Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.

Science.gov (United States)

Heald, Emerson F.

1978-01-01

Presents a computer method for teaching chemical equilibrium concepts using material balance conditions and the minimization of the free energy. Method for the calculation of chemical equilibrium, the computer program used to solve equilibrium problems and applications of the method are also included. (HM)

Rapid computation of chemical equilibrium composition - An application to hydrocarbon combustion

Science.gov (United States)

Erickson, W. D.; Prabhu, R. K.

1986-01-01

A scheme for rapidly computing the chemical equilibrium composition of hydrocarbon combustion products is derived. A set of ten governing equations is reduced to a single equation that is solved by the Newton iteration method. Computation speeds are approximately 80 times faster than the often used free-energy minimization method. The general approach also has application to many other chemical systems.

Molecular computing: paths to chemical Turing machines.

Science.gov (United States)

Varghese, Shaji; Elemans, Johannes A A W; Rowan, Alan E; Nolte, Roeland J M

2015-11-13

To comply with the rapidly increasing demand of information storage and processing, new strategies for computing are needed. The idea of molecular computing, where basic computations occur through molecular, supramolecular, or biomolecular approaches, rather than electronically, has long captivated researchers. The prospects of using molecules and (bio)macromolecules for computing is not without precedent. Nature is replete with examples where the handling and storing of data occurs with high efficiencies, low energy costs, and high-density information encoding. The design and assembly of computers that function according to the universal approaches of computing, such as those in a Turing machine, might be realized in a chemical way in the future; this is both fascinating and extremely challenging. In this perspective, we highlight molecular and (bio)macromolecular systems that have been designed and synthesized so far with the objective of using them for computing purposes. We also present a blueprint of a molecular Turing machine, which is based on a catalytic device that glides along a polymer tape and, while moving, prints binary information on this tape in the form of oxygen atoms.

Introduction to computational mass transfer with applications to chemical engineering

CERN Document Server

Yu, Kuo-Tsong

2014-01-01

This book presents a new computational methodology called Computational Mass Transfer (CMT). It offers an approach to rigorously simulating the mass, heat and momentum transfer under turbulent flow conditions with the help of two newly published models, namely the C’2—εC’ model and the Reynolds  mass flux model, especially with regard to predictions of concentration, temperature and velocity distributions in chemical and related processes. The book will also allow readers to understand the interfacial phenomena accompanying the mass transfer process and methods for modeling the interfacial effect, such as the influences of Marangoni convection and Rayleigh convection. The CMT methodology is demonstrated by means of its applications to typical separation and chemical reaction processes and equipment, including distillation, absorption, adsorption and chemical reactors. Professor Kuo-Tsong Yu is a Member of the Chinese Academy of Sciences. Dr. Xigang Yuan is a Professor at the School of Chemical Engine...

Foreign Language Translation of Chemical Nomenclature by Computer

Science.gov (United States)

2009-01-01

Chemical compound names remain the primary method for conveying molecular structures between chemists and researchers. In research articles, patents, chemical catalogues, government legislation, and textbooks, the use of IUPAC and traditional compound names is universal, despite efforts to introduce more machine-friendly representations such as identifiers and line notations. Fortunately, advances in computing power now allow chemical names to be parsed and generated (read and written) with almost the same ease as conventional connection tables. A significant complication, however, is that although the vast majority of chemistry uses English nomenclature, a significant fraction is in other languages. This complicates the task of filing and analyzing chemical patents, purchasing from compound vendors, and text mining research articles or Web pages. We describe some issues with manipulating chemical names in various languages, including British, American, German, Japanese, Chinese, Spanish, Swedish, Polish, and Hungarian, and describe the current state-of-the-art in software tools to simplify the process. PMID:19239237

Computer-Aided Multiscale Modelling for Chemical Process Engineering

DEFF Research Database (Denmark)

Morales Rodriguez, Ricardo; Gani, Rafiqul

2007-01-01

Chemical processes are generally modeled through monoscale approaches, which, while not adequate, satisfy a useful role in product-process design. In this case, use of a multi-dimensional and multi-scale model-based approach has importance in product-process development. A computer-aided framework...

In silico toxicology: computational methods for the prediction of chemical toxicity

KAUST Repository

Raies, Arwa B.; Bajic, Vladimir B.

2016-01-01

Determining the toxicity of chemicals is necessary to identify their harmful effects on humans, animals, plants, or the environment. It is also one of the main steps in drug design. Animal models have been used for a long time for toxicity testing. However, in vivo animal tests are constrained by time, ethical considerations, and financial burden. Therefore, computational methods for estimating the toxicity of chemicals are considered useful. In silico toxicology is one type of toxicity assessment that uses computational methods to analyze, simulate, visualize, or predict the toxicity of chemicals. In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design. There are various methods for generating models to predict toxicity endpoints. We provide a comprehensive overview, explain, and compare the strengths and weaknesses of the existing modeling methods and algorithms for toxicity prediction with a particular (but not exclusive) emphasis on computational tools that can implement these methods and refer to expert systems that deploy the prediction models. Finally, we briefly review a number of new research directions in in silico toxicology and provide recommendations for designing in silico models.

In silico toxicology: computational methods for the prediction of chemical toxicity

KAUST Repository

Raies, Arwa B.

2016-01-06

Determining the toxicity of chemicals is necessary to identify their harmful effects on humans, animals, plants, or the environment. It is also one of the main steps in drug design. Animal models have been used for a long time for toxicity testing. However, in vivo animal tests are constrained by time, ethical considerations, and financial burden. Therefore, computational methods for estimating the toxicity of chemicals are considered useful. In silico toxicology is one type of toxicity assessment that uses computational methods to analyze, simulate, visualize, or predict the toxicity of chemicals. In silico toxicology aims to complement existing toxicity tests to predict toxicity, prioritize chemicals, guide toxicity tests, and minimize late-stage failures in drugs design. There are various methods for generating models to predict toxicity endpoints. We provide a comprehensive overview, explain, and compare the strengths and weaknesses of the existing modeling methods and algorithms for toxicity prediction with a particular (but not exclusive) emphasis on computational tools that can implement these methods and refer to expert systems that deploy the prediction models. Finally, we briefly review a number of new research directions in in silico toxicology and provide recommendations for designing in silico models.

A computational environment for creating and testing reduced chemical kinetic mechanisms

Energy Technology Data Exchange (ETDEWEB)

Montgomery, C.J.; Swensen, D.A.; Harding, T.V.; Cremer, M.A.; Bockelie, M.J. [Reaction Engineering International, Salt Lake City, UT (USA)

2002-02-01

This paper describes software called computer assisted reduced mechanism problem solving environment (CARM-PSE) that gives the engineer the ability to rapidly set up, run and examine large numbers of problems comparing detailed and reduced (approximate) chemistry. CARM-PSE integrates the automatic chemical mechanism reduction code CARM and the codes that simulate perfectly stirred reactors and plug flow reactors into a user-friendly computational environment. CARM-PSE gives the combustion engineer the ability to easily test chemical approximations over many hundreds of combinations of inputs in a multidimensional parameter space. The demonstration problems compare detailed and reduced chemical kinetic calculations for methane-air combustion, including nitrogen oxide formation, in a stirred reactor and selective non-catalytic reduction of NOx, in coal combustion flue gas.

Computer-Aided Construction of Chemical Kinetic Models

Energy Technology Data Exchange (ETDEWEB)

Green, William H. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

2014-12-31

The combustion chemistry of even simple fuels can be extremely complex, involving hundreds or thousands of kinetically significant species. The most reasonable way to deal with this complexity is to use a computer not only to numerically solve the kinetic model, but also to construct the kinetic model in the first place. Because these large models contain so many numerical parameters (e.g. rate coefficients, thermochemistry) one never has sufficient data to uniquely determine them all experimentally. Instead one must work in “predictive” mode, using theoretical rather than experimental values for many of the numbers in the model, and as appropriate refining the most sensitive numbers through experiments. Predictive chemical kinetics is exactly what is needed for computer-aided design of combustion systems based on proposed alternative fuels, particularly for early assessment of the value and viability of proposed new fuels before those fuels are commercially available. This project was aimed at making accurate predictive chemical kinetics practical; this is a challenging goal which requires a range of science advances. The project spanned a wide range from quantum chemical calculations on individual molecules and elementary-step reactions, through the development of improved rate/thermo calculation procedures, the creation of algorithms and software for constructing and solving kinetic simulations, the invention of methods for model-reduction while maintaining error control, and finally comparisons with experiment. Many of the parameters in the models were derived from quantum chemistry calculations, and the models were compared with experimental data measured in our lab or in collaboration with others.

Computational singular perturbation analysis of stochastic chemical systems with stiffness

Science.gov (United States)

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; Najm, Habib N.

2017-04-01

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to not only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. The algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.

A computer investigation of chemically mediated detachment in bacterial biofilms.

Science.gov (United States)

Hunt, Stephen M; Hamilton, Martin A; Sears, John T; Harkin, Gary; Reno, Jason

2003-05-01

A three-dimensional computer model was used to evaluate the effect of chemically mediated detachment on biofilm development in a negligible-shear environment. The model, BacLAB, combines conventional diffusion-reaction equations for chemicals with a cellular automata algorithm to simulate bacterial growth, movement and detachment. BacLAB simulates the life cycle of a bacterial biofilm from its initial colonization of a surface to the development of a mature biofilm with cell areal densities comparable to those in the laboratory. A base model founded on well established transport equations that are easily adaptable to investigate conjectures at the biological level has been created. In this study, the conjecture of a detachment mechanism involving a bacterially produced chemical detachment factor in which high local concentrations of this detachment factor cause the bacteria to detach from the biofilm was examined. The results show that the often observed 'mushroom'-shaped structure can occur if detachment events create voids so that the remaining attached cells look like mushrooms.

A rapid method for the computation of equilibrium chemical composition of air to 15000 K

Science.gov (United States)

Prabhu, Ramadas K.; Erickson, Wayne D.

1988-01-01

A rapid computational method has been developed to determine the chemical composition of equilibrium air to 15000 K. Eleven chemically reacting species, i.e., O2, N2, O, NO, N, NO+, e-, N+, O+, Ar, and Ar+ are included. The method involves combining algebraically seven nonlinear equilibrium equations and four linear elemental mass balance and charge neutrality equations. Computational speeds for determining the equilibrium chemical composition are significantly faster than the often used free energy minimization procedure. Data are also included from which the thermodynamic properties of air can be computed. A listing of the computer program together with a set of sample results are included.

Computer integrated manufacturing in the chemical industry : Theory & practice

NARCIS (Netherlands)

Ashayeri, J.; Teelen, A.; Selen, W.J.

1995-01-01

This paper addresses the possibilities of implementing Computer Integrated Manufacturing in the process industry, and the chemical industry in particular. After presenting some distinct differences of the process industry in relation to discrete manufacturing, a number of focal points are discussed.

Computational thermal, chemical, fluid, and solid mechanics for geosystems management.

Energy Technology Data Exchange (ETDEWEB)

Davison, Scott; Alger, Nicholas; Turner, Daniel Zack; Subia, Samuel Ramirez; Carnes, Brian; Martinez, Mario J.; Notz, Patrick K.; Klise, Katherine A.; Stone, Charles Michael; Field, Richard V., Jr.; Newell, Pania; Jove-Colon, Carlos F.; Red-Horse, John Robert; Bishop, Joseph E.; Dewers, Thomas A.; Hopkins, Polly L.; Mesh, Mikhail; Bean, James E.; Moffat, Harry K.; Yoon, Hongkyu

2011-09-01

This document summarizes research performed under the SNL LDRD entitled - Computational Mechanics for Geosystems Management to Support the Energy and Natural Resources Mission. The main accomplishment was development of a foundational SNL capability for computational thermal, chemical, fluid, and solid mechanics analysis of geosystems. The code was developed within the SNL Sierra software system. This report summarizes the capabilities of the simulation code and the supporting research and development conducted under this LDRD. The main goal of this project was the development of a foundational capability for coupled thermal, hydrological, mechanical, chemical (THMC) simulation of heterogeneous geosystems utilizing massively parallel processing. To solve these complex issues, this project integrated research in numerical mathematics and algorithms for chemically reactive multiphase systems with computer science research in adaptive coupled solution control and framework architecture. This report summarizes and demonstrates the capabilities that were developed together with the supporting research underlying the models. Key accomplishments are: (1) General capability for modeling nonisothermal, multiphase, multicomponent flow in heterogeneous porous geologic materials; (2) General capability to model multiphase reactive transport of species in heterogeneous porous media; (3) Constitutive models for describing real, general geomaterials under multiphase conditions utilizing laboratory data; (4) General capability to couple nonisothermal reactive flow with geomechanics (THMC); (5) Phase behavior thermodynamics for the CO2-H2O-NaCl system. General implementation enables modeling of other fluid mixtures. Adaptive look-up tables enable thermodynamic capability to other simulators; (6) Capability for statistical modeling of heterogeneity in geologic materials; and (7) Simulator utilizes unstructured grids on parallel processing computers.

An integrated computer aided system for integrated design of chemical processes

DEFF Research Database (Denmark)

Gani, Rafiqul; Hytoft, Glen; Jaksland, Cecilia

1997-01-01

In this paper, an Integrated Computer Aided System (ICAS), which is particularly suitable for solving problems related to integrated design of chemical processes; is presented. ICAS features include a model generator (generation of problem specific models including model simplification and model ...... form the basis for the toolboxes. The available features of ICAS are highlighted through a case study involving the separation of binary azeotropic mixtures. (C) 1997 Elsevier Science Ltd....

Some Matrix Iterations for Computing Generalized Inverses and Balancing Chemical Equations

Directory of Open Access Journals (Sweden)

Farahnaz Soleimani

2015-11-01

Full Text Available An application of iterative methods for computing the Moore–Penrose inverse in balancing chemical equations is considered. With the aim to illustrate proposed algorithms, an improved high order hyper-power matrix iterative method for computing generalized inverses is introduced and applied. The improvements of the hyper-power iterative scheme are based on its proper factorization, as well as on the possibility to accelerate the iterations in the initial phase of the convergence. Although the effectiveness of our approach is confirmed on the basis of the theoretical point of view, some numerical comparisons in balancing chemical equations, as well as on randomly-generated matrices are furnished.

Novel scheme to compute chemical potentials of chain molecules on a lattice

Science.gov (United States)

Mooij, G. C. A. M.; Frenkel, D.

We present a novel method that allows efficient computation of the total number of allowed conformations of a chain molecule in a dense phase. Using this method, it is possible to estimate the chemical potential of such a chain molecule. We have tested the present method in simulations of a two-dimensional monolayer of chain molecules on a lattice (Whittington-Chapman model) and compared it with existing schemes to compute the chemical potential. We find that the present approach is two to three orders of magnitude faster than the most efficient of the existing methods.

Quantum chemical studies of estrogenic compounds

Science.gov (United States)

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

Computational chemical imaging for cardiovascular pathology: chemical microscopic imaging accurately determines cardiac transplant rejection.

Directory of Open Access Journals (Sweden)

Saumya Tiwari

Full Text Available Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients' biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures.

Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

Science.gov (United States)

Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

Computational Analyses of Complex Flows with Chemical Reactions

Science.gov (United States)

Bae, Kang-Sik

The heat and mass transfer phenomena in micro-scale for the mass transfer phenomena on drug in cylindrical matrix system, the simulation of oxygen/drug diffusion in a three dimensional capillary network, and a reduced chemical kinetic modeling of gas turbine combustion for Jet propellant-10 have been studied numerically. For the numerical analysis of the mass transfer phenomena on drug in cylindrical matrix system, the governing equations are derived from the cylindrical matrix systems, Krogh cylinder model, which modeling system is comprised of a capillary to a surrounding cylinder tissue along with the arterial distance to veins. ADI (Alternative Direction Implicit) scheme and Thomas algorithm are applied to solve the nonlinear partial differential equations (PDEs). This study shows that the important factors which have an effect on the drug penetration depth to the tissue are the mass diffusivity and the consumption of relevant species during the time allowed for diffusion to the brain tissue. Also, a computational fluid dynamics (CFD) model has been developed to simulate the blood flow and oxygen/drug diffusion in a three dimensional capillary network, which are satisfied in the physiological range of a typical capillary. A three dimensional geometry has been constructed to replicate the one studied by Secomb et al. (2000), and the computational framework features a non-Newtonian viscosity model for blood, the oxygen transport model including in oxygen-hemoglobin dissociation and wall flux due to tissue absorption, as well as an ability to study the diffusion of drugs and other materials in the capillary streams. Finally, a chemical kinetic mechanism of JP-10 has been compiled and validated for a wide range of combustion regimes, covering pressures of 1atm to 40atm with temperature ranges of 1,200 K--1,700 K, which is being studied as a possible Jet propellant for the Pulse Detonation Engine (PDE) and other high-speed flight applications such as hypersonic

Tailor-made Design of Chemical Blends using Decomposition-based Computer-aided Approach

DEFF Research Database (Denmark)

Yunus, Nor Alafiza; Manan, Zainuddin Abd.; Gernaey, Krist

(properties). In this way, first the systematic computer-aided technique establishes the search space, and then narrows it down in subsequent steps until a small number of feasible and promising candidates remain and then experimental work may be conducted to verify if any or all the candidates satisfy......Computer aided technique is an efficient approach to solve chemical product design problems such as design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product attributes...... is decomposed into two stages. The first stage investigates the mixture stability where all unstable mixtures are eliminated and the stable blend candidates are retained for further testing. In the second stage, the blend candidates have to satisfy a set of target properties that are ranked according...

Performance predictions for solar-chemical convertors by computer simulation

Energy Technology Data Exchange (ETDEWEB)

Luttmer, J.D.; Trachtenberg, I.

1985-08-01

A computer model which simulates the operation of Texas Instruments solar-chemical convertor (SCC) was developed. The model allows optimization of SCC processes, material, and configuration by facilitating decisions on tradeoffs among ease of manufacturing, power conversion efficiency, and cost effectiveness. The model includes various algorithms which define the electrical, electrochemical, and resistance parameters and which describ the operation of the discrete components of the SCC. Results of the model which depict the effect of material and geometric changes on various parameters are presented. The computer-calculated operation is compared with experimentall observed hydrobromic acid electrolysis rates.

Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions

Science.gov (United States)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such observables as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method with the Dunning correlation consistent basis sets to obtain accurate energetics, gives useful results for a number of chemically important systems. Applications to complex reactions leading to NO and soot formation in hydrocarbon combustion are discussed.

Pushing the frontiers of first-principles based computer simulations of chemical and biological systems.

Science.gov (United States)

Brunk, Elizabeth; Ashari, Negar; Athri, Prashanth; Campomanes, Pablo; de Carvalho, F Franco; Curchod, Basile F E; Diamantis, Polydefkis; Doemer, Manuel; Garrec, Julian; Laktionov, Andrey; Micciarelli, Marco; Neri, Marilisa; Palermo, Giulia; Penfold, Thomas J; Vanni, Stefano; Tavernelli, Ivano; Rothlisberger, Ursula

2011-01-01

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these methods to larger systems, longer time scales and increased accuracies. Their versatility is illustrated with a diverse range of applications, ranging from the determination of the gas phase structure of the cyclic decapeptide gramicidin S, to the study of G protein coupled receptors, the interaction of transition metal based anti-cancer agents with protein targets, the mechanism of action of DNA repair enzymes, the role of metal ions in neurodegenerative diseases and the computational design of dye-sensitized solar cells. Many of these projects are done in collaboration with experimental groups from the Institute of Chemical Sciences and Engineering (ISIC) at the EPFL.

Computer program determines chemical composition of physical system at equilibrium

Science.gov (United States)

Kwong, S. S.

1966-01-01

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

Some Matrix Iterations for Computing Generalized Inverses and Balancing Chemical Equations

OpenAIRE

Soleimani, Farahnaz; Stanimirovi´c, Predrag; Soleymani, Fazlollah

2015-01-01

An application of iterative methods for computing the Moore–Penrose inverse in balancing chemical equations is considered. With the aim to illustrate proposed algorithms, an improved high order hyper-power matrix iterative method for computing generalized inverses is introduced and applied. The improvements of the hyper-power iterative scheme are based on its proper factorization, as well as on the possibility to accelerate the iterations in the initial phase of the convergence. Although the ...

Computational Chemical Synthesis Analysis and Pathway Design

Directory of Open Access Journals (Sweden)

Fan Feng

2018-06-01

Full Text Available With the idea of retrosynthetic analysis, which was raised in the 1960s, chemical synthesis analysis and pathway design have been transformed from a complex problem to a regular process of structural simplification. This review aims to summarize the developments of computer-assisted synthetic analysis and design in recent years, and how machine-learning algorithms contributed to them. LHASA system started the pioneering work of designing semi-empirical reaction modes in computers, with its following rule-based and network-searching work not only expanding the databases, but also building new approaches to indicating reaction rules. Programs like ARChem Route Designer replaced hand-coded reaction modes with automatically-extracted rules, and programs like Chematica changed traditional designing into network searching. Afterward, with the help of machine learning, two-step models which combine reaction rules and statistical methods became the main stream. Recently, fully data-driven learning methods using deep neural networks which even do not require any prior knowledge, were applied into this field. Up to now, however, these methods still cannot replace experienced human organic chemists due to their relatively low accuracies. Future new algorithms with the aid of powerful computational hardware will make this topic promising and with good prospects.

RICE: a computer program for multicomponent chemically reactive flows at all speeds

International Nuclear Information System (INIS)

Rivard, W.C.; Farmer, O.A.; Butler, T.D.

1974-11-01

The fluid dynamics of chemically reactive mixtures are calculated at arbitrary flow speeds with the RICE program. The dynamics are governed by the two-dimensional, time-dependent Navier-Stokes equations together with the species transport equations and the mass-action rate equations for the chemical reactions. The mass and momentum equations for the mixture are solved implicitly by the ICE technique. The equations for total energy and species transport are solved explicitly while the chemical rate equations are solved implicitly with a time step that may be a submultiple of the hydrodynamic time step. Application is made to continuous wave HF chemical lasers to compute the supersonic mixing and chemical reactions that take place in the lasing cavity. (U.S.)

Computational Methods to Assess the Production Potential of Bio-Based Chemicals

DEFF Research Database (Denmark)

Campodonico, Miguel A; Sukumara, Sumesh; Feist, Adam M.

2018-01-01

are described in detail. The first tool is GEM-Path: an algorithm to compute all structurally possible pathways from one target molecule to the host metabolome. The second tool is a framework for Modeling Sustainable Industrial Chemicals production (MuSIC), which integrates modeling approaches for cellular...... metabolism, bioreactor design, upstream/downstream processes, and economic impact assessment. Integrating GEM-Path and MuSIC will play a vital role in supporting early phases of research efforts and guide the policy makers with decisions, as we progress toward planning a sustainable chemical industry....

Incorporating Computer-Aided Software in the Undergraduate Chemical Engineering Core Courses

Science.gov (United States)

Alnaizy, Raafat; Abdel-Jabbar, Nabil; Ibrahim, Taleb H.; Husseini, Ghaleb A.

2014-01-01

Introductions of computer-aided software and simulators are implemented during the sophomore-year of the chemical engineering (ChE) curriculum at the American University of Sharjah (AUS). Our faculty concurs that software integration within the curriculum is beneficial to our students, as evidenced by the positive feedback received from industry…

Evaluating amber force fields using computed NMR chemical shifts.

Science.gov (United States)

Koes, David R; Vries, John K

2017-10-01

NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

Computer Aided Methods & Tools for Separation & Purification of Fine Chemical & Pharmaceutical Products

DEFF Research Database (Denmark)

Afonso, Maria B.C.; Soni, Vipasha; Mitkowski, Piotr Tomasz

2006-01-01

An integrated approach that is particularly suitable for solving problems related to product-process design from the fine chemicals, agrochemicals, food and pharmaceutical industries is presented together with the corresponding methods and tools, which forms the basis for an integrated computer...

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

Science.gov (United States)

Das, A K; Meuwly, M

2016-01-01

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed. © 2016 Elsevier Inc. All rights reserved.

Design of tailor-made chemical blend using a decomposition-based computer-aided approach

DEFF Research Database (Denmark)

Yunus, Nor Alafiza; Gernaey, Krist; Manan, Z.A.

2011-01-01

Computer aided techniques form an efficient approach to solve chemical product design problems such as the design of blended liquid products (chemical blending). In chemical blending, one tries to find the best candidate, which satisfies the product targets defined in terms of desired product...... methodology for blended liquid products that identifies a set of feasible chemical blends. The blend design problem is formulated as a Mixed Integer Nonlinear Programming (MINLP) model where the objective is to find the optimal blended gasoline or diesel product subject to types of chemicals...... and their compositions and a set of desired target properties of the blended product as design constraints. This blend design problem is solved using a decomposition approach, which eliminates infeasible and/or redundant candidates gradually through a hierarchy of (property) model based constraints. This decomposition...

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

Science.gov (United States)

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

2015-02-11

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

AMDTreat 5.0+ with PHREEQC titration module to compute caustic chemical quantity, effluent quality, and sludge volume

Science.gov (United States)

Cravotta, Charles A.; Means, Brent P; Arthur, Willam; McKenzie, Robert M; Parkhurst, David L.

2015-01-01

Alkaline chemicals are commonly added to discharges from coal mines to increase pH and decrease concentrations of acidity and dissolved aluminum, iron, manganese, and associated metals. The annual cost of chemical treatment depends on the type and quantities of chemicals added and sludge produced. The AMDTreat computer program, initially developed in 2003, is widely used to compute such costs on the basis of the user-specified flow rate and water quality data for the untreated AMD. Although AMDTreat can use results of empirical titration of net-acidic or net-alkaline effluent with caustic chemicals to accurately estimate costs for treatment, such empirical data are rarely available. A titration simulation module using the geochemical program PHREEQC has been incorporated with AMDTreat 5.0+ to improve the capability of AMDTreat to estimate: (1) the quantity and cost of caustic chemicals to attain a target pH, (2) the chemical composition of the treated effluent, and (3) the volume of sludge produced by the treatment. The simulated titration results for selected caustic chemicals (NaOH, CaO, Ca(OH)2, Na2CO3, or NH3) without aeration or with pre-aeration can be compared with or used in place of empirical titration data to estimate chemical quantities, treated effluent composition, sludge volume (precipitated metals plus unreacted chemical), and associated treatment costs. This paper describes the development, evaluation, and potential utilization of the PHREEQC titration module with the new AMDTreat 5.0+ computer program available at http://www.amd.osmre.gov/.

