discussion in the undergraduate neuroscience education community. Hopefully this will lead to greater interaction between chemistry and neuroscience at the undergraduate level in other institutions. PMID:23626488

[Computational chemistry in structure-based drug design].

PubMed

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

2013-07-01

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

REVIEWS OF TOPICAL PROBLEMS: Analytic calculations on digital computers for applications in physics and mathematics

NASA Astrophysics Data System (ADS)

Gerdt, V. P.; Tarasov, O. V.; Shirkov, Dmitrii V.

1980-01-01

The present state of analytic calculations on computers is reviewed. Several programming systems which are used for analytic calculations are discussed: SCHOONSCHIP, CLAM, REDUCE-2, SYMBAL, CAMAL, AVTO-ANALITIK, MACSYMA, etc. It is shown that these systems can be used to solve a wide range of problems in physics and mathematics. Some physical applications are discussed in celestial mechanics, the general theory of relativity, quantum field theory, plasma physics, hydrodynamics, atomic and molecular physics, and quantum chemistry. Some mathematical applications which are discussed are evaluating indefinite integrals, solving differential equations, and analyzing mathematical expressions. This review is addressed to physicists and mathematicians working in a wide range of fields.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids.

PubMed

Aradi, Bálint; Niklasson, Anders M N; Frauenheim, Thomas

2015-07-14

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born-Oppenheimer molecular dynamics. For systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can be applied to a broad range of problems in materials science, chemistry, and biology.

LABORATORY AND COMPUTATIONAL INVESTIGATIONS OF THE ATMOSPHERIC CHEMISTRY OF KEY OXIDATION PRODUCTS CONTROLLING TROPOSPHERIC OZONE FORMATION

EPA Science Inventory

Major uncertainties remain in our ability to identify the key reactions and primary oxidation products of volatile hydrocarbons that contribute to ozone formation in the troposphere. To reduce these uncertainties, computational chemistry, mechanistic and process analysis techniqu...

Establishing the Basis for Validated Predictions of Highly Non-Equilibrium Flows. (With 9 Attachments)

DTIC Science & Technology

1993-10-14

expansion in Figure 8, a finite rate chemistry, inviscid flow solution was calculated using a One Dimensional Kinetics ( ODK ) computer program2 0...T Temperature range (K) 300 < T < 2000 Units cm3 mo-L’ sec-, [able 2: Reaction rate used in ODK compuiations. Working Gas 12 Stagnation pressure (atm...and proceeding to shorter wavelengths. The laser beam was focused on the probed volume with a 30 cm focal length lens. The LIF signal was collected in

Cumulative Index to NASA Tech Briefs 1963-1969

NASA Technical Reports Server (NTRS)

1970-01-01

Tech Briefs are short announcements of new technology derived from the research and development activities of the National Aeronautics and Space Administration. These briefs emphasize information considered likely to be transferrable across industrial, regional, or disciplinary lines and are issued to encourage commercial application. This Cumulative index to NASA Tech Briefs lists those published from 1963 through 1969. The main listing is divided into six categokies: Electrical (Electronic), Physical Sciences (Energy Sources), Materials (Chemistry), Life Sciences, Mechanical, and Computer Programs.

24th Current Trends in Computational Chemistry

DTIC Science & Technology

2017-05-17

Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 Final Report W911NF-16-1-0470 69708-CH-CF.1 601-979-3723 a. REPORT 14. ABSTRACT 16...5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 5c. PROGRAM ELEMENT NUMBER 5b. GRANT NUMBER 5a. CONTRACT NUMBER Form Approved OMB NO...number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. Jackson State University 1400 John R. Lynch Street Jackson, MS 39217 -0002 Agency Code

Training the Future - Interns Harvesting & Testing Plant Experim

NASA Image and Video Library

2017-07-19

In the Space Life Sciences Laboratory at NASA's Kennedy Space Center in Florida, student interns such as Ayla Grandpre, left, and Payton Barnwell are joining agency scientists, contributing in the area of plant growth research for food production in space. Grandpre is pursuing a degree in computer science and chemistry at Rocky Mountain College in Billings, Montana. Barnwell is a mechanical engineering and nanotechnology major at Florida Polytechnic University. The agency attracts its future workforce through the NASA Internship, Fellowships and Scholarships, or NIFS, Program.

Supercomputing in Aerospace

NASA Technical Reports Server (NTRS)

Kutler, Paul; Yee, Helen

1987-01-01

Topics addressed include: numerical aerodynamic simulation; computational mechanics; supercomputers; aerospace propulsion systems; computational modeling in ballistics; turbulence modeling; computational chemistry; computational fluid dynamics; and computational astrophysics.

Investigating the Viability of a Competency-Based, Qualitative Laboratory Assessment Model in First-Year Undergraduate Chemistry

ERIC Educational Resources Information Center

Pullen, Reyne; Thickett, Stuart C.; Bissember, Alex C.

2018-01-01

In chemistry curricula, both the role of the laboratory program and the method of assessment used are subject to scrutiny and debate. The ability to identify clearly defined competencies for the chemistry laboratory program is crucial, given the numerous other disciplines that rely on foundation-level chemistry knowledge and practical skills. In…

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennit - A Computational Modeling Study

DTIC Science & Technology

2014-01-01

Study Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to...understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus...find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance are required. A computational material

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…

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language.

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

PubMed Central

2013-01-01

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910

Monthly Progress Report No. 60 for April 1948

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

Various

This report gives a short summary of each of the following programs: (1) 184-inch Cyclotron Program; (2) 60-inch Cyclotron Program; (3) Synchrotron Program; (4) Linear Accelerator Program; (5) Experimental Physics; (6) Theoretical Physics; (7) Chemistry; (8) Medical Physics; and (9) Health Physics and Chemistry.

Chemistry Division: Annual progress report for period ending March 31, 1987

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

Not Available

1987-08-01

This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics. (DLC)

Development of the Connected Chemistry as Formative Assessment Pedagogy for High School Chemistry Teaching

ERIC Educational Resources Information Center

Park, Mihwa; Liu, Xiufeng; Waight, Noemi

2017-01-01

This paper describes the development of Connected Chemistry as Formative Assessment (CCFA) pedagogy, which integrates three promising teaching and learning approaches, computer models, formative assessments, and learning progressions, to promote student understanding in chemistry. CCFA supports student learning in making connections among the…

Medicinal Chemistry Projects Requiring Imaginative Structure-Based Drug Design Methods.

PubMed

Moitessier, Nicolas; Pottel, Joshua; Therrien, Eric; Englebienne, Pablo; Liu, Zhaomin; Tomberg, Anna; Corbeil, Christopher R

2016-09-20

Computational methods for docking small molecules to proteins are prominent in drug discovery. There are hundreds, if not thousands, of documented examples-and several pertinent cases within our research program. Fifteen years ago, our first docking-guided drug design project yielded nanomolar metalloproteinase inhibitors and illustrated the potential of structure-based drug design. Subsequent applications of docking programs to the design of integrin antagonists, BACE-1 inhibitors, and aminoglycosides binding to bacterial RNA demonstrated that available docking programs needed significant improvement. At that time, docking programs primarily considered flexible ligands and rigid proteins. We demonstrated that accounting for protein flexibility, employing displaceable water molecules, and using ligand-based pharmacophores improved the docking accuracy of existing methods-enabling the design of bioactive molecules. The success prompted the development of our own program, Fitted, implementing all of these aspects. The primary motivation has always been to respond to the needs of drug design studies; the majority of the concepts behind the evolution of Fitted are rooted in medicinal chemistry projects and collaborations. Several examples follow: (1) Searching for HDAC inhibitors led us to develop methods considering drug-zinc coordination and its effect on the pKa of surrounding residues. (2) Targeting covalent prolyl oligopeptidase (POP) inhibitors prompted an update to Fitted to identify reactive groups and form bonds with a given residue (e.g., a catalytic residue) when the geometry allows it. Fitted-the first fully automated covalent docking program-was successfully applied to the discovery of four new classes of covalent POP inhibitors. As a result, efficient stereoselective syntheses of a few screening hits were prioritized rather than synthesizing large chemical libraries-yielding nanomolar inhibitors. (3) In order to study the metabolism of POP inhibitors by cytochrome P450 enzymes (CYPs)-for toxicology studies-the program Impacts was derived from Fitted and helped us to reveal a complex metabolism with unforeseen stereocenter isomerizations. These efforts, combined with those of other docking software developers, have strengthened our understanding of the complex drug-protein binding process while providing the medicinal chemistry community with useful tools that have led to drug discoveries. In this Account, we describe our contributions over the past 15 years-within their historical context-to the design of drug candidates, including BACE-1 inhibitors, POP covalent inhibitors, G-quadruplex binders, and aminoglycosides binding to nucleic acids. We also remark the necessary developments of docking programs, specifically Fitted, that enabled structure-based design to flourish and yielded multiple fruitful, rational medicinal chemistry campaigns.

The Student-to-Student Chemistry Initiative: Training High School Students To Perform Chemistry Demonstration Programs for Elementary School Students

NASA Astrophysics Data System (ADS)

Voegel, Phillip D.; Quashnock, Kathryn A.; Heil, Katrina M.

