NREL Receives Editors' Choice Awards for Supercomputer Research | News |

Science.gov Websites

function," Beckham said. "We followed up these molecular simulations with experimental work to Award. The awards recognize outstanding research in computational molecular science and engineering Mechanisms of Cellulose-Active Enzymes Using Molecular Simulation" at the AIChE 2014 Annual Meeting

Grid computing in large pharmaceutical molecular modeling.

PubMed

Claus, Brian L; Johnson, Stephen R

2008-07-01

Most major pharmaceutical companies have employed grid computing to expand their compute resources with the intention of minimizing additional financial expenditure. Historically, one of the issues restricting widespread utilization of the grid resources in molecular modeling is the limited set of suitable applications amenable to coarse-grained parallelization. Recent advances in grid infrastructure technology coupled with advances in application research and redesign will enable fine-grained parallel problems, such as quantum mechanics and molecular dynamics, which were previously inaccessible to the grid environment. This will enable new science as well as increase resource flexibility to load balance and schedule existing workloads.

| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to

Demystifying computer science for molecular ecologists.

PubMed

Belcaid, Mahdi; Toonen, Robert J

2015-06-01

In this age of data-driven science and high-throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long-standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373-389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context-specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade-offs that are not obvious to the uninitiated. © 2015 John Wiley & Sons Ltd.

Molecular computational elements encode large populations of small objects

NASA Astrophysics Data System (ADS)

Prasanna de Silva, A.; James, Mark R.; McKinney, Bernadine O. F.; Pears, David A.; Weir, Sheenagh M.

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1nm) and large `on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100μm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a `wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.

Molecular computational elements encode large populations of small objects.

PubMed

de Silva, A Prasanna; James, Mark R; McKinney, Bernadine O F; Pears, David A; Weir, Sheenagh M

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1 nm) and large 'on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100 microm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a 'wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.

Strategic Vision for Adopting 21st Century Science Methodologies

EPA Pesticide Factsheets

To better protect human health and the environment, EPA’s OPP is developing and evaluating new technologies in molecular, cellular, computational sciences to supplement or replace more traditional methods of toxicity testing and risk assessment.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

77 FR 57571 - Center For Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-18

...: Genes, Genomes, and Genetics Integrated Review Group; Genomics, Computational Biology and Technology... Reproductive Sciences Integrated Review Group; Cellular, Molecular and Integrative Reproduction Study Section...: Immunology Integrated Review Group; Cellular and Molecular Immunology--B Study Section. [[Page 57572

Biotechnology Computing: Information Science for the Era of Molecular Medicine.

ERIC Educational Resources Information Center

Masys, Daniel R.

1989-01-01

The evolution from classical genetics to biotechnology, an area of research involving key macromolecules in living cells, is chronicled and the current state of biotechnology is described, noting related advances in computing and clinical medicine. (MSE)

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

EPA Science Inventory

The US EPA National Center for Computational Toxicology (NCCT) has a mission to integrate modern computing and information technology with molecular biology to improve Agency prioritization of data requirements and risk assessment of chemicals. Recognizing the critical need for ...

Computational Science in Armenia (Invited Talk)

NASA Astrophysics Data System (ADS)

Marandjian, H.; Shoukourian, Yu.

This survey is devoted to the development of informatics and computer science in Armenia. The results in theoretical computer science (algebraic models, solutions to systems of general form recursive equations, the methods of coding theory, pattern recognition and image processing), constitute the theoretical basis for developing problem-solving-oriented environments. As examples can be mentioned: a synthesizer of optimized distributed recursive programs, software tools for cluster-oriented implementations of two-dimensional cellular automata, a grid-aware web interface with advanced service trading for linear algebra calculations. In the direction of solving scientific problems that require high-performance computing resources, examples of completed projects include the field of physics (parallel computing of complex quantum systems), astrophysics (Armenian virtual laboratory), biology (molecular dynamics study of human red blood cell membrane), meteorology (implementing and evaluating the Weather Research and Forecast Model for the territory of Armenia). The overview also notes that the Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia has established a scientific and educational infrastructure, uniting computing clusters of scientific and educational institutions of the country and provides the scientific community with access to local and international computational resources, that is a strong support for computational science in Armenia.

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.

Computer-aided design of polymers and composites

NASA Technical Reports Server (NTRS)

Kaelble, D. H.

1985-01-01

This book on computer-aided design of polymers and composites introduces and discusses the subject from the viewpoint of atomic and molecular models. Thus, the origins of stiffness, strength, extensibility, and fracture toughness in composite materials can be analyzed directly in terms of chemical composition and molecular structure. Aspects of polymer composite reliability are considered along with characterization techniques for composite reliability, relations between atomic and molecular properties, computer aided design and manufacture, polymer CAD/CAM models, and composite CAD/CAM models. Attention is given to multiphase structural adhesives, fibrous composite reliability, metal joint reliability, polymer physical states and transitions, chemical quality assurance, processability testing, cure monitoring and management, nondestructive evaluation (NDE), surface NDE, elementary properties, ionic-covalent bonding, molecular analysis, acid-base interactions, the manufacturing science, and peel mechanics.

ISMB 2016 offers outstanding science, networking, and celebration

PubMed Central

Fogg, Christiana

2016-01-01

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 23 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. ISMB 2016 will be the year's most important computational biology event globally. The conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems. ISMB 2016 offers the strongest scientific program and the broadest scope of any international bioinformatics/computational biology conference. Building on past successes, the conference is designed to cater to variety of disciplines within the bioinformatics/computational biology community.  ISMB 2016 takes place July 8 - 12 at the Swan and Dolphin Hotel in Orlando, Florida, United States. For two days preceding the conference, additional opportunities including Satellite Meetings, Student Council Symposium, and a selection of Special Interest Group Meetings and Applied Knowledge Exchange Sessions (AKES) are all offered to enable registered participants to learn more on the latest methods and tools within specialty research areas. PMID:27347392

ISMB 2016 offers outstanding science, networking, and celebration.

PubMed

Fogg, Christiana

2016-01-01

The annual international conference on Intelligent Systems for Molecular Biology (ISMB) is the major meeting of the International Society for Computational Biology (ISCB). Over the past 23 years the ISMB conference has grown to become the world's largest bioinformatics/computational biology conference. ISMB 2016 will be the year's most important computational biology event globally. The conferences provide a multidisciplinary forum for disseminating the latest developments in bioinformatics/computational biology. ISMB brings together scientists from computer science, molecular biology, mathematics, statistics and related fields. Its principal focus is on the development and application of advanced computational methods for biological problems. ISMB 2016 offers the strongest scientific program and the broadest scope of any international bioinformatics/computational biology conference. Building on past successes, the conference is designed to cater to variety of disciplines within the bioinformatics/computational biology community.  ISMB 2016 takes place July 8 - 12 at the Swan and Dolphin Hotel in Orlando, Florida, United States. For two days preceding the conference, additional opportunities including Satellite Meetings, Student Council Symposium, and a selection of Special Interest Group Meetings and Applied Knowledge Exchange Sessions (AKES) are all offered to enable registered participants to learn more on the latest methods and tools within specialty research areas.

Molecular mechanics and dynamics characterization of an in silico mutated protein: a stand-alone lab module or support activity for in vivo and in vitro analyses of targeted proteins.

PubMed

Chiang, Harry; Robinson, Lucy C; Brame, Cynthia J; Messina, Troy C

2013-01-01

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems. Computer simulations of molecular events can now be accomplished quickly and with standard computer technology. Also, simulation software is freely available for most computing platforms, and online support for the novice user is ample. We have therefore created a molecular dynamics laboratory module to enhance undergraduate student understanding of molecular events underlying organismal phenotype. This module builds on a previously described project in which students use site-directed mutagenesis to investigate functions of conserved sequence features in members of a eukaryotic protein kinase family. In this report, we detail the laboratory activities of a MD module that provide a complement to phenotypic outcomes by providing a hypothesis-driven and quantifiable measure of predicted structural changes caused by targeted mutations. We also present examples of analyses students may perform. These laboratory activities can be integrated with genetics or biochemistry experiments as described, but could also be used independently in any course that would benefit from a quantitative approach to protein structure-function relationships. Copyright © 2013 Wiley Periodicals, Inc.

Life sciences and environmental sciences

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

Not Available

1992-02-01

The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment,more » applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.« less

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

Molecular robots with sensors and intelligence.

PubMed

Hagiya, Masami; Konagaya, Akihiko; Kobayashi, Satoshi; Saito, Hirohide; Murata, Satoshi

2014-06-17

CONSPECTUS: What we can call a molecular robot is a set of molecular devices such as sensors, logic gates, and actuators integrated into a consistent system. The molecular robot is supposed to react autonomously to its environment by receiving molecular signals and making decisions by molecular computation. Building such a system has long been a dream of scientists; however, despite extensive efforts, systems having all three functions (sensing, computation, and actuation) have not been realized yet. This Account introduces an ongoing research project that focuses on the development of molecular robotics funded by MEXT (Ministry of Education, Culture, Sports, Science and Technology, Japan). This 5 year project started in July 2012 and is titled "Development of Molecular Robots Equipped with Sensors and Intelligence". The major issues in the field of molecular robotics all correspond to a feedback (i.e., plan-do-see) cycle of a robotic system. More specifically, these issues are (1) developing molecular sensors capable of handling a wide array of signals, (2) developing amplification methods of signals to drive molecular computing devices, (3) accelerating molecular computing, (4) developing actuators that are controllable by molecular computers, and (5) providing bodies of molecular robots encapsulating the above molecular devices, which implement the conformational changes and locomotion of the robots. In this Account, the latest contributions to the project are reported. There are four research teams in the project that specialize on sensing, intelligence, amoeba-like actuation, and slime-like actuation, respectively. The molecular sensor team is focusing on the development of molecular sensors that can handle a variety of signals. This team is also investigating methods to amplify signals from the molecular sensors. The molecular intelligence team is developing molecular computers and is currently focusing on a new photochemical technology for accelerating DNA-based computations. They also introduce novel computational models behind various kinds of molecular computers necessary for designing such computers. The amoeba robot team aims at constructing amoeba-like robots. The team is trying to incorporate motor proteins, including kinesin and microtubules (MTs), for use as actuators implemented in a liposomal compartment as a robot body. They are also developing a methodology to link DNA-based computation and molecular motor control. The slime robot team focuses on the development of slime-like robots. The team is evaluating various gels, including DNA gel and BZ gel, for use as actuators, as well as the body material to disperse various molecular devices in it. They also try to control the gel actuators by DNA signals coming from molecular computers.

Reasoning with Atomic-Scale Molecular Dynamic Models

ERIC Educational Resources Information Center

Pallant, Amy; Tinker, Robert F.

2004-01-01

The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

Workflow Management Systems for Molecular Dynamics on Leadership Computers

NASA Astrophysics Data System (ADS)

Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu

Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.

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…

Three-Dimensional Printing of Human Skeletal Muscle Cells: An Interdisciplinary Approach for Studying Biological Systems

ERIC Educational Resources Information Center

Bagley, James R.; Galpin, Andrew J.

2015-01-01

Interdisciplinary exploration is vital to education in the 21st century. This manuscript outlines an innovative laboratory-based teaching method that combines elements of biochemistry/molecular biology, kinesiology/health science, computer science, and manufacturing engineering to give students the ability to better conceptualize complex…

Annual Progress Report (17th) and 1992-97 Renewal Proposal Interactive Graphics for Molecular Studies

DTIC Science & Technology

1991-01-24

Molecular Graphics, vol. 6, No. 4 (Dec. 1988), p. 223. Turk, Greg, "Interactive Collision Detection for Molecular Graphics," M.S. thesis , UNC-Chapel Hill...Problem," Master’s thesis , UNC Department of Computer Science Technical Report #TR87-013, May 1987. Pique, ME., "Technical Trends in Molecular Graphics...AD-A236 598 Seventeenth Annual Progress Report and 1992-97 Renewal Proposal Interactive Graphics for Molecular Studies TR91-020 January 24, 1991 red

A Combined Experimental and Computational Study on the Stability of Nanofluids Containing Metal Organic Frameworks

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

Annapureddy, Harsha Vardhan Reddy; Nune, Satish K.; Motkuri, Radha K.

2015-01-08

Computational studies on nanofluids composed of metal organic frameworks (MOFs) were performed using molecular modeling techniques. Grand Canonical Monte Carlo (GCMC) simulations were used to study adsorption behavior of 1,1,1,3,3-pentafluoropropane (R-245fa) in a MIL-101 MOF at various temperatures. To understand the stability of the nanofluid composed of MIL-101 particles, we performed molecular dynamics simulations to compute potentials of mean force between hypothetical MIL-101 fragments terminated with two different kinds of modulators in R-245fa and water. Our computed potentials of mean force results indicate that the MOF particles tend to disperse better in water than in R-245fa. The reasons for thismore » observation were analyzed and discussed. Our results agree with experimental results indicating that the employed potential models and modeling approaches provide good description of molecular interactions and the reliabilities. Work performed by LXD was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. Work performed by HVRA, SKN, RKM, and PBM was supported by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory is a multiprogram national laboratory operated for DOE by Battelle.« less

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

Toward integration of in vivo molecular computing devices: successes and challenges

PubMed Central

Hayat, Sikander; Hinze, Thomas

2008-01-01

The computing power unleashed by biomolecule based massively parallel computational units has been the focus of many interdisciplinary studies that couple state of the art ideas from mathematical logic, theoretical computer science, bioengineering, and nanotechnology to fulfill some computational task. The output can influence, for instance, release of a drug at a specific target, gene expression, cell population, or be a purely mathematical entity. Analysis of the results of several studies has led to the emergence of a general set of rules concerning the implementation and optimization of in vivo computational units. Taking two recent studies on in vivo computing as examples, we discuss the impact of mathematical modeling and simulation in the field of synthetic biology and on in vivo computing. The impact of the emergence of gene regulatory networks and the potential of proteins acting as “circuit wires” on the problem of interconnecting molecular computing device subunits is also highlighted. PMID:19404433

New Genetics

MedlinePlus

... Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is a science education ... the basics of DNA and its molecular cousin RNA, and new directions in genetic research. The New ...

Dehydration of 1-octadecanol over H-BEA: A combined experimental and computational study

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

Song, Wenji; Liu, Yuanshuai; Barath, Eszter

Liquid phase dehydration of 1-octdecanol, which is intermediately formed during the hydrodeoxygenation of microalgae oil, has been explored in a combined experimental and computational study. The alkyl chain of C18 alcohol interacts with acid sites during diffusion inside the zeolite pores, resulting in an inefficient utilization of the Brønsted acid sites for samples with high acid site concentrations. The parallel intra- and inter- molecular dehydration pathways having different activation energies pass through alternative reaction intermediates. Formation of surface-bound alkoxide species is the rate-limiting step during intramolecular dehydration, whereas intermolecular dehydration proceeds via a bulky dimer intermediate. Octadecene is the primarymore » dehydration product over H-BEA at 533 K. Despite of the main contribution of Brønsted acid sites towards both dehydration pathways, Lewis acid sites are also active in the formation of dioctadecyl ether. The intramolecular dehydration to octadecene and cleavage of the intermediately formed ether, however, require strong BAS. L. Wang, D. Mei and J. A. Lercher, acknowledge the partial support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Laboratory Directed Research and Development Annual Report for 2009

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

Hughes, Pamela J.

This report documents progress made on all LDRD-funded projects during fiscal year 2009. As a US Department of Energy (DOE) Office of Science (SC) national laboratory, Pacific Northwest National Laboratory (PNNL) has an enduring mission to bring molecular and environmental sciences and engineering strengths to bear on DOE missions and national needs. Their vision is to be recognized worldwide and valued nationally for leadership in accelerating the discovery and deployment of solutions to challenges in energy, national security, and the environment. To achieve this mission and vision, they provide distinctive, world-leading science and technology in: (1) the design and scalablemore » synthesis of materials and chemicals; (2) climate change science and emissions management; (3) efficient and secure electricity management from generation to end use; and (4) signature discovery and exploitation for threat detection and reduction. PNNL leadership also extends to operating EMSL: the Environmental Molecular Sciences Laboratory, a national scientific user facility dedicated to providing itnegrated experimental and computational resources for discovery and technological innovation in the environmental molecular sciences.« less

Enhanced Molecular Dynamics Methods Applied to Drug Design Projects.

PubMed

Ziada, Sonia; Braka, Abdennour; Diharce, Julien; Aci-Sèche, Samia; Bonnet, Pascal

2018-01-01

Nobel Laureate Richard P. Feynman stated: "[…] everything that living things do can be understood in terms of jiggling and wiggling of atoms […]." The importance of computer simulations of macromolecules, which use classical mechanics principles to describe atom behavior, is widely acknowledged and nowadays, they are applied in many fields such as material sciences and drug discovery. With the increase of computing power, molecular dynamics simulations can be applied to understand biological mechanisms at realistic timescales. In this chapter, we share our computational experience providing a global view of two of the widely used enhanced molecular dynamics methods to study protein structure and dynamics through the description of their characteristics, limits and we provide some examples of their applications in drug design. We also discuss the appropriate choice of software and hardware. In a detailed practical procedure, we describe how to set up, run, and analyze two main molecular dynamics methods, the umbrella sampling (US) and the accelerated molecular dynamics (aMD) methods.

ISMB Conference Funding to Support Attendance of Early Researchers and Students

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

Gaasterland, Terry

ISMB Conference Funding for Students and Young Scientists Historical Description The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 22 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on “intelligent systems” and actual biological data makes ISMB a unique and highly important meeting.more » 21 years of experience in holding the conference has resulted in a consistently well-organized, well attended, and highly respected annual conference. "Intelligent systems" include any software which goes beyond straightforward, closed-form algorithms or standard database technologies, and encompasses those that view data in a symbolic fashion, learn from examples, consolidate multiple levels of abstraction, or synthesize results to be cognitively tractable to a human, including the development and application of advanced computational methods for biological problems. Relevant computational techniques include, but are not limited to: machine learning, pattern recognition, knowledge representation, databases, combinatorics, stochastic modeling, string and graph algorithms, linguistic methods, robotics, constraint satisfaction, and parallel computation. Biological areas of interest include molecular structure, genomics, molecular sequence analysis, evolution and phylogenetics, molecular interactions, metabolic pathways, regulatory networks, developmental control, and molecular biology generally. Emphasis is placed on the validation of methods using real data sets, on practical applications in the biological sciences, and on development of novel computational techniques. The ISMB conferences are distinguished from many other conferences in computational biology or artificial intelligence by an insistence that the researchers work with real molecular biology data, not theoretical or toy examples; and from many other biological conferences by providing a forum for technical advances as they occur, which otherwise may be shunned until a firm experimental result is published. The resulting intellectual richness and cross-disciplinary diversity provides an important opportunity for both students and senior researchers. ISMB has become the premier conference series in this field with refereed, published proceedings, establishing an infrastructure to promote the growing body of research.« less

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

PubMed

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations

PubMed Central

2013-01-01

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins. PMID:23298176

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…

Software Reviews.

ERIC Educational Resources Information Center

Wulfson, Stephen, Ed.

1987-01-01

Reviews seven computer software programs that can be used in science education programs. Describes courseware which deals with muscles and bones, terminology, classifying animals without backbones, molecular structures, drugs, genetics, and shaping the earth's surface. (TW)

International Conference on Intelligent Systems for Molecular Biology (ISMB)

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

Goldberg, Debra; Hibbs, Matthew; Kall, Lukas

The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference hasmore » resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.« less

1976 annual summary report

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

Not Available

1978-03-01

Abstracts of papers published during the previous calendar year, arranged in accordance with the project titles used in the USDOE Schedule 189 Budget Proposals, are presented. The collection of abstracts supplements the listing of papers published in the Schedule 189. The following subject areas are represented: high-energy physics; nuclear physics; basic energy sciences (nuclear science, materials sciences, solid state physics, materials chemistry); molecular, mathematical, and earth sciences (fundamental interactions, processes and techniques, mathematical and computer sciences); environmental research and development; physical and technological studies (characterization, measurement and monitoring); and nuclear research and applications.

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

Baker, Ann E; Barker, Ashley D; Bland, Arthur S Buddy

Oak Ridge National Laboratory's Leadership Computing Facility (OLCF) continues to deliver the most powerful resources in the U.S. for open science. At 2.33 petaflops peak performance, the Cray XT Jaguar delivered more than 1.4 billion core hours in calendar year (CY) 2011 to researchers around the world for computational simulations relevant to national and energy security; advancing the frontiers of knowledge in physical sciences and areas of biological, medical, environmental, and computer sciences; and providing world-class research facilities for the nation's science enterprise. Users reported more than 670 publications this year arising from their use of OLCF resources. Of thesemore » we report the 300 in this review that are consistent with guidance provided. Scientific achievements by OLCF users cut across all range scales from atomic to molecular to large-scale structures. At the atomic scale, researchers discovered that the anomalously long half-life of Carbon-14 can be explained by calculating, for the first time, the very complex three-body interactions between all the neutrons and protons in the nucleus. At the molecular scale, researchers combined experimental results from LBL's light source and simulations on Jaguar to discover how DNA replication continues past a damaged site so a mutation can be repaired later. Other researchers combined experimental results from ORNL's Spallation Neutron Source and simulations on Jaguar to reveal the molecular structure of ligno-cellulosic material used in bioethanol production. This year, Jaguar has been used to do billion-cell CFD calculations to develop shock wave compression turbo machinery as a means to meet DOE goals for reducing carbon sequestration costs. General Electric used Jaguar to calculate the unsteady flow through turbo machinery to learn what efficiencies the traditional steady flow assumption is hiding from designers. Even a 1% improvement in turbine design can save the nation billions of gallons of fuel.« less

Acid/base equilibria in clusters and their role in proton exchange membranes: Computational insight

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

Glezakou, Vanda A; Dupuis, Michel; Mundy, Christopher J

2007-10-24

We describe molecular orbital theory and ab initio molecular dynamics studies of acid/base equilibria of clusters AH:(H 2O) n↔A -:H +(H 2O) n in low hydration regime (n = 1-4), where AH is a model of perfluorinated sulfonic acids, RSO 3H (R = CF 3CF 2), encountered in polymeric electrolyte membranes of fuel cells. Free energy calculations on the neutral and ion pair structures for n = 3 indicate that the two configurations are close in energy and are accessible in the fluctuation dynamics of proton transport. For n = 1,2 the only relevant configuration is the neutral form. Thismore » was verified through ab initio metadynamics simulations. These findings suggest that bases are directly involved in the proton transport at low hydration levels. In addition, the gas phase proton affinity of the model sulfonic acid RSO 3H was found to be comparable to the proton affinity of water. Thus, protonated acids can also play a role in proton transport under low hydration conditions and under high concentration of protons. This work was supported by the Division of Chemical Science, Office of Basic Energy Sciences, US Department of Energy (DOE under Contract DE-AC05-76RL)1830. Computations were performed on computers of the Molecular Interactions and Transformations (MI&T) group and MSCF facility of EMSL, sponsored by US DOE and OBER located at PNNL. This work was benefited from resource of the National Energy Research Scientific Computing Centre, supported by the Office of Science of the US DOE, under Contract No. DE-AC03-76SF00098.« less

CSBB: synthetic biology research at Newcastle University.

PubMed

Goñi-Moreno, Angel; Wipat, Anil; Krasnogor, Natalio

2017-06-15

The Centre for Synthetic Biology and the Bioeconomy (CSBB) brings together a far-reaching multidisciplinary community across all Newcastle University's faculties - Medical Sciences, Science, Agriculture and Engineering, and Humanities, Arts and Social Sciences. The CSBB focuses on many different areas of Synthetic Biology, including bioprocessing, computational design and in vivo computation, as well as improving understanding of basic molecular machinery. Such breadth is supported by major national and international research funding, a range of industrial partners in the North East of England and beyond, as well as a large number of doctoral and post-doctoral researchers. The CSBB trains the next generation of scientists through a 1-year MSc in Synthetic Biology. © 2017 The Author(s).

Molecular Evolution in Historical Perspective.

PubMed

Suárez-Díaz, Edna

2016-12-01

In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms. These developments sparked important debates between defendants of the molecular and organismic approaches. The most vocal confrontations focused on the relation between primates and humans, and the neutral theory of molecular evolution. By the 1980s and 1990s, the construction of large protein and DNA sequences databases, and the development of computer-based statistical tools, facilitated the coming together of molecular and evolutionary biology. Although in its contemporary form the field of molecular evolution can be traced back to the last five decades, the field has deep roots in twentieth century experimental life sciences. For historians of science, the origins and consolidation of molecular evolution provide a privileged field for the study of scientific debates, the relation between technological advances and scientific knowledge, and the connection between science and broader social concerns.

A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model.

PubMed

Wang, Zhaocai; Ji, Zuwen; Wang, Xiaoming; Wu, Tunhua; Huang, Wei

2017-12-01

As a promising approach to solve the computationally intractable problem, the method based on DNA computing is an emerging research area including mathematics, computer science and molecular biology. The task scheduling problem, as a well-known NP-complete problem, arranges n jobs to m individuals and finds the minimum execution time of last finished individual. In this paper, we use a biologically inspired computational model and describe a new parallel algorithm to solve the task scheduling problem by basic DNA molecular operations. In turn, we skillfully design flexible length DNA strands to represent elements of the allocation matrix, take appropriate biological experiment operations and get solutions of the task scheduling problem in proper length range with less than O(n 2 ) time complexity. Copyright © 2017. Published by Elsevier B.V.

Exploring the role of pendant amines in transition metal complexes for the reduction of N2 to hydrazine and ammonia

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

Bhattacharya, Papri; Prokopchuk, Demyan E.; Mock, Michael T.

2017-03-01

This review examines the synthesis and acid reactivity of transition metal dinitrogen complexes bearing diphosphine ligands containing pendant amine groups in the second coordination sphere. This manuscript is a review of the work performed in the Center for Molecular Electrocatalysis. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences. EPR studies on Fe were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located atmore » PNNL. Computational resources were provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. DOE.« less

Text-mining and information-retrieval services for molecular biology

PubMed Central

Krallinger, Martin; Valencia, Alfonso

2005-01-01

Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators. PMID:15998455

Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data.

PubMed

Salvadori, Andrea; Del Frate, Gianluca; Pagliai, Marco; Mancini, Giordano; Barone, Vincenzo

2016-11-15

The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation.

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.

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

NONE

This document comprises Pacific Northwest National Laboratory`s report for Fiscal Year 1996 on research and development programs. The document contains 161 project summaries in 16 areas of research and development. The 16 areas of research and development reported on are: atmospheric sciences, biotechnology, chemical instrumentation and analysis, computer and information science, ecological science, electronics and sensors, health protection and dosimetry, hydrological and geologic sciences, marine sciences, materials science and engineering, molecular science, process science and engineering, risk and safety analysis, socio-technical systems analysis, statistics and applied mathematics, and thermal and energy systems. In addition, this report provides an overview ofmore » the research and development program, program management, program funding, and Fiscal Year 1997 projects.« less

The impact of computer science in molecular medicine: enabling high-throughput research.

PubMed

de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

2013-01-01

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

Exploratory Research and Development Fund, FY 1990

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

Not Available

1992-05-01

The Lawrence Berkeley Laboratory Exploratory R D Fund FY 1990 report is compiled from annual reports submitted by principal investigators following the close of the fiscal year. This report describes the projects supported and summarizes their accomplishments. It constitutes a part of an Exploratory R D Fund (ERF) planning and documentation process that includes an annual planning cycle, projection selection, implementation, and review. The research areas covered in this report are: Accelerator and fusion research; applied science; cell and molecular biology; chemical biodynamics; chemical sciences; earth sciences; engineering; information and computing sciences; materials sciences; nuclear science; physics and research medicinemore » and radiation biophysics.« less

On the Reaction Mechanism of Acetaldehyde Decomposition on Mo(110)

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

Mei, Donghai; Karim, Ayman M.; Wang, Yong

2012-02-16

The strong Mo-O bond strength provides promising reactivity of Mo-based catalysts for the deoxygenation of biomass-derived oxygenates. Combining the novel dimer saddle point searching method with periodic spin-polarized density functional theory calculations, we investigated the reaction pathways of a acetaldehyde decomposition on the clean Mo(110) surface. Two reaction pathways were identified, a selective deoxygenation and a nonselective fragmentation pathways. We found that acetaldehyde preferentially adsorbs at the pseudo 3-fold hollow site in the η2(C,O) configuration on Mo(110). Among four possible bond (β-C-H, γ-C-H, C-O and C-C) cleavages, the initial decomposition of the adsorbed acetaldehyde produces either ethylidene via the C-Omore » bond scission or acetyl via the β-C-H bond scission while the C-C and the γ-C-H bond cleavages of acetaldehyde leading to the formation of methyl (and formyl) and formylmethyl are unlikely. Further dehydrogenations of ethylidene into either ethylidyne or vinyl are competing and very facile with low activation barriers of 0.24 and 0.31 eV, respectively. Concurrently, the formed acetyl would deoxygenate into ethylidyne via the C-O cleavage rather than breaking the C-C or the C-H bonds. The selective deoxygenation of acetaldehyde forming ethylene is inhibited by relatively weaker hydrogenation capability of the Mo(110) surface. Instead, the nonselective pathway via vinyl and vinylidene dehydrogenations to ethynyl as the final hydrocarbon fragment is kinetically favorable. On the other hand, the strong interaction between ethylene and the Mo(110) surface also leads to ethylene decomposition instead of desorption into the gas phase. This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). This work was financially supported by the National Advanced Biofuels Consortium (NABC). Computing time was granted by a user project (emsl42292) at the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). The EMSL is a U.S. Department of Energy (DOE) national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and supported by the DOE Office of Biological and Environmental Research. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

2001: Things to come.

PubMed

Apuzzo, M L; Liu, C Y

2001-10-01

THIS ARTICLE DISCUSSES elements in the definition of modernity and emerging futurism in neurological surgery. In particular, it describes evolution, discovery, and paradigm shifts in the field and forces responsible for their realization. It analyzes the cyclical reinvention of the discipline experienced during the past generation and attempts to identify apertures to the near and more remote future. Subsequently, it focuses on forces and discovery in computational science, imaging, molecular science, biomedical engineering, and information processing as they relate to the theme of minimalism that is evident in the field. These areas are explained in the light of future possibilities offered by the emerging field of nanotechnology with molecular engineering.

On the Implications of Neuroscience Research for Science Teaching and Learning: Are There Any?

ERIC Educational Resources Information Center

Lawson, Anton E.

2006-01-01

What, if anything, do teachers need to know about how the brain works to improve teaching and learning? After all, a plumber needs to know how to stop leaks--not the molecular structure of water. And one can learn how to use a computer without knowing how a computer chip works. Likewise, teachers need to know how to help students develop…

In Vitro Models of Human Toxicity Pathways

EPA Science Inventory

For toxicity testing and assessment programs to address the large numbers of substances of potential concern, a paradigm shift in the assessment of chemical hazard and risk is needed that takes advantage of advances in molecular toxicology, computational sciences, and information...

Employee Spotlight: Clarence Chang | Argonne National Laboratory

Science.gov Websites

batteries --Electricity transmission --Smart Grid Environment -Biology --Computational biology --Environmental biology ---Metagenomics ---Terrestrial ecology --Molecular biology ---Clinical proteomics and biomarker discovery ---Interventional biology ---Proteomics --Structural biology -Environmental science &

Hierarchy, determinism, and specificity in theories of development and evolution.

PubMed

Deichmann, Ute

2017-10-16

The concepts of hierarchical organization, genetic determinism and biological specificity (for example of species, biologically relevant macromolecules, or genes) have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information (specificity) and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled "reductionist". However, the concepts have been marginalized or rejected in some of the research that in the late 1960s began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that 'molecular reductionism' has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular 'reductionism', in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology.

Advances in visual representation of molecular potentials.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.

Molecular Mechanics and Dynamics Characterization of an "in silico" Mutated Protein: A Stand-Alone Lab Module or Support Activity for "in vivo" and "in vitro" Analyses of Targeted Proteins

ERIC Educational Resources Information Center

Chiang, Harry; Robinson, Lucy C.; Brame, Cynthia J.; Messina, Troy C.

2013-01-01

Over the past 20 years, the biological sciences have increasingly incorporated chemistry, physics, computer science, and mathematics to aid in the development and use of mathematical models. Such combined approaches have been used to address problems from protein structure-function relationships to the workings of complex biological systems.…

Exploratory Research and Development Fund, FY 1990. Report on Lawrence Berkeley Laboratory

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

Not Available

1992-05-01

The Lawrence Berkeley Laboratory Exploratory R&D Fund FY 1990 report is compiled from annual reports submitted by principal investigators following the close of the fiscal year. This report describes the projects supported and summarizes their accomplishments. It constitutes a part of an Exploratory R&D Fund (ERF) planning and documentation process that includes an annual planning cycle, projection selection, implementation, and review. The research areas covered in this report are: Accelerator and fusion research; applied science; cell and molecular biology; chemical biodynamics; chemical sciences; earth sciences; engineering; information and computing sciences; materials sciences; nuclear science; physics and research medicine and radiationmore » biophysics.« less

2017 ISCB Overton Prize: Christoph Bock

PubMed Central

Fogg, Christiana N.; Kovats, Diane E.; Berger, Bonnie

2017-01-01

The International Society for Computational Biology (ISCB) each year recognizes the achievements of an early to mid-career scientist with the Overton Prize. This prize honors the untimely death of Dr. G. Christian Overton, an admired computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators who are in the early to middle phases of their careers and are selected because of their significant contributions to computational biology through research, teaching, and service. ISCB is pleased to recognize Dr. Christoph Bock, Principal Investigator at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, Austria, as the 2017 winner of the Overton Prize. Bock will be presenting a keynote presentation at the 2017 International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) in Prague, Czech Republic being held during July 21-25, 2017. PMID:28713546

2017 ISCB Overton Prize: Christoph Bock.

PubMed

Fogg, Christiana N; Kovats, Diane E; Berger, Bonnie

2017-01-01

The International Society for Computational Biology (ISCB) each year recognizes the achievements of an early to mid-career scientist with the Overton Prize. This prize honors the untimely death of Dr. G. Christian Overton, an admired computational biologist and founding ISCB Board member. Winners of the Overton Prize are independent investigators who are in the early to middle phases of their careers and are selected because of their significant contributions to computational biology through research, teaching, and service. ISCB is pleased to recognize Dr. Christoph Bock, Principal Investigator at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences in Vienna, Austria, as the 2017 winner of the Overton Prize. Bock will be presenting a keynote presentation at the 2017 International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) in Prague, Czech Republic being held during July 21-25, 2017.

The evolution and future of minimalism in neurological surgery.

PubMed

Liu, Charles Y; Wang, Michael Y; Apuzzo, Michael L J

2004-11-01

The evolution of the field of neurological surgery has been marked by a progressive minimalism. This has been evident in the development of an entire arsenal of modern neurosurgical enterprises, including microneurosurgery, neuroendoscopy, stereotactic neurosurgery, endovascular techniques, radiosurgical systems, intraoperative and navigational devices, and in the last decade, cellular and molecular adjuvants. In addition to reviewing the major developments and paradigm shifts in the cyclic reinvention of the field as it currently stands, this paper attempts to identify forces and developments that are likely to fuel the irresistible escalation of minimalism into the future. These forces include discoveries in computational science, imaging, molecular science, biomedical engineering, and information processing as they relate to the theme of minimalism. These areas are explained in the light of future possibilities offered by the emerging field of nanotechnology with molecular engineering.

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

Roy, Santanu; Dang, Liem X.

In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occursmore » at a nanosecond time scale for Na+ and at a picosecond time scale for other ions. We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

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

Dang, Liem X.; Vo, Quynh N.; Nilsson, Mikael

We report one of the first simulations using a classical rate theory approach to predict the mechanism of the exchange process between water and aqueous uranyl ions. Using our water and ion-water polarizable force fields and molecular dynamics techniques, we computed the potentials of mean force for the uranyl ion-water pair as the function of pressures at ambient temperature. Subsequently, these simulated potentials of mean force were used to calculate rate constants using the transition rate theory; the time dependent transmission coefficients were also examined using the reactive flux method and Grote-Hynes treatments of the dynamic response of the solvent.more » The computed activation volumes using transition rate theory and the corrected rate constants are positive, thus the mechanism of this particular water-exchange is a dissociative process. We discuss our rate theory results and compare them with previously studies in which non-polarizable force fields were used. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description

PubMed Central

2013-01-01

With the publication of the first eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data, GigaScience and Pensoft demonstrate how classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. This 'holistic’ approach in taxonomic description of a new species of cave-dwelling centipede is published in the Biodiversity Data Journal (BDJ), with coordinated data release in the GigaScience GigaDB database. PMID:24229463

Biodiversity research in the "big data" era: GigaScience and Pensoft work together to publish the most data-rich species description.

PubMed

Edmunds, Scott C; Hunter, Chris I; Smith, Vincent; Stoev, Pavel; Penev, Lyubomir

2013-10-28

With the publication of the first eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data, GigaScience and Pensoft demonstrate how classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. This 'holistic' approach in taxonomic description of a new species of cave-dwelling centipede is published in the Biodiversity Data Journal (BDJ), with coordinated data release in the GigaScience GigaDB database.

Towards the simulation of molecular collisions with a superconducting quantum computer

NASA Astrophysics Data System (ADS)

Geller, Michael

2013-05-01

I will discuss the prospects for the use of large-scale, error-corrected quantum computers to simulate complex quantum dynamics such as molecular collisions. This will likely require millions qubits. I will also discuss an alternative approach [M. R. Geller et al., arXiv:1210.5260] that is ideally suited for today's superconducting circuits, which uses the single-excitation subspace (SES) of a system of n tunably coupled qubits. The SES method allows many operations in the unitary group SU(n) to be implemented in a single step, bypassing the need for elementary gates, thereby making large computations possible without error correction. The method enables universal quantum simulation, including simulation of the time-dependent Schrodinger equation, and we argue that a 1000-qubit SES processor should be capable of achieving quantum speedup relative to a petaflop supercomputer. We speculate on the utility and practicality of such a simulator for atomic and molecular collision physics. Work supported by the US National Science Foundation CDI program.

Molecular dynamics simulations through GPU video games technologies

PubMed Central

Loukatou, Styliani; Papageorgiou, Louis; Fakourelis, Paraskevas; Filntisi, Arianna; Polychronidou, Eleftheria; Bassis, Ioannis; Megalooikonomou, Vasileios; Makałowski, Wojciech; Vlachakis, Dimitrios; Kossida, Sophia

2016-01-01

Bioinformatics is the scientific field that focuses on the application of computer technology to the management of biological information. Over the years, bioinformatics applications have been used to store, process and integrate biological and genetic information, using a wide range of methodologies. One of the most de novo techniques used to understand the physical movements of atoms and molecules is molecular dynamics (MD). MD is an in silico method to simulate the physical motions of atoms and molecules under certain conditions. This has become a state strategic technique and now plays a key role in many areas of exact sciences, such as chemistry, biology, physics and medicine. Due to their complexity, MD calculations could require enormous amounts of computer memory and time and therefore their execution has been a big problem. Despite the huge computational cost, molecular dynamics have been implemented using traditional computers with a central memory unit (CPU). A graphics processing unit (GPU) computing technology was first designed with the goal to improve video games, by rapidly creating and displaying images in a frame buffer such as screens. The hybrid GPU-CPU implementation, combined with parallel computing is a novel technology to perform a wide range of calculations. GPUs have been proposed and used to accelerate many scientific computations including MD simulations. Herein, we describe the new methodologies developed initially as video games and how they are now applied in MD simulations. PMID:27525251

Heterolysis of H2 Across a Classical Lewis Pair, 2,6-Lutidine-BCl3: Synthesis, Characterization, and Mechanism

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

Ginovska-Pangovska, Bojana; Autrey, Thomas; Parab, Kshitij K.

We report on a combined computational and experimental study of the activation of hydrogen using for 2,6-lutidine (Lut)/BCl3 Lewis pairs. Herein we describe the synthetic approach used to obtain a new FLP, Lut-BCl3 that activates molecular H2 at ~10 bar, 100 °C in toluene or lutidine as the solvent. The resulting compound is an unexpected neutral hydride, LutBHCl2, rather than the ion pair, which we attribute to ligand redistribution. The mechanism for activation was modeled with density functional theory and accurate G3(MP2)B3 theory. The dative bond in Lut-BCl3 is calculated to have a bond enthalpy of 15 kcal/mol. The separatedmore » pair is calculated to react with H2 and form the [LutH+][HBCl3–] ion pair with a barrier of 13 kcal/mol. Metathesis with LutBCl3 produces LutBHCl2 and [LutH][BCl4]. The overall reaction is exothermic by 8.5 kcal/mol. An alternative pathway was explored involving lutidine–borenium cation pair activating H2. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Biosciences, and Geosciences, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

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

Raugei, Simone; DuBois, Daniel L.; Rousseau, Roger J.

Rational design of molecular catalysts requires a systematic approach to designing ligands with specific functionality and precisely tailored electronic and steric properties. It then becomes possible to devise computer protocols to predict accurately the required properties and ultimately to design catalysts by computer. In this account we first review how thermodynamic properties such as oxidation-reduction potentials (E0), acidities (pKa), and hydride donor abilities (ΔGH-) form the basis for a systematic design of molecular catalysts for reactions that are critical for a secure energy future (hydrogen evolution and oxidation, oxygen and nitrogen reduction, and carbon dioxide reduction). We highlight how densitymore » functional theory allows us to determine and predict these properties within “chemical” accuracy (~ 0.06 eV for redox potentials, ~ 1 pKa unit for pKa values, and ~ 1.5 kcal/mol for hydricities). These quantities determine free energy maps and profiles associated with catalytic cycles, i.e. the relative energies of intermediates, and help us distinguish between desirable and high-energy pathways and mechanisms. Good catalysts have flat profiles that avoid high activation barriers due to low and high energy intermediates. We illustrate how the criterion of a flat energy profile lends itself to the prediction of design points by computer for optimum catalysts. This research was carried out in the Center for Molecular Electro-catalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences. Pacific Northwest National Laboratory (PNNL) is operated for the DOE by Battelle.« less

Homology Modeling and Molecular Docking for the Science Curriculum

ERIC Educational Resources Information Center

McDougal, Owen M.; Cornia, Nic; Sambasivarao, S. V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim

2014-01-01

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular…

Computer-Aided Design of Thermostable Proteins.

DTIC Science & Technology

1988-03-31

bA -𔄀* ’ resolution (Pabo and Lewis, 1982). We have much better data from our repressor-operator cocrystals (Jordan et. al., 1985) and this... Cocrystals Science 230, 1383-1385. Pabo, C.O. (1983) Molecular Technology: Designing Peptides and Proteins Nature 301, 200. Pabo, C.O. and Lewis, M. (1982

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP),

Materials Science | NREL

Science.gov Websites

sulfide (SnS). The top image represents output from atomic force microscopy for the molecular sections and computations. The image shows modeled electronic density of states (top panel) of the the bandgap of the narrow-gap crystalline semiconductors (left and right sides of the image) when it

AFOSR/AFRPL Rocket Propulsion Research Meeting Held at Lancaster, California on 12-15 March 1984. Abstracts and Agenda

DTIC Science & Technology

1984-02-01

MA 0900 28 HIGH TEMPERATURE MOLECULAR ABSORBERS FOR CW LASER PROPULSION. David 0 Rosen, David 0 Ham , and Lauren M Cowles, Physical Sciences Inc...been put into the dcvulopmunt of* computer codes uo wodel various aspects of rocket propellant behavior such a cobustion :..echawica and DSDT. However...Differential Scanning Calorimeter, and (2) thermal diffusivit- using U laser flash apparatus. All measurements are madc under digital computer contro

Operation of micro and molecular machines: a new concept with its origins in interface science.