Combined use of computational chemistry and chemoinformatics methods for chemical discovery

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, Manabu, E-mail: sugimoto@kumamoto-u.ac.jp [Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555 (Japan); Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585 (Japan); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Ideo, Toshihiro; Iwane, Ryo [Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555 (Japan)

2015-12-31

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

Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

2010-09-15

To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

Science.gov (United States)

Egan, C. K.; Jacques, S. D. M.; Wilson, M. D.; Veale, M. C.; Seller, P.; Beale, A. M.; Pattrick, R. A. D.; Withers, P. J.; Cernik, R. J.

2015-01-01

We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography. PMID:26514938

Computed Tomography Imaging findings in Chemical Warfare Victims with pulmonary Complications

Directory of Open Access Journals (Sweden)

Zahra Salehinezhad

2013-05-01

Full Text Available Introduction: Data on imaging findings in pulmonary complications of chemical agents is scarce. The current study aimed to evaluate radiological findings of late onset pulmonary complications in chemical warfare victims (CWV and to guide pulmonologists in diagnosis of these subjects. Materials and Methods: Ninety- three male CWV were enrolled in this prospective study, 20-25 years (mean=23 after exposure. Demographic and clinical data were recorded. High resolution computed Tomography (HRCT of the lung was performed during inspiration and expiration and was double reported blindly by two radiologists. Final diagnosis was made according to HRCT findings. The HRCT findings, final diagnosis, and distribution of the abnormalities were compared between subjects whom had been exposed to more complex chemical agents used during the second half of the war and simpler agents during the first half. Results: The most frequent HRCT findings were air trapping (56.7% and mosaic attenuation (35.1%. The distribution of abnormalities was mostly local (79.4% and bilateral (73% especially in lower regions (61.3%. The diagnosed respiratory diseases included bronchiolitis obliterans (43%, chronic obstructive pulmonary disease (COPD (27.9%, asthma (23.6%, bronchiectasis (13.9% and interstitial lung disease (ILD (9.6%. Frequency of subjects involved in the second half of the period of war was more than the first period (P-value < 0.05 but the HRCT findings were similar. Conclusions: Bronchiolitis obliterans with picture of focal bilateral air trapping was the most common finding in CWV but asthma appeared to have become a new problem in these subjects.

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

Directory of Open Access Journals (Sweden)

Phadungsukanan Weerapong

2012-08-01

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

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

Science.gov (United States)

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

2012-08-07

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

Computer program for calculation of complex chemical equilibrium compositions and applications. Part 1: Analysis

Science.gov (United States)

Gordon, Sanford; Mcbride, Bonnie J.

1994-01-01

This report presents the latest in a number of versions of chemical equilibrium and applications programs developed at the NASA Lewis Research Center over more than 40 years. These programs have changed over the years to include additional features and improved calculation techniques and to take advantage of constantly improving computer capabilities. The minimization-of-free-energy approach to chemical equilibrium calculations has been used in all versions of the program since 1967. The two principal purposes of this report are presented in two parts. The first purpose, which is accomplished here in part 1, is to present in detail a number of topics of general interest in complex equilibrium calculations. These topics include mathematical analyses and techniques for obtaining chemical equilibrium; formulas for obtaining thermodynamic and transport mixture properties and thermodynamic derivatives; criteria for inclusion of condensed phases; calculations at a triple point; inclusion of ionized species; and various applications, such as constant-pressure or constant-volume combustion, rocket performance based on either a finite- or infinite-chamber-area model, shock wave calculations, and Chapman-Jouguet detonations. The second purpose of this report, to facilitate the use of the computer code, is accomplished in part 2, entitled 'Users Manual and Program Description'. Various aspects of the computer code are discussed, and a number of examples are given to illustrate its versatility.

An implicit multigrid algorithm for computing hypersonic, chemically reacting viscous flows

International Nuclear Information System (INIS)

Edwards, J.R.

1996-01-01

An implicit algorithm for computing viscous flows in chemical nonequilibrium is presented. Emphasis is placed on the numerical efficiency of the time integration scheme, both in terms of periteration workload and overall convergence rate. In this context, several techniques are introduced, including a stable, O(m 2 ) approximate factorization of the chemical source Jacobian and implementations of V-cycle and filtered multigrid acceleration methods. A five species-seventeen reaction air model is used to calculate hypersonic viscous flow over a cylinder at conditions corresponding to flight at 5 km/s, 60 km altitude and at 11.36 km/s, 76.42 km altitude. Inviscid calculations using an eleven-species reaction mechanism including ionization are presented for a case involving 11.37 km/s flow at an altitude of 84.6 km. Comparisons among various options for the implicit treatment of the chemical source terms and among different multilevel approaches for convergence acceleration are presented for all simulations

Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

Walch, Stephen P.; Langhoff, S. R. (Technical Monitor)

1994-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. For some dynamics methods, global potential energy surfaces are required. In this case, it is necessary to obtain the energy at a complete sampling of all the possible arrangements of the nuclei, which are energetically accessible, and then a fitting function must be obtained to interpolate between the computed points. In other cases, characterization of the stationary points and the reaction pathway connecting them is sufficient. These properties may be readily obtained using analytical derivative methods. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives usefull results for a number of chemically important systems. The talk will focus on a number of applications including global potential energy surfaces, H + O2, H + N2, O(3p) + H2, and reaction pathways for complex reactions, including reactions leading to NO and soot formation in hydrocarbon combustion.

Computing multi-species chemical equilibrium with an algorithm based on the reaction extents

DEFF Research Database (Denmark)

Paz-Garcia, Juan Manuel; Johannesson, Björn; Ottosen, Lisbeth M.

2013-01-01

-negative constrains. The residual function, representing the distance to the equilibrium, is defined from the chemical potential (or Gibbs energy) of the chemical system. Local minimums are potentially avoided by the prioritization of the aqueous reactions with respect to the heterogeneous reactions. The formation......A mathematical model for the solution of a set of chemical equilibrium equations in a multi-species and multiphase chemical system is described. The computer-aid solution of model is achieved by means of a Newton-Raphson method enhanced with a line-search scheme, which deals with the non...... and release of gas bubbles is taken into account in the model, limiting the concentration of volatile aqueous species to a maximum value, given by the gas solubility constant.The reaction extents are used as state variables for the numerical method. As a result, the accepted solution satisfies the charge...

Computational Systems Chemical Biology

OpenAIRE

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

Ultrastructural Analysis of Urinary Stones by Microfocus Computed Tomography and Comparison with Chemical Analysis

Directory of Open Access Journals (Sweden)

Tolga Karakan

2016-06-01

Full Text Available Objective: To investigate the ultra-structure of urinary system stones using micro-focus computed tomography (MCT, which makes non-destructive analysis and to compare with wet chemical analysis. Methods: This study was carried out at the Ankara Train­ing and Research hospital. Renal stones, removed from 30 patients during percutaneous nephrolithotomy (PNL surgery, were included in the study. The stones were blindly evaluated by the specialists with MCT and chemi­cal analysis. Results: The comparison of the stone components be­tween chemical analysis and MCT, showed that the rate of consistence was very low (p0.05. It was also seen that there was no significant relation between its 3D structure being heterogeneous or homogenous. Conclusion: The stone analysis with MCT is a time con­suming and costly method. This method is useful to un­derstand the mechanisms of stone formation and an im­portant guide to develop the future treatment modalities.

A survey of process control computers at the Idaho Chemical Processing Plant

International Nuclear Information System (INIS)

Dahl, C.A.

1989-01-01

The Idaho Chemical Processing Plant (ICPP) at the Idaho National Engineering Laboratory is charged with the safe processing of spent nuclear fuel elements for the United States Department of Energy. The ICPP was originally constructed in the late 1950s and used state-of-the-art technology for process control at that time. The state of process control instrumentation at the ICPP has steadily improved to keep pace with emerging technology. Today, the ICPP is a college of emerging computer technology in process control with some systems as simple as standalone measurement computers while others are state-of-the-art distributed control systems controlling the operations in an entire facility within the plant. The ICPP has made maximal use of process computer technology aimed at increasing surety, safety, and efficiency of the process operations. Many benefits have been derived from the use of the computers for minimal costs, including decreased misoperations in the facility, and more benefits are expected in the future

Plant exposure chambers for study of toxic chemical-plant interactions (journal version)

International Nuclear Information System (INIS)

McFarlane, J.C.; Pfleeger, T.

1987-01-01

Chambers for the study of plant uptake and phytotoxicity of toxic, radio-labeled chemicals are described. The chambers are designed to meet the criteria of continuously stirred tank reactors while providing containment for toxic chemicals. They are computer managed and operated within a controlled-environment room. Besides providing controlled conditions within the contained spaces, continuous measurements are made of various environmental parameters and plant transpiration, net photosynthesis, and dark respiration in up to 18 separate chambers

Progress report on SYVAC chemical speciation modelling studies during 1983/4

International Nuclear Information System (INIS)

Cross, J.; Smith, G.L.; Williams, D.R.

1984-01-01

This report summarises progress made on the SYVAC (System Variability Analysis program) chemical speciation project during 1983-4. Chemical speciation is defined and its importance in the SYVAC approach to Radioactive Waste Management is discussed. Computer modelling of chemical equilibria is described and the two programs presently operational at UWIST - SOLMNQ and MINEQL - are compared and discussed in detail. In view of the shortcomings of the databases supplied with these programs, a new database of equilibrium constants has been compiled containing 483 aqueous species and 329 solid phases, including data for the radionuclides uranium, plutonium, americium, neptunium and thorium. The collaborative work with AERE, Harwell, is reported. A leaching experiment carried out at Harwell has been modelled using the chemical speciation programs. The results for uranium, plutonium, americium and neptunium, are presented. However, the experimental data provided by AERE is insufficient for accurate simulations. Chemical speciation studies relating to specific sites require accurate characterisation of the groundwater, i.e. chemical composition, Eh and pH. In the absence of such information, preliminary studies have been made using an average granite groundwater. The results of these studies are presented and include solubility and speciation plots for uranium, plutonium, thorium and neptunium. The future aims of the project are discussed. (author)

Gas-Phase Molecular Dynamics: Theoretical Studies in Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu, H.G.; Muckerman, J.T.

2010-06-01

The goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods.

SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery.

Directory of Open Access Journals (Sweden)

Paul A Novick

Full Text Available In the face of drastically rising drug discovery costs, strategies promising to reduce development timelines and expenditures are being pursued. Computer-aided virtual screening and repurposing approved drugs are two such strategies that have shown recent success. Herein, we report the creation of a highly-curated in silico database of chemical structures representing approved drugs, chemical isolates from traditional medicinal herbs, and regulated chemicals, termed the SWEETLEAD database. The motivation for SWEETLEAD stems from the observance of conflicting information in publicly available chemical databases and the lack of a highly curated database of chemical structures for the globally approved drugs. A consensus building scheme surveying information from several publicly accessible databases was employed to identify the correct structure for each chemical. Resulting structures are filtered for the active pharmaceutical ingredient, standardized, and differing formulations of the same drug were combined in the final database. The publically available release of SWEETLEAD (https://simtk.org/home/sweetlead provides an important tool to enable the successful completion of computer-aided repurposing and drug discovery campaigns.

Oxygen-vacancy defects on BaTiO3 (001) surface: a quantum chemical study

International Nuclear Information System (INIS)

Duque, Carlos; Stashans, Arvids

2003-01-01

A quantum-chemical study of technologically important BaTiO 3 crystal and oxygen-vacancy defects on its (001) surface is reported in the present work. The computations are made using a quantum-chemical method developed for periodic systems (crystals), which is based on the Hartree-Fock theory. The atomic rearrangement due to the surface creation is obtained for a pure BaTiO 3 by means of the periodic large unit cell (LUC) model and using an automated geometry optimisation procedure. The same technique is employed to study the electronic and structural properties of the material due to the presence of an O vacancy and F centre (two electrons trapped in an oxygen vacancy). The computations are carried out for both cubic and tetragonal lattices

Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

Science.gov (United States)

Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

2015-01-01

An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

Text-mining strategies to support computational research in chemical toxicity (ACS 2017 Spring meeting)

Science.gov (United States)

With 26 million citations, PubMed is one of the largest sources of information about the activity of chemicals in biological systems. Because this information is expressed in natural language and not stored as data, using the biomedical literature directly in computational resear...

Exploring Natural Products from the Biodiversity of Pakistan for Computational Drug Discovery Studies: Collection, Optimization, Design and Development of A Chemical Database (ChemDP).

Science.gov (United States)

Mirza, Shaher Bano; Bokhari, Habib; Fatmi, Muhammad Qaiser

2015-01-01

Pakistan possesses a rich and vast source of natural products (NPs). Some of these secondary metabolites have been identified as potent therapeutic agents. However, the medicinal usage of most of these compounds has not yet been fully explored. The discoveries for new scaffolds of NPs as inhibitors of certain enzymes or receptors using advanced computational drug discovery approaches are also limited due to the unavailability of accurate 3D structures of NPs. An organized database incorporating all relevant information, therefore, can facilitate to explore the medicinal importance of the metabolites from Pakistani Biodiversity. The Chemical Database of Pakistan (ChemDP; release 01) is a fully-referenced, evolving, web-based, virtual database which has been designed and developed to introduce natural products (NPs) and their derivatives from the biodiversity of Pakistan to Global scientific communities. The prime aim is to provide quality structures of compounds with relevant information for computer-aided drug discovery studies. For this purpose, over 1000 NPs have been identified from more than 400 published articles, for which 2D and 3D molecular structures have been generated with a special focus on their stereochemistry, where applicable. The PM7 semiempirical quantum chemistry method has been used to energy optimize the 3D structure of NPs. The 2D and 3D structures can be downloaded as .sdf, .mol, .sybyl, .mol2, and .pdb files - readable formats by many chemoinformatics/bioinformatics software packages. Each entry in ChemDP contains over 100 data fields representing various molecular, biological, physico-chemical and pharmacological properties, which have been properly documented in the database for end users. These pieces of information have been either manually extracted from the literatures or computationally calculated using various computational tools. Cross referencing to a major data repository i.e. ChemSpider has been made available for overlapping

Chemical Industry Bandwidth Study

Energy Technology Data Exchange (ETDEWEB)

none,

2006-12-01

The Chemical Bandwidth Study provides a snapshot of potentially recoverable energy losses during chemical manufacturing. The advantage of this study is the use of "exergy" analysis as a tool for pinpointing inefficiencies.

Computer tool to evaluate the cue reactivity of chemically dependent individuals.

Science.gov (United States)

Silva, Meire Luci da; Frère, Annie France; Oliveira, Henrique Jesus Quintino de; Martucci Neto, Helio; Scardovelli, Terigi Augusto

2017-03-01

Anxiety is one of the major influences on the dropout of relapse and treatment of substance abuse treatment. Chemically dependent individuals need (CDI) to be aware of their emotional state in situations of risk during their treatment. Many patients do not agree with the diagnosis of the therapist when considering them vulnerable to environmental stimuli related to drugs. This research presents a cue reactivity detection tool based on a device acquiring physiological signals connected to personal computer. Depending on the variations of the emotional state of the drug addict, alteration of the physiological signals will be detected by the computer tool (CT) which will modify the displayed virtual sets without intervention of the therapist. Developed in 3ds Max® software, the CT is composed of scenarios and objects that are in the habit of marijuana and cocaine dependent individual's daily life. The interaction with the environment is accomplished using a Human-Computer Interface (HCI) that converts incoming physiological signals indicating anxiety state into commands that change the scenes. Anxiety was characterized by the average variability from cardiac and respiratory rate of 30 volunteers submitted stress environment situations. To evaluate the effectiveness of cue reactivity a total of 50 volunteers who were marijuana, cocaine or both dependent were accompanied. Prior to CT, the results demonstrated a poor correlation between the therapists' predictions and those of the chemically dependent individuals. After exposure to the CT, there was a significant increase of 73% in awareness of the risks of relapse. We confirmed the hypothesis that the CT, controlled only by physiological signals, increases the perception of vulnerability to risk situations of individuals with dependence on marijuana, cocaine or both. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Investigation of Spark Ignition and Autoignition in Methane and Air Using Computational Fluid Dynamics and Chemical Reaction Kinetics. A numerical Study of Ignition Processes in Internal Combustion Engines

Energy Technology Data Exchange (ETDEWEB)

Nordrik, R.

1993-12-01

The processes in the combustion chamber of internal combustion engines have received increased attention in recent years because their efficiencies are important both economically and environmentally. This doctoral thesis studies the ignition phenomena by means of numerical simulation methods. The fundamental physical relations include flow field conservation equations, thermodynamics, chemical reaction kinetics, transport properties and spark modelling. Special attention is given to the inclusion of chemical kinetics in the flow field equations. Using his No Transport of Radicals Concept method, the author reduces the computational efforts by neglecting the transport of selected intermediate species. The method is validated by comparison with flame propagation data. A computational method is described and used to simulate spark ignition in laminar premixed methane-air mixtures and the autoignition process of a methane bubble surrounded by hot air. The spark ignition simulation agrees well with experimental results from the literature. The autoignition simulation identifies the importance of diffusive and chemical processes acting together. The ignition delay times exceed the experimental values found in the literature for premixed ignition delay, presumably because of the mixing process and lack of information on low temperature reactions in the skeletal kinetic mechanism. Transient turbulent methane jet autoignition is simulated by means of the KIVA-II code. Turbulent combustion is modelled by the Eddy Dissipation Concept. 90 refs., 81 figs., 3 tabs.

Computational Modeling | Bioenergy | NREL

Science.gov (United States)

cell walls and are the source of biofuels and biomaterials. Our modeling investigates their properties . Quantum Mechanical Models NREL studies chemical and electronic properties and processes to reduce barriers Computational Modeling Computational Modeling NREL uses computational modeling to increase the

Isolation, characterization, spectroscopic properties and quantum chemical computations of an important phytoalexin resveratrol as antioxidant component from Vitis labrusca L. and their chemical compositions

Science.gov (United States)

Güder, Aytaç; Korkmaz, Halil; Gökce, Halil; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

2014-12-01

In this study, isolation and characterization of trans-resveratrol (RES) as an antioxidant compound were carried out from VLE, VLG and VLS. Furthermore, antioxidant activities were evaluated by using six different methods. Finally, total phenolic, flavonoid, ascorbic acid, anthocyanin, lycopene, β-carotene and vitamin E contents were carried out. In addition, the FT-IR, 13C and 1H NMR chemical shifts and UV-vis. spectra of trans-resveratrol were experimentally recorded. Quantum chemical computations such as the molecular geometry, vibrational frequencies, UV-vis. spectroscopic parameters, HOMOs-LUMOs energies, molecular electrostatic potential (MEP), natural bond orbitals (NBO) and nonlinear optics (NLO) properties of title molecule have been calculated by using DFT/B3PW91 method with 6-311++G(d,p) basis set in ground state for the first time. The obtained results show that the calculated spectroscopic data are in a good agreement with experimental data.

Use of computer-assisted prediction of toxic effects of chemical substances

International Nuclear Information System (INIS)

Simon-Hettich, Brigitte; Rothfuss, Andreas; Steger-Hartmann, Thomas

2006-01-01

The current revision of the European policy for the evaluation of chemicals (REACH) has lead to a controversy with regard to the need of additional animal safety testing. To avoid increases in animal testing but also to save time and resources, alternative in silico or in vitro tests for the assessment of toxic effects of chemicals are advocated. The draft of the original document issued in 29th October 2003 by the European Commission foresees the use of alternative methods but does not give further specification on which methods should be used. Computer-assisted prediction models, so-called predictive tools, besides in vitro models, will likely play an essential role in the proposed repertoire of 'alternative methods'. The current discussion has urged the Advisory Committee of the German Toxicology Society to present its position on the use of predictive tools in toxicology. Acceptable prediction models already exist for those toxicological endpoints which are based on well-understood mechanism, such as mutagenicity and skin sensitization, whereas mechanistically more complex endpoints such as acute, chronic or organ toxicities currently cannot be satisfactorily predicted. A potential strategy to assess such complex toxicities will lie in their dissection into models for the different steps or pathways leading to the final endpoint. Integration of these models should result in a higher predictivity. Despite these limitations, computer-assisted prediction tools already today play a complementary role for the assessment of chemicals for which no data is available or for which toxicological testing is impractical due to the lack of availability of sufficient compounds for testing. Furthermore, predictive tools offer support in the screening and the subsequent prioritization of compound for further toxicological testing, as expected within the scope of the European REACH program. This program will also lead to the collection of high-quality data which will broaden the

Computing Properties Of Chemical Mixtures At Equilibrium

Science.gov (United States)

Mcbride, B. J.; Gordon, S.

1995-01-01

Scientists and engineers need data on chemical equilibrium compositions to calculate theoretical thermodynamic properties of chemical systems. Information essential in design and analysis of such equipment as compressors, turbines, nozzles, engines, shock tubes, heat exchangers, and chemical-processing equipment. CET93 is general program that calculates chemical equilibrium compositions and properties of mixtures for any chemical system for which thermodynamic data are available. Includes thermodynamic data for more than 1,300 gaseous and condensed species and thermal-transport data for 151 gases. Written in FORTRAN 77.

Aligator: A computational tool for optimizing total chemical synthesis of large proteins.

Science.gov (United States)

Jacobsen, Michael T; Erickson, Patrick W; Kay, Michael S

2017-09-15

The scope of chemical protein synthesis (CPS) continues to expand, driven primarily by advances in chemical ligation tools (e.g., reversible solubilizing groups and novel ligation chemistries). However, the design of an optimal synthesis route can be an arduous and fickle task due to the large number of theoretically possible, and in many cases problematic, synthetic strategies. In this perspective, we highlight recent CPS tool advances and then introduce a new and easy-to-use program, Aligator (Automated Ligator), for analyzing and designing the most efficient strategies for constructing large targets using CPS. As a model set, we selected the E. coli ribosomal proteins and associated factors for computational analysis. Aligator systematically scores and ranks all feasible synthetic strategies for a particular CPS target. The Aligator script methodically evaluates potential peptide segments for a target using a scoring function that includes solubility, ligation site quality, segment lengths, and number of ligations to provide a ranked list of potential synthetic strategies. We demonstrate the utility of Aligator by analyzing three recent CPS projects from our lab: TNFα (157 aa), GroES (97 aa), and DapA (312 aa). As the limits of CPS are extended, we expect that computational tools will play an increasingly important role in the efficient execution of ambitious CPS projects such as production of a mirror-image ribosome. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computer-Aided Chemical Product Design Framework: Design of High Performance and Environmentally Friendly Refrigerants

DEFF Research Database (Denmark)

Cignitti, Stefano; Zhang, Lei; Gani, Rafiqul

properties and needs should carefully be selected for a given heat pump cycle to ensure that an optimum refrigerant is found? How can cycle performance and environmental criteria be integrated at the product design stage and not in post-design analysis? Computer-aided product design methods enable...... the possibility of designing novel molecules, mixtures and blends, such as refrigerants through a systematic framework (Cignitti et al., 2015; Yunus et al., 2014). In this presentation a computer-aided framework is presented for chemical product design through mathematical optimization. Here, molecules, mixtures...... and blends, are systematically designed through a decomposition based solution method. Given a problem definition, computer-aided molecular design (CAMD) problem is defined, which is formulated into a mixed integer nonlinear program (MINLP). The decomposed solution method then sequentially divides the MINLP...

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

Science.gov (United States)

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

2000-01-01

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

Asymmetric energy flow in liquid alkylbenzenes: A computational study

International Nuclear Information System (INIS)

Leitner, David M.; Pandey, Hari Datt

2015-01-01

Ultrafast IR-Raman experiments on substituted benzenes [B. C. Pein et al., J. Phys. Chem. B 117, 10898–10904 (2013)] reveal that energy can flow more efficiently in one direction along a molecule than in others. We carry out a computational study of energy flow in the three alkyl benzenes, toluene, isopropylbenzene, and t-butylbenzene, studied in these experiments, and find an asymmetry in the flow of vibrational energy between the two chemical groups of the molecule due to quantum mechanical vibrational relaxation bottlenecks, which give rise to a preferred direction of energy flow. We compare energy flow computed for all modes of the three alkylbenzenes over the relaxation time into the liquid with energy flow through the subset of modes monitored in the time-resolved Raman experiments and find qualitatively similar results when using the subset compared to all the modes

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

Science.gov (United States)

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

Gas-Phase Molecular Dynamics: Theoretical Studies In Spectroscopy and Chemical Dynamics

Energy Technology Data Exchange (ETDEWEB)

Yu H. G.; Muckerman, J.T.

2012-05-29

The main goal of this program is the development and application of computational methods for studying chemical reaction dynamics and molecular spectroscopy in the gas phase. We are interested in developing rigorous quantum dynamics algorithms for small polyatomic systems and in implementing approximate approaches for complex ones. Particular focus is on the dynamics and kinetics of chemical reactions and on the rovibrational spectra of species involved in combustion processes. This research also explores the potential energy surfaces of these systems of interest using state-of-the-art quantum chemistry methods, and extends them to understand some important properties of materials in condensed phases and interstellar medium as well as in combustion environments.

A NEW TOOL FOR THE STUDY OF RESONANCE IN CHEMICAL EDUCATION

Directory of Open Access Journals (Sweden)

Francisco Torrens

2014-03-01

Full Text Available The objective of this study is to present a computer-based project, for which our program POLAR and our version of PAPID were written for the study of the subject of resonance in chemistry. Both algorithms allow a better didactic strategy and methodological adaptation for the study of molecular properties in chemical education. Teachers will find the options of POLAR and PAPID useful for demonstrations. It is still to be explored the methodological application of these computational programs enriching the present teaching techniques. Implementing new algorithms in learning situations is technically simple, but checking their usefulness in teaching practice is extraordinarily complex and requires a research that has hardly begun. The topic of resonance in chemistry represents an opportunity for the integration of teaching and research into the European Space for Higher Education.

Experimental research on the contrast production of the chemical elements with the atomic numbers 1-83 in a computer-totalbody-tomogram

International Nuclear Information System (INIS)

Kirschner, H.; Burmester, U.; Stringaris, K.