2004-05-01

The Student-to-Student Chemistry Initiative is an outreach program started in the fall of 2001 at Midwestern State University (MSU). The oncampus program trains high school science students to perform a series of chemistry demonstrations and subsequently provides kits containing necessary supplies and reagents for the high school students to perform demonstration programs at elementary schools. The program focuses on improving student perception of science. The program's impact on high school student perception is evaluated through statistical analysis of paired preparticipation and postparticipation surveys. The surveys focus on four areas of student perception: general attitude toward science, interest in careers in science, science awareness, and interest in attending MSU for postsecondary education. Increased scores were observed in all evaluation areas including a statistically significant increase in science awareness following participation.

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a ``glass like`` material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

APOLLO: A computer program for the calculation of chemical equilibrium and reaction kinetics of chemical systems

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

Nguyen, H.D.

1991-11-01

Several of the technologies being evaluated for the treatment of waste material involve chemical reactions. Our example is the in situ vitrification (ISV) process where electrical energy is used to melt soil and waste into a glass like'' material that immobilizes and encapsulates any residual waste. During the ISV process, various chemical reactions may occur that produce significant amounts of products which must be contained and treated. The APOLLO program was developed to assist in predicting the composition of the gases that are formed. Although the development of this program was directed toward ISV applications, it should be applicable tomore » other technologies where chemical reactions are of interest. This document presents the mathematical methodology of the APOLLO computer code. APOLLO is a computer code that calculates the products of both equilibrium and kinetic chemical reactions. The current version, written in FORTRAN, is readily adaptable to existing transport programs designed for the analysis of chemically reacting flow systems. Separate subroutines EQREACT and KIREACT for equilibrium ad kinetic chemistry respectively have been developed. A full detailed description of the numerical techniques used, which include both Lagrange multiplies and a third-order integrating scheme is presented. Sample test problems are presented and the results are in excellent agreement with those reported in the literature.« less

Biennial Conference on Chemical Education: Abstracts of Papers (9th, Bozeman, Montana, July 27-August 2, 1986).

ERIC Educational Resources Information Center

1986

This document includes summaries of conference presentations dealing with a wide variety of topics, including chemistry units for the elementary classroom, science experimentation in the secondary school, computer simulations, computer interfaces, videodisc technology, correspondence teaching of general chemistry, interdisciplinary energy courses,…

Using Computer Simulations in Chemistry Problem Solving

ERIC Educational Resources Information Center

Avramiotis, Spyridon; Tsaparlis, Georgios

2013-01-01

This study is concerned with the effects of computer simulations of two novel chemistry problems on the problem solving ability of students. A control-experimental group, equalized by pair groups (n[subscript Exp] = n[subscript Ctrl] = 78), research design was used. The students had no previous experience of chemical practical work. Student…

RESEARCH STRATEGIES FOR THE APPLICATION OF THE TECHNIQUES OF COMPUTATIONAL BIOLOGICAL CHEMISTRY TO ENVIRONMENTAL PROBLEMS

EPA Science Inventory

On October 25 and 26, 1984, the U.S. EPA sponsored a workshop to consider the potential applications of the techniques of computational biological chemistry to problems in environmental health. Eleven extramural scientists from the various related disciplines and a similar number...

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...

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…

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…

The NATA code: Theory and analysis, volume 1. [user manuals (computer programming) - gas dynamics, wind tunnels

NASA Technical Reports Server (NTRS)

Bade, W. L.; Yos, J. M.

1975-01-01

A computer program for calculating quasi-one-dimensional gas flow in axisymmetric and two-dimensional nozzles and rectangular channels is presented. Flow is assumed to start from a state of thermochemical equilibrium at a high temperature in an upstream reservoir. The program provides solutions based on frozen chemistry, chemical equilibrium, and nonequilibrium flow with finite reaction rates. Electronic nonequilibrium effects can be included using a two-temperature model. An approximate laminar boundary layer calculation is given for the shear and heat flux on the nozzle wall. Boundary layer displacement effects on the inviscid flow are considered also. Chemical equilibrium and transport property calculations are provided by subroutines. The code contains precoded thermochemical, chemical kinetic, and transport cross section data for high-temperature air, CO2-N2-Ar mixtures, helium, and argon. It provides calculations of the stagnation conditions on axisymmetric or two-dimensional models, and of the conditions on the flat surface of a blunt wedge. The primary purpose of the code is to describe the flow conditions and test conditions in electric arc heated wind tunnels.

Caring for the Environment while Teaching Organic Chemistry

ERIC Educational Resources Information Center

Santos, Elvira Santos; Gavilan Garcia, Irma Cruz; Lejarazo Gomez, Eva Florencia

2004-01-01

A comprehensive program in the field of green chemistry, which concentrates on processing and managing of wastes produced during laboratory experiments, is presented. The primary aim of the program is to instill a sense of responsibility and a concern for the environment through organic chemistry education.

Cookbook Versus Creative Chemistry

ERIC Educational Resources Information Center

Venkatachelam, Chaya; Rudolph, R. W.

1974-01-01

A new approach to a research-oriented general chemistry laboratory is described. Objectives for the laboratory program are specified, details are provided concerning the program design, and the results of an experiment to evaluate the program are reported. (DT)

Laboratory-directed research and development: FY 1996 progress report

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

Vigil, J.; Prono, J.

1997-05-01

This report summarizes the FY 1996 goals and accomplishments of Laboratory-Directed Research and Development (LDRD) projects. It gives an overview of the LDRD program, summarizes work done on individual research projects, and provides an index to the projects` principal investigators. Projects are grouped by their LDRD component: Individual Projects, Competency Development, and Program Development. Within each component, they are further divided into nine technical disciplines: (1) materials science, (2) engineering and base technologies, (3) plasmas, fluids, and particle beams, (4) chemistry, (5) mathematics and computational sciences, (6) atomic and molecular physics, (7) geoscience, space science, and astrophysics, (8) nuclear andmore » particle physics, and (9) biosciences.« less

75 FR 48698 - Medicare, Medicaid and CLIA Programs; COLA (Formerly the Commission on Office Laboratory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-11

..., including Syphilis Serology, General Immunology. Chemistry, including Routine Chemistry, Urinalysis.... Chemistry, including Routine Chemistry, Urinalysis, Endocrinology, Toxicology. Hematology. Immunohematology...

Inorganic Chemistry at the Undergraduate Level: Are We All on the Same Page?

ERIC Educational Resources Information Center

Pesterfield, Les L.; Henrickson, Charles H.

2001-01-01

Summarizes and presents results of a national survey on undergraduate inorganic chemistry which asked faculty to describe the general layout of their undergraduate program and course content. Reveals both similarities in the structure of undergraduate inorganic chemistry programs across the country and diversity in content. (ASK)

The Chemistry Teaching Fellowship Program: Developing Curricula and Graduate Student Professionalism

ERIC Educational Resources Information Center

Kim, Kris S.; Rackus, Darius G.; Mabury, Scott A.; Morra, Barbora; Dicks, Andrew P.

2017-01-01

The Chemistry Teaching Fellowship Program (CTFP) is offered to graduate students and postdoctoral researchers at the University of Toronto as an opportunity to undertake curriculum development and chemistry education research. Projects are run with faculty supervision and focus on designing new laboratory activities, lectures, tutorials,…

Chemistry 20-30: Background, Exemplars and Resources.

ERIC Educational Resources Information Center

Hackman, Desiree; And Others

This document is designed to provide practical information for teaching the Chemistry 20-30 Program of Studies. The first section provides an overview of Chemistry 20, explaining the program philosophy and the relationships among science, technology, and society. The use of concept connections and teaching a course around major science themes is…

The Chemistry Teaching Program for Developing the Senior High School Students' Entrepreneurial Attitudes

ERIC Educational Resources Information Center

Susianna, Nancy

2011-01-01

The objectives of this research were to identify the characteristics and effectiveness of chemistry teaching programs that increase students' entrepreneurial attitudes, chemistry concepts understanding and creativity. The research design application refers to the R & D (Research and Development) Design. Seventy-three senior high school students…

General Chemistry Collection for Students (CD-ROM), Abstract of Special Issue 16, 4th Edition

NASA Astrophysics Data System (ADS)

2000-07-01

The General Chemistry Collection contains both new and previously published JCE Software programs that are intended for use by introductory-level chemistry students. These peer-reviewed programs for Macintosh and for Windows are available on a single CD-ROM for convenient distribution to and access by students, and the CD may be adopted for students to purchase as they would a textbook. General Chemistry Collection covers a broad range of topics providing students with interesting information, tutorials, and simulations that will be useful to them as they study chemistry for the first time. There are 22 programs included in the General Chemistry Collection 4th Edition. Their titles and the general chemistry topics they cover are listed in Table 1. Features in This Edition General Chemistry Collection, 4th edition includes:

• Lessons for Introductory Chemistry and INQUAL-S, two new programs not previously published by JCE Software (abstracts appear below)
• Writing Electron Dot Structures (1) and Viscosity Measurement: A Virtual Experiment for Windows (2), two programs published individually by JCE Software
• Periodic Table Live! LE, a limited edition of Periodic Table Live!, 2nd Edition (3) (this replaces Chemistry Navigator (4) and Illustrated Periodic Table (5))
• Many of the programs from previous editions (6)1

Laboratory manual: mineral X-ray diffraction data retrieval/plot computer program

USGS Publications Warehouse

Hauff, Phoebe L.; VanTrump, George

1976-01-01

The Mineral X-Ray Diffraction Data Retrieval/Plot Computer Program--XRDPLT (VanTrump and Hauff, 1976a) is used to retrieve and plot mineral X-ray diffraction data. The program operates on a file of mineral powder diffraction data (VanTrump and Hauff, 1976b) which contains two-theta or 'd' values, and intensities, chemical formula, mineral name, identification number, and mineral group code. XRDPLT is a machine-independent Fortran program which operates in time-sharing mode on a DEC System i0 computer and the Gerber plotter (Evenden, 1974). The program prompts the user to respond from a time-sharing terminal in a conversational format with the required input information. The program offers two major options: retrieval only; retrieval and plot. The first option retrieves mineral names, formulas, and groups from the file by identification number, by the mineral group code (a classification by chemistry or structure), or by searches based on the formula components. For example, it enables the user to search for minerals by major groups (i.e., feldspars, micas, amphiboles, oxides, phosphates, carbonates) by elemental composition (i.e., Fe, Cu, AI, Zn), or by a combination of these (i.e., all copper-bearing arsenates). The second option retrieves as the first, but also plots the retrieved 2-theta and intensity values as diagrammatic X-ray powder patterns on mylar sheets or overlays. These plots can be made using scale combinations compatible with chart recorder diffractograms and 114.59 mm powder camera films. The overlays are then used to separate or sieve out unrelated minerals until unknowns are matched and identified.