PubMed

Ariga, Katsuhiko; Ishihara, Shinsuke; Izawa, Hironori; Xia, Hong; Hill, Jonathan P

2011-03-21

A landmark accomplishment of nanotechnology would be successful fabrication of ultrasmall machines that can work like tweezers, motors, or even computing devices. Now we must consider how operation of micro- and molecular machines might be implemented for a wide range of applications. If these machines function only under limited conditions and/or require specialized apparatus then they are useless for practical applications. Therefore, it is important to carefully consider the access of functionality of the molecular or nanoscale systems by conventional stimuli at the macroscopic level. In this perspective, we will outline the position of micro- and molecular machines in current science and technology. Most of these machines are operated by light irradiation, application of electrical or magnetic fields, chemical reactions, and thermal fluctuations, which cannot always be applied in remote machine operation. We also propose strategies for molecular machine operation using the most conventional of stimuli, that of macroscopic mechanical force, achieved through mechanical operation of molecular machines located at an air-water interface. The crucial roles of the characteristics of an interfacial environment, i.e. connection between macroscopic dimension and nanoscopic function, and contact of media with different dielectric natures, are also described.

US-Latin American Workshop on Molecular and Materials Sciences: Theoretical and Computational Aspects Held at the University of Florida, Gainesville, on February 8-10, 1994

DTIC Science & Technology

1994-08-09

Observables During a Collision Inst. de Fisica , Cuernavaca, Mexico Ruben D. Santiago Acosta An Algebraic Model for 3-dimensional Atom-Diatom Inst C...STRUCTURES. MOLECULAR DYNAMICS SIMULATION M. C .Donnamaria and J. R. Grigera Instituto de Fisica de Liquidos y Sistemas Biologicos (IFLYSIB),CONICET...Crybiology, 1981, 18, 631. ACKNOWLEDGMENTS This work has been partially funded by the Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) of

Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

First-principles characterization of formate and carboxyl adsorption on the stoichiometric CeO2(111) and CeO2(110) surfaces

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

Mei, Donghai

2013-05-20

Molecular adsorption of formate and carboxyl on the stoichiometric CeO2(111) and CeO2(110) surfaces was studied using periodic density functional theory (DFT+U) calculations. Two distinguishable adsorption modes (strong and weak) of formate are identified. The bidentate configuration is more stable than the monodentate adsorption configuration. Both formate and carboxyl bind at the more open CeO2(110) surface are stronger. The calculated vibrational frequencies of two adsorbed species are consistent with experimental measurements. Finally, the effects of U parameters on the adsorption of formate and carboxyl over both CeO2 surfaces were investigated. We found that the geometrical configurations of two adsorbed species aremore » not affected by using different U parameters (U=0, 5, and 7). However, the calculated adsorption energy of carboxyl pronouncedly increases with the U value while the adsorption energy of formate only slightly changes (<0.2 eV). The Bader charge analysis shows the opposite charge transfer occurs for formate and carboxyl adsorption where the adsorbed formate is negatively charge whiled the adsorbed carboxyl is positively charged. Interestingly, with the increasing U parameter, the amount of charge is also increased. This work was supported by the Laboratory Directed Research and Development (LDRD) project of the Pacific Northwest National Laboratory (PNNL) and by a Cooperative Research and Development Agreement (CRADA) with General Motors. The computations were performed using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at PNNL in Richland, Washington. Part of the computing time was also granted by the National Energy Research Scientific Computing Center (NERSC)« less

Computer-Assisted Drug Formulation Design: Novel Approach in Drug Delivery.

PubMed

Metwally, Abdelkader A; Hathout, Rania M

2015-08-03

We hypothesize that, by using several chemo/bio informatics tools and statistical computational methods, we can study and then predict the behavior of several drugs in model nanoparticulate lipid and polymeric systems. Accordingly, two different matrices comprising tripalmitin, a core component of solid lipid nanoparticles (SLN), and PLGA were first modeled using molecular dynamics simulation, and then the interaction of drugs with these systems was studied by means of computing the free energy of binding using the molecular docking technique. These binding energies were hence correlated with the loadings of these drugs in the nanoparticles obtained experimentally from the available literature. The obtained relations were verified experimentally in our laboratory using curcumin as a model drug. Artificial neural networks were then used to establish the effect of the drugs' molecular descriptors on the binding energies and hence on the drug loading. The results showed that the used soft computing methods can provide an accurate method for in silico prediction of drug loading in tripalmitin-based and PLGA nanoparticulate systems. These results have the prospective of being applied to other nano drug-carrier systems, and this integrated statistical and chemo/bio informatics approach offers a new toolbox to the formulation science by proposing what we present as computer-assisted drug formulation design (CADFD).

An interactive computer lab of the galvanic cell for students in biochemistry.

PubMed

Ahlstrand, Emma; Buetti-Dinh, Antoine; Friedman, Ran

2018-01-01

We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δ r G, Δ r H, and Δ r S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material. Cloud computing platforms such as CoCalc facilitate the distribution of computer codes and allow students to access and apply interactive course tools beyond the course's scope. Despite some limitations imposed by cloud computing, the students appreciated the approach and the enhanced opportunities to discuss study questions with their classmates and instructor as facilitated by the interactive tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):58-65, 2018. © 2017 The International Union of Biochemistry and Molecular Biology.

The Early Years of Molecular Dynamics and Computers at UCRL, LRL, LLL, and LLNL

NASA Astrophysics Data System (ADS)

Mansigh Karlsen, Mary Ann

I'm the young woman in the picture shown in Fig. 12.1 that appeared with the invitation to the Symposium to celebrate Berni Alder's ninetieth birthday. I worked with Berni for over 25 years on the computer programs that provided the data he needed to write the fifteen papers published in scientific journals on Studies in Molecular Dynamics. My name appears at the end of each one thanking me for computer support. It has been interesting to look on the Internet to find my name in the middle of many foreign languages, including Japanese characters and Russian Cyrillic script. It shows how Berni's work has been of interest to many scientists all over the world from the earliest years. Figure 12.1 was also included with articles written when he received the National Medal of Science from President Obama in 2009…

ChemPreview: an augmented reality-based molecular interface.

PubMed

Zheng, Min; Waller, Mark P

2017-05-01

Human computer interfaces make computational science more comprehensible and impactful. Complex 3D structures such as proteins or DNA are magnified by digital representations and displayed on two-dimensional monitors. Augmented reality has recently opened another door to access the virtual three-dimensional world. Herein, we present an augmented reality application called ChemPreview with the potential to manipulate bio-molecular structures at an atomistic level. ChemPreview is available at https://github.com/wallerlab/chem-preview/releases, and is built on top of the Meta 1 platform https://www.metavision.com/. ChemPreview can be used to interact with a protein in an intuitive way using natural hand gestures, thereby making it appealing to computational chemists or structural biologists. The ability to manipulate atoms in real world could eventually provide new and more efficient ways of extracting structural knowledge, or designing new molecules in silico. Copyright © 2017 Elsevier Inc. All rights reserved.

Elucidation of the Chromatographic Enantiomer Elution Order Through Computational Studies.

PubMed

Sardella, Roccaldo; Ianni, Federica; Macchiarulo, Antonio; Pucciarini, Lucia; Carotti, Andrea; Natalini, Benedetto

2018-01-01

During the last twenty years, the interest towards the development of chiral compound has exponentially been increased. Indeed, the set-up of suitable asymmetric enantioselective synthesis protocols is currently one of the focuses of many pharmaceutical research projects. In this scenario, chiral HPLC separations have gained great importance as well, both for analytical- and preparative-scale applications, the latter devoted to the quantitative isolation of enantiopure compounds. Molecular modelling and quantum chemistry methods can be fruitfully applied to solve chirality related problems especially when enantiomerically pure reference standards are missing. In this framework, with the aim to explain the molecular basis of the enantioselective retention, we performed computational studies to rationalize the enantiomer elution order with both low- and high-molecular weight chiral selectors. Semi-empirical and quantum mechanical computational procedures were successfully applied in the domains of chiral ligand-exchange and chiral ion-exchange chromatography, as well as in studies dealing with the use of polysaccharide-based enantioresolving materials. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Mapping the Materials Genome through Combinatorial Informatics

NASA Astrophysics Data System (ADS)

Rajan, Krishna

2012-02-01

The recently announced White House Materials Genome Initiative provides an exciting challenge to the materials science community. To meet that challenge one needs to address a critical question, namely what is the materials genome? Some guide on how to the answer this question can be gained by recognizing that a ``gene'' is a carrier of information. In the biological sciences, discovering how to manipulate these genes has generated exciting discoveries in fundamental molecular biology as well as significant advances in biotechnology. Scaling that up to molecular, cellular length scales and beyond, has spawned from genomics, fields such as proteomics, metabolomics and essentially systems biology. The ``omics'' approach requires that one needs to discover and track these ``carriers of information'' and then correlate that information to predict behavior. A similar challenge lies in materials science, where there is a diverse array of modalities of materials ``discovery'' ranging from new materials chemistries and molecular arrangements with novel properties, to the development and design of new micro- and mesoscale structures. Hence to meaningfully adapt the spirit of ``genomics'' style research in materials science, we need to first identify and map the ``genes'' across different materials science applications On the experimental side, combinatorial experiments have opened a new approach to generate data in a high throughput manner, but without a clear way to link that to models, the full value of that data is not realized. Hence along with experimental and computational materials science, we need to add a ``third leg'' to our toolkit to make the ``Materials Genome'' a reality, the science of Materials Informatics. In this presentation we provide an overview of how information science coupled to materials science can in fact achieve the goal of mapping the ``Materials Genome''.

Local Aqueous Solvation Structure Around Ca2+ During Ca2+---Cl– Pair Formation

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

Baer, Marcel D.; Mundy, Christopher J.

2016-03-03

The molecular details of single ion solvation around Ca2+ and ion-pairing of Ca2--Cl- are investigated using ab initio molecular dynamics. The use of empirical dispersion corrections to the BLYP functional are investigated by comparison to experimentally available extended X-ray absorption fine structure (EXAFS) measurements, which probes the first solvation shell in great detail. Besides finding differences in the free-energy for both ion-pairing and the coordination number of ion solvation between the quantum and classical descriptions of interaction, there were important differences found between dispersion corrected and uncorrected density functional theory (DFT). Specifically, we show significantly different free-energy landscapes for bothmore » coordination number of Ca2+ and its ion-pairing with Cl- depending on the DFT simulation protocol. Our findings produce a self-consistent treatment of short-range solvent response to the ion and the intermediate to long-range collective response of the electrostatics of the ion-ion interaction to produce a detailed picture of ion-pairing that is consistent with experiment. MDB is supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory. It was conducted under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. CJM acknowledges support from US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program. The authors thank Prof. Tom Beck for discussions regarding QCT, and Drs. Greg Schenter and Shawn Kathmann for insightful comments.« less

Equation-free and variable free modeling for complex/multiscale systems. Coarse-grained computation in science and engineering using fine-grained models

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

Kevrekidis, Ioannis G.

The work explored the linking of modern developing machine learning techniques (manifold learning and in particular diffusion maps) with traditional PDE modeling/discretization/scientific computation techniques via the equation-free methodology developed by the PI. The result (in addition to several PhD degrees, two of them by CSGF Fellows) was a sequence of strong developments - in part on the algorithmic side, linking data mining with scientific computing, and in part on applications, ranging from PDE discretizations to molecular dynamics and complex network dynamics.

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

ERIC Educational Resources Information Center

Roy, Urmi

2016-01-01

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

Earth System Grid II, Turning Climate Datasets into Community Resources

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

Middleton, Don

2006-08-01

The Earth System Grid (ESG) II project, funded by the Department of Energy’s Scientific Discovery through Advanced Computing program, has transformed climate data into community resources. ESG II has accomplished this goal by creating a virtual collaborative environment that links climate centers and users around the world to models and data via a computing Grid, which is based on the Department of Energy’s supercomputing resources and the Internet. Our project’s success stems from partnerships between climate researchers and computer scientists to advance basic and applied research in the terrestrial, atmospheric, and oceanic sciences. By interfacing with other climate science projects,more » we have learned that commonly used methods to manage and remotely distribute data among related groups lack infrastructure and under-utilize existing technologies. Knowledge and expertise gained from ESG II have helped the climate community plan strategies to manage a rapidly growing data environment more effectively. Moreover, approaches and technologies developed under the ESG project have impacted datasimulation integration in other disciplines, such as astrophysics, molecular biology and materials science.« less

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

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

Prakash, Arushi; Baer, Marcel D.; Mundy, Christopher J.

Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with amore » hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.« less

Quantum Testbeds Stakeholder Workshop (QTSW) Report meeting purpose and agenda.

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

Hebner, Gregory A.

Quantum computing (QC) is a promising early-stage technology with the potential to provide scientific computing capabilities far beyond what is possible with even an Exascale computer in specific problems of relevance to the Office of Science. These include (but are not limited to) materials modeling, molecular dynamics, and quantum chromodynamics. However, commercial QC systems are not yet available and the technical maturity of current QC hardware, software, algorithms, and systems integration is woefully incomplete. Thus, there is a significant opportunity for DOE to define the technology building blocks, and solve the system integration issues to enable a revolutionary tool. Oncemore » realized, QC will have world changing impact on economic competitiveness, the scientific enterprise, and citizen well-being. Prior to this workshop, DOE / Office of Advanced Scientific Computing Research (ASCR) hosted a workshop in 2015 to explore QC scientific applications. The goal of that workshop was to assess the viability of QC technologies to meet the computational requirements in support of DOE’s science and energy mission and to identify the potential impact of these technologies.« less

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity

PubMed Central

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand “complex behavior” and complexity theory, and from which important biological insight can be gained. PMID:24999297

Computational Cellular Dynamics Based on the Chemical Master Equation: A Challenge for Understanding Complexity.

PubMed

Liang, Jie; Qian, Hong

2010-01-01

Modern molecular biology has always been a great source of inspiration for computational science. Half a century ago, the challenge from understanding macromolecular dynamics has led the way for computations to be part of the tool set to study molecular biology. Twenty-five years ago, the demand from genome science has inspired an entire generation of computer scientists with an interest in discrete mathematics to join the field that is now called bioinformatics. In this paper, we shall lay out a new mathematical theory for dynamics of biochemical reaction systems in a small volume (i.e., mesoscopic) in terms of a stochastic, discrete-state continuous-time formulation, called the chemical master equation (CME). Similar to the wavefunction in quantum mechanics, the dynamically changing probability landscape associated with the state space provides a fundamental characterization of the biochemical reaction system. The stochastic trajectories of the dynamics are best known through the simulations using the Gillespie algorithm. In contrast to the Metropolis algorithm, this Monte Carlo sampling technique does not follow a process with detailed balance. We shall show several examples how CMEs are used to model cellular biochemical systems. We shall also illustrate the computational challenges involved: multiscale phenomena, the interplay between stochasticity and nonlinearity, and how macroscopic determinism arises from mesoscopic dynamics. We point out recent advances in computing solutions to the CME, including exact solution of the steady state landscape and stochastic differential equations that offer alternatives to the Gilespie algorithm. We argue that the CME is an ideal system from which one can learn to understand "complex behavior" and complexity theory, and from which important biological insight can be gained.

A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors.

PubMed

Glowacki, David R; O'Connor, Michael; Calabró, Gaetano; Price, James; Tew, Philip; Mitchell, Thomas; Hyde, Joseph; Tew, David P; Coughtrie, David J; McIntosh-Smith, Simon

2014-01-01

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human-computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone the motion of the simulated atoms, affecting both graphics and sonified simulation data. GPU acceleration has been key to achieving our target of 60 frames per second (FPS), giving an extremely fluid interactive experience. GPU acceleration has also allowed us to scale the system for use in immersive 360° spaces with an array of up to ten depth sensors, allowing several users to simultaneously chaperone the dynamics. The flexibility of our platform for carrying out molecular dynamics simulations has been considerably enhanced by wrappers that facilitate fast communication with a portable selection of GPU-accelerated molecular force evaluation routines. In this paper, we describe a 360° atmospheric molecular dynamics simulation we have run in a chemistry/physics education context. We also describe initial tests in which users have been able to chaperone the dynamics of 10-alanine peptide embedded in an explicit water solvent. Using this system, both expert and novice users have been able to accelerate peptide rare event dynamics by 3-4 orders of magnitude.

Exploring Do-It-Yourself Approaches in Computational Quantum Chemistry: The Pedagogical Benefits of the Classical Boys Algorithm

ERIC Educational Resources Information Center

Orsini, Gabriele

2015-01-01

The ever-increasing impact of molecular quantum calculations over chemical sciences implies a strong and urgent need for the elaboration of proper teaching strategies in university curricula. In such perspective, this paper proposes an extensive project for a student-driven, cooperative, from-scratch implementation of a general Hartree-Fock…

Sanibel Symposium in the Petascale-Exascale Computational Era

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

Cheng, Hai-Ping

The 56 th Sanibel Symposium was held February 14-19 2016 at the King and Prince Hotel, St. Simons Island, GA. It successfully brought quantum chemists and chemical and condensed matter physicists together in presentations, posters, and informal discussions bridging those two communities. The Symposium has had a significant role in preparing generations of quantum theorists. As computational potency and algorithmic sophistication have grown, the Symposium has evolved to emphasize more heavily computationally oriented method development in chemistry and materials physics, including nanoscience, complex molecular phenomena, and even bio-molecular methods and problems. Given this context, the 56 th Sanibel meeting systematicallymore » and deliberately had sessions focused on exascale computation. A selection of outstanding theoretical problems that need serious attention was included. Five invited sessions, two contributed sessions (hot topics), and a poster session were organized with the exascale theme. This was a historic milestone in the evolution of the Symposia. Just as years ago linear algebra, perturbation theory, density matrices, and band-structure methods dominated early Sanibel Symposia, the exascale sessions of the 56 thmeeting contributed a transformative influence to add structure and strength to the computational physical science community in an unprecedented way. A copy of the full program of the 56 th Symposium is attached. The exascale sessions were Linear Scaling, Non-Adabatic Dynamics, Interpretive Theory and Models, Computation, Software, and Algorithms, and Quantum Monte Carlo. The Symposium Proceedings will be published in Molecular Physics (2017). Note that the Sanibel proceedings from 2015 and 2014 were published as Molecular Physics vol. 114, issue 3-4 (2016) and vol. 113, issue 3-4 (2015) respectively.« less

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

Temperature specification in atomistic molecular dynamics and its impact on simulation efficacy

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

Temperature is a vital thermodynamical function for physical systems. Knowledge of system temperature permits assessment of system ergodicity, entropy, system state and stability. Rapid theoretical and computational developments in the fields of condensed matter physics, chemistry, material science, molecular biology, nanotechnology and others necessitate clarity in the temperature specification. Temperature-based materials simulations, both standalone and distributed computing, are projected to grow in prominence over diverse research fields. In this article we discuss the apparent variability of temperature modeling formalisms used currently in atomistic molecular dynamics simulations, with respect to system energetics,dynamics and structural evolution. Commercial simulation programs, which by nature are heuristic, do not openly discuss this fundamental question. We address temperature specification in the context of atomistic molecular dynamics. We define a thermostat at 400K relative to a heat bath at 300K firstly using a modified ab-initio Newtonian method, and secondly using a Monte-Carlo method. The thermostatic vacancy formation and cohesion energies, equilibrium lattice constant for FCC copper is then calculated. Finally we compare and contrast the results.

Computational Study of the Bulk Properties of a Novel Molecule: alpha-Tocopherol-Ascorbic Acid Surfactant

NASA Astrophysics Data System (ADS)

Stirling, Shannon; Kim, Hye-Young

Alpha-tocopherol-ascorbic acid surfactant (EC) is a novel amphiphilic molecule of antioxidant properties, which has a hydrophobic vitamin E and a hydrophilic vitamin C chemically linked. We have developed atomistic force fields (g54a7) for a protonated (neutral) EC molecule. Our goal is to carry out molecular dynamics (MD) simulations of protonated EC molecules using the newly developed force fields and study the molecular properties. First we ran energy minimization (EM) with one molecule in a vacuum to obtain the low energy molecular configuration with emtol =10. We then used Packmol to insert 125 EC molecules in a 3nm cube. We then performed MD simulations of the bulk system composed of 125 EC molecules, from which we measured the bulk density and the evaporation energy of the molecular system. Gromacs2016 is used for the EM and MD simulation studies. We will present the results of the ongoing research. National Institute Of General Medical Sciences of the National Institutes of Health under Award Number P20GM103424 (Kim). Computational resources were provided by the Louisiana Optical Network Initiative.

Dependence of the rate of LiF ion pairing on the description of molecular interaction

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

Pluharova, Eva; Baer, Marcel D.; Schenter, Gregory K.

2016-03-03

We present an analysis of the dynamics of ion-pairing of Lithium Fluoride (LiF) in aqueous solvent using both detailed molecular simulation as well as reduced models within a Gener- alized Langevin Equation (GLE) framework. We explored the sensitivity of the ion-pairing phenomena to the details of descriptions of molecular interaction, comparing two empirical potentials to explicit quantum based density functional theory. We find quantitative differences in the potentials of mean force for ion-pairing as well as time dependent frictions that lead to variations in the rate constant and reactive flux correlation functions. These details reflect differences in solvent response tomore » ion-pairing between different representations of molecular interaction and influence anharmonicity of the dynamic response. We find that the short time anharmonic response is recovered with a GLE parameterization. Recovery of the details of long time response may require extensions to the reduced model. We show that the utility of using a reduced model leads to a straight forward application of variational transition state the- ory concepts to the condensed phase system. The significance of this is reflected in the analysis of committor distributions and the variation of planar hypersurfaces, leading to an improved understanding of factors that determine the rate of LiF ion-pairing. CJM and GKS are supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest Na- tional Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of Laboratory Directed Research and Development funding under the auspices of PNNL’s Laboratory Initiative Materials Synthesis and Simulation across Scales (MS3). Additional computing resources were generously allocated by PNNL’s Institutional Computing program. EP acknowledges support from PNNL’s Alternate Sponsored Fellowship program and IMPRS Dres- den.Support to P.J. from the Czech Science Foundation (grant P208/12/G016) and the Academy of Sciences (Praemium Academie award) is gratefully acknowledged.« less

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

Molecular Docking and Drug Discovery in β-Adrenergic Receptors.

PubMed

Vilar, Santiago; Sobarzo-Sanchez, Eduardo; Santana, Lourdes; Uriarte, Eugenio

2017-01-01

Evolution in computer engineering, availability of increasing amounts of data and the development of new and fast docking algorithms and software have led to improved molecular simulations with crucial applications in virtual high-throughput screening and drug discovery. Moreover, analysis of protein-ligand recognition through molecular docking has become a valuable tool in drug design. In this review, we focus on the applicability of molecular docking on a particular class of G protein-coupled receptors: the β-adrenergic receptors, which are relevant targets in clinic for the treatment of asthma and cardiovascular diseases. We describe the binding site in β-adrenergic receptors to understand key factors in ligand recognition along with the proteins activation process. Moreover, we focus on the discovery of new lead compounds that bind the receptors, on the evaluation of virtual screening using the active/ inactive binding site states, and on the structural optimization of known families of binders to improve β-adrenergic affinity. We also discussed strengths and challenges related to the applicability of molecular docking in β-adrenergic receptors. Molecular docking is a valuable technique in computational chemistry to deeply analyze ligand recognition and has led to important breakthroughs in drug discovery and design in the field of β-adrenergic receptors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics

PubMed Central

Steinhauser, Martin O.; Hiermaier, Stefan

2009-01-01

This review discusses several computational methods used on different length and time scales for the simulation of material behavior. First, the importance of physical modeling and its relation to computer simulation on multiscales is discussed. Then, computational methods used on different scales are shortly reviewed, before we focus on the molecular dynamics (MD) method. Here we survey in a tutorial-like fashion some key issues including several MD optimization techniques. Thereafter, computational examples for the capabilities of numerical simulations in materials research are discussed. We focus on recent results of shock wave simulations of a solid which are based on two different modeling approaches and we discuss their respective assets and drawbacks with a view to their application on multiscales. Then, the prospects of computer simulations on the molecular length scale using coarse-grained MD methods are covered by means of examples pertaining to complex topological polymer structures including star-polymers, biomacromolecules such as polyelectrolytes and polymers with intrinsic stiffness. This review ends by highlighting new emerging interdisciplinary applications of computational methods in the field of medical engineering where the application of concepts of polymer physics and of shock waves to biological systems holds a lot of promise for improving medical applications such as extracorporeal shock wave lithotripsy or tumor treatment. PMID:20054467

Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities

PubMed Central

Bardhan, Jaydeep P.

2014-01-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics. PMID:25505358

Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.

PubMed

Bardhan, Jaydeep P

2013-12-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

Gradient models in molecular biophysics: progress, challenges, opportunities

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.

2013-12-01

In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

Analysing and Rationalising Molecular and Materials Databases Using Machine-Learning

NASA Astrophysics Data System (ADS)

de, Sandip; Ceriotti, Michele

Computational materials design promises to greatly accelerate the process of discovering new or more performant materials. Several collaborative efforts are contributing to this goal by building databases of structures, containing between thousands and millions of distinct hypothetical compounds, whose properties are computed by high-throughput electronic-structure calculations. The complexity and sheer amount of information has made manual exploration, interpretation and maintenance of these databases a formidable challenge, making it necessary to resort to automatic analysis tools. Here we will demonstrate how, starting from a measure of (dis)similarity between database items built from a combination of local environment descriptors, it is possible to apply hierarchical clustering algorithms, as well as dimensionality reduction methods such as sketchmap, to analyse, classify and interpret trends in molecular and materials databases, as well as to detect inconsistencies and errors. Thanks to the agnostic and flexible nature of the underlying metric, we will show how our framework can be applied transparently to different kinds of systems ranging from organic molecules and oligopeptides to inorganic crystal structures as well as molecular crystals. Funded by National Center for Computational Design and Discovery of Novel Materials (MARVEL) and Swiss National Science Foundation.

Towards computational materials design from first principles using alchemical changes and derivatives.

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

von Lilienfeld-Toal, Otto Anatole

2010-11-01

The design of new materials with specific physical, chemical, or biological properties is a central goal of much research in materials and medicinal sciences. Except for the simplest and most restricted cases brute-force computational screening of all possible compounds for interesting properties is beyond any current capacity due to the combinatorial nature of chemical compound space (set of stoichiometries and configurations). Consequently, when it comes to computationally optimizing more complex systems, reliable optimization algorithms must not only trade-off sufficient accuracy and computational speed of the models involved, they must also aim for rapid convergence in terms of number of compoundsmore » 'visited'. I will give an overview on recent progress on alchemical first principles paths and gradients in compound space that appear to be promising ingredients for more efficient property optimizations. Specifically, based on molecular grand canonical density functional theory an approach will be presented for the construction of high-dimensional yet analytical property gradients in chemical compound space. Thereafter, applications to molecular HOMO eigenvalues, catalyst design, and other problems and systems shall be discussed.« less

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.

Mechanistic insights into aqueous phase propanol dehydration in H-ZSM-5 zeolite

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

Mei, Donghai; Lercher, Johannes A.

Aqueous phase dehydration of 1-propanol over H-ZSM-5 zeolite was investigated using density functional theory (DFT) calculations. The water molecules in the zeolite pores prefer to aggregate via the hydrogen bonding network and be protonated at the Brønsted acidic sites (BAS). Two typical configurations, i.e., dispersed and clustered, of water molecules were identified by ab initio molecular dynamics simulation of the mimicking aqueous phase H-ZSM-5 zeolite unit cell with 20 water molecules per unit cell. DFT calculated Gibbs free energies suggest that the dimeric propanol-propanol, the propanol-water complex, and the trimeric propanol-propanol-water are formed at high propanol concentrations, which provide amore » kinetically feasible dehydration reaction channel of 1-propanol to propene. However, calculation results also indicate that the propanol dehydration via the unimolecular mechanism becomes kinetically discouraged due to the enhanced stability of the protonated dimeric propanol and the protonated water cluster acting as the BAS site for alcohol dehydration reaction. This work was supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

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

Computational biology and bioinformatics in Nigeria.

PubMed

Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

2014-04-01

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

Computational Biology and Bioinformatics in Nigeria

PubMed Central

Fatumo, Segun A.; Adoga, Moses P.; Ojo, Opeolu O.; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

2014-01-01

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

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

Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.

2014-07-03

Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinitiesmore » and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL.« less

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

Structure, dynamics and stability of water/scCO 2/mineral interfaces from ab initio molecular dynamics simulations

DOE PAGES

Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; ...

2015-10-12

Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO 2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca 2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO 2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences, Geosciences and Biosciences (R.R.), and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle. Computational resources were provided by PNNL’s Platform for Institutional Computing (PIC), the W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at PNNL and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory.« less

Addressing the challenges of standalone multi-core simulations in molecular dynamics

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-07-01

Computational modelling in material science involves mathematical abstractions of force fields between particles with the aim to postulate, develop and understand materials by simulation. The aggregated pairwise interactions of the material's particles lead to a deduction of its macroscopic behaviours. For practically meaningful macroscopic scales, a large amount of data are generated, leading to vast execution times. Simulation times of hours, days or weeks for moderately sized problems are not uncommon. The reduction of simulation times, improved result accuracy and the associated software and hardware engineering challenges are the main motivations for many of the ongoing researches in the computational sciences. This contribution is concerned mainly with simulations that can be done on a "standalone" computer based on Message Passing Interfaces (MPI), parallel code running on hardware platforms with wide specifications, such as single/multi- processor, multi-core machines with minimal reconfiguration for upward scaling of computational power. The widely available, documented and standardized MPI library provides this functionality through the MPI_Comm_size (), MPI_Comm_rank () and MPI_Reduce () functions. A survey of the literature shows that relatively little is written with respect to the efficient extraction of the inherent computational power in a cluster. In this work, we discuss the main avenues available to tap into this extra power without compromising computational accuracy. We also present methods to overcome the high inertia encountered in single-node-based computational molecular dynamics. We begin by surveying the current state of the art and discuss what it takes to achieve parallelism, efficiency and enhanced computational accuracy through program threads and message passing interfaces. Several code illustrations are given. The pros and cons of writing raw code as opposed to using heuristic, third-party code are also discussed. The growing trend towards graphical processor units and virtual computing clouds for high-performance computing is also discussed. Finally, we present the comparative results of vacancy formation energy calculations using our own parallelized standalone code called Verlet-Stormer velocity (VSV) operating on 30,000 copper atoms. The code is based on the Sutton-Chen implementation of the Finnis-Sinclair pairwise embedded atom potential. A link to the code is also given.

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

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

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less

Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

PubMed

Zhang, Qiang; Bhattacharya, Sudin; Andersen, Melvin E; Conolly, Rory B

2010-02-01

The new paradigm envisioned for toxicity testing in the 21st century advocates shifting from the current animal-based testing process to a combination of in vitro cell-based studies, high-throughput techniques, and in silico modeling. A strategic component of the vision is the adoption of the systems biology approach to acquire, analyze, and interpret toxicity pathway data. As key toxicity pathways are identified and their wiring details elucidated using traditional and high-throughput techniques, there is a pressing need to understand their qualitative and quantitative behaviors in response to perturbation by both physiological signals and exogenous stressors. The complexity of these molecular networks makes the task of understanding cellular responses merely by human intuition challenging, if not impossible. This process can be aided by mathematical modeling and computer simulation of the networks and their dynamic behaviors. A number of theoretical frameworks were developed in the last century for understanding dynamical systems in science and engineering disciplines. These frameworks, which include metabolic control analysis, biochemical systems theory, nonlinear dynamics, and control theory, can greatly facilitate the process of organizing, analyzing, and understanding toxicity pathways. Such analysis will require a comprehensive examination of the dynamic properties of "network motifs"--the basic building blocks of molecular circuits. Network motifs like feedback and feedforward loops appear repeatedly in various molecular circuits across cell types and enable vital cellular functions like homeostasis, all-or-none response, memory, and biological rhythm. These functional motifs and associated qualitative and quantitative properties are the predominant source of nonlinearities observed in cellular dose response data. Complex response behaviors can arise from toxicity pathways built upon combinations of network motifs. While the field of computational cell biology has advanced rapidly with increasing availability of new data and powerful simulation techniques, a quantitative orientation is still lacking in life sciences education to make efficient use of these new tools to implement the new toxicity testing paradigm. A revamped undergraduate curriculum in the biological sciences including compulsory courses in mathematics and analysis of dynamical systems is required to address this gap. In parallel, dissemination of computational systems biology techniques and other analytical tools among practicing toxicologists and risk assessment professionals will help accelerate implementation of the new toxicity testing vision.

Workflow based framework for life science informatics.

PubMed

Tiwari, Abhishek; Sekhar, Arvind K T

2007-10-01

Workflow technology is a generic mechanism to integrate diverse types of available resources (databases, servers, software applications and different services) which facilitate knowledge exchange within traditionally divergent fields such as molecular biology, clinical research, computational science, physics, chemistry and statistics. Researchers can easily incorporate and access diverse, distributed tools and data to develop their own research protocols for scientific analysis. Application of workflow technology has been reported in areas like drug discovery, genomics, large-scale gene expression analysis, proteomics, and system biology. In this article, we have discussed the existing workflow systems and the trends in applications of workflow based systems.

Genomics, proteomics, MEMS and SAIF: which role for diagnostic imaging?

PubMed

Grassi, R; Lagalla, R; Rotondo, A

2008-09-01

In these three words--genomics, proteomics and nanotechnologies--is the future of medicine of the third millennium, which will be characterised by more careful attention to disease prevention, diagnosis and treatment. Molecular imaging appears to satisfy this requirement. It is emerging as a new science that brings together molecular biology and in vivo imaging and represents the key for the application of personalized medicine. Micro-PET (positron emission tomography), micro-SPECT (single photon emission computed tomography), micro-CT (computed tomography), micro-MR (magnetic resonance), micro-US (ultrasound) and optical imaging are all molecular imaging techniques, several of which are applied only in preclinical settings on animal models. Others, however, are applied routinely in both clinical and preclinical setting. Research on small animals allows investigation of the genesis and development of diseases, as well as drug efficacy and the development of personalized therapies, through the study of biological processes that precede the expression of common symptoms of a pathology. Advances in molecular imaging were made possible only by collaboration among scientists in the fields of radiology, chemistry, molecular and cell biology, physics, mathematics, pharmacology, gene therapy and oncology. Although until now researchers have traditionally limited their interactions, it is only by increasing these connections that the current gaps in terminology, methods and approaches that inhibit scientific progress can be eliminated.

Crystal structure of channelrhodopsin, a light-gated cation channel – all cations lead through the monomer –

PubMed Central

Kato, Hideaki E.; Nureki, Osamu

2013-01-01

Channelrhodopsin (ChR) is a light-gated cation channel derived from green algae. Since the inward flow of cations triggers the neuron firing, neurons expressing ChRs can be optically controlled even within freely moving mammals. Although ChR has been broadly applied to neuro-science research, little is known about its molecular mechanisms. We determined the crystal structure of chimeric ChR at 2.3 Å resolution and revealed its molecular architecture. The integration of structural, electrophysio-logical, and computational analyses provided insight into the molecular basis for the channel function of ChR, and paved the way for the principled design of ChR variants with novel properties. PMID:27493541

[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.

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

PubMed

Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf

2017-11-20

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S N 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

NASA Astrophysics Data System (ADS)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

A classical reactive potential for molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2015-10-12

We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, itmore » is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.« less

Designer drugs: the evolving science of drug discovery.

PubMed

Wanke, L A; DuBose, R F

1998-07-01

Drug discovery and design are fundamental to drug development. Until recently, most drugs were discovered through random screening or developed through molecular modification. New technologies are revolutionizing this phase of drug development. Rational drug design, using powerful computers and computational chemistry and employing X-ray crystallography, nuclear magnetic resonance spectroscopy, and three-dimensional quantitative structure activity relationship analysis, is creating highly specific, biologically active molecules by virtual reality modeling. Sophisticated screening technologies are eliminating all but the most active lead compounds. These new technologies promise more efficacious, safe, and cost-effective medications, while minimizing drug development time and maximizing profits.

Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

PubMed Central

Da Silva, Franck; Empereur-mot, Charly; Chavent, Matthieu; Baaden, Marc

2013-01-01

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/. PMID:23483961

Game on, science - how video game technology may help biologists tackle visualization challenges.

PubMed

Lv, Zhihan; Tek, Alex; Da Silva, Franck; Empereur-mot, Charly; Chavent, Matthieu; Baaden, Marc

2013-01-01

The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.

Crop improvement using life cycle datasets acquired under field conditions.

PubMed

Mochida, Keiichi; Saisho, Daisuke; Hirayama, Takashi

2015-01-01

Crops are exposed to various environmental stresses in the field throughout their life cycle. Modern plant science has provided remarkable insights into the molecular networks of plant stress responses in laboratory conditions, but the responses of different crops to environmental stresses in the field need to be elucidated. Recent advances in omics analytical techniques and information technology have enabled us to integrate data from a spectrum of physiological metrics of field crops. The interdisciplinary efforts of plant science and data science enable us to explore factors that affect crop productivity and identify stress tolerance-related genes and alleles. Here, we describe recent advances in technologies that are key components for data driven crop design, such as population genomics, chronological omics analyses, and computer-aided molecular network prediction. Integration of the outcomes from these technologies will accelerate our understanding of crop phenology under practical field situations and identify key characteristics to represent crop stress status. These elements would help us to genetically engineer "designed crops" to prevent yield shortfalls because of environmental fluctuations due to future climate change.

The graph neural network model.

PubMed

Scarselli, Franco; Gori, Marco; Tsoi, Ah Chung; Hagenbuchner, Markus; Monfardini, Gabriele

2009-01-01

Many underlying relationships among data in several areas of science and engineering, e.g., computer vision, molecular chemistry, molecular biology, pattern recognition, and data mining, can be represented in terms of graphs. In this paper, we propose a new neural network model, called graph neural network (GNN) model, that extends existing neural network methods for processing the data represented in graph domains. This GNN model, which can directly process most of the practically useful types of graphs, e.g., acyclic, cyclic, directed, and undirected, implements a function tau(G,n) is an element of IR(m) that maps a graph G and one of its nodes n into an m-dimensional Euclidean space. A supervised learning algorithm is derived to estimate the parameters of the proposed GNN model. The computational cost of the proposed algorithm is also considered. Some experimental results are shown to validate the proposed learning algorithm, and to demonstrate its generalization capabilities.

Molecular Imaging in the College of Optical Sciences – An Overview of Two Decades of Instrumentation Development

PubMed Central

Furenlid, Lars R.; Barrett, Harrison H.; Barber, H. Bradford; Clarkson, Eric W.; Kupinski, Matthew A.; Liu, Zhonglin; Stevenson, Gail D.; Woolfenden, James M.

2015-01-01

During the past two decades, researchers at the University of Arizona’s Center for Gamma-Ray Imaging (CGRI) have explored a variety of approaches to gamma-ray detection, including scintillation cameras, solid-state detectors, and hybrids such as the intensified Quantum Imaging Device (iQID) configuration where a scintillator is followed by optical gain and a fast CCD or CMOS camera. We have combined these detectors with a variety of collimation schemes, including single and multiple pinholes, parallel-hole collimators, synthetic apertures, and anamorphic crossed slits, to build a large number of preclinical molecular-imaging systems that perform Single-Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), and X-Ray Computed Tomography (CT). In this paper, we discuss the themes and methods we have developed over the years to record and fully use the information content carried by every detected gamma-ray photon. PMID:26236069

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

Dang, Liem X.; Schenter, Gregory K.

To enhance our understanding of the solvent exchange mechanism in liquid methanol, we report a systematic study of this process using molecular dynamics simulations. We use transition state theory, the Impey-Madden-McDonald method, the reactive flux method, and Grote-Hynes theory to compute the rate constants for this process. Solvent coupling was found to dominate, resulting in a significantly small transmission coefficient. We predict a positive activation volume for the methanol exchange process. The essential features of the dynamics of the system as well as the pressure dependence are recovered from a Generalized Langevin Equation description of the dynamics. We find thatmore » the dynamics and response to anharmonicity can be decomposed into two time regimes, one corresponding to short time response (< 0.1 ps) and long time response (> 5 ps). An effective characterization of the process results from launching dynamics from the planar hypersurface corresponding to Grote-Hynes theory. This results in improved numerical convergence of correlation functions. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Graphene Oxide Catalyzed C-H Bond Activation: The Importance Oxygen Functional Groups for Biaryl Construction

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

Gao, Yongjun; Tang, Pei; Zhou, Hu

A heterogeneous, inexpensive and environment-friendly carbon catalytic system was developed for the C-H bond arylation of benzene resulting in the subsequent formation of biaryl compounds. The oxygen-containing groups on these graphene oxide sheets play an essential role in the observed catalytic activity. The catalytic results of model compounds and DFT calculations show that these functional groups promote this reaction by stabilization and activation of K ions at the same time of facilitating the leaving of I. And further mechanisms studies show that it is the charge induced capabilities of oxygen groups connected to specific carbon skeleton together with the giantmore » π-reaction platform provided by the π-domain of graphene that played the vital roles in the observed excellent catalytic activity. D. Mei acknowledges the support from the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory.« less

Computational studies of adsorption in metal organic frameworks and interaction of nanoparticles in condensed phases

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

Annapureddy, Harsha V.; Motkuri, Radha K.; Nguyen, Phuong T.

In this review, we describe recent efforts in which computer simulations were used to systematically study nano-structured metal organic frameworks, with particular emphasis on their application in heating and cooling processes. These materials also are known as metal organic heat carriers. We used both molecular dynamics and Grand Canonical Monte Carlo simulation techniques to gain a molecular-level understanding of the adsorption mechanism of gases in these porous materials. We investigated the uptake of various gases such as refrigerants R12 and R143a and also the elemental gases Xe and Rn by the metal organic framework (i.e., Ni2(dhtp)). We also evaluated themore » effects of temperature and pressure on the uptake mechanism. Our computed results compared reasonably well with available experimental measurements, thus validating our potential models and approaches. In addition, we also investigated the structural, diffusive, and adsorption properties of different hydrocarbons in Ni2(dhtp). To elucidate the mechanism of nanoparticle dispersion in condensed phases, we also studied the interactions among nanoparticles in various liquids, such as n-hexane, water and methanol. This work was performed at Pacific Northwest National Laboratory (PNNL) and was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences, U.S. Department of Energy (DOE). PNNL is operated by Battelle for the DOE. The authors also gratefully acknowledge support received from the National Energy Technology Laboratory of DOE's Office of Fossil Energy.« less

Educational aspects of molecular simulation

NASA Astrophysics Data System (ADS)

Allen, Michael P.

This article addresses some aspects of teaching simulation methods to undergraduates and graduate students. Simulation is increasingly a cross-disciplinary activity, which means that the students who need to learn about simulation methods may have widely differing backgrounds. Also, they may have a wide range of views on what constitutes an interesting application of simulation methods. Almost always, a successful simulation course includes an element of practical, hands-on activity: a balance always needs to be struck between treating the simulation software as a 'black box', and becoming bogged down in programming issues. With notebook computers becoming widely available, students often wish to take away the programs to run themselves, and access to raw computer power is not the limiting factor that it once was; on the other hand, the software should be portable and, if possible, free. Examples will be drawn from the author's experience in three different contexts. (1) An annual simulation summer school for graduate students, run by the UK CCP5 organization, in which practical sessions are combined with an intensive programme of lectures describing the methodology. (2) A molecular modelling module, given as part of a doctoral training centre in the Life Sciences at Warwick, for students who might not have a first degree in the physical sciences. (3) An undergraduate module in Physics at Warwick, also taken by students from other disciplines, teaching high performance computing, visualization, and scripting in the context of a physical application such as Monte Carlo simulation.