1979-01-01

The contrast production for the chemical elements with the atomic numbers Z=1-83 were determined by computer-tomography. With the formula relation of the Δ-number and the atomic number can one compute the contrast production of any chosen chemical compound. Iodine-free and inorganic iodine-containing contrast media are examined for their contrast production and compared with presently used organic iodine-containing contrast media. The contrast enhancement of organic contrast media in tissue are discussed. (orig.) [de

In-cylinder diesel spray combustion simulations using parallel computation: A performance benchmarking study

International Nuclear Information System (INIS)

Pang, Kar Mun; Ng, Hoon Kiat; Gan, Suyin

2012-01-01

Highlights: ► A performance benchmarking exercise is conducted for diesel combustion simulations. ► The reduced chemical mechanism shows its advantages over base and skeletal models. ► High efficiency and great reduction of CPU runtime are achieved through 4-node solver. ► Increasing ISAT memory from 0.1 to 2 GB reduces the CPU runtime by almost 35%. ► Combustion and soot processes are predicted well with minimal computational cost. - Abstract: In the present study, in-cylinder diesel combustion simulation was performed with parallel processing on an Intel Xeon Quad-Core platform to allow both fluid dynamics and chemical kinetics of the surrogate diesel fuel model to be solved simultaneously on multiple processors. Here, Cartesian Z-Coordinate was selected as the most appropriate partitioning algorithm since it computationally bisects the domain such that the dynamic load associated with fuel particle tracking was evenly distributed during parallel computations. Other variables examined included number of compute nodes, chemistry sizes and in situ adaptive tabulation (ISAT) parameters. Based on the performance benchmarking test conducted, parallel configuration of 4-compute node was found to reduce the computational runtime most efficiently whereby a parallel efficiency of up to 75.4% was achieved. The simulation results also indicated that accuracy level was insensitive to the number of partitions or the partitioning algorithms. The effect of reducing the number of species on computational runtime was observed to be more significant than reducing the number of reactions. Besides, the study showed that an increase in the ISAT maximum storage of up to 2 GB reduced the computational runtime by 50%. Also, the ISAT error tolerance of 10 −3 was chosen to strike a balance between results accuracy and computational runtime. The optimised parameters in parallel processing and ISAT, as well as the use of the in-house reduced chemistry model allowed accurate

How computational methods and relativistic effects influence the study of chemical reactions involving Ru-NO complexes?

Science.gov (United States)

Orenha, Renato Pereira; Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade; Galembeck, Sérgio Emanuel

2017-05-05

Two treatments of relativistic effects, namely effective core potentials (ECP) and all-electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2-TZVP calculations. Specifically, the reaction energies of reduction (A-F), isomerization (G-I), and Cl - negative trans influence in relation to NH 3 (J-L) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A-L. From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC-wPBE, and CCSD(T) (reference method). For reactions A-I, B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J-L. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Experimental and computational development of a natural breast phantom for dosimetry studies

International Nuclear Information System (INIS)

Nogueira, Luciana B.; Campos, Tarcisio P.R.

2013-01-01

This paper describes the experimental and computational development of a natural breast phantom, anthropomorphic and anthropometric for studies in dosimetry of brachytherapy and teletherapy of breast. The natural breast phantom developed corresponding to fibroadipose breasts of women aged 30 to 50 years, presenting radiographically medium density. The experimental breast phantom was constituted of three tissue-equivalents (TE's): glandular TE, adipose TE and skin TE. These TE's were developed according to chemical composition of human breast and present radiological response to exposure. Completed the construction of experimental breast phantom this was mounted on a thorax phantom previously developed by the research group NRI/UFMG. Then the computational breast phantom was constructed by performing a computed tomography (CT) by axial slices of the chest phantom. Through the images generated by CT a computational model of voxels of the thorax phantom was developed by SISCODES computational program, being the computational breast phantom represented by the same TE's of the experimental breast phantom. The images generated by CT allowed evaluating the radiological equivalence of the tissues. The breast phantom is being used in studies of experimental dosimetry both in brachytherapy as in teletherapy of breast. Dosimetry studies by MCNP-5 code using the computational model of the phantom breast are in progress. (author)

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

Science.gov (United States)

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.

Computer Controlled Chemical Micro-Reactor

International Nuclear Information System (INIS)

Mechtilde, Schaefer; Eduard, Stach; Adreas, Foitzik

2006-01-01

Chemical reactions or chemical equilibria can be influenced and controlled by several parameters. The ratio of two liquid ingredients, the so called reactants or educts, plays an important role in determining the end product and its yield. The reactants must be weighed and accordingly mixed with the conventional batch mode. If the reaction is done in a microreactor or in several parallel working micro-reactors, units for allotting the educts in appropriate quantities are required. In this report we present a novel micro-reactor that allows the constant monitoring of the chemical reaction via Raman spectroscopy. Such monitoring enables an appropriate feedback on the steering parameters for the PC controlled micro-pumps for the appropriate educt flow rate of both liquids to get optimised ratios of ingredients at an optimised total flow rate. The micro-reactors are the core pieces of the design and are easily removable and can therefore be changed at any time to adapt the requirements of the chemical reaction. One type of reactor consists of a stainless steel base containing small scale milled channels covered with anodically bonded Pyrex glass. Another type of reactor has a base of anisotropically etched silicon, and is also covered with anodically bonded Pyrex glass. The glass window allows visual observation of the initial phase interface of the two educts in the reaction channels by optical microscopy and does not affect, in contrast to infrared spectroscopy, the Raman spectroscopic signal for detection of the reaction kinetics. On the basis of a test reaction, we present non-invasive and spatially highly resolved in-situ reaction analysis using Raman spectroscopy measured along the reaction channel at different locations

A computational methodology for formulating gasoline surrogate fuels with accurate physical and chemical kinetic properties

KAUST Repository

Ahmed, Ahfaz

2015-03-01

Gasoline is the most widely used fuel for light duty automobile transportation, but its molecular complexity makes it intractable to experimentally and computationally study the fundamental combustion properties. Therefore, surrogate fuels with a simpler molecular composition that represent real fuel behavior in one or more aspects are needed to enable repeatable experimental and computational combustion investigations. This study presents a novel computational methodology for formulating surrogates for FACE (fuels for advanced combustion engines) gasolines A and C by combining regression modeling with physical and chemical kinetics simulations. The computational methodology integrates simulation tools executed across different software platforms. Initially, the palette of surrogate species and carbon types for the target fuels were determined from a detailed hydrocarbon analysis (DHA). A regression algorithm implemented in MATLAB was linked to REFPROP for simulation of distillation curves and calculation of physical properties of surrogate compositions. The MATLAB code generates a surrogate composition at each iteration, which is then used to automatically generate CHEMKIN input files that are submitted to homogeneous batch reactor simulations for prediction of research octane number (RON). The regression algorithm determines the optimal surrogate composition to match the fuel properties of FACE A and C gasoline, specifically hydrogen/carbon (H/C) ratio, density, distillation characteristics, carbon types, and RON. The optimal surrogate fuel compositions obtained using the present computational approach was compared to the real fuel properties, as well as with surrogate compositions available in the literature. Experiments were conducted within a Cooperative Fuels Research (CFR) engine operating under controlled autoignition (CAI) mode to compare the formulated surrogates against the real fuels. Carbon monoxide measurements indicated that the proposed surrogates

Studies in Chemical Dynamics

International Nuclear Information System (INIS)

Rabitz, Herschel; Ho, Tak-San

2003-01-01

This final report draws together the research carried from February, 1986 through January, 2003 concerning a series of topics in chemical dynamics. The specific areas of study include molecular collisions, chemical kinetics, data inversion to extract potential energy surfaces, and model reduction of complex kinetic systems

What can we learn by computing 13Cα chemical shifts for X-ray protein models?

International Nuclear Information System (INIS)

Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

2009-01-01

The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

Exploiting the Complementarity between Dereplication and Computer-Assisted Structure Elucidation for the Chemical Profiling of Natural Cosmetic Ingredients: Tephrosia purpurea as a Case Study.

Science.gov (United States)

Hubert, Jane; Chollet, Sébastien; Purson, Sylvain; Reynaud, Romain; Harakat, Dominique; Martinez, Agathe; Nuzillard, Jean-Marc; Renault, Jean-Hugues

2015-07-24

The aqueous-ethanolic extract of Tephrosia purpurea seeds is currently exploited in the cosmetic industry as a natural ingredient of skin lotions. The aim of this study was to chemically characterize this ingredient by combining centrifugal partition extraction (CPE) as a fractionation tool with two complementary identification approaches involving dereplication and computer-assisted structure elucidation. Following two rapid fractionations of the crude extract (2 g), seven major compounds namely, caffeic acid, quercetin-3-O-rutinoside, ethyl galactoside, ciceritol, stachyose, saccharose, and citric acid, were unambiguously identified within the CPE-generated simplified mixtures by a recently developed (13)C NMR-based dereplication method. The structures of four additional compounds, patuletin-3-O-rutinoside, kaempferol-3-O-rutinoside, guaiacylglycerol 8-vanillic acid ether, and 2-methyl-2-glucopyranosyloxypropanoic acid, were automatically elucidated by using the Logic for Structure Determination program based on the interpretation of 2D NMR (HSQC, HMBC, and COSY) connectivity data. As more than 80% of the crude extract mass was characterized without need for tedious and labor-intensive multistep purification procedures, the identification tools involved in this work constitute a promising strategy for an efficient and time-saving chemical profiling of natural extracts.

Computer program to solve two-dimensional shock-wave interference problems with an equilibrium chemically reacting air model

Science.gov (United States)

Glass, Christopher E.

1990-08-01

The computer program EASI, an acronym for Equilibrium Air Shock Interference, was developed to calculate the inviscid flowfield, the maximum surface pressure, and the maximum heat flux produced by six shock wave interference patterns on a 2-D, cylindrical configuration. Thermodynamic properties of the inviscid flowfield are determined using either an 11-specie, 7-reaction equilibrium chemically reacting air model or a calorically perfect air model. The inviscid flowfield is solved using the integral form of the conservation equations. Surface heating calculations at the impingement point for the equilibrium chemically reacting air model use variable transport properties and specific heat. However, for the calorically perfect air model, heating rate calculations use a constant Prandtl number. Sample calculations of the six shock wave interference patterns, a listing of the computer program, and flowcharts of the programming logic are included.

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

Science.gov (United States)

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

2014-01-14

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

Interaction of anthraquinone anti-cancer drugs with DNA:Experimental and computational quantum chemical study

Science.gov (United States)

Al-Otaibi, Jamelah S.; Teesdale Spittle, Paul; El Gogary, Tarek M.

2017-01-01

Anthraquinones form the basis of several anticancer drugs. Anthraquinones anticancer drugs carry out their cytotoxic activities through their interaction with DNA, and inhibition of topoisomerase II activity. Anthraquinones (AQ4 and AQ4H) were synthesized and studied along with 1,4-DAAQ by computational and experimental tools. The purpose of this study is to shade more light on mechanism of interaction between anthraquinone DNA affinic agents and different types of DNA. This study will lead to gain of information useful for drug design and development. Molecular structures were optimized using DFT B3LYP/6-31 + G(d). Depending on intramolecular hydrogen bonding interactions two conformers of AQ4 were detected and computed as 25.667 kcal/mol apart. Molecular reactivity of the anthraquinone compounds was explored using global and condensed descriptors (electrophilicity and Fukui functions). Molecular docking studies for the inhibition of CDK2 and DNA binding were carried out to explore the anti cancer potency of these drugs. NMR and UV-VIS electronic absorption spectra of anthraquinones/DNA were investigated at the physiological pH. The interaction of the three anthraquinones (AQ4, AQ4H and 1,4-DAAQ) were studied with three DNA (calf thymus DNA, (Poly[dA].Poly[dT]) and (Poly[dG].Poly[dC]). NMR study shows a qualitative pattern of drug/DNA interaction in terms of band shift and broadening. UV-VIS electronic absorption spectra were employed to measure the affinity constants of drug/DNA binding using Scatchard analysis.

Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

Energy Technology Data Exchange (ETDEWEB)

Paul, Bijan Kumar [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India); Guchhait, Nikhil, E-mail: nikhil.guchhait@rediffmail.com [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India)

2012-07-25

Highlights: Black-Right-Pointing-Pointer Experimental and computational studies on the photophysics of 4-chlorosalicylic acid. Black-Right-Pointing-Pointer Spectroscopically established ESIPT reaction substantiated by theoretical calculation. Black-Right-Pointing-Pointer Quantum chemical treatment of IMHB unveils strength, nature and directional nature. Black-Right-Pointing-Pointer Superiority of quantum chemical treatment of H-bond over geometric criteria. Black-Right-Pointing-Pointer Role of H-bond as a modulator of aromaticity. -- Abstract: The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S{sub 1}-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

Combustion of hydrogen-air jets in local chemical equilibrium: A guide to the CHARNAL computer program

Science.gov (United States)

Spalding, D. B.; Launder, B. E.; Morse, A. P.; Maples, G.

1974-01-01

A guide to a computer program, written in FORTRAN 4, for predicting the flow properties of turbulent mixing with combustion of a circular jet of hydrogen into a co-flowing stream of air is presented. The program, which is based upon the Imperial College group's PASSA series, solves differential equations for diffusion and dissipation of turbulent kinetic energy and also of the R.M.S. fluctuation of hydrogen concentration. The effective turbulent viscosity for use in the shear stress equation is computed. Chemical equilibrium is assumed throughout the flow.

An integrated multi-label classifier with chemical-chemical interactions for prediction of chemical toxicity effects.

Science.gov (United States)

Liu, Tao; Chen, Lei; Pan, Xiaoyong

2018-05-31

Chemical toxicity effect is one of the major reasons for declining candidate drugs. Detecting the toxicity effects of all chemicals can accelerate the procedures of drug discovery. However, it is time-consuming and expensive to identify the toxicity effects of a given chemical through traditional experiments. Designing quick, reliable and non-animal-involved computational methods is an alternative way. In this study, a novel integrated multi-label classifier was proposed. First, based on five types of chemical-chemical interactions retrieved from STITCH, each of which is derived from one aspect of chemicals, five individual classifiers were built. Then, several integrated classifiers were built by integrating some or all individual classifiers. By testing the integrated classifiers on a dataset with chemicals and their toxicity effects in Accelrys Toxicity database and non-toxic chemicals with their performance evaluated by jackknife test, an optimal integrated classifier was selected as the proposed classifier, which provided quite high prediction accuracies and wide applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

Science.gov (United States)

Wu, Xin; Koslowski, Axel; Thiel, Walter

2012-07-10

In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

Computational studies of free radical-scavenging properties of phenolic compounds.

Science.gov (United States)

Alov, Petko; Tsakovska, Ivanka; Pajeva, Ilza

2015-01-01

For more than half a century free radical-induced alterations at cellular and organ levels have been investigated as a probable underlying mechanism of a number of adverse health conditions. Consequently, significant research efforts have been spent for discovering more effective and potent antioxidants / free radical scavengers for treatment of these adverse conditions. Being by far the most used antioxidants among natural and synthetic compounds, mono- and polyphenols have been the focus of both experimental and computational research on mechanisms of free radical scavenging. Quantum chemical studies have provided a significant amount of data on mechanisms of reactions between phenolic compounds and free radicals outlining a number of properties with a key role for the radical scavenging activity and capacity of phenolics. The obtained quantum chemical parameters together with other molecular descriptors have been used in quantitative structure-activity relationship (QSAR) analyses for the design of new more effective phenolic antioxidants and for identification of the most useful natural antioxidant phenolics. This review aims at presenting the state of the art in quantum chemical and QSAR studies of phenolic antioxidants and at analysing the trends observed in the field in the last decade.

Chemical Product Design

DEFF Research Database (Denmark)

Gani, Rafiqul

2004-01-01

This paper highlights for a class of chemical products, the design process, their design with respect to the important issues, the need for appropriate tools and finally, lists some of the challenges and opportunities for the process systems engineering (PSE)/computer-aided process engineering...... (CAPE) community. The chemical products considered belong to the following types: chemical/biochemical/agrochemical products, coatings and solvents, food (nutraceuticals), HIM (household, industrial and institutional), personal care, pharmaceuticals and drugs. The challenges and opportunities...... are highlighted in terms of the needs for multi-level modeling with emphasis on property models that are suitable for computer-aided applications, flexible solution strategies that are able to solve a large range of chemical product design problems and finally, a systems chemical product design framework...

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

Science.gov (United States)

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

Computational toxicology as implemented by the U.S. EPA: providing high throughput decision support tools for screening and assessing chemical exposure, hazard and risk.

Science.gov (United States)

Kavlock, Robert; Dix, David

2010-02-01

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, the U.S. Environmental Protection Agency EPA is developing robust and flexible computational tools that can be applied to the thousands of chemicals in commerce, and contaminant mixtures found in air, water, and hazardous-waste sites. The Office of Research and Development (ORD) Computational Toxicology Research Program (CTRP) is composed of three main elements. The largest component is the National Center for Computational Toxicology (NCCT), which was established in 2005 to coordinate research on chemical screening and prioritization, informatics, and systems modeling. The second element consists of related activities in the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL). The third and final component consists of academic centers working on various aspects of computational toxicology and funded by the U.S. EPA Science to Achieve Results (STAR) program. Together these elements form the key components in the implementation of both the initial strategy, A Framework for a Computational Toxicology Research Program (U.S. EPA, 2003), and the newly released The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the Toxicity of Chemicals (U.S. EPA, 2009a). Key intramural projects of the CTRP include digitizing legacy toxicity testing information toxicity reference database (ToxRefDB), predicting toxicity (ToxCast) and exposure (ExpoCast), and creating virtual liver (v-Liver) and virtual embryo (v-Embryo) systems models. U.S. EPA-funded STAR centers are also providing bioinformatics, computational toxicology data and models, and developmental toxicity data and models. The models and underlying data are being made publicly

ACToR-AGGREGATED COMPUTATIONAL TOXICOLOGY ...

Science.gov (United States)

One goal of the field of computational toxicology is to predict chemical toxicity by combining computer models with biological and toxicological data. predict chemical toxicity by combining computer models with biological and toxicological data

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

Science.gov (United States)

Lin, Yen Ting; Chylek, Lily A; Lemons, Nathan W; Hlavacek, William S

2018-06-21

The chemical kinetics of many complex systems can be concisely represented by reaction rules, which can be used to generate reaction events via a kinetic Monte Carlo method that has been termed network-free simulation. Here, we demonstrate accelerated network-free simulation through a novel approach to equation-free computation. In this process, variables are introduced that approximately capture system state. Derivatives of these variables are estimated using short bursts of exact stochastic simulation and finite differencing. The variables are then projected forward in time via a numerical integration scheme, after which a new exact stochastic simulation is initialized and the whole process repeats. The projection step increases efficiency by bypassing the firing of numerous individual reaction events. As we show, the projected variables may be defined as populations of building blocks of chemical species. The maximal number of connected molecules included in these building blocks determines the degree of approximation. Equation-free acceleration of network-free simulation is found to be both accurate and efficient.

Chemical Mechanism Solvers in Air Quality Models

Directory of Open Access Journals (Sweden)

John C. Linford

2011-09-01

Full Text Available The solution of chemical kinetics is one of the most computationally intensivetasks in atmospheric chemical transport simulations. Due to the stiff nature of the system,implicit time stepping algorithms which repeatedly solve linear systems of equations arenecessary. This paper reviews the issues and challenges associated with the construction ofefficient chemical solvers, discusses several families of algorithms, presents strategies forincreasing computational efficiency, and gives insight into implementing chemical solverson accelerated computer architectures.

Computer Program for Calculation of Complex Chemical Equilibrium Compositions, Rocket Performance, Incident and Reflected Shocks, and Chapman-Jouguet Detonations. Interim Revision, March 1976

Science.gov (United States)

Gordon, S.; Mcbride, B. J.

1976-01-01

A detailed description of the equations and computer program for computations involving chemical equilibria in complex systems is given. A free-energy minimization technique is used. The program permits calculations such as (1) chemical equilibrium for assigned thermodynamic states (T,P), (H,P), (S,P), (T,V), (U,V), or (S,V), (2) theoretical rocket performance for both equilibrium and frozen compositions during expansion, (3) incident and reflected shock properties, and (4) Chapman-Jouguet detonation properties. The program considers condensed species as well as gaseous species.

Towards reaction-diffusion computing devices based on minority-carrier transport in semiconductors

International Nuclear Information System (INIS)

Asai, Tetsuya; Adamatzky, Andrew; Amemiya, Yoshihito

2004-01-01

Reaction-diffusion (RD) chemical systems are known to realize sensible computation when both data and results of the computation are encoded in concentration profiles of chemical species; the computation is implemented via spreading and interaction of either diffusive or phase waves. Thin-layer chemical systems are thought of therefore as massively-parallel locally-connected computing devices, where micro-volume of the medium is analogous to an elementary processor. Practical applications of the RD chemical systems are reduced however due to very low speed of traveling waves which makes real-time computation senseless. To overcome the speed-limitations while preserving unique features of RD computers we propose a semiconductor RD computing device where minority carriers diffuse as chemical species and reaction elements are represented by p-n-p-n diodes. We offer blue-prints of the RD semiconductor devices, and study in computer simulation propagation phenomena of the density wave of minority carriers. We then demonstrate what computational problems can be solved in RD semiconductor devices and evaluate space-time complexity of computation in the devices

Identification of new candidate drugs for lung cancer using chemical-chemical interactions, chemical-protein interactions and a K-means clustering algorithm.

Science.gov (United States)

Lu, Jing; Chen, Lei; Yin, Jun; Huang, Tao; Bi, Yi; Kong, Xiangyin; Zheng, Mingyue; Cai, Yu-Dong

2016-01-01

Lung cancer, characterized by uncontrolled cell growth in the lung tissue, is the leading cause of global cancer deaths. Until now, effective treatment of this disease is limited. Many synthetic compounds have emerged with the advancement of combinatorial chemistry. Identification of effective lung cancer candidate drug compounds among them is a great challenge. Thus, it is necessary to build effective computational methods that can assist us in selecting for potential lung cancer drug compounds. In this study, a computational method was proposed to tackle this problem. The chemical-chemical interactions and chemical-protein interactions were utilized to select candidate drug compounds that have close associations with approved lung cancer drugs and lung cancer-related genes. A permutation test and K-means clustering algorithm were employed to exclude candidate drugs with low possibilities to treat lung cancer. The final analysis suggests that the remaining drug compounds have potential anti-lung cancer activities and most of them have structural dissimilarity with approved drugs for lung cancer.

Vibrational studies of Thyroxine hormone: Comparative study with quantum chemical calculations

Science.gov (United States)

Borah, Mukunda Madhab; Devi, Th. Gomti

2017-11-01

The FTIR and Raman techniques have been used to record spectra of Thyroxine. The stable geometrical parameters and vibrational wave numbers were calculated based on potential energy distribution (PED) using vibrational energy distribution analysis (VEDA) program. The vibrational energies are assigned to monomer, chain dimer and cyclic dimers of this molecule using the basis set B3LYP/LANL2DZ. The computational scaled frequencies are in good agreements with the experimental results. The study is extended to calculate the HOMO-LUMO energy gap, Molecular Electrostatic Potential (MEP) surface, hardness (η), chemical potential (μ), Global electrophilicity index (ω) and different thermo dynamical properties of Thyroxine in different states. The calculated HOMO-LUMO energies show the charge transfer occurs within the molecule. The calculated Natural bond orbital (NBO) analysis confirms the presence of intra-molecular charge transfer as well as the hydrogen bonding interaction.

Computational models of neuromodulation.

Science.gov (United States)

Fellous, J M; Linster, C

1998-05-15

Computational modeling of neural substrates provides an excellent theoretical framework for the understanding of the computational roles of neuromodulation. In this review, we illustrate, with a large number of modeling studies, the specific computations performed by neuromodulation in the context of various neural models of invertebrate and vertebrate preparations. We base our characterization of neuromodulations on their computational and functional roles rather than on anatomical or chemical criteria. We review the main framework in which neuromodulation has been studied theoretically (central pattern generation and oscillations, sensory processing, memory and information integration). Finally, we present a detailed mathematical overview of how neuromodulation has been implemented at the single cell and network levels in modeling studies. Overall, neuromodulation is found to increase and control computational complexity.

Computational enzymology for degradation of chemical warfare agents: promising technologies for remediation processes

Directory of Open Access Journals (Sweden)

2017-03-01

Full Text Available Chemical weapons are a major worldwide problem, since they are inexpensive, easy to produce on a large scale and difficult to detect and control. Among the chemical warfare agents, we can highlight the organophosphorus compounds (OP, which contain the phosphorus element and that have a large number of applications. They affect the central nervous system and can lead to death, so there are a lot of works in order to design new effective antidotes for the intoxication caused by them. The standard treatment includes the use of an anticholinergic combined to a central nervous system depressor and an oxime. Oximes are compounds that reactivate Acetylcholinesterase (AChE, a regulatory enzyme responsible for the transmission of nerve impulses, which is one of the molecular targets most vulnerable to neurotoxic agents. Increasingly, enzymatic treatment becomes a promising alternative; therefore, other enzymes have been studied for the OP degradation function, such as phosphotriesterase (PTE from bacteria, human serum paraoxonase 1 (HssPON1 and diisopropyl fluorophosphatase (DFPase that showed significant performances in OP detoxification. The understanding of mechanisms by which enzymes act is of extreme importance for the projection of antidotes for warfare agents, and computational chemistry comes to aid and reduce the time and costs of the process. Molecular Docking, Molecular Dynamics and QM/MM (quantum-mechanics/molecular-mechanics are techniques used to investigate the molecular interactions between ligands and proteins.

Advanced Chemical Propulsion Study

Science.gov (United States)

Woodcock, Gordon; Byers, Dave; Alexander, Leslie A.; Krebsbach, Al

2004-01-01

A study was performed of advanced chemical propulsion technology application to space science (Code S) missions. The purpose was to begin the process of selecting chemical propulsion technology advancement activities that would provide greatest benefits to Code S missions. Several missions were selected from Code S planning data, and a range of advanced chemical propulsion options was analyzed to assess capabilities and benefits re these missions. Selected beneficial applications were found for higher-performing bipropellants, gelled propellants, and cryogenic propellants. Technology advancement recommendations included cryocoolers and small turbopump engines for cryogenic propellants; space storable propellants such as LOX-hydrazine; and advanced monopropellants. It was noted that fluorine-bearing oxidizers offer performance gains over more benign oxidizers. Potential benefits were observed for gelled propellants that could be allowed to freeze, then thawed for use.

Chemical, computational and functional insights into the chemical stability of the Hedgehog pathway inhibitor GANT61.

Science.gov (United States)

Calcaterra, Andrea; Iovine, Valentina; Botta, Bruno; Quaglio, Deborah; D'Acquarica, Ilaria; Ciogli, Alessia; Iazzetti, Antonia; Alfonsi, Romina; Lospinoso Severini, Ludovica; Infante, Paola; Di Marcotullio, Lucia; Mori, Mattia; Ghirga, Francesca

2018-12-01

This work aims at elucidating the mechanism and kinetics of hydrolysis of GANT61, the first and most-widely used inhibitor of the Hedgehog (Hh) signalling pathway that targets Glioma-associated oncogene homologue (Gli) proteins, and at confirming the chemical nature of its bioactive form. GANT61 is poorly stable under physiological conditions and rapidly hydrolyses into an aldehyde species (GANT61-A), which is devoid of the biological activity against Hh signalling, and a diamine derivative (GANT61-D), which has shown inhibition of Gli-mediated transcription. Here, we combined chemical synthesis, NMR spectroscopy, analytical studies, molecular modelling and functional cell assays to characterise the GANT61 hydrolysis pathway. Our results show that GANT61-D is the bioactive form of GANT61 in NIH3T3 Shh-Light II cells and SuFu -/- mouse embryonic fibroblasts, and clarify the structural requirements for GANT61-D binding to Gli1. This study paves the way to the design of GANT61 derivatives with improved potency and chemical stability.