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…

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…

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…

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…

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…

Perception of the Relevance of Organic Chemistry in a German Pharmacy Students’ Course

PubMed Central

Wehle, Sarah

2016-01-01

Objective. To investigate German pharmacy students’ attitudes toward the relevance of organic chemistry training in Julius Maximilian University (JMU) of Würzburg with regard to subsequent courses in the curricula and in later prospective career options. Methods. Surveys were conducted in the second-year organic chemistry course (50 participants) as well as during the third-year and fourth-year lecture cycle on medicinal and pharmaceutical chemistry (66 participants) in 2014. Results. Students’ attitudes were surprisingly consistent throughout the progress of the degree course. Students considered organic chemistry very relevant to the pharmacy study program (95% junior and 97% senior students), and of importance for their future pharmacy program (88% junior and 94% senior students). With regard to prospective career options, the perceived relevance was considerably lower and attitudes were less homogenous. Conclusions. German pharmacy students at JMU Würzburg consider organic chemistry of high relevance for medicinal chemistry and other courses in JMU’s pharmacy program. PMID:27170811

Perception of the Relevance of Organic Chemistry in a German Pharmacy Students' Course.

PubMed

Wehle, Sarah; Decker, Michael

2016-04-25

Objective. To investigate German pharmacy students' attitudes toward the relevance of organic chemistry training in Julius Maximilian University (JMU) of Würzburg with regard to subsequent courses in the curricula and in later prospective career options. Methods. Surveys were conducted in the second-year organic chemistry course (50 participants) as well as during the third-year and fourth-year lecture cycle on medicinal and pharmaceutical chemistry (66 participants) in 2014. Results. Students' attitudes were surprisingly consistent throughout the progress of the degree course. Students considered organic chemistry very relevant to the pharmacy study program (95% junior and 97% senior students), and of importance for their future pharmacy program (88% junior and 94% senior students). With regard to prospective career options, the perceived relevance was considerably lower and attitudes were less homogenous. Conclusions. German pharmacy students at JMU Würzburg consider organic chemistry of high relevance for medicinal chemistry and other courses in JMU's pharmacy program.

The Professional Development of High School Chemistry Coordinators

NASA Astrophysics Data System (ADS)

Hofstein, Avi; Carmeli, Miriam; Shore, Relly

2004-02-01

The implementation of new content and pedagogical standards in science education necessitates intensive, long-term professional development of science teachers. In this paper, we describe the rationale and structure of a comprehensive and intensive professional development program of school-based leaders, namely school chemistry coordinators. The year-long program was designed so that the chemistry teachers who enrolled in the program were able to develop in three interrelated aspects: content knowledge, pedagogical content knowledge, and leadership ability. Several strategies for the development of these aspects were adopted from Loucks-Horsley, Hewson, Love, & Stiles (1998). The evaluation of the program focused on the changes that participating teachers underwent regarding their personal beliefs and their functioning as school chemistry coordinators in their schools.

Impact of Chemistry Teachers' Knowledge and Practices on Student Achievement

NASA Astrophysics Data System (ADS)

Scantlebury, Kathryn

2008-10-01

Professional development programs promoting inquiry-based teaching are challenged with providing teachers content knowledge and using pedagogical approaches that model standards based instruction. Inquiry practices are also important for undergraduate students. This paper focuses on the evaluation of an extensive professional development program for chemistry teachers that included chemistry content tests for students and the teachers and the impact of undergraduate research experiences on college students' attitudes towards chemistry. Baseline results for the students showed that there were no gender differences on the achievement test but white students scored significantly higher than non-white students. However, parent/adult involvement with chemistry homework and projects, was a significant negative predictor of 11th grade students' test chemistry achievement score. This paper will focus on students' achievement and attitude results for teachers who are mid-way through the program providing evidence that on-going, sustained professional development in content and pedagogy is critical for improving students' science achievement.

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

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

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Extended Lagrangian Density Functional Tight-Binding Molecular Dynamics for Molecules and Solids

DOE PAGES

Aradi, Bálint; Niklasson, Anders M. N.; Frauenheim, Thomas

2015-06-26

A computationally fast quantum mechanical molecular dynamics scheme using an extended Lagrangian density functional tight-binding formulation has been developed and implemented in the DFTB+ electronic structure program package for simulations of solids and molecular systems. The scheme combines the computational speed of self-consistent density functional tight-binding theory with the efficiency and long-term accuracy of extended Lagrangian Born–Oppenheimer molecular dynamics. Furthermore, for systems without self-consistent charge instabilities, only a single diagonalization or construction of the single-particle density matrix is required in each time step. The molecular dynamics simulation scheme can also be applied to a broad range of problems in materialsmore » science, chemistry, and biology.« less

Mass spectrometry. [in organic chemistry

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

1978-01-01

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.

Role of theory in space science

NASA Technical Reports Server (NTRS)

1983-01-01

The goal of theory is to understand how the fundamental laws of physics laws of physics and chemistry give rise to the features of the universe. It is recommended that NASA establish independent theoretical research programs in planetary sciences and in astrophysics similar to the solar-system plasma-physics theory program, which is characterized by stable, long-term support for theorists in university departments, NASA centers, and other organizations engaged in research in topics relevant to present and future space-derived data. It is recommended that NASA keep these programs under review to full benefit from the resulting research and to assure opportunities for inflow of new ideas and investigators. Also, provisions should be made by NASA for the computing needs of the theorists in the programs. Finally, it is recommended that NASA involve knowledgeable theorists in mission planning activities at all levels, from the formulation of long-term scientific strategies through the planning and operation of specific missions.

Integrative Biological Chemistry Program Includes the Use of Informatics Tools, GIS and SAS Software Applications

ERIC Educational Resources Information Center

D'Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

2015-01-01

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning…

Turn on Chemistry Program with a Focus on Community Values.

ERIC Educational Resources Information Center

Kalra, R. M.

The program is a terminal course in chemistry for 9-12 grade students who are non-science majors, low achievers, and/or American Indians. Its objectives include to provide a systematic and practical overview of the discipline of chemistry; to change student behavior through this knowledge; to develop social responsibility, scientific attitude, and…

Reactivity of Household Oxygen Bleaches: A Stepwise Laboratory Exercise in High School Chemistry Course

ERIC Educational Resources Information Center

Nakano, Masayoshi; Ogasawara, Haruka; Wada, Takeshi; Koga, Nobuyoshi

2016-01-01

This paper reports on a learning program designed for high school chemistry classes that involves laboratory exercises using household oxygen bleaches. In this program, students are taught the chemistry of oxygen bleaches through a stepwise inquiry using laboratory exercises organized with different pedagogical intents. Through comparative…

Organic Chemistry for the Gifted.

ERIC Educational Resources Information Center

deBeer, W. H. J.

In response to a serious shortage of chemists in South Africa, gifted secondary school students are enrolled in an enrichment program in organic chemistry and encouraged to consider chemistry or one of its related fields as a career. The introductory portion of the program involves approximately 90 hours over a 3-year period while the advanced…

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…

Symbolic Mathematics Engines in Teaching Chemistry: A Symposium Report

ERIC Educational Resources Information Center

Ellison, Mark

2004-01-01

The use of Symbolic Mathematics Engines (SMEs) in chemical education as a part of the Division of Computers in Chemistry was discussed by a panel of educators at the Symbolic Calculation in Chemistry symposium in Philadelphia in 2004. The panelists agreed that many more topics in chemistry are amenable to SME's exploration and that symbolic…

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...

Discovering H-bonding rules in crystals with inductive logic programming.

PubMed

Ando, Howard Y; Dehaspe, Luc; Luyten, Walter; Van Craenenbroeck, Elke; Vandecasteele, Henk; Van Meervelt, Luc

2006-01-01

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Extensible Computational Chemistry Environment

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

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 the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » 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

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 with practical computer time.

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…

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…

Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997

Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.

A novel computational approach towards the certification of large-scale boson sampling

NASA Astrophysics Data System (ADS)

Huh, Joonsuk

Recent proposals of boson sampling and the corresponding experiments exhibit the possible disproof of extended Church-Turning Thesis. Furthermore, the application of boson sampling to molecular computation has been suggested theoretically. Till now, however, only small-scale experiments with a few photons have been successfully performed. The boson sampling experiments of 20-30 photons are expected to reveal the computational superiority of the quantum device. A novel theoretical proposal for the large-scale boson sampling using microwave photons is highly promising due to the deterministic photon sources and the scalability. Therefore, the certification protocol of large-scale boson sampling experiments should be presented to complete the exciting story. We propose, in this presentation, a computational protocol towards the certification of large-scale boson sampling. The correlations of paired photon modes and the time-dependent characteristic functional with its Fourier component can show the fingerprint of large-scale boson sampling. This work was supported by Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education, Science and Technology(NRF-2015R1A6A3A04059773), the ICT R&D program of MSIP/IITP [2015-019, Fundamental Research Toward Secure Quantum Communication] and Mueunjae Institute for Chemistry (MIC) postdoctoral fellowship.