Conformational Dynamics and Proton Relay Positioning in Nickel Catalysts for Hydrogen Production and Oxidation

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

Franz, James A.; O'Hagan, Molly J.; Ho, Ming-Hsun

2013-12-09

The [Ni(PR2NR’2)2]2+ catalysts, (where PR2NR´2 is 1,5-R´-3,7-R-1,5-diaza-3,7-diphosphacyclooctane), are some of the fastest reported for hydrogen production and oxidation, however, chair/boat isomerization and the presence of a fifth solvent ligand have the potential to slow catalysis by incorrectly positioning the pendant amines or blocking the addition of hydrogen. Here, we report the structural dynamics of a series of [Ni(PR2NR’2)2]n+ complexes, characterized by NMR spectroscopy and theoretical modeling. A fast exchange process was observed for the [Ni(CH3CN)(PR2NR’2)2]2+ complexes which depends on the ligand. This exchange process was identified to occur through a three step mechanism including dissociation of the acetonitrile, boat/chair isomerizationmore » of each of the four rings identified by the phosphine ligands (including nitrogen inversion), and reassociation of acetonitrile on the opposite side of the complex. The rate of the chair/boat inversion can be influenced by varying the substituent on the nitrogen atom, but the rate of the overall exchange process is at least an order of magnitude faster than the catalytic rate in acetonitrile demonstrating that the structural dynamics of the [Ni(PR2NR´2)2]2+ complexes does not hinder catalysis. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under FWP56073. Research by J.A.F., M.O., M-H. H., M.L.H, D.L.D. A.M.A., S. R. and R.M.B. was carried out in the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. W.J.S. and S.L. were funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. T.L. was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory; the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory; and the Jaguar supercomputer at Oak Ridge National Laboratory (INCITE 2008-2011 award supported by the Office of Science of the U.S. DOE under Contract No. DE-AC0500OR22725).« less

Molecular modeling in structural nano-toxicology: interactions of nano-particles with nano-machinery of cells.

PubMed

Yanamala, Naveena; Kagan, Valerian E; Shvedova, Anna A

2013-12-01

Over the past two decades, nanotechnology has emerged as a key player in various disciplines of science and technology. Some of the most exciting applications are in the field of biomedicine - for theranostics (for combined diagnostic and therapeutic purposes) as well as for exploration of biological systems. A detailed understanding of the molecular interactions between nanoparticles and biological nano-machinery - macromolecules, membranes, and intracellular organelles - is crucial for obtaining adequate information on mechanisms of action of nanomaterials as well as a perspective on the long term effects of these materials and their possible toxicological outcomes. This review focuses on the use of structure-based computational molecular modeling as a tool to understand and to predict the interactions between nanomaterials and nano-biosystems. We review major approaches and provide examples of computational analysis of the structural principles behind such interactions. A rationale on how nanoparticles of different sizes, shape, structure and chemical properties can affect the organization and functions of nano-machinery of cells is also presented. Published by Elsevier B.V.

Computing exponentially faster: implementing a non-deterministic universal Turing machine using DNA

PubMed Central

Currin, Andrew; Korovin, Konstantin; Ababi, Maria; Roper, Katherine; Kell, Douglas B.; Day, Philip J.

2017-01-01

The theory of computer science is based around universal Turing machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of classical UTMs. For the most important class of problem in computer science, non-deterministic polynomial complete problems, non-deterministic UTMs (NUTMs) are theoretically exponentially faster than both classical UTMs and quantum mechanical UTMs (QUTMs). However, no attempt has previously been made to build an NUTM, and their construction has been regarded as impossible. Here, we demonstrate the first physical design of an NUTM. This design is based on Thue string rewriting systems, and thereby avoids the limitations of most previous DNA computing schemes: all the computation is local (simple edits to strings) so there is no need for communication, and there is no need to order operations. The design exploits DNA's ability to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that the design works using both computational modelling and in vitro molecular biology experimentation: the design is thermodynamically favourable, microprogramming can be used to encode arbitrary Thue rules, all classes of Thue rule can be implemented, and non-deterministic rule implementation. In an NUTM, the resource limitation is space, which contrasts with classical UTMs and QUTMs where it is time. This fundamental difference enables an NUTM to trade space for time, which is significant for both theoretical computer science and physics. It is also of practical importance, for to quote Richard Feynman ‘there's plenty of room at the bottom’. This means that a desktop DNA NUTM could potentially utilize more processors than all the electronic computers in the world combined, and thereby outperform the world's current fastest supercomputer, while consuming a tiny fraction of its energy. PMID:28250099

Introduction to bioinformatics.

PubMed

Can, Tolga

2014-01-01

Bioinformatics is an interdisciplinary field mainly involving molecular biology and genetics, computer science, mathematics, and statistics. Data intensive, large-scale biological problems are addressed from a computational point of view. The most common problems are modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution usually involves the following steps: Collect statistics from biological data. Build a computational model. Solve a computational modeling problem. Test and evaluate a computational algorithm. This chapter gives a brief introduction to bioinformatics by first providing an introduction to biological terminology and then discussing some classical bioinformatics problems organized by the types of data sources. Sequence analysis is the analysis of DNA and protein sequences for clues regarding function and includes subproblems such as identification of homologs, multiple sequence alignment, searching sequence patterns, and evolutionary analyses. Protein structures are three-dimensional data and the associated problems are structure prediction (secondary and tertiary), analysis of protein structures for clues regarding function, and structural alignment. Gene expression data is usually represented as matrices and analysis of microarray data mostly involves statistics analysis, classification, and clustering approaches. Biological networks such as gene regulatory networks, metabolic pathways, and protein-protein interaction networks are usually modeled as graphs and graph theoretic approaches are used to solve associated problems such as construction and analysis of large-scale networks.

UC Merced Center for Computational Biology Final Report

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

Colvin, Michael; Watanabe, Masakatsu

Final report for the UC Merced Center for Computational Biology. The Center for Computational Biology (CCB) was established to support multidisciplinary scientific research and academic programs in computational biology at the new University of California campus in Merced. In 2003, the growing gap between biology research and education was documented in a report from the National Academy of Sciences, Bio2010 Transforming Undergraduate Education for Future Research Biologists. We believed that a new type of biological sciences undergraduate and graduate programs that emphasized biological concepts and considered biology as an information science would have a dramatic impact in enabling the transformationmore » of biology. UC Merced as newest UC campus and the first new U.S. research university of the 21st century was ideally suited to adopt an alternate strategy - to create a new Biological Sciences majors and graduate group that incorporated the strong computational and mathematical vision articulated in the Bio2010 report. CCB aimed to leverage this strong commitment at UC Merced to develop a new educational program based on the principle of biology as a quantitative, model-driven science. Also we expected that the center would be enable the dissemination of computational biology course materials to other university and feeder institutions, and foster research projects that exemplify a mathematical and computations-based approach to the life sciences. As this report describes, the CCB has been successful in achieving these goals, and multidisciplinary computational biology is now an integral part of UC Merced undergraduate, graduate and research programs in the life sciences. The CCB began in fall 2004 with the aid of an award from U.S. Department of Energy (DOE), under its Genomes to Life program of support for the development of research and educational infrastructure in the modern biological sciences. This report to DOE describes the research and academic programs made possible by the CCB from its inception until August, 2010, at the end of the final extension. Although DOE support for the center ended in August 2010, the CCB will continue to exist and support its original objectives. The research and academic programs fostered by the CCB have led to additional extramural funding from other agencies, and we anticipate that CCB will continue to provide support for quantitative and computational biology program at UC Merced for many years to come. Since its inception in fall 2004, CCB research projects have continuously had a multi-institutional collaboration with Lawrence Livermore National Laboratory (LLNL), and the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign, as well as individual collaborators at other sites. CCB affiliated faculty cover a broad range of computational and mathematical research including molecular modeling, cell biology, applied math, evolutional biology, bioinformatics, etc. The CCB sponsored the first distinguished speaker series at UC Merced, which had an important role is spreading the word about the computational biology emphasis at this new campus. One of CCB's original goals is to help train a new generation of biologists who bridge the gap between the computational and life sciences. To archive this goal, by summer 2006, a new program - summer undergraduate internship program, have been established under CCB to train the highly mathematical and computationally intensive Biological Science researchers. By the end of summer 2010, 44 undergraduate students had gone through this program. Out of those participants, 11 students have been admitted to graduate schools and 10 more students are interested in pursuing graduate studies in the sciences. The center is also continuing to facilitate the development and dissemination of undergraduate and graduate course materials based on the latest research in computational biology.« less

Computational and theoretical modeling of pH and flow effects on the early-stage non-equilibrium self-assembly of optoelectronic peptides

NASA Astrophysics Data System (ADS)

Mansbach, Rachael; Ferguson, Andrew

Self-assembling π-conjugated peptides are attractive candidates for the fabrication of bioelectronic materials possessing optoelectronic properties due to electron delocalization over the conjugated peptide groups. We present a computational and theoretical study of an experimentally-realized optoelectronic peptide that displays triggerable assembly in low pH to resolve the microscopic effects of flow and pH on the non-equilibrium morphology and kinetics of assembly. Using a combination of molecular dynamics simulations and hydrodynamic modeling, we quantify the time and length scales at which convective flows employed in directed assembly compete with microscopic diffusion to influence assembly. We also show that there is a critical pH below which aggregation proceeds irreversibly, and quantify the relationship between pH, charge density, and aggregate size. Our work provides new fundamental understanding of pH and flow of non-equilibrium π-conjugated peptide assembly, and lays the groundwork for the rational manipulation of environmental conditions and peptide chemistry to control assembly and the attendant emergent optoelectronic properties. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award # DE-SC0011847, and by the Computational Science and Engineering Fellowship from the University of Illinois at Urbana-Champaign.

[Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer].

PubMed

Fang, Xiang; Li, Ning-qiu; Fu, Xiao-zhe; Li, Kai-bin; Lin, Qiang; Liu, Li-hui; Shi, Cun-bin; Wu, Shu-qin

2015-07-01

As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects.

An Introduction to Programming for Bioscientists: A Python-Based Primer

PubMed Central

Mura, Cameron

2016-01-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a “variable,” the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences. PMID:27271528

An Introduction to Programming for Bioscientists: A Python-Based Primer.

PubMed

Ekmekci, Berk; McAnany, Charles E; Mura, Cameron

2016-06-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a "variable," the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.

Mechanisms and Dynamics of Abiotic and Biotic Interactions at Environmental Interfaces

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

Roso, Kevin M.

The Stanford EMSI (SEMSI) was established in 2004 through joint funding by the National Science Foundation and the OBER-ERSD. It encompasses a number of universities and national laboratories. The PNNL component of the SEMSI is funded by ERSD and is the focus of this report. This component has the objective of providing theory support to the SEMSI by bringing computational capabilities and expertise to bear on important electron transfer problems at mineral/water and mineral/microbe interfaces. PNNL staff member Dr. Kevin Rosso, who is also ''matrixed'' into the Environmental Molecular Sciences Laboratory (EMSL) at PNNL, is a co-PI on the SEMSImore » project and the PNNL lead. The EMSL computational facilities being applied to the SEMSI project include the 11.8 teraflop massively-parallel supercomputer. Science goals of this EMSL/SEMSI partnership include advancing our understanding of: (1) The kinetics of U(VI) and Cr(VI) reduction by aqueous and solid-phase Fe(II), (2) The structure of mineral surfaces in equilibrium with solution, and (3) Mechanisms of bacterial electron transfer to iron oxide surfaces via outer-membrane cytochromes.« less

Polymerization and Structure of Bio-Based Plastics: A Computer Simulation

NASA Astrophysics Data System (ADS)

Khot, Shrikant N.; Wool, Richard P.

2001-03-01

We recently examined several hundred chemical pathways to convert chemically functionalized plant oil triglycerides, monoglycerides and reactive diluents into high performance plastics with a broad range of properties (US Patent No. 6,121,398). The resulting polymers had linear, branched, light- and highly-crosslinked chain architectures and could be used as pressure sensitive adhesives, elastomers and high performance rigid thermoset composite resins. To optimize the molecular design and minimize the number of chemical trials in this system with excess degrees of freedom, we developed a computer simulation of the free radical polymerization process. The triglyceride structure, degree of chemical substitution, mole fractions, fatty acid distribution function, and reaction kinetic parameters were used as initial inputs on a 3d lattice simulation. The evolution of the network fractal structure was computed and used to measure crosslink density, dangling ends, degree of reaction and defects in the lattice. The molecular connectivity was used to determine strength via a vector percolation model of fracture. The simulation permitted the optimal design of new bio-based materials with respect to monomer selection, cure reaction conditions and desired properties. Supported by the National Science Foundation

Molecularization in nutritional science: a view from philosophy of science.

PubMed

Ströhle, Alexander; Döring, Frank

2010-10-01

Over the past decade, a trend toward molecularization, which could be observed in almost all bioscientific disciplines, now appears to have also developed in nutritional science. However, molecular nutrition research gives birth to a series of questions. Therefore, we take a look at the epistemological foundation of (molecular) nutritional science. We (i) analyze the scientific status of (molecular) nutritional science and its position in the canon of other scientific disciplines, (ii) focus on the cognitive aims of nutritional science in general and (iii) on the chances and limits of molecular nutrition research in particular. By taking up the thoughts of an earlier work, we are analyzing (molecular) nutritional science from a strictly realist and emergentist-naturalist perspective. Methodologically, molecular nutrition research is bound to a microreductive research approach. We emphasize, however, that it need not be a radical microreductionism whose scientific reputation is not the best. Instead we favor moderate microreductionism, which combines reduction with integration. As mechanismic explanations are one of the primary aims of factual sciences, we consider it as the task of molecular nutrition research to find profound, i.e. molecular-mechanismic, explanations for the conditions, characteristics and changes of organisms related to the organism-nutrition environment interaction.

Computed tomography of subchondral bone and osteophytes in hip osteoarthritis: the shape of things to come?

PubMed

Turmezei, Tom D; Poole, Ken E S

2011-01-01

Bone is a fundamental component of the disordered joint homeostasis seen in osteoarthritis, a disease that has been primarily characterized by the breakdown of articular cartilage accompanied by local bone changes and a limited degree of joint inflammation. In this review we consider the role of computed tomography imaging and computational analysis in osteoarthritis research, focusing on subchondral bone and osteophytes in the hip. We relate what is already known in this area to what could be explored through this approach in the future in relation to both clinical research trials and the underlying cellular and molecular science of osteoarthritis. We also consider how this area of research could impact on our understanding of the genetics of osteoarthritis.

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

Microbiome Tools for Forensic Science.

PubMed

Metcalf, Jessica L; Xu, Zhenjiang Z; Bouslimani, Amina; Dorrestein, Pieter; Carter, David O; Knight, Rob

2017-09-01

Microbes are present at every crime scene and have been used as physical evidence for over a century. Advances in DNA sequencing and computational approaches have led to recent breakthroughs in the use of microbiome approaches for forensic science, particularly in the areas of estimating postmortem intervals (PMIs), locating clandestine graves, and obtaining soil and skin trace evidence. Low-cost, high-throughput technologies allow us to accumulate molecular data quickly and to apply sophisticated machine-learning algorithms, building generalizable predictive models that will be useful in the criminal justice system. In particular, integrating microbiome and metabolomic data has excellent potential to advance microbial forensics. Copyright © 2017. Published by Elsevier Ltd.

Molecular simulations for energy, environmental and pharmaceutical applications of nanoporous materials: from zeolites, metal-organic frameworks to protein crystals.

PubMed

Jiang, Jianwen; Babarao, Ravichandar; Hu, Zhongqiao

2011-07-01

Nanoporous materials have widespread applications in chemical industry, but the pathway from laboratory synthesis and testing to practical utilization of nanoporous materials is substantially challenging and requires fundamental understanding from the bottom up. With ever-growing computational resources, molecular simulations have become an indispensable tool for material characterization, screening and design. This tutorial review summarizes the recent simulation studies in zeolites, metal-organic frameworks and protein crystals, and provides a molecular overview for energy, environmental and pharmaceutical applications of nanoporous materials with increasing degree of complexity in building blocks. It is demonstrated that molecular-level studies can bridge the gap between physical and engineering sciences, unravel microscopic insights that are otherwise experimentally inaccessible, and assist in the rational design of new materials. The review is concluded with major challenges in future simulation exploration of novel nanoporous materials for emerging applications.

Molecular-dynamics simulations of urea nucleation from aqueous solution

PubMed Central

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-01

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932

Molecular-dynamics simulations of urea nucleation from aqueous solution.

PubMed

Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

2015-01-06

Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

Surface tension and contact angles: Molecular origins and associated microstructure

NASA Technical Reports Server (NTRS)

Davis, H. T.

1982-01-01

Gradient theory converts the molecular theory of inhomogeneous fluid into nonlinear boundary value problems for density and stress distributions in fluid interfaces, contact line regions, nuclei and microdroplets, and other fluid microstructures. The relationship between the basic patterns of fluid phase behavior and the occurrence and stability of fluid microstructures was clearly established by the theory. All the inputs of the theory have molecular expressions which are computable from simple models. On another level, the theory becomes a phenomenological framework in which the equation of state of homogeneous fluid and sets of influence parameters of inhomogeneous fluids are the inputs and the structures, stress tensions and contact angles of menisci are the outputs. These outputs, which find applications in the science and technology of drops and bubbles, are discussed.

Accelerating scientific discovery : 2007 annual report.

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

Beckman, P.; Dave, P.; Drugan, C.

2008-11-14

As a gateway for scientific discovery, the Argonne Leadership Computing Facility (ALCF) works hand in hand with the world's best computational scientists to advance research in a diverse span of scientific domains, ranging from chemistry, applied mathematics, and materials science to engineering physics and life sciences. Sponsored by the U.S. Department of Energy's (DOE) Office of Science, researchers are using the IBM Blue Gene/L supercomputer at the ALCF to study and explore key scientific problems that underlie important challenges facing our society. For instance, a research team at the University of California-San Diego/ SDSC is studying the molecular basis ofmore » Parkinson's disease. The researchers plan to use the knowledge they gain to discover new drugs to treat the disease and to identify risk factors for other diseases that are equally prevalent. Likewise, scientists from Pratt & Whitney are using the Blue Gene to understand the complex processes within aircraft engines. Expanding our understanding of jet engine combustors is the secret to improved fuel efficiency and reduced emissions. Lessons learned from the scientific simulations of jet engine combustors have already led Pratt & Whitney to newer designs with unprecedented reductions in emissions, noise, and cost of ownership. ALCF staff members provide in-depth expertise and assistance to those using the Blue Gene/L and optimizing user applications. Both the Catalyst and Applications Performance Engineering and Data Analytics (APEDA) teams support the users projects. In addition to working with scientists running experiments on the Blue Gene/L, we have become a nexus for the broader global community. In partnership with the Mathematics and Computer Science Division at Argonne National Laboratory, we have created an environment where the world's most challenging computational science problems can be addressed. Our expertise in high-end scientific computing enables us to provide guidance for applications that are transitioning to petascale as well as to produce software that facilitates their development, such as the MPICH library, which provides a portable and efficient implementation of the MPI standard--the prevalent programming model for large-scale scientific applications--and the PETSc toolkit that provides a programming paradigm that eases the development of many scientific applications on high-end computers.« less

Know Your Discipline: Teaching the Philosophy of Computer Science

ERIC Educational Resources Information Center

Tedre, Matti

2007-01-01

The diversity and interdisciplinarity of computer science and the multiplicity of its uses in other sciences make it hard to define computer science and to prescribe how computer science should be carried out. The diversity of computer science also causes friction between computer scientists from different branches. Computer science curricula, as…

Promotional effect of surface hydroxyls on electrochemical reduction of CO2 over SnOx/Sn electrode

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

Cui, Chaonan; Han, Jinyu; Zhu, Xinli

Tin oxide (SnOx) formation on tin-based electrode surfaces during CO2 electrochemical reduction can have a significant impact on the activity and selectivity of the reaction. In the present study, density functional theory (DFT) calculations have been performed to understand the role of SnOx in CO2 reduction using a SnO monolayer on the Sn(112) surface as a model for SnOx. Water molecules have been treated explicitly and considered actively participating in the reaction. The results showed that H2O dissociates on the perfect SnO monolayer into two hydroxyl groups symmetrically on the surface. CO2 energetically prefers to react with the hydroxyl, formingmore » a bicarbonate (HCO3(t)*) intermediate, which can then be reduced to either formate (HCOO*) by hydrogenating the carbon atom or carboxyl (COOH*) by protonating the oxygen atom. Both steps involve a simultaneous C-O bond breaking. Further reduction of HCOO* species leads to the formation of formic acid in the acidic solution at pH < 4, while the COOH* will decompose to CO and H2O via protonation. Whereas the oxygen vacancy (VO) in the monolayer maybe formed by the reduction of the monolayer, it can be recovered by H2O dissociation, resulting in two embedded hydroxyl groups. However, the hydroxylated surface with two symmetric hydroxyls is energetically more favorable for CO2 reduction than the hydroxylated VO surface with two embedded hydroxyls. The reduction potential for the former has a limiting-potential of -0.20 V (RHE), lower than that for the latter (-0.74 V (RHE)). Compared to the pure Sn electrode, the formation of SnOx monolayer on the electrode under the operating conditions promotes CO2 reduction more effectively by forming surface hydroxyls, thereby, providing a new channel via COOH* to the CO formation, although formic acid is still the major reduction product. The work was supported in part by National Natural Sciences Foundation of China (Grant #21373148 and #21206117). The High Performance Computing Center of Tianjin University is acknowledged for providing services to the computing cluster. CC acknowledges the support of 24 China Scholarship Council (CSC). QG acknowledges the support of NSF-CBET program (Award no. CBET-1438440). DM was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. The computations were performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory (PNNL) in Richland, Washington.« less

Report of the matrix of biological knowledge workshop

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

Morowitz, H.J.; Smith, T.

1987-10-30

Current understanding of biology involves complex relationships rooted in enormous amounts of data. These data include entries from biochemistry, ecology, genetics, human and veterinary medicine, molecular structure studies, agriculture, embryology, systematics, and many other disciplines. The present wealth of biological data goes beyond past accumulations now include new understandings from molecular biology. Several important biological databases are currently being supported, and more are planned; however, major problems of interdatabase communication and management efficiency abound. Few scientists are currently capable of keeping up with this ever-increasing wealth of knowledge, let alone searching it efficiently for new or unsuspected links and importantmore » analogies. Yet this is what is required if the continued rapid generation of such data is to lead most effectively to the major conceptual, medical, and agricultural advances anticipated over the coming decades in the United States. The opportunity exists to combine the potential of modern computer science, database management, and artificial intelligence in a major effort to organize the vast wealth of biological and clinical data. The time is right because the amount of data is still manageable even in its current highly-fragmented form; important hardware and computer science tools have been greatly improved; and there have been recent fundamental advances in our comprehension of biology. This latter is particularly true at the molecular level where the information for nearly all higher structure and function is encoded. The organization of all biological experimental data coordinately within a structure incorporating our current understanding - the Matrix of Biological Knowledge - will provide the data and structure for the major advances foreseen in the years ahead.« less

Proceedings ICASS 2017

NASA Astrophysics Data System (ADS)

Fu, Qiang; Schaaf, Peter

2018-07-01

This special issue of the high impact international peer reviewed journal Applied Surface Science represents the proceedings of the 2nd International Conference on Applied Surface Science ICASS held 12-16 June 2017 in Dalian China. The conference provided a forum for researchers in all areas of applied surface science to present their work. The main topics of the conference are in line with the most popular areas of research reported in Applied Surface Science. Thus, this issue includes current research on the role and use of surfaces in chemical and physical processes, related to catalysis, electrochemistry, surface engineering and functionalization, biointerfaces, semiconductors, 2D-layered materials, surface nanotechnology, energy, new/functional materials and nanotechnology. Also the various techniques and characterization methods will be discussed. Hence, scientific research on the atomic and molecular level of material properties investigated with specific surface analytical techniques and/or computational methods is essential for any further progress in these fields.

26TH AFOSR Chemical & Atmospheric Sciences Program Review FY81.

DTIC Science & Technology

1982-03-01

AFOSR-80-0020, 2310/A2 N. Larsen Department of Electrical Engineering Cornell University Ithaca, New York 14853 Light Scattering and Absorption Kuo-Nan...0011; University of Florida 80-0015 (To MRO Contract DAAM 1816 NW G Street 29-78-G-0024), 2310/Al Gainesville, FL 32601 Atmospheric Absorption of...parameters for use in the theoretical spectroscopy, for updating the transmission/emission codes, and for computing molecular absorption /emission line

`Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny

NASA Astrophysics Data System (ADS)

Kolekar, Pandurang S.; Kale, Mohan M.; Kulkarni-Kale, Urmila

2010-10-01

Bioinformatics, being multidisciplinary field, involves applications of various methods from allied areas of Science for data mining using computational approaches. Clustering and molecular phylogeny is one of the key areas in Bioinformatics, which help in study of classification and evolution of organisms. Molecular phylogeny algorithms can be divided into distance based and character based methods. But most of these methods are dependent on pre-alignment of sequences and become computationally intensive with increase in size of data and hence demand alternative efficient approaches. `Inter arrival time distribution' (IATD) is a popular concept in the theory of stochastic system modeling but its potential in molecular data analysis has not been fully explored. The present study reports application of IATD in Bioinformatics for clustering and molecular phylogeny. The proposed method provides IATDs of nucleotides in genomic sequences. The distance function based on statistical parameters of IATDs is proposed and distance matrix thus obtained is used for the purpose of clustering and molecular phylogeny. The method is applied on a dataset of 3' non-coding region sequences (NCR) of Dengue virus type 3 (DENV-3), subtype III, reported in 2008. The phylogram thus obtained revealed the geographical distribution of DENV-3 isolates. Sri Lankan DENV-3 isolates were further observed to be clustered in two sub-clades corresponding to pre and post Dengue hemorrhagic fever emergence groups. These results are consistent with those reported earlier, which are obtained using pre-aligned sequence data as an input. These findings encourage applications of the IATD based method in molecular phylogenetic analysis in particular and data mining in general.

Exascale computing and what it means for shock physics

NASA Astrophysics Data System (ADS)

Germann, Timothy

2015-06-01

The U.S. Department of Energy is preparing to launch an Exascale Computing Initiative, to address the myriad challenges required to deploy and effectively utilize an exascale-class supercomputer (i.e., one capable of performing 1018 operations per second) in the 2023 timeframe. Since physical (power dissipation) requirements limit clock rates to at most a few GHz, this will necessitate the coordination of on the order of a billion concurrent operations, requiring sophisticated system and application software, and underlying mathematical algorithms, that may differ radically from traditional approaches. Even at the smaller workstation or cluster level of computation, the massive concurrency and heterogeneity within each processor will impact computational scientists. Through the multi-institutional, multi-disciplinary Exascale Co-design Center for Materials in Extreme Environments (ExMatEx), we have initiated an early and deep collaboration between domain (computational materials) scientists, applied mathematicians, computer scientists, and hardware architects, in order to establish the relationships between algorithms, software stacks, and architectures needed to enable exascale-ready materials science application codes within the next decade. In my talk, I will discuss these challenges, and what it will mean for exascale-era electronic structure, molecular dynamics, and engineering-scale simulations of shock-compressed condensed matter. In particular, we anticipate that the emerging hierarchical, heterogeneous architectures can be exploited to achieve higher physical fidelity simulations using adaptive physics refinement. This work is supported by the U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research.

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.

International Journal of Molecular Science 2017 Best Paper Award.

PubMed

2017-11-02

The Editors of the International Journal of Molecular Sciences have established the Best Paper Award to recognize the most outstanding articles published in the areas of molecular biology, molecular physics and chemistry that have been published in the International Journal of Molecular Sciences. The prizes have been awarded annually since 2012 [...].

NIST Role in Advancing Innovation

NASA Astrophysics Data System (ADS)

Semerjian, Hratch

2006-03-01

According to the National Innovation Initiative, a report of the Council on Competitiveness, innovation will be the single most important factor in determining America's success through the 21^st century. NIST mission is to promote U.S. innovation and industrial competitiveness by advancing measurement science, standards, and technology -- in ways that enhance economic security and improve the quality of life for all Americans. NIST innovations in measurement science and technology often become the basis for new industrial capabilities. Several examples of such developments will be discussed, including the development of techniques for manipulation and measurement of biomolecules which may become the building blocks for molecular electronics; expansion of the frontiers of quantum theory to develop the field of quantum computing and communication; development of atomic scale measurement capabilities for future nano- and molecular scale electronic devices; development of a lab-on-a-chip that can detect within seconds trace amounts of toxic chemicals in water, or can be used for rapid DNA analysis; and standards to facilitate supply chain interoperability.

Computational Approaches to Nucleic Acid Origami.

PubMed

Jabbari, Hosna; Aminpour, Maral; Montemagno, Carlo

2015-10-12

Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.

Li + solvation and kinetics of Li +–BF 4 -/PF 6 - ion pairs in ethylene carbonate. A molecular dynamics study with classical rate theories

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

Chang, Tsun-Mei; Dang, Liem X.

Using our polarizable force-field models and employing classical rate theories of chemical reactions, we examine the ethylene carbonate (EC) exchange process between the first and second solvation shells around Li+ and the dissociation kinetics of ion pairs Li+-[BF4] and Li+-[PF6] in this solvent. We calculate the exchange rates using transition state theory and correct them with transmission coefficients computed by the reactive flux; Impey, Madden, and McDonald approaches; and Grote-Hynes theory. We found the residence times of EC around Li+ ions varied from 70 to 450 ps, depending on the correction method used. We found the relaxation times changed significantlymore » from Li+-[BF4] to Li+-[PF6] ion pairs in EC. Our results also show that, in addition to affecting the free energy of dissociation in EC, the anion type also significantly influence the dissociation kinetics of ion pairing. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Molecular science for drug development and biomedicine.

PubMed

Zhong, Wei-Zhu; Zhou, Shu-Feng

2014-11-04

With the avalanche of biological sequences generated in the postgenomic age, molecular science is facing an unprecedented challenge, i.e., how to timely utilize the huge amount of data to benefit human beings. Stimulated by such a challenge, a rapid development has taken place in molecular science, particularly in the areas associated with drug development and biomedicine, both experimental and theoretical. The current thematic issue was launched with the focus on the topic of "Molecular Science for Drug Development and Biomedicine", in hopes to further stimulate more useful techniques and findings from various approaches of molecular science for drug development and biomedicine.[...].

Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

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

Hansmann, Ulrich H.E.

2012-07-02

This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previousmore » years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.« less

In Situ Fabrication of PtCo Alloy Embedded in Nitrogen-Doped Graphene Nanopores as Synergistic Catalyst for Oxygen Reduction Reaction

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

Zhong, Xing; Wang, Lei; Zhou, Hu

A novel PtCo alloy in situ etched and embedded in graphene nanopores (PtCo/NPG) as a high-performance catalyst for ORR was reported. Graphene nanopores were fabricated in situ while forming PtCo nanoparticles that were uniformly embedded in the graphene nanopores. Given the synergistic effect between PtCo alloy and nanopores, PtCo/NPG exhibited 11.5 times higher mass activity than that of the commercial Pt/C cathode electrocatalyst. DFT calculations indicated that the nanopores in NPG cannot only stabilize PtCo nanoparticles but can also definitely change the electronic structures, thereby change its adsorption abilities. This enhancement can lead to a favorable reaction pathway on PtCo/NPGmore » for ORR. This study showed that PtCo/NPG is a potential candidate for the next generation of Pt-based catalysts in fuel cells. This study also offered a promising alternative strategy and enabled the fabrication of various kinds of metal/graphene nanopore nanohybrids with potential applications in catalysts and potential use for other technological devices. The authors acknowledge the financial support from the National Basic Research Program (973 program, No. 2013CB733501), Zhejiang Provincial Education Department Research Program (Y201326554) and the National Natural Science Foundation of China (No. 21306169, 21101137, 21136001, 21176221 and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC).« less

Factors influencing exemplary science teachers' levels of computer use

NASA Astrophysics Data System (ADS)

Hakverdi, Meral

This study examines exemplary science teachers' use of technology in science instruction, factors influencing their level of computer use, their level of knowledge/skills in using specific computer applications for science instruction, their use of computer-related applications/tools during their instruction, and their students' use of computer applications/tools in or for their science class. After a relevant review of the literature certain variables were selected for analysis. These variables included personal self-efficacy in teaching with computers, outcome expectancy, pupil-control ideology, level of computer use, age, gender, teaching experience, personal computer use, professional computer use and science teachers' level of knowledge/skills in using specific computer applications for science instruction. The sample for this study includes middle and high school science teachers who received the Presidential Award for Excellence in Science Teaching Award (sponsored by the White House and the National Science Foundation) between the years 1997 and 2003 from all 50 states and U.S. territories. Award-winning science teachers were contacted about the survey via e-mail or letter with an enclosed return envelope. Of the 334 award-winning science teachers, usable responses were received from 92 science teachers, which made a response rate of 27.5%. Analysis of the survey responses indicated that exemplary science teachers have a variety of knowledge/skills in using computer related applications/tools. The most commonly used computer applications/tools are information retrieval via the Internet, presentation tools, online communication, digital cameras, and data collection probes. Results of the study revealed that students' use of technology in their science classroom is highly correlated with the frequency of their science teachers' use of computer applications/tools. The results of the multiple regression analysis revealed that personal self-efficacy related to the exemplary science teachers' level of computer use suggesting that computer use is dependent on perceived abilities at using computers. The teachers' use of computer-related applications/tools during class, and their personal self-efficacy, age, and gender are highly related with their level of knowledge/skills in using specific computer applications for science instruction. The teachers' level of knowledge/skills in using specific computer applications for science instruction and gender related to their use of computer-related applications/tools during class and the students' use of computer-related applications/tools in or for their science class. In conclusion, exemplary science teachers need assistance in learning and using computer-related applications/tool in their science class.

Review Article: The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-neoplastic Diseases in the Era of Precision Medicine.

PubMed

Ogino, Shuji; Nishihara, Reiko; VanderWeele, Tyler J; Wang, Molin; Nishi, Akihiro; Lochhead, Paul; Qian, Zhi Rong; Zhang, Xuehong; Wu, Kana; Nan, Hongmei; Yoshida, Kazuki; Milner, Danny A; Chan, Andrew T; Field, Alison E; Camargo, Carlos A; Williams, Michelle A; Giovannucci, Edward L

2016-07-01

Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases, such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical/radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational/systems biology, there are wide open opportunities in MPE to contribute to public health.

Cajal and consciousness. Introduction.

PubMed

Marijuán, P C

2001-04-01

One hundred years after Santiago Ramón Cajal established the bases of modern neuroscience in his masterpiece Textura del sistema nervioso del hombre y de los vertebrados, the question is stated again: What is the status of consciousness today? The responses in this book, by contemporary leading figures of neuroscience, evolution, molecular biology, computer science, and quantum physics, collectively compose a fascinating conceptual landscape. Both the evolutionary emergence of consciousness and its development towards the highest level may be analyzed by a wealth of new theories and hypotheses, including Cajal's prescient ones. Some noticeable gaps remain, however. Celebrating the centennial of Textura is a timely occasion to reassess how close--and how far--our system of the sciences is to explaining consciousness.

National Synchrotron Light Source annual report 1991

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

Hulbert, S.L.; Lazarz, N.M.

1992-04-01

This report discusses the following research conducted at NSLS: atomic and molecular science; energy dispersive diffraction; lithography, microscopy and tomography; nuclear physics; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; workshop on surface structure; workshop on electronic and chemical phenomena at surfaces; workshop on imaging; UV FEL machine reviews; VUV machine operations; VUV beamline operations; VUV storage ring parameters; x-ray machine operations; x-ray beamline operations; x-ray storage ring parameters; superconducting x-ray lithography source; SXLS storage ring parameters; the accelerator test facility; proposed UV-FEL user facility at the NSLS; global orbit feedback systems; and NSLSmore » computer system.« less

Quantum Simulation of Helium Hydride Cation in a Solid-State Spin Register.

PubMed

Wang, Ya; Dolde, Florian; Biamonte, Jacob; Babbush, Ryan; Bergholm, Ville; Yang, Sen; Jakobi, Ingmar; Neumann, Philipp; Aspuru-Guzik, Alán; Whitfield, James D; Wrachtrup, Jörg

2015-08-25

Ab initio computation of molecular properties is one of the most promising applications of quantum computing. While this problem is widely believed to be intractable for classical computers, efficient quantum algorithms exist which have the potential to vastly accelerate research throughput in fields ranging from material science to drug discovery. Using a solid-state quantum register realized in a nitrogen-vacancy (NV) defect in diamond, we compute the bond dissociation curve of the minimal basis helium hydride cation, HeH(+). Moreover, we report an energy uncertainty (given our model basis) of the order of 10(-14) hartree, which is 10 orders of magnitude below the desired chemical precision. As NV centers in diamond provide a robust and straightforward platform for quantum information processing, our work provides an important step toward a fully scalable solid-state implementation of a quantum chemistry simulator.

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.

A molecular orbital study of the energy spectrum, exchange interaction and gate crosstalk of a four-quantum-dot system

NASA Astrophysics Data System (ADS)

Yang, Xu-Chen; Wang, Xin

The manipulation of coupled quantum dot devices is crucial to scalable, fault-tolerant quantum computation. We present a theoretical study of a four-electron four-quantum-dot system based on molecular orbital methods, which depicts a pair of singlet-triplet (S-T) qubits. We find that while the two S-T qubits are coupled by the capacitive interaction when they are sufficiently far away, the admixture of wave functions undergoes a substantial change as the two S-T qubits get closer. We find that in certain parameter regime the exchange interaction may only be defined in the sense of an effective one when the computational basis states no longer dominate the eigenstates. We further discuss the gate crosstalk as a consequence of this wave function mixing. This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China (No. CityU 21300116) and the National Natural Science Foundation of China (No. 11604277).

Programming Enzyme-Initiated Autonomous DNAzyme Nanodevices in Living Cells.

PubMed

Chen, Feng; Bai, Min; Cao, Ke; Zhao, Yue; Cao, Xiaowen; Wei, Jing; Wu, Na; Li, Jiang; Wang, Lihua; Fan, Chunhai; Zhao, Yongxi

2017-12-26

Molecular nanodevices are computational assemblers that switch defined states upon external stimulation. However, interfacing artificial nanodevices with natural molecular machineries in living cells remains a great challenge. Here, we delineate a generic method for programming assembly of enzyme-initiated DNAzyme nanodevices (DzNanos). Two programs including split assembly of two partzymes and toehold exchange displacement assembly of one intact DNAzyme initiated by telomerase are computed. The intact one obtains higher assembly yield and catalytic performance ascribed to proper conformation folding and active misplaced assembly. By employing MnO 2 nanosheets as both DNA carriers and source of Mn 2+ as DNAzyme cofactor, we find that this DzNano is well assembled via a series of conformational states in living cells and operates autonomously with sustained cleavage activity. Other enzymes can also induce corresponding DzNano assembly with defined programming modules. These DzNanos not only can monitor enzyme catalysis in situ but also will enable the implementation of cellular stages, behaviors, and pathways for basic science, diagnostic, and therapeutic applications as genetic circuits.

ISCR FY2005 Annual Report

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

Keyes, D E; McGraw, J R

2006-02-02

Large-scale scientific computation and all of the disciplines that support and help validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of simulation as a fundamental tool of scientific and engineering research is underscored in the President's Information Technology Advisory Committee (PITAC) June 2005 finding that ''computational science has become critical to scientific leadership, economic competitiveness, and nationalmore » security''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed, most notably the molecular dynamics simulation that sustained more than 100 Teraflop/s and won the 2005 Gordon Bell Prize. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use in an efficient manner. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of data. Advances in scientific computing research have, therefore, never been more vital to the core missions of LLNL than at present. Computational science is evolving so rapidly along every one of its research fronts that to remain on the leading edge, LLNL must engage researchers at many academic centers of excellence. In FY 2005, the Institute for Scientific Computing Research (ISCR) served as one of LLNL's main bridges to the academic community with a program of collaborative subcontracts, visiting faculty, student internships, workshops, and an active seminar series. The ISCR identifies researchers from the academic community for computer science and computational science collaborations with LLNL and hosts them for both brief and extended visits with the aim of encouraging long-term academic research agendas that address LLNL research priorities. Through these collaborations, ideas and software flow in both directions, and LLNL cultivates its future workforce. The Institute strives to be LLNL's ''eyes and ears'' in the computer and information sciences, keeping the Laboratory aware of and connected to important external advances. It also attempts to be the ''hands and feet'' that carry those advances into the Laboratory and incorporate them into practice. ISCR research participants are integrated into LLNL's Computing Applications and Research (CAR) Department, especially into its Center for Applied Scientific Computing (CASC). In turn, these organizations address computational challenges arising throughout the rest of the Laboratory. Administratively, the ISCR flourishes under LLNL's University Relations Program (URP). Together with the other four institutes of the URP, the ISCR navigates a course that allows LLNL to benefit from academic exchanges while preserving national security. While it is difficult to operate an academic-like research enterprise within the context of a national security laboratory, the results declare the challenges well met and worth the continued effort. The pages of this annual report summarize the activities of the faculty members, postdoctoral researchers, students, and guests from industry and other laboratories who participated in LLNL's computational mission under the auspices of the ISCR during FY 2005.« less

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

PubMed

Scully, John R

2015-01-01

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

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

uPy: a ubiquitous computer graphics Python API with Biological Modeling Applications

PubMed Central

Autin, L.; Johnson, G.; Hake, J.; Olson, A.; Sanner, M.

2015-01-01

In this paper we describe uPy, an extension module for the Python programming language that provides a uniform abstraction of the APIs of several 3D computer graphics programs called hosts, including: Blender, Maya, Cinema4D, and DejaVu. A plugin written with uPy is a unique piece of code that will run in all uPy-supported hosts. We demonstrate the creation of complex plug-ins for molecular/cellular modeling and visualization and discuss how uPy can more generally simplify programming for many types of projects (not solely science applications) intended for multi-host distribution. uPy is available at http://upy.scripps.edu PMID:24806987

Modelling the spread of innovation in wild birds.

PubMed

Shultz, Thomas R; Montrey, Marcel; Aplin, Lucy M

2017-06-01

We apply three plausible algorithms in agent-based computer simulations to recent experiments on social learning in wild birds. Although some of the phenomena are simulated by all three learning algorithms, several manifestations of social conformity bias are simulated by only the approximate majority (AM) algorithm, which has roots in chemistry, molecular biology and theoretical computer science. The simulations generate testable predictions and provide several explanatory insights into the diffusion of innovation through a population. The AM algorithm's success raises the possibility of its usefulness in studying group dynamics more generally, in several different scientific domains. Our differential-equation model matches simulation results and provides mathematical insights into the dynamics of these algorithms. © 2017 The Author(s).