An Origin of Life in Cycling Hot Spring Pools: Emerging Evidence from Chemistry, Geology and Computational Studies

Science.gov (United States)

Deamer, D. W.; Damer, B. F.; Van Kranendonk, M. J.; Djokic, T.

2017-07-01

New evidence for an origin of life in a hot spring setting on land is supported by three studies: chemical (polymerization in wet-dry cycles), geological (stromatolites in a 3.48 Ga geothermal field) and computational (verifying the kinetic trap).

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. AYOUB KANAANI. Articles written in Journal of Chemical Sciences. Volume 128 Issue 8 August 2016 pp 1211-1221 Regular Article. Synthesis, molecular structure, spectroscopic investigations and computational study of a potential molecular switch of 2-([1 ...

Abstracts Book of Jubilee Scientific Assembly of Polish Chemical Society and Association of Engineers and Technicians of Chemical Industry

International Nuclear Information System (INIS)

2000-01-01

Scientific Assemblies of Polish Chemical Society and Association of Engineers and Technicians of Chemical Industry are most important chemical discussion forum organised annually in Poland. Basic as well as application studies in all chemical branches have been extensively presented. The next subjects was proposed as sections and symposia topics: organic chemistry, physical chemistry (chemical kinetics, catalysis, thermodynamics), membranes and membrane processes, biological chemistry, biotechnology, metalorganic compounds and complexes, polymer chemistry, crystallochemical study, spectroscopy in nowadays chemistry, supramolecular chemistry, chemistry and technology of coal, high-energetic materials, environment protection, didactics in chemistry, radiation chemistry, photochemistry, electrochemistry, chemistry and technology of carbohydrates, theoretical and computer chemistry, young scientists forum, history of chemistry

Advances in unconventional computing

CERN Document Server

2017-01-01

The unconventional computing is a niche for interdisciplinary science, cross-bred of computer science, physics, mathematics, chemistry, electronic engineering, biology, material science and nanotechnology. The aims of this book are to uncover and exploit principles and mechanisms of information processing in and functional properties of physical, chemical and living systems to develop efficient algorithms, design optimal architectures and manufacture working prototypes of future and emergent computing devices. This first volume presents theoretical foundations of the future and emergent computing paradigms and architectures. The topics covered are computability, (non-)universality and complexity of computation; physics of computation, analog and quantum computing; reversible and asynchronous devices; cellular automata and other mathematical machines; P-systems and cellular computing; infinity and spatial computation; chemical and reservoir computing. The book is the encyclopedia, the first ever complete autho...

Early detection and identification of anomalies in chemical regime based on computational intelligence techniques

International Nuclear Information System (INIS)

Figedy, Stefan; Smiesko, Ivan

2012-01-01

This article provides brief information about the fundamental features of a newly-developed diagnostic system for early detection and identification of anomalies being generated in water chemistry regime of the primary and secondary circuit of the VVER-440 reactor. This system, which is called SACHER (System of Analysis of CHEmical Regime), was installed within the major modernization project at the NPP-V2 Bohunice in the Slovak Republic. The SACHER system has been fully developed on MATLAB environment. It is based on computational intelligence techniques and inserts various elements of intelligent data processing modules for clustering, diagnosing, future prediction, signal validation, etc, into the overall chemical information system. The application of SACHER would essentially assist chemists to identify the current situation regarding anomalies being generated in the primary and secondary circuit water chemistry. This system is to be used for diagnostics and data handling, however it is not intended to fully replace the presence of experienced chemists to decide upon corrective actions. (author)

Rational Design of Mixed-Metal Oxides for Chemical Looping Combustion of Coal via Coupled Computational-Experimental Studies

Energy Technology Data Exchange (ETDEWEB)

Mishra, Amit [North Carolina State Univ., Raleigh, NC (United States); Li, Fanxing [North Carolina State Univ., Raleigh, NC (United States); Santiso, Erik [North Carolina State Univ., Raleigh, NC (United States)

2017-09-18

Energy and global climate change are two grand challenges to the modern society. An urgent need exists for development of clean and efficient energy conversion processes. The chemical looping strategy, which utilizes regenerable oxygen carriers (OCs) to indirectly convert carbonaceous fuels via redox reactions, is considered to be one of the more promising approaches for CO2 capture by the U.S. Department of Energy (USDOE). To date, most long-term chemical looping operations were conducted using gaseous fuels, even though direct conversion of coal is more desirable from both economics and CO2 capture viewpoints. The main challenges for direct coal conversion reside in the stringent requirements on oxygen carrier performances. In addition, coal char and volatile compounds are more challenging to convert than gaseous fuels. A promising approach for direct conversion of coal is the so called chemical looping with oxygen uncoupling (CLOU) technique. In the CLOU process, a metal oxide that decomposes at the looping temperature, and releases oxygen to the gas phase is used as the OC. The overarching objective of this project was to discover the fundamental principles for rational design and optimization of oxygen carriers (OC) in coal chemical looping combustion (CLC) processes. It directly addresses Topic Area B of the funding opportunity announcement (FOA) in terms of “predictive description of the phase behavior and mechanical properties” of “mixed metal oxide” based OCs and rational development of new OC materials with superior functionality. This was achieved through studies exploring i) iron-containing mixed-oxide composites as oxygen carriers for CLOU, ii) Ca1-xAxMnO3-δ (A = Sr and Ba) as oxygen carriers for CLOU, iii) CaMn1-xBxO3-δ (B=Al, V, Fe, Co, and Ni) as oxygen carrier for CLOU and iv) vacancy creation energy in Mn-containing perovskites as an indicator chemical looping with oxygen uncoupling.

Modeling chemical kinetics graphically

NARCIS (Netherlands)

Heck, A.

2012-01-01

In literature on chemistry education it has often been suggested that students, at high school level and beyond, can benefit in their studies of chemical kinetics from computer supported activities. Use of system dynamics modeling software is one of the suggested quantitative approaches that could

Selected bibliography for the extraction of uranium from seawater: chemical process and plant design feasibility study

Energy Technology Data Exchange (ETDEWEB)

Binney, S.E.; Polkinghorne, S.T.; Jante, R.R.; Rodman, M.R.; Chen, A.C.T.; Gordon, L.I.

1979-02-01

A selected annotated bibliography of 521 references was prepared as a part of a feasibility study of the extraction of uranium from seawater. For the most part, these references are related to the chemical processes whereby the uranium is removed from the seawater. A companion docment contains a similar bibliography of 471 references related to oceanographic and uranium extraction plant siting considerations, although some of the references are in common. The bibliography was prepared by computer retrieval from Chemical Abstracts, Nuclear Science Abstracts, Energy Data Base, NTIS, and Oceanic Abstracts. References are listed by author, country of author, and selected keywords.

Selected bibliography for the extraction of uranium from seawater: chemical process and plant design feasibility study

International Nuclear Information System (INIS)

Binney, S.E.; Polkinghorne, S.T.; Jante, R.R.; Rodman, M.R.; Chen, A.C.T.; Gordon, L.I.

1979-02-01

A selected annotated bibliography of 521 references was prepared as a part of a feasibility study of the extraction of uranium from seawater. For the most part, these references are related to the chemical processes whereby the uranium is removed from the seawater. A companion docment contains a similar bibliography of 471 references related to oceanographic and uranium extraction plant siting considerations, although some of the references are in common. The bibliography was prepared by computer retrieval from Chemical Abstracts, Nuclear Science Abstracts, Energy Data Base, NTIS, and Oceanic Abstracts. References are listed by author, country of author, and selected keywords

Computational modeling of chemical reactions and interstitial growth and remodeling involving charged solutes and solid-bound molecules.

Science.gov (United States)

Ateshian, Gerard A; Nims, Robert J; Maas, Steve; Weiss, Jeffrey A

2014-10-01

Mechanobiological processes are rooted in mechanics and chemistry, and such processes may be modeled in a framework that couples their governing equations starting from fundamental principles. In many biological applications, the reactants and products of chemical reactions may be electrically charged, and these charge effects may produce driving forces and constraints that significantly influence outcomes. In this study, a novel formulation and computational implementation are presented for modeling chemical reactions in biological tissues that involve charged solutes and solid-bound molecules within a deformable porous hydrated solid matrix, coupling mechanics with chemistry while accounting for electric charges. The deposition or removal of solid-bound molecules contributes to the growth and remodeling of the solid matrix; in particular, volumetric growth may be driven by Donnan osmotic swelling, resulting from charged molecular species fixed to the solid matrix. This formulation incorporates the state of strain as a state variable in the production rate of chemical reactions, explicitly tying chemistry with mechanics for the purpose of modeling mechanobiology. To achieve these objectives, this treatment identifies the specific theoretical and computational challenges faced in modeling complex systems of interacting neutral and charged constituents while accommodating any number of simultaneous reactions where reactants and products may be modeled explicitly or implicitly. Several finite element verification problems are shown to agree with closed-form analytical solutions. An illustrative tissue engineering analysis demonstrates tissue growth and swelling resulting from the deposition of chondroitin sulfate, a charged solid-bound molecular species. This implementation is released in the open-source program FEBio ( www.febio.org ). The availability of this framework may be particularly beneficial to optimizing tissue engineering culture systems by examining the

Ch. 33 Modeling: Computational Thermodynamics

International Nuclear Information System (INIS)

Besmann, Theodore M.

2012-01-01

This chapter considers methods and techniques for computational modeling for nuclear materials with a focus on fuels. The basic concepts for chemical thermodynamics are described and various current models for complex crystalline and liquid phases are illustrated. Also included are descriptions of available databases for use in chemical thermodynamic studies and commercial codes for performing complex equilibrium calculations.

A computer code simulating multistage chemical exchange column under wide range of operating conditions

International Nuclear Information System (INIS)

Yamanishi, Toshihiko; Okuno, Kenji

1996-09-01

A computer code has been developed to simulate a multistage CECE(Combined Electrolysis Chemical Exchange) column. The solution of basic equations can be found out by the Newton-Raphson method. The independent variables are the atom fractions of D and T in each stage for the case where H is dominant within the column. These variables are replaced by those of H and T under the condition that D is dominant. Some effective techniques have also been developed to get a set of solutions of the basic equations: a setting procedure of initial values of the independent variables; and a procedure for the convergence of the Newton-Raphson method. The computer code allows us to simulate the column behavior under a wide range of the operating conditions. Even for a severe case, where the dominant species changes along the column height, the code can give a set of solutions of the basic equations. (author)

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. SUDIP PAN. Articles written in Journal of Chemical Sciences. Volume 128 Issue 10 October 2016 pp 1537-1548 Regular Article. A computational study on structure, stability and bonding in Noble Gas bound metal Nitrates, Sulfates and Carbonates (Metal = Cu, Ag, Au).

Progress report on SYVAC chemical modelling studies during 1984/85

International Nuclear Information System (INIS)

Cross, J.E.; Read, D.; Smith, G.L.; Williams, D.R.

1985-05-01

This report summarises progress made from April 1984 to May 1985 on chemical modelling within the DOE SYVAC project. Three new computer programs; the reaction path codes, PHREEQE and EQ3/6, and the chemical transport simulator CHEMTRN, have been acquired. Their applicability, overall capabilities, ease of use and database requirements are assessed. Coupled approaches to geochemical - hydrological modelling and the use of CHEMTRN is discussed. Modelling has been performed in connection with the ''Dry Run Assessment''. Speciation and solubilities of the actinides were simulated, assuming the vault to be a concrete solution and the geosphere to be represented by Harwell site groundwater analyses. Model verification and validation by collaboration with experimentalists and other modellers is discussed. (author)

Computational electromagnetic-aerodynamics

CERN Document Server

Shang, Joseph J S

2016-01-01

Presents numerical algorithms, procedures, and techniques required to solve engineering problems relating to the interactions between electromagnetic fields, fluid flow, and interdisciplinary technology for aerodynamics, electromagnetics, chemical-physics kinetics, and plasmadynamics This book addresses modeling and simulation science and technology for studying ionized gas phenomena in engineering applications. Computational Electromagnetic-Aerodynamics is organized into ten chapters. Chapter one to three introduce the fundamental concepts of plasmadynamics, chemical-physics of ionization, classical magnetohydrodynamics, and their extensions to plasma-based flow control actuators, high-speed flows of interplanetary re-entry, and ion thrusters in space exploration. Chapter four to six explain numerical algorithms and procedures for solving Maxwell’s equation in the time domain for computational electromagnetics, plasma wave propagation, and the time-dependent c mpressible Navier-Stokes equation for aerodyn...

A computational study of the supersonic coherent jet

International Nuclear Information System (INIS)

Jeong, Mi Seon; Kim, Heuy Dong

2003-01-01

In steel-making process of iron and steel industry, the purity and quality of steel can be dependent on the amount of CO contained in the molten metal. Recently, the supersonic oxygen jet is being applied to the molten metal in the electric furnace and thus reduces the CO amount through the chemical reactions between the oxygen jet and molten metal, leading to a better quality of steel. In this application, the supersonic oxygen jet is limited in the distance over which the supersonic velocity is maintained. In order to get longer supersonic jet propagation into the molten metal, a supersonic coherent jet is suggested as one of the alternatives which are applicable to the electric furnace system. It has a flame around the conventional supersonic jet and thus the entrainment effect of the surrounding gas into the supersonic jet is reduced, leading to a longer propagation of the supersonic jet. In this regard, gasdynamics mechanism about why the combustion phenomenon surrounding the supersonic jet causes the jet core length to be longer is not yet clarified. The present study investigates the major characteristics of the supersonic coherent jet, compared with the conventional supersonic jet. A computational study is carried out to solve the compressible, axisymmetric Navier-Stokes equations. The computational results of the supersonic coherent jet are compared with the conventional supersonic jets

Estimation of Radiative Efficiency of Chemicals with Potentially Significant Global Warming Potential.

Science.gov (United States)

Betowski, Don; Bevington, Charles; Allison, Thomas C

2016-01-19

Halogenated chemical substances are used in a broad array of applications, and new chemical substances are continually being developed and introduced into commerce. While recent research has considerably increased our understanding of the global warming potentials (GWPs) of multiple individual chemical substances, this research inevitably lags behind the development of new chemical substances. There are currently over 200 substances known to have high GWP. Evaluation of schemes to estimate radiative efficiency (RE) based on computational chemistry are useful where no measured IR spectrum is available. This study assesses the reliability of values of RE calculated using computational chemistry techniques for 235 chemical substances against the best available values. Computed vibrational frequency data is used to estimate RE values using several Pinnock-type models, and reasonable agreement with reported values is found. Significant improvement is obtained through scaling of both vibrational frequencies and intensities. The effect of varying the computational method and basis set used to calculate the frequency data is discussed. It is found that the vibrational intensities have a strong dependence on basis set and are largely responsible for differences in computed RE values.

Exploring the role of quantum chemical descriptors in modeling acute toxicity of diverse chemicals to Daphnia magna.

Science.gov (United States)

Reenu; Vikas

2015-09-01

Various quantum-mechanically computed molecular and thermodynamic descriptors along with physico-chemical, electrostatic and topological descriptors are compared while developing quantitative structure-activity relationships (QSARs) for the acute toxicity of 252 diverse organic chemicals towards Daphnia magna. QSAR models based on the quantum-chemical descriptors, computed with routinely employed advanced semi-empirical and ab-initio methods, along with the electron-correlation contribution (CORR) of the descriptors, are analyzed for the external predictivity of the acute toxicity. The models with reliable internal stability and external predictivity are found to be based on the HOMO energy along with the physico-chemical, electrostatic and topological descriptors. Besides this, the total energy and electron-correlation energy are also observed as highly reliable descriptors, suggesting that the intra-molecular interactions between the electrons play an important role in the origin of the acute toxicity, which is in fact an unexplored phenomenon. The models based on quantum-chemical descriptors such as chemical hardness, absolute electronegativity, standard Gibbs free energy and enthalpy are also observed to be reliable. A comparison of the robust models based on the quantum-chemical descriptors computed with various quantum-mechanical methods suggests that the advanced semi-empirical methods such as PM7 can be more reliable than the ab-initio methods which are computationally more expensive. Copyright © 2015 Elsevier Inc. All rights reserved.

Computational study of sheath structure in oxygen containing plasmas at medium pressures

Science.gov (United States)

Hrach, Rudolf; Novak, Stanislav; Ibehej, Tomas; Hrachova, Vera

2016-09-01

Plasma mixtures containing active species are used in many plasma-assisted material treatment technologies. The analysis of such systems is rather difficult, as both physical and chemical processes affect plasma properties. A combination of experimental and computational approaches is the best suited, especially at higher pressures and/or in chemically active plasmas. The first part of our study of argon-oxygen mixtures was based on experimental results obtained in the positive column of DC glow discharge. The plasma was analysed by the macroscopic kinetic approach which is based on the set of chemical reactions in the discharge. The result of this model is a time evolution of the number densities of each species. In the second part of contribution the detailed analysis of processes taking place during the interaction of oxygen containing plasma with immersed substrates was performed, the results of the first model being the input parameters. The used method was the particle simulation technique applied to multicomponent plasma. The sheath structure and fluxes of charged particles to substrates were analysed in the dependence on plasma pressure, plasma composition and surface geometry.

Computational studies of atmospherically-relevant chemical reactions in water clusters and on liquid water and ice surfaces.

Science.gov (United States)

Gerber, R Benny; Varner, Mychel E; Hammerich, Audrey D; Riikonen, Sampsa; Murdachaew, Garold; Shemesh, Dorit; Finlayson-Pitts, Barbara J

2015-02-17

CONSPECTUS: Reactions on water and ice surfaces and in other aqueous media are ubiquitous in the atmosphere, but the microscopic mechanisms of most of these processes are as yet unknown. This Account examines recent progress in atomistic simulations of such reactions and the insights provided into mechanisms and interpretation of experiments. Illustrative examples are discussed. The main computational approaches employed are classical trajectory simulations using interaction potentials derived from quantum chemical methods. This comprises both ab initio molecular dynamics (AIMD) and semiempirical molecular dynamics (SEMD), the latter referring to semiempirical quantum chemical methods. Presented examples are as follows: (i) Reaction of the (NO(+))(NO3(-)) ion pair with a water cluster to produce the atmospherically important HONO and HNO3. The simulations show that a cluster with four water molecules describes the reaction. This provides a hydrogen-bonding network supporting the transition state. The reaction is triggered by thermal structural fluctuations, and ultrafast changes in atomic partial charges play a key role. This is an example where a reaction in a small cluster can provide a model for a corresponding bulk process. The results support the proposed mechanism for production of HONO by hydrolysis of NO2 (N2O4). (ii) The reactions of gaseous HCl with N2O4 and N2O5 on liquid water surfaces. Ionization of HCl at the water/air interface is followed by nucleophilic attack of Cl(-) on N2O4 or N2O5. Both reactions proceed by an SN2 mechanism. The products are ClNO and ClNO2, precursors of atmospheric atomic chlorine. Because this mechanism cannot result from a cluster too small for HCl ionization, an extended water film model was simulated. The results explain ClNO formation experiments. Predicted ClNO2 formation is less efficient. (iii) Ionization of acids at ice surfaces. No ionization is found on ideal crystalline surfaces, but the process is efficient on

Development and Performance of the Modularized, High-performance Computing and Hybrid-architecture Capable GEOS-Chem Chemical Transport Model

Science.gov (United States)

Long, M. S.; Yantosca, R.; Nielsen, J.; Linford, J. C.; Keller, C. A.; Payer Sulprizio, M.; Jacob, D. J.

2014-12-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been reengineered to serve as a platform for a range of computational atmospheric chemistry science foci and applications. Development included modularization for coupling to general circulation and Earth system models (ESMs) and the adoption of co-processor capable atmospheric chemistry solvers. This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of GEOS-Chem scientific code to permit seamless transition from the GEOS-Chem stand-alone serial CTM to deployment as a coupled ESM module. In this manner, the continual stream of updates contributed by the CTM user community is automatically available for broader applications, which remain state-of-science and directly referenceable to the latest version of the standard GEOS-Chem CTM. These developments are now available as part of the standard version of the GEOS-Chem CTM. The system has been implemented as an atmospheric chemistry module within the NASA GEOS-5 ESM. The coupled GEOS-5/GEOS-Chem system was tested for weak and strong scalability and performance with a tropospheric oxidant-aerosol simulation. Results confirm that the GEOS-Chem chemical operator scales efficiently for any number of processes. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemical operator means that the relative cost goes down with increasing number of processes, making fine-scale resolution simulations possible.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. HARI JI SINGH. Articles written in Journal of Chemical Sciences. Volume 123 Issue 5 September 2011 pp 733-741. Computational study on decomposition kinetics of CH3CFClO radical · Hari Ji Singh Bhupesh Kumar Mishra · More Details Abstract Fulltext PDF. The present ...

A computational approach to extinction events in chemical reaction networks with discrete state spaces.

Science.gov (United States)

Johnston, Matthew D

2017-12-01

Recent work of Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist of a series of systems of equalities and inequalities on the edges of a modified reaction network called a domination-expanded reaction network. In this paper, we present a computational implementation of these conditions written in Python and apply the program on examples drawn from the biochemical literature. We also run the program on 458 models from the European Bioinformatics Institute's BioModels Database and report our results. Copyright © 2017 Elsevier Inc. All rights reserved.

Design of chemical plant

International Nuclear Information System (INIS)

Lee, Dong Il; Kim, Seung Jae; Yang, Jae Ho; Ryu, Hwa Won

1993-01-01

This book describes design of chemical plant, which includes chemical engineer and plan for chemical plant, development of chemical process, cost engineering pattern, design and process development, general plant construction plan, project engineering, foundation for economy on assets and depreciation, estimation for cost on capital investment and manufacturing cost, design with computers optimal design and method like fluid mechanics design chemical device and estimation for cost, such as dispatch of material and device writing on design report and appendixes.

Downloadable Computational Toxicology Data

Science.gov (United States)

EPA’s computational toxicology research generates data that investigates the potential harm, or hazard of a chemical, the degree of exposure to chemicals as well as the unique chemical characteristics. This data is publicly available here.

Argonne Chemical Sciences & Engineering - Awards Home

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Application of computer-aided multi-scale modelling framework – Aerosol case study

DEFF Research Database (Denmark)

Heitzig, Martina; Sin, Gürkan; Glarborg, Peter

2011-01-01

Model-based computer aided product-process engineering has attained increased importance in a number of industries, including pharmaceuticals, petrochemicals, fine chemicals, polymers, biotechnology, food, energy and water. This trend is set to continue due to the substantial benefits computer-aided...... methods provide. The key prerequisite of computer-aided product-process engineering is however the availability of models of different types, forms and application modes. The development of the models required for the systems under investigation tends to be a challenging and time-consuming task involving...... numerous steps, expert skills and different modelling tools. This motivates the development of a computer-aided modelling framework that supports the user during model development, documentation, analysis, identification, application and re-use with the goal to increase the efficiency of the modelling...

Real-time nonlinear feedback control of pattern formation in (bio)chemical reaction-diffusion processes: a model study.

Science.gov (United States)

Brandt-Pollmann, U; Lebiedz, D; Diehl, M; Sager, S; Schlöder, J

2005-09-01

Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.

Modification of silicon nitride surfaces with GOPES and APTES for antibody immobilization: computational and experimental studies

International Nuclear Information System (INIS)

To, Thien Dien; Nguyen, Anh Tuan; Phan, Khoa Nhat Thanh; Truong, An Thu Thi; Doan, Tin Chanh Duc; Dang, Chien Mau

2015-01-01

Chemical modification of silicon nitride (SiN) surfaces by silanization has been widely studied especially with 3-(aminopropyl)triethoxysilane (APTES) and 3-(glycidyloxypropyl) dimethylethoxysilane (GOPES). However few reports performed the experimental and computational studies together. In this study, surface modification of SiN surfaces with GOPES and APTES covalently bound with glutaraldehyde (GTA) was investigated for antibody immobilization. The monoclonal anti-cytokeratin-FITC (MACF) antibody was immobilized on the modified SiN surfaces. The modified surfaces were characterized by water contact angle measurements, atomic force microscopy and fluorescence microscopy. The FITC-fluorescent label indicated the existence of MACF antibody on the SiN surfaces and the efficiency of the silanization reaction. Absorption of APTES and GOPES on the oxidized SiN surfaces was computationally modeled and calculated by Materials Studio software. The computational and experimental results showed that modification of the SiN surfaces with APTES and GTA was more effective than the modification with GOPES. (paper)

Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

Science.gov (United States)

Pineda, M.; Stamatakis, M.

2017-07-01

Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks.

Molecular activation analysis for chemical speciation studies

International Nuclear Information System (INIS)

Chai-Chifang

1998-01-01

The term of Molecular Activation Analysis (MAA) refers to an activation analysis method that is able to provide information about the chemical species of elements in system of interests, though its definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the total concentrations are often without any meaning when assessing health or environmental risks of trace elements.In practice, the MAA is a combination of conventional instrumental or radiochemical activation analysis and physical, chemical or biochemical separation techniques. The MAA is able to play a particular role in speciation studies. However, the critical point in the MAA is that it is not permitted to change the primitive chemical species of elements in systems, or the change has to be under control; in the meantime it is not allowed to form the 'new artifact' originally not present in systems. Some practical examples of MAA for chemical species research performed recently in our laboratory will be presented as follows: Chemical species of platinum group elements in sediment; Chemical species of iodine in marine algae; Chemical species of mercury in human tissues; Chemical species of selenium in corn; Chemical species of rare earth elements in natural plant, etc. The merits and limitations of MAA will be described as well. (author)

Model reduction of multiscale chemical langevin equations: a numerical case study.