An Integrative and Collaborative Approach to Creating a Diverse and Computationally Competent Geoscience Workforce

NASA Astrophysics Data System (ADS)

Moore, S. L.; Kar, A.; Gomez, R.

2015-12-01

A partnership between Fort Valley State University (FVSU), the Jackson School of Geosciences at The University of Texas (UT) at Austin, and the Texas Advanced Computing Center (TACC) is engaging computational geoscience faculty and researchers with academically talented underrepresented minority (URM) students, training them to solve grand challenges . These next generation computational geoscientists are being trained to solve some of the world's most challenging geoscience grand challenges requiring data intensive large scale modeling and simulation on high performance computers . UT Austin's geoscience outreach program GeoFORCE, recently awarded the Presidential Award in Excellence in Science, Mathematics and Engineering Mentoring, contributes to the collaborative best practices in engaging researchers with URM students. Collaborative efforts over the past decade are providing data demonstrating that integrative pipeline programs with mentoring and paid internship opportunities, multi-year scholarships, computational training, and communication skills development are having an impact on URMs developing middle skills for geoscience careers. Since 1997, the Cooperative Developmental Energy Program at FVSU and its collaborating universities have graduated 87 engineers, 33 geoscientists, and eight health physicists. Recruited as early as high school, students enroll for three years at FVSU majoring in mathematics, chemistry or biology, and then transfer to UT Austin or other partner institutions to complete a second STEM degree, including geosciences. A partnership with the Integrative Computational Education and Research Traineeship (ICERT), a National Science Foundation (NSF) Research Experience for Undergraduates (REU) Site at TACC provides students with a 10-week summer research experience at UT Austin. Mentored by TACC researchers, students with no previous background in computational science learn to use some of the world's most powerful high performance computing resources to address a grand geosciences problem. Students increase their ability to understand and explain the societal impact of their research and communicate the research to multidisciplinary and lay audiences via near-peer mentoring, poster presentations, and publication opportunities.

An Intensive Training Program for Effective Teaching Assistants in Chemistry

ERIC Educational Resources Information Center

Dragisich, Vera; Keller, Valerie; Zhao, Meishan

2016-01-01

We report an intensive graduate teaching assistant (GTA) training program developed at The University of Chicago. The program has been assessed and has been successful in preparing GTAs for effective discussion and laboratory teaching for both general and organic chemistry. We believe that this training program can provide insightful information…

Development and application of the GIM code for the Cyber 203 computer

NASA Technical Reports Server (NTRS)

Stainaker, J. F.; Robinson, M. A.; Rawlinson, E. G.; Anderson, P. G.; Mayne, A. W.; Spradley, L. W.

1982-01-01

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.

Systemic Changes in the Undergraduate Chemistry Curriculum Program Awards

NASA Astrophysics Data System (ADS)

1995-07-01

The National Science Foundation has awarded over 10 million in awards to four coalitions in the first round of full awards in the Systemic Changes in the Undergraduate Chemistry Curriculum program. Overall, more than 50 institutions, ranging from large universities to four-year and community colleges, are formally involved in these projects. Each of the projects will involve five years of curricular development and evaluation and dissemination of the results by the participating institutions, as described in the abstracts below. We encourage faculty who are interested in becoming involved in any of these projects to contact the appropriate coalition. In addition, we expect to begin offering an emphasis in 1997 under the Course and Curriculum Development program in which faculty can request funds to assist them in adapting and adopting at their own institutions curricular innovations that have been developed by these coalitions. Another round of proposals for full awards was accepted in June of 1995, and we expect to make one more award in the program during FY1996. We do not expect to accept proposals for either planning or full grants in this program in June of 1996. However, the regular Course and Curriculum Development program will continue to accept and fund proposals requesting support for smaller-scale changes in the chemistry curriculum. ChemLinks Coalition: Making Chemical Connections Brock Spencer Beloit College, Beloit, WI 53511 DUE 9455918: FY1995, 705,000; FY 1996, 655,000; FY1997, 655,000; FY1998, 350,00; FY1999, 350,000 The ChemLinks Coalition is undertaking a five-year project to change the way students learn chemistry, increase scientific literacy for all students taking chemistry, and promote the process of educational reform. In collaboration with the ModularChem Consortium, faculty are developing, testing, and disseminating modular course materials that use active and collaborative approaches to learning. These materials, focused on the first two years of the chemistry curriculum, start with interdisciplinary questions important to students and to society (the molecular basis of life, the environment, technology), and in answering them develop an appreciation of how science is actually done. This approach is designed to reach a broader student audience more effectively than do traditional courses, an audience that includes students who are members of groups traditionally underrepresented in science, nonscience majors, and those taking chemistry as a supporting course, as well as chemistry majors. By providing a model for students preparing for careers in teaching, this approach has an impact on Teacher Preparation Programs. Collaboration among faculty from different disciplines and a number of institutions supports and reinforces those who want to make changes. These leading liberal arts colleges (Beloit, Carleton, Colorado, Grinnell, Hope, Kalamazoo, Knox, Lawrence, Macalester, Rhodes, Spelman, St. Olaf, Wooster) and research universities (Chicago, Washington - St. Louis) already have experience working together on chemistry curricular reform. An alliance with the Advanced Technology Environmental Education Center's coalition of 2-year institutions assures an impact on Advanced Technology Education Programs. By using the extensive Project Kaleidoscope network to promote reform, the ChemLinks Coalition involves a much larger and more diverse group of institutions in making systemic and sustainable changes in undergraduate chemistry education. A Workshop Chemistry Curriculum David K. Gosser CUNY City College, New York, NY 10031 DUE 9455920: FY1995, 425,000; FY1996, 400,000; FY1997, 400,000; FY1998, 150,000; FY1999, 150,000 The City College Consortium, which includes ten senior and community colleges at the City University of New York, and the Universities of Pittsburgh, Pennsylvania, and Rochester, is developing and applying widely a new model of teaching. This model, called Workshop Chemistry, introduces participation and mentorship by recent completers of the course. Small group, student-led workshops are integral to the course structure. Every week two workshops, each an hour long, complement the lecture and laboratory components. The workshop model provides a collaborative learning experience that increases student involvement and provides a new role for students as mentors. In Workshop Chemistry, students learn the problem solving, communication, and teamwork skills crucial for success in the workplace while learning chemistry more effectively. Working together with the faculty, students become an active part of the community of the department. A prototype workshop model has been developed at City College in a general chemistry course for science and engineering majors and is being expanded and refined for a broad range of courses including preparatory chemistry, chemistry for allied health sciences, organic chemistry, instrumental, and analytical chemistry. The experience of students as workshop leaders provides a natural introduction to teaching that is being formalized through a Teacher Preparation component of the project. The workshop method is also being exploited and applied in curricula for technician education, an initiative relevant to Advanced Technology Education. The project evaluates Workshop Chemistry and disseminates it beyond the bounds of the consortium. Student Workshop Manuals that include the problem solving, model building, and simulation activities of the workshops are being produced for each course. New project partners will be invited to view workshops, to participate in faculty developments, and to implement pilot workshop courses at their own institutions. Sweeping Change in Manageable Units: A Modular Approach for Chemistry Curriculum Reform C. Bradley Moore University of California-Berkeley, Berkeley, CA 94720 DUE 9455924: FY1995, 755,000; FY1996, 705,000; FY1997, 705,000; FY1998, 350,000; FY1999, 350,000 The purpose of this program is to develop new curricula, materials and methods that will enhance the appreciation and learning of science, especially chemistry, for every undergraduate student such that all college graduates will command the knowledge and skills necessary to permit continued learning, lead productive lives, and make informed decisions. To accomplish this mission, a modular approach to teaching chemistry in the first two years of the undergraduate curriculum is being developed and evaluated. Modules of 1-4 weeks present fundamental chemistry to students in the context of a real-world problem or application and emphasize the links between chemistry and other disciplines. In collaboration with the ChemLinks Coalition, modules are being developed, tested and refined at the two- and four-year colleges and research universities comprising the two consortia. Curriculum materials, including text, lab, and multimedia components suitable for students from diverse cultural and ethnic backgrounds and usable at a wide variety of undergraduate institutions are being produced and distributed by an established publisher. Teaching methods that utilize current understanding of learning processes and emphasize active learning and the full spectrum of modern technologies are being supported, tested, and promulgated. A model support infrastructure for development and assessment of new materials and methods is being provided. A framework for continuous improvement of curricula should result from the work and be institutionalized within the consortium. Faculty workshops and sessions at national and regional meetings will be conducted to guarantee dissemination. Our consortium institutions now participate significantly in pre-service teacher training and education of advanced science or engineering technicians and are developing new programs in these areas. Thus, our program will strongly impact the Advanced Technological Education and Teacher Preparation Programs by developing modular materials appropriate to the task of educating future teachers and technicians. Establishing New Traditions: Revitalizing the Curriculum John W. Moore University of Wisconsin-Madison, Madison, WI 53706 DUE 9455928: FY1995, 949,968; FY1996, 899,999; FY1997, 899,941; FY1998, 499,941; FY1999, $499,742 This project establishes new traditions in the chemistry curriculum that optimize opportunities for all students to learn chemical facts and concepts, develop and pursue interests in chemistry and chemistry-related disciplines, and appreciate how an understanding of chemistry is important to life and living. We are changing fundamentally the ways students, faculty, and administrators view their roles, creating a student-centered, active-learning emphasis. We have a broad range of reforms, each of which is developed, tested, modified, thoroughly evaluated, and widely disseminated. We address five main areas that apply to all levels of the curriculum: student-focused active learning; inquiry-based/open-ended laboratories; interdisciplinary course clusters to create learning communities; a topic-oriented curriculum; and information technology/computer tools. Each development in each area is carefully evaluated, and only the best survive. Evaluation provides important information about the process of transfer of innovations among institutions of different types. To insure that our reforms are useful for all students, our consortium includes industry, public and private four-year institutions, minority institutions, and two-year colleges. The project gives special emphasis to students who choose teaching as a career option by main-streaming these students in courses that benefit them in both content and pedagogy. Students, including those in Science Education, are fully integrated into the development and implementation of the project, working on both research topics and evaluation. The project also gives special emphasis to community college students in Advanced Technological Education programs to ensure that they share in using the newly developed curriculum. The students in the ATE program will clearly benefit by being provided the five main areas of thrust that this coalition is developing. All the students emerge with greater comprehension and better retention of chemical knowledge, improved ability to apply chemical concepts to new problems, enhanced appreciation of the relation between chemistry and other disciplines, and skills that enable them to work effectively in multidisciplinary teams.