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Gender differences in the use of computers, programming, and peer interactions in computer science classrooms

NASA Astrophysics Data System (ADS)

Stoilescu, Dorian; Egodawatte, Gunawardena

2010-12-01

Research shows that female and male students in undergraduate computer science programs view computer culture differently. Female students are interested more in the use of computers than in doing programming, whereas male students see computer science mainly as a programming activity. The overall purpose of our research was not to find new definitions for computer science culture but to see how male and female students see themselves involved in computer science practices, how they see computer science as a successful career, and what they like and dislike about current computer science practices. The study took place in a mid-sized university in Ontario. Sixteen students and two instructors were interviewed to get their views. We found that male and female views are different on computer use, programming, and the pattern of student interactions. Female and male students did not have any major issues in using computers. In computing programming, female students were not so involved in computing activities whereas male students were heavily involved. As for the opinions about successful computer science professionals, both female and male students emphasized hard working, detailed oriented approaches, and enjoying playing with computers. The myth of the geek as a typical profile of successful computer science students was not found to be true.

Controlling Proton Delivery through Catalyst Structural Dynamics

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

Cardenas, Allan Jay P.; Ginovska, Bojana; Kumar, Neeraj

The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates ofmore » electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

Learning nucleic acids solving by bioinformatics problems.

PubMed

Nunes, Rhewter; Barbosa de Almeida Júnior, Edivaldo; Pessoa Pinto de Menezes, Ivandilson; Malafaia, Guilherme

2015-01-01

The article describes the development of a new approach to teach molecular biology to undergraduate biology students. The 34 students who participated in this research belonged to the first period of the Biological Sciences teaching course of the Instituto Federal Goiano at Urutaí Campus, Brazil. They were registered in Cell Biology in the first semester of 2013. They received four 55 min-long expository/dialogued lectures that covered the content of "structure and functions of nucleic acids". Later the students were invited to attend four meetings (in a computer laboratory) in which some concepts of Bioinformatics were presented and some problems of the Rosalind platform were solved. The observations we report here are very useful as a broad groundwork to development new research. An interesting possibility is research into the effects of bioinformatics interventions that improve molecular biology learning. © 2015 The International Union of Biochemistry and Molecular Biology.

Rational Design of Pathogen-Mimicking Amphiphilic Materials as Nanoadjuvants

NASA Astrophysics Data System (ADS)

Ulery, Bret D.; Petersen, Latrisha K.; Phanse, Yashdeep; Kong, Chang Sun; Broderick, Scott R.; Kumar, Devender; Ramer-Tait, Amanda E.; Carrillo-Conde, Brenda; Rajan, Krishna; Wannemuehler, Michael J.; Bellaire, Bryan H.; Metzger, Dennis W.; Narasimhan, Balaji

2011-12-01

An opportunity exists today for cross-cutting research utilizing advances in materials science, immunology, microbial pathogenesis, and computational analysis to effectively design the next generation of adjuvants and vaccines. This study integrates these advances into a bottom-up approach for the molecular design of nanoadjuvants capable of mimicking the immune response induced by a natural infection but without the toxic side effects. Biodegradable amphiphilic polyanhydrides possess the unique ability to mimic pathogens and pathogen associated molecular patterns with respect to persisting within and activating immune cells, respectively. The molecular properties responsible for the pathogen-mimicking abilities of these materials have been identified. The value of using polyanhydride nanovaccines was demonstrated by the induction of long-lived protection against a lethal challenge of Yersinia pestis following a single administration ten months earlier. This approach has the tantalizing potential to catalyze the development of next generation vaccines against diseases caused by emerging and re-emerging pathogens.

Flow in porous media, phase and ultralow interfacial tensions: Mechanisms of enhanced petroleum recovery

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

Davis, H.T.; Scriven, L.E.

1991-07-01

A major program of university research, longer-ranged and more fundamental in approach than industrial research, into basic mechanisms of enhancing petroleum recovery and into underlying physics, chemistry, geology, applied mathematics, computation, and engineering science has been built at Minnesota. The original focus was surfactant-based chemical flooding, but the approach taken was sufficiently fundamental that the research, longer-ranged than industrial efforts, has become quite multidirectional. Topics discussed are volume controlled porosimetry; fluid distribution and transport in porous media at low wetting phase saturation; molecular dynamics of fluids in ultranarrow pores; molecular dynamics and molecular theory of wetting and adsorption; new numericalmore » methods to handle initial and boundary conditions in immiscible displacement; electron microscopy of surfactant fluid microstructure; low cost system for animating liquid crystallites viewed with polarized light; surfaces of constant mean curvature with prescribed contact angle.« less

Final Technical Report

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

Kirkpatrick, R. James

This document serves as the final report for United States Department of Energy Basic Energy Sciences Grant DE-FG02-08ER15929, “Computational and Spectroscopic Investigations of the Molecular Scale Structure and Dynamics of Geologically Important Fluids and Mineral-Fluid Interfaces” (R. James Kirkpatrick, P.I., A. O. Yazaydin, co-P.I.). The research under this grant was intimately tied to that supported by the parallel the grant of the same title at Alfred (DOE DE-FG02-10ER16128; Geoffrey M. Bowers, P.I.).

Molecular Beam Epitaxial Growth, Characterization and Electronic Device Processing of HgCdTe, HgZnTe, Related Heterojunctions and HgCdTe-CdTe Superlattices

DTIC Science & Technology

1989-11-13

Workshopon thePhysicsand Chemitry of HC,Oct. 1937,ovilne aemuch better than those currently achieved using the or- result). aretalcvprpaeeiay(M )got...temperature. The corresponding high-tempera- 5-mV steps. All the data acquisition was computerized . ture activation energies are systematically higher...Boukerche, M. DeSouza and J. P. Faurie Department of Physics Electrical Engineering and Computer Science University of Illinois at Chicago Chicago, Illinois

Exploring the Relationships between Self-Efficacy and Preference for Teacher Authority among Computer Science Majors

ERIC Educational Resources Information Center

Lin, Che-Li; Liang, Jyh-Chong; Su, Yi-Ching; Tsai, Chin-Chung

2013-01-01

Teacher-centered instruction has been widely adopted in college computer science classrooms and has some benefits in training computer science undergraduates. Meanwhile, student-centered contexts have been advocated to promote computer science education. How computer science learners respond to or prefer the two types of teacher authority,…

Free energy calculation of permeant-membrane interactions using molecular dynamics simulations.

PubMed

Elvati, Paolo; Violi, Angela

2012-01-01

Nanotoxicology, the science concerned with the safe use of nanotechnology and nanostructure design for biological applications, is a field of research that has recently received great attention, as a result of the rapid growth in nanotechnology. Many nanostructures are of a scale and chemical composition similar to many biomolecular environments, and recent papers have reported evident toxicity of selected nanoparticles. Molecular simulations can help develop a mechanistic understanding of how structural properties affect bioactivity. In this chapter, we describe how to compute the free energy of interactions between cellular membranes and benzene, the main constituent of some toxic carbonaceous particles, with well-tempered metadynamics. This algorithm reconstructs the free energy surface and accelerates rare events in a coarse-grained representation of the system.

Investigating the significance of zero-point motion in small molecular clusters of sulphuric acid and water

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

Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

2014-01-14

The nucleation of particles from trace gases in the atmosphere is an important source of cloud condensation nuclei (CCN), and these are vital for the formation of clouds in view of the high supersaturations required for homogeneous water droplet nucleation. The methods of quantum chemistry have increasingly been employed to model nucleation due to their high accuracy and efficiency in calculating configurational energies; and nucleation rates can be obtained from the associated free energies of particle formation. However, even in such advanced approaches, it is typically assumed that the nuclei have a classical nature, which is questionable for some systems.more » The importance of zero-point motion (also known as quantum nuclear dynamics) in modelling small clusters of sulphuric acid and water is tested here using the path integral molecular dynamics (PIMD) method at the density functional theory (DFT) level of theory. We observe a small zero-point effect on the the equilibrium structures of certain clusters. One configuration is found to display a bimodal behaviour at 300 K in contrast to the stable ionised state suggested from a zero temperature classical geometry optimisation. The general effect of zero-point motion is to promote the extent of proton transfer with respect to classical behaviour. We thank Prof. Angelos Michaelides and his group in University College London (UCL) for practical advice and helpful discussions. This work benefited from interactions with the Thomas Young Centre through seminar and discussions involving the PIMD method. SMK was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. JLS and IJF were supported by the IMPACT scheme at UCL and by the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. We are grateful for use of the UCL Legion High Performance Computing Facility and the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy, Office of Science of the under Contract No. DE-AC02-05CH11231.« less

Academic computer science and gender: A naturalistic study investigating the causes of attrition

NASA Astrophysics Data System (ADS)

Declue, Timothy Hall

Far fewer women than men take computer science classes in high school, enroll in computer science programs in college, or complete advanced degrees in computer science. The computer science pipeline begins to shrink for women even before entering college, but it is at the college level that the "brain drain" is the most evident numerically, especially in the first class taken by most computer science majors called "Computer Science 1" or CS-I. The result, for both academia and industry, is a pronounced technological gender disparity in academic and industrial computer science. The study revealed the existence of several factors influencing success in CS-I. First, and most clearly, the effect of attribution processes seemed to be quite strong. These processes tend to work against success for females and in favor of success for males. Likewise, evidence was discovered which strengthens theories related to prior experience and the perception that computer science has a culture which is hostile to females. Two unanticipated themes related to the motivation and persistence of successful computer science majors. The findings did not support the belief that females have greater logistical problems in computer science than males, or that females tend to have a different programming style than males which adversely affects the females' ability to succeed in CS-I.

Explorative search of distributed bio-data to answer complex biomedical questions

PubMed Central

2014-01-01

Background The huge amount of biomedical-molecular data increasingly produced is providing scientists with potentially valuable information. Yet, such data quantity makes difficult to find and extract those data that are most reliable and most related to the biomedical questions to be answered, which are increasingly complex and often involve many different biomedical-molecular aspects. Such questions can be addressed only by comprehensively searching and exploring different types of data, which frequently are ordered and provided by different data sources. Search Computing has been proposed for the management and integration of ranked results from heterogeneous search services. Here, we present its novel application to the explorative search of distributed biomedical-molecular data and the integration of the search results to answer complex biomedical questions. Results A set of available bioinformatics search services has been modelled and registered in the Search Computing framework, and a Bioinformatics Search Computing application (Bio-SeCo) using such services has been created and made publicly available at http://www.bioinformatics.deib.polimi.it/bio-seco/seco/. It offers an integrated environment which eases search, exploration and ranking-aware combination of heterogeneous data provided by the available registered services, and supplies global results that can support answering complex multi-topic biomedical questions. Conclusions By using Bio-SeCo, scientists can explore the very large and very heterogeneous biomedical-molecular data available. They can easily make different explorative search attempts, inspect obtained results, select the most appropriate, expand or refine them and move forward and backward in the construction of a global complex biomedical query on multiple distributed sources that could eventually find the most relevant results. Thus, it provides an extremely useful automated support for exploratory integrated bio search, which is fundamental for Life Science data driven knowledge discovery. PMID:24564278

The Role of Molecular Pathological Epidemiology in the Study of Neoplastic and Non-Neoplastic Diseases in the Era of Precision Medicine

PubMed Central

Ogino, Shuji; Nishihara, Reiko; VanderWeele, Tyler J.; Wang, Molin; Nishi, Akihiro; Lochhead, Paul; Qian, Zhi Rong; Zhang, Xuehong; Wu, Kana; Nan, Hongmei; Yoshida, Kazuki; Milner, Danny A; Chan, Andrew T.; Field, Alison E.; Camargo, Carlos A; Williams, Michelle A; Giovannucci, Edward L.

2016-01-01

Molecular pathology diagnostics to subclassify diseases based on pathogenesis are increasingly common in clinical translational medicine. Molecular pathological epidemiology (MPE) is an integrative transdisciplinary science based on the unique disease principle and the disease continuum theory. While it has been most commonly applied to research on breast, lung, and colorectal cancers, MPE can investigate etiologic heterogeneity in non-neoplastic diseases such as cardiovascular diseases, obesity, diabetes mellitus, drug toxicity, and immunity-related and infectious diseases. This science can enhance causal inference by linking putative etiologic factors to specific molecular biomarkers as outcomes. Technological advances increasingly enable analyses of various -omics, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, microbiome, immunomics, interactomics, etc. Challenges in MPE include sample size limitations (depending on availability of biospecimens or biomedical / radiological imaging), need for rigorous validation of molecular assays and study findings, and paucities of interdisciplinary experts, education programs, international forums, and standardized guidelines. To address these challenges, there are ongoing efforts such as multidisciplinary consortium pooling projects, the International Molecular Pathological Epidemiology (MPE) Meeting Series, and the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE)-MPE guideline project. Efforts should be made to build biorepository and biobank networks, and worldwide population-based MPE databases. These activities match with the purposes of the Big Data to Knowledge (BD2K), Genetic Associations and Mechanisms in Oncology (GAME-ON), and Precision Medicine Initiatives of the United States National Institute of Health. Given advances in biotechnology, bioinformatics, and computational / systems biology, there are wide open opportunities in MPE to contribute to public health. PMID:26928707

Life science research and drug discovery at the turn of the 21st century: the experience of SwissBioGrid.

PubMed

den Besten, Matthijs; Thomas, Arthur J; Schroeder, Ralph

2009-04-22

It is often said that the life sciences are transforming into an information science. As laboratory experiments are starting to yield ever increasing amounts of data and the capacity to deal with those data is catching up, an increasing share of scientific activity is seen to be taking place outside the laboratories, sifting through the data and modelling "in silico" the processes observed "in vitro." The transformation of the life sciences and similar developments in other disciplines have inspired a variety of initiatives around the world to create technical infrastructure to support the new scientific practices that are emerging. The e-Science programme in the United Kingdom and the NSF Office for Cyberinfrastructure are examples of these. In Switzerland there have been no such national initiatives. Yet, this has not prevented scientists from exploring the development of similar types of computing infrastructures. In 2004, a group of researchers in Switzerland established a project, SwissBioGrid, to explore whether Grid computing technologies could be successfully deployed within the life sciences. This paper presents their experiences as a case study of how the life sciences are currently operating as an information science and presents the lessons learned about how existing institutional and technical arrangements facilitate or impede this operation. SwissBioGrid gave rise to two pilot projects: one for proteomics data analysis and the other for high-throughput molecular docking ("virtual screening") to find new drugs for neglected diseases (specifically, for dengue fever). The proteomics project was an example of a data management problem, applying many different analysis algorithms to Terabyte-sized datasets from mass spectrometry, involving comparisons with many different reference databases; the virtual screening project was more a purely computational problem, modelling the interactions of millions of small molecules with a limited number of protein targets on the coat of the dengue virus. Both present interesting lessons about how scientific practices are changing when they tackle the problems of large-scale data analysis and data management by means of creating a novel technical infrastructure. In the experience of SwissBioGrid, data intensive discovery has a lot to gain from close collaboration with industry and harnessing distributed computing power. Yet the diversity in life science research implies only a limited role for generic infrastructure; and the transience of support means that researchers need to integrate their efforts with others if they want to sustain the benefits of their success, which are otherwise lost.

National Synchrotron Light Source annual report 1991. Volume 1, October 1, 1990--September 30, 1991

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

Hulbert, S.L.; Lazarz, N.M.

1992-04-01

This report discusses the following research conducted at NSLS: atomic and molecular science; energy dispersive diffraction; lithography, microscopy and tomography; nuclear physics; UV photoemission and surface science; x-ray absorption spectroscopy; x-ray scattering and crystallography; x-ray topography; workshop on surface structure; workshop on electronic and chemical phenomena at surfaces; workshop on imaging; UV FEL machine reviews; VUV machine operations; VUV beamline operations; VUV storage ring parameters; x-ray machine operations; x-ray beamline operations; x-ray storage ring parameters; superconducting x-ray lithography source; SXLS storage ring parameters; the accelerator test facility; proposed UV-FEL user facility at the NSLS; global orbit feedback systems; and NSLSmore » computer system.« less

INVENTION IS NOT AN OPTION

PubMed Central

Comedy, Yolanda L.; Gilbert, Juan E.; Pun, Suzie H.

2017-01-01

Inventors help solve all kinds of problems. The AAAS-Lemelson Invention Ambassador program celebrates inventors who have an impact on global challenges, making our communities and the globe better, one invention at a time. In this paper, we introduce two of these invention ambassadors: Dr. Suzie Pun and Dr. Juan Gilbert. Dr. Suzie Pun is the Robert F. Rushmer Professor of Bioengineering, an adjunct professor of chemical engineering, and a member of the Molecular Engineering and Sciences Institute at the University of Washington. Dr. Juan Gilbert is the Andrew Banks Family Preeminence Endowed Professor and chair of the Computer & Information Science & Engineering Department at the University of Florida. Both have a passion for solving problems and are dedicated to teaching their students to change the world. PMID:29527271

Looking back: forward looking

PubMed Central

2017-01-01

Abstract GigaScience is now 5 years old, having been launched at the 2012 Intelligent Systems for Molecular Biology conference. Anyone who has attended what is the largest computational biology conference since then has had the opportunity to join us for each birthday celebration—and receive 1 of our fun T-shirts as a party prize. Since launching, we have pushed our agenda of openness, transparency, reproducibility, and reusability. Here, we look back at our first 5 years and what we have done to forward our open science goals in scientific publishing. Our mainstay has been to create a process that allows the availability and publication of as many “research objects” as possible to create a more complete way of communicating how the research process is done. PMID:28938718

Computer-Game Construction: A Gender-Neutral Attractor to Computing Science

ERIC Educational Resources Information Center

Carbonaro, Mike; Szafron, Duane; Cutumisu, Maria; Schaeffer, Jonathan

2010-01-01

Enrollment in Computing Science university programs is at a dangerously low level. A major reason for this is the general lack of interest in Computing Science by females. In this paper, we discuss our experience with using a computer game construction environment as a vehicle to encourage female participation in Computing Science. Experiments…

Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

PubMed

Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

2016-09-20

The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic progress. An accurate and efficient theoretical computational approach could drastically decrease this time by screening potential dielectric materials and providing reliable design rules for future molecular dielectrics. Until recently, accurate calculation of dielectric responses in molecular materials was difficult and highly approximate. Most previous modeling efforts relied on classical formalisms to relate molecular polarizability to macroscopic dielectric properties. These efforts often vastly overestimated polarizability in the subject materials and ignored crucial material properties that can affect dielectric response. Recent advances in first-principles calculations via density functional theory (DFT) with periodic boundary conditions have allowed accurate computation of dielectric properties in molecular materials. In this Account, we outline the methodology used to calculate dielectric properties of molecular materials. We demonstrate the validity of this approach on model systems, capturing the frequency dependence of the dielectric response and achieving quantitative accuracy compared with experiment. This method is then used as a guide to new high-capacitance molecular dielectrics by determining what materials and chemical properties are important in maximizing dielectric response in self-assembled monolayers (SAMs). It will be seen that this technique is a powerful tool for understanding and designing new molecular dielectric systems, the properties of which are fundamental to many scientific areas.

2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner

PubMed Central

Fogg, Christiana N.; Kovats, Diane E.; Berger, Bonnie

2017-01-01

The International Society for Computational Biology ( ISCB) recognizes an established scientist each year with the Accomplishment by a Senior Scientist Award for significant contributions he or she has made to the field. This award honors scientists who have contributed to the advancement of computational biology and bioinformatics through their research, service, and education work. Pavel Pevzner, PhD, Ronald R. Taylor Professor of Computer Science and Director of the NIH Center for Computational Mass Spectrometry at University of California, San Diego, has been selected as the winner of the 2017 Accomplishment by a Senior Scientist Award. The ISCB awards committee, chaired by Dr. Bonnie Berger of the Massachusetts Institute of Technology, selected Pevzner as the 2017 winner. Pevzner will receive his award and deliver a keynote address at the 2017 Intelligent Systems for Molecular Biology-European Conference on Computational Biology joint meeting ( ISMB/ECCB 2017) held in Prague, Czech Republic from July 21-July 25, 2017. ISMB/ECCB is a biennial joint meeting that brings together leading scientists in computational biology and bioinformatics from around the globe. PMID:28713548

A Comparative Framework for Studying the Histories of the Humanities and Science.

PubMed

Bod, Rens

2015-06-01

While the humanities and the sciences have a closely connected history, there are no general histories that bring the two fields together on an equal footing. This paper argues that there is a level at which some humanistic and scientific disciplines can be brought under a common denominator and compared. This is at the level of underlying methods, especially at the level of formalisms and rule systems used by different disciplines. The essay formally compares linguistics and computer science by noting that the same grammar formalism was used in the 1950s for describing both human and. programming languages. Additionally, it examines the influence of philology on molecular biology, and vice versa, by recognizing that the tree-formalism and rule system used for text reconstruction was also employed in DNA genetics. It also shows that rule systems for source criticism in history are used in forensic science, evidence-based medicine, and jurisprudence. This paper thus opens up a new comparative approach within which the histories of the humanities and the sciences can be examined on a common level.

The challenge of cardiac modeling--interaction and integration.

PubMed

Sideman, Samuel

2006-10-01

The goal of clinical cardiology is to obtain an integrated picture of the interacting parameters of muscle and vessel mechanics, blood circulation and myocardial perfusion, oxygen consumption and energy metabolism, and electrical activation and heart rate, thus relating to the true physiological and pathophysiological characteristics of the heart. Scientific insight into the cardiac physiology and performance is achieved by utilizing life sciences, for example, molecular biology, genetics and related intra- and intercellular phenomena, as well as the exact sciences, for example, mathematics, computer science, and related imaging and visualization techniques. The tools to achieve these goals are based on the intimate interactions between engineering science and medicine and the developments of modern, medically oriented technology. Most significant is the beneficiary effect of the globalization of science, the Internet, and the unprecedented international interaction and scientific cooperation in facing difficult multidisciplined challenges. This meeting aims to explore some important interactions in the cardiac system and relate to the integration of spatial and temporal interacting system parameters, so as to gain better insight into the structure and function of the cardiac system, thus leading to better therapeutic modalities.

Central Computer Science Concepts to Research-Based Teacher Training in Computer Science: An Experimental Study

ERIC Educational Resources Information Center

Zendler, Andreas; Klaudt, Dieter

2012-01-01

The significance of computer science for economics and society is undisputed. In particular, computer science is acknowledged to play a key role in schools (e.g., by opening multiple career paths). The provision of effective computer science education in schools is dependent on teachers who are able to properly represent the discipline and whose…

Molecular Dynamics Study of the Proposed Proton Transport Pathways in [FeFe]-Hydrogenase

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

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.

2014-01-15

Possible proton channels in Clostridium pasteurianum [FeFe]-hydrogenase were investigated with molecular dynamics simulations. This study was undertaken to discern proposed channels, compare their properties, evaluate the functional channel, and to provide insight into the features of an active proton channel. Our simulations suggest that protons are not transported through water wires. Instead, a five-residue motif (E282, S319, E279, HOH, C299) was found to be the likely channel, consistent with experimental observations. This channel connects the surface of the enzyme and the di-thiomethylamine bridge of the catalytic H-cluster, permitting the transport of protons. The channel was found to have a persistentmore » hydrogen bonded core (residues E279 to S319), with less persistent hydrogen bonds at the ends of the channel. The hydrogen bond occupancy in this network was found to be sensitive to the protonation state of the residues in the channel, with different protonation states enhancing or stabilizing hydrogen bonding in different regions of the network. Single site mutations to non-hydrogen bonding residues break the hydrogen bonding network at that residue, consistent with experimental observations showing catalyst inactivation. In many cases, these mutations alter the hydrogen bonding in other regions of the channel which may be equally important in catalytic failure. A correlation between the protein dynamics near the proton channel and the redox partner binding regions was also found as a function of protonation state. The likely mechanism of proton movement in [FeFe]-hydrogenases is discussed based on the structural analysis presented here. This work was funded by the DOE Office of Science Early Career Research Program through the Office of Basic Energy Sciences. Computational resources were provided at W. R. Wiley Environmental Molecular Science Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research located at Pacific Northwest National Laboratory, and a portion of the research was performed using PNNL Institutional Computing at Pacific Northwest National Laboratory. Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.« less

Using spatial principles to optimize distributed computing for enabling the physical science discoveries

PubMed Central

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-01-01

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century. PMID:21444779

Using spatial principles to optimize distributed computing for enabling the physical science discoveries.

PubMed

Yang, Chaowei; Wu, Huayi; Huang, Qunying; Li, Zhenlong; Li, Jing

2011-04-05

Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century.

Recent science and its exploration: the case of molecular biology.

PubMed

Rheinberger, Hans-Jörg

2009-03-01

This paper is about the interaction and the intertwinement between history of science as a historical process and history of science as the historiography of this process, taking molecular biology as an example. In the first part, two historical shifts are briefly characterized that appear to have punctuated the emergence of molecular biology between the 1930s and the 1980s, one connected to a new generation of analytical apparatus, the other to properly molecular tools. The second part concentrates on the historiography of this development. Basically, it distinguishes three phases. The first phase was largely dominated by accounts of the actors themselves. The second coincided with the general 'practical turn' in history of science at large, and today's historical appropriations of the molecularization of the life sciences appear to be marked by the changing disciplinary status of the science under review. In a closing remark, an argument is made for differentiating between long-range, middle-range and short-range perspectives in dealing with the history of the sciences.

A Financial Technology Entrepreneurship Program for Computer Science Students

ERIC Educational Resources Information Center

Lawler, James P.; Joseph, Anthony

2011-01-01

Education in entrepreneurship is becoming a critical area of curricula for computer science students. Few schools of computer science have a concentration in entrepreneurship in the computing curricula. The paper presents Technology Entrepreneurship in the curricula at a leading school of computer science and information systems, in which students…

Synthetic Molecular Machines for Active Self-Assembly: Prototype Algorithms, Designs, and Experimental Study

NASA Astrophysics Data System (ADS)

Dabby, Nadine L.

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast--all while remaining functional. This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of "active self-assembly" of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology's numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules. One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved. One might think that because a system is Turing-complete, capable of computing "anything," that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not "computations" in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface. Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors "energetically incomplete" programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time. As we will demonstrate and prove, a sufficiently expressive implementation of an "active" molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the problem, so the system is not "energetically incomplete." But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive. Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly. We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self-assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics. We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this reaction over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction. In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molecular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

The role of broken symmetry in solvation of a spherical cavity in classical and quantum water models

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

Remsing, Richard C.; Baer, Marcel D.; Schenter, Gregory K.

2014-08-21

Insertion of a hard sphere cavity in liquid water breaks translational symmetry and generates an electrostatic potential difference between the region near the cavity and the bulk. Here, we clarify the physical interpretation of this potential and its calculation. We also show that the electrostatic potential in the center of small, medium, and large cavities depends very sensitively on the form of the assumed molecular interactions for dfferent classical simple point-charge models and quantum mechanical DFT-based interaction potentials, as reected in their description of donor and acceptor hydrogen bonds near the cavity. These dfferences can signifcantly affect the magnitude ofmore » the scalar electrostatic potential. We argue that the result of these studies will have direct consequences toward our understanding of the thermodynamics of ion solvation through the cavity charging process. JDW and RCR are supported by the National Science Foundation (Grants CHE0848574 and CHE1300993). CJM and GKS are supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the Department of Energy by Battelle. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL. We acknowledge illuminating discussions and sharing of ideas and preprints with Dr. Shawn M. Kathmann and Prof. Tom Beck. The DFT simulations used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional computing resources were generously allocated by PNNL's Institutional Computing program.« less

Computer Science Teacher Professional Development in the United States: A Review of Studies Published between 2004 and 2014

ERIC Educational Resources Information Center

Menekse, Muhsin

2015-01-01

While there has been a remarkable interest to make computer science a core K-12 academic subject in the United States, there is a shortage of K-12 computer science teachers to successfully implement computer sciences courses in schools. In order to enhance computer science teacher capacity, training programs have been offered through teacher…

Educational challenges of molecular life science: Characteristics and implications for education and research.

PubMed

Tibell, Lena A E; Rundgren, Carl-Johan

2010-01-01

Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life-often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from "pure sciences," such as math, chemistry, and physics, through "applied sciences," such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences.

Redox biotransformation and delivery of anthracycline anticancer antibiotics: How interpretable structure-activity relationships of lethality using electrophilicity and the London formula for dispersion interaction work.

PubMed

Pang, Siu-Kwong

2017-03-30

Quantum chemical methods and molecular mechanics approaches face a lot of challenges in drug metabolism study because of their either insufficient accuracy or huge computational cost, or lack of clear molecular level pictures for building computational models. Low-cost QSAR methods can often be carried out even though molecular level pictures are not well defined; however, they show difficulty in identifying the mechanisms of drug metabolism and delineating the effects of chemical structures on drug toxicity because a certain amount of molecular descriptors are difficult to be interpreted. In order to make a breakthrough, it was proposed that mechanistically interpretable molecular descriptors were used to correlate with biological activity to establish structure-activity plots. The mechanistically interpretable molecular descriptors used in this study include electrophilicity and the mathematical function in the London formula for dispersion interaction, and they were calculated using quantum chemical methods. The biological activity is the lethality of anthracycline anticancer antibiotics denoted as log LD50, which were obtained by intraperitoneal injection into mice. The results reveal that the plots for electrophilicity, which can be interpreted as redox reactivity of anthracyclines, can describe oxidative degradation for detoxification and reductive bioactivation for toxicity induction. The plots for the dispersion interaction function, which represent the attraction between anthracyclines and biomolecules, can describe efflux from and influx into target cells of toxicity. The plots can also identify three structural scaffolds of anthracyclines that have different metabolic pathways, resulting in their different toxicity behavior. This structure-dependent toxicity behavior revealed in the plots can provide perspectives on design of anthracycline anticancer antibiotics. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Enhancing coherence in molecular spin qubits via atomic clock transitions

NASA Astrophysics Data System (ADS)

Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

2016-03-01

Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a ‘bottom-up’ approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits.

Three-dimensional printing of human skeletal muscle cells: An interdisciplinary approach for studying biological systems.

PubMed

Bagley, James R; Galpin, Andrew J

2015-01-01

Interdisciplinary exploration is vital to education in the 21st century. This manuscript outlines an innovative laboratory-based teaching method that combines elements of biochemistry/molecular biology, kinesiology/health science, computer science, and manufacturing engineering to give students the ability to better conceptualize complex biological systems. Here, we utilize technology available at most universities to print three-dimensional (3D) scale models of actual human muscle cells (myofibers) out of bioplastic materials. The same methodological approach could be applied to nearly any cell type or molecular structure. This advancement is significant because historically, two-dimensional (2D) myocellular images have proven insufficient for detailed analysis of organelle organization and morphology. 3D imaging fills this void by providing accurate and quantifiable myofiber structural data. Manipulating tangible 3D models combats 2D limitation and gives students new perspectives and alternative learning experiences that may assist their understanding. This approach also exposes learners to 1) human muscle cell extraction and isolation, 2) targeted fluorescence labeling, 3) confocal microscopy, 4) image processing (via open-source software), and 5) 3D printing bioplastic scale-models (×500 larger than the actual cells). Creating these physical models may further student's interest in the invisible world of molecular and cellular biology. Furthermore, this interdisciplinary laboratory project gives instructors of all biological disciplines a new teaching tool to foster integrative thinking. © 2015 The International Union of Biochemistry and Molecular Biology.

NETTAB 2012 on "Integrated Bio-Search"

PubMed Central

2014-01-01

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement. PMID:24564635

Expanding Your Laboratory by Accessing Collaboratory Resources

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

Hoyt, David W.; Burton, Sarah D.; Peterson, Michael R.

2004-03-01

The Environmental Molecular Sciences Laboratory (EMSL) in Richland, Washington, is the home of a research facility setup by the United States Department of Energy (DOE). The facility is atypical because it houses over 100 cutting-edge research systems for the use of researchers all over the United States and the world. Access to the lab is requested through a peer-review proposal process and the scientists who use the facility are generally referred to as ‘users’. There are six main research facilities housed in EMSL, all of which host visiting researchers. Several of these facilities also participate in the EMSL Collaboratory, amore » remote access capability supported by EMSL operations funds. Of these, the High-Field Magnetic Resonance Facility (HFMRF) and Molecular Science Computing Facility (MSCF) have a significant number of their users performing remote work. The HFMRF in EMSL currently houses 12 NMR spectrometers that range in magnet field strength from 7.05T to 21.1T. Staff associated with the NMR facility offers scientific expertise in the areas of structural biology, solid-state materials/catalyst characterization, and magnetic resonance imaging (MRI) techniques. The way in which the HFMRF operates, with a high level of dedication to remote operation across the full suite of High-Field NMR spectrometers, has earned it the name “Virtual NMR Facility”. This review will focus on the operational aspects of remote research done in the High-Field Magnetic Resonance Facility and the computer tools that make remote experiments possible.« less

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP), Basic Science Program, HLA Immunogenetics Section, under the leadership of Dr. Mary Carrington, studies the influence of human leukocyte antigens (HLA) and specific KIR/HLA genotypes on risk of and outcomes to infection, cancer, autoimmune disease, and maternal-fetal disease. Recent studies have focused on the impact of HLA gene expression in disease, the molecular mechanism regulating expression levels, and the functional basis for the effect of differential expression on disease outcome. The lab’s further focus is on the genetic basis for resistance/susceptibility to disease conferred by immunogenetic variation. KEY ROLES/RESPONSIBILITIES The Senior Computational Scientist will provide research support to the CIP-BSP-HLA Immunogenetics Section performing bio-statistical design, analysis and reporting of research projects conducted in the lab. This individual will be involved in the implementation of statistical models and data preparation. Successful candidate should have 5 or more years of competent, innovative biostatistics/bioinformatics research experience, beyond doctoral training Considerable experience with statistical software, such as SAS, R and S-Plus Sound knowledge, and demonstrated experience of theoretical and applied statistics Write program code to analyze data using statistical analysis software Contribute to the interpretation and publication of research results

Development of a structured undergraduate research experience: Framework and implications.

PubMed

Brown, Anne M; Lewis, Stephanie N; Bevan, David R

2016-09-10

Participating in undergraduate research can be a pivotal experience for students in life science disciplines. Development of critical thinking skills, in addition to conveying scientific ideas in oral and written formats, is essential to ensuring that students develop a greater understanding of basic scientific knowledge and the research process. Modernizing the current life sciences research environment to accommodate the growing demand by students for experiential learning is needed. By developing and implementing a structured, theory-based approach to undergraduate research in the life sciences, specifically biochemistry, it has been successfully shown that more students can be provided with a high-quality, high-impact research experience. The structure of this approach allowed students to develop novel, independent projects in a computational molecular modeling lab. Students engaged in an experience in which career goals, problem-solving skills, time management skills, and independence in a research lab were developed. After experiencing this approach to undergraduate research, students reported feeling challenged to think critically and prepared for future career paths. The approach allowed for a progressive learning environment where more undergraduate students could participate in publishable research. Future areas for development include implementation in a bench-top lab and extension to disciplines beyond biochemistry. In this study, it has been shown that utilizing the structured approach to undergraduate research could allow for more students to experience undergraduate research and develop into more confident, independent life scientists well prepared for graduate schools and professional research environments. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):463-474, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Photofragment slice imaging studies of pyrrole and the Xe…pyrrole cluster

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

Rubio-Lago, L.; Zaouris, D.; Sakellariou, Y.

The photolysis of pyrrole has been studied in a molecular beam at wavelengths 250 nm, 240 nm and 193.3 nm, using 2 different carrier gases, He and Xe. A broad bimodal distribution of H atom fragment velocities has been observed at all wavelengths. Near threshold at both 240 and 250 nm, , sharp features have been observed in the fast part of the H-atom distribution. Under appropriate molecular beam conditions, these sharp features and the photolysis of pyrrole at both 240 and 250 nm disappear when using Xe as opposed to He as the carrier gas. We attribute this phenomenonmore » to cluster formation between Xe and pyrrole, and this assumption is supported by observation of resonance enhanced multiphoton ionization spectra for the (Xe…pyrrole) cluster followed by photofragmentation of the nascent cation cluster. Ab initio calculations are performed to support the experimental data. Part of this work is supported by the transfer of knowledge program SOUTHERN DYNAMICS MTKD-CT-2004-014306. The experimental work was performed at the Ultraviolet Laser Facility operating at IESL-FORTH and has been supported in part by the European Commission through the Research Infrastructures activity of FP6 (“Laserlab- Europe” RII3-CT-2003-506350). We also wish to thank the graduate program Applied Molecular Spectroscopy (EPEAEK). Part of this work was supported by the Division of Chemical Sciences, Geosciences and Biosciences, Office of Basic Energy Sciences, US Department of Energy with Battelle Memorial Institute, which operates the Pacific Northwest National Laboratory. Computer resources were provided by the Office of Science, US Department of Energy.« less

Active Oxygen Vacancy Site for Methanol Synthesis from CO2 Hydrogenation on In2O3(110): A DFT Study

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

Ye, Jingyun; Liu, Changjun; Mei, Donghai

2013-06-03

Methanol synthesis from CO2 hydrogenation on the defective In2O3(110) surface with surface oxygen vacancies has been investigated using periodic density functional theory calculations. The relative stabilities of six possible surface oxygen vacancies numbered from Ov1 to Ov6 on the perfect In2O3(110) surface were examined. The calculated oxygen vacancy formation energies show that the D1 surface with the Ov1 defective site is the most thermodynamically favorable while the D4 surface with the Ov4 defective site is the least stable. Two different methanol synthesis routes from CO2 hydrogenation over both D1 and D4 surfaces were studied and the D4 surface was foundmore » to be more favorable for CO2 activation and hydrogenation. On the D4 surface, one of the O atoms of the CO2 molecule fills in the Ov4 site upon adsorption. Hydrogenation of CO2 to HCOO on the D4 surface is both thermodynamically and kinetically favorable. Further hydrogenation of HCOO involves both forming the C-H bond and breaking the C-O bond, resulting in H2CO and hydroxyl. The HCOO hydrogenation is slightly endothermic with an activation barrier of 0.57 eV. A high barrier of 1.14 eV for the hydrogenation of H2CO to H3CO indicates that this step is the rate-limiting step in the methanol synthesis on the defective In2O3(110) surface. We gratefully acknowledge the supports from the National Natural Science Foundation of China (#20990223) and from US Department of Energy, Basic Energy Science program (DE-FG02-05ER46231). D. Mei was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. The computations were performed in part using the Molecular Science Computing Facility in the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), which is a U.S. Department of Energy national scientific user facility located at Pacific Northwest National Laboratory in Richland, Washington. PNNL is a multiprogram national laboratory operated for DOE by Battelle.« less

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

NASA Astrophysics Data System (ADS)

Mrugalla, Florian; Kast, Stefan M.

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory.

PubMed

Mrugalla, Florian; Kast, Stefan M

2016-09-01

Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems.

Computer Science | Classification | College of Engineering & Applied

Science.gov Websites

EMS 1011 profile photo Adrian Dumitrescu, Ph.D.ProfessorComputer Science(414) 229-4265Eng & Math @uwm.eduEng & Math Sciences 919 profile photo Hossein Hosseini, Ph.D.ProfessorComputer Science(414) 229 -5184hosseini@uwm.eduEng & Math Sciences 1091 profile photo Amol Mali, Ph.D.Associate ProfessorComputer

Computers in Science Education: Can They Go Far Enough? Have We Gone Too Far?

ERIC Educational Resources Information Center

Schrock, John Richard

1984-01-01

Indicates that although computers may churn out creative research, science is still dependent on science education, and that science education consists of increasing human experience. Also considers uses and misuses of computers in the science classroom, examining Edgar Dale's "cone of experience" related to laboratory computer and "extended…

Computational Nanotechnology of Molecular Materials, Electronics, and Actuators with Carbon Nanotubes and Fullerenes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, Madhu; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

The role of computational nanotechnology in developing next generation of multifunctional materials, molecular scale electronic and computing devices, sensors, actuators, and machines is described through a brief review of enabling computational techniques and few recent examples derived from computer simulations of carbon nanotube based molecular nanotechnology.

Applications of modern statistical methods to analysis of data in physical science

NASA Astrophysics Data System (ADS)

Wicker, James Eric

Modern methods of statistical and computational analysis offer solutions to dilemmas confronting researchers in physical science. Although the ideas behind modern statistical and computational analysis methods were originally introduced in the 1970's, most scientists still rely on methods written during the early era of computing. These researchers, who analyze increasingly voluminous and multivariate data sets, need modern analysis methods to extract the best results from their studies. The first section of this work showcases applications of modern linear regression. Since the 1960's, many researchers in spectroscopy have used classical stepwise regression techniques to derive molecular constants. However, problems with thresholds of entry and exit for model variables plagues this analysis method. Other criticisms of this kind of stepwise procedure include its inefficient searching method, the order in which variables enter or leave the model and problems with overfitting data. We implement an information scoring technique that overcomes the assumptions inherent in the stepwise regression process to calculate molecular model parameters. We believe that this kind of information based model evaluation can be applied to more general analysis situations in physical science. The second section proposes new methods of multivariate cluster analysis. The K-means algorithm and the EM algorithm, introduced in the 1960's and 1970's respectively, formed the basis of multivariate cluster analysis methodology for many years. However, several shortcomings of these methods include strong dependence on initial seed values and inaccurate results when the data seriously depart from hypersphericity. We propose new cluster analysis methods based on genetic algorithms that overcomes the strong dependence on initial seed values. In addition, we propose a generalization of the Genetic K-means algorithm which can accurately identify clusters with complex hyperellipsoidal covariance structures. We then use this new algorithm in a genetic algorithm based Expectation-Maximization process that can accurately calculate parameters describing complex clusters in a mixture model routine. Using the accuracy of this GEM algorithm, we assign information scores to cluster calculations in order to best identify the number of mixture components in a multivariate data set. We will showcase how these algorithms can be used to process multivariate data from astronomical observations.

Perspective: Ring-polymer instanton theory

NASA Astrophysics Data System (ADS)

Richardson, Jeremy O.

2018-05-01

Since the earliest explorations of quantum mechanics, it has been a topic of great interest that quantum tunneling allows particles to penetrate classically insurmountable barriers. Instanton theory provides a simple description of these processes in terms of dominant tunneling pathways. Using a ring-polymer discretization, an efficient computational method is obtained for applying this theory to compute reaction rates and tunneling splittings in molecular systems. Unlike other quantum-dynamics approaches, the method scales well with the number of degrees of freedom, and for many polyatomic systems, the method may provide the most accurate predictions which can be practically computed. Instanton theory thus has the capability to produce useful data for many fields of low-temperature chemistry including spectroscopy, atmospheric and astrochemistry, as well as surface science. There is however still room for improvement in the efficiency of the numerical algorithms, and new theories are under development for describing tunneling in nonadiabatic transitions.

High-Performance Computation of Distributed-Memory Parallel 3D Voronoi and Delaunay Tessellation

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

Peterka, Tom; Morozov, Dmitriy; Phillips, Carolyn

2014-11-14

Computing a Voronoi or Delaunay tessellation from a set of points is a core part of the analysis of many simulated and measured datasets: N-body simulations, molecular dynamics codes, and LIDAR point clouds are just a few examples. Such computational geometry methods are common in data analysis and visualization; but as the scale of simulations and observations surpasses billions of particles, the existing serial and shared-memory algorithms no longer suffice. A distributed-memory scalable parallel algorithm is the only feasible approach. The primary contribution of this paper is a new parallel Delaunay and Voronoi tessellation algorithm that automatically determines which neighbormore » points need to be exchanged among the subdomains of a spatial decomposition. Other contributions include periodic and wall boundary conditions, comparison of our method using two popular serial libraries, and application to numerous science datasets.« less

Quantum computing applied to calculations of molecular energies: CH2 benchmark.