Science.gov (United States)

Sotiropoulos, Vassilios; Contou-Carrere, Marie-Nathalie; Daoutidis, Prodromos; Kaznessis, Yiannis N

2009-01-01

Two very important characteristics of biological reaction networks need to be considered carefully when modeling these systems. First, models must account for the inherent probabilistic nature of systems far from the thermodynamic limit. Often, biological systems cannot be modeled with traditional continuous-deterministic models. Second, models must take into consideration the disparate spectrum of time scales observed in biological phenomena, such as slow transcription events and fast dimerization reactions. In the last decade, significant efforts have been expended on the development of stochastic chemical kinetics models to capture the dynamics of biomolecular systems, and on the development of robust multiscale algorithms, able to handle stiffness. In this paper, the focus is on the dynamics of reaction sets governed by stiff chemical Langevin equations, i.e., stiff stochastic differential equations. These are particularly challenging systems to model, requiring prohibitively small integration step sizes. We describe and illustrate the application of a semianalytical reduction framework for chemical Langevin equations that results in significant gains in computational cost.

Computational Model of the Fathead Minnow Hypothalamic-Pituitary-Gonadal Axis: Incorporating Protein Synthesis in Improving Predictability of Responses to Endocrine Active Chemicals

Science.gov (United States)

There is international concern about chemicals that alter endocrine system function in humans and/or wildlife and subsequently cause adverse effects. We previously developed a mechanistic computational model of the hypothalamic-pituitary-gonadal (HPG) axis in female fathead minno...

Vibrational spectroscopic studies of Isoleucine by quantum chemical calculations.

Science.gov (United States)

Moorthi, P P; Gunasekaran, S; Ramkumaar, G R

2014-04-24

In this work, we reported a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of Isoleucine (2-Amino-3-methylpentanoic acid). The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments, thermodynamics properties, NBO analyses, NMR chemical shifts and ultraviolet-visible spectral interpretation of Isoleucine have been studied by performing MP2 and DFT/cc-pVDZ level of theory. The FTIR, FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. The UV-visible absorption spectra of the compound were recorded in the range of 200-800 nm. Computational calculations at MP2 and B3LYP level with basis set of cc-pVDZ is employed in complete assignments of Isoleucine molecule on the basis of the potential energy distribution (PED) of the vibrational modes, calculated using VEDA-4 program. The calculated wavenumbers are compared with the experimental values. The difference between the observed and calculated wavenumber values of most of the fundamentals is very small. (13)C and (1)H nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method and compared with experimental results. The formation of hydrogen bond was investigated in terms of the charge density by the NBO calculations. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. Besides, molecular electrostatic potential (MEP) were investigated using theoretical calculations. Copyright © 2014 Elsevier B.V. All rights reserved.

Intracellular chemical gradients: morphing principle in bacteria

Directory of Open Access Journals (Sweden)

Endres Robert G

2012-09-01

Full Text Available Abstract Advances in computational biology allow systematic investigations to ascertain whether internal chemical gradients can be maintained in bacteria – an open question at the resolution limit of fluorescence microscopy. While it was previously believed that the small bacterial cell size and fast diffusion in the cytoplasm effectively remove any such gradient, a new computational study published in BMC Biophysics supports the emerging view that gradients can exist. The study arose from the recent observation that phosphorylated CtrA forms a gradient prior to cell division in Caulobacter crescentus, a bacterium known for its complicated cell cycle. Tropini et al. (2012 postulate that such gradients can provide an internal chemical compass, directing protein localization, cell division and cell development. More specifically, they describe biochemical and physical constraints on the formation of such gradients and explore a number of existing bacterial cell morphologies. These chemical gradients may limit in vitro analyses, and may ensure timing control and robustness to fluctuations during critical stages in cell development.

Simulating chemistry using quantum computers.

Science.gov (United States)

Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán

2011-01-01

The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.

Computational quantum chemistry website

International Nuclear Information System (INIS)

1997-01-01

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

An experimental study on prediction of gallstone composition by ultrasonography and computed tomography

International Nuclear Information System (INIS)

Lee, Jong Beum; Chung, Sae Yul; Kim, Kun Sang; Lee, Yong Chul; Han, Man Chung; Kim, Jin Kyu

1992-01-01

Prediction of chemical composition of gallstones is a prerequisite in contemplating the chemical dissolution or extracorporeal shock wave lithotripsy of gallstones. The author retrospectively analysed the correlation between quantitative chemical composition of gallstones and their ultrasonographic and computed tomographic findings. The ultrasonography(US) and computed tomography(CT) of 100 consecutive stones obtained from 100 patients were performed under the in vitro condition. Their US and CT findings were grouped with certain pattern and each group was compared with the chemical composition of the stones. Stones with entirely discernible circumference and homogeneous internal echo on US had high bilirubin and low cholesterol content. Acoustic shadows were frequently absent with those stones. Stones with variable internal echo on US had relatively high cholesterol content but their distribution range were wide. There was no correlationship between the cholesterol content and the CT No. of the gallstones. There was positive correlationship between the calcium content and the CT No. of gallstones. The near totally calcified gallstones had very low cholesterol and high residue content. There was no relationship between the calcification type and the ultrasonographic pattern. In conclusion, those stones with entirely discernible circumference and homogeneous internal echo on US were pigment stones. On the contrary, stones with variable internal echo had relatively high cholesterol content. CT could predict the calcium content with CT No., but could not predict the cholesterol content

de novo computational enzyme design.

Science.gov (United States)

Zanghellini, Alexandre

2014-10-01

Recent advances in systems and synthetic biology as well as metabolic engineering are poised to transform industrial biotechnology by allowing us to design cell factories for the sustainable production of valuable fuels and chemicals. To deliver on their promises, such cell factories, as much as their brick-and-mortar counterparts, will require appropriate catalysts, especially for classes of reactions that are not known to be catalyzed by enzymes in natural organisms. A recently developed methodology, de novo computational enzyme design can be used to create enzymes catalyzing novel reactions. Here we review the different classes of chemical reactions for which active protein catalysts have been designed as well as the results of detailed biochemical and structural characterization studies. We also discuss how combining de novo computational enzyme design with more traditional protein engineering techniques can alleviate the shortcomings of state-of-the-art computational design techniques and create novel enzymes with catalytic proficiencies on par with natural enzymes. Copyright © 2014 Elsevier Ltd. All rights reserved.

COMPUTATIONAL SCIENCE CENTER

Energy Technology Data Exchange (ETDEWEB)

DAVENPORT,J.

2004-11-01

The Brookhaven Computational Science Center brings together researchers in biology, chemistry, physics, and medicine with applied mathematicians and computer scientists to exploit the remarkable opportunities for scientific discovery which have been enabled by modern computers. These opportunities are especially great in computational biology and nanoscience, but extend throughout science and technology and include for example, nuclear and high energy physics, astrophysics, materials and chemical science, sustainable energy, environment, and homeland security.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 119; Issue 5 ... We present here results of ab-initio studies of structures and interaction energies of ... Center for Computational Natural Sciences and Bioinformatics, International Institute ...

A model ecosystem experiment and its computational simulation studies

International Nuclear Information System (INIS)

Doi, M.

2002-01-01

Simplified microbial model ecosystem and its computer simulation model are introduced as eco-toxicity test for the assessment of environmental responses from the effects of environmental impacts. To take the effects on the interactions between species and environment into account, one option is to select the keystone species on the basis of ecological knowledge, and to put it in the single-species toxicity test. Another option proposed is to put the eco-toxicity tests as experimental micro ecosystem study and a theoretical model ecosystem analysis. With these tests, the stressors which are more harmful to the ecosystems should be replace with less harmful ones on the basis of unified measures. Management of radioactive materials, chemicals, hyper-eutrophic, and other artificial disturbances of ecosystem should be discussed consistently from the unified view point of environmental protection. (N.C.)

From Interfaces to Bulk: Experimental-Computational Studies Across Time and Length Scales of Multi-Functional Ionic Polymers

Energy Technology Data Exchange (ETDEWEB)

Perahia, Dvora [Clemson Univ., SC (United States); Grest, Gary S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-01-25

Neutron experiments coupled with computational components have resulted in unprecedented understanding of the factors that impact the behavior of ionic structured polymers. Additionally, new computational tools to study macromolecules, were developed. In parallel, this DOE funding have enabled the education of the next generation of material researchers who are able to take the advantage neutron tools offer to the understanding and design of advanced materials. Our research has provided unprecedented insight into one of the major factors that limits the use of ionizable polymers, combining the macroscopic view obtained from the experimental techniques with molecular insight extracted from computational studies leading to transformative knowledge that will impact the design of nano-structured, materials. With the focus on model systems, of broad interest to the scientific community and to industry, the research addressed challenges that cut across a large number of polymers, independent of the specific chemical structure or the transported species.

East-West paths to unconventional computing.

Science.gov (United States)

Adamatzky, Andrew; Akl, Selim; Burgin, Mark; Calude, Cristian S; Costa, José Félix; Dehshibi, Mohammad Mahdi; Gunji, Yukio-Pegio; Konkoli, Zoran; MacLennan, Bruce; Marchal, Bruno; Margenstern, Maurice; Martínez, Genaro J; Mayne, Richard; Morita, Kenichi; Schumann, Andrew; Sergeyev, Yaroslav D; Sirakoulis, Georgios Ch; Stepney, Susan; Svozil, Karl; Zenil, Hector

2017-12-01

Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured. This article includes idiosyncratic accounts of 'unconventional computing' scientists reflecting on their personal experiences, what attracted them to the field, their inspirations and discoveries. Copyright © 2017 Elsevier Ltd. All rights reserved.

First principle chemical kinetics in zeolites: the methanol-to-olefin process as a case study.

Science.gov (United States)

Van Speybroeck, Veronique; De Wispelaere, Kristof; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Waroquier, Michel

2014-11-07

To optimally design next generation catalysts a thorough understanding of the chemical phenomena at the molecular scale is a prerequisite. Apart from qualitative knowledge on the reaction mechanism, it is also essential to be able to predict accurate rate constants. Molecular modeling has become a ubiquitous tool within the field of heterogeneous catalysis. Herein, we review current computational procedures to determine chemical kinetics from first principles, thus by using no experimental input and by modeling the catalyst and reacting species at the molecular level. Therefore, we use the methanol-to-olefin (MTO) process as a case study to illustrate the various theoretical concepts. This process is a showcase example where rational design of the catalyst was for a long time performed on the basis of trial and error, due to insufficient knowledge of the mechanism. For theoreticians the MTO process is particularly challenging as the catalyst has an inherent supramolecular nature, for which not only the Brønsted acidic site is important but also organic species, trapped in the zeolite pores, must be essentially present during active catalyst operation. All these aspects give rise to specific challenges for theoretical modeling. It is shown that present computational techniques have matured to a level where accurate enthalpy barriers and rate constants can be predicted for reactions occurring at a single active site. The comparison with experimental data such as apparent kinetic data for well-defined elementary reactions has become feasible as current computational techniques also allow predicting adsorption enthalpies with reasonable accuracy. Real catalysts are truly heterogeneous in a space- and time-like manner. Future theory developments should focus on extending our view towards phenomena occurring at longer length and time scales and integrating information from various scales towards a unified understanding of the catalyst. Within this respect molecular

Computational model of collagen turnover in carotid arteries during hypertension.

Science.gov (United States)

Sáez, P; Peña, E; Tarbell, J M; Martínez, M A

2015-02-01

It is well known that biological tissues adapt their properties because of different mechanical and chemical stimuli. The goal of this work is to study the collagen turnover in the arterial tissue of hypertensive patients through a coupled computational mechano-chemical model. Although it has been widely studied experimentally, computational models dealing with the mechano-chemical approach are not. The present approach can be extended easily to study other aspects of bone remodeling or collagen degradation in heart diseases. The model can be divided into three different stages. First, we study the smooth muscle cell synthesis of different biological substances due to over-stretching during hypertension. Next, we study the mass-transport of these substances along the arterial wall. The last step is to compute the turnover of collagen based on the amount of these substances in the arterial wall which interact with each other to modify the turnover rate of collagen. We simulate this process in a finite element model of a real human carotid artery. The final results show the well-known stiffening of the arterial wall due to the increase in the collagen content. Copyright © 2015 John Wiley & Sons, Ltd.

Key study on the potential of hydrazine bisborane for solid- and liquid-state chemical hydrogen storage.

Science.gov (United States)

Pylypko, Sergii; Petit, Eddy; Yot, Pascal G; Salles, Fabrice; Cretin, Marc; Miele, Philippe; Demirci, Umit B

2015-05-04

Hydrazine bisborane N2H4(BH3)2 (HBB; 16.8 wt %) recently re-emerged as a potential hydrogen storage material. However, such potential is controversial: HBB was seen as a hazardous compound up to 2010, but now it would be suitable for hydrogen storage. In this context, we focused on fundamentals of HBB because they are missing in the literature and should help to shed light on its effective potential while taking into consideration any risk. Experimental/computational methods were used to get a complete characterization data sheet, including, e.g., XRD, NMR, FTIR, Raman, TGA, and DSC. From the reported results and discussion, it is concluded that HBB has potential in the field of chemical hydrogen storage given that both thermolytic and hydrolytic dehydrogenations were analyzed. In solid-state chemical hydrogen storage, it cannot be used in the pristine state (risk of explosion during dehydrogenation) but can be used for the synthesis of derivatives with improved dehydrogenation properties. In liquid-state chemical hydrogen storage, it can be studied for room-temperature dehydrogenation, but this requires the development of an active and selective metal-based catalyst. HBB is a thus a candidate for chemical hydrogen storage.

Human Environmental Disease Network: A computational model to assess toxicology of contaminants.

Science.gov (United States)

Taboureau, Olivier; Audouze, Karine

2017-01-01

During the past decades, many epidemiological, toxicological and biological studies have been performed to assess the role of environmental chemicals as potential toxicants associated with diverse human disorders. However, the relationships between diseases based on chemical exposure rarely have been studied by computational biology. We developed a human environmental disease network (EDN) to explore and suggest novel disease-disease and chemical-disease relationships. The presented scored EDN model is built upon the integration of systems biology and chemical toxicology using information on chemical contaminants and their disease relationships reported in the TDDB database. The resulting human EDN takes into consideration the level of evidence of the toxicant-disease relationships, allowing inclusion of some degrees of significance in the disease-disease associations. Such a network can be used to identify uncharacterized connections between diseases. Examples are discussed for type 2 diabetes (T2D). Additionally, this computational model allows confirmation of already known links between chemicals and diseases (e.g., between bisphenol A and behavioral disorders) and also reveals unexpected associations between chemicals and diseases (e.g., between chlordane and olfactory alteration), thus predicting which chemicals may be risk factors to human health. The proposed human EDN model allows exploration of common biological mechanisms of diseases associated with chemical exposure, helping us to gain insight into disease etiology and comorbidity. This computational approach is an alternative to animal testing supporting the 3R concept.

Accessing and using chemical databases

DEFF Research Database (Denmark)

Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell

2013-01-01

Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval......, and dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples....

Silicene Catalyzed Reduction of Nitrobenzene to Aniline: a Computational Study

Science.gov (United States)

Morrissey, Christopher; He, Haiying

The reduction of nitrobenzene to aniline has a broad range of applications in the production of rubbers, dyes, agrochemicals, and pharmaceuticals. Currently, use of metal catalysts is the most popular method of performing this reaction on a large scale. These metal catalysts usually require high-temperature and/or high-pressure reaction conditions, and produce hazardous chemicals. This has led to a call for more environmentally friendly nonmetal catalysts. Recent studies suggest that silicene, the recently discovered silicon counterpart of graphene, could potentially work as a nonmetal catalyst due to its unique electronic property and strong interactions with molecules containing nitrogen and oxygen. In this computational study, we have investigated the plausibility of using silicene as a catalyst for the reduction of nitrobenzene. Possible reaction mechanisms will be discussed with a highlight of the difference between silicene and metal catalysts. . All calculations were performed in the framework of density functional theory.

Influence of ionization on the Gupta and on the Park chemical models

Science.gov (United States)

Morsa, Luigi; Zuppardi, Gennaro

2014-12-01

This study is an extension of former works by the present authors, in which the influence of the chemical models by Gupta and by Park was evaluated on thermo-fluid-dynamic parameters in the flow field, including transport coefficients, related characteristic numbers and heat flux on two current capsules (EXPERT and Orion) during the high altitude re-entry path. The results verified that the models, even computing different air compositions in the flow field, compute only slight different compositions on the capsule surface, therefore the difference in the heat flux is not very relevant. In the above mentioned studies, ionization was neglected because the velocities of the capsules (about 5000 m/s for EXPERT and about 7600 m/s for Orion) were not high enough to activate meaningful ionization. The aim of the present work is to evaluate the incidence of ionization, linked to the chemical models by Gupta and by Park, on both heat flux and thermo fluid-dynamic parameters. The present computer tests were carried out by a direct simulation Monte Carlo code (DS2V) in the velocity interval 7600-12000 m/s, considering only the Orion capsule at an altitude of 85 km. The results verified what already found namely when ionization is not considered, the chemical models compute only a slight different gas composition in the core of the shock wave and practically the same composition on the surface therefore the same heat flux. On the opposite, the results verified that when ionization is considered, the chemical models compute different compositions in the whole shock layer and on the surface therefore different heat flux. The analysis of the results relies on a qualitative and a quantitative evaluation of the effects of ionization on both chemical models. The main result of the study is that when ionization is taken into account, the Park model is more reactive than the Gupta model; consequently, the heat flux computed by Park is lower than the one computed by Gupta; using the

Contribution to chemical-mineralogical study of carbonatites

International Nuclear Information System (INIS)

Costa, M.Q. da; Lima, W.N. de; Correa, S.L.A.

1982-01-01

A preliminary chemical-mineralogical study of carbonatites from Jacupiranga (SP,Brazil) and Alto Pinheiros (SC,Brazil) enabled not only to ratify hypotheses previously described by Brazilian researchers but also made clear certain aspects related to the geochemistry of carbonatites concerning their occurrence, the probable genesis of these species and their chemical and mineralogical characteristics.(Author) [pt

A study of computer-related upper limb discomfort and computer vision syndrome.

Science.gov (United States)

Sen, A; Richardson, Stanley

2007-12-01

Personal computers are one of the commonest office tools in Malaysia today. Their usage, even for three hours per day, leads to a health risk of developing Occupational Overuse Syndrome (OOS), Computer Vision Syndrome (CVS), low back pain, tension headaches and psychosocial stress. The study was conducted to investigate how a multiethnic society in Malaysia is coping with these problems that are increasing at a phenomenal rate in the west. This study investigated computer usage, awareness of ergonomic modifications of computer furniture and peripherals, symptoms of CVS and risk of developing OOS. A cross-sectional questionnaire study of 136 computer users was conducted on a sample population of university students and office staff. A 'Modified Rapid Upper Limb Assessment (RULA) for office work' technique was used for evaluation of OOS. The prevalence of CVS was surveyed incorporating a 10-point scoring system for each of its various symptoms. It was found that many were using standard keyboard and mouse without any ergonomic modifications. Around 50% of those with some low back pain did not have an adjustable backrest. Many users had higher RULA scores of the wrist and neck suggesting increased risk of developing OOS, which needed further intervention. Many (64%) were using refractive corrections and still had high scores of CVS commonly including eye fatigue, headache and burning sensation. The increase of CVS scores (suggesting more subjective symptoms) correlated with increase in computer usage spells. It was concluded that further onsite studies are needed, to follow up this survey to decrease the risks of developing CVS and OOS amongst young computer users.

FastChem: A computer program for efficient complex chemical equilibrium calculations in the neutral/ionized gas phase with applications to stellar and planetary atmospheres

Science.gov (United States)

Stock, Joachim W.; Kitzmann, Daniel; Patzer, A. Beate C.; Sedlmayr, Erwin

2018-06-01

For the calculation of complex neutral/ionized gas phase chemical equilibria, we present a semi-analytical versatile and efficient computer program, called FastChem. The applied method is based on the solution of a system of coupled nonlinear (and linear) algebraic equations, namely the law of mass action and the element conservation equations including charge balance, in many variables. Specifically, the system of equations is decomposed into a set of coupled nonlinear equations in one variable each, which are solved analytically whenever feasible to reduce computation time. Notably, the electron density is determined by using the method of Nelder and Mead at low temperatures. The program is written in object-oriented C++ which makes it easy to couple the code with other programs, although a stand-alone version is provided. FastChem can be used in parallel or sequentially and is available under the GNU General Public License version 3 at https://github.com/exoclime/FastChem together with several sample applications. The code has been successfully validated against previous studies and its convergence behavior has been tested even for extreme physical parameter ranges down to 100 K and up to 1000 bar. FastChem converges stable and robust in even most demanding chemical situations, which posed sometimes extreme challenges for previous algorithms.

Computer-Aided Modeling of Lipid Processing Technology

DEFF Research Database (Denmark)

Diaz Tovar, Carlos Axel

2011-01-01

increase along with growing interest in biofuels, the oleochemical industry faces in the upcoming years major challenges in terms of design and development of better products and more sustainable processes to make them. Computer-aided methods and tools for process synthesis, modeling and simulation...... are widely used for design, analysis, and optimization of processes in the chemical and petrochemical industries. These computer-aided tools have helped the chemical industry to evolve beyond commodities toward specialty chemicals and ‘consumer oriented chemicals based products’. Unfortunately...... to develop systematic computer-aided methods (property models) and tools (database) related to the prediction of the necessary physical properties suitable for design and analysis of processes employing lipid technologies. The methods and tools include: the development of a lipid-database (CAPEC...

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Science.gov (United States)

Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

2011-01-01

Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

Directory of Open Access Journals (Sweden)

Janna Hastings

Full Text Available Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA.

The Chemical Information Ontology: Provenance and Disambiguation for Chemical Data on the Biological Semantic Web

Science.gov (United States)

Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

2011-01-01

Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA). PMID:21991315

Ab initio computational study of vincristine as a biological active compound: NMR and NBO analyses

Directory of Open Access Journals (Sweden)

Shiva Joohari

2015-06-01

Full Text Available Vincristine is a biological active alkaloid that has been used clinically against a variety of neoplasms. In the current study we have theoretically investigated the magnetic properties of titled compound to predict physical and chemical properties of vincristine as a biological inhibitor. Ab initio computation using HF and B3LYP with 3-21G(d and 6-31G(d level of theory have been performed and then magnetic shielding tensor (, ppm, shielding asymmetry (, magnetic shielding anisotropy (aniso, ppm, the skew of a tensor (K, chemical shift anisotropy ( and chemical shift ( were calculated to indicate the details of the interaction mechanism between microtubules and vincristine. Moreover, EHOMO, ELUMO and Ebg were evaluated. The maximum and minimum values of Ebg were found in HF/3-21g and B3LYP/3-21g respectively. It was also uggested that O24, O37, O49 and O55 with minimum values of iso, are active sites of titled compound. Furthermore the calculated chemical shifts were compared with experimental data in DMSO and CDCl3 solvents.

Aggregated Computational Toxicology Resource (ACTOR)

Data.gov (United States)

U.S. Environmental Protection Agency — The Aggregated Computational Toxicology Resource (ACTOR) is a database on environmental chemicals that is searchable by chemical name and other identifiers, and by...

Mg co-ordination with potential carcinogenic molecule acrylamide: Spectroscopic, computational and cytotoxicity studies

Science.gov (United States)

Singh, Ranjana; Mishra, Vijay K.; Singh, Hemant K.; Sharma, Gunjan; Koch, Biplob; Singh, Bachcha; Singh, Ranjan K.

2018-03-01

Acrylamide (acr) is a potential toxic molecule produced in thermally processed food stuff. Acr-Mg complex has been synthesized chemically and characterized by spectroscopic techniques. The binding sites of acr with Mg were identified by experimental and computational methods. Both experimental and theoretical results suggest that Mg coordinated with the oxygen atom of Cdbnd O group of acr. In-vitro cytotoxicity studies revealed significant decrease in the toxic level of acr-Mg complex as compared to pure acr. The decrease in toxicity on complexation with Mg may be a useful step for future research to reduce the toxicity of acr.

COMPUTATIONAL SCIENCE CENTER

Energy Technology Data Exchange (ETDEWEB)

DAVENPORT, J.

2005-11-01

The Brookhaven Computational Science Center brings together researchers in biology, chemistry, physics, and medicine with applied mathematicians and computer scientists to exploit the remarkable opportunities for scientific discovery which have been enabled by modern computers. These opportunities are especially great in computational biology and nanoscience, but extend throughout science and technology and include, for example, nuclear and high energy physics, astrophysics, materials and chemical science, sustainable energy, environment, and homeland security. To achieve our goals we have established a close alliance with applied mathematicians and computer scientists at Stony Brook and Columbia Universities.

Modeling reaction histories to study chemical pathways in condensed phase detonation

International Nuclear Information System (INIS)

Scott Stewart, D.; Hernández, Alberto; Lee, Kibaek

2016-01-01

The estimation of pressure and temperature histories, which are required to understand chemical pathways in condensed phase explosives during detonation, is discussed. We argue that estimates made from continuum models, calibrated by macroscopic experiments, are essential to inform modern, atomistic-based reactive chemistry simulations at detonation pressures and temperatures. We present easy to implement methods for general equation of state and arbitrarily complex chemical reaction schemes that can be used to compute reactive flow histories for the constant volume, the energy process, and the expansion process on the Rayleigh line of a steady Chapman-Jouguet detonation. A brief review of state-of-the-art of two-component reactive flow models is given that highlights the Ignition and Growth model of Lee and Tarver [Phys. Fluids 23, 2362 (1980)] and the Wide-Ranging Equation of State model of Wescott, Stewart, and Davis [J. Appl. Phys. 98, 053514 (2005)]. We discuss evidence from experiments and reactive molecular dynamic simulations that motivate models that have several components, instead of the two that have traditionally been used to describe the results of macroscopic detonation experiments. We present simplified examples of a formulation for a hypothetical explosive that uses simple (ideal) equation of state forms and detailed comparisons. Then, we estimate pathways computed from two-component models of real explosive materials that have been calibrated with macroscopic experiments.

A Study of Interactions between Mixing and Chemical Reaction Using the Rate-Controlled Constrained-Equilibrium Method

Science.gov (United States)

Hadi, Fatemeh; Janbozorgi, Mohammad; Sheikhi, M. Reza H.; Metghalchi, Hameed

2016-10-01

The rate-controlled constrained-equilibrium (RCCE) method is employed to study the interactions between mixing and chemical reaction. Considering that mixing can influence the RCCE state, the key objective is to assess the accuracy and numerical performance of the method in simulations involving both reaction and mixing. The RCCE formulation includes rate equations for constraint potentials, density and temperature, which allows taking account of mixing alongside chemical reaction without splitting. The RCCE is a dimension reduction method for chemical kinetics based on thermodynamics laws. It describes the time evolution of reacting systems using a series of constrained-equilibrium states determined by RCCE constraints. The full chemical composition at each state is obtained by maximizing the entropy subject to the instantaneous values of the constraints. The RCCE is applied to a spatially homogeneous constant pressure partially stirred reactor (PaSR) involving methane combustion in oxygen. Simulations are carried out over a wide range of initial temperatures and equivalence ratios. The chemical kinetics, comprised of 29 species and 133 reaction steps, is represented by 12 RCCE constraints. The RCCE predictions are compared with those obtained by direct integration of the same kinetics, termed detailed kinetics model (DKM). The RCCE shows accurate prediction of combustion in PaSR with different mixing intensities. The method also demonstrates reduced numerical stiffness and overall computational cost compared to DKM.