Piquing Student Interest with Pharmacology: An Interdisciplinary Program Helps High School Students Learn Biology and Chemistry Principles

ERIC Educational Resources Information Center

Halpin, Myra J.; Hoeffler, Leanne; Schwartz-Bloom, Rochelle D.

2005-01-01

To help students learn science concepts, Pharmacology Education Partnership (PEP)--a science education program that incorporates relevant topics related to drugs and drug abuse into standard biology and chemistry curricula was developed. The interdisciplinary PEP curriculum provides six modules to teach biology and chemistry principles within the…

Mobilizing EPA's Comptox Chemistry Dashboard Data on Mobile Devices (ACS Spring Meeting)

EPA Science Inventory

The EPA’s National Center of Computational Toxicology (NCCT) Chemistry Dashboard provides access to chemistry data for about 720,000 chemical substances. The application is used to source, for example: physicochemical property data, bioassay screening data and functional use, and...

Students' Learning with the Connected Chemistry (CC1) Curriculum: Navigating the Complexities of the Particulate World

ERIC Educational Resources Information Center

Levy, Sharona T.; Wilensky, Uri

2009-01-01

The focus of this study is students' learning with a Connected Chemistry unit, CC1 (denotes Connected Chemistry, chapter 1), a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry (Levy and Wilensky 2009). An investigation was conducted into high-school students' learning with Connected…

A survey of upwind methods for flows with equilibrium and non-equilibrium chemistry and thermodynamics

NASA Technical Reports Server (NTRS)

Grossman, B.; Garrett, J.; Cinnella, P.

1989-01-01

Several versions of flux-vector split and flux-difference split algorithms were compared with regard to general applicability and complexity. Test computations were performed using curve-fit equilibrium air chemistry for an M = 5 high-temperature inviscid flow over a wedge, and an M = 24.5 inviscid flow over a blunt cylinder for test computations; for these cases, little difference in accuracy was found among the versions of the same flux-split algorithm. For flows with nonequilibrium chemistry, the effects of the thermodynamic model on the development of flux-vector split and flux-difference split algorithms were investigated using an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Several numerical examples are presented, including nonequilibrium air chemistry in a high-temperature shock tube and nonequilibrium hydrogen-air chemistry in a supersonic diffuser.

40 CFR 158.310 - Product chemistry data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Product chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Product Chemistry § 158.310 Product chemistry data... the product chemistry data requirements for a particular pesticide product. Notes that apply to an...

76 FR 24922 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-03

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance... announces the following meeting: Name: Proposal Review Panel for Chemistry 1191. Date and Time: May 17, 2011...: Katharine Covert, Acting Deputy Division Director, Chemistry Centers Program, Division of Chemistry, Room...

40 CFR 158.1410 - Residue chemistry data requirements table.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Residue chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Residue Chemistry § 158.1410 Residue chemistry data... the residue chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.1410 - Residue chemistry data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Residue chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Residue Chemistry § 158.1410 Residue chemistry data... the residue chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.310 - Product chemistry data requirements table.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Product chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Product Chemistry § 158.310 Product chemistry data... the product chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.1410 - Residue chemistry data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Residue chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Residue Chemistry § 158.1410 Residue chemistry data... the residue chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.1410 - Residue chemistry data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Residue chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Residue Chemistry § 158.1410 Residue chemistry data... the residue chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.310 - Product chemistry data requirements table.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Product chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Product Chemistry § 158.310 Product chemistry data... the product chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.1410 - Residue chemistry data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Residue chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Residue Chemistry § 158.1410 Residue chemistry data... the residue chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.310 - Product chemistry data requirements table.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Product chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Product Chemistry § 158.310 Product chemistry data... the product chemistry data requirements for a particular pesticide product. Notes that apply to an...

40 CFR 158.310 - Product chemistry data requirements table.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Product chemistry data requirements...) PESTICIDE PROGRAMS DATA REQUIREMENTS FOR PESTICIDES Product Chemistry § 158.310 Product chemistry data... the product chemistry data requirements for a particular pesticide product. Notes that apply to an...

Chemistry on the Go: Review of Chemistry Apps on Smartphones

ERIC Educational Resources Information Center

Libman, Diana; Huang, Ling

2013-01-01

touch-controlled computers such as smartphones and iPods are seeing dramatic growth with increasing adoption rates. This review covers about 30 popular and mostly free apps that can be used to learn chemistry and to serve as reference or research tools. The target…

Richard J. French, Ph.D. | NREL

Science.gov Websites

J. French, Ph.D. Photo of Richard J. French Rick French Researcher IV-Chemistry Richard.French Laboratory equipment design and construction Computer-aided design (CAD) Education Ph.D., Chemistry, Oregon State University B.S., Chemistry, Wheaton College Professional Experience Research Scientist, National

Effectiveness of Using Computer-Assisted Supplementary Instruction for Teaching the Mole Concept

NASA Astrophysics Data System (ADS)

Yalçinalp, Serpil; Geban, Ömer; Özkan, Ilker

This study examined the effect of computer-assisted instruction (CAI), used as a problem-solving supplement to classroom instruction, on students' understanding of chemical formulas and mole concept, their attitudes toward chemistry subjects, and CAI. The objective was to assess the effectiveness of CAI over recitation hours when both teaching methods were used as a supplement to the traditional chemistry instruction. We randomly selected two classes in a secondary school. Each teaching strategy was randomly assigned to one class. The experimental group received supplementary instruction delivered via CAI, while the control group received similar instruction through recitation hours. The data were analyzed using two-way analysis of variance and t-test. It was found that the students who used the CAI accompanied with lectures scored significantly higher than those who attended recitation hours, in terms of school subject achievement in chemistry and attitudes toward chemistry subjects. In addition, there was a significant improvement in the attitudes of students in the experimental group toward the use of computers in a chemistry course. There was no significant difference between the performances of females versus males in each treatment group.Received: 26 April 1994; Revised: 6 April 1995;

Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126

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…

Using a Tablet PC to Enhance Student Engagement and Learning in an Introductory Organic Chemistry Course

ERIC Educational Resources Information Center

Derting, Terry L.; Cox, James R.

2008-01-01

Over the past three decades, computer-based technologies have influenced all aspects of chemistry, including chemical education. Pen-based computing applications, such as the tablet PC, have reemerged in the past few years and are providing new ways for educators to deliver content and engage students inside and outside the classroom and…

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…

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…

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…

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…

Networked Instructional Chemistry: Using Technology To Teach Chemistry

NASA Astrophysics Data System (ADS)

Smith, Stanley; Stovall, Iris

1996-10-01

Networked multimedia microcomputers provide new ways to help students learn chemistry and to help instructors manage the learning environment. This technology is used to replace some traditional laboratory work, collect on-line experimental data, enhance lectures and quiz sections with multimedia presentations, provide prelaboratory training for beginning nonchemistry- major organic laboratory, provide electronic homework for organic chemistry students, give graduate students access to real NMR data for analysis, and provide access to molecular modeling tools. The integration of all of these activities into an active learning environment is made possible by a client-server network of hundreds of computers. This requires not only instructional software but also classroom and course management software, computers, networking, and room management. Combining computer-based work with traditional course material is made possible with software management tools that allow the instructor to monitor the progress of each student and make available an on-line gradebook so students can see their grades and class standing. This client-server based system extends the capabilities of the earlier mainframe-based PLATO system, which was used for instructional computing. This paper outlines the components of a technology center used to support over 5,000 students per semester.