PubMed

Veis, Libor; Pittner, Jiří

2010-11-21

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.

Digital pathology in nephrology clinical trials, research, and pathology practice.

PubMed

Barisoni, Laura; Hodgin, Jeffrey B

2017-11-01

In this review, we will discuss (i) how the recent advancements in digital technology and computational engineering are currently applied to nephropathology in the setting of clinical research, trials, and practice; (ii) the benefits of the new digital environment; (iii) how recognizing its challenges provides opportunities for transformation; and (iv) nephropathology in the upcoming era of kidney precision and predictive medicine. Recent studies highlighted how new standardized protocols facilitate the harmonization of digital pathology database infrastructure and morphologic, morphometric, and computer-aided quantitative analyses. Digital pathology enables robust protocols for clinical trials and research, with the potential to identify previously underused or unrecognized clinically useful parameters. The integration of digital pathology with molecular signatures is leading the way to establishing clinically relevant morpho-omic taxonomies of renal diseases. The introduction of digital pathology in clinical research and trials, and the progressive implementation of the modern software ecosystem, opens opportunities for the development of new predictive diagnostic paradigms and computer-aided algorithms, transforming the practice of renal disease into a modern computational science.

Atomistic Simulations of High-intensity XFEL Pulses on Diffractive Imaging of Nano-sized System Dynamics

NASA Astrophysics Data System (ADS)

Ho, Phay; Knight, Christopher; Bostedt, Christoph; Young, Linda; Tegze, Miklos; Faigel, Gyula

2016-05-01

We have developed a large-scale atomistic computational method based on a combined Monte Carlo and Molecular Dynamics (MC/MD) method to simulate XFEL-induced radiation damage dynamics of complex materials. The MD algorithm is used to propagate the trajectories of electrons, ions and atoms forward in time and the quantum nature of interactions with an XFEL pulse is accounted for by a MC method to calculate probabilities of electronic transitions. Our code has good scalability with MPI/OpenMP parallelization, and it has been run on Mira, a petascale system at the Argonne Leardership Computing Facility, with particle number >50 million. Using this code, we have examined the impact of high-intensity 8-keV XFEL pulses on the x-ray diffraction patterns of argon clusters. The obtained patterns show strong pulse parameter dependence, providing evidence of significant lattice rearrangement and diffuse scattering. Real-space electronic reconstruction was performed using phase retrieval methods. We found that the structure of the argon cluster can be recovered with atomic resolution even in the presence of considerable radiation damage. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

EDITORIAL: Design and function of molecular and bioelectronics devices

NASA Astrophysics Data System (ADS)

Krstic, Predrag; Forzani, Erica; Tao, Nongjian; Korkin, Anatoli

2007-10-01

Further rapid progress of electronics, in particular the increase of computer power and breakthroughs in sensor technology for industrial, medical diagnostics and environmental applications, strongly depends on the scaling of electronic devices, ultimately to the size of molecules. Design of controllable molecular-scale devices may resolve the problem of energy dissipation at the nanoscale and take advantage of molecular self-assembly in the so-called bottom-up approach. This special issue of Nanotechnology is devoted to a better understanding of the function and design of molecular-scale devices that are relevant to future electronics and sensor technology. Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (12-16 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. The conference series Nano and Giga Challenges in Electronics and Photonics was launched as a truly interdisciplinary forum to bridge scientists and engineers to work across boundaries in the design of future information technologies, from atoms to materials to devices to system architecture. Following the first two successful meetings in Moscow, Russia (NGCM2002) and Krakow, Poland (NGCM2004), the third Nano and Giga Forum (NGC2007) was held in 2007 hosted by Arizona State University. Besides this special issue of Nanotechnology, two other collections (in the journal Solid State Electronics and the tutorial book in the series Nanostructure Science and Technology Springer) have published additional selected and invited papers from NGC2007. The NGC2007 meeting, which included two days of tutorials (Spring School) and a three day symposium, attracted approximately 400 participants from academic, industrial and governmental research institutions from 41 countries, and covered recent developments in the fabrication and functionality of nano-scale materials, devices and system architecture from advanced CMOS to molecular electronics, photonics, optoelectronics and magnetic materials and devices. The success of the conference would not have been possible without generous support from many sponsors and research institutions, especially from Arizona State University (conference host and co-organizer), International Science and Technology Center (ISTC), National Science Foundation (NSFT), Defense Advanced Research Agency (DARPA), Office of Naval Research, Army Research Office, Computational Chemistry List (CCL), Springer Publisher, City of Tempe, STMicroelectronics, Quarles & Brady LLP, Oak Ridge National Laboratory, Canadian Consulate in Phoenix, Salt River Project (SRP) and many other local, national and international and individual supporters. We would like to acknowledge the shared responsibility for this special issue of Nanotechnology on molecular and bioelectronics, and the highly professional support from Dr Nina Couzin, Dr Alex Wotherspoon and the Nanotechnology team from the IOP Publishing. We also acknowledge the exception made in allowing the publication of some material that is outside the normal scope of Nanotechnology.

Design and function of molecular and bioelectronics devices.

PubMed

Krstic, Predrag; Forzani, Erica; Tao, Nongjian; Korkin, Anatoli

2007-10-24

Further rapid progress of electronics, in particular the increase of computer power and breakthroughs in sensor technology for industrial, medical diagnostics and environmental applications, strongly depends on the scaling of electronic devices, ultimately to the size of molecules. Design of controllable molecular-scale devices may resolve the problem of energy dissipation at the nanoscale and take advantage of molecular self-assembly in the so-called bottom-up approach. This special issue of Nanotechnology is devoted to a better understanding of the function and design of molecular-scale devices that are relevant to future electronics and sensor technology. Papers contained in this special issue are selected from the symposium Nano and Giga Challenges in Electronics and Photonics: From Atoms to Materials to Devices to System Architecture (12-16 March, 2007, Phoenix, Arizona, USA), as well as from original and novel scientific contributions of invited world-renown researchers. It addresses both theoretical and experimental achievements in the fields of molecular and bioelectronics, chemical and biosensors at the molecular level, including carbon nanotubes, novel nanostructures, as well as related research areas and industrial applications. The conference series Nano and Giga Challenges in Electronics and Photonics was launched as a truly interdisciplinary forum to bridge scientists and engineers to work across boundaries in the design of future information technologies, from atoms to materials to devices to system architecture. Following the first two successful meetings in Moscow, Russia (NGCM2002) and Krakow, Poland (NGCM2004), the third Nano and Giga Forum (NGC2007) was held in 2007 hosted by Arizona State University. Besides this special issue of Nanotechnology, two other collections (in the journal Solid State Electronics and the tutorial book in the series Nanostructure Science and Technology Springer) have published additional selected and invited papers from NGC2007. The NGC2007 meeting, which included two days of tutorials (Spring School) and a three day symposium, attracted approximately 400 participants from academic, industrial and governmental research institutions from 41 countries, and covered recent developments in the fabrication and functionality of nano-scale materials, devices and system architecture from advanced CMOS to molecular electronics, photonics, optoelectronics and magnetic materials and devices. The success of the conference would not have been possible without generous support from many sponsors and research institutions, especially from Arizona State University (conference host and co-organizer), International Science and Technology Center (ISTC), National Science Foundation (NSFT), Defense Advanced Research Agency (DARPA), Office of Naval Research, Army Research Office, Computational Chemistry List (CCL), Springer Publisher, City of Tempe, STMicroelectronics, Quarles & Brady LLP, Oak Ridge National Laboratory, Canadian Consulate in Phoenix, Salt River Project (SRP) and many other local, national and international and individual supporters. We would like to acknowledge the shared responsibility for this special issue of Nanotechnology on molecular and bioelectronics, and the highly professional support from Dr Nina Couzin, Dr Alex Wotherspoon and the Nanotechnology team from the IOP Publishing. We also acknowledge the exception made in allowing the publication of some material that is outside the normal scope of Nanotechnology.

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science

NASA Technical Reports Server (NTRS)

1987-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period April, 1986 through September 30, 1986 is summarized.

78 FR 10180 - Annual Computational Science Symposium; Conference

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-13

...] Annual Computational Science Symposium; Conference AGENCY: Food and Drug Administration, HHS. ACTION... Computational Science Symposium.'' The purpose of the conference is to help the broader community align and share experiences to advance computational science. At the conference, which will bring together FDA...

Joint density-functional theory for energetics and spectroscopy in complex aqueous and nonaqueous solvents

NASA Astrophysics Data System (ADS)

Gunceler, Deniz

Solvents are of great importance in many technological applications, but are difficult to study using standard, off-the-shelf ab initio electronic structure methods. This is because a single configuration of molecular positions in the solvent (a "snapshot" of the fluid) is not necessarily representative of the thermodynamic average. To obtain any thermodynamic averages (e.g. free energies), the phase space of the solvent must be sampled, typically using molecular dynamics. This greatly increases the computational cost involved in studying solvated systems. Joint density-functional theory has made its mark by being a computationally efficient yet rigorous theory by which to study solvation. It replaces the need for thermodynamic sampling with an effective continuum description of the solvent environment that is in-principle exact, computationally efficient and intuitive (easier to interpret). It has been very successful in aqueous systems, with potential applications in (among others) energy materials discovery, catalysis and surface science. In this dissertation, we develop accurate and fast joint density functional theories for complex, non-aqueous solvent enviroments, including organic solvents and room temperature ionic liquids, as well as new methods for calculating electron excitation spectra in such systems. These theories are then applied to a range of physical problems, from dendrite formation in lithium-metal batteries to the optical spectra of solvated ions.

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

Hules, John

This 1998 annual report from the National Scientific Energy Research Computing Center (NERSC) presents the year in review of the following categories: Computational Science; Computer Science and Applied Mathematics; and Systems and Services. Also presented are science highlights in the following categories: Basic Energy Sciences; Biological and Environmental Research; Fusion Energy Sciences; High Energy and Nuclear Physics; and Advanced Scientific Computing Research and Other Projects.

Computation Directorate and Science& Technology Review Computational Science and Research Featured in 2002

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

Alchorn, A L

Thank you for your interest in the activities of the Lawrence Livermore National Laboratory Computation Directorate. This collection of articles from the Laboratory's Science & Technology Review highlights the most significant computational projects, achievements, and contributions during 2002. In 2002, LLNL marked the 50th anniversary of its founding. Scientific advancement in support of our national security mission has always been the core of the Laboratory. So that researchers could better under and predict complex physical phenomena, the Laboratory has pushed the limits of the largest, fastest, most powerful computers in the world. In the late 1950's, Edward Teller--one of themore » LLNL founders--proposed that the Laboratory commission a Livermore Advanced Research Computer (LARC) built to Livermore's specifications. He tells the story of being in Washington, DC, when John Von Neumann asked to talk about the LARC. He thought Teller wanted too much memory in the machine. (The specifications called for 20-30,000 words.) Teller was too smart to argue with him. Later Teller invited Von Neumann to the Laboratory and showed him one of the design codes being prepared for the LARC. He asked Von Neumann for suggestions on fitting the code into 10,000 words of memory, and flattered him about ''Labbies'' not being smart enough to figure it out. Von Neumann dropped his objections, and the LARC arrived with 30,000 words of memory. Memory, and how close memory is to the processor, is still of interest to us today. Livermore's first supercomputer was the Remington-Rand Univac-1. It had 5600 vacuum tubes and was 2 meters wide by 4 meters long. This machine was commonly referred to as a 1 KFlop machine [E+3]. Skip ahead 50 years. The ASCI White machine at the Laboratory today, produced by IBM, is rated at a peak performance of 12.3 TFlops or E+13. We've improved computer processing power by 10 orders of magnitude in 50 years, and I do not believe there's any reason to think we won't improve another 10 orders of magnitude in the next 50 years. For years I have heard talk of hitting the physical limits of Moore's Law, but new technologies will take us into the next phase of computer processing power such as 3-D chips, molecular computing, quantum computing, and more. Big computers are icons or symbols of the culture and larger infrastructure that exists at LLNL to guide scientific discovery and engineering development. We have dealt with balance issues for 50 years and will continue to do so in our quest for a digital proxy of the properties of matter at extremely high temperatures and pressures. I believe that the next big computational win will be the merger of high-performance computing with information management. We already create terabytes--soon to be petabytes--of data. Efficiently storing, finding, visualizing and extracting data and turning that into knowledge which aids decision-making and scientific discovery is an exciting challenge. In the meantime, please enjoy this retrospective on computational physics, computer science, advanced software technologies, and applied mathematics performed by programs and researchers at LLNL during 2002. It offers a glimpse into the stimulating world of computational science in support of the national missions and homeland defense.« less

Enduring Influence of Stereotypical Computer Science Role Models on Women's Academic Aspirations

ERIC Educational Resources Information Center

Cheryan, Sapna; Drury, Benjamin J.; Vichayapai, Marissa

2013-01-01

The current work examines whether a brief exposure to a computer science role model who fits stereotypes of computer scientists has a lasting influence on women's interest in the field. One-hundred undergraduate women who were not computer science majors met a female or male peer role model who embodied computer science stereotypes in appearance…

A Web of Resources for Introductory Computer Science.

ERIC Educational Resources Information Center

Rebelsky, Samuel A.

As the field of Computer Science has grown, the syllabus of the introductory Computer Science course has changed significantly. No longer is it a simple introduction to programming or a tutorial on computer concepts and applications. Rather, it has become a survey of the field of Computer Science, touching on a wide variety of topics from digital…

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science

NASA Technical Reports Server (NTRS)

1988-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period April l, 1988 through September 30, 1988.

Summary of research in applied mathematics, numerical analysis and computer science at the Institute for Computer Applications in Science and Engineering

NASA Technical Reports Server (NTRS)

1984-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science during the period October 1, 1983 through March 31, 1984 is summarized.

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science

NASA Technical Reports Server (NTRS)

1987-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period October 1, 1986 through March 31, 1987 is summarized.

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation.

PubMed

Michaels, Thomas C T; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M; Knowles, Tuomas P J

2018-04-20

Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation

NASA Astrophysics Data System (ADS)

Michaels, Thomas C. T.; Šarić, Anđela; Habchi, Johnny; Chia, Sean; Meisl, Georg; Vendruscolo, Michele; Dobson, Christopher M.; Knowles, Tuomas P. J.

2018-04-01

Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.

Coding considerations for standalone molecular dynamics simulations of atomistic structures

NASA Astrophysics Data System (ADS)

Ocaya, R. O.; Terblans, J. J.

2017-10-01

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

High school computer science education paves the way for higher education: the Israeli case

NASA Astrophysics Data System (ADS)

Armoni, Michal; Gal-Ezer, Judith

2014-07-01

The gap between enrollments in higher education computing programs and the high-tech industry's demands is widely reported, and is especially prominent for women. Increasing the availability of computer science education in high school is one of the strategies suggested in order to address this gap. We look at the connection between exposure to computer science in high school and pursuing computing in higher education. We also examine the gender gap, in the context of high school computer science education. We show that in Israel, students who took the high-level computer science matriculation exam were more likely to pursue computing in higher education. Regarding the issue of gender, we will show that, in general, in Israel the difference between males and females who take computer science in high school is relatively small, and a larger, though still not very large difference exists only for the highest exam level. In addition, exposing females to high-level computer science in high school has more relative impact on pursuing higher education in computing.

Effect of Graphene with Nanopores on Metal Clusters

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

Zhou, Hu; Chen, Xianlang; Wang, Lei

Porous graphene, which is a novel type of defective graphene, shows excellent potential as a support material for metal clusters. In this work, the stability and electronic structures of metal clusters (Pd, Ir, Rh) supported on pristine graphene and graphene with different sizes of nanopore were investigated by first-principle density functional theory (DFT) calculations. Thereafter, CO adsorption and oxidation reaction on the Pd-graphene system were chosen to evaluate its catalytic performance. Graphene with nanopore can strongly stabilize the metal clusters and cause a substantial downshift of the d-band center of the metal clusters, thus decreasing CO adsorption. All binding energies,more » d-band centers, and adsorption energies show a linear change with the size of the nanopore: a bigger size of nanopore corresponds to a stronger metal clusters bond to the graphene, lower downshift of the d-band center, and weaker CO adsorption. By using a suitable size nanopore, supported Pd clusters on the graphene will have similar CO and O2 adsorption ability, thus leading to superior CO tolerance. The DFT calculated reaction energy barriers show that graphene with nanopore is a superior catalyst for CO oxidation reaction. These properties can play an important role in instructing graphene-supported metal catalyst preparation to prevent the diffusion or agglomeration of metal clusters and enhance catalytic performance. This work was supported by National Basic Research Program of China (973Program) (2013CB733501), the National Natural Science Foundation of China (NSFC-21176221, 21136001, 21101137, 21306169, and 91334013). D. Mei acknowledges the support from the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC).« less

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Argonne National Laboratory Annual Report of Laboratory Directed Research and Development program activities FY 2011.

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

Office of The Director)

As a national laboratory Argonne concentrates on scientific and technological challenges that can only be addressed through a sustained, interdisciplinary focus at a national scale. Argonne's eight major initiatives, as enumerated in its strategic plan, are Hard X-ray Sciences, Leadership Computing, Materials and Molecular Design and Discovery, Energy Storage, Alternative Energy and Efficiency, Nuclear Energy, Biological and Environmental Systems, and National Security. The purposes of Argonne's Laboratory Directed Research and Development (LDRD) Program are to encourage the development of novel technical concepts, enhance the Laboratory's research and development (R and D) capabilities, and pursue its strategic goals. projects are selectedmore » from proposals for creative and innovative R and D studies that require advance exploration before they are considered to be sufficiently developed to obtain support through normal programmatic channels. Among the aims of the projects supported by the LDRD Program are the following: establishment of engineering proof of principle, assessment of design feasibility for prospective facilities, development of instrumentation or computational methods or systems, and discoveries in fundamental science and exploratory development.« less

Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology.

PubMed

Salazar, Brittany M; Balczewski, Emily A; Ung, Choong Yong; Zhu, Shizhen

2016-12-27

Pediatric cancers rarely exhibit recurrent mutational events when compared to most adult cancers. This poses a challenge in understanding how cancers initiate, progress, and metastasize in early childhood. Also, due to limited detected driver mutations, it is difficult to benchmark key genes for drug development. In this review, we use neuroblastoma, a pediatric solid tumor of neural crest origin, as a paradigm for exploring "big data" applications in pediatric oncology. Computational strategies derived from big data science-network- and machine learning-based modeling and drug repositioning-hold the promise of shedding new light on the molecular mechanisms driving neuroblastoma pathogenesis and identifying potential therapeutics to combat this devastating disease. These strategies integrate robust data input, from genomic and transcriptomic studies, clinical data, and in vivo and in vitro experimental models specific to neuroblastoma and other types of cancers that closely mimic its biological characteristics. We discuss contexts in which "big data" and computational approaches, especially network-based modeling, may advance neuroblastoma research, describe currently available data and resources, and propose future models of strategic data collection and analyses for neuroblastoma and other related diseases.

Defining Computational Thinking for Mathematics and Science Classrooms

NASA Astrophysics Data System (ADS)

Weintrop, David; Beheshti, Elham; Horn, Michael; Orton, Kai; Jona, Kemi; Trouille, Laura; Wilensky, Uri

2016-02-01

Science and mathematics are becoming computational endeavors. This fact is reflected in the recently released Next Generation Science Standards and the decision to include "computational thinking" as a core scientific practice. With this addition, and the increased presence of computation in mathematics and scientific contexts, a new urgency has come to the challenge of defining computational thinking and providing a theoretical grounding for what form it should take in school science and mathematics classrooms. This paper presents a response to this challenge by proposing a definition of computational thinking for mathematics and science in the form of a taxonomy consisting of four main categories: data practices, modeling and simulation practices, computational problem solving practices, and systems thinking practices. In formulating this taxonomy, we draw on the existing computational thinking literature, interviews with mathematicians and scientists, and exemplary computational thinking instructional materials. This work was undertaken as part of a larger effort to infuse computational thinking into high school science and mathematics curricular materials. In this paper, we argue for the approach of embedding computational thinking in mathematics and science contexts, present the taxonomy, and discuss how we envision the taxonomy being used to bring current educational efforts in line with the increasingly computational nature of modern science and mathematics.

Distance education through the Internet: the GNA-VSNS biocomputing course.

PubMed

de la Vega, F M; Giegerich, R; Fuellen, G

1996-01-01

A prototype course on biocomputing was delivered via international computer networks in early summer 1995. The course lasted 11 weeks, and was offered free of charge. It was organized by the BioComputing Division of the Virtual School of Natural Sciences, which is a member school of the Globewide Network Academy. It brought together 34 students and 7 instructors from all over the world, and covered the basics of sequence analysis. Five authors from Germany and USA prepared a hypertext book which was discussed in weekly study sessions that took place in a virtual classroom at the BioMOO electronic conferencing system. The course aimed at students with backgrounds in molecular biology, biomedicine or computer science, complementing and extending their skills with an interdisciplinary curriculum. Special emphasis was placed on the use of Internet resources, and the development of new teaching tools. The hypertext book includes direct links to sequence analysis and databank search services on the Internet. A tool for the interactive visualization of unit-cost pairwise sequence alignment was developed for the course. All course material will stay accessible at the World Wide Web address (Uniform Resource Locator) http://+www.techfak.uni-bielefeld.de/bcd/welcome .html. This paper describes the aims and organization of the course, and gives a preliminary account of this novel experience in distance education.

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

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

Crabtree, George; Glotzer, Sharon; McCurdy, Bill

This report is based on a SC Workshop on Computational Materials Science and Chemistry for Innovation on July 26-27, 2010, to assess the potential of state-of-the-art computer simulations to accelerate understanding and discovery in materials science and chemistry, with a focus on potential impacts in energy technologies and innovation. The urgent demand for new energy technologies has greatly exceeded the capabilities of today's materials and chemical processes. To convert sunlight to fuel, efficiently store energy, or enable a new generation of energy production and utilization technologies requires the development of new materials and processes of unprecedented functionality and performance. Newmore » materials and processes are critical pacing elements for progress in advanced energy systems and virtually all industrial technologies. Over the past two decades, the United States has developed and deployed the world's most powerful collection of tools for the synthesis, processing, characterization, and simulation and modeling of materials and chemical systems at the nanoscale, dimensions of a few atoms to a few hundred atoms across. These tools, which include world-leading x-ray and neutron sources, nanoscale science facilities, and high-performance computers, provide an unprecedented view of the atomic-scale structure and dynamics of materials and the molecular-scale basis of chemical processes. For the first time in history, we are able to synthesize, characterize, and model materials and chemical behavior at the length scale where this behavior is controlled. This ability is transformational for the discovery process and, as a result, confers a significant competitive advantage. Perhaps the most spectacular increase in capability has been demonstrated in high performance computing. Over the past decade, computational power has increased by a factor of a million due to advances in hardware and software. This rate of improvement, which shows no sign of abating, has enabled the development of computer simulations and models of unprecedented fidelity. We are at the threshold of a new era where the integrated synthesis, characterization, and modeling of complex materials and chemical processes will transform our ability to understand and design new materials and chemistries with predictive power. In turn, this predictive capability will transform technological innovation by accelerating the development and deployment of new materials and processes in products and manufacturing. Harnessing the potential of computational science and engineering for the discovery and development of materials and chemical processes is essential to maintaining leadership in these foundational fields that underpin energy technologies and industrial competitiveness. Capitalizing on the opportunities presented by simulation-based engineering and science in materials and chemistry will require an integration of experimental capabilities with theoretical and computational modeling; the development of a robust and sustainable infrastructure to support the development and deployment of advanced computational models; and the assembly of a community of scientists and engineers to implement this integration and infrastructure. This community must extend to industry, where incorporating predictive materials science and chemistry into design tools can accelerate the product development cycle and drive economic competitiveness. The confluence of new theories, new materials synthesis capabilities, and new computer platforms has created an unprecedented opportunity to implement a "materials-by-design" paradigm with wide-ranging benefits in technological innovation and scientific discovery. The Workshop on Computational Materials Science and Chemistry for Innovation was convened in Bethesda, Maryland, on July 26-27, 2010. Sponsored by the Department of Energy (DOE) Offices of Advanced Scientific Computing Research and Basic Energy Sciences, the workshop brought together 160 experts in materials science, chemistry, and computational science representing more than 65 universities, laboratories, and industries, and four agencies. The workshop examined seven foundational challenge areas in materials science and chemistry: materials for extreme conditions, self-assembly, light harvesting, chemical reactions, designer fluids, thin films and interfaces, and electronic structure. Each of these challenge areas is critical to the development of advanced energy systems, and each can be accelerated by the integrated application of predictive capability with theory and experiment. The workshop concluded that emerging capabilities in predictive modeling and simulation have the potential to revolutionize the development of new materials and chemical processes. Coupled with world-leading materials characterization and nanoscale science facilities, this predictive capability provides the foundation for an innovation ecosystem that can accelerate the discovery, development, and deployment of new technologies, including advanced energy systems. Delivering on the promise of this innovation ecosystem requires the following: Integration of synthesis, processing, characterization, theory, and simulation and modeling. Many of the newly established Energy Frontier Research Centers and Energy Hubs are exploiting this integration. Achieving/strengthening predictive capability in foundational challenge areas. Predictive capability in the seven foundational challenge areas described in this report is critical to the development of advanced energy technologies. Developing validated computational approaches that span vast differences in time and length scales. This fundamental computational challenge crosscuts all of the foundational challenge areas. Similarly challenging is coupling of analytical data from multiple instruments and techniques that are required to link these length and time scales. Experimental validation and quantification of uncertainty in simulation and modeling. Uncertainty quantification becomes increasingly challenging as simulations become more complex. Robust and sustainable computational infrastructure, including software and applications. For modeling and simulation, software equals infrastructure. To validate the computational tools, software is critical infrastructure that effectively translates huge arrays of experimental data into useful scientific understanding. An integrated approach for managing this infrastructure is essential. Efficient transfer and incorporation of simulation-based engineering and science in industry. Strategies for bridging the gap between research and industrial applications and for widespread industry adoption of integrated computational materials engineering are needed.« less

Nicholas Brunhart-Lupo | NREL

Science.gov Websites

. Education Ph.D., Computer Science, Colorado School of Mines M.S., Computer Science, University of Queensland B.S., Computer Science, Colorado School of Mines Brunhart-Lupo Nicholas Brunhart-Lupo Computational Science Nicholas.Brunhart-Lupo@nrel.gov

The Need for Computer Science

ERIC Educational Resources Information Center

Margolis, Jane; Goode, Joanna; Bernier, David

2011-01-01

Broadening computer science learning to include more students is a crucial item on the United States' education agenda, these authors say. Although policymakers advocate more computer science expertise, computer science offerings in high schools are few--and actually shrinking. In addition, poorly resourced schools with a high percentage of…

Summary of research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science

NASA Technical Reports Server (NTRS)

1989-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period October 1, 1988 through March 31, 1989 is summarized.

Alliance for Computational Science Collaboration HBCU Partnership at Fisk University. Final Report 2001

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

Collins, W. E.

2004-08-16

Computational Science plays a big role in research and development in mathematics, science, engineering and biomedical disciplines. The Alliance for Computational Science Collaboration (ACSC) has the goal of training African-American and other minority scientists in the computational science field for eventual employment with the Department of Energy (DOE). The involvements of Historically Black Colleges and Universities (HBCU) in the Alliance provide avenues for producing future DOE African-American scientists. Fisk University has been participating in this program through grants from the DOE. The DOE grant supported computational science activities at Fisk University. The research areas included energy related projects, distributed computing,more » visualization of scientific systems and biomedical computing. Students' involvement in computational science research included undergraduate summer research at Oak Ridge National Lab, on-campus research involving the participation of undergraduates, participation of undergraduate and faculty members in workshops, and mentoring of students. These activities enhanced research and education in computational science, thereby adding to Fisk University's spectrum of research and educational capabilities. Among the successes of the computational science activities are the acceptance of three undergraduate students to graduate schools with full scholarships beginning fall 2002 (one for master degree program and two for Doctoral degree program).« less

Educational Challenges of Molecular Life Science: Characteristics and Implications for Education and Research

PubMed Central

Rundgren, Carl-Johan

2010-01-01

Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life—often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from “pure sciences,” such as math, chemistry, and physics, through “applied sciences,” such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences. PMID:20194805

Curricular Influences on Female Afterschool Facilitators' Computer Science Interests and Career Choices

NASA Astrophysics Data System (ADS)

Koch, Melissa; Gorges, Torie

2016-10-01

Underrepresented populations such as women, African-Americans, and Latinos/as often come to STEM (science, technology, engineering, and mathematics) careers by less traditional paths than White and Asian males. To better understand how and why women might shift toward STEM, particularly computer science, careers, we investigated the education and career direction of afterschool facilitators, primarily women of color in their twenties and thirties, who taught Build IT, an afterschool computer science curriculum for middle school girls. Many of these women indicated that implementing Build IT had influenced their own interest in technology and computer science and in some cases had resulted in their intent to pursue technology and computer science education. We wanted to explore the role that teaching Build IT may have played in activating or reactivating interest in careers in computer science and to see whether in the years following implementation of Build IT, these women pursued STEM education and/or careers. We reached nine facilitators who implemented the program in 2011-12 or shortly after. Many indicated that while facilitating Build IT, they learned along with the participants, increasing their interest in and confidence with technology and computer science. Seven of the nine participants pursued further STEM or computer science learning or modified their career paths to include more of a STEM or computer science focus. Through interviews, we explored what aspects of Build IT influenced these facilitators' interest and confidence in STEM and when relevant their pursuit of technology and computer science education and careers.

The NASA computer science research program plan

NASA Technical Reports Server (NTRS)

1983-01-01

A taxonomy of computer science is included, one state of the art of each of the major computer science categories is summarized. A functional breakdown of NASA programs under Aeronautics R and D, space R and T, and institutional support is also included. These areas were assessed against the computer science categories. Concurrent processing, highly reliable computing, and information management are identified.

Looking back: forward looking.

PubMed

Edmunds, Scott C; Nogoy, Nicole A; Zauner, Hans; Li, Peter; Hunter, Christopher I; Zhe, Xiao Si; Goodman, Laurie

2017-09-01

GigaScience is now 5 years old, having been launched at the 2012 Intelligent Systems for Molecular Biology conference. Anyone who has attended what is the largest computational biology conference since then has had the opportunity to join us for each birthday celebration-and receive 1 of our fun T-shirts as a party prize. Since launching, we have pushed our agenda of openness, transparency, reproducibility, and reusability. Here, we look back at our first 5 years and what we have done to forward our open science goals in scientific publishing. Our mainstay has been to create a process that allows the availability and publication of as many "research objects" as possible to create a more complete way of communicating how the research process is done. © The Authors 2017. Published by Oxford University Press.

On teaching computer ethics within a computer science department.

PubMed

Quinn, Michael J

2006-04-01

The author has surveyed a quarter of the accredited undergraduate computer science programs in the United States. More than half of these programs offer a 'social and ethical implications of computing' course taught by a computer science faculty member, and there appears to be a trend toward teaching ethics classes within computer science departments. Although the decision to create an 'in house' computer ethics course may sometimes be a pragmatic response to pressure from the accreditation agency, this paper argues that teaching ethics within a computer science department can provide students and faculty members with numerous benefits. The paper lists topics that can be covered in a computer ethics course and offers some practical suggestions for making the course successful.

Proceedings of US-Latin American Workshop on Molecular and Materials Sciences: Theoretical and Computational Aspects Held in Gainesville, Florida on 10-12 March 1993

DTIC Science & Technology

1994-08-09

City Josd Rdamier and R. Iterative Bogoliubov Transformations and Applications Jauregui Inst. de Fisica , Cuernavaca, Meiico Peter J. Reynolds Quantum...University, Provo, UT 84602 J. R•camier Instituto de Fisica , UNAM, Cuernavaca, Mor., MWxico Gamow states are solutions to the Schr6dinger equation with a...Coutinho Departamento de FAsica do UFPE 50732-910 Recife, PE, Brazil and Jnstituto de Fisica da USP, Czp 20516 01498-970 Sdo Paulo, SP, Brasil The

Microbes to Biomes at Berkeley Lab

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

None

2015-10-28

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Fundamental approaches in molecular biology for communication sciences and disorders.

PubMed

Bartlett, Rebecca S; Jetté, Marie E; King, Suzanne N; Schaser, Allison; Thibeault, Susan L

2012-08-01

This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has increased at a remarkable pace. Most of this progress can be attributed to concomitant advances in basic molecular biology and, specifically, the development of an ever-expanding armamentarium of technologies for analysis of DNA, RNA, and protein structure and function. Details of these methodologies, their limitations, and examples from the communication sciences and disorders literature are presented. Results/Conclusions The use of molecular biology techniques in the fields of speech, language, and hearing sciences is increasing, facilitating the need for an understanding of molecular biology fundamentals and common experimental assays.

Computational Science News | Computational Science | NREL

Science.gov Websites

-Cooled High-Performance Computing Technology at the ESIF February 28, 2018 NREL Launches New Website for High-Performance Computing System Users The National Renewable Energy Laboratory (NREL) Computational Science Center has launched a revamped website for users of the lab's high-performance computing (HPC

Stability Analysis of Finite Difference Approximations to Hyperbolic Systems, and Problems in Applied and Computational Matrix Theory

DTIC Science & Technology

1988-07-08

Marcus and C. Baczynski), Computer Science Press, Rockville, Maryland, 1986. 3. An Introduction to Pascal and Precalculus , Computer Science Press...Science Press, Rockville, Maryland, 1986. 35. An Introduction to Pascal and Precalculus , Computer Science Press, Rockville, Maryland, 1986. 36

Empirical Determination of Competence Areas to Computer Science Education

ERIC Educational Resources Information Center

Zendler, Andreas; Klaudt, Dieter; Seitz, Cornelia

2014-01-01

The authors discuss empirically determined competence areas to K-12 computer science education, emphasizing the cognitive level of competence. The results of a questionnaire with 120 professors of computer science serve as a database. By using multi-dimensional scaling and cluster analysis, four competence areas to computer science education…

Factors Influencing Exemplary Science Teachers' Levels of Computer Use

ERIC Educational Resources Information Center

Hakverdi, Meral; Dana, Thomas M.; Swain, Colleen

2011-01-01

The purpose of this study was to examine exemplary science teachers' use of technology in science instruction, factors influencing their level of computer use, their level of knowledge/skills in using specific computer applications for science instruction, their use of computer-related applications/tools during their instruction, and their…

Preparing Future Secondary Computer Science Educators

ERIC Educational Resources Information Center

Ajwa, Iyad

2007-01-01

Although nearly every college offers a major in computer science, many computer science teachers at the secondary level have received little formal training. This paper presents details of a project that could make a significant contribution to national efforts to improve computer science education by combining teacher education and professional…

OPENING REMARKS: SciDAC: Scientific Discovery through Advanced Computing

NASA Astrophysics Data System (ADS)

Strayer, Michael

2005-01-01

Good morning. Welcome to SciDAC 2005 and San Francisco. SciDAC is all about computational science and scientific discovery. In a large sense, computational science characterizes SciDAC and its intent is change. It transforms both our approach and our understanding of science. It opens new doors and crosses traditional boundaries while seeking discovery. In terms of twentieth century methodologies, computational science may be said to be transformational. There are a number of examples to this point. First are the sciences that encompass climate modeling. The application of computational science has in essence created the field of climate modeling. This community is now international in scope and has provided precision results that are challenging our understanding of our environment. A second example is that of lattice quantum chromodynamics. Lattice QCD, while adding precision and insight to our fundamental understanding of strong interaction dynamics, has transformed our approach to particle and nuclear science. The individual investigator approach has evolved to teams of scientists from different disciplines working side-by-side towards a common goal. SciDAC is also undergoing a transformation. This meeting is a prime example. Last year it was a small programmatic meeting tracking progress in SciDAC. This year, we have a major computational science meeting with a variety of disciplines and enabling technologies represented. SciDAC 2005 should position itself as a new corner stone for Computational Science and its impact on science. As we look to the immediate future, FY2006 will bring a new cycle to SciDAC. Most of the program elements of SciDAC will be re-competed in FY2006. The re-competition will involve new instruments for computational science, new approaches for collaboration, as well as new disciplines. There will be new opportunities for virtual experiments in carbon sequestration, fusion, and nuclear power and nuclear waste, as well as collaborations with industry and virtual prototyping. New instruments of collaboration will include institutes and centers while summer schools, workshops and outreach will invite new talent and expertise. Computational science adds new dimensions to science and its practice. Disciplines of fusion, accelerator science, and combustion are poised to blur the boundaries between pure and applied science. As we open the door into FY2006 we shall see a landscape of new scientific challenges: in biology, chemistry, materials, and astrophysics to name a few. The enabling technologies of SciDAC have been transformational as drivers of change. Planning for major new software systems assumes a base line employing Common Component Architectures and this has become a household word for new software projects. While grid algorithms and mesh refinement software have transformed applications software, data management and visualization have transformed our understanding of science from data. The Gordon Bell prize now seems to be dominated by computational science and solvers developed by TOPS ISIC. The priorities of the Office of Science in the Department of Energy are clear. The 20 year facilities plan is driven by new science. High performance computing is placed amongst the two highest priorities. Moore's law says that by the end of the next cycle of SciDAC we shall have peta-flop computers. The challenges of petascale computing are enormous. These and the associated computational science are the highest priorities for computing within the Office of Science. Our effort in Leadership Class computing is just a first step towards this goal. Clearly, computational science at this scale will face enormous challenges and possibilities. Performance evaluation and prediction will be critical to unraveling the needed software technologies. We must not lose sight of our overarching goal—that of scientific discovery. Science does not stand still and the landscape of science discovery and computing holds immense promise. In this environment, I believe it is necessary to institute a system of science based performance metrics to help quantify our progress towards science goals and scientific computing. As a final comment I would like to reaffirm that the shifting landscapes of science will force changes to our computational sciences, and leave you with the quote from Richard Hamming, 'The purpose of computing is insight, not numbers'.

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

PubMed

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

2014-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Measurement Frontiers in Molecular Biology

NASA Astrophysics Data System (ADS)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

Enabling Wide-Scale Computer Science Education through Improved Automated Assessment Tools

NASA Astrophysics Data System (ADS)

Boe, Bryce A.

There is a proliferating demand for newly trained computer scientists as the number of computer science related jobs continues to increase. University programs will only be able to train enough new computer scientists to meet this demand when two things happen: when there are more primary and secondary school students interested in computer science, and when university departments have the resources to handle the resulting increase in enrollment. To meet these goals, significant effort is being made to both incorporate computational thinking into existing primary school education, and to support larger university computer science class sizes. We contribute to this effort through the creation and use of improved automated assessment tools. To enable wide-scale computer science education we do two things. First, we create a framework called Hairball to support the static analysis of Scratch programs targeted for fourth, fifth, and sixth grade students. Scratch is a popular building-block language utilized to pique interest in and teach the basics of computer science. We observe that Hairball allows for rapid curriculum alterations and thus contributes to wide-scale deployment of computer science curriculum. Second, we create a real-time feedback and assessment system utilized in university computer science classes to provide better feedback to students while reducing assessment time. Insights from our analysis of student submission data show that modifications to the system configuration support the way students learn and progress through course material, making it possible for instructors to tailor assignments to optimize learning in growing computer science classes.

Programmers, professors, and parasites: credit and co-authorship in computer science.

PubMed

Solomon, Justin

2009-12-01

This article presents an in-depth analysis of past and present publishing practices in academic computer science to suggest the establishment of a more consistent publishing standard. Historical precedent for academic publishing in computer science is established through the study of anecdotes as well as statistics collected from databases of published computer science papers. After examining these facts alongside information about analogous publishing situations and standards in other scientific fields, the article concludes with a list of basic principles that should be adopted in any computer science publishing standard. These principles would contribute to the reliability and scientific nature of academic publications in computer science and would allow for more straightforward discourse in future publications.

Increasing Diversity in Computer Science: Acknowledging, yet Moving Beyond, Gender

NASA Astrophysics Data System (ADS)

Larsen, Elizabeth A.; Stubbs, Margaret L.

Lack of diversity within the computer science field has, thus far, been examined most fully through the lens of gender. This article is based on a follow-on to Margolis and Fisher's (2002) study and includes interviews with 33 Carnegie Mellon University students from the undergraduate senior class of 2002 in the School of Computer Science. We found evidence of similarities among the perceptions of these women and men on definitions of computer science, explanations for the notoriously low proportion of women in the field, characterizations of a typical computer science student, impressions of recent curricular changes, a sense of the atmosphere/culture in the program, views of the Women@SCS campus organization, and suggestions for attracting and retaining well-rounded students in computer science. We conclude that efforts to increase diversity in the computer science field will benefit from a more broad-based approach that considers, but is not limited to, notions of gender difference.

Democratizing Computer Science

ERIC Educational Resources Information Center

Margolis, Jane; Goode, Joanna; Ryoo, Jean J.

2015-01-01

Computer science programs are too often identified with a narrow stratum of the student population, often white or Asian boys who have access to computers at home. But because computers play such a huge role in our world today, all students can benefit from the study of computer science and the opportunity to build skills related to computing. The…

Implementing an Affordable High-Performance Computing for Teaching-Oriented Computer Science Curriculum

ERIC Educational Resources Information Center

Abuzaghleh, Omar; Goldschmidt, Kathleen; Elleithy, Yasser; Lee, Jeongkyu

2013-01-01

With the advances in computing power, high-performance computing (HPC) platforms have had an impact on not only scientific research in advanced organizations but also computer science curriculum in the educational community. For example, multicore programming and parallel systems are highly desired courses in the computer science major. However,…

78 FR 59927 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., Computational, and Systems Biology [External Review Draft]'' (EPA/600/R-13/214A). EPA is also announcing that... Advances in Molecular, Computational, and Systems Biology [External Review Draft]'' is available primarily...

78 FR 68058 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-13

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., computational, and systems biology data can better inform risk assessment. This draft document is available for...

Computer Science and the Liberal Arts

ERIC Educational Resources Information Center

Shannon, Christine

2010-01-01

Computer science and the liberal arts have much to offer each other. Yet liberal arts colleges, in particular, have been slow to recognize the opportunity that the study of computer science provides for achieving the goals of a liberal education. After the precipitous drop in computer science enrollments during the first decade of this century,…

Marrying Content and Process in Computer Science Education

ERIC Educational Resources Information Center

Zendler, A.; Spannagel, C.; Klaudt, D.

2011-01-01

Constructivist approaches to computer science education emphasize that as well as knowledge, thinking skills and processes are involved in active knowledge construction. K-12 computer science curricula must not be based on fashions and trends, but on contents and processes that are observable in various domains of computer science, that can be…

Computing Whether She Belongs: Stereotypes Undermine Girls' Interest and Sense of Belonging in Computer Science

ERIC Educational Resources Information Center

Master, Allison; Cheryan, Sapna; Meltzoff, Andrew N.

2016-01-01

Computer science has one of the largest gender disparities in science, technology, engineering, and mathematics. An important reason for this disparity is that girls are less likely than boys to enroll in necessary "pipeline courses," such as introductory computer science. Two experiments investigated whether high-school girls' lower…

Approaching Gender Parity: Women in Computer Science at Afghanistan's Kabul University

ERIC Educational Resources Information Center

Plane, Jandelyn

2010-01-01

This study explores the representation of women in computer science at the tertiary level through data collected about undergraduate computer science education at Kabul University in Afghanistan. Previous studies have theorized reasons for underrepresentation of women in computer science, and while many of these reasons are indeed present in…

Some Hail 'Computational Science' as Biggest Advance Since Newton, Galileo.