Energetics of 2- and 3-coumaranone isomers: A combined calorimetric and computational study

International Nuclear Information System (INIS)

Sousa, Clara C.S.; Matos, M. Agostinha R.; Santos, Luís M.N.B.F.; Morais, Victor M.F.

2013-01-01

Highlights: • Experimental standard molar enthalpies of formation, sublimation of 2- and 3-coumaranone. • Mini-bomb combustion calorimetry, sublimation Calvet microcalorimetry. • DFT methods and high level composite ab initio calculations. • Theoretical estimate of the enthalpy of formation of isobenzofuranone. • Chemical shift (NICS) and the relative stability of the isomers. -- Abstract: Condensed phase standard (p° = 0.1 MPa) molar enthalpies of formation for 2-coumaranone and 3-coumaranone were derived from the standard molar enthalpies of combustion, in oxygen, at T = 298.15 K, measured by mini-bomb combustion calorimetry. Standard molar enthalpies of sublimation of both isomers were determined by Calvet microcalorimetry. These results were combined to derive the standard molar enthalpies of formation of the compounds, in gas phase, at T = 298.15 K. Additionally, accurate quantum chemical calculations have been performed using DFT methods and high level composite ab initio calculations. Theoretical estimates of the enthalpies of formation of the compounds are in good agreement with the experimental values thus supporting the predictions of the same parameters for isobenzofuranone, an isomer which has not been experimentally studied. The relative stability of these isomers has been evaluated by experimental and computational results. The importance of some stabilizing electronic intramolecular interactions has been studied and quantitatively evaluated through Natural Bonding Orbital (NBO) analysis of the wave functions and the nucleus independent chemical shift (NICS) of the studied systems have been calculated in order to study and establish the effect of electronic delocalization upon the relative stability of the isomers

Parallel execution of chemical software on EGEE Grid

CERN Document Server

Sterzel, Mariusz

2008-01-01

Constant interest among chemical community to study larger and larger molecules forces the parallelization of existing computational methods in chemistry and development of new ones. These are main reasons of frequent port updates and requests from the community for the Grid ports of new packages to satisfy their computational demands. Unfortunately some parallelization schemes used by chemical packages cannot be directly used in Grid environment. Here we present a solution for Gaussian package. The current state of development of Grid middleware allows easy parallel execution in case of software using any of MPI flavour. Unfortunately many chemical packages do not use MPI for parallelization therefore special treatment is needed. Gaussian can be executed in parallel on SMP architecture or via Linda. These require reservation of certain number of processors/cores on a given WN and the equal number of processors/cores on each WN, respectively. The current implementation of EGEE middleware does not offer such f...

Computational chemistry

Science.gov (United States)

Arnold, J. O.

1987-01-01

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

Laboratory of Chemical Physics

Data.gov (United States)

Federal Laboratory Consortium — Current research in the Laboratory of Chemical Physics is primarily concerned with experimental, theoretical, and computational problems in the structure, dynamics,...

Introduction to chemical reaction engineering

International Nuclear Information System (INIS)

Kim, Yeong Geol

1990-10-01

This deals with chemical reaction engineering with thirteen chapters. The contents of this book are introduction on reaction engineering, chemical kinetics, thermodynamics and chemical reaction, abnormal reactor, non-isothermal reactor, nonideal reactor, catalysis in nonuniform system, diffusion and reaction in porosity catalyst, design catalyst heterogeneous reactor in solid bed, a high molecule polymerization, bio reaction engineering, reaction engineering in material process, control multi-variable reactor process using digital computer.

Chapter 3 – VPPD-Lab: The Chemical Product Simulator

DEFF Research Database (Denmark)

Kalakul, Sawitree; Cignitti, Stefano; Zhang, L.

2017-01-01

for computer-aided chemical product design and evaluation, implemented in the software called VPPD-Lab, is presented. In the same way a typical process simulator works, the VPPD-Lab allows users to: (1) analyze chemical-based products by performing virtual experiments (product property and performance......Computer-aided methods and tools for current and future product–process design and development need to manage problems requiring efficient handling of models, data, and knowledge from different sources and at different times and size scales. In this chapter, a systematic model-based framework...... lotion design. Through these case studies, the use of design templates, associated workflows (methods), data flows (software integration), and solution strategies (database and tools) are highlighted....

Computational approaches to the chemical conversion of carbon dioxide

Energy Technology Data Exchange (ETDEWEB)

Cheng, Daojian; Negreiros, Fabio R.; Apra, Edoardo; Fortunelli, Alessandro

2013-06-01

The conversion of CO2 into fuels and chemicals is viewed as an attractive route for controlling the atmospheric concentration of this greenhouse gas and recycling it, but its industrial application is limited by the low selectivity and activity of the current catalysts. Theoretical modeling, in particular density-functional theory (DFT) simulations, provides a powerful and effective tool to discover chemical reaction mechanisms and design new catalysts for the chemical conversion of CO2, overcoming the repetitious and time/labor consuming trial-and-error experimental processes. In this article we give a comprehensive survey of recent advances on mechanism determination by DFT calculations for the catalytic hydrogenation of CO2 into CO, CH4, CH3OH, and HCOOH, and CO2 methanation, as well as the photo- and electrochemical reduction of CO2. DFT-guided design procedures of new catalytic systems are also reviewed, and challenges and perspectives in this field are outlined.

Thermalization with chemical potentials, and higher spin black holes

International Nuclear Information System (INIS)

Mandal, Gautam; Sinha, Ritam; Sorokhaibam, Nilakash

2015-01-01

We study the long time behaviour of local observables following a quantum quench in 1+1 dimensional conformal field theories possessing additional conserved charges besides the energy. We show that the expectation value of an arbitrary string of local observables supported on a finite interval exponentially approaches an equilibrium value. The equilibrium is characterized by a temperature and chemical potentials defined in terms of the quenched state. For an infinite number of commuting conserved charges, the equilibrium ensemble is a generalized Gibbs ensemble (GGE). We compute the thermalization rate in a systematic perturbation in the chemical potentials, using a new technique to sum over an infinite number of Feynman diagrams. The above technique also allows us to compute relaxation times for thermal Green’s functions in the presence of an arbitrary number of chemical potentials. In the context of a higher spin (hs[λ]) holography, the partition function of the final equilibrium GGE is known to agree with that of a higher spin black hole. The thermalization rate from the CFT computed in our paper agrees with the quasinormal frequency of a scalar field in this black hole.

Computational Study of Stratified Combustion in an Optical Diesel Engine

KAUST Repository

Jaasim, Mohammed

2017-03-28

Full cycle simulations of KAUST optical diesel engine were conducted in order to provide insights into the details of fuel spray, mixing, and combustion characteristics at different start of injection (SOI) conditions. Although optical diagnostics provide valuable information, the high fidelity simulations with matched parametric conditions improve fundamental understanding of relevant physical and chemical processes by accessing additional observables such as the local mixture distribution, intermediate species concentrations, and detailed chemical reaction rates. Commercial software, CONVERGE™, was used as the main simulation tool, with the Reynolds averaged Navier-Stokes (RANS) turbulence model and the multi-zone (SAGE) combustion model to compute the chemical reaction terms. SOI is varied from late compression ignition (CI) to early partially premixed combustion (PPC) conditions. The simulation results revealed a stronger correlation between fuel injection timing and combustion phasing for late SOI conditions, whereas the combustion phasing starts to decouple from SOI for early SOI cases. The predictions are consistent with the experimental observations, in terms of the overall trends in combustion and emission characteristics, while the high fidelity simulations provided further insights into the effects of mixture stratifications resulting from different SOI conditions.

Educational NASA Computational and Scientific Studies (enCOMPASS)

Science.gov (United States)

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

A Computer Oriented Scheme for Coding Chemicals in the Field of Biomedicine.

Science.gov (United States)

Bobka, Marilyn E.; Subramaniam, J.B.

The chemical coding scheme of the Medical Coding Scheme (MCS), developed for use in the Comparative Systems Laboratory (CSL), is outlined and evaluated in this report. The chemical coding scheme provides a classification scheme and encoding method for drugs and chemical terms. Using the scheme complicated chemical structures may be expressed…

Multi-scenario modelling of uncertainty in stochastic chemical systems

International Nuclear Information System (INIS)

Evans, R. David; Ricardez-Sandoval, Luis A.

2014-01-01

Uncertainty analysis has not been well studied at the molecular scale, despite extensive knowledge of uncertainty in macroscale systems. The ability to predict the effect of uncertainty allows for robust control of small scale systems such as nanoreactors, surface reactions, and gene toggle switches. However, it is difficult to model uncertainty in such chemical systems as they are stochastic in nature, and require a large computational cost. To address this issue, a new model of uncertainty propagation in stochastic chemical systems, based on the Chemical Master Equation, is proposed in the present study. The uncertain solution is approximated by a composite state comprised of the averaged effect of samples from the uncertain parameter distributions. This model is then used to study the effect of uncertainty on an isomerization system and a two gene regulation network called a repressilator. The results of this model show that uncertainty in stochastic systems is dependent on both the uncertain distribution, and the system under investigation. -- Highlights: •A method to model uncertainty on stochastic systems was developed. •The method is based on the Chemical Master Equation. •Uncertainty in an isomerization reaction and a gene regulation network was modelled. •Effects were significant and dependent on the uncertain input and reaction system. •The model was computationally more efficient than Kinetic Monte Carlo

Chemical substructure analysis in toxicology

Energy Technology Data Exchange (ETDEWEB)

Beauchamp, R.O. Jr. [Center for Information on Toxicology and Environment, Raleigh, NC (United States)

1990-12-31

A preliminary examination of chemical-substructure analysis (CSA) demonstrates the effective use of the Chemical Abstracts compound connectivity file in conjunction with the bibliographic file for relating chemical structures to biological activity. The importance of considering the role of metabolic intermediates under a variety of conditions is illustrated, suggesting structures that should be examined that may exhibit potential activity. This CSA technique, which utilizes existing large files accessible with online personal computers, is recommended for use as another tool in examining chemicals in drugs. 2 refs., 4 figs.

COMPARATIVE STUDY OF CLOUD COMPUTING AND MOBILE CLOUD COMPUTING

OpenAIRE

Nidhi Rajak*, Diwakar Shukla

2018-01-01

Present era is of Information and Communication Technology (ICT) and there are number of researches are going on Cloud Computing and Mobile Cloud Computing such security issues, data management, load balancing and so on. Cloud computing provides the services to the end user over Internet and the primary objectives of this computing are resource sharing and pooling among the end users. Mobile Cloud Computing is a combination of Cloud Computing and Mobile Computing. Here, data is stored in...

Thermodynamics of natural selection III: Landauer's principle in computation and chemistry.

Science.gov (United States)

Smith, Eric

2008-05-21

This is the third in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and their relations to the thermodynamics of computation. The previous two papers have developed reversible chemical transformations as idealizations for studying physiology and natural selection, and derived bounds from the second law of thermodynamics, between information gain in an ensemble and the chemical work required to produce it. This paper concerns the explicit mapping of chemistry to computation, and particularly the Landauer decomposition of irreversible computations, in which reversible logical operations generating no heat are separated from heat-generating erasure steps which are logically irreversible but thermodynamically reversible. The Landauer arrangement of computation is shown to produce the same entropy-flow diagram as that of the chemical Carnot cycles used in the second paper of the series to idealize physiological cycles. The specific application of computation to data compression and error-correcting encoding also makes possible a Landauer analysis of the somewhat different problem of optimal molecular recognition, which has been considered as an information theory problem. It is shown here that bounds on maximum sequence discrimination from the enthalpy of complex formation, although derived from the same logical model as the Shannon theorem for channel capacity, arise from exactly the opposite model for erasure.

Creating and maintaining chemical artificial life by robotic symbiosis

DEFF Research Database (Denmark)

Hanczyc, Martin M.; Parrilla, Juan M.; Nicholson, Arwen

2015-01-01

We present a robotic platform based on the open source RepRap 3D printer that can print and maintain chemical artificial life in the form of a dynamic, chemical droplet. The robot uses computer vision, a self-organizing map, and a learning program to automatically categorize the behavior of the d......We present a robotic platform based on the open source RepRap 3D printer that can print and maintain chemical artificial life in the form of a dynamic, chemical droplet. The robot uses computer vision, a self-organizing map, and a learning program to automatically categorize the behavior...... confluence of chemical, artificial intelligence, and robotic approaches to artificial life....

Creating and Maintaining Chemical Artificial Life by Robotic Symbiosis

DEFF Research Database (Denmark)

Hanczyc, Martin; Parrilla, Juan M.; Nicholson, Arwen

2015-01-01

We present a robotic platform based on the open source RepRap 3D printer that can print and maintain chemical artificial life in the form of a dynamic, chemical droplet. The robot uses computer vision, a self-organizing map, and a learning program to automatically categorize the behavior of the d......We present a robotic platform based on the open source RepRap 3D printer that can print and maintain chemical artificial life in the form of a dynamic, chemical droplet. The robot uses computer vision, a self-organizing map, and a learning program to automatically categorize the behavior...... confluence of chemical, artificial intelligence, and robotic approaches to artificial life....

Investigation of Evaluation method of chemical runaway reaction

International Nuclear Information System (INIS)

Sato, Yoshihiko; Sasaya, Shinji; Kurakata, Koichiro; Nojiri, Ichiro

2002-02-01

Safety study 'Study of evaluation of abnormal occurrence for chemical substances in the nuclear fuel facilities' will be carried out from 2001 to 2005. In this study, the prediction of thermal hazards of chemical substances will be investigated and prepared. The hazard prediction method of chemical substances will be constructed from these results. Therefore, the hazard prediction methods applied in the chemical engineering in which the chemical substances with the hazard of fire and explosion were often treated were investigated. CHETAH (The ASTM Computer Program for Chemical Thermodynamic and Energy Release Evaluation) developed by ASTM (American Society for Testing and Materials) and TSS (Thermal Safety Software) developed by CISP (ChemInform St. Petersburg) were introduced and the fire and explosion hazards of chemical substances and reactions in the reprocessing process were evaluated. From these evaluated results, CHETAH could almost estimate the heat of reaction at 10% accuracy. It was supposed that CHETAH was useful as a screening for the hazards of fire and explosion of the new chemical substances and so on. TSS could calculate the reaction rate and the reaction behavior from the data measured by the various calorimeters rapidly. It was supposed that TSS was useful as an evaluation method for the hazards of fire and explosion of the new chemical reactions and so on. (author)

Metal-organic frameworks for the removal of toxic industrial chemicals and chemical warfare agents.

Science.gov (United States)

Bobbitt, N Scott; Mendonca, Matthew L; Howarth, Ashlee J; Islamoglu, Timur; Hupp, Joseph T; Farha, Omar K; Snurr, Randall Q

2017-06-06

Owing to the vast diversity of linkers, nodes, and topologies, metal-organic frameworks can be tailored for specific tasks, such as chemical separations or catalysis. Accordingly, these materials have attracted significant interest for capture and/or detoxification of toxic industrial chemicals and chemical warfare agents. In this paper, we review recent experimental and computational work pertaining to the capture of several industrially-relevant toxic chemicals, including NH 3 , SO 2 , NO 2 , H 2 S, and some volatile organic compounds, with particular emphasis on the challenging issue of designing materials that selectively adsorb these chemicals in the presence of water. We also examine recent research on the capture and catalytic degradation of chemical warfare agents such as sarin and sulfur mustard using metal-organic frameworks.

Predicting Chemical Toxicity from Proteomics and Computational Chemistry

Science.gov (United States)

2008-07-30

perfluorooctanoic acid , perfluorodecanoic acid , clofibrate , and diethylhexyl phthalate) show that the leading eigenvalue of the D/D matrix derived from embedded... clofibrate , and DEHP, show that this approach clusters the first three highly-fluorinated and mechanistically similar chemicals together, while

Quantitative Study on Computer Self-Efficacy and Computer Anxiety Differences in Academic Major and Residential Status

Science.gov (United States)

Binkley, Zachary Wayne McClellan

2017-01-01

This study investigates computer self-efficacy and computer anxiety within 61 students across two academic majors, Aviation and Sports and Exercise Science, while investigating the impact residential status, age, and gender has on those two psychological constructs. The purpose of the study is to find if computer self-efficacy and computer anxiety…

Introduction to computational mass transfer with applications to chemical engineering

CERN Document Server

Yu, Kuo-Tsung

2017-01-01

This book offers an easy-to-understand introduction to the computational mass transfer (CMT) method. On the basis of the contents of the first edition, this new edition is characterized by the following additional materials. It describes the successful application of this method to the simulation of the mass transfer process in a fluidized bed, as well as recent investigations and computing methods for predictions for the multi-component mass transfer process. It also demonstrates the general issues concerning computational methods for simulating the mass transfer of the rising bubble process. This new edition has been reorganized by moving the preparatory materials for Computational Fluid Dynamics (CFD) and Computational Heat Transfer into appendices, additions of new chapters, and including three new appendices on, respectively, generalized representation of the two-equation model for the CMT, derivation of the equilibrium distribution function in the lattice-Boltzmann method, and derivation of the Navier-S...

Study guide to accompany computers data and processing

CERN Document Server

Deitel, Harvey M

1985-01-01

Study Guide to Accompany Computer and Data Processing provides information pertinent to the fundamental aspects of computers and computer technology. This book presents the key benefits of using computers.Organized into five parts encompassing 19 chapters, this book begins with an overview of the evolution of modern computing systems from the earliest mechanical calculating devices to microchips. This text then introduces computer hardware and describes the processor. Other chapters describe how microprocessors are made and describe the physical operation of computers. This book discusses as w

CHEMICAL PROPERTIES STUDYS OF PEATLANDON VARIOUS LANDUSE

Directory of Open Access Journals (Sweden)

Yondra Yondra

2017-12-01

Full Text Available Natural peat swamp forests converted can alter the soil chemical properties. This study aims to determine the extent to which changes in soil chemical properties that occur after the conversion of land from peat swamp forest to palm oil plantation, HTI Acacia crasicarpa, and sago plantation and to know which types of plants are sustainable on peatlands. The results showed that soil pH increased after the change of land function. While the water content decreased. Chemical properties such as C-organic, ash content, CEC, alkaline saturation, macro nutrients (NPK and bases can be changed also undergo changes after undergoing landuse changes, but no violations based on the law made by the government in pp No 25 of 2000 on the criteria of peatland damage and government regulation no. 150 of 2000 on the control of soil damage for biomass production. Sago is the most sustainable plant compared to others due to changes in soil chemical properties not too much different from other landuse although planted in the long term.

Formal modeling of a system of chemical reactions under uncertainty.

Science.gov (United States)

Ghosh, Krishnendu; Schlipf, John

2014-10-01

We describe a novel formalism representing a system of chemical reactions, with imprecise rates of reactions and concentrations of chemicals, and describe a model reduction method, pruning, based on the chemical properties. We present two algorithms, midpoint approximation and interval approximation, for construction of efficient model abstractions with uncertainty in data. We evaluate computational feasibility by posing queries in computation tree logic (CTL) on a prototype of extracellular-signal-regulated kinase (ERK) pathway.

Recent development in computational actinide chemistry

International Nuclear Information System (INIS)

Li Jun

2008-01-01

Ever since the Manhattan project in World War II, actinide chemistry has been essential for nuclear science and technology. Yet scientists still seek the ability to interpret and predict chemical and physical properties of actinide compounds and materials using first-principle theory and computational modeling. Actinide compounds are challenging to computational chemistry because of their complicated electron correlation effects and relativistic effects, including spin-orbit coupling effects. There have been significant developments in theoretical studies on actinide compounds in the past several years. The theoretical capabilities coupled with new experimental characterization techniques now offer a powerful combination for unraveling the complexities of actinide chemistry. In this talk, we will provide an overview of our own research in this field, with particular emphasis on applications of relativistic density functional and ab initio quantum chemical methods to the geometries, electronic structures, spectroscopy and excited-state properties of small actinide molecules such as CUO and UO 2 and some large actinide compounds relevant to separation and environment science. The performance of various density functional approaches and wavefunction theory-based electron correlation methods will be compared. The results of computational modeling on the vibrational, electronic, and NMR spectra of actinide compounds will be briefly discussed as well [1-4]. We will show that progress in relativistic quantum chemistry, computer hardware and computational chemistry software has enabled computational actinide chemistry to emerge as a powerful and predictive tool for research in actinide chemistry. (authors)

Study of Intelligent Secure Chemical Inventory Management System

Science.gov (United States)

Shukran, Mohd Afizi Mohd; Naim Abdullah, Muhammad; Nazri Ismail, Mohd; Maskat, Kamaruzaman; Isa, Mohd Rizal Mohd; Shahfee Ishak, Muhammad; Adib Khairuddin, Muhamad

2017-08-01

Chemical inventory management system has been experiencing a new revolution from traditional inventory system which is manual to an automated inventory management system. In this paper, some review of the classic and modern approaches to chemical inventory management system has been discussed. This paper also describe about both type of inventory management. After a comparative analysis of the traditional method and automated method, it can be said that both methods have some distinctive characteristics. Moreover, the automated inventory management method has higher accuracy of calculation because the calculations are handled by software, eliminating possible errors and saving time. The automated inventory system also allows users and administrators to track the availability, location and consumption of chemicals. The study of this paper can provide forceful review analysis support for the chemical inventory management related research.

Higher spin entanglement entropy at finite temperature with chemical potential

Energy Technology Data Exchange (ETDEWEB)

Chen, Bin [Department of Physics and State Key Laboratory of Nuclear Physics and Technology,Peking University,Beijing 100871 (China); Collaborative Innovation Center of Quantum Matter,5 Yiheyuan Rd, Beijing 100871 (China); Center for High Energy Physics, Peking University,5 Yiheyuan Rd, Beijing 100871 (China); Beijing Center for Mathematics and Information Interdisciplinary Sciences, Beijing 100048 (China); Wu, Jie-qiang [Department of Physics and State Key Laboratory of Nuclear Physics and Technology,Peking University,Beijing 100871 (China)

2016-07-11

It is generally believed that the semiclassical AdS{sub 3} higher spin gravity could be described by a two dimensional conformal field theory with W-algebra symmetry in the large central charge limit. In this paper, we study the single interval entanglement entropy on the torus in the CFT with a W{sub 3} deformation. More generally we develop the monodromy analysis to compute the two-point function of the light operators under a thermal density matrix with a W{sub 3} chemical potential to the leading order. Holographically we compute the probe action of the Wilson line in the background of the spin-3 black hole with a chemical potential. We find exact agreement.

Integrating process safety with molecular modeling-based risk assessment of chemicals within the REACH regulatory framework: benefits and future challenges.

Science.gov (United States)

Lewis, Amanda; Kazantzis, Nikolaos; Fishtik, Ilie; Wilcox, Jennifer

2007-04-11

Registration, evaluation and authorization of chemicals (REACH) represents a recent regulatory initiative by the European union commission to protect human health and the environment from potentially hazardous chemicals. Under REACH, all stakeholders must submit (thermo)physical, thermochemical, and toxicological data for certain chemicals. The commission's impact assessment studies estimate that the costs of REACH will be approximately 3-5 billion Euros. The present study advocates the systematic incorporation of computational chemistry and computer-assisted chemical risk assessment methods into REACH to reduce regulatory compliance costs. Currently powerful computer-aided ab initio techniques can be used to generate predictions of key properties of broad classes of chemicals, without resorting to costly experimentation and potentially hazardous testing. These data could be integrated into a centralized IT decision and compliance support system, and stored in a retrievable, easily communicable manner should new regulatory and/or production requirements necessitate the introduction of different uses of chemicals under different conditions. For illustration purposes, ab initio calculations are performed on heterocyclic nitrogen-containing compounds which currently serve as high energy density materials in the chemical industry. Since investigations of these compounds are still in their infancy, stability studies are imperative regarding their safe handling and storage, as well as registration under REACH.

Integrating process safety with molecular modeling-based risk assessment of chemicals within the REACH regulatory framework: Benefits and future challenges

International Nuclear Information System (INIS)

Lewis, Amanda; Kazantzis, Nikolaos; Fishtik, Ilie; Wilcox, Jennifer

2007-01-01

Registration, evaluation and authorization of chemicals (REACH) represents a recent regulatory initiative by the European union commission to protect human health and the environment from potentially hazardous chemicals. Under REACH, all stakeholders must submit (thermo)physical, thermochemical, and toxicological data for certain chemicals. The commission's impact assessment studies estimate that the costs of REACH will be approximately 3-5 billion Euros. The present study advocates the systematic incorporation of computational chemistry and computer-assisted chemical risk assessment methods into REACH to reduce regulatory compliance costs. Currently powerful computer-aided ab initio techniques can be used to generate predictions of key properties of broad classes of chemicals, without resorting to costly experimentation and potentially hazardous testing. These data could be integrated into a centralized IT decision and compliance support system, and stored in a retrievable, easily communicable manner should new regulatory and/or production requirements necessitate the introduction of different uses of chemicals under different conditions. For illustration purposes, ab initio calculations are performed on heterocyclic nitrogen-containing compounds which currently serve as high energy density materials in the chemical industry. Since investigations of these compounds are still in their infancy, stability studies are imperative regarding their safe handling and storage, as well as registration under REACH

Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

Science.gov (United States)

Kravchenko, Alexandra; Grandy, Stuart A.

2014-05-01

Understanding chemical structure of soil organic matter (SOM) and factors that affect it are vital for gaining understanding of mechanisms of C sequestration by soil. Physical protection of C by adsorption to mineral particles and physical disconnection between C sources and microbial decomposers is now regarded as the key component of soil C sequestration. Both of the processes are greatly influenced by micro-scale structure and distribution of soil pores. However, because SOM chemical structure is typically studied in disturbed (ground and sieved) soil samples the experimental evidence of the relationships between soil pore structure and chemical structure of SOM are still scarce. Our study takes advantage of the X-ray computed micro-tomography (µ-CT) tools that enable non-destructive analysis of pore structure in intact soil samples. The objective of this study is to examine the relationship between SOM chemical structure and pore-characteristics in intact soil macro-aggregates from two contrasting long-term land uses. The two studied land use treatments are a conventionally tilled corn-soybean-wheat rotation treatment and a native succession vegetation treatment removed from agricultural use >20 years ago. The study is located in southwest Michigan, USA, on sandy-loam Typic Hapludalfs. For this study we used soil macro-aggregates 4-6 mm in size collected at 0-15 cm depth. The aggregate size was selected so as both to enable high resolution of µ-CT and to provide sufficient amount of soil for C measurements. X-ray µ-CT scanning was conducted at APS Argonne at a scanning resolution of 14 µm. Two scanned aggregates (1 per treatment) were used in this preliminary study. Each aggregate was cut into 7 "geo-referenced" sections. Analyses of pore characteristics in each section were conducted using 3DMA and ImageJ image analysis tools. SOM chemistry was analyzed using pyrolysis/gas chromatography-mass spectroscopy. Results demonstrated that the relationships

Computer applications in thermochemistry

International Nuclear Information System (INIS)

Vana Varamban, S.