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.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Using Touch-Screen Technology, Apps, and Blogs to Engage and Sustain High School Students' Interest in Chemistry Topics

ERIC Educational Resources Information Center

Kim, Heejoo; Chacko, Priya; Zhao, Jinhui; Montclare, Jin Kim

2014-01-01

As part of an outreach program, we integrated chemistry apps with blogging to enhance the learning experience of students in and outside the classroom. Our outreach program involved college mentors who participated in the development and implementation of chemistry lessons alongside the classroom teacher. Three technology-rich modules that focused…

Promoting Chemistry Learning through Undergraduate Work Experience in the Chemistry Lab: A Practical Approach

ERIC Educational Resources Information Center

Yu, Hong-Bin

2015-01-01

Hiring undergraduate lab assistants in chemistry departments is common in college. However, few studies have focused on promoting undergraduate chemistry learning and thinking skills through this work experience in chemistry teaching laboratories. This article discusses the strategy we implemented in the lab assistant program. The…

76 FR 12996 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-09

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance... Awardees by NSF Division of Chemistry (CHE), 1191. Dates and Times: March 31, 2011; 8 a.m.-5:30 p.m. April... Director, Chemistry Centers Program, Division of Chemistry, Room 1055, National Science Foundation, 4201...

76 FR 6499 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-04

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance... Awardees by NSF Division of Chemistry (1191). Dates and Times: February 17, 2011; 8 a.m.-6 p.m. February 18... Director, Chemistry Centers Program, Division of Chemistry, Room 1055, National Science Foundation, 4201...

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...

CPT Special Report: Survey of Ph.D. Programs in Chemistry.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1997

1997-01-01

Presents preliminary results from a survey taken by the American Chemical Society (ACS) Committee on Professional Training (CPT) to determine the current practices among 155 Ph.D. programs in chemistry. (DKM)

Focus Groups and Exit Interviews Are Components of Chemistry Department Program Assessment

NASA Astrophysics Data System (ADS)

Dreisbach, Joseph H.; Hogan, Thomas P.; Stamford, Anne Marie; Greggo, John W.

1998-10-01

The Chemistry Department, in conjunction with the Assessment and Institutional Research Office (AIRO) and the Department of Counseling and Human Services developed an assessment plan which incorporates use of focus groups and exit interviews. As part of the five-year departmental review, a number of student focus groups were facilitated to evaluate (a) the freshman and sophomore organic chemistry programs which also service other departments and (b) the upper division lecture and laboratory program for majors. Use of direct conversation in program assessment yields less ambiguous results compared with other methods because responses can be clarified with careful follow up questions. Success of this project gave rise to use of annual exit interviews with graduating seniors from the chemistry department. The approach described can easily be modified to meet the needs of any academic setting.

Laboratory Sequence in Computational Methods for Introductory Chemistry

NASA Astrophysics Data System (ADS)

Cody, Jason A.; Wiser, Dawn C.

2003-07-01

A four-exercise laboratory sequence for introductory chemistry integrating hands-on, student-centered experience with computer modeling has been designed and implemented. The progression builds from exploration of molecular shapes to intermolecular forces and the impact of those forces on chemical separations made with gas chromatography and distillation. The sequence ends with an exploration of molecular orbitals. The students use the computers as a tool; they build the molecules, submit the calculations, and interpret the results. Because of the construction of the sequence and its placement spanning the semester break, good laboratory notebook practices are reinforced and the continuity of course content and methods between semesters is emphasized. The inclusion of these techniques in the first year of chemistry has had a positive impact on student perceptions and student learning.

77 FR 5852 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance with the Federal Advisory Committee Act (Pub. L. 92- 463, as amended), the National Science Foundation... and Computation for Chemistry Presentations. 11:45 a.m.-1 p.m. Closed--Executive Session, review and...

Public Access to Environmental Chemistry Data via the CompTox Chemistry Dashboard (ACS Fall Meeting 6 of 12)

EPA Science Inventory

The National Center for Computational Toxicology (NCCT) has assembled and delivered an enormous quantity and diversity of data for the environmental sciences through the CompTox Chemistry Dashboard. These data include high-throughput in vitro screening data, in vivo and functiona...

Computational and Physical Analysis of Catalytic Compounds

NASA Astrophysics Data System (ADS)

Wu, Richard; Sohn, Jung Jae; Kyung, Richard

2015-03-01

Nanoparticles exhibit unique physical and chemical properties depending on their geometrical properties. For this reason, synthesis of nanoparticles with controlled shape and size is important to use their unique properties. Catalyst supports are usually made of high-surface-area porous oxides or carbon nanomaterials. These support materials stabilize metal catalysts against sintering at high reaction temperatures. Many studies have demonstrated large enhancements of catalytic behavior due to the role of the oxide-metal interface. In this paper, the catalyzing ability of supported nano metal oxides, such as silicon oxide and titanium oxide compounds as catalysts have been analyzed using computational chemistry method. Computational programs such as Gamess and Chemcraft has been used in an effort to compute the efficiencies of catalytic compounds, and bonding energy changes during the optimization convergence. The result illustrates how the metal oxides stabilize and the steps that it takes. The graph of the energy computation step(N) versus energy(kcal/mol) curve shows that the energy of the titania converges faster at the 7th iteration calculation, whereas the silica converges at the 9th iteration calculation.

Chemistry 20-30: Program of Studies.

ERIC Educational Resources Information Center

Alberta Dept. of Education, Edmonton. Curriculum Branch.

Presented in English and French, Chemistry 20-30 is an academic program that helps students in Alberta, Canada, better understand and apply fundamental concepts and skills. The major goals of the program are: (1) to develop in students an understanding of the interconnecting ideas and principles that transcend and unify the natural science…

A Field Study Program in Analytical Chemistry for College Seniors.

ERIC Educational Resources Information Center

Langhus, D. L.; Flinchbaugh, D. A.

1986-01-01

Describes an elective field study program at Moravian College (Pennsylvania) in which seniors in analytical chemistry obtain first-hand experience at Bethlehem Steel Corporation. Discusses the program's planning phase, some method development projects done by students, experiences received in laboratory operations, and the evaluation of student…

Employing Popular Children's Literature to Teach Elementary School Chemistry: An Engaging Outreach Program

ERIC Educational Resources Information Center

Wally, Laura M.; Levinger, Nancy E.; Grainger, David W.

2005-01-01

A chemistry outreach program to enthuse students of elementary school levels through employing popular children's literature Harry Potter is presented. The outreach activity performance found the students discovering new skills, learning more about science, and participating enthusiastically in the program without any added incentive from their…

Introductory Linear Regression Programs in Undergraduate Chemistry.

ERIC Educational Resources Information Center

Gale, Robert J.

1982-01-01

Presented are simple programs in BASIC and FORTRAN to apply the method of least squares. They calculate gradients and intercepts and express errors as standard deviations. An introduction of undergraduate students to such programs in a chemistry class is reviewed, and issues instructors should be aware of are noted. (MP)

Exemplary Programs in Physics, Chemistry, Biology, and Earth Science.

ERIC Educational Resources Information Center

Yager, Robert E., Ed.

The 1982 Search for Excellence in Science Education project has identified 50 exemplary programs in physics, chemistry, biology, and earth science. Descriptions of four of these programs and the criteria used in their selection are presented. The first section reviews the direction established by Project Synthesis in searching for exemplary…

Additional support for the TDK/MABL computer program

NASA Technical Reports Server (NTRS)

Nickerson, G. R.; Dunn, Stuart S.

1993-01-01

An advanced version of the Two-Dimensional Kinetics (TDK) computer program was developed under contract and released to the propulsion community in early 1989. Exposure of the code to this community indicated a need for improvements in certain areas. In particular, the TDK code needed to be adapted to the special requirements imposed by the Space Transportation Main Engine (STME) development program. This engine utilizes injection of the gas generator exhaust into the primary nozzle by means of a set of slots. The subsequent mixing of this secondary stream with the primary stream with finite rate chemical reaction can have a major impact on the engine performance and the thermal protection of the nozzle wall. In attempting to calculate this reacting boundary layer problem, the Mass Addition Boundary Layer (MABL) module of TDK was found to be deficient in several respects. For example, when finite rate chemistry was used to determine gas properties, (MABL-K option) the program run times became excessive because extremely small step sizes were required to maintain numerical stability. A robust solution algorithm was required so that the MABL-K option could be viable as a rocket propulsion industry design tool. Solving this problem was a primary goal of the phase 1 work effort.

ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe; Paulus, Beate; Hege, Hans-Christian; Schild, Axel

2016-06-15

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

PubMed Central

2014-01-01

Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

Preparing Physics and Chemistry Teachers at the University of Arizona

NASA Astrophysics Data System (ADS)

Novodvorsky, Ingrid

2006-04-01

Beginning in 2000, science majors at the University of Arizona who wish to teach in middle or high schools have enrolled in the College of Science Teacher Preparation Program (CoS TPP). Students in the program take General Education courses, content courses, and science pedagogy courses that make them eligible for teacher certification. Students can remain in their science degree programs, and take the required science pedagogy courses, or they can enroll in a BS in Science Education degree that includes the pedagogy courses, with concentrations available in Biology, Chemistry, Earth Science, and Physics. Science educators from six different departments, two permanent Adjunct Instructors, and two Teachers in Residence teach the program's courses. (One of the Teachers in Residence is supported by the PhysTEC project.) Most of the pedagogy courses include field experiences in area science classrooms; the program works with some 115 mentor teachers from throughout the Tucson area, who host preservice teachers in their field experiences. In the first six years of the program, 14 program graduates have been chemistry and physics teachers. This compares to a total of six chemistry and physics teachers produced by the College of Education program in the four years preceding the creation of the CoS TPP. In this presentation, I will describe the unique features of the courses that prospective chemistry and physics teachers take and the field experiences in which they participate. In addition, I will describe how PhysTEC-supplied resources have been used to improve the program, and the ways in which we are assessing the program's success.