ERIC Educational Resources Information Center

Turner, Judith Axler

1987-01-01

Computational science is defined as science done on a computer. A computer can serve as a laboratory for researchers who cannot experiment with their subjects, and as a calculator for those who otherwise might need centuries to solve some problems mathematically. The National Science Foundation's support of supercomputers is discussed. (MLW)

African-American males in computer science---Examining the pipeline for clogs

NASA Astrophysics Data System (ADS)

Stone, Daryl Bryant

The literature on African-American males (AAM) begins with a statement to the effect that "Today young Black men are more likely to be killed or sent to prison than to graduate from college." Why are the numbers of African-American male college graduates decreasing? Why are those enrolled in college not majoring in the science, technology, engineering, and mathematics (STEM) disciplines? This research explored why African-American males are not filling the well-recognized industry need for Computer Scientist/Technologists by choosing college tracks to these careers. The literature on STEM disciplines focuses largely on women in STEM, as opposed to minorities, and within minorities, there is a noticeable research gap in addressing the needs and opportunities available to African-American males. The primary goal of this study was therefore to examine the computer science "pipeline" from the African-American male perspective. The method included a "Computer Science Degree Self-Efficacy Scale" be distributed to five groups of African-American male students, to include: (1) fourth graders, (2) eighth graders, (3) eleventh graders, (4) underclass undergraduate computer science majors, and (5) upperclass undergraduate computer science majors. In addition to a 30-question self-efficacy test, subjects from each group were asked to participate in a group discussion about "African-American males in computer science." The audio record of each group meeting provides qualitative data for the study. The hypotheses include the following: (1) There is no significant difference in "Computer Science Degree" self-efficacy between fourth and eighth graders. (2) There is no significant difference in "Computer Science Degree" self-efficacy between eighth and eleventh graders. (3) There is no significant difference in "Computer Science Degree" self-efficacy between eleventh graders and lower-level computer science majors. (4) There is no significant difference in "Computer Science Degree" self-efficacy between lower-level computer science majors and upper-level computer science majors. (5) There is no significant difference in "Computer Science Degree" self-efficacy between each of the five groups of students. Finally, the researcher selected African-American male students attending six primary schools, including the predominately African-American elementary, middle and high school that the researcher attended during his own academic career. Additionally, a racially mixed elementary, middle and high school was selected from the same county in Maryland. Bowie State University provided both the underclass and upperclass computer science majors surveyed in this study. Of the five hypotheses, the sample provided enough evidence to support the claim that there are significant differences in the "Computer Science Degree" self-efficacy between each of the five groups of students. ANOVA analysis by question and total self-efficacy scores provided more results of statistical significance. Additionally, factor analysis and review of the qualitative data provide more insightful results. Overall, the data suggest 'a clog' may exist in the middle school level and students attending racially mixed schools were more confident in their computer, math and science skills. African-American males admit to spending lots of time on social networking websites and emailing, but are 'dis-aware' of the skills and knowledge needed to study in the computing disciplines. The majority of the subjects knew little, if any, AAMs in the 'computing discipline pipeline'. The collegian African-American males, in this study, agree that computer programming is a difficult area and serves as a 'major clog in the pipeline'.

Girls in computer science: A female only introduction class in high school

NASA Astrophysics Data System (ADS)

Drobnis, Ann W.

This study examined the impact of an all girls' classroom environment in a high school introductory computer science class on the student's attitudes towards computer science and their thoughts on future involvement with computer science. It was determined that an all girls' introductory class could impact the declining female enrollment and female students' efficacy towards computer science. This research was conducted in a summer school program through a regional magnet school for science and technology which these students attend during the school year. Three different groupings of students were examined for the research: female students in an all girls' class, female students in mixed-gender classes and male students in mixed-gender classes. A survey, Attitudes about Computers and Computer Science (ACCS), was designed to obtain an understanding of the students' thoughts, preconceptions, attitude, knowledge of computer science, and future intentions around computer science, both in education and career. Students in all three groups were administered the ACCS prior to taking the class and upon completion of the class. In addition, students in the all girls' class wrote in a journal throughout the course, and some of those students were also interviewed upon completion of the course. The data was analyzed using quantitative and qualitative techniques. While there were no major differences found in the quantitative data, it was determined that girls in the all girls' class were truly excited by what they had learned and were more open to the idea of computer science being a part of their future.

Dehydration pathways of 1-propanol on HZSM-5 in the presence and absence of water

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

Zhi, Yuchun; Shi, Hui; Mu, Linyu

The Brønsted acid-catalyzed gas-phase dehydration of 1-propanol (0.075-4 kPa) was studied on zeolite H-MFI (Si/Al = 26, containing minimal amounts of extraframework Al moieties) in the absence and presence of co-fed water (0-2.5 kPa) at 413-443 K. It is shown that propene can be formed from monomeric and dimeric adsorbed 1-propanol. The stronger adsorption of 1-propanol relative to water indicates that the reduced dehydration rates in the presence of water are not a consequence of the competitive adsorption between 1-propanol and water. Instead, the deleterious effect is related to the different extents of stabilization of adsorbed intermediates and the relevantmore » elimination/substitution transition states by water. Water stabilizes the adsorbed 1-propanol monomer significantly more than the elimination transition state, leading to a higher activation barrier and a greater entropy gain for the rate-limiting step, which eventually leads to propene. In a similar manner, an excess of 1-propanol stabilizes the adsorbed state of 1-propanol more than the elimination transition state. In comparison with the monomer-mediated pathway, adsorbed dimer and the relevant transition states for propene and ether formation are similarly, while less effectively, stabilized by intrazeolite water molecules. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, and was performed in part using the Molecular Sciences Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located and the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

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

PubMed

Eirín-López, José M

2013-01-01

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

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology⋆

PubMed Central

Fu, Wenjiang J.; Stromberg, Arnold J.; Viele, Kert; Carroll, Raymond J.; Wu, Guoyao

2009-01-01

Over the past two decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine fetal retardation). PMID:20233650

Water condensation: a multiscale phenomenon.

PubMed

Jensen, Kasper Risgaard; Fojan, Peter; Jensen, Rasmus Lund; Gurevich, Leonid

2014-02-01

The condensation of water is a phenomenon occurring in multiple situations in everyday life, e.g., when fog is formed or when dew forms on the grass or on windows. This means that this phenomenon plays an important role within the different fields of science including meteorology, building physics, and chemistry. In this review we address condensation models and simulations with the main focus on heterogeneous condensation of water. The condensation process is, at first, described from a thermodynamic viewpoint where the nucleation step is described by the classical nucleation theory. Further, we address the shortcomings of the thermodynamic theory in describing the nucleation and emphasize the importance of nanoscale effects. This leads to the description of condensation from a molecular viewpoint. Also presented is how the nucleation can be simulated by use of molecular models, and how the condensation process is simulated on the macroscale using computational fluid dynamics. Finally, examples of hybrid models combining molecular and macroscale models for the simulation of condensation on a surface are presented.

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

PubMed

Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conceptual Considerations in Molecular Science

ERIC Educational Resources Information Center

Sawyer, Donald T.

2005-01-01

There are significant misconceptions within the chemical community and molecular science, particularly in the undergraduate curriculum and the associated textbooks. Some of the misconceptions are described, which give poor basis to understand molecular bonding and structure, and reaction mechanisms.

Bringing computational science to the public.

PubMed

McDonagh, James L; Barker, Daniel; Alderson, Rosanna G

2016-01-01

The increasing use of computers in science allows for the scientific analyses of large datasets at an increasing pace. We provided examples and interactive demonstrations at Dundee Science Centre as part of the 2015 Women in Science festival, to present aspects of computational science to the general public. We used low-cost Raspberry Pi computers to provide hands on experience in computer programming and demonstrated the application of computers to biology. Computer games were used as a means to introduce computers to younger visitors. The success of the event was evaluated by voluntary feedback forms completed by visitors, in conjunction with our own self-evaluation. This work builds on the original work of the 4273π bioinformatics education program of Barker et al. (2013, BMC Bioinform. 14:243). 4273π provides open source education materials in bioinformatics. This work looks at the potential to adapt similar materials for public engagement events. It appears, at least in our small sample of visitors (n = 13), that basic computational science can be conveyed to people of all ages by means of interactive demonstrations. Children as young as five were able to successfully edit simple computer programs with supervision. This was, in many cases, their first experience of computer programming. The feedback is predominantly positive, showing strong support for improving computational science education, but also included suggestions for improvement. Our conclusions are necessarily preliminary. However, feedback forms suggest methods were generally well received among the participants; "Easy to follow. Clear explanation" and "Very easy. Demonstrators were very informative." Our event, held at a local Science Centre in Dundee, demonstrates that computer games and programming activities suitable for young children can be performed alongside a more specialised and applied introduction to computational science for older visitors.

The Future of Pharmaceutical Manufacturing Sciences.

PubMed

Rantanen, Jukka; Khinast, Johannes

2015-11-01

The entire pharmaceutical sector is in an urgent need of both innovative technological solutions and fundamental scientific work, enabling the production of highly engineered drug products. Commercial-scale manufacturing of complex drug delivery systems (DDSs) using the existing technologies is challenging. This review covers important elements of manufacturing sciences, beginning with risk management strategies and design of experiments (DoE) techniques. Experimental techniques should, where possible, be supported by computational approaches. With that regard, state-of-art mechanistic process modeling techniques are described in detail. Implementation of materials science tools paves the way to molecular-based processing of future DDSs. A snapshot of some of the existing tools is presented. Additionally, general engineering principles are discussed covering process measurement and process control solutions. Last part of the review addresses future manufacturing solutions, covering continuous processing and, specifically, hot-melt processing and printing-based technologies. Finally, challenges related to implementing these technologies as a part of future health care systems are discussed. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association.

A Haptic-Enhanced System for Molecular Sensing

NASA Astrophysics Data System (ADS)

Comai, Sara; Mazza, Davide

The science of haptics has received an enormous attention in the last decade. One of the major application trends of haptics technology is data visualization and training. In this paper, we present a haptically-enhanced system for manipulation and tactile exploration of molecules.The geometrical models of molecules is extracted either from theoretical or empirical data using file formats widely adopted in chemical and biological fields. The addition of information computed with computational chemistry tools, allows users to feel the interaction forces between an explored molecule and a charge associated to the haptic device, and to visualize a huge amount of numerical data in a more comprehensible way. The developed tool can be used either for teaching or research purposes due to its high reliance on both theoretical and experimental data.

Single-molecule protein sequencing through fingerprinting: computational assessment

NASA Astrophysics Data System (ADS)

Yao, Yao; Docter, Margreet; van Ginkel, Jetty; de Ridder, Dick; Joo, Chirlmin

2015-10-01

Proteins are vital in all biological systems as they constitute the main structural and functional components of cells. Recent advances in mass spectrometry have brought the promise of complete proteomics by helping draft the human proteome. Yet, this commonly used protein sequencing technique has fundamental limitations in sensitivity. Here we propose a method for single-molecule (SM) protein sequencing. A major challenge lies in the fact that proteins are composed of 20 different amino acids, which demands 20 molecular reporters. We computationally demonstrate that it suffices to measure only two types of amino acids to identify proteins and suggest an experimental scheme using SM fluorescence. When achieved, this highly sensitive approach will result in a paradigm shift in proteomics, with major impact in the biological and medical sciences.

Computer Science and Telecommunications Board summary of activities

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

Blumenthal, M.S.

1992-03-27

The Computer Science and Telecommunications Board (CSTB) considers technical and policy issues pertaining to computer science, telecommunications, and associated technologies. CSTB actively disseminates the results of its completed projects to those in a position to help implement their recommendations or otherwise use their insights. It provides a forum for the exchange of information on computer science, computing technology, and telecommunications. This report discusses the major accomplishments of CSTB.

The inhibition of methane hydrate formation by water alignment underneath surface adsorption of surfactants

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

Nguyen, Ngoc N.; Nguyen, Anh V.; Dang, Liem X.

Sodium dodecyl sulfate (SDS) has been widely shown to strongly promote the formation of methane hydrate. Here we show that SDS displays an extraordinary inhibition effect on methane hydrate formation when the surfactant is used in sub-millimolar concentration (around 0.3 mM). We have also employed Sum Frequency Generation vibrational spectroscopy (SFG) and molecular dynamics simulation (MDS) to elucidate the molecular mechanism of this inhibition. The SFG and MDS results revealed a strong alignment of water molecules underneath surface adsorption of SDS in its sub-millimolar solution. Interestingly, both the alignment of water and the inhibition effect (in 0.3 mM SDS solution)more » went vanishing when an oppositely-charged surfactant (tetra-n-butylammonium bromide, TBAB) was suitably added to produce a mixed solution of 0.3 mM SDS and 3.6 mM TBAB. Combining structural and kinetic results, we pointed out that the alignment of water underneath surface adsorption of dodecyl sulfate (DS-) anions gave rise to the unexpected inhibition of methane hydration formation in sub-millimolar solution of SDS. The adoption of TBAB mitigated the SDS-induced electrostatic field at the solution’s surface and, therefore, weakened the alignment of interfacial water which, in turn, erased the inhibition effect. We discussed this finding using the concept of activation energy of the interfacial formation of gas hydrate. The main finding of this work is to reveal the interplay of interfacial water in governing gas hydrate formation which sheds light on a universal molecular-scale understanding of the influence of surfactants on gas hydrate formation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Hispanic women overcoming deterrents to computer science: A phenomenological study

NASA Astrophysics Data System (ADS)

Herling, Lourdes

The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the U.S. population which they represent. The overall enrollment in computer science programs has continued to decline with the enrollment of women declining at a higher rate than that of men. This study addressed three aspects of underrepresentation about which there has been little previous research: addressing computing disciplines specifically rather than embedding them within the STEM disciplines, what attracts women and minorities to computer science, and addressing the issues of race/ethnicity and gender in conjunction rather than in isolation. Since women of underrepresented ethnicities are more severely underrepresented than women in general, it is important to consider whether race and ethnicity play a role in addition to gender as has been suggested by previous research. Therefore, this study examined what attracted Hispanic women to computer science specifically. The study determines whether being subjected to multiple marginalizations---female and Hispanic---played a role in the experiences of Hispanic women currently in computer science. The study found five emergent themes within the experiences of Hispanic women in computer science. Encouragement and role models strongly influenced not only the participants' choice to major in the field, but to persist as well. Most of the participants experienced a negative atmosphere and feelings of not fitting in while in college and industry. The interdisciplinary nature of computer science was the most common aspect that attracted the participants to computer science. The aptitudes participants commonly believed are needed for success in computer science are the Twenty-First Century skills problem solving, creativity, and critical thinking. While not all the participants had experience with computers or programming prior to attending college, experience played a role in the self-confidence of those who did.

Research in applied mathematics, numerical analysis, and computer science

NASA Technical Reports Server (NTRS)

1984-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering (ICASE) in applied mathematics, numerical analysis, and computer science is summarized and abstracts of published reports are presented. The major categories of the ICASE research program are: (1) numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; (2) control and parameter identification; (3) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, and structural analysis; and (4) computer systems and software, especially vector and parallel computers.

Science-Driven Computing: NERSC's Plan for 2006-2010

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

Simon, Horst D.; Kramer, William T.C.; Bailey, David H.

NERSC has developed a five-year strategic plan focusing on three components: Science-Driven Systems, Science-Driven Services, and Science-Driven Analytics. (1) Science-Driven Systems: Balanced introduction of the best new technologies for complete computational systems--computing, storage, networking, visualization and analysis--coupled with the activities necessary to engage vendors in addressing the DOE computational science requirements in their future roadmaps. (2) Science-Driven Services: The entire range of support activities, from high-quality operations and user services to direct scientific support, that enable a broad range of scientists to effectively use NERSC systems in their research. NERSC will concentrate on resources needed to realize the promise ofmore » the new highly scalable architectures for scientific discovery in multidisciplinary computational science projects. (3) Science-Driven Analytics: The architectural and systems enhancements and services required to integrate NERSC's powerful computational and storage resources to provide scientists with new tools to effectively manipulate, visualize, and analyze the huge data sets derived from simulations and experiments.« less

Adsorption and self-assembly of bio-organic molecules at model surfaces: A route towards increased complexity

NASA Astrophysics Data System (ADS)

Costa, Dominique; Pradier, Claire-Marie; Tielens, Frederik; Savio, Letizia

2015-12-01

Understanding the bio-physical-chemical interactions at nanostructured biointerfaces and the assembly mechanisms of so-called hybrid nano-composites is nowadays a key issue for nanoscience in view of the many possible applications foreseen. The contribution of surface science in this field is noteworthy since, using a bottom-up approach, it allows the investigation of the fundamental processes at the basis of complex interfacial phenomena and thus it helps to unravel the elementary mechanisms governing them. Nowadays it is well demonstrated that a wide variety of different molecular assemblies can form upon adsorption of small biomolecules at surfaces. The geometry of such self-organized structures can often be tuned by a careful control of the experimental conditions during the deposition process. Indeed an impressive number of studies exists (both experimental and - to a lesser extent - theoretical), which demonstrates the ability of molecular self-assembly to create different structural motifs in a more or less predictable manner, by tuning the molecular building blocks as well as the metallic substrate. In this frame, amino acids and small peptides at surfaces are key, basic, systems to be studied. The amino acids structure is simple enough to serve as a model for the chemisorption of biofunctional molecules, but their adsorption at surfaces has applications in surface functionalization, in enantiospecific catalysis, biosensing, shape control of nanoparticles or in emerging fields such as "green" corrosion inhibition. In this paper we review the most recent advances in this field. We shall start from the adsorption of amino acids at metal surfaces and we will evolve then in the direction of more complex systems, in the light of the latest improvements of surface science techniques and of computational methods. On one side, we will focus on amino acids adsorption at oxide surfaces, on the other on peptide adsorption both at metal and oxide substrates. Particular attention will be drawn to the added value provided by the combination of several experimental surface science techniques and to the precious contribution of advanced complementary computational methods to resolve the details of systems of increased complexity. Finally, some hints on experiments performed in presence of water and then characterized in UHV and on the related theoretical work will be presented. This is a further step towards a better approximation of real biological systems. However, since the methods employed are often not typical of surface science, this topic is not developed in detail.

Bacteria as computers making computers

PubMed Central

Danchin, Antoine

2009-01-01

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments. PMID:19016882

Bacteria as computers making computers.

PubMed

Danchin, Antoine

2009-01-01

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.

Gender Differences in the Use of Computers, Programming, and Peer Interactions in Computer Science Classrooms

ERIC Educational Resources Information Center

Stoilescu, Dorian; Egodawatte, Gunawardena

2010-01-01

Research shows that female and male students in undergraduate computer science programs view computer culture differently. Female students are interested more in the use of computers than in doing programming, whereas male students see computer science mainly as a programming activity. The overall purpose of our research was not to find new…

Engineering and physical sciences in oncology: challenges and opportunities.

PubMed

Mitchell, Michael J; Jain, Rakesh K; Langer, Robert

2017-11-01

The principles of engineering and physics have been applied to oncology for nearly 50 years. Engineers and physical scientists have made contributions to all aspects of cancer biology, from quantitative understanding of tumour growth and progression to improved detection and treatment of cancer. Many early efforts focused on experimental and computational modelling of drug distribution, cell cycle kinetics and tumour growth dynamics. In the past decade, we have witnessed exponential growth at the interface of engineering, physics and oncology that has been fuelled by advances in fields including materials science, microfabrication, nanomedicine, microfluidics, imaging, and catalysed by new programmes at the National Institutes of Health (NIH), including the National Institute of Biomedical Imaging and Bioengineering (NIBIB), Physical Sciences in Oncology, and the National Cancer Institute (NCI) Alliance for Nanotechnology. Here, we review the advances made at the interface of engineering and physical sciences and oncology in four important areas: the physical microenvironment of the tumour and technological advances in drug delivery; cellular and molecular imaging; and microfluidics and microfabrication. We discussthe research advances, opportunities and challenges for integrating engineering and physical sciences with oncology to develop new methods to study, detect and treat cancer, and we also describe the future outlook for these emerging areas.

What is bioinformatics? A proposed definition and overview of the field.

PubMed

Luscombe, N M; Greenbaum, D; Gerstein, M

2001-01-01

The recent flood of data from genome sequences and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. Here we propose a definition for this new field and review some of the research that is being pursued, particularly in relation to transcriptional regulatory systems. Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (e.g. expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks. Bioinformatics employs a wide range of computational techniques including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches integrating a variety of computational methods and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the web at http://bioinfo.mbb.yale.edu/what-is-it.

Molecular Dynamics Simulations, Challenges and Opportunities: A Biologist's Prospective.

PubMed

Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf

2017-08-30

Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules. MD analysis has unravelled the various biological mechanisms (protein folding/unfolding, protein-small molecule interactions, protein-protein interactions, DNA/RNA-protein interactions, proteins embedded in membrane, lipid-lipid interactions, drug transport etc.) operating at the atomic and molecular levels. However, there are still some parameters including torsions in amino acids, carbohydrates (whose structure is extended and not well defined like that of proteins) and single stranded nucleic acids for which the force fields need further improvement, although there are several workers putting in constant efforts in these directions. The existing force fields are not efficient for studying the crowded environment inside the cells, since these interactions involve multiple factors in real time. Therefore, the improved force fields may provide the opportunities for their wider applications on the complex biosystems in diverse cellular conditions. In conclusion, the intervention of MD in the basic sciences involving interdisciplinary approaches will be helpful for understanding many fundamental biological and physiological processes at the molecular levels that may be further applied in various fields including biotechnology, fisheries, sustainable agriculture and biomedical research. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Opportunities for Computational Discovery in Basic Energy Sciences

NASA Astrophysics Data System (ADS)

Pederson, Mark

2011-03-01

An overview of the broad-ranging support of computational physics and computational science within the Department of Energy Office of Science will be provided. Computation as the third branch of physics is supported by all six offices (Advanced Scientific Computing, Basic Energy, Biological and Environmental, Fusion Energy, High-Energy Physics, and Nuclear Physics). Support focuses on hardware, software and applications. Most opportunities within the fields of~condensed-matter physics, chemical-physics and materials sciences are supported by the Officeof Basic Energy Science (BES) or through partnerships between BES and the Office for Advanced Scientific Computing. Activities include radiation sciences, catalysis, combustion, materials in extreme environments, energy-storage materials, light-harvesting and photovoltaics, solid-state lighting and superconductivity.~ A summary of two recent reports by the computational materials and chemical communities on the role of computation during the next decade will be provided. ~In addition to materials and chemistry challenges specific to energy sciences, issues identified~include a focus on the role of the domain scientist in integrating, expanding and sustaining applications-oriented capabilities on evolving high-performance computing platforms and on the role of computation in accelerating the development of innovative technologies. ~~

Research | Computational Science | NREL

Science.gov Websites

Research Research NREL's computational science experts use advanced high-performance computing (HPC technologies, thereby accelerating the transformation of our nation's energy system. Enabling High-Impact Research NREL's computational science capabilities enable high-impact research. Some recent examples

Artificial intelligence in hematology.

PubMed

Zini, Gina

2005-10-01

Artificial intelligence (AI) is a computer based science which aims to simulate human brain faculties using a computational system. A brief history of this new science goes from the creation of the first artificial neuron in 1943 to the first artificial neural network application to genetic algorithms. The potential for a similar technology in medicine has immediately been identified by scientists and researchers. The possibility to store and process all medical knowledge has made this technology very attractive to assist or even surpass clinicians in reaching a diagnosis. Applications of AI in medicine include devices applied to clinical diagnosis in neurology and cardiopulmonary diseases, as well as the use of expert or knowledge-based systems in routine clinical use for diagnosis, therapeutic management and for prognostic evaluation. Biological applications include genome sequencing or DNA gene expression microarrays, modeling gene networks, analysis and clustering of gene expression data, pattern recognition in DNA and proteins, protein structure prediction. In the field of hematology the first devices based on AI have been applied to the routine laboratory data management. New tools concern the differential diagnosis in specific diseases such as anemias, thalassemias and leukemias, based on neural networks trained with data from peripheral blood analysis. A revolution in cancer diagnosis, including the diagnosis of hematological malignancies, has been the introduction of the first microarray based and bioinformatic approach for molecular diagnosis: a systematic approach based on the monitoring of simultaneous expression of thousands of genes using DNA microarray, independently of previous biological knowledge, analysed using AI devices. Using gene profiling, the traditional diagnostic pathways move from clinical to molecular based diagnostic systems.

Charge separation and carrier dynamics in donor-acceptor heterojunction photovoltaic systems.

PubMed

Teuscher, Joël; Brauer, Jan C; Stepanov, Andrey; Solano, Alicia; Boziki, Ariadni; Chergui, Majed; Wolf, Jean-Pierre; Rothlisberger, Ursula; Banerji, Natalie; Moser, Jacques-E

2017-11-01

Electron transfer and subsequent charge separation across donor-acceptor heterojunctions remain the most important areas of study in the field of third-generation photovoltaics. In this context, it is particularly important to unravel the dynamics of individual ultrafast processes (such as photoinduced electron transfer, carrier trapping and association, and energy transfer and relaxation), which prevail in materials and at their interfaces. In the frame of the National Center of Competence in Research "Molecular Ultrafast Science and Technology," a research instrument of the Swiss National Science Foundation, several groups active in the field of ultrafast science in Switzerland have applied a number of complementary experimental techniques and computational simulation tools to scrutinize these critical photophysical phenomena. Structural, electronic, and transport properties of the materials and the detailed mechanisms of photoinduced charge separation in dye-sensitized solar cells, conjugated polymer- and small molecule-based organic photovoltaics, and high-efficiency lead halide perovskite solar energy converters have been scrutinized. Results yielded more than thirty research articles, an overview of which is provided here.

NASA's computer science research program

NASA Technical Reports Server (NTRS)

Larsen, R. L.

1983-01-01

Following a major assessment of NASA's computing technology needs, a new program of computer science research has been initiated by the Agency. The program includes work in concurrent processing, management of large scale scientific databases, software engineering, reliable computing, and artificial intelligence. The program is driven by applications requirements in computational fluid dynamics, image processing, sensor data management, real-time mission control and autonomous systems. It consists of university research, in-house NASA research, and NASA's Research Institute for Advanced Computer Science (RIACS) and Institute for Computer Applications in Science and Engineering (ICASE). The overall goal is to provide the technical foundation within NASA to exploit advancing computing technology in aerospace applications.

Girls Save the World through Computer Science

ERIC Educational Resources Information Center

Murakami, Christine

2011-01-01

It's no secret that fewer and fewer women are entering computer science fields. Attracting high school girls to computer science is only part of the solution. Retaining them while they are in higher education or the workforce is also a challenge. To solve this, there is a need to show girls that computer science is a wide-open field that offers…

The Assessment of Taiwanese College Students' Conceptions of and Approaches to Learning Computer Science and Their Relationships

ERIC Educational Resources Information Center

Liang, Jyh-Chong; Su, Yi-Ching; Tsai, Chin-Chung

2015-01-01

The aim of this study was to explore Taiwanese college students' conceptions of and approaches to learning computer science and then explore the relationships between the two. Two surveys, Conceptions of Learning Computer Science (COLCS) and Approaches to Learning Computer Science (ALCS), were administered to 421 college students majoring in…

Hispanic Women Overcoming Deterrents to Computer Science: A Phenomenological Study

ERIC Educational Resources Information Center

Herling, Lourdes

2011-01-01

The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the…

The Effects of Integrating Service Learning into Computer Science: An Inter-Institutional Longitudinal Study

ERIC Educational Resources Information Center

Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

2015-01-01

This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of…

Non-Determinism: An Abstract Concept in Computer Science Studies

ERIC Educational Resources Information Center

Armoni, Michal; Gal-Ezer, Judith

2007-01-01

Non-determinism is one of the most important, yet abstract, recurring concepts of Computer Science. It plays an important role in Computer Science areas such as formal language theory, computability theory, distributed computing, and operating systems. We conducted a series of studies on the perception of non-determinism. In the current research,…

An Investigation of Primary School Science Teachers' Use of Computer Applications

ERIC Educational Resources Information Center

Ocak, Mehmet Akif; Akdemir, Omur

2008-01-01

This study investigated the level and frequency of science teachers' use of computer applications as an instructional tool in the classroom. The manner and frequency of science teachers' use of computer, their perceptions about integration of computer applications, and other factors contributed to changes in their computer literacy are…

Methodical Approaches to Teaching of Computer Modeling in Computer Science Course

ERIC Educational Resources Information Center

Rakhimzhanova, B. Lyazzat; Issabayeva, N. Darazha; Khakimova, Tiyshtik; Bolyskhanova, J. Madina

2015-01-01

The purpose of this study was to justify of the formation technique of representation of modeling methodology at computer science lessons. The necessity of studying computer modeling is that the current trends of strengthening of general education and worldview functions of computer science define the necessity of additional research of the…

Alzheimer's disease in the omics era.

PubMed

Sancesario, Giulia M; Bernardini, Sergio

2018-06-18

Recent progresses in high-throughput technologies have led to a new scenario in investigating pathologies, named the "Omics era", which integrate the opportunity to collect large amounts of data and information at the molecular and protein levels together with the development of novel computational and statistical tools that are able to analyze and filter such data. Subsequently, advances in genotyping arrays, next generation sequencing, mass spectrometry technology, and bioinformatics allowed for the simultaneous large-scale study of thousands of genes (genomics), epigenetics factors (epigenomics), RNA (transcriptomics), metabolites (metabolomics) and proteins(proteomics), with the possibility of integrating multiple types of omics data ("multi -omics"). All of these technological innovations have modified the approach to the study of complex diseases, such as Alzheimer's Disease (AD), thus representing a promising tool to investigate the relationship between several molecular pathways in AD as well as other pathologies. This review focuses on the current knowledge on the pathology of AD, the recent findings from Omics sciences, and the challenge of the use of Big Data. We then focus on future perspectives for Omics sciences, such as the discovery of novel diagnostic biomarkers or drugs. Copyright © 2018. Published by Elsevier Inc.

Understanding nanofluid stability through molecular simulation

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

Dang, Liem X.; Annapureddy, Harsha V.; Sun, Xiuquan

We performed molecular dynamics simulations to study solvation of a nanoparticle and nanoparticle-nanoparticle interactions in an n-hexane solution. Structural signatures are barely observed between the nanoparticle and n-hexane molecules because of weak binding and steric effects. The dynamic properties of the n-hexane molecule, on the other hand, are significantly influenced by the solvated nanoparticle. The diffusion of n-hexane molecules inside the nanoparticle is significantly decreased mainly because of the loss of dimensions of translation. Because one translational degree of freedom is lost by colliding with the wall of nanoparticle, the n-hexane molecules outside the nanoparticle diffuse 30% slower than themore » molecules in pure solution. The computed free energy profiles illustrate that the arrangement of the nanoparticles in bulk n-hexane solution are dependent on the orientation and functional group. We found that the n-hexane solvent exerts some effects on the interactions between the solvated nanoparticles. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences and by the Office of Energy Efficiency and Renewable Energy, Geothermal Technologies Program. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.« less

Thermodynamic and transport properties of spiro-(1,1')-bipyrrolidinium tetrafluoroborate and acetonitrile mixtures: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Qing-Yin, Zhang; Peng, Xie; Xin, Wang; Xue-Wen, Yu; Zhi-Qiang, Shi; Shi-Huai, Zhao

2016-06-01

Organic salts such as spiro-(1,1')-bipyrrolidinium tetrafluoroborate ([SBP][BF4]) dissolved in liquid acetonitrile (ACN) are a new kind of organic salt solution, which is expected to be used as an electrolyte in electrical double layer capacitors (EDLCs). To explore the physicochemical properties of the solution, an all-atom force field is established on the basis of AMBER parameter values and quantum mechanical calculations. Molecular dynamics (MD) simulations are carried out to explore the liquid structure and physicochemical properties of [SBP][BF4] electrolyte at room temperature. The computed thermodynamic and transport properties match the available experimental results very well. The microscopic structures of [SBP][BF4] salt solution are also discussed in detail. The method used in this work provides an efficient way of predicting the properties of organic salt solvent as an electrolyte in EDLCs. Project supported by the National Natural Science Foundation of China (Grant Nos. 21476172 and 51172160), the National High Technology Research and Development Program of China (Grant No. 2013AA050905), and the Natural Science Foundation of Tianjin, China (Grant Nos. 12JCZDJC28400, 14RCHZGX00859, 14JCTPJC00484, and 14JCQNJC07200).

Expanding the foundation for personalized medicine: implications and challenges for dentistry.

PubMed

Garcia, I; Kuska, R; Somerman, M J

2013-07-01

Personalized medicine aims to individualize care based on a person's unique genetic, environmental, and clinical profile. Dentists and physicians have long recognized variations between and among patients, and have customized care based on each individual's health history, environment, and behavior. However, the sequencing of the human genome in 2003 and breakthroughs in regenerative medicine, imaging, and computer science redefined "personalized medicine" as clinical care that takes advantage of new molecular tools to facilitate highly precise health care based on an individual's unique genomic and molecular characteristics. Major investments in science bring a new urgency toward realizing the promise of personalized medicine; yet, many challenges stand in the way. In this article, we present an overview of the opportunities and challenges that influence the oral health community's full participation in personalized medicine. We highlight selected research advances that are solidifying the foundation of personalized oral health care, elaborate on their impact on dentistry, and explore obstacles toward their adoption into practice. It is our view that now is the time for oral health professionals, educators, students, researchers, and patients to engage fully in preparations for the arrival of personalized medicine as a means to provide quality, customized, and effective oral health care for all.

Climate Modeling Computing Needs Assessment

NASA Astrophysics Data System (ADS)

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

2011-12-01

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

Kenny Gruchalla | NREL

Science.gov Websites

feature extraction, human-computer interaction, and physics-based modeling. Professional Experience 2009 ., computer science, University of Colorado at Boulder M.S., computer science, University of Colorado at Boulder B.S., computer science, New Mexico Institute of Mining and Technology

2008 ALCF annual report.

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

Drugan, C.

2009-12-07

The word 'breakthrough' aptly describes the transformational science and milestones achieved at the Argonne Leadership Computing Facility (ALCF) throughout 2008. The number of research endeavors undertaken at the ALCF through the U.S. Department of Energy's (DOE) Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program grew from 9 in 2007 to 20 in 2008. The allocation of computer time awarded to researchers on the Blue Gene/P also spiked significantly - from nearly 10 million processor hours in 2007 to 111 million in 2008. To support this research, we expanded the capabilities of Intrepid, an IBM Blue Gene/P systemmore » at the ALCF, to 557 teraflops (TF) for production use. Furthermore, we enabled breakthrough levels of productivity and capability in visualization and data analysis with Eureka, a powerful installation of NVIDIA Quadro Plex S4 external graphics processing units. Eureka delivered a quantum leap in visual compute density, providing more than 111 TF and more than 3.2 terabytes of RAM. On April 21, 2008, the dedication of the ALCF realized DOE's vision to bring the power of the Department's high performance computing to open scientific research. In June, the IBM Blue Gene/P supercomputer at the ALCF debuted as the world's fastest for open science and third fastest overall. No question that the science benefited from this growth and system improvement. Four research projects spearheaded by Argonne National Laboratory computer scientists and ALCF users were named to the list of top ten scientific accomplishments supported by DOE's Advanced Scientific Computing Research (ASCR) program. Three of the top ten projects used extensive grants of computing time on the ALCF's Blue Gene/P to model the molecular basis of Parkinson's disease, design proteins at atomic scale, and create enzymes. As the year came to a close, the ALCF was recognized with several prestigious awards at SC08 in November. We provided resources for Linear Scaling Divide-and-Conquer Electronic Structure Calculations for Thousand Atom Nanostructures, a collaborative effort between Argonne, Lawrence Berkeley National Laboratory, and Oak Ridge National Laboratory that received the ACM Gordon Bell Prize Special Award for Algorithmic Innovation. The ALCF also was named a winner in two of the four categories in the HPC Challenge best performance benchmark competition.« less

Computer-aided design and computer science technology

NASA Technical Reports Server (NTRS)

Fulton, R. E.; Voigt, S. J.

1976-01-01

A description is presented of computer-aided design requirements and the resulting computer science advances needed to support aerospace design. The aerospace design environment is examined, taking into account problems of data handling and aspects of computer hardware and software. The interactive terminal is normally the primary interface between the computer system and the engineering designer. Attention is given to user aids, interactive design, interactive computations, the characteristics of design information, data management requirements, hardware advancements, and computer science developments.

The effects of integrating service learning into computer science: an inter-institutional longitudinal study

NASA Astrophysics Data System (ADS)

Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

2015-07-01

This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of the Students & Technology in Academia, Research, and Service (STARS) Alliance, an NSF-supported broadening participation in computing initiative that aims to diversify the computer science pipeline through innovative pedagogy and inter-institutional partnerships. The current paper describes how the STARS Alliance has expanded to diverse institutions, all using service learning as a vehicle for broadening participation in computing and enhancing attitudes and behaviors associated with student success. Results supported the STARS model of service learning for enhancing computing efficacy and computing commitment and for providing diverse students with many personal and professional development benefits.

ICASE Computer Science Program

NASA Technical Reports Server (NTRS)

1985-01-01

The Institute for Computer Applications in Science and Engineering computer science program is discussed in outline form. Information is given on such topics as problem decomposition, algorithm development, programming languages, and parallel architectures.

Synergistic Effect of Nitrogen in Cobalt Nitride and Nitrogen-Doped Hollow Carbon Spheres for Oxygen Reduction Reaction

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

Zhong, Xing; Liu, Lin; Jiang, Yu

The need for inexpensive and high-activity oxygen reduction reaction (ORR) electrocatalysts has attracted considerable research interest over the past years. Here we report a novel hybrid that contains cobalt nitride/nitrogen-rich hollow carbon spheres (CoxN/NHCS) as a high-performance catalyst for ORR. The CoxN nanoparticles were uniformly dispersed and confined in the hollow NHCS shell. The performance of the resulting CoxN/NHCS hybrid was comparable with that of a commercial Pt/C at the same catalyst loading toward ORR, but the mass activity of the former was 5.7 times better than that of the latter. The nitrogen in both CoxN and NHCS, especially CoxN,more » could weaken the adsorption of reaction intermediates (O and OOH), which follows the favourable reaction pathway on CoxN/NHCS according to the DFT-calculated Gibbs free energy diagrams. Our results demonstrated a new strategy for designing and developing inexpensive, non-precious metal electrocatalysts for next-generation fuels. The authors acknowledge the financial support from the National Basic Research Program (973 program, No. 2013CB733501) and the National Natural Science Foundation of China (No. 21306169, 21101137, 21136001, 21176221 and 91334013). Dr. D. Mei is supported by the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

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

Roy, Santanu; Baer, Marcel D.; Mundy, Christopher J.

2016-04-14

Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable andmore » structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.« less

A review of bioinformatics training applied to research in molecular medicine, agriculture and biodiversity in Costa Rica and Central America.

PubMed

Orozco, Allan; Morera, Jessica; Jiménez, Sergio; Boza, Ricardo

2013-09-01

Today, Bioinformatics has become a scientific discipline with great relevance for the Molecular Biosciences and for the Omics sciences in general. Although developed countries have progressed with large strides in Bioinformatics education and research, in other regions, such as Central America, the advances have occurred in a gradual way and with little support from the Academia, either at the undergraduate or graduate level. To address this problem, the University of Costa Rica's Medical School, a regional leader in Bioinformatics in Central America, has been conducting a series of Bioinformatics workshops, seminars and courses, leading to the creation of the region's first Bioinformatics Master's Degree. The recent creation of the Central American Bioinformatics Network (BioCANET), associated to the deployment of a supporting computational infrastructure (HPC Cluster) devoted to provide computing support for Molecular Biology in the region, is providing a foundational stone for the development of Bioinformatics in the area. Central American bioinformaticians have participated in the creation of as well as co-founded the Iberoamerican Bioinformatics Society (SOIBIO). In this article, we review the most recent activities in education and research in Bioinformatics from several regional institutions. These activities have resulted in further advances for Molecular Medicine, Agriculture and Biodiversity research in Costa Rica and the rest of the Central American countries. Finally, we provide summary information on the first Central America Bioinformatics International Congress, as well as the creation of the first Bioinformatics company (Indromics Bioinformatics), spin-off the Academy in Central America and the Caribbean.

Towards efficient data exchange and sharing for big-data driven materials science: metadata and data formats

NASA Astrophysics Data System (ADS)

Ghiringhelli, Luca M.; Carbogno, Christian; Levchenko, Sergey; Mohamed, Fawzi; Huhs, Georg; Lüders, Martin; Oliveira, Micael; Scheffler, Matthias

2017-11-01

With big-data driven materials research, the new paradigm of materials science, sharing and wide accessibility of data are becoming crucial aspects. Obviously, a prerequisite for data exchange and big-data analytics is standardization, which means using consistent and unique conventions for, e.g., units, zero base lines, and file formats. There are two main strategies to achieve this goal. One accepts the heterogeneous nature of the community, which comprises scientists from physics, chemistry, bio-physics, and materials science, by complying with the diverse ecosystem of computer codes and thus develops "converters" for the input and output files of all important codes. These converters then translate the data of each code into a standardized, code-independent format. The other strategy is to provide standardized open libraries that code developers can adopt for shaping their inputs, outputs, and restart files, directly into the same code-independent format. In this perspective paper, we present both strategies and argue that they can and should be regarded as complementary, if not even synergetic. The represented appropriate format and conventions were agreed upon by two teams, the Electronic Structure Library (ESL) of the European Center for Atomic and Molecular Computations (CECAM) and the NOvel MAterials Discovery (NOMAD) Laboratory, a European Centre of Excellence (CoE). A key element of this work is the definition of hierarchical metadata describing state-of-the-art electronic-structure calculations.

Applications of Out-of-Domain Knowledge in Students' Reasoning about Computer Program State

ERIC Educational Resources Information Center

Lewis, Colleen Marie

2012-01-01

To meet a growing demand and a projected deficit in the supply of computer professionals (NCWIT, 2009), it is of vital importance to expand students' access to computer science. However, many researchers in the computer science education community unproductively assume that some students lack an innate ability for computer science and…

Scientific Computing Strategic Plan for the Idaho National Laboratory

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

Whiting, Eric Todd

Scientific computing is a critical foundation of modern science. Without innovations in the field of computational science, the essential missions of the Department of Energy (DOE) would go unrealized. Taking a leadership role in such innovations is Idaho National Laboratory’s (INL’s) challenge and charge, and is central to INL’s ongoing success. Computing is an essential part of INL’s future. DOE science and technology missions rely firmly on computing capabilities in various forms. Modeling and simulation, fueled by innovations in computational science and validated through experiment, are a critical foundation of science and engineering. Big data analytics from an increasing numbermore » of widely varied sources is opening new windows of insight and discovery. Computing is a critical tool in education, science, engineering, and experiments. Advanced computing capabilities in the form of people, tools, computers, and facilities, will position INL competitively to deliver results and solutions on important national science and engineering challenges. A computing strategy must include much more than simply computers. The foundational enabling component of computing at many DOE national laboratories is the combination of a showcase like data center facility coupled with a very capable supercomputer. In addition, network connectivity, disk storage systems, and visualization hardware are critical and generally tightly coupled to the computer system and co located in the same facility. The existence of these resources in a single data center facility opens the doors to many opportunities that would not otherwise be possible.« less

A Cognitive Model for Problem Solving in Computer Science

ERIC Educational Resources Information Center

Parham, Jennifer R.