1996-01-01

Knowledge of equilibrium is needed under many practical situations. Simple stoichiometric calculations can be performed by the use of hand calculators. Multi-component, multi-phase gas - solid chemical equilibrium calculations are far beyond the conventional devices and methods. Iterative techniques have to be resorted. Such problems are most elegantly handled by the use of modern computers. This report demonstrates the possible use of computers for chemical equilibrium calculations in the field of thermochemistry and chemical metallurgy. Four modules are explained. To fit the experimental C p data and to generate the thermal functions, to perform equilibrium calculations to the defined conditions, to prepare the elaborate input to the equilibrium and to analyse the calculated results graphically. The principles of thermochemical calculations are briefly described. An extensive input guide is given. Several illustrations are included to help the understanding and usage. (author)

Computing in Engineering Education: From There, to Here, to Where? Part 1: Computing.

Science.gov (United States)

Carnahan, Brice

1991-01-01

Presents the 1990 American Society for Engineering Education award lecture for the Chemical Engineering Division. Following a brief outline of what the computing world includes, the lecture traces computing technology from the early years to milestones, as well as current trends, in both hardware and software development. Highlights the…

On Emulation of Flueric Devices in Excitable Chemical Medium.

Science.gov (United States)

Adamatzky, Andrew

2016-01-01

Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ) medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies.

On Emulation of Flueric Devices in Excitable Chemical Medium.

Directory of Open Access Journals (Sweden)

Andrew Adamatzky

Full Text Available Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences; Volume 128; Issue 1. Formation of BH3 Adducts with Pyridine-2-Methylaminophosphine ligands: An experimental and computational study. Harinath Adimulam Dwijendra P Kukri Bhabani S Mallik Tarun K Panda. Regular Articles Volume 128 Issue 1 January 2016 pp 53-60 ...

Reduced Chemical Kinetic Mechanisms for JP-8 Combustion

National Research Council Canada - National Science Library

Montgomery, Christopher J; Cannon, S. M; Mawid, M. A; Sekar, B

2002-01-01

Using CARM (Computer Aided Reduction Method), a computer program that automates the mechanism reduction process, six different reduced chemical kinetic mechanisms for JP-8 combustion have been generated...

A priori modeling of chemical reactions on computational grid platforms: Workflows and data models

International Nuclear Information System (INIS)

Rampino, S.; Monari, A.; Rossi, E.; Evangelisti, S.; Laganà, A.

2012-01-01

Graphical abstract: The quantum framework of the Grid Empowered Molecular Simulator GEMS assembled on the European Grid allows the ab initio evaluation of the dynamics of small systems starting from the calculation of the electronic properties. Highlights: ► The grid based GEMS simulator accurately models small chemical systems. ► Q5Cost and D5Cost file formats provide interoperability in the workflow. ► Benchmark runs on H + H 2 highlight the Grid empowering. ► O + O 2 and N + N 2 calculated k (T)’s fall within the error bars of the experiment. - Abstract: The quantum framework of the Grid Empowered Molecular Simulator GEMS has been assembled on the segment of the European Grid devoted to the Computational Chemistry Virtual Organization. The related grid based workflow allows the ab initio evaluation of the dynamics of small systems starting from the calculation of the electronic properties. Interoperability between computational codes across the different stages of the workflow was made possible by the use of the common data formats Q5Cost and D5Cost. Illustrative benchmark runs have been performed on the prototype H + H 2 , N + N 2 and O + O 2 gas phase exchange reactions and thermal rate coefficients have been calculated for the last two. Results are discussed in terms of the modeling of the interaction and advantages of using the Grid is highlighted.

Chapter 6 – Computer-Aided Molecular Design and Property Prediction

DEFF Research Database (Denmark)

Gani, Rafiqul; Zhang, L.; Kalakul, Sawitree

2017-01-01

for the initial stages of the design/development process. Therefore, computer-aided molecular design and property prediction techniques are two topics that play important roles in chemical product design, analysis, and application. In this chapter, an overview of the concepts, methods, and tools related......Today's society needs many chemical-based products for its survival, nutrition, health, transportation, agriculture, and the functioning of processes. Chemical-based products have to be designed/developed in order to meet these needs, while at the same time, they must be innovative and sustainable...... to these two topics are given. In addition, a generic computer-aided framework for the design of molecules, mixtures, and blends is presented. The application of the framework is highlighted for molecular products through two case studies involving the design of refrigerants and surfactants....

ACToR - Aggregated Computational Toxicology Resource

International Nuclear Information System (INIS)

Judson, Richard; Richard, Ann; Dix, David; Houck, Keith; Elloumi, Fathi; Martin, Matthew; Cathey, Tommy; Transue, Thomas R.; Spencer, Richard; Wolf, Maritja

2008-01-01

ACToR (Aggregated Computational Toxicology Resource) is a database and set of software applications that bring into one central location many types and sources of data on environmental chemicals. Currently, the ACToR chemical database contains information on chemical structure, in vitro bioassays and in vivo toxicology assays derived from more than 150 sources including the U.S. Environmental Protection Agency (EPA), Centers for Disease Control (CDC), U.S. Food and Drug Administration (FDA), National Institutes of Health (NIH), state agencies, corresponding government agencies in Canada, Europe and Japan, universities, the World Health Organization (WHO) and non-governmental organizations (NGOs). At the EPA National Center for Computational Toxicology, ACToR helps manage large data sets being used in a high-throughput environmental chemical screening and prioritization program called ToxCast TM

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

Science.gov (United States)

Wainwright, Camille L.

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

Interactive Chemical Safety for Sustainablity Toxicity Forecaster Dashboard

Data.gov (United States)

U.S. Environmental Protection Agency — EPA researchers have been using advances in computational toxicology to address lack of data on the thousands of chemicals. EPA released chemical data on 1,800...

Combinatorial computational chemistry approach of tight-binding quantum chemical molecular dynamics method to the design of the automotive catalysts

International Nuclear Information System (INIS)

Ito, Yuki; Jung, Changho; Luo, Yi; Koyama, Michihisa; Endou, Akira; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

2006-01-01

Recently, we have developed a new tight-binding quantum chemical molecular dynamics program 'Colors' for combinatorial computational chemistry approach. This methodology is based on our original tight-binding approximation and realized over 5000 times acceleration compared to the conventional first-principles molecular dynamics method. In the present study, we applied our new program to the simulations on various realistic large-scale models of the automotive three-way catalysts, ultrafine Pt particle/CeO 2 (111) support. Significant electron transfer from the Pt particle to the CeO 2 (111) surface was observed and it was found to strongly depend on the size of the Pt particle. Furthermore, our simulation results suggest that the reduction of the Ce atom due to the electron transfer from the Pt particle to the CeO 2 surface is a main reason for the strong interaction of the Pt particle and CeO 2 (111) support

Mathematical modeling and computational intelligence in engineering applications

CERN Document Server

Silva Neto, Antônio José da; Silva, Geraldo Nunes

2016-01-01

This book brings together a rich selection of studies in mathematical modeling and computational intelligence, with application in several fields of engineering, like automation, biomedical, chemical, civil, electrical, electronic, geophysical and mechanical engineering, on a multidisciplinary approach. Authors from five countries and 16 different research centers contribute with their expertise in both the fundamentals and real problems applications based upon their strong background on modeling and computational intelligence. The reader will find a wide variety of applications, mathematical and computational tools and original results, all presented with rigorous mathematical procedures. This work is intended for use in graduate courses of engineering, applied mathematics and applied computation where tools as mathematical and computational modeling, numerical methods and computational intelligence are applied to the solution of real problems.

A computational methodology for formulating gasoline surrogate fuels with accurate physical and chemical kinetic properties

KAUST Repository

Ahmed, Ahfaz; Goteng, Gokop; Shankar, Vijai; Al-Qurashi, Khalid; Roberts, William L.; Sarathy, Mani

2015-01-01

simpler molecular composition that represent real fuel behavior in one or more aspects are needed to enable repeatable experimental and computational combustion investigations. This study presents a novel computational methodology for formulating

Students' Computing Use and Study: When More is Less

Directory of Open Access Journals (Sweden)

Christine A McLachlan

2016-02-01

Full Text Available Since the turn of the century there has been a steady decline in enrolments of students in senior secondary computing classes in Australia. A flow on effect has seen reduced enrolments in tertiary computing courses and the subsequent predictions of shortages in skilled computing professionals. This paper investigates the relationship between students’ computing literacy levels, their use and access to computing tools, and students’ interest in and attitudes to formal computing study. Through the use of secondary data obtained from Australian and international reports, a reverse effect was discovered indicating that the more students used computing tools, the less interested they become in computing studies. Normal 0 false false false EN-AU X-NONE X-NONE

PHYSICO-CHEMICAL STUDIES OF DISAZO DYES DERIVED ...

African Journals Online (AJOL)

DJFLEX

with disazo disperse dyes on synthetic polymer-fibres. (Venkataraman, 1974; Otutu et al., 2008). In this present study, the physico-chemical studies of disazo dyes derived from p-aminophenol recently prepared by our research group is described. We also described the kinetics of the dyes on nylon 6 fibre. In another study.

Chemical kinetics of detonation in some liquid mixtures

Energy Technology Data Exchange (ETDEWEB)

Raikova, Vlada M.; Likholatov, Evgeny A. [Mendeleev University of Chemical Technology, Moscow (Russian Federation)

2005-09-01

The main objective of this work is to study the chemical kinetics of detonation reactions in some nitroester mixtures and solutions of nitrocompounds in concentrated nitric acid. The main source of information on chemical kinetics in the detonation wave was the experimental dependence of failure diameter on composition of mixtures. Calculations were carried out in terms of classic theory of Dremin using the SGKR computer code. Effective values for the activation energies and pre-exponential factors for detonation reactions in the mixtures under investigation have been defined. (Abstract Copyright [2005], Wiley Periodicals, Inc.)

Galaxy formation with radiative and chemical feedback

NARCIS (Netherlands)

Graziani, L.; Salvadori, S.; Schneider, R.; Kawata, D.; de Bennassuti, M.; Maselli, A.

Here we introduce GAMESH, a novel pipeline that implements self-consistent radiative and chemical feedback in a computational model of galaxy formation. By combining the cosmological chemical-evolution model GAMETE with the radiative transfer code CRASH, GAMESH can post-process realistic outputs of

The ORNL Chemical Technology Division, 1950-1994

Energy Technology Data Exchange (ETDEWEB)

Jolley, R.L.; Genung, R.K.; McNeese, L.E.; Mrochek, J.E.

1994-10-01

This document attempts to reconstruct the role played by the Chemical Technology Division (Chem Tech) of the Oak Ridge National Laboratory (ORNL) in the atomic era since the 1940`s related to the development and production of nuclear weapons and power reactors. Chem Tech`s early contributions were landmark pioneering studies. Unknown and dimly perceived problems like chemical hazards, radioactivity, and criticality had to be dealt with. New chemical concepts and processes had to be developed to test the new theories being developed by physicists. New engineering concepts had to be developed and demonstrated in order to build facilities and equipment that had never before been attempted. Chem Tech`s role was chemical separations, especially uranium and plutonium, and nuclear fuel reprocessing. With diversification of national and ORNL missions, Chem Tech undertook R&D studies in many areas including biotechnology; clinical and environmental chemistry; nuclear reactors; safety regulations; effective and safe waste management and disposal; computer modeling and informational databases; isotope production; and environmental control. The changing mission of Chem Tech are encapsulated in the evolving activities.

Mind the Gap! A Journey towards Computational Toxicology.

Science.gov (United States)

Mangiatordi, Giuseppe Felice; Alberga, Domenico; Altomare, Cosimo Damiano; Carotti, Angelo; Catto, Marco; Cellamare, Saverio; Gadaleta, Domenico; Lattanzi, Gianluca; Leonetti, Francesco; Pisani, Leonardo; Stefanachi, Angela; Trisciuzzi, Daniela; Nicolotti, Orazio

2016-09-01

Computational methods have advanced toxicology towards the development of target-specific models based on a clear cause-effect rationale. However, the predictive potential of these models presents strengths and weaknesses. On the good side, in silico models are valuable cheap alternatives to in vitro and in vivo experiments. On the other, the unconscious use of in silico methods can mislead end-users with elusive results. The focus of this review is on the basic scientific and regulatory recommendations in the derivation and application of computational models. Attention is paid to examine the interplay between computational toxicology and drug discovery and development. Avoiding the easy temptation of an overoptimistic future, we report our view on what can, or cannot, realistically be done. Indeed, studies of safety/toxicity represent a key element of chemical prioritization programs carried out by chemical industries, and primarily by pharmaceutical companies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bridging the Gap between Chemical Flooding and Independent Oil Producers

Energy Technology Data Exchange (ETDEWEB)

Stan McCool; Tony Walton; Paul Whillhite; Mark Ballard; Miguel Rondon; Kaixu Song; Zhijun Liu; Shahab Ahmed; Peter Senior

2012-03-31

Ten Kanas oil reservoirs/leases were studied through geological and engineering analysis to assess the potential performance of chemical flooding to recover oil. Reservoirs/leases that have been efficiently waterflooded have the highest performance potential for chemical flooding. Laboratory work to identify efficient chemical systems and to test the oil recovery performance of the systems was the major effort of the project. Efficient chemical systems were identified for crude oils from nine of the reservoirs/leases. Oil recovery performance of the identified chemical systems in Berea sandstone rocks showed 90+ % recoveries of waterflood residual oil for seven crude oils. Oil recoveries increased with the amount of chemical injected. Recoveries were less in Indiana limestone cores. One formulation recovered 80% of the tertiary oil in the limestone rock. Geological studies for nine of the oil reservoirs are presented. Pleasant Prairie, Trembley, Vinland and Stewart Oilfields in Kansas were the most favorable of the studied reservoirs for a pilot chemical flood from geological considerations. Computer simulations of the performance of a laboratory coreflood were used to predict a field application of chemical flooding for the Trembley Oilfield. Estimates of field applications indicated chemical flooding is an economically viable technology for oil recovery.

Quantum chemical investigation of levofloxacin-boron complexes: A computational approach

Science.gov (United States)

Sayin, Koray; Karakaş, Duran

2018-04-01

Quantum chemical calculations are performed over some boron complexes with levofloxacin. Boron complex with fluorine atoms are optimized at three different methods (HF, B3LYP and M062X) with 6-31 + G(d) basis set. The best level is determined as M062X/6-31 + G(d) by comparison of experimental and calculated results of complex (1). The other complexes are optimized by using the best level. Structural properties, IR and NMR spectrum are examined in detail. Biological activities of mentioned complexes are investigated by some quantum chemical descriptors and molecular docking analyses. As a result, biological activities of complex (2) and (4) are close to each other and higher than those of other complexes. Additionally, NLO properties of mentioned complexes are investigated by some quantum chemical parameters. It is found that complex (3) is the best candidate for NLO applications.

Measurement of breast tissue composition with dual energy cone-beam computed tomography: A postmortem study

Energy Technology Data Exchange (ETDEWEB)

Ding Huanjun; Ducote, Justin L.; Molloi, Sabee [Department of Radiological Sciences, University of California, Irvine, California 92697 (United States)

2013-06-15

Purpose: To investigate the feasibility of a three-material compositional measurement of water, lipid, and protein content of breast tissue with dual kVp cone-beam computed tomography (CT) for diagnostic purposes. Methods: Simulations were performed on a flat panel-based computed tomography system with a dual kVp technique in order to guide the selection of experimental acquisition parameters. The expected errors induced by using the proposed calibration materials were also estimated by simulation. Twenty pairs of postmortem breast samples were imaged with a flat-panel based dual kVp cone-beam CT system, followed by image-based material decomposition using calibration data obtained from a three-material phantom consisting of water, vegetable oil, and polyoxymethylene plastic. The tissue samples were then chemically decomposed into their respective water, lipid, and protein contents after imaging to allow direct comparison with data from dual energy decomposition. Results: Guided by results from simulation, the beam energies for the dual kVp cone-beam CT system were selected to be 50 and 120 kVp with the mean glandular dose divided equally between each exposure. The simulation also suggested that the use of polyoxymethylene as the calibration material for the measurement of pure protein may introduce an error of -11.0%. However, the tissue decomposition experiments, which employed a calibration phantom made out of water, oil, and polyoxymethylene, exhibited strong correlation with data from the chemical analysis. The average root-mean-square percentage error for water, lipid, and protein contents was 3.58% as compared with chemical analysis. Conclusions: The results of this study suggest that the water, lipid, and protein contents can be accurately measured using dual kVp cone-beam CT. The tissue compositional information may improve the sensitivity and specificity for breast cancer diagnosis.

Chemical structure and dynamics: Annual report 1993

Energy Technology Data Exchange (ETDEWEB)

Colson, S.D.

1994-07-01

The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

Synthesis, antimicrobial activities and computational studies of some ...

African Journals Online (AJOL)

The quantitative structure-antibacterial activity relationship was studied using some quantum chemical parameters with the aid of Spartan 10 (V1.0.1) and XLSTAT (add-in) software. A good correlation was observed between the antibacterial activity of the compounds and the calculated quantum chemical descriptors.

SCREENING CHEMICALS FOR ESTROGEN RECEPTOR BIOACTIVITY USING A COMPUTATIONAL MODEL

Science.gov (United States)

The U.S. Environmental Protection Agency (EPA) is considering the use high-throughput and computational methods for regulatory applications in the Endocrine Disruptor Screening Program (EDSP). To use these new tools for regulatory decision making, computational methods must be a...

Reprint of: Energetics of 2- and 3-coumaranone isomers: A combined calorimetric and computational study

International Nuclear Information System (INIS)

Sousa, Clara C.S.; Matos, M. Agostinha R.; Santos, Luís M.N.B.F.; Morais, Victor M.F.

2014-01-01

Highlights: • Experimental standard molar enthalpies of formation, sublimation of 2- and 3-coumaranone. • Mini-bomb combustion calorimetry, sublimation Calvet microcalorimetry. • DFT methods and high level composite ab initio calculations. • Theoretical estimate of the enthalpy of formation of isobenzofuranone. • Chemical shift (NICS) and the relative stability of the isomers. - Abstract: Condensed phase standard (p° = 0.1 MPa) molar enthalpies of formation for 2-coumaranone and 3-coumaranone were derived from the standard molar enthalpies of combustion, in oxygen, at T = 298.15 K, measured by mini-bomb combustion calorimetry. Standard molar enthalpies of sublimation of both isomers were determined by Calvet microcalorimetry. These results were combined to derive the standard molar enthalpies of formation of the compounds, in gas phase, at T = 298.15 K. Additionally, accurate quantum chemical calculations have been performed using DFT methods and high level composite ab initio calculations. Theoretical estimates of the enthalpies of formation of the compounds are in good agreement with the experimental values thus supporting the predictions of the same parameters for isobenzofuranone, an isomer which has not been experimentally studied. The relative stability of these isomers has been evaluated by experimental and computational results. The importance of some stabilizing electronic intramolecular interactions has been studied and quantitatively evaluated through Natural Bonding Orbital (NBO) analysis of the wave functions and the nucleus independent chemical shift (NICS) of the studied systems have been calculated in order to study and establish the effect of electronic delocalization upon the relative stability of the isomers

Computer stress study of bone with computed tomography

International Nuclear Information System (INIS)

Linden, M.J.; Marom, S.A.; Linden, C.N.

1986-01-01

A computer processing tool has been developed which, together with a finite element program, determines the stress-deformation pattern in a long bone, utilizing Computed Tomography (CT) data files for the geometry and radiographic density information. The geometry, together with mechanical properties and boundary conditions: loads and displacements, comprise the input of the Finite element (FE) computer program. The output of the program is the stresses and deformations in the bone. The processor is capable of developing an accurate three-dimensional finite element model from a scanned human long bone due to the CT high pixel resolution and the local mechanical properties determined from the radiographic densities of the scanned bone. The processor, together with the finite element program, serves first as an analysis tool towards improved understanding of bone function and remodelling. In this first stage, actual long bones may be scanned and analyzed under applied loads and displacements, determined from existing gait analyses. The stress-deformation patterns thus obtained may be used for studying the biomechanical behavior of particular long bones such as bones with implants and with osteoporosis. As a second stage, this processor may serve as a diagnostic tool for analyzing the biomechanical response of a specific patient's long long bone under applied loading by utilizing a CT data file of the specific bone as an input to the processor with the FE program

Positron computed tomography: current state, clinical results and future trends

International Nuclear Information System (INIS)

Schelbert, H.R.; Phelps, M.E.; Kuhl, D.E.

1980-01-01

An overview is presented of positron computed tomography: its advantages over single photon emission tomography, its use in metabolic studies of the heart and chemical investigation of the brain, and future trends

Computational Fluid Dynamics Methods and Their Applications in Medical Science

Directory of Open Access Journals (Sweden)

Kowalewski Wojciech

2016-12-01

Full Text Available As defined by the National Institutes of Health: “Biomedical engineering integrates physical, chemical, mathematical, and computational sciences and engineering principles to study biology, medicine, behavior, and health”. Many issues in this area are closely related to fluid dynamics. This paper provides an overview of the basic concepts concerning Computational Fluid Dynamics and its applications in medicine.

Interactive Chemical Safety for Sustainablity Toxicity Forecaster Dashboard

Science.gov (United States)

EPA researchers have been using advances in computational toxicology to address lack of data on the thousands of chemicals. EPA released chemical data on 1,800 chemicals. The 1,800 chemicals were screened in more than 800 rapid, automated tests (called high-throughput screening assays) to determine potential human health effects. The data is available through the interactive Chemical Safety for Sustainability Dashboards (iCSS dashboard) and the complete data sets are also available for download.

Kinetic studies of elementary chemical reactions

Energy Technology Data Exchange (ETDEWEB)

Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)

1993-12-01

This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

Study of the chemical sputtering in Tore-Supra

International Nuclear Information System (INIS)

Cambe, A.

2002-01-01

The work presented in this thesis focuses on the interactions between energetic particles coming from thermonuclear plasma and the inner components of a fusion machine. This interaction induces two major problems: erosion of the wall, and tritium retention. This report treats the erosion of carbon based materials. The first part is devoted to chemical sputtering, that appears to be the principal erosion mechanism, compared to physical sputtering and radiation enhanced sublimation that both can be limited. Chemical sputtering has been studied in situ in the tokamak Tore-Supra for ohmic and lower hybrid (LH) heated discharges, by means of mass spectrometry and optical spectroscopy. We have shown that it is necessary to take into account both methane and heavier hydrocarbons (C 2 D x and C 3 D y ) in the determination of the chemical sputtering yield. It is found that for the ohmic discharges, the sputtering yield of CD 4 (Y CD4 ) is highly flux (φ) dependent, showing a variation of the form: Y CD4 ∝ φ -0.23 . The experimental study also reveals that an increase of the surface temperature induces an augmentation of Y CD4 . The interpretation and the modelling of the experimental results have been performed with a Monte Carlo code (BBQ. In the second part of this work, we have developed and installed an infrared spectroscopy diagnostic in the 0.8-1.6, μm wavelength range dedicated to the measurement of surface temperature, and the identification of atomic and molecular lines emitted during plasma/wall interactions. In the third part, we present the feasibility study of an in situ tungsten deposition process at low temperature(<80 deg C) in order to suppress the chemical sputtering. This study shows that, with this method call Plasma Assisted Chemical Vapor Deposition (PACVD), we are able to coat the whole inner vessel of a tokamak with 1 μm of tungsten. (author)

Abstracts Book of 42. Scientific Assembly of Polish Chemical Society and Association of Engineers and Technicians of Chemical Industry

International Nuclear Information System (INIS)

1999-01-01

Scientific Assembly of Polish Chemical Society and Association of Engineers and Technicians of Chemical Industry is the most important chemical forum of Polish chemists organised annually. The state of art of many fundamental and applied investigations have been presented and discussed. The following scientific sessions and microsymposia have been proposed: plenary session, analytical chemistry, inorganic chemistry, organic chemistry, chemistry and environment, chemistry and technology of polymers, chemistry didactics, electrochemistry, young scientists forum, chemical technology, chemical engineering, high energetics materials, computers in research and teaching of chemistry, structure modelling and polymer properties, silicon-organic compounds

Computer Technology for Industry

Science.gov (United States)

1982-01-01

Shell Oil Company used a COSMIC program, called VISCEL to insure the accuracy of the company's new computer code for analyzing polymers, and chemical compounds. Shell reported that there were no other programs available that could provide the necessary calculations. Shell produces chemicals for plastic products used in the manufacture of automobiles, housewares, appliances, film, textiles, electronic equipment and furniture.

Computational Toxicology as Implemented by the US EPA ...

Science.gov (United States)

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, the U.S. Environmental Protection Agency EPA is developing robust and flexible computational tools that can be applied to the thousands of chemicals in commerce, and contaminant mixtures found in air, water, and hazardous-waste sites. The Office of Research and Development (ORD) Computational Toxicology Research Program (CTRP) is composed of three main elements. The largest component is the National Center for Computational Toxicology (NCCT), which was established in 2005 to coordinate research on chemical screening and prioritization, informatics, and systems modeling. The second element consists of related activities in the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL). The third and final component consists of academic centers working on various aspects of computational toxicology and funded by the U.S. EPA Science to Achieve Results (STAR) program. Together these elements form the key components in the implementation of both the initial strategy, A Framework for a Computational Toxicology Research Program (U.S. EPA, 2003), and the newly released The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the T

KinChem: A Computational Resource for Teaching and Learning Chemical Kinetics

Science.gov (United States)

da Silva, Jose´ Nunes, Jr.; Sousa Lima, Mary Anne; Silva Sousa, Eduardo Henrique; Oliveira Alexandre, Francisco Serra; Melo Leite, Antonio Jose´, Jr.