PRN 98-1: Self-Certification of Product Chemistry Data with Attachments

EPA Pesticide Factsheets

The Office of Pesticide Programs has established a self-certification program for certain product chemistry data of manufacturing-use products and end-use products produced by a non-integrated formulation system.

Open Babel: An open chemical toolbox

PubMed Central

2011-01-01

Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

Lincoln Advanced Science and Engineering Reinforcement (LASER) program

NASA Technical Reports Server (NTRS)

Williams, Willie E.

1989-01-01

Lincoln University, under the Lincoln Advanced Science and Engineering Reinforcement (LASER) Program, has identified and successfully recruited over 100 students for majors in technical fields. To date, over 70 percent of these students have completed or will complete technical degrees in engineering, physics, chemistry, and computer science. Of those completing the undergraduate degree, over 40 percent have gone on to graduate and professional schools. This success is attributable to well planned approaches to student recruitment, training, personal motivation, retention, and program staff. Very closely coupled to the above factors is a focus designed to achieve excellence in program services and student performance. Future contributions by the LASER Program to the pool of technical minority graduates will have a significant impact. This is already evident from the success of the students that began the first year of the program. With program plans to refine many of the already successful techniques, follow-on activities are expected to make even greater contributions to the availability of technically trained minorities. For example, undergraduate research exposure, broadened summer, and co-op work experiences will be enhanced.

The Inorganic Illustrator: A 3-D Graphical Supplement for Inorganic and Bioinorganic Chemistry Courses Distributed on CD-ROM

NASA Astrophysics Data System (ADS)

Childs, Scott L.; Hagen, Karl S.

1996-10-01

The visualization of molecular and solid state chemical structures in three dimensions is a particularly difficult problem for students to overcome when the primary means of communication is the two-dimensional world of textbooks, blackboards, and overhead projector screens. Recent editions of popular textbooks in organic, inorganic, and biochemistry have included stereoviews of molecules to aid the student, and stereoviews of crystal structures have been used in inorganic chemistry publications for many years. These are powerful aids for visualizing complex molecules, but with the exception of the biochemistry text mentioned above, they are limited to single, static images generally in black and white. Molecular model kits are routinely used very effectively in organic chemistry but their utility in inorganic chemistry is limited to all but the most simple molecules encountered. Now that personal computers are generally accessible and multimedia tools are starting to make an appearance in chemistry lecture halls (1), we can make our inorganic and bioinorganic chemistry and crystallography lectures come alive with the aid of the computer-based resources, which are the essence of this project. As part of this project we are accumulating a database of representative crystal structures of main group molecules, coordination complexes, organometallic compounds, small metalloproteins, bioinorganic model complexes, clusters, and solid state materials in Chem3D Plus format to be viewed with Chem3D Viewer, which is free software from Cambridge Scientific Computing. We are also generating a library of high-quality graphic images of these same molecules and structures using Cerius2 package from Molecular Simulations. These include polyhedral representations of clusters and solid state structures (see Fig. 1). Figure 1. Representation of the user interface: the title page and an example of polyhedral and ball-and-stick representation of an octanuclear iron-oxo cluster. The files of solid state structures will not be limited to single unit cells that are common in textbooks, but will present multiple cells such that the extended lattice of the material is evident. Navigation through these resources is through a unique open hypertext-based interface using Authorware, which allows the user to create complex applications that support movies, animation, and other graphics seamlessly. Chem3D Viewer is a powerful program that allows not only multiple visualization modes, but also the detailed analysis of both bonded and nonbonded distances and angles. This is particularly useful for recognizing symmetry elements within molecules, as the student can precisely align atoms along the screen's Cartesian axes or within its planes and subsequently rotate the molecules about the axes at precise angles. We are developing stand-alone interactive tutorials to assign point groups to molecules and clusters. In addition, tutorials are being developed that show how the Chem3D Viewer software can be most effectively used in a classroom setting for lectures or for home or lab use by the students. The Inorganic Illustrator will be made available to the education community for the cost of materials plus shipping and handling. Acknowledgment We would like to thank the NSF for financial support through the Division of Undergraduate Education Course and Curriculum Program (DUE-CCD 9455567). Literature Cited 1. Illman, D. L. Chem. Eng. News 1994, 72(May 9), 34.

Rural Outreach Chemistry for Kids (R.O.C.K.): The Program and Its Evaluation

ERIC Educational Resources Information Center

Lynch, Mark; Zovinka, Edward P.; Zhang, Lening; Hruska, Jenna L.; Lee, Angela

2005-01-01

The Rural Outreach Chemistry for Kids (R.O.C.K.) program was designed as a service-learning project for students at Saint Francis University to serve the local communities by organizing chemistry activities in high schools. It was initiated in 1995 and has involved a large number of Saint Francis University students and local high school students.…

Laboratory experiments in the study of the chemistry of the outer planets.

PubMed

Scattergood, T W

1987-01-01

The investigation of chemical evolution of bodies in our solar system has, in the past, included observations, theoretical modeling, and laboratory simulations. Of these programs, the last one has been the most criticized due to the inherent difficulties in accurately recreating alien environments in the laboratory. Processes such as wall reactions and changes in chemistry due to difficulties in achieving realistic conditions of temperature, pressure, composition, and energy flux may yield results which are not truly representative of the systems being modeled. However, many laboratory studies have been done which have yielded data useful in planetary science. Gross simulations of atmospheric chemistry have placed constraints on the nature of complex molecules expected in planetary atmospheres. More precise studies of specific chemical processes have provided information about the sources and properties of product gases and aerosols. Determinations of basic properties such as spectral features and reaction rate constants yield data useful in the interpretation of observations and in computational modeling. Alone, and in conjunction with modeling, laboratory experiments will continue to be used to further our understanding of the outer solar system, and some experiments that need to be done are listed.

The Effectiveness of a Computer-Assisted Instruction Package in Supplementing Teaching of Selected Concepts in High School Chemistry: Writing Formulas and Balancing Chemical Equations.

ERIC Educational Resources Information Center

Wainwright, Camille L.

Four classes of high school chemistry students (N=108) were randomly assigned to experimental and control groups to investigate the effectiveness of a computer assisted instruction (CAI) package during a unit on writing/naming of chemical formulas and balancing equations. Students in the experimental group received drill, review, and reinforcement…

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…

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…

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…

XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely available to the scientific community for use and collaboration under the GNU Public License. Running time: User dependent. The program runs until stopped by the user.

Attitudes and Beliefs of Pathology Residents Regarding the Subspecialty of Clinical Chemistry: Results of a Survey.

PubMed

Haidari, Mehran; Yared, Marwan; Olano, Juan P; Alexander, C Bruce; Powell, Suzanne Z

2017-02-01

-Previous studies suggest that training in pathology residency programs does not adequately prepare pathology residents to become competent in clinical chemistry. -To define the beliefs of pathology residents in the United States regarding their preparation for practicing clinical chemistry in their career, their attitude toward the discipline, and the attractiveness of clinical chemistry as a career. -The residents of all pathology residency programs in the United States were given the opportunity to participate in an online survey. -Three hundred thirty-six pathology residents responded to the survey. Analysis of the survey results indicates that pathology residents are more likely to believe that their income may be lower if they select a career that has a clinical chemistry focus and that their faculty do not value clinical chemistry as much as the anatomic pathology part of the residency. Residents also report that clinical chemistry is not as enjoyable as anatomic pathology rotations during residency or preferable as a sole career path. A large proportion of residents also believe that they will be slightly prepared or not prepared to practice clinical chemistry by the end of their residency and that they do not have enough background and/or time to learn clinical chemistry during their residency programs to be able to practice this specialty effectively post graduation. -Our survey results suggest that many pathology residents do not have a positive attitude toward clinical chemistry and do not experience a supportive learning environment with an expectation that they will become competent in clinical chemistry with a residency alone.

Numerical computation of linear instability of detonations

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry; Kasimov, Aslan

2017-11-01

We propose a method to study linear stability of detonations by direct numerical computation. The linearized governing equations together with the shock-evolution equation are solved in the shock-attached frame using a high-resolution numerical algorithm. The computed results are processed by the Dynamic Mode Decomposition technique to generate dispersion relations. The method is applied to the reactive Euler equations with simple-depletion chemistry as well as more complex multistep chemistry. The results are compared with those known from normal-mode analysis. We acknowledge financial support from King Abdullah University of Science and Technology.

Enabling drug discovery project decisions with integrated computational chemistry and informatics

NASA Astrophysics Data System (ADS)

Tsui, Vickie; Ortwine, Daniel F.; Blaney, Jeffrey M.

2017-03-01

Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.

Building "My First NMRviewer": A Project Incorporating Coding and Programming Tasks in the Undergraduate Chemistry Curricula

ERIC Educational Resources Information Center

Arrabal-Campos, Francisco M.; Cortés-Villena, Alejandro; Fernández, Ignacio

2017-01-01

This paper presents a programming project named NMRviewer that allows students to visualize transformed and processed 1 H NMR data in an accessible, interactive format while allowing instructors to incorporate programming content into the chemistry curricula. Using the MATLAB graphical user interface development environment (GUIDE), students can…

An Exemplary Program in Higher Education for Chemists, Engineers, and Chemistry Teachers.