2009-01-01

According to industry representatives, computer science education needs to emphasize the processes involved in solving computing problems rather than their solutions. Most of the current assessment tools used by universities and computer science departments analyze student answers to problems rather than investigating the processes involved in…

Approaches to Classroom-Based Computational Science.

ERIC Educational Resources Information Center

Guzdial, Mark

Computational science includes the use of computer-based modeling and simulation to define and test theories about scientific phenomena. The challenge for educators is to develop techniques for implementing computational science in the classroom. This paper reviews some previous work on the use of simulation alone (without modeling), modeling…

Defining Computational Thinking for Mathematics and Science Classrooms

ERIC Educational Resources Information Center

Weintrop, David; Beheshti, Elham; Horn, Michael; Orton, Kai; Jona, Kemi; Trouille, Laura; Wilensky, Uri

2016-01-01

Science and mathematics are becoming computational endeavors. This fact is reflected in the recently released Next Generation Science Standards and the decision to include "computational thinking" as a core scientific practice. With this addition, and the increased presence of computation in mathematics and scientific contexts, a new…

NASA Center for Computational Sciences: History and Resources

NASA Technical Reports Server (NTRS)

2000-01-01

The Nasa Center for Computational Sciences (NCCS) has been a leading capacity computing facility, providing a production environment and support resources to address the challenges facing the Earth and space sciences research community.

Institute for Computer Applications in Science and Engineering (ICASE)

NASA Technical Reports Server (NTRS)

1984-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis and computer science during the period April 1, 1983 through September 30, 1983 is summarized.

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…

78 FR 64255 - Advisory Committee for Computer and Information Science and Engineering; Cancellation of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-28

... NATIONAL SCIENCE FOUNDATION Advisory Committee for Computer and Information Science and Engineering; Cancellation of Meeting SUMMARY: As a result of the impact of the recent government shutdown, the... Committee for Computer and Information Science and Engineering meeting. The public notice for this committee...

Exemplary Science Teachers' Use of Technology

ERIC Educational Resources Information Center

Hakverdi-Can, Meral; Dana, Thomas M.

2012-01-01

The purpose of this study is to examine exemplary science teachers' level of computer use, their knowledge/skills in using specific computer applications for science instruction, their use of computer-related applications/tools during their instruction, how often they required their students to use those applications in or for their science class…

Marine molecular biology: an emerging field of biological sciences.

PubMed

Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

2008-01-01

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.

PubMed

Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro

2012-11-21

In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1990

1990-01-01

Reviewed are seven computer software packages for IBM and/or Apple Computers. Included are "Windows on Science: Volume 1--Physical Science"; "Science Probe--Physical Science"; "Wildlife Adventures--Grizzly Bears"; "Science Skills--Development Programs"; "The Clean Machine"; "Rock Doctor";…

Computation Through Neuronal Oscillations

NASA Astrophysics Data System (ADS)

Hepp, K.

Some of us believe that natural sciences are governed by simple and predictive general principles. This hope has not yet been fulfilled in physics for unifying gravitation and quantum mechanics. Epigenetics has shaken the monopoly of the genetic code to determine inheritance (Alberts et al., Molecular Biology of the Cell. Garland, New York, 2008). It is therefore not surprising that quantum mechanics does not explain consciousness or more generally the coherence of the brain in perception, action and cognition. In an other context, others (Tegmark, Phys Rev E 61:4194-4206, 2000) and we (Koch and Hepp, Nature 440:611-612, 2006; Koch and Hepp, Visions of Discovery: New Light on Physics, Cosmology, and Consciousness. Cambridge University Press, Cambridge, 2011) have strongly argued against the absurdity of such a claim, because consciousness is a higher brain function and not a molecular binding mechanism. Decoherence in the warm and wet brain is by many orders of magnitude too strong. Moreover, there are no efficient algorithms for neural quantum computations. However, the controversy over classical and quantum consciousness will probably never be resolved (see e.g. Hepp, J Math Phys 53:095222, 2012; Hameroff and Penrose, Phys Life Rev 11:39-78, 2013).

Therapeutic, Molecular and Computational Aspects of Novel Monoamine Oxidase (MAO) Inhibitors.

PubMed

Ramesh, Muthusamy; Dokurugu, Yussif M; Thompson, Michael D; Soliman, Mahmoud E

2017-01-01

Background Due to the limited number of MAO inhibitors in the clinics, several research efforts are aimed at the discovery of novel MAO inhibitors. At present, a high specificity and a reversible mode of inhibition of MAO-A/B are cited as desirable traits in drug discovery process. This will help to reduce the probability of causing target disruption and may increase the duration of action of drug. Most of the existing MAO inhibitors lead to side effects due to the lack of affinity and selectivity. Therefore, there is an urgent need to design novel, potent, reversible and selective inhibitors for MAO-A/B. Selective inhibition of MAO-A results in the elevated level of serotonin and noradrenaline. Hence, MAO-A inhibitors can be used for improving the symptoms of depression. The selective MAO-B inhibitors are used with L-DOPA and/or dopamine agonists in the symptomatic treatment of Parkinson's disease. The present study was aimed to describe the recently developed hits of MAO inhibitors. At present, CADD techniques are gaining an attention in rationale drug discovery of MAO inhibitors, and several research groups employed CADD approaches on various chemical scaffolds to identify novel MAO inhibitors. These computational techniques assisted in the development of lead molecules with improved pharmacodynamics / pharmacokinetic properties toward MAOs. Further, CADD techniques provided a better understanding of structural aspects of molecular targets and lead molecules. The present review describes the importance of structural features of potential chemical scaffolds as well as the role of computational approaches like ligand docking, molecular dynamics, QSAR and pharmacophore modeling in the development of novel MAO inhibitors. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Towards a unified picture of the water self-ions at the air-water interface: a density functional theory perspective

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

Baer, Marcel D.; Kuo, I-F W.; Tobias, Douglas J.

2014-07-17

The propensities of the water self ions, H3O+ and OH- , for the air-water interface has implications for interfacial acid-base chemistry. Despite numerous experimental and computational studies, no consensus has been reached on the question of whether or not H3O+ and/or OH- prefer to be at the water surface or in the bulk. Here we report a molecular dynamics simulation study of the bulk vs. interfacial behavior of H3O+ and OH- that employs forces derived from density functional theory with a generalized gradient approximation exchangecorrelation functional (specifically, BLYP) and empirical dispersion corrections. We computed the potential of mean force (PMF)more » for H3O+ as a function of the position of the ion in a 215-molecule water slab. The PMF is flat, suggesting that H3O+ has equal propensity for the air-water interface and the bulk. We compare the PMF for H3O+ to our previously computed PMF for OH- adsorption, which contains a shallow minimum at the interface, and we explore how differences in solvation of each ion at the interface vs. the bulk are connected with interfacial propensity. We find that the solvation shell of H3O+ is only slightly dependent on its position in the water slab, while OH- partially desolvates as it approaches the interface, and we examine how this difference in solvation behavior is manifested in the electronic structure and chemistry of the two ions. DJT was supported by National Science Foundation grant CHE-0909227. CJM was supported by the U.S. Department of Energy‘s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the Department of Energy by Battelle. The potential of mean force required resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DEAC05-00OR22725. The remaining simulations and analysis used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. at at Lawrence Berkeley National Laboratory. MDB is grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship Program at PNNL.« less

A reconfigurable NAND/NOR genetic logic gate

PubMed Central

2012-01-01

Background Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations. Results We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs. Conclusions We present a dynamically-reconfigurable NAND/NOR genetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications. PMID:22989145

Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex

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

Bhattacharya, Papri; Heiden, Zachariah M.; Wiedner, Eric S.

We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo-15NH3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo=15NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo=15NR generates a terminal Mo≡N nitride, and a [Mo-15NH]+ complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo-15NH3 complex and the formation of Mo=15NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Officemore » of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.« less

A reconfigurable NAND/NOR genetic logic gate.

PubMed

Goñi-Moreno, Angel; Amos, Martyn

2012-09-18

Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is still in its infancy, with few agreed standards. In this paper we focus on the interpretation of logical values in terms of molecular concentrations. We describe the results of computational investigations of a novel circuit that is able to trigger specific differential responses depending on the input standard used. The circuit can therefore be dynamically reconfigured (without modification) to serve as both a NAND/NOR logic gate. This multi-functional behaviour is achieved by a) varying the meanings of inputs, and b) using branch predictions (as in computer science) to display a constrained output. A thorough computational study is performed, which provides valuable insights for the future laboratory validation. The simulations focus on both single-cell and population behaviours. The latter give particular insights into the spatial behaviour of our engineered cells on a surface with a non-homogeneous distribution of inputs. We present a dynamically-reconfigurable NAND/NOR genetic logic circuit that can be switched between modes of operation via a simple shift in input signal concentration. The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications.

Computer Science Techniques Applied to Parallel Atomistic Simulation

NASA Astrophysics Data System (ADS)

Nakano, Aiichiro

1998-03-01

Recent developments in parallel processing technology and multiresolution numerical algorithms have established large-scale molecular dynamics (MD) simulations as a new research mode for studying materials phenomena such as fracture. However, this requires large system sizes and long simulated times. We have developed: i) Space-time multiresolution schemes; ii) fuzzy-clustering approach to hierarchical dynamics; iii) wavelet-based adaptive curvilinear-coordinate load balancing; iv) multilevel preconditioned conjugate gradient method; and v) spacefilling-curve-based data compression for parallel I/O. Using these techniques, million-atom parallel MD simulations are performed for the oxidation dynamics of nanocrystalline Al. The simulations take into account the effect of dynamic charge transfer between Al and O using the electronegativity equalization scheme. The resulting long-range Coulomb interaction is calculated efficiently with the fast multipole method. Results for temperature and charge distributions, residual stresses, bond lengths and bond angles, and diffusivities of Al and O will be presented. The oxidation of nanocrystalline Al is elucidated through immersive visualization in virtual environments. A unique dual-degree education program at Louisiana State University will also be discussed in which students can obtain a Ph.D. in Physics & Astronomy and a M.S. from the Department of Computer Science in five years. This program fosters interdisciplinary research activities for interfacing High Performance Computing and Communications with large-scale atomistic simulations of advanced materials. This work was supported by NSF (CAREER Program), ARO, PRF, and Louisiana LEQSF.

An Overview of NASA's Intelligent Systems Program

NASA Technical Reports Server (NTRS)

Cooke, Daniel E.; Norvig, Peter (Technical Monitor)

2001-01-01

NASA and the Computer Science Research community are poised to enter a critical era. An era in which - it seems - that each needs the other. Market forces, driven by the immediate economic viability of computer science research results, place Computer Science in a relatively novel position. These forces impact how research is done, and could, in worst case, drive the field away from significant innovation opting instead for incremental advances that result in greater stability in the market place. NASA, however, requires significant advances in computer science research in order to accomplish the exploration and science agenda it has set out for itself. NASA may indeed be poised to advance computer science research in this century much the way it advanced aero-based research in the last.

A Review of Models for Teacher Preparation Programs for Precollege Computer Science Education.

ERIC Educational Resources Information Center

Deek, Fadi P.; Kimmel, Howard

2002-01-01

Discusses the need for adequate precollege computer science education and focuses on the issues of teacher preparation programs and requirements needed to teach high school computer science. Presents models of teacher preparation programs and compares state requirements with Association for Computing Machinery (ACM) recommendations. (Author/LRW)

A DDC Bibliography on Computers in Information Sciences. Volume II. Information Sciences Series.

ERIC Educational Resources Information Center

Defense Documentation Center, Alexandria, VA.

The unclassified and unlimited bibliography compiles references dealing specifically with the role of computers in information sciences. The volume contains 239 annotated references grouped under three major headings: Artificial and Programming Languages, Computer Processing of Analog Data, and Computer Processing of Digital Data. The references…

Making Advanced Computer Science Topics More Accessible through Interactive Technologies

ERIC Educational Resources Information Center

Shao, Kun; Maher, Peter

2012-01-01

Purpose: Teaching advanced technical concepts in a computer science program to students of different technical backgrounds presents many challenges. The purpose of this paper is to present a detailed experimental pedagogy in teaching advanced computer science topics, such as computer networking, telecommunications and data structures using…

Deterministic Function Computation with Chemical Reaction Networks*

PubMed Central

Chen, Ho-Lin; Doty, David; Soloveichik, David

2013-01-01

Chemical reaction networks (CRNs) formally model chemistry in a well-mixed solution. CRNs are widely used to describe information processing occurring in natural cellular regulatory networks, and with upcoming advances in synthetic biology, CRNs are a promising language for the design of artificial molecular control circuitry. Nonetheless, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs is not well understood. CRNs have been shown to be efficiently Turing-universal (i.e., able to simulate arbitrary algorithms) when allowing for a small probability of error. CRNs that are guaranteed to converge on a correct answer, on the other hand, have been shown to decide only the semilinear predicates (a multi-dimensional generalization of “eventually periodic” sets). We introduce the notion of function, rather than predicate, computation by representing the output of a function f : ℕk → ℕl by a count of some molecular species, i.e., if the CRN starts with x1, …, xk molecules of some “input” species X1, …, Xk, the CRN is guaranteed to converge to having f(x1, …, xk) molecules of the “output” species Y1, …, Yl. We show that a function f : ℕk → ℕl is deterministically computed by a CRN if and only if its graph {(x, y) ∈ ℕk × ℕl ∣ f(x) = y} is a semilinear set. Finally, we show that each semilinear function f (a function whose graph is a semilinear set) can be computed by a CRN on input x in expected time O(polylog ∥x∥1). PMID:25383068

ASCR Workshop on Quantum Computing for Science

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

Aspuru-Guzik, Alan; Van Dam, Wim; Farhi, Edward

This report details the findings of the DOE ASCR Workshop on Quantum Computing for Science that was organized to assess the viability of quantum computing technologies to meet the computational requirements of the DOE’s science and energy mission, and to identify the potential impact of quantum technologies. The workshop was held on February 17-18, 2015, in Bethesda, MD, to solicit input from members of the quantum computing community. The workshop considered models of quantum computation and programming environments, physical science applications relevant to DOE's science mission as well as quantum simulation, and applied mathematics topics including potential quantum algorithms formore » linear algebra, graph theory, and machine learning. This report summarizes these perspectives into an outlook on the opportunities for quantum computing to impact problems relevant to the DOE’s mission as well as the additional research required to bring quantum computing to the point where it can have such impact.« less

BIOCOMPUTATION: some history and prospects.

PubMed

Cull, Paul

2013-06-01

At first glance, biology and computer science are diametrically opposed sciences. Biology deals with carbon based life forms shaped by evolution and natural selection. Computer Science deals with electronic machines designed by engineers and guided by mathematical algorithms. In this brief paper, we review biologically inspired computing. We discuss several models of computation which have arisen from various biological studies. We show what these have in common, and conjecture how biology can still suggest answers and models for the next generation of computing problems. We discuss computation and argue that these biologically inspired models do not extend the theoretical limits on computation. We suggest that, in practice, biological models may give more succinct representations of various problems, and we mention a few cases in which biological models have proved useful. We also discuss the reciprocal impact of computer science on biology and cite a few significant contributions to biological science. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The Need for Integrated Approaches in Metabolic Engineering

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

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must b e considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

The Need for Integrated Approaches in Metabolic Engineering

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

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

Highlights include state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. A combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the “system” that is being manipulated: transcriptome, translatome, proteome, or reactome. Here, by bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

The Need for Integrated Approaches in Metabolic Engineering

DOE PAGES

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

2016-08-15

Highlights include state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. A combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the “system” that is being manipulated: transcriptome, translatome, proteome, or reactome. Here, by bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

Microbes to Biomes at Berkeley Lab

ScienceCinema

None

2018-06-21

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Advanced technology and truth in advertising

NASA Astrophysics Data System (ADS)

Landauer, Rolf

1990-09-01

Most proposals for new technological approaches fail, and that is reasonable. Despite that, most of the technological proposals arising from basic science are promoted unhesitantly, with little attention to critical appraisal, even little opportunity for the presentation of criticism. We discuss several case histories related to devices intended to displace the transistor in computer logic. Our list includes devices using control of quantum mechanically coherent electron transmission, devices operating at a molecular level, and devices using nonlinear electromagnetic interaction. Neural networks are placed in a different category; something seems to be coming out of this field after several decades of effort.

A Case Study of the Introduction of Computer Science in NZ Schools

ERIC Educational Resources Information Center

Bell, Tim; Andreae, Peter; Robins, Anthony

2014-01-01

For many years computing in New Zealand schools was focused on teaching students how to use computers, and there was little opportunity for students to learn about programming and computer science as formal subjects. In this article we review a series of initiatives that occurred from 2007 to 2009 that led to programming and computer science being…

Research in Applied Mathematics, Fluid Mechanics and Computer Science

NASA Technical Reports Server (NTRS)

1999-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period October 1, 1998 through March 31, 1999.

[Research activities in applied mathematics, fluid mechanics, and computer science

NASA Technical Reports Server (NTRS)

1995-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period April 1, 1995 through September 30, 1995.

Activities of the Institute for Computer Applications in Science and Engineering

NASA Technical Reports Server (NTRS)

1985-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period April 1, 1985 through October 2, 1985 is summarized.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

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

Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

2016-06-13

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

QSAR Methods.

PubMed

Gini, Giuseppina

2016-01-01

In this chapter, we introduce the basis of computational chemistry and discuss how computational methods have been extended to some biological properties and toxicology, in particular. Since about 20 years, chemical experimentation is more and more replaced by modeling and virtual experimentation, using a large core of mathematics, chemistry, physics, and algorithms. Then we see how animal experiments, aimed at providing a standardized result about a biological property, can be mimicked by new in silico methods. Our emphasis here is on toxicology and on predicting properties through chemical structures. Two main streams of such models are available: models that consider the whole molecular structure to predict a value, namely QSAR (Quantitative Structure Activity Relationships), and models that find relevant substructures to predict a class, namely SAR. The term in silico discovery is applied to chemical design, to computational toxicology, and to drug discovery. We discuss how the experimental practice in biological science is moving more and more toward modeling and simulation. Such virtual experiments confirm hypotheses, provide data for regulation, and help in designing new chemicals.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

PubMed

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

Computational Design of Molecularly Imprinted Polymers

NASA Astrophysics Data System (ADS)

Subrahmanyam, Sreenath; Piletsky, Sergey A.

Artificial receptors have been in use for several decades as sensor elements, in affinity separation, and as models for investigation of molecular recognition. Although there have been numerous publications on the use of molecular modeling in characterization of their affinity and selectivity, very few attempts have been made on the application of molecular modeling in computational design of synthetic receptors. This chapter discusses recent successes in the use of computational design for the development of one particular branch of synthetic receptors - molecularly imprinted polymers.

A Quantitative Model for Assessing Visual Simulation Software Architecture

DTIC Science & Technology

2011-09-01

Software Engineering Arnold Buss Research Associate Professor of MOVES LtCol Jeff Boleng, PhD Associate Professor of Computer Science U.S. Air Force Academy... science (operating and programming systems series). New York, NY, USA: Elsevier Science Ltd. Henry, S., & Kafura, D. (1984). The evaluation of software...Rudy Darken Professor of Computer Science Dissertation Supervisor Ted Lewis Professor of Computer Science Richard Riehle Professor of Practice

K-16 Computationally Rich Science Education: A Ten-Year Review of the "Journal of Science Education and Technology" (1998-2008)

ERIC Educational Resources Information Center

Wofford, Jennifer

2009-01-01

Computing is anticipated to have an increasingly expansive impact on the sciences overall, becoming the third, crucial component of a "golden triangle" that includes mathematics and experimental and theoretical science. However, even more true with computing than with math and science, we are not preparing our students for this new reality. It is…

Interactive Synthesis of Code Level Security Rules

DTIC Science & Technology

2017-04-01

Interactive Synthesis of Code-Level Security Rules A Thesis Presented by Leo St. Amour to The Department of Computer Science in partial fulfillment...of the requirements for the degree of Master of Science in Computer Science Northeastern University Boston, Massachusetts April 2017 DISTRIBUTION...Abstract of the Thesis Interactive Synthesis of Code-Level Security Rules by Leo St. Amour Master of Science in Computer Science Northeastern University

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.

Integral equation and discontinuous Galerkin methods for the analysis of light-matter interaction

NASA Astrophysics Data System (ADS)

Baczewski, Andrew David

Light-matter interaction is among the most enduring interests of the physical sciences. The understanding and control of this physics is of paramount importance to the design of myriad technologies ranging from stained glass, to molecular sensing and characterization techniques, to quantum computers. The development of complex engineered systems that exploit this physics is predicated at least partially upon in silico design and optimization that properly capture the light-matter coupling. In this thesis, the details of computational frameworks that enable this type of analysis, based upon both Integral Equation and Discontinuous Galerkin formulations will be explored. There will be a primary focus on the development of efficient and accurate software, with results corroborating both. The secondary focus will be on the use of these tools in the analysis of a number of exemplary systems.

Approaching gender parity: Women in computer science at Afghanistan's Kabul University

NASA Astrophysics Data System (ADS)

Plane, Jandelyn

This study explores the representation of women in computer science at the tertiary level through data collected about undergraduate computer science education at Kabul University in Afghanistan. Previous studies have theorized reasons for underrepresentation of women in computer science, and while many of these reasons are indeed present in Afghanistan, they appear to hinder advancement to degree to a lesser extent. Women comprise at least 36% of each graduating class from KU's Computer Science Department; however, in 2007 women were 25% of the university population. In the US, women comprise over 50% of university populations while only graduating on average 25% women in undergraduate computer science programs. Representation of women in computer science in the US is 50% below the university rate, but at KU, it is 50% above the university rate. This mixed methods study of KU was conducted in the following three stages: setting up focus groups with women computer science students, distributing surveys to all students in the CS department, and conducting a series of 22 individual interviews with fourth year CS students. The analysis of the data collected and its comparison to literature on university/department retention in Science, Technology, Engineering and Mathematics gender representation and on women's education in underdeveloped Islamic countries illuminates KU's uncharacteristic representation of women in its Computer Science Department. The retention of women in STEM through the education pipeline has several characteristics in Afghanistan that differ from countries often studied in available literature. Few Afghan students have computers in their home and few have training beyond secretarial applications before considering studying CS at university. University students in Afghanistan are selected based on placement exams and are then assigned to an area of study, and financially supported throughout their academic career, resulting in a low attrition rate from the program. Gender and STEM literature identifies parental encouragement, stereotypes and employment perceptions as influential characteristics. Afghan women in computer science received significant parental encouragement even from parents with no computer background. They do not seem to be influenced by any negative "geek" stereotypes, but they do perceive limitations when considering employment after graduation.

Getting the Right Answers for the Right Reasons: Toward Predictive Molecular Simulations of Water with Many-Body Potential Energy Functions.

PubMed

Paesani, Francesco

2016-09-20

The central role played by water in fundamental processes relevant to different disciplines, including chemistry, physics, biology, materials science, geology, and climate research, cannot be overemphasized. It is thus not surprising that, since the pioneering work by Stillinger and Rahman, many theoretical and computational studies have attempted to develop a microscopic description of the unique properties of water under different thermodynamic conditions. Consequently, numerous molecular models based on either molecular mechanics or ab initio approaches have been proposed over the years. However, despite continued progress, the correct prediction of the properties of water from small gas-phase clusters to the liquid phase and ice through a single molecular model remains challenging. To large extent, this is due to the difficulties encountered in the accurate modeling of the underlying hydrogen-bond network in which both number and strength of the hydrogen bonds vary continuously as a result of a subtle interplay between energetic, entropic, and nuclear quantum effects. In the past decade, the development of efficient algorithms for correlated electronic structure calculations of small molecular complexes, accompanied by tremendous progress in the analytical representation of multidimensional potential energy surfaces, opened the doors to the design of highly accurate potential energy functions built upon rigorous representations of the many-body expansion (MBE) of the interaction energies. This Account provides a critical overview of the performance of the MB-pol many-body potential energy function through a systematic analysis of energetic, structural, thermodynamic, and dynamical properties as well as of vibrational spectra of water from the gas to the condensed phase. It is shown that MB-pol achieves unprecedented accuracy across all phases of water through a quantitative description of each individual term of the MBE, with a physically correct representation of both short- and long-range many-body contributions. Comparisons with experimental data probing different regions of the water potential energy surface from clusters to bulk demonstrate that MB-pol represents a major step toward the long-sought-after "universal model" capable of accurately describing the molecular properties of water under different conditions and in different environments. Along this path, future challenges include the extension of the many-body scheme adopted by MB-pol to the description of generic solutes as well as the integration of MB-pol in an efficient theoretical and computational framework to model acid-base reactions in aqueous environments. In this context, given the nontraditional form of the MB-pol energy and force expressions, synergistic efforts by theoretical/computational chemists/physicists and computer scientists will be critical for the development of high-performance software for many-body molecular dynamics simulations.

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…

Science-Technology Coupling: The Case of Mathematical Logic and Computer Science.

ERIC Educational Resources Information Center

Wagner-Dobler, Roland

1997-01-01

In the history of science, there have often been periods of sudden rapprochements between pure science and technology-oriented branches of science. Mathematical logic as pure science and computer science as technology-oriented science have experienced such a rapprochement, which is studied in this article in a bibliometric manner. (Author)

Cognitive computing and eScience in health and life science research: artificial intelligence and obesity intervention programs.

PubMed

Marshall, Thomas; Champagne-Langabeer, Tiffiany; Castelli, Darla; Hoelscher, Deanna

2017-12-01

To present research models based on artificial intelligence and discuss the concept of cognitive computing and eScience as disruptive factors in health and life science research methodologies. The paper identifies big data as a catalyst to innovation and the development of artificial intelligence, presents a framework for computer-supported human problem solving and describes a transformation of research support models. This framework includes traditional computer support; federated cognition using machine learning and cognitive agents to augment human intelligence; and a semi-autonomous/autonomous cognitive model, based on deep machine learning, which supports eScience. The paper provides a forward view of the impact of artificial intelligence on our human-computer support and research methods in health and life science research. By augmenting or amplifying human task performance with artificial intelligence, cognitive computing and eScience research models are discussed as novel and innovative systems for developing more effective adaptive obesity intervention programs.

78 FR 61870 - Advisory Committee for Computer and Information Science and Engineering; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-04

... NATIONAL SCIENCE FOUNDATION Advisory Committee for Computer and Information Science and Engineering; Notice of Meeting In accordance with Federal Advisory Committee Act (Pub. L. 92-463, as amended... Committee for Computer and Information Science and Engineering (1115). Date/Time: Oct 31, 2013: 12:30 p.m...

Activities of the Institute for Computer Applications in Science and Engineering (ICASE)

NASA Technical Reports Server (NTRS)

1985-01-01

Research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period October 1, 1984 through March 31, 1985 is summarized.

[Research Conducted at the Institute for Computer Applications in Science and Engineering

NASA Technical Reports Server (NTRS)

1997-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period 1 Oct. 1996 - 31 Mar. 1997.

Activities of the Institute for Computer Applications in Science and Engineering (ICASE)

NASA Technical Reports Server (NTRS)

1988-01-01

This report summarizes research conducted at the Institute for Computer Applications Science and Engineering in applied mathematics, numerical analysis, and computer science during the period October 2, 1987 through March 31, 1988.

[Activities of Institute for Computer Applications in Science and Engineering (ICASE)

NASA Technical Reports Server (NTRS)

1999-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics. fluid mechanics, and computer science during the period April 1, 1999 through September 30. 1999.

First-principles Study of Phenol Hydrogenation on Pt and Ni Catalysts in Aqueous Phase

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

Yoon, Yeohoon; Rousseau, Roger J.; Weber, Robert S.

2014-07-23

The effects of aqueous phase on the reactivity of phenol hydrogenation over Pt and Ni catalysts were investigated using density functional theory based ab initio molecular dynamics (AIMD) calculations. The adsorption of phenol and the first hydrogenation steps via three carbon positions (ortho, meta and para) with respect to the phenolic OH group were studied in both vacuum and liquid phase conditions. To gain insight into how the aqueous phase affects the metal catalyst surface, increasing water environments including singly adsorbed water molecule, mono- (9 water molecules), double layers (24 water molecules), and the bulk liquid water which (52 watermore » molecules) on the Pt(111) and the Ni(111) surfaces were modeled. Compared to the vacuum/metal interfaces, AIMD simulation results suggest that the aqueous Pt(111) and Ni(111) interfaces have a lower metal work function in the order of 0.8 - 0.9 eV, thus, making the metals in aqueous phase stronger reducing agents and poorer oxidizing agents. Phenol adsorption from the aqueous phase is found to be slightly weaker that from the vapor phase. The first hydrogenation step of phenol at the ortho position of the phenolic ring is slightly favored over the other two positions. The polarization induced by the surrounding water molecules and the solvation effect play important roles in stabilizing the transition states associated with phenol hydrogenation by lowering the barriers of 0.1 - 0.4 eV. The detailed discussion on the basis of the interfacial electrostatics from the current study is very useful to understand the nature of a broader class of metal catalyzed reactions in liquid solution phase. This work was supported by the US Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences and Office of Energy Efficiency and Renewable Energy. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) and by the National Energy Research Scientific Computing Center (NERSC). EMSL is a national scientific user facility located at Pacific Northwest National Laboratory (PNNL) and sponsored by DOE’s Office of Biological and Environmental Research.« less

Practical Measurement of Complexity In Dynamic Systems

DTIC Science & Technology

2012-01-01

policies that produce highly complex behaviors , yet yield no benefit. 21Jason B. Clark and David R. Jacques / Procedia Computer Science 8 (2012) 14... Procedia Computer Science 8 (2012) 14 – 21 1877-0509 © 2012 Published by Elsevier B.V. doi:10.1016/j.procs.2012.01.008 Available online at...www.sciencedirect.com Procedia Computer Science Procedia Computer Science 00 (2012) 000–000 www.elsevier.com/locate/ procedia Available online at

The role of physicality in rich programming environments

NASA Astrophysics Data System (ADS)

Liu, Allison S.; Schunn, Christian D.; Flot, Jesse; Shoop, Robin

2013-12-01

Computer science proficiency continues to grow in importance, while the number of students entering computer science-related fields declines. Many rich programming environments have been created to motivate student interest and expertise in computer science. In the current study, we investigated whether a recently created environment, Robot Virtual Worlds (RVWs), can be used to teach computer science principles within a robotics context by examining its use in high-school classrooms. We also investigated whether the lack of physicality in these environments impacts student learning by comparing classrooms that used either virtual or physical robots for the RVW curriculum. Results suggest that the RVW environment leads to significant gains in computer science knowledge, that virtual robots lead to faster learning, and that physical robots may have some influence on algorithmic thinking. We discuss the implications of physicality in these programming environments for learning computer science.

Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

ERIC Educational Resources Information Center

Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

2012-01-01

Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

The emerging role of cloud computing in molecular modelling.

PubMed

Ebejer, Jean-Paul; Fulle, Simone; Morris, Garrett M; Finn, Paul W

2013-07-01

There is a growing recognition of the importance of cloud computing for large-scale and data-intensive applications. The distinguishing features of cloud computing and their relationship to other distributed computing paradigms are described, as are the strengths and weaknesses of the approach. We review the use made to date of cloud computing for molecular modelling projects and the availability of front ends for molecular modelling applications. Although the use of cloud computing technologies for molecular modelling is still in its infancy, we demonstrate its potential by presenting several case studies. Rapid growth can be expected as more applications become available and costs continue to fall; cloud computing can make a major contribution not just in terms of the availability of on-demand computing power, but could also spur innovation in the development of novel approaches that utilize that capacity in more effective ways. Copyright © 2013 Elsevier Inc. All rights reserved.

Path Not Found: Disparities in Access to Computer Science Courses in California High Schools

ERIC Educational Resources Information Center

Martin, Alexis; McAlear, Frieda; Scott, Allison

2015-01-01

"Path Not Found: Disparities in Access to Computer Science Courses in California High Schools" exposes one of the foundational causes of underrepresentation in computing: disparities in access to computer science courses in California's public high schools. This report provides new, detailed data on these disparities by student body…

Developing Oral and Written Communication Skills in Undergraduate Computer Science and Information Systems Curriculum

ERIC Educational Resources Information Center

Kortsarts, Yana; Fischbach, Adam; Rufinus, Jeff; Utell, Janine M.; Yoon, Suk-Chung

2010-01-01

Developing and applying oral and written communication skills in the undergraduate computer science and computer information systems curriculum--one of the ABET accreditation requirements - is a very challenging and, at the same time, a rewarding task that provides various opportunities to enrich the undergraduate computer science and computer…

EOS MLS Science Data Processing System: A Description of Architecture and Capabilities

NASA Technical Reports Server (NTRS)

Cuddy, David T.; Echeverri, Mark D.; Wagner, Paul A.; Hanzel, Audrey T.; Fuller, Ryan A.

2006-01-01

This paper describes the architecture and capabilities of the Science Data Processing System (SDPS) for the EOS MLS. The SDPS consists of two major components--the Science Computing Facility and the Science Investigator-led Processing System. The Science Computing Facility provides the facilities for the EOS MLS Science Team to perform the functions of scientific algorithm development, processing software development, quality control of data products, and scientific analyses. The Science Investigator-led Processing System processes and reprocesses the science data for the entire mission and delivers the data products to the Science Computing Facility and to the Goddard Space Flight Center Earth Science Distributed Active Archive Center, which archives and distributes the standard science products.

Simulation and understanding of atomic and molecular quantum crystals

NASA Astrophysics Data System (ADS)

Cazorla, Claudio; Boronat, Jordi

2017-07-01

Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

Women in computer science: An interpretative phenomenological analysis exploring common factors contributing to women's selection and persistence in computer science as an academic major

NASA Astrophysics Data System (ADS)

Thackeray, Lynn Roy

The purpose of this study is to understand the meaning that women make of the social and cultural factors that influence their reasons for entering and remaining in study of computer science. The twenty-first century presents many new challenges in career development and workforce choices for both men and women. Information technology has become the driving force behind many areas of the economy. As this trend continues, it has become essential that U.S. citizens need to pursue a career in technologies, including the computing sciences. Although computer science is a very lucrative profession, many Americans, especially women, are not choosing it as a profession. Recent studies have shown no significant differences in math, technical and science competency between men and women. Therefore, other factors, such as social, cultural, and environmental influences seem to affect women's decisions in choosing an area of study and career choices. A phenomenological method of qualitative research was used in this study, based on interviews of seven female students who are currently enrolled in a post-secondary computer science program. Their narratives provided meaning into the social and cultural environments that contribute to their persistence in their technical studies, as well as identifying barriers and challenges that are faced by female students who choose to study computer science. It is hoped that the data collected from this study may provide recommendations for the recruiting, retention and support for women in computer science departments of U.S. colleges and universities, and thereby increase the numbers of women computer scientists in industry. Keywords: gender access, self-efficacy, culture, stereotypes, computer education, diversity.

Multiscale Computational Analysis of Nitrogen and Oxygen Gas-Phase Thermochemistry in Hypersonic Flows

NASA Astrophysics Data System (ADS)

Bender, Jason D.

Understanding hypersonic aerodynamics is important for the design of next-generation aerospace vehicles for space exploration, national security, and other applications. Ground-level experimental studies of hypersonic flows are difficult and expensive; thus, computational science plays a crucial role in this field. Computational fluid dynamics (CFD) simulations of extremely high-speed flows require models of chemical and thermal nonequilibrium processes, such as dissociation of diatomic molecules and vibrational energy relaxation. Current models are outdated and inadequate for advanced applications. We describe a multiscale computational study of gas-phase thermochemical processes in hypersonic flows, starting at the atomic scale and building systematically up to the continuum scale. The project was part of a larger effort centered on collaborations between aerospace scientists and computational chemists. We discuss the construction of potential energy surfaces for the N4, N2O2, and O4 systems, focusing especially on the multi-dimensional fitting problem. A new local fitting method named L-IMLS-G2 is presented and compared with a global fitting method. Then, we describe the theory of the quasiclassical trajectory (QCT) approach for modeling molecular collisions. We explain how we implemented the approach in a new parallel code for high-performance computing platforms. Results from billions of QCT simulations of high-energy N2 + N2, N2 + N, and N2 + O2 collisions are reported and analyzed. Reaction rate constants are calculated and sets of reactive trajectories are characterized at both thermal equilibrium and nonequilibrium conditions. The data shed light on fundamental mechanisms of dissociation and exchange reactions -- and their coupling to internal energy transfer processes -- in thermal environments typical of hypersonic flows. We discuss how the outcomes of this investigation and other related studies lay a rigorous foundation for new macroscopic models for hypersonic CFD. This research was supported by the Department of Energy Computational Science Graduate Fellowship and by the Air Force Office of Scientific Research Multidisciplinary University Research Initiative.

77 FR 38630 - Open Internet Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-28

... Computer Science and Co-Founder of the Berkman Center for Internet and Society, Harvard University, is... of Technology Computer Science and Artificial Intelligence Laboratory, is appointed vice-chairperson... Jennifer Rexford, Professor of Computer Science, Princeton University Dennis Roberson, Vice Provost...

Research in progress at the Institute for Computer Applications in Science and Engineering

NASA Technical Reports Server (NTRS)

1987-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, numerical analysis, and computer science during the period April 1, 1987 through October 1, 1987.

Integrated Genomic and Network-Based Analyses of Complex Diseases and Human Disease Network.

PubMed

Al-Harazi, Olfat; Al Insaif, Sadiq; Al-Ajlan, Monirah A; Kaya, Namik; Dzimiri, Nduna; Colak, Dilek

2016-06-20

A disease phenotype generally reflects various pathobiological processes that interact in a complex network. The highly interconnected nature of the human protein interaction network (interactome) indicates that, at the molecular level, it is difficult to consider diseases as being independent of one another. Recently, genome-wide molecular measurements, data mining and bioinformatics approaches have provided the means to explore human diseases from a molecular basis. The exploration of diseases and a system of disease relationships based on the integration of genome-wide molecular data with the human interactome could offer a powerful perspective for understanding the molecular architecture of diseases. Recently, subnetwork markers have proven to be more robust and reliable than individual biomarker genes selected based on gene expression profiles alone, and achieve higher accuracy in disease classification. We have applied one of these methodologies to idiopathic dilated cardiomyopathy (IDCM) data that we have generated using a microarray and identified significant subnetworks associated with the disease. In this paper, we review the recent endeavours in this direction, and summarize the existing methodologies and computational tools for network-based analysis of complex diseases and molecular relationships among apparently different disorders and human disease network. We also discuss the future research trends and topics of this promising field. Copyright © 2015 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Ltd. All rights reserved.

A parallel-processing approach to computing for the geographic sciences; applications and systems enhancements

USGS Publications Warehouse

Crane, Michael; Steinwand, Dan; Beckmann, Tim; Krpan, Greg; Liu, Shu-Guang; Nichols, Erin; Haga, Jim; Maddox, Brian; Bilderback, Chris; Feller, Mark; Homer, George

2001-01-01

The overarching goal of this project is to build a spatially distributed infrastructure for information science research by forming a team of information science researchers and providing them with similar hardware and software tools to perform collaborative research. Four geographically distributed Centers of the U.S. Geological Survey (USGS) are developing their own clusters of low-cost, personal computers into parallel computing environments that provide a costeffective way for the USGS to increase participation in the high-performance computing community. Referred to as Beowulf clusters, these hybrid systems provide the robust computing power required for conducting information science research into parallel computing systems and applications.

Enabling Earth Science Through Cloud Computing

NASA Technical Reports Server (NTRS)

Hardman, Sean; Riofrio, Andres; Shams, Khawaja; Freeborn, Dana; Springer, Paul; Chafin, Brian

2012-01-01

Cloud Computing holds tremendous potential for missions across the National Aeronautics and Space Administration. Several flight missions are already benefiting from an investment in cloud computing for mission critical pipelines and services through faster processing time, higher availability, and drastically lower costs available on cloud systems. However, these processes do not currently extend to general scientific algorithms relevant to earth science missions. The members of the Airborne Cloud Computing Environment task at the Jet Propulsion Laboratory have worked closely with the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) mission to integrate cloud computing into their science data processing pipeline. This paper details the efforts involved in deploying a science data system for the CARVE mission, evaluating and integrating cloud computing solutions with the system and porting their science algorithms for execution in a cloud environment.

The effects of computer-based dynamic visualization simulations on student learning in high school science

NASA Astrophysics Data System (ADS)

Moodley, Sadha

The purpose of this study was to determine whether the use of dynamic computer-based visualizations of the classical model of particle behavior helps to improve student understanding, performance, and interest in science when used by teachers as visual presentations to complement their traditional methods of teaching. The software, Virtual Molecular Dynamics Laboratory (VMDL), was developed at the Center for Polymer Studies at Boston University through funding from the National Science Foundation. The design of the study included five pairs of classes in four different schools in New England from the inner city and from advantaged suburbs. The study employed a treatment-control group design for testing the impact of several VMDL simulations on student learning in several content areas from traditional chemistry and physical science courses. The study employed a mixed qualitative and quantitative design. The quantitative part involved administering the Group Assessment of Logical Thinking (GALT) as well as post-tests that were topic specific. An Analysis of Covariance (ANCOVA) was conducted on the test scores with the GALT scores serving as a covariate. Results of the ANCOVA showed that students' understanding and performance were better in classes where teachers used the computer-based dynamic visualizations to complement their traditional teaching. GALT scores were significantly different among schools but very similar within schools. They were significant in adjusting post-test scores for pre-treatment differences for only two of the schools. The treatment groups outscored the control groups in all five comparisons. The mean differences reached statistical significance at the p < .01 level in only four of the comparisons. The qualitative part of the study involved classroom observations and student interviews. Analysis of classroom observations revealed a shift in classroom dynamics to more learner-centeredness with greater engagement by students, especially in classes that tended to have little student participation without the simulations. Analysis of the student interviews indicated that the dynamic visualizations made learning more enjoyable, helped with remembering, and enhanced students abilities to make connections between the nanoscopic and macroscopic science.

Teaching and Learning Methodologies Supported by ICT Applied in Computer Science

ERIC Educational Resources Information Center

Capacho, Jose

2016-01-01

The main objective of this paper is to show a set of new methodologies applied in the teaching of Computer Science using ICT. The methodologies are framed in the conceptual basis of the following sciences: Psychology, Education and Computer Science. The theoretical framework of the research is supported by Behavioral Theory, Gestalt Theory.…

76 FR 61118 - Advisory Committee for Computer and Information Science and Engineering; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-03

... Engineering; Notice of Meeting In accordance with the Federal Advisory Committee Act (Pub. L. 92- 463, as... Computer and Information Science and Engineering (1115). Date and Time: November 1, 2011 from 12 p.m.-5:30... Computer and Information Science and Engineering, National Science Foundation, 4201 Wilson Blvd., Suite...

Computer Science in High School Graduation Requirements. ECS Education Trends (Updated)

ERIC Educational Resources Information Center

Zinth, Jennifer

2016-01-01

Allowing high school students to fulfill a math or science high school graduation requirement via a computer science credit may encourage more student to pursue computer science coursework. This Education Trends report is an update to the original report released in April 2015 and explores state policies that allow or require districts to apply…

A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course

ERIC Educational Resources Information Center

Elmore, Donald E.; Guayasamin, Ryann C.; Kieffer, Madeleine E.