2014-01-01

This paper presents a piece of educational software covering a comprehensive number of topics of chemical kinetics, which is available free of charge in Portuguese and English. The software was developed to support chemistry educators and students in the teaching-learning process of chemical kinetics by using animations, calculations, and…

Positron Computed Tomography: Current State, Clinical Results and Future Trends

Science.gov (United States)

Schelbert, H. R.; Phelps, M. E.; Kuhl, D. E.

1980-09-01

An overview is presented of positron computed tomography: its advantages over single photon emission tomography, its use in metabolic studies of the heart and chemical investigation of the brain, and future trends. (ACR)

Positron computed tomography: current state, clinical results and future trends

Energy Technology Data Exchange (ETDEWEB)

Schelbert, H.R.; Phelps, M.E.; Kuhl, D.E.

1980-09-01

An overview is presented of positron computed tomography: its advantages over single photon emission tomography, its use in metabolic studies of the heart and chemical investigation of the brain, and future trends. (ACR)

X-ray micro computed tomography characterization of cellular SiC foams for their applications in chemical engineering

Energy Technology Data Exchange (ETDEWEB)

Ou, Xiaoxia [School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL (United Kingdom); Zhang, Xun; Lowe, Tristan [Henry Moseley X-ray Imaging Facility, Materials Science Centre, School of Materials, The University of Manchester, M13 9PL (United Kingdom); Blanc, Remi [FEI, 3 Impasse Rudolf Diesel, BP 50227, 33708 Mérignac (France); Rad, Mansoureh Norouzi [School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL (United Kingdom); Wang, Ying [Henry Moseley X-ray Imaging Facility, Materials Science Centre, School of Materials, The University of Manchester, M13 9PL (United Kingdom); Batail, Nelly; Pham, Charlotte [SICAT SARL, 20 Place des Halles, 67000 Strasbourg (France); Shokri, Nima; Garforth, Arthur A. [School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL (United Kingdom); Withers, Philip J. [Henry Moseley X-ray Imaging Facility, Materials Science Centre, School of Materials, The University of Manchester, M13 9PL (United Kingdom); Fan, Xiaolei, E-mail: xiaolei.fan@manchester.ac.uk [School of Chemical Engineering and Analytical Science, The University of Manchester, M13 9PL (United Kingdom)

2017-01-15

Open-cell SiC foams clearly are promising materials for continuous-flow chemical applications such as heterogeneous catalysis and distillation. X-ray micro computed tomography characterization of cellular β-SiC foams at a spatial voxel size of 13.6{sup 3} μm{sup 3} and the interpretation of morphological properties of SiC open-cell foams with implications to their transport properties are presented. Static liquid hold-up in SiC foams was investigated through in-situ draining experiments for the first time using the μ-CT technique providing thorough 3D information about the amount and distribution of liquid hold-up inside the foam. This will enable better modeling and design of structured reactors based on SiC foams in the future. In order to see more practical uses, μ-CT data of cellular foams must be exploited to optimize the design of the morphology of foams for a specific application. - Highlights: •Characterization of SiC foams using novel X-ray micro computed tomography. •Interpretation of structural properties of SiC foams regarding to their transport properties. •Static liquid hold-up analysis of SiC foams through in-situ draining experiments.

Computer Aided Methodology for Simultaneous Synthesis, Design & Analysis of Chemical Products-Processes

DEFF Research Database (Denmark)

d'Anterroches, Loïc; Gani, Rafiqul

2006-01-01

A new combined methodology for computer aided molecular design and process flowsheet design is presented. The methodology is based on the group contribution approach for prediction of molecular properties and design of molecules. Using the same principles, process groups have been developed...... a wide range of problems. In this paper, only the computer aided flowsheet design related features are presented....... together with their corresponding flowsheet property models. To represent the process flowsheets in the same way as molecules, a unique but simple notation system has been developed. The methodology has been converted into a prototype software, which has been tested with several case studies covering...

China's Chemical Information Online Service: ChI2Net.

Science.gov (United States)

Naiyan, Yu; And Others

1997-01-01

Describes the Chemical Integrated Information Service Network (ChI2Net), a comprehensive online information service system which includes chemical, technical, economic, market, news, and management information based on computer and modern communication technology that was built by the China National Chemical Information Centre. (Author/LRW)

General method and thermodynamic tables for computation of equilibrium composition and temperature of chemical reactions

Science.gov (United States)

Huff, Vearl N; Gordon, Sanford; Morrell, Virginia E

1951-01-01

A rapidly convergent successive approximation process is described that simultaneously determines both composition and temperature resulting from a chemical reaction. This method is suitable for use with any set of reactants over the complete range of mixture ratios as long as the products of reaction are ideal gases. An approximate treatment of limited amounts of liquids and solids is also included. This method is particularly suited to problems having a large number of products of reaction and to problems that require determination of such properties as specific heat or velocity of sound of a dissociating mixture. The method presented is applicable to a wide variety of problems that include (1) combustion at constant pressure or volume; and (2) isentropic expansion to an assigned pressure, temperature, or Mach number. Tables of thermodynamic functions needed with this method are included for 42 substances for convenience in numerical computations.

Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

Science.gov (United States)

Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

2008-06-01

A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

On several computer-oriented studies

International Nuclear Information System (INIS)

Takahashi, Ryoichi

1982-01-01

To utilize fully digital techniques for solving various difficult problems, nuclear engineers have recourse to computer-oriented approaches. The current trend, in such fields as optimization theory, control system theory and computational fluid dynamics reflect the ability to use computers to obtain numerical solutions to complex problems. Special purpose computers will be used as the integral part of the solving system to process a large amount of data, to implement a control law and even to produce a decision-making. Many problem-solving systems designed in the future will incorporate special-purpose computers as system component. The optimum use of computer system is discussed: why are energy model, energy data base and a big computer used; why will the economic process-computer be allocated to nuclear plants in the future; why should the super-computer be demonstrated at once. (Mori, K.)

Bayesian molecular design with a chemical language model

Science.gov (United States)

Ikebata, Hisaki; Hongo, Kenta; Isomura, Tetsu; Maezono, Ryo; Yoshida, Ryo

2017-04-01

The aim of computational molecular design is the identification of promising hypothetical molecules with a predefined set of desired properties. We address the issue of accelerating the material discovery with state-of-the-art machine learning techniques. The method involves two different types of prediction; the forward and backward predictions. The objective of the forward prediction is to create a set of machine learning models on various properties of a given molecule. Inverting the trained forward models through Bayes' law, we derive a posterior distribution for the backward prediction, which is conditioned by a desired property requirement. Exploring high-probability regions of the posterior with a sequential Monte Carlo technique, molecules that exhibit the desired properties can computationally be created. One major difficulty in the computational creation of molecules is the exclusion of the occurrence of chemically unfavorable structures. To circumvent this issue, we derive a chemical language model that acquires commonly occurring patterns of chemical fragments through natural language processing of ASCII strings of existing compounds, which follow the SMILES chemical language notation. In the backward prediction, the trained language model is used to refine chemical strings such that the properties of the resulting structures fall within the desired property region while chemically unfavorable structures are successfully removed. The present method is demonstrated through the design of small organic molecules with the property requirements on HOMO-LUMO gap and internal energy. The R package iqspr is available at the CRAN repository.

Cost effectiveness of dilute chemical decontamination

International Nuclear Information System (INIS)

LeSurf, J.E.; Weyman, G.D.

The basic principles of dilute chemical decontamination are described, as well as the method of application. Methods of computing savings in radiation dose and costs are presented, with results from actual experience and illustrative examples. It is concluded that dilute chemical decontamination is beneficial in many cases. It reduces radiation exposure of workers, saves money, and simplifies maintenance work

Measuring Impact of EPAs Computational Toxicology Research (BOSC)

Science.gov (United States)

Computational Toxicology (CompTox) research at the EPA was initiated in 2005. Since 2005, CompTox research efforts have made tremendous advances in developing new approaches to evaluate thousands of chemicals for potential health effects. The purpose of this case study is to trac...

Accurate quantum chemical calculations

Science.gov (United States)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Theoretical studies of chemical reaction dynamics

Energy Technology Data Exchange (ETDEWEB)

Schatz, G.C. [Argonne National Laboratory, IL (United States)

1993-12-01

This collaborative program with the Theoretical Chemistry Group at Argonne involves theoretical studies of gas phase chemical reactions and related energy transfer and photodissociation processes. Many of the reactions studied are of direct relevance to combustion; others are selected they provide important examples of special dynamical processes, or are of relevance to experimental measurements. Both classical trajectory and quantum reactive scattering methods are used for these studies, and the types of information determined range from thermal rate constants to state to state differential cross sections.

Flow-Injection Responses of Diffusion Processes and Chemical Reactions

DEFF Research Database (Denmark)

Andersen, Jens Enevold Thaulov

2000-01-01

tool of automated analytical chemistry. The need for an even lower consumption of chemicals and for computer analysis has motivated a study of the FIA peak itself, that is, a theoretical model was developed, that provides detailed knowledge of the FIA profile. It was shown that the flow in a FIA...... manifold may be characterised by a diffusion coefficient that depends on flow rate, denoted as the kinematic diffusion coefficient. The description was applied to systems involving species of chromium, both in the case of simple diffusion and in the case of chemical reactions. It is suggested that it may...... be used in the resolution of FIA profiles to obtain information about the content of interference’s, in the study of chemical reaction kinetics and to measure absolute concentrations within the FIA-detector cell....

Application of X-ray computed micro-tomography to the study of damage and oxidation kinetics of thermostructural composites

Energy Technology Data Exchange (ETDEWEB)

Caty, Olivier, E-mail: caty@lcts.u-bordeaux1.fr [Laboratory of Thermostructural Composites (LCTS), Université de Bordeaux, CNRS, SAFRAN, CEA, 3 Allée La Boétie, 33600 Pessac (France); Ibarroule, Philippe; Herbreteau, Mathieu; Rebillat, Francis [Laboratory of Thermostructural Composites (LCTS), Université de Bordeaux, CNRS, SAFRAN, CEA, 3 Allée La Boétie, 33600 Pessac (France); Maire, Eric [MATEIS Laboratory, INSA Lyon, 7 Avenue Jean Capelle, 69621 Villeurbanne Cedex (France); Vignoles, Gérard L. [Laboratory of Thermostructural Composites (LCTS), Université de Bordeaux, CNRS, SAFRAN, CEA, 3 Allée La Boétie, 33600 Pessac (France)

2014-04-01

Thermostructural composites are three-dimensionally (3D) structured materials. Weakening phenomena (mechanical and chemical) take place inside the material following its 3D structure and are thus hard to describe accurately. X-ray computed micro-tomography (μCT) is a recent solution that allows their experimental investigation. The technique is applied here to the study of failure under tensile loading and to the self healing processes during oxidation. Results are useful data to verify or invalidate hypotheses or estimations made in current models.

Study of interfacial phenomena for bio/chemical sensing applications

Science.gov (United States)

Min, Hwall

This work presents the fundamental study of biological and chemical interfacial phenomena and (bio)chemical sensing applications using high frequency resonator arrays. To realize a versatile (bio)chemical sensing system for the fundamental study as well as their practical applications, the following three distinct components were studied and developed: i) detection platforms with high sensitivity, ii) novel innovative sensing materials with high selectivity, iii) analytical model for data interpretation. 8-pixel micromachined quartz crystal resonator (muQCR) arrays with a fundamental resonance frequency of 60 ¡V 90 MHz have been used to provide a reliable detection platform with high sensitivity. Room temperature ionic liquid (RTIL) has been explored and integrated into the sensing system as a smart chemical sensing material. The use of nanoporous gold (np-Au) enables the combination of the resonator and surface-enhanced Raman spectroscopy for both quantitative and qualitative measurement. A statistical model for the characterization of resonator behavior to study the protein adsorption kinetics is developed by random sequential adsorption (RSA) approach with the integration of an effective surface depletion theory. The investigation of the adsorption kinetics of blood proteins is reported as the fundamental study of biological phenomena using the proposed sensing system. The aim of this work is to study different aspects of protein adsorption and kinetics of adsorption process with blood proteins on different surfaces. We specifically focus on surface depletion effect in conjunction with the RSA model to explain the observed adsorption isotherm characteristics. A number of case studies on protein adsorption conducted using the proposed sensing system has been discussed. Effort is specifically made to understand adsorption kinetics, and the effect of surface on the adsorption process as well as the properties of the adsorbed protein layer. The second half of the

A Codesign Case Study in Computer Graphics

DEFF Research Database (Denmark)

Brage, Jens P.; Madsen, Jan

1994-01-01

The paper describes a codesign case study where a computer graphics application is examined with the intention to speed up its execution. The application is specified as a C program, and is characterized by the lack of a simple compute-intensive kernel. The hardware/software partitioning is based...

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

Science.gov (United States)

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

2016-03-21

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

Mathematical study of chemical kinetics schemes. Application to air pollution models; Etude mathematique de schemas de cinetique chimique. Application a des modeles de pollution atmospherique

Energy Technology Data Exchange (ETDEWEB)

Billette, E.

1997-06-23

Complex chemical kinetics modelling is relevant in numerous fields related to the petroleum industry, for instance engine combustion, petrochemistry and atmospheric pollution. Many numerical difficulties are encountered in the computation of these models, mainly due to the large size, the non-linearity and the stiffness of the associated ordinary differential systems. We first studied systems that have an asymptotic behaviour which may be derived from an algebraic analysis. Then we reviewed different methods that make possible the reduction of size and stiffness for chemical kinetics-related differential systems, and suggest possible improvements for some of those methods. We also studied their application to atmospheric chemistry models. Finally, we started to extend those reduction methods to partial differential systems that include, in addition to chemical kinetics, other phenomena such as species emission, advection or diffusion. (author) 44 refs.

Computational studies of tokamak plasmas

International Nuclear Information System (INIS)

Takizuka, Tomonori; Tsunematsu, Toshihide; Tokuda, Shinji

1981-02-01

Computational studies of tokamak plasmas are extensively advanced. Many computational codes have been developed by using several kinds of models, i.e., the finite element formulation of MHD equations, the time dependent multidimensional fluid model, and the particle model with the Monte-Carlo method. These codes are applied to the analyses of the equilibrium of an axisymmetric toroidal plasma (SELENE), the time evolution of the high-beta tokamak plasma (APOLLO), the low-n MHD stability (ERATO-J) and high-n ballooning mode stability (BOREAS) in the INTOR tokamak, the nonlinear MHD stability, such as the positional instability (AEOLUS-P), resistive internal mode (AEOLUS-I) etc., and the divertor functions. (author)

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Science.gov (United States)

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

Catalytic Deoxydehydration of Carbohydrates and Polyols to Chemicals and Fuels

Energy Technology Data Exchange (ETDEWEB)

Nicholas, Kenneth M. [Univ. of Oklahoma, Norman, OK (United States)

2016-01-15

As the world's fossil fuel resources are being depleted and their costs increase, there is an urgent need to discover and develop new processes for the conversion of renewable, biomass resources into fuels and chemical feedstocks. Research and development in this area have been given high priority by both governmental agencies and industry. To increase the energy content and decrease the boiling points of biomass-derived carbohydrates and polyols to the useful liquid range it is necessary to chemically remove water (dehydrate) and, preferably, oxygen (deoxygenate/reduce). The poly-hydroxylic nature of carbohydrates is attractive for their use as functionalized chemical building blocks, but it presents a daunting challenge for their selective conversion to single product chemicals or fuels. The long term, practical objective of this project is to develop catalytic processes for the deoxydehydration (DODH) of biomass-derived carbohydrates and polyols to produce unsaturated alcohols and hydrocarbons of value as chemical feedstocks and fuels; DODH: polyol + reductant --(LMOx catalyst)--> unsaturate + oxidized reductant + H2O. Limited prior studies have established the viability of the DODH process with expensive phosphine reductants and rhenium-catalysts. Initial studies in the PI's laboratory have now demonstrated: 1) the moderately efficient conversion of glycols to olefins by the economical sulfite salts is catalyzed by MeReO3 and Z+ReO4-; 2) effective phosphine-based catalytic DODH of representative glycols to olefins by cheap LMoO2 complexes; and 3) computational studies (with K. Houk, UCLA) have identified several Mo-, W-, and V-oxo complexes that are likely to catalyze glycol DODH. Seeking practically useful DODH reactions of complex polyols and new understanding of the reactivity of polyoxo-metal species with biomass-oxygenates we will employ a two-pronged approach: 1) investigate experimentally the reactivity, both stoichiometric and catalytic, of

Sensitivity analysis of the Gupta and Park chemical models on the heat flux by DSMC and CFD codes

Science.gov (United States)

Morsa, Luigi; Festa, Giandomenico; Zuppardi, Gennaro

2012-11-01

The present study is the logical continuation of a former paper by the first author in which the influence of the chemical models by Gupta and by Park on the computation of heat flux on the Orion and EXPERT capsules was evaluated. Tests were carried out by the direct simulation Monte Carlo code DS2V and by the computational fluiddynamic (CFD) code H3NS. DS2V implements the Gupta model, while H3NS implements the Park model. In order to compare the effects of the chemical models, the Park model was implemented also in DS2V. The results showed that DS2V and H3NS compute a different composition both in the flow field and on the surface, even using the same chemical model (Park). Furthermore DS2V computes, by the two chemical models, different compositions in the flow field but the same composition on the surface, therefore the same heat flux. In the present study, in order to evaluate the influence of these chemical models also in a CFD code, the Gupta and the Park models have been implemented in FLUENT. Tests by DS2V and by FLUENT, have been carried out for the EXPERT capsule at the altitude of 70 km and with velocity of 5000 m/s. The capsule experiences a hypersonic, continuum low density regime. Due to the energy level of the flow, the vibration equation, lacking in the original version of FLUENT, has been implemented. The results of the heat flux computation verify that FLUENT is quite sensitive to the Gupta and to the Park chemical models. In fact, at the stagnation point, the percentage difference between the models is about 13%. On the opposite the DS2V results by the two models are practically equivalent.

NEW CHEMICAL PROFILES FOR THE ASTEROSEISMOLOGY OF ZZ CETI STARS

International Nuclear Information System (INIS)

Althaus, L. G.; Corsico, A. H.; Romero, A. D.; Miller Bertolami, M. M.; Bischoff-Kim, A.; Renedo, I.; Garcia-Berro, E.

2010-01-01

We compute new chemical profiles for the core and envelope of white dwarfs appropriate for pulsational studies of ZZ Ceti stars. These profiles are extracted from the complete evolution of progenitor stars, evolved through the main sequence and the thermally pulsing asymptotic giant branch (AGB) stages, and from time-dependent element diffusion during white dwarf evolution. We discuss the importance of the initial-final mass relationship for the white dwarf carbon-oxygen composition. In particular, we find that the central oxygen abundance may be underestimated by about 15% if the white dwarf mass is assumed to be the hydrogen-free core mass before the first thermal pulse. We also discuss the importance for the chemical profiles expected in the outermost layers of ZZ Ceti stars of the computation of the thermally pulsing AGB phase and of the phase in which element diffusion is relevant. We find a strong dependence of the outer layer chemical stratification on the stellar mass. In particular, in the less massive models, the double-layered structure in the helium layer built up during the thermally pulsing AGB phase is not removed by diffusion by the time the ZZ Ceti stage is reached. Finally, we perform adiabatic pulsation calculations and discuss the implications of our new chemical profiles for the pulsational properties of ZZ Ceti stars. We find that the whole g-mode period spectrum and the mode-trapping properties of these pulsating white dwarfs as derived from our new chemical profiles are substantially different from those based on chemical profiles widely used in existing asteroseismological studies. Thus, we expect the asteroseismological models derived from our chemical profiles to be significantly different from those found thus far.

Human volunteer studies with non-pharmaceutical chemicals: metabolism and pharmacokinetic studies.

Science.gov (United States)

Wilks, M F; Woollen, B H

1994-06-01

1. Human volunteer studies are an essential part of drug development but their use in the area of non-pharmaceutical chemicals has so far been very limited. Such studies can have considerable value in the assessment and improvement of the safe use of chemicals. 2. Once metabolic pathways and target metabolites have been identified in volunteers this information can be used in studies in the workplace or in the general population. Studies should be performed selectively only if there is both a toxic hazard and a significant exposure potential. In addition, they should only be carried out if the required information cannot be obtained in any other way. 3. Volunteer studies with non-pharmaceuticals have become increasingly acceptable in the light of established international guidelines, no-fault compensation, improvements in study design and technical developments which allow the use of very low dose levels. The final decision on whether to carry out a study must always rest with an independent ethical committee. 4. The practical aspects of the study should be specified in a detailed protocol conforming with the principles of good clinical practice. The safety of volunteers must be of paramount concern throughout. Depending on the nature of the chemical and the study, it may be advisable to carry out studies in a clinical facility where equipment is available for the treatment of any emergencies that might occur. 5. Numerous investigators have now shown that human volunteer studies are ethically acceptable, practicable and yield important information. The risk to volunteers is minimal and this approach can lead to an improved foundation for occupational hygiene standards, more accurate risk assessment and thus better protection of the workforce and the general population.

Using Computer Simulations in Chemistry Problem Solving

Science.gov (United States)

Avramiotis, Spyridon; Tsaparlis, Georgios

2013-01-01

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

Chemical and radiation environmental risk management at the crossroads: Case studies

International Nuclear Information System (INIS)

Tran, N.; Burke, T.; Locke, P.

1999-01-01

Although many of the major environmental risk management decisions we face today require the simultaneous evaluation and control of both radiological and chemical risks, the separation of radiation and chemical risk management persists along legal, regulatory, programmatic, training and professional practice levels. In June 1998, a panel of 40 chemical and radiation risk experts met at an interactive workshop entitled 'Addressing the Similarities and Differences in Chemical and Radiation Environmental Risk Management,' in Annapolis, Maryland to discuss several perspectives on harmonizing chemical and radiation risk management approaches. At the conclusion of the meeting, workshop participants recommended that case studies of clean-up sites at which radioactive materials and hazardous chemical risks were addressed, be developed to help educate participants in the harmonization dialogue about their counterpart's issues, stimulate discussion and sharpen issues in a way that they can be resolved. Several key risk management issues that were highlighted from the discussion at the Annapolis meeting are being evaluated in the case studies. They include: decision criteria, costs and public/stakeholder input. This paper presents these key issues and the approach taken in the case studies. (author)

The Challenge '88 Project: Interfacing of Chemical Instruments to Computers.

Science.gov (United States)

Lyons, Jim; Verghese, Manoj

The main part of this project involved using a computer, either an Apple or an IBM, as a chart recorder for the infrared (IR) and nuclear magnetic resonance (NMR) spectrophotometers. The computer "reads" these machines and displays spectra on its monitor. The graphs can then be stored for future reference and manipulation. The program to…

Computer Simulation of Temperature Parameter for Diamond Formation by Using Hot-Filament Chemical Vapor Deposition

Directory of Open Access Journals (Sweden)

Chang Weon Song

2017-12-01

Full Text Available To optimize the deposition parameters of diamond films, the temperature, pressure, and distance between the filament and the susceptor need to be considered. However, it is difficult to precisely measure and predict the filament and susceptor temperature in relation to the applied power in a hot filament chemical vapor deposition (HF-CVD system. In this study, the temperature distribution inside the system was numerically calculated for the applied powers of 12, 14, 16, and 18 kW. The applied power needed to achieve the appropriate temperature at a constant pressure and other conditions was deduced, and applied to actual experimental depositions. The numerical simulation was conducted using the commercial computational fluent dynamics software ANSYS-FLUENT. To account for radiative heat-transfer in the HF-CVD reactor, the discrete ordinate (DO model was used. The temperatures of the filament surface and the susceptor at different power levels were predicted to be 2512–2802 K and 1076–1198 K, respectively. Based on the numerical calculations, experiments were performed. The simulated temperatures for the filament surface were in good agreement with the experimental temperatures measured using a two-color pyrometer. The results showed that the highest deposition rate and the lowest deposition of non-diamond was obtained at a power of 16 kW.

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Journal of Chemical Sciences. Dhurairajan senthilnathan. Articles written in Journal of Chemical Sciences. Volume 123 Issue 3 May 2011 pp 279-290. Biocatalysis of azidolysis of epoxides: Computational evidences on the role of halohydrin dehalogenase (HheC) · Dhurairajan senthilnathan ...

Non-Determinism: An Abstract Concept in Computer Science Studies

Science.gov (United States)

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,…

Versatile Optimization of Chemical Ordering in Bimetallic Nanoparticles

KAUST Repository

Kovács, Gábor

2017-01-05

Chemical ordering in bimetallic nanocrystallites can now be efficiently determined by density-functional calculations with the help of topological energy expressions. Herein, we deal with extending the usage of that computational scheme. We show that it enables one to structurally characterize bimetallic nanoparticles of less regular shapes than previously studied magic-type particles. In fcc Pd–Au particles of different shapes (cuboctahedral Pd58Au58, C3v Pd61Au61, cubic Pd68Au67, and truncated octahedral Pd70Au70), we identify the surface segregation of gold as the driving force to the lowest-energy chemical ordering. We applied the calculated descriptor values quantifying the segregation propensity of Au and energies of Pd–Au bonds in these ∼1.5 nm large particles to optimize and analyze the chemical ordering in 3.7–6 nm large Pd–Au particles. We also discuss how to predict the chemical ordering in nanoalloys at elevated temperatures. The present study paves the way to advanced structural investigations of nanoalloys to substantially accelerate their knowledge-driven engineering and manufacturing.

Versatile Optimization of Chemical Ordering in Bimetallic Nanoparticles

KAUST Repository

Ková cs, Gá bor; Kozlov, Sergey M.; Neyman, Konstantin M.

2017-01-01

Chemical ordering in bimetallic nanocrystallites can now be efficiently determined by density-functional calculations with the help of topological energy expressions. Herein, we deal with extending the usage of that computational scheme. We show that it enables one to structurally characterize bimetallic nanoparticles of less regular shapes than previously studied magic-type particles. In fcc Pd–Au particles of different shapes (cuboctahedral Pd58Au58, C3v Pd61Au61, cubic Pd68Au67, and truncated octahedral Pd70Au70), we identify the surface segregation of gold as the driving force to the lowest-energy chemical ordering. We applied the calculated descriptor values quantifying the segregation propensity of Au and energies of Pd–Au bonds in these ∼1.5 nm large particles to optimize and analyze the chemical ordering in 3.7–6 nm large Pd–Au particles. We also discuss how to predict the chemical ordering in nanoalloys at elevated temperatures. The present study paves the way to advanced structural investigations of nanoalloys to substantially accelerate their knowledge-driven engineering and manufacturing.

Quantifying chemical uncertainties in simulations of the ISM

Science.gov (United States)

Glover, Simon

2018-06-01

The ever-increasing power of large parallel computers now makes it possible to include increasingly sophisticated chemical