ERIC Educational Resources Information Center

Ayers, Jerry B.; And Others

This paper presents the rationale, structure, and specifications for a model program for the preparation of chemists, chemical engineers, and high school chemistry teachers. The model (an application of systems technology to program development in higher education) is based on the structure provided by the Georgia Educational Model Specifications…

A Three-Year Chemistry Seminar Program Focusing on Career Development Skills

ERIC Educational Resources Information Center

Tucci, Valerie K.; O'Connor, Abby R.; Bradley, Lynn M.

2014-01-01

An innovative, three-year seminar program was developed for undergraduates at The College of New Jersey (TCNJ) that supplements the core chemistry curriculum by teaching the auxiliary skills necessary for life as a professional chemist. Advising, good laboratory practice, and information literacy are the strategic components of this program that…

Computational Investigations for Undergraduate Organic Chemistry: Predicting the Mechanism of the Ritter Reaction

NASA Astrophysics Data System (ADS)

Hessley, Rita K.

2000-02-01

In an effort to engage students more deeply in their laboratory work and provide them with valuable learning experiences in the applications and limitations of computational chemistry as a research tool, students are instructed to carry out a computational pre-lab exercise. Before carrying out a laboratory experiment that investigates the mechanism for the formation of N-t-butylbenzamide, students construct and obtain heats of formation for reactants, products, postulated reaction intermediates, and one transition state structure for each proposed mechanism. This is designed as a companion to an open-ended laboratory experiment that hones skills learned early in most traditional organic chemistry courses. The incorporation of a preliminary computational exercise enables students to move beyond guessing what the outcome of the reaction will be. It challenges them to test what they believe they "know" about such fundamental concepts as stability of carbocations, or the significance and utility of thermodynamic data relative to kinetic data. On the basis of their computations and their own experimental data, students then verify or dispute their hypothesis, finally arriving at a defensible and logical conclusion about the course of the reaction mechanism. The manner of implementation of the exercise and typical computational data are described.

Physiology undergraduate degree requirements in the U.S.

PubMed

VanRyn, Valerie S; Poteracki, James M; Wehrwein, Erica A

2017-12-01

Course-level learning objectives and core concepts for undergraduate physiology teaching exist. The next step is to consider how these resources fit into generalizable program-level guidelines for Bachelor of Science (BS) degrees in Physiology. In the absence of program-level guidelines for Physiology degree programs, we compiled a selective internal report to review degree requirements from 18 peer BS programs entitled "Physiology" in the United States (U.S.). There was a range of zero to three required semesters of math, physics, physics laboratory, general biology, biology laboratory, general chemistry, chemistry laboratory, organic chemistry, organic chemistry laboratory, biochemistry, biochemistry laboratory, anatomy, anatomy laboratory, core systems physiology, and physiology laboratory. Required upper division credits ranged from 11 to 31 and included system-specific, exercise and environmental, clinically relevant, pathology/disease-related, and basic science options. We hope that this information will be useful for all programs that consider themselves to be physiology, regardless of name. Reports such as this can serve as a starting point for collaboration among BS programs to improve physiology undergraduate education and best serve our students. Copyright © 2017 the American Physiological Society.

Structure Identification Using High Resolution Mass Spectrometry Data and the EPAs Chemistry Dashboard (ACS Fall meeting)

EPA Science Inventory

The iCSS Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and Exp...

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

PubMed

Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

2012-05-21

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

A two-dimensional numerical simulation of a supersonic, chemically reacting mixing layer

NASA Technical Reports Server (NTRS)

Drummond, J. Philip

1988-01-01

Research has been undertaken to achieve an improved understanding of physical phenomena present when a supersonic flow undergoes chemical reaction. A detailed understanding of supersonic reacting flows is necessary to successfully develop advanced propulsion systems now planned for use late in this century and beyond. In order to explore such flows, a study was begun to create appropriate physical models for describing supersonic combustion, and to develop accurate and efficient numerical techniques for solving the governing equations that result from these models. From this work, two computer programs were written to study reacting flows. Both programs were constructed to consider the multicomponent diffusion and convection of important chemical species, the finite rate reaction of these species, and the resulting interaction of the fluid mechanics and the chemistry. The first program employed a finite difference scheme for integrating the governing equations, whereas the second used a hybrid Chebyshev pseudospectral technique for improved accuracy.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

PubMed

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

2017-03-27

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Analytical Chemistry Division annual progress report for period ending December 31, 1985

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

Shultz, W.D.

1986-05-01

Progress reports are presented for the four major sections of the division: analytical spectroscopy, radioactive materials laboratories, inorganic chemistry, and organic chemistry. A brief discussion of the division's role in the Laboratory's Environmental Restoration and Facilities Upgrade is given. Information about quality assurance and safety programs is presented, along with a tabulation of analyses rendered. Publications, oral presentations, professional activities, educational programs, and seminars are cited.

Chemistry for the Life Sciences. An Instructor Resource Guide. Appendix to a Final Report on the Paraprofessional Rurally Oriented Family Home Health Training Program.

ERIC Educational Resources Information Center

Odom, H. Clyde; Myer, Donna Foster

This instructor's resource guide, one in a series of products from a project to develop an associate degree program for paraprofessional rural family health promoters, deals with teaching chemistry for the life sciences. Covered in the first section of the volume are the role of chemistry in rural health promotional training, general objectives…

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

The international water conference proceedings

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

Guseman, J.R.

1984-10-01

This book provides information on computer applications to water chemistry control, groundwater, membrane technology, instrumentation/analytical techniques and ion exchange. Other topics of discussion include cooling water, biocontrol, the hydraulic properties of ion exchange resins, steam electric power plant aqueous discharges and colorimetric determination of trace benzotriazole or tolytriazole. Water chemistry guidelines for large steam generating power plants is discussed, as well as wastewater treatment, boiler water conditioning and ion exchange/computer related topics.

Understanding Solubility through Excel Spreadsheets

NASA Astrophysics Data System (ADS)

Brown, Pamela

2001-02-01

This article describes assignments related to the solubility of inorganic salts that can be given in an introductory general chemistry course. Le Châtelier's principle, solubility, unit conversion, and thermodynamics are tied together to calculate heats of solution by two methods: heats of formation and an application of the van't Hoff equation. These assignments address the need for math, graphing, and computer skills in the chemical technology program by developing skill in the use of Microsoft Excel to prepare spreadsheets and graphs and to perform linear and nonlinear curve-fitting. Background information on the value of understanding and predicting solubility is provided.

CHARMM: The Biomolecular Simulation Program

PubMed Central

Brooks, B.R.; Brooks, C.L.; MacKerell, A.D.; Nilsson, L.; Petrella, R.J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A.R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R.W.; Post, C.B.; Pu, J.Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D.M.; Karplus, M.

2009-01-01

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. In addition, the CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This paper provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM paper in 1983. PMID:19444816

Deep learning for computational chemistry.

PubMed

Goh, Garrett B; Hodas, Nathan O; Vishnu, Abhinav

2017-06-15

The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the last few years, we have seen the transformative impact of deep learning in many domains, particularly in speech recognition and computer vision, to the extent that the majority of expert practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. In this review, we provide an introductory overview into the theory of deep neural networks and their unique properties that distinguish them from traditional machine learning algorithms used in cheminformatics. By providing an overview of the variety of emerging applications of deep neural networks, we highlight its ubiquity and broad applicability to a wide range of challenges in the field, including quantitative structure activity relationship, virtual screening, protein structure prediction, quantum chemistry, materials design, and property prediction. In reviewing the performance of deep neural networks, we observed a consistent outperformance against non-neural networks state-of-the-art models across disparate research topics, and deep neural network-based models often exceeded the "glass ceiling" expectations of their respective tasks. Coupled with the maturity of GPU-accelerated computing for training deep neural networks and the exponential growth of chemical data on which to train these networks on, we anticipate that deep learning algorithms will be a valuable tool for computational chemistry. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

19. VIEW OF THE GENERAL CHEMISTRY LABORATORY IN BUILDING 881. ...

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

19. VIEW OF THE GENERAL CHEMISTRY LABORATORY IN BUILDING 881. (4/12/62) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

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

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

77 FR 42341 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-18

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance... announces the following meeting: Name: ChemMatCARS Site Visit, 2011 Awardees by NSF Division of Chemistry.... Carlos Murillo, Program Director, Division of Chemistry, Room 1055, National Science Foundation, 4201...

What Teaching Teaches: Mentoring and the Performance Gains of Mentors

NASA Astrophysics Data System (ADS)

Amaral, Katie E.; Vala, Martin

2009-05-01

A peer mentoring program was added to an introductory chemistry course at a large university. The introductory chemistry course prepares students with little or no previous chemistry background to enter the mainstream general chemistry sequence and is part lecture and part small-group problem-solving. Faculty instructors are responsible for the lecture while peer mentors handle the group problem-solving portion. Peer mentors, recruited from previous introductory chemistry course, are chosen for their knowledge of the material and their helpfulness in group activities. While a number of studies on peer mentoring have reported the benefits to the mentored students, the present study looks at the benefits to the mentors. Grade enhancement in the main-stream general chemistry sequence, withdrawal rates, and number of additional chemistry courses taken by the mentors have been compared to under-prepared students who took the introductory chemistry course but did not serve as mentors and well-prepared students who did not need the introductory chemistry course. Our results show that mentors earned higher grades, withdrew from chemistry courses at a lower rate, and took more courses in chemistry than their counterparts. The enhanced achievement and retention of the mentors in chemistry suggests that programs that encourage under-prepared students to mentor are worthwhile endeavors.