2010-01-01

As computational modeling plays an increasingly central role in biochemical research, it is important to provide students with exposure to common modeling methods in their undergraduate curriculum. This article describes a series of computer labs designed to introduce undergraduate students to energy minimization, molecular dynamics simulations,…

Using a Computer Animation to Teach High School Molecular Biology

ERIC Educational Resources Information Center

Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

2008-01-01

We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

Supramolecular ferroelectrics.

PubMed

Tayi, Alok S; Kaeser, Adrien; Matsumoto, Michio; Aida, Takuzo; Stupp, Samuel I

2015-04-01

Supramolecular chemistry uses non-covalent interactions to coax molecules into forming ordered assemblies. The construction of ordered materials with these reversible bonds has led to dramatic innovations in organic electronics, polymer science and biomaterials. Here, we review how supramolecular strategies can advance the burgeoning field of organic ferroelectricity. Ferroelectrics - materials with a spontaneous and electrically reversible polarization - are touted for use in non-volatile computer memories, sensors and optics. Historically, this physical phenomenon has been studied in inorganic materials, although some organic examples are known and strong interest exists to extend the search for ferroelectric molecular systems. Other undiscovered applications outside this regime could also emerge. We describe the key features necessary for molecular and supramolecular dipoles in organic ferroelectrics and their incorporation into ordered systems, such as porous frameworks and liquid crystals. The goal of this Review is to motivate the development of innovative supramolecular ferroelectrics that exceed the performance and usefulness of known systems.

Extracting biomarkers of commitment to cancer development: potential role of vibrational spectroscopy in systems biology.

PubMed

Theophilou, Georgios; Paraskevaidi, Maria; Lima, Kássio M G; Kyrgiou, Maria; Martin-Hirsch, Pierre L; Martin, Francis L

2015-05-01

The complex processes driving cancer have so far impeded the discovery of dichotomous biomarkers associated with its initiation and progression. Reductionist approaches utilizing 'omics' technologies have met some success in identifying molecular alterations associated with carcinogenesis. Systems biology is an emerging science that combines high-throughput investigation techniques to define the dynamic interplay between regulatory biological systems in response to internal and external cues. Vibrational spectroscopy has the potential to play an integral role within systems biology research approaches. It is capable of examining global models of carcinogenesis by scrutinizing chemical bond alterations within molecules. The application of infrared or Raman spectroscopic approaches coupled with computational analysis under the systems biology umbrella can assist the transition of biomarker research from the molecular level to the system level. The comprehensive representation of carcinogenesis as a multilevel biological process will inevitably revolutionize cancer-related healthcare by personalizing risk prediction and prevention.

Conception and development of the Second Life® Embryo Physics Course.

PubMed

Gordon, Richard

2013-06-01

The study of embryos with the tools and mindset of physics, started by Wilhelm His in the 1880s, has resumed after a hiatus of a century. The Embryo Physics Course convenes online allowing interested researchers and students, who are scattered around the world, to gather weekly in one place, the virtual world of Second Life®. It attracts people from a wide variety of disciplines and walks of life: applied mathematics, artificial life, bioengineering, biophysics, cancer biology, cellular automata, civil engineering, computer science, embryology, electrical engineering, evolution, finite element methods, history of biology, human genetics, mathematics, molecular developmental biology, molecular biology, nanotechnology, philosophy of biology, phycology, physics, self-reproducing systems, stem cells, tensegrity structures, theoretical biology, and tissue engineering. Now in its fifth year, the Embryo Physics Course provides a focus for research on the central question of how an embryo builds itself.

High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction

PubMed Central

Carter, Charles W.

2017-01-01

Understanding how distinct parts of proteins produce coordinated behavior has driven and continues to drive advances in protein science and enzymology. However, despite consensus about the conceptual basis for allostery, the idiosyncratic nature of allosteric mechanisms resists general approaches. Computational methods can identify conformational transition states from structural changes, revealing common switching mechanisms that impose multistate behavior. Thermodynamic cycles use factorial perturbations to measure coupling energies between side chains in molecular switches that mediate shear during domain motion. Such cycles have now been complemented by modular cycles that measure energetic coupling between separable domains. For one model system, energetic coupling between domains has been shown to be quantitatively equivalent to that between dynamic side chains. Linkages between domain motion, switching residues, and catalysis make nucleoside triphosphate hydrolysis conditional on domain movement, confirming an essential yet neglected aspect of free energy transduction and suggesting the potential generality of these studies. PMID:28375734

Computer-Aided Screening of Conjugated Polymers for Organic Solar Cell: Classification by Random Forest.

PubMed

Nagasawa, Shinji; Al-Naamani, Eman; Saeki, Akinori

2018-05-17

Owing to the diverse chemical structures, organic photovoltaic (OPV) applications with a bulk heterojunction framework have greatly evolved over the last two decades, which has produced numerous organic semiconductors exhibiting improved power conversion efficiencies (PCEs). Despite the recent fast progress in materials informatics and data science, data-driven molecular design of OPV materials remains challenging. We report a screening of conjugated molecules for polymer-fullerene OPV applications by supervised learning methods (artificial neural network (ANN) and random forest (RF)). Approximately 1000 experimental parameters including PCE, molecular weight, and electronic properties are manually collected from the literature and subjected to machine learning with digitized chemical structures. Contrary to the low correlation coefficient in ANN, RF yields an acceptable accuracy, which is twice that of random classification. We demonstrate the application of RF screening for the design, synthesis, and characterization of a conjugated polymer, which facilitates a rapid development of optoelectronic materials.

Lattice-free prediction of three-dimensional structure of programmed DNA assemblies

PubMed Central

Pan, Keyao; Kim, Do-Nyun; Zhang, Fei; Adendorff, Matthew R.; Yan, Hao; Bathe, Mark

2014-01-01

DNA can be programmed to self-assemble into high molecular weight 3D assemblies with precise nanometer-scale structural features. Although numerous sequence design strategies exist to realize these assemblies in solution, there is currently no computational framework to predict their 3D structures on the basis of programmed underlying multi-way junction topologies constrained by DNA duplexes. Here, we introduce such an approach and apply it to assemblies designed using the canonical immobile four-way junction. The procedure is used to predict the 3D structure of high molecular weight planar and spherical ring-like origami objects, a tile-based sheet-like ribbon, and a 3D crystalline tensegrity motif, in quantitative agreement with experiments. Our framework provides a new approach to predict programmed nucleic acid 3D structure on the basis of prescribed secondary structure motifs, with possible application to the design of such assemblies for use in biomolecular and materials science. PMID:25470497

Characteristics of the Navy Laboratory Warfare Center Technical Workforce

DTIC Science & Technology

2013-09-29

Mathematics and Information Science (M&IS) Actuarial Science 1510 Computer Science 1550 Gen. Math & Statistics 1501 Mathematics 1520 Operations...Admin. Network Systems & Data Communication Analysts Actuaries Mathematicians Operations Research Analyst Statisticians Social Science (SS...workforce was sub-divided into six broad occupational groups: Life Science , Physical Science , Engineering, Mathematics, Computer Science and Information

Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency.

PubMed

Kepper, Nick; Ettig, Ramona; Dickmann, Frank; Stehr, Rene; Grosveld, Frank G; Wedemann, Gero; Knoch, Tobias A

2010-01-01

Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we-can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency.

The Development of a Post-Baccalaureate Certificate Program in Molecular Diagnostics

PubMed Central

Williams, Gail S.; Brown, Judith D.; Keagle, Martha B.

2000-01-01

A post-baccalaureate certificate program in diagnostic molecular sciences was created in 1995 by the Diagnostic Genetic Sciences Program in the School of Allied Health at the University of Connecticut. The required on-campus lecture and laboratory courses include basic laboratory techniques, health care issues, cell biology, immunology, human genetics, research, management, and molecular diagnostic techniques and laboratory in molecular diagnostics. These courses precede a 6-month, full-time practicum at an affiliated full-service molecular laboratory. The practicum includes amplification and blotting methods, a research project, and a choice of specialized electives including DNA sequencing, mutagenesis, in situ hybridization methods, or molecular diagnostic applications in microbiology. Graduates of the program are immediately eligible to sit for the National Credentialing Agency examination in molecular biology to obtain the credential Clinical Laboratory Specialist in Molecular Biology (CLSp(MB). This description of the University of Connecticut program may assist other laboratory science programs in creating similar curricula. PMID:11232107

A Review of Computer Science Resources for Learning and Teaching with K-12 Computing Curricula: An Australian Case Study

ERIC Educational Resources Information Center

Falkner, Katrina; Vivian, Rebecca

2015-01-01

To support teachers to implement Computer Science curricula into classrooms from the very first year of school, teachers, schools and organisations seek quality curriculum resources to support implementation and teacher professional development. Until now, many Computer Science resources and outreach initiatives have targeted K-12 school-age…

Technology, Pedagogy, and Epistemology: Opportunities and Challenges of Using Computer Modeling and Simulation Tools in Elementary Science Methods

ERIC Educational Resources Information Center

Schwarz, Christina V.; Meyer, Jason; Sharma, Ajay

2007-01-01

This study infused computer modeling and simulation tools in a 1-semester undergraduate elementary science methods course to advance preservice teachers' understandings of computer software use in science teaching and to help them learn important aspects of pedagogy and epistemology. Preservice teachers used computer modeling and simulation tools…

Prospective Students' Reactions to the Presentation of the Computer Science Major

ERIC Educational Resources Information Center

Weaver, Daniel Scott

2010-01-01

The number of students enrolling in Computer Science in colleges and Universities has declined since its peak in the early 2000s. Some claim contributing factors that intimate that prospective students fear the lack of employment opportunities if they study computing in college. However, the lack of understanding of what Computer Science is and…

Science at the interstices: an evolution in the academy.

PubMed

Balser, Jeffrey R; Baruchin, Andrea

2008-09-01

Biomedical science is at an evolutionary turning point. Many of the rate-limiting steps to realizing the next generation of personalized, highly targeted diagnostics and therapeutics rest at the interstices between biomedical science and the classic, university-based disciplines, such as physics, mathematics, computational science, engineering, social sciences, business, and law. Institutes, centers, or other entities created to foster interdisciplinary science are rapidly forming to tackle these formidable challenges, but they are plagued with substantive barriers, born of traditions, processes, and culture, which impede scientific progress and endanger success. Without a more seamless interdisciplinary framework, academic health centers will struggle to move transformative advances in technology into the foundation of biomedical science, and the equally challenging advancement of models that effectively integrate new molecular diagnostics and therapies into the business and social fabric of our population will be similarly hampered. At the same time, excess attention on rankings tied to competition for National Institutes of Health and other federal funds adversely encourages academic medical centers (AMCs) and universities to hoard, rather than share, resources effectively and efficiently. To fully realize their discovery potential, AMCs must consider a substantive realignment relative to one another, as well as with their associated universities, as the academy looks toward innovative approaches to provide a more supportive foundation for the emergent biomedical research enterprise. The authors discuss potential models that could serve to lower barriers to interdisciplinary science, promoting a new synergy between AMCs and their parent universities.

Does Geophysics Need "A new kind of Science"?

NASA Astrophysics Data System (ADS)

Turcotte, D. L.; Rundle, J. B.

2002-12-01

Stephen Wolfram's book "A New Kind of Science" has received a great deal of attention in the last six months, both positive and negative. The theme of the book is that "cellular automata", which arise from spatial and temporal coarse-graining of equations of motion, provide the foundations for a new nonlinear science of "complexity". The old science is the science of partial differential equations. Some of the major contributions of this old science have been in geophysics, i.e. gravity, magnetics, seismic waves, heat flow. The basis of the new science is the use of massive computing and numerical simulations. The new science is motivated by the observations that many physical systems display a vast multiplicity of space and time scales, and have hidden dynamics that in many cases are impossible to directly observe. An example would be molecular dynamics. Statistical physics derives continuum equations from the discrete interactions between atoms and molecules, in the modern world the continuum equations are then discretized using finite differences, finite elements, etc. in order to obtain numerical solutions. Examples of widely used cellular automata models include diffusion limited aggregation and site percolation. Also the class of models that are said to exhibit self-organized criticality, the sand-pile model, the slider-block model, the forest-fire model. Applications of these models include drainage networks, seismicity, distributions of minerals,and the evolution of landforms and coastlines. Simple cellular automata models generate deterministic chaos, i.e. the logistic map.

PREPARING FOR EXASCALE: ORNL Leadership Computing Application Requirements and Strategy

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

Joubert, Wayne; Kothe, Douglas B; Nam, Hai Ah

2009-12-01

In 2009 the Oak Ridge Leadership Computing Facility (OLCF), a U.S. Department of Energy (DOE) facility at the Oak Ridge National Laboratory (ORNL) National Center for Computational Sciences (NCCS), elicited petascale computational science requirements from leading computational scientists in the international science community. This effort targeted science teams whose projects received large computer allocation awards on OLCF systems. A clear finding of this process was that in order to reach their science goals over the next several years, multiple projects will require computational resources in excess of an order of magnitude more powerful than those currently available. Additionally, for themore » longer term, next-generation science will require computing platforms of exascale capability in order to reach DOE science objectives over the next decade. It is generally recognized that achieving exascale in the proposed time frame will require disruptive changes in computer hardware and software. Processor hardware will become necessarily heterogeneous and will include accelerator technologies. Software must undergo the concomitant changes needed to extract the available performance from this heterogeneous hardware. This disruption portends to be substantial, not unlike the change to the message passing paradigm in the computational science community over 20 years ago. Since technological disruptions take time to assimilate, we must aggressively embark on this course of change now, to insure that science applications and their underlying programming models are mature and ready when exascale computing arrives. This includes initiation of application readiness efforts to adapt existing codes to heterogeneous architectures, support of relevant software tools, and procurement of next-generation hardware testbeds for porting and testing codes. The 2009 OLCF requirements process identified numerous actions necessary to meet this challenge: (1) Hardware capabilities must be advanced on multiple fronts, including peak flops, node memory capacity, interconnect latency, interconnect bandwidth, and memory bandwidth. (2) Effective parallel programming interfaces must be developed to exploit the power of emerging hardware. (3) Science application teams must now begin to adapt and reformulate application codes to the new hardware and software, typified by hierarchical and disparate layers of compute, memory and concurrency. (4) Algorithm research must be realigned to exploit this hierarchy. (5) When possible, mathematical libraries must be used to encapsulate the required operations in an efficient and useful way. (6) Software tools must be developed to make the new hardware more usable. (7) Science application software must be improved to cope with the increasing complexity of computing systems. (8) Data management efforts must be readied for the larger quantities of data generated by larger, more accurate science models. Requirements elicitation, analysis, validation, and management comprise a difficult and inexact process, particularly in periods of technological change. Nonetheless, the OLCF requirements modeling process is becoming increasingly quantitative and actionable, as the process becomes more developed and mature, and the process this year has identified clear and concrete steps to be taken. This report discloses (1) the fundamental science case driving the need for the next generation of computer hardware, (2) application usage trends that illustrate the science need, (3) application performance characteristics that drive the need for increased hardware capabilities, (4) resource and process requirements that make the development and deployment of science applications on next-generation hardware successful, and (5) summary recommendations for the required next steps within the computer and computational science communities.« less

Using the Tower of Hanoi puzzle to infuse your mathematics classroom with computer science concepts

NASA Astrophysics Data System (ADS)

Marzocchi, Alison S.

2016-07-01

This article suggests that logic puzzles, such as the well-known Tower of Hanoi puzzle, can be used to introduce computer science concepts to mathematics students of all ages. Mathematics teachers introduce their students to computer science concepts that are enacted spontaneously and subconsciously throughout the solution to the Tower of Hanoi puzzle. These concepts include, but are not limited to, conditionals, iteration, and recursion. Lessons, such as the one proposed in this article, are easily implementable in mathematics classrooms and extracurricular programmes as they are good candidates for 'drop in' lessons that do not need to fit into any particular place in the typical curriculum sequence. As an example for readers, the author describes how she used the puzzle in her own Number Sense and Logic course during the federally funded Upward Bound Math/Science summer programme for college-intending low-income high school students. The article explains each computer science term with real-life and mathematical examples, applies each term to the Tower of Hanoi puzzle solution, and describes how students connected the terms to their own solutions of the puzzle. It is timely and important to expose mathematics students to computer science concepts. Given the rate at which technology is currently advancing, and our increased dependence on technology in our daily lives, it has become more important than ever for children to be exposed to computer science. Yet, despite the importance of exposing today's children to computer science, many children are not given adequate opportunity to learn computer science in schools. In the United States, for example, most students finish high school without ever taking a computing course. Mathematics lessons, such as the one described in this article, can help to make computer science more accessible to students who may have otherwise had little opportunity to be introduced to these increasingly important concepts.

Rate Theory of Ion Pairing at the Water Liquid–Vapor Interface

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

Dang, Liem X.; Schenter, Gregory K.; Wick, Collin D.

There is overwhelming evidence that certain ions are present near the vapor–liquid interface of aqueous salt solutions. Despite their importance in many chemical reactive phenomena, how ion–ion interactions are affected by interfaces and their influence on kinetic processes is not well understood. Molecular simulations were carried out to exam the thermodynamics and kinetics of small alkali halide ions in the bulk and near the water vapor–liquid interface. We calculated dissociation rates using classical transition state theory, and corrected them with transmission coefficients determined by the reactive flux method and Grote-Hynes theory. Our results show that, in addition to affecting themore » free energy of ions in solution, the interfacial environments significantly influence the kinetics of ion pairing. The results obtained from the reactive flux method and Grote-Hynes theory on the relaxation time present an unequivocal picture of the interface suppressing ion dissociation. This work was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.« less

Engineering and physical sciences in oncology: challenges and opportunities

PubMed Central

Mitchell, Michael J.; Jain, Rakesh K.; Langer, Robert

2017-01-01

The principles of engineering and physics have been applied to oncology for nearly 50 years. Engineers and physical scientists have made contributions to all aspects of cancer biology, from quantitative understanding of tumour growth and progression to improved detection and treatment of cancer. Many early efforts focused on experimental and computational modelling of drug distribution, cell cycle kinetics and tumour growth dynamics. In the past decade, we have witnessed exponential growth at the interface of engineering, physics and oncology that has been fuelled by advances in fields including materials science, microfabrication, nanomedicine, microfluidics, imaging, and catalysed by new programmes at the National Institutes of Health (NIH), including the National Institute of Biomedical Imaging and Bioengineering (NIBIB), Physical Sciences in Oncology, and the National Cancer Institute (NCI) Alliance for Nanotechnology. Here, we review the advances made at the interface of engineering and physical sciences and oncology in four important areas: the physical microenvironment of the tumour and technological advances in drug delivery; cellular and molecular imaging; and microfluidics and microfabrication. We discussthe research advances, opportunities and challenges for integrating engineering and physical sciences with oncology to develop new methods to study, detect and treat cancer, and we also describe the future outlook for these emerging areas. PMID:29026204

Utilization of computer technology by science teachers in public high schools and the impact of standardized testing

NASA Astrophysics Data System (ADS)

Priest, Richard Harding

A significant percentage of high school science teachers are not using computers to teach their students or prepare them for standardized testing. A survey of high school science teachers was conducted to determine how they are having students use computers in the classroom, why science teachers are not using computers in the classroom, which variables were relevant to their not using computers, and what are the effects of standardized testing on the use of technology in the high school science classroom. A self-administered questionnaire was developed to measure these aspects of computer integration and demographic information. A follow-up telephone interview survey of a portion of the original sample was conducted in order to clarify questions, correct misunderstandings, and to draw out more holistic descriptions from the subjects. The primary method used to analyze the quantitative data was frequency distributions. Multiple regression analysis was used to investigate the relationships between the barriers and facilitators and the dimensions of instructional use, frequency, and importance of the use of computers. All high school science teachers in a large urban/suburban school district were sent surveys. A response rate of 58% resulted from two mailings of the survey. It was found that contributing factors to why science teachers do not use computers were not enough up-to-date computers in their classrooms and other educational commitments and duties do not leave them enough time to prepare lessons that include technology. While a high percentage of science teachers thought their school and district administrations were supportive of technology, they also believed more inservice technology training and follow-up activities to support that training are needed and more software needs to be created. The majority of the science teachers do not use the computer to help students prepare for standardized tests because they believe they can prepare students more efficiently without a computer. Nearly half of the teachers, however, gave lack of time to prepare instructional materials and lack of a means to project a computer image to the whole class as reasons they do not use computers. A significant percentage thought science standardized testing was having a negative effect on computer use.

Educational NASA Computational and Scientific Studies (enCOMPASS)

NASA Technical Reports Server (NTRS)

Memarsadeghi, Nargess

2013-01-01

Educational NASA Computational and Scientific Studies (enCOMPASS) is an educational project of NASA Goddard Space Flight Center aimed at bridging the gap between computational objectives and needs of NASA's scientific research, missions, and projects, and academia's latest advances in applied mathematics and computer science. enCOMPASS achieves this goal via bidirectional collaboration and communication between NASA and academia. Using developed NASA Computational Case Studies in university computer science/engineering and applied mathematics classes is a way of addressing NASA's goals of contributing to the Science, Technology, Education, and Math (STEM) National Objective. The enCOMPASS Web site at http://encompass.gsfc.nasa.gov provides additional information. There are currently nine enCOMPASS case studies developed in areas of earth sciences, planetary sciences, and astrophysics. Some of these case studies have been published in AIP and IEEE's Computing in Science and Engineering magazines. A few university professors have used enCOMPASS case studies in their computational classes and contributed their findings to NASA scientists. In these case studies, after introducing the science area, the specific problem, and related NASA missions, students are first asked to solve a known problem using NASA data and past approaches used and often published in a scientific/research paper. Then, after learning about the NASA application and related computational tools and approaches for solving the proposed problem, students are given a harder problem as a challenge for them to research and develop solutions for. This project provides a model for NASA scientists and engineers on one side, and university students, faculty, and researchers in computer science and applied mathematics on the other side, to learn from each other's areas of work, computational needs and solutions, and the latest advances in research and development. This innovation takes NASA science and engineering applications to computer science and applied mathematics university classes, and makes NASA objectives part of the university curricula. There is great potential for growth and return on investment of this program to the point where every major university in the U.S. would use at least one of these case studies in one of their computational courses, and where every NASA scientist and engineer facing a computational challenge (without having resources or expertise to solve it) would use enCOMPASS to formulate the problem as a case study, provide it to a university, and get back their solutions and ideas.

Research in progress and other activities of the Institute for Computer Applications in Science and Engineering

NASA Technical Reports Server (NTRS)

1993-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics and computer science during the period April 1, 1993 through September 30, 1993. The major categories of the current ICASE research program are: (1) applied and numerical mathematics, including numerical analysis and algorithm development; (2) theoretical and computational research in fluid mechanics in selected areas of interest to LaRC, including acoustic and combustion; (3) experimental research in transition and turbulence and aerodynamics involving LaRC facilities and scientists; and (4) computer science.

Research in progress in applied mathematics, numerical analysis, fluid mechanics, and computer science

NASA Technical Reports Server (NTRS)

1994-01-01

This report summarizes research conducted at the Institute for Computer Applications in Science and Engineering in applied mathematics, fluid mechanics, and computer science during the period October 1, 1993 through March 31, 1994. The major categories of the current ICASE research program are: (1) applied and numerical mathematics, including numerical analysis and algorithm development; (2) theoretical and computational research in fluid mechanics in selected areas of interest to LaRC, including acoustics and combustion; (3) experimental research in transition and turbulence and aerodynamics involving LaRC facilities and scientists; and (4) computer science.

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

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

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Medical physics practice in the next decade

PubMed Central

Paliwal, Bhudatt

2006-01-01

Impressive advances in computers and materials science have fueled a broad-based confluence of basic science breakthroughs. These advances are making us reformulate our learning, teaching and credentialing methodologies and research and development frontiers. We are now in the age of molecular medicine. In the entire field of health care, a paradigm shift from population-based solutions to individual specific care is taking place. These trends are reshaping the practice of medical physics. In this short presentation, examples are given to illustrate developments in image-guided intensity-modulated and adaptive helical tomotherapy, enhanced application of intensity modulation radiotherapy (IMRT) using adaptive radiotherapy and conformal avoidance. These advances include improved normal tissue sparing and permit dose reconstruction and verification, thereby allowing significant biologically effective dose escalation and reduced radiation toxicity. The intrinsic capability of helical TomoTherapy for megavoltage CT imaging for IMRT image-guidance is also discussed. Finally developments in motion management are described. PMID:22275799

Publications of LASL research, 1972--1976

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

Petersen, L.

1977-04-01

This bibliography is a compilation of unclassified work done at the Los Alamos Scientific Laboratory and published during the years 1972 to 1976. Publications too late for inclusion in earlier compilations are also listed. Declassification of previously classified reports is considered to constitute publication. The bibliography includes LASL reports, journal articles, books, conference papers, papers published in congressional hearings, theses, patents, etc. The following subject areas are included: aerospace studies; analytical technology; astrophysics; atomic and molecular physics, equation of state, opacity; biology and medicine; chemical dynamics and kinetics; chemistry; cryogenics; crystallography; CTR and plasma physics; earth science and engineering; energymore » (nonnuclear); engineering and equipment; EPR, ESR, NMR studies; explosives and detonations; fission physics; health and safety; hydrodynamics and radiation transport; instruments; lasers; mathematics and computers; medium-energy physics; metallurgy and ceramics technology; neutronics and criticality studies; nuclear physics; nuclear safeguards; physics; reactor technology; solid state science; and miscellaneous (including Project Rover). (RWR)« less

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

DOE PAGES

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.; ...

2016-03-07

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Creating Science Simulations through Computational Thinking Patterns

ERIC Educational Resources Information Center

Basawapatna, Ashok Ram

2012-01-01

Computational thinking aims to outline fundamental skills from computer science that everyone should learn. As currently defined, with help from the National Science Foundation (NSF), these skills include problem formulation, logically organizing data, automating solutions through algorithmic thinking, and representing data through abstraction.…

77 FR 65417 - Proposal Review Panel for Computing Communication Foundations; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-26

...: To assess the progress of the EIC Award, ``Collaborative Research: Computational Behavioral Science... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Computing Communication Foundations; Notice... National Science Foundation announces the following meeting: Name: Site Visit, Proposal Panel Review for...

Chemodiversity and molecular plasticity: recognition processes as explored by property spaces.

PubMed

Vistoli, Giulio; Pedretti, Alessandro; Testa, Bernard

2011-06-01

In the last few years, a need to account for molecular flexibility in drug-design methodologies has emerged, even if the dynamic behavior of molecular properties is seldom made explicit. For a flexible molecule, it is indeed possible to compute different values for a given conformation-dependent property and the ensemble of such values defines a property space that can be used to describe its molecular variability; a most representative case is the lipophilicity space. In this review, a number of applications of lipophilicity space and other property spaces are presented, showing that this concept can be fruitfully exploited: to investigate the constraints exerted by media of different levels of structural organization, to examine processes of molecular recognition and binding at an atomic level, to derive informative descriptors to be included in quantitative structure--activity relationships and to analyze protein simulations extracting the relevant information. Much molecular information is neglected in the descriptors used by medicinal chemists, while the concept of property space can fill this gap by accounting for the often-disregarded dynamic behavior of both small ligands and biomacromolecules. Property space also introduces some innovative concepts such as molecular sensitivity and plasticity, which appear best suited to explore the ability of a molecule to adapt itself to the environment variously modulating its property and conformational profiles. Globally, such concepts can enhance our understanding of biological phenomena providing fruitful descriptors in drug-design and pharmaceutical sciences.

Crosscut report: Exascale Requirements Reviews, March 9–10, 2017 – Tysons Corner, Virginia. An Office of Science review sponsored by: Advanced Scientific Computing Research, Basic Energy Sciences, Biological and Environmental Research, Fusion Energy Sciences, High Energy Physics, Nuclear Physics

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

Gerber, Richard; Hack, James; Riley, Katherine

The mission of the U.S. Department of Energy Office of Science (DOE SC) is the delivery of scientific discoveries and major scientific tools to transform our understanding of nature and to advance the energy, economic, and national security missions of the United States. To achieve these goals in today’s world requires investments in not only the traditional scientific endeavors of theory and experiment, but also in computational science and the facilities that support large-scale simulation and data analysis. The Advanced Scientific Computing Research (ASCR) program addresses these challenges in the Office of Science. ASCR’s mission is to discover, develop, andmore » deploy computational and networking capabilities to analyze, model, simulate, and predict complex phenomena important to DOE. ASCR supports research in computational science, three high-performance computing (HPC) facilities — the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and Leadership Computing Facilities at Argonne (ALCF) and Oak Ridge (OLCF) National Laboratories — and the Energy Sciences Network (ESnet) at Berkeley Lab. ASCR is guided by science needs as it develops research programs, computers, and networks at the leading edge of technologies. As we approach the era of exascale computing, technology changes are creating challenges for science programs in SC for those who need to use high performance computing and data systems effectively. Numerous significant modifications to today’s tools and techniques will be needed to realize the full potential of emerging computing systems and other novel computing architectures. To assess these needs and challenges, ASCR held a series of Exascale Requirements Reviews in 2015–2017, one with each of the six SC program offices,1 and a subsequent Crosscut Review that sought to integrate the findings from each. Participants at the reviews were drawn from the communities of leading domain scientists, experts in computer science and applied mathematics, ASCR facility staff, and DOE program managers in ASCR and the respective program offices. The purpose of these reviews was to identify mission-critical scientific problems within the DOE Office of Science (including experimental facilities) and determine the requirements for the exascale ecosystem that would be needed to address those challenges. The exascale ecosystem includes exascale computing systems, high-end data capabilities, efficient software at scale, libraries, tools, and other capabilities. This effort will contribute to the development of a strategic roadmap for ASCR compute and data facility investments and will help the ASCR Facility Division establish partnerships with Office of Science stakeholders. It will also inform the Office of Science research needs and agenda. The results of the six reviews have been published in reports available on the web at http://exascaleage.org/. This report presents a summary of the individual reports and of common and crosscutting findings, and it identifies opportunities for productive collaborations among the DOE SC program offices.« less

High School Students Learning University Level Computer Science on the Web: A Case Study of the "DASK"-Model

ERIC Educational Resources Information Center

Grandell, Linda

2005-01-01

Computer science is becoming increasingly important in our society. Meta skills, such as problem solving and logical and algorithmic thinking, are emphasized in every field, not only in the natural sciences. Still, largely due to gaps in tuition, common misunderstandings exist about the true nature of computer science. These are especially…

Non-parallel processing: Gendered attrition in academic computer science

NASA Astrophysics Data System (ADS)

Cohoon, Joanne Louise Mcgrath

2000-10-01

This dissertation addresses the issue of disproportionate female attrition from computer science as an instance of gender segregation in higher education. By adopting a theoretical framework from organizational sociology, it demonstrates that the characteristics and processes of computer science departments strongly influence female retention. The empirical data identifies conditions under which women are retained in the computer science major at comparable rates to men. The research for this dissertation began with interviews of students, faculty, and chairpersons from five computer science departments. These exploratory interviews led to a survey of faculty and chairpersons at computer science and biology departments in Virginia. The data from these surveys are used in comparisons of the computer science and biology disciplines, and for statistical analyses that identify which departmental characteristics promote equal attrition for male and female undergraduates in computer science. This three-pronged methodological approach of interviews, discipline comparisons, and statistical analyses shows that departmental variation in gendered attrition rates can be explained largely by access to opportunity, relative numbers, and other characteristics of the learning environment. Using these concepts, this research identifies nine factors that affect the differential attrition of women from CS departments. These factors are: (1) The gender composition of enrolled students and faculty; (2) Faculty turnover; (3) Institutional support for the department; (4) Preferential attitudes toward female students; (5) Mentoring and supervising by faculty; (6) The local job market, starting salaries, and competitiveness of graduates; (7) Emphasis on teaching; and (8) Joint efforts for student success. This work contributes to our understanding of the gender segregation process in higher education. In addition, it contributes information that can lead to effective solutions for an economically significant issue in modern American society---gender equality in computer science.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

PubMed

Ionescu, Crina-Maria; Sehnal, David; Falginella, Francesco L; Pant, Purbaj; Pravda, Lukáš; Bouchal, Tomáš; Svobodová Vařeková, Radka; Geidl, Stanislav; Koča, Jaroslav

2015-01-01

Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.

Coherent manipulation of quantum spin states in a single molecular nanomagnet

NASA Astrophysics Data System (ADS)

Wernsdorfer, Wolfgang

The endeavour of quantum electronics is driven by one of the most ambitious technological goals of today's scientists: the realization of an operational quantum computer (http://qurope.eu). We started to address this goal by the new research field of molecular quantum spintronics. The building blocks are magnetic molecules, i.e. well-defined spin qubits. We will discuss this still largely unexplored field and present our first results: For example, using a molecular spin-transistor, we achieved the electronic read-out of the nuclear spin of an individual metal atom embedded in an SMM. We could show very long spin lifetimes (>10 s). Using the hyperfine Stark effect, which transforms electric fields into local effective magnetic fields, we could not only tune the resonance frequency by several MHz, but also perform coherent quantum manipulations on a single nuclear qubit faster than a μs by means of electrical fields only, establishing the individual addressability of identical nuclear qubits. Using three different microwave frequencies, we could implement a simple four-level Grover algorithm. S. Thiele, F. Balestro, R. Ballou, S. Klyatskaya, M. Ruben, W. Wernsdorfer, Science 344, 1135 (2014).

Report on Computing and Networking in the Space Science Laboratory by the SSL Computer Committee

NASA Technical Reports Server (NTRS)

Gallagher, D. L. (Editor)

1993-01-01

The Space Science Laboratory (SSL) at Marshall Space Flight Center is a multiprogram facility. Scientific research is conducted in four discipline areas: earth science and applications, solar-terrestrial physics, astrophysics, and microgravity science and applications. Representatives from each of these discipline areas participate in a Laboratory computer requirements committee, which developed this document. The purpose is to establish and discuss Laboratory objectives for computing and networking in support of science. The purpose is also to lay the foundation for a collective, multiprogram approach to providing these services. Special recognition is given to the importance of the national and international efforts of our research communities toward the development of interoperable, network-based computer applications.

A review of Computer Science resources for learning and teaching with K-12 computing curricula: an Australian case study

NASA Astrophysics Data System (ADS)

Falkner, Katrina; Vivian, Rebecca

2015-10-01

To support teachers to implement Computer Science curricula into classrooms from the very first year of school, teachers, schools and organisations seek quality curriculum resources to support implementation and teacher professional development. Until now, many Computer Science resources and outreach initiatives have targeted K-12 school-age children, with the intention to engage children and increase interest, rather than to formally teach concepts and skills. What is the educational quality of existing Computer Science resources and to what extent are they suitable for classroom learning and teaching? In this paper, an assessment framework is presented to evaluate the quality of online Computer Science resources. Further, a semi-systematic review of available online Computer Science resources was conducted to evaluate resources available for classroom learning and teaching and to identify gaps in resource availability, using the Australian curriculum as a case study analysis. The findings reveal a predominance of quality resources, however, a number of critical gaps were identified. This paper provides recommendations and guidance for the development of new and supplementary resources and future research.

Ambient belonging: how stereotypical cues impact gender participation in computer science.

PubMed

Cheryan, Sapna; Plaut, Victoria C; Davies, Paul G; Steele, Claude M

2009-12-01

People can make decisions to join a group based solely on exposure to that group's physical environment. Four studies demonstrate that the gender difference in interest in computer science is influenced by exposure to environments associated with computer scientists. In Study 1, simply changing the objects in a computer science classroom from those considered stereotypical of computer science (e.g., Star Trek poster, video games) to objects not considered stereotypical of computer science (e.g., nature poster, phone books) was sufficient to boost female undergraduates' interest in computer science to the level of their male peers. Further investigation revealed that the stereotypical broadcast a masculine stereotype that discouraged women's sense of ambient belonging and subsequent interest in the environment (Studies 2, 3, and 4) but had no similar effect on men (Studies 3, 4). This masculine stereotype prevented women's interest from developing even in environments entirely populated by other women (Study 2). Objects can thus come to broadcast stereotypes of a group, which in turn can deter people who do not identify with these stereotypes from joining that group.

Debunking the Computer Science Digital Library: Lessons Learned in Collection Development at Seneca College of Applied Arts & Technology

ERIC Educational Resources Information Center

Buczynski, James Andrew

2005-01-01

Developing a library collection to support the curriculum of Canada's largest computer studies school has debunked many myths about collecting computer science and technology information resources. Computer science students are among the heaviest print book and e-book users in the library. Circulation statistics indicate that the demand for print…

Snatching Defeat from the Jaws of Victory: When Good Projects Go Bad. Girls and Computer Science.

ERIC Educational Resources Information Center

Sanders, Jo

In week-long semesters in the summers of 1997, 1998, and 1999, the 6APT (Summer Institute in Computer Science for Advanced Placement Teachers) project taught 240 high school teachers of Advanced Placement Computer Science (APCS) about gender equity in computers. Teachers were then followed through 2000. Results indicated that while teachers, did…

77 FR 12823 - Advanced Scientific Computing Advisory Committee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-02

... Exascale ARRA projects--Magellan final report, Advanced Networking update Status from Computer Science COV Early Career technical talks Summary of Applied Math and Computer Science Workshops ASCR's new SBIR..., Office of Science. ACTION: Notice of Open Meeting. SUMMARY: This notice announces a meeting of the...

75 FR 18407 - Investing in Innovation Fund

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-12

... include computer science rather than science. To correct this error, the Department makes the following..., in footnote number eight, in line six, ``including science'' is replaced with ``including computer... obtain this document in an accessible format (e.g., Braille, large print, audiotape, or computer diskette...

Innovative Science Experiments Using Phoenix

ERIC Educational Resources Information Center

Kumar, B. P. Ajith; Satyanarayana, V. V. V.; Singh, Kundan; Singh, Parmanand

2009-01-01

A simple, flexible and very low cost hardware plus software framework for developing computer-interfaced science experiments is presented. It can be used for developing computer-interfaced science experiments without getting into the details of electronics or computer programming. For developing experiments this is a middle path between…

The Metamorphosis of an Introduction to Computer Science.

ERIC Educational Resources Information Center

Ben-Jacob, Marion G.

1997-01-01

Introductory courses in computer science at colleges and universities have undergone significant changes in 20 years. This article provides an overview of the history of introductory computer science (FORTRAN, ANSI flowchart symbols, BASIC, data processing concepts, and PASCAL) and its future (robotics and C++). (PEN)

All Roads Lead to Computing: Making, Participatory Simulations, and Social Computing as Pathways to Computer Science

ERIC Educational Resources Information Center

Brady, Corey; Orton, Kai; Weintrop, David; Anton, Gabriella; Rodriguez, Sebastian; Wilensky, Uri

2017-01-01

Computer science (CS) is becoming an increasingly diverse domain. This paper reports on an initiative designed to introduce underrepresented populations to computing using an eclectic, multifaceted approach. As part of a yearlong computing course, students engage in Maker activities, participatory simulations, and computing projects that…

Frames of scientific evidence: How journalists represent the (un)certainty of molecular medicine in science television programs.

PubMed

Ruhrmann, Georg; Guenther, Lars; Kessler, Sabrina Heike; Milde, Jutta

2015-08-01

For laypeople, media coverage of science on television is a gateway to scientific issues. Defining scientific evidence is central to the field of science, but there are still questions if news coverage of science represents scientific research findings as certain or uncertain. The framing approach is a suitable framework to classify different media representations; it is applied here to investigate the frames of scientific evidence in film clips (n=207) taken from science television programs. Molecular medicine is the domain of interest for this analysis, due to its high proportion of uncertain and conflicting research findings and risks. The results indicate that television clips vary in their coverage of scientific evidence of molecular medicine. Four frames were found: Scientific Uncertainty and Controversy, Scientifically Certain Data, Everyday Medical Risks, and Conflicting Scientific Evidence. They differ in their way of framing scientific evidence and risks of molecular medicine. © The Author(s) 2013.

After-Hours Science: Microchips and Onion Dip.

ERIC Educational Resources Information Center

Brugger, Steve

1984-01-01

Computer programs were developed for a science center nutrition exhibit. The exhibit was recognized by the National Science Teachers Association Search for Excellence in Science Education as an outstanding science program. The computer programs (Apple II) and their use in the exhibit are described. (BC)

Computational design of protein interactions: designing proteins that neutralize influenza by inhibiting its hemagglutinin surface protein

NASA Astrophysics Data System (ADS)

Fleishman, Sarel

2012-02-01

Molecular recognition underlies all life processes. Design of interactions not seen in nature is a test of our understanding of molecular recognition and could unlock the vast potential of subtle control over molecular interaction networks, allowing the design of novel diagnostics and therapeutics for basic and applied research. We developed the first general method for designing protein interactions. The method starts by computing a region of high affinity interactions between dismembered amino acid residues and the target surface and then identifying proteins that can harbor these residues. Designs are tested experimentally for binding the target surface and successful ones are affinity matured using yeast cell surface display. Applied to the conserved stem region of influenza hemagglutinin we designed two unrelated proteins that, following affinity maturation, bound hemagglutinin at subnanomolar dissociation constants. Co-crystal structures of hemagglutinin bound to the two designed binders were within 1Angstrom RMSd of their models, validating the accuracy of the design strategy. One of the designed proteins inhibits the conformational changes that underlie hemagglutinin's cell-invasion functions and blocks virus infectivity in cell culture, suggesting that such proteins may in future serve as diagnostics and antivirals against a wide range of pathogenic influenza strains. We have used this method to obtain experimentally validated binders of several other target proteins, demonstrating the generality of the approach. We discuss the combination of modeling and high-throughput characterization of design variants which has been key to the success of this approach, as well as how we have used the data obtained in this project to enhance our understanding of molecular recognition. References: Science 332:816 JMB, in press Protein Sci 20:753

Computing Education in Korea--Current Issues and Endeavors

ERIC Educational Resources Information Center

Choi, Jeongwon; An, Sangjin; Lee, Youngjun

2015-01-01

Computer education has been provided for a long period of time in Korea. Starting as a vocational program, the content of computer education for students evolved to include content on computer literacy, Information Communication Technology (ICT) literacy, and brand-new computer science. While a new curriculum related to computer science was…

75 FR 18492 - Investing in Innovation Fund; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-12

... those disciplines, we intended to include computer science rather than science. To correct this error... ``including computer science.'' Program Authority: Section 14007 of division A of the American Recovery and....g., braille, large print, audiotape, or computer diskette) on request to the contact listed in this...

Process-Based Development of Competence Models to Computer Science Education

ERIC Educational Resources Information Center

Zendler, Andreas; Seitz, Cornelia; Klaudt, Dieter

2016-01-01

A process model ("cpm.4.CSE") is introduced that allows the development of competence models in computer science education related to curricular requirements. It includes eight subprocesses: (a) determine competence concept, (b) determine competence areas, (c) identify computer science concepts, (d) assign competence dimensions to…

The Role of Physicality in Rich Programming Environments

ERIC Educational Resources Information Center

Liu, Allison S.; Schunn, Christian D.; Flot, Jesse; Shoop, Robin

2013-01-01

Computer science proficiency continues to grow in importance, while the number of students entering computer science-related fields declines. Many rich programming environments have been created to motivate student interest and expertise in computer science. In the current study, we investigated whether a recently created environment, Robot…

Studies in Mathematics, Volume 22. Studies in Computer Science.

ERIC Educational Resources Information Center

Pollack, Seymour V., Ed.

The nine articles in this collection were selected because they represent concerns central to computer science, emphasize topics of particular interest to mathematicians, and underscore the wide range of areas deeply and continually affected by computer science. The contents consist of: "Introduction" (S. V. Pollack), "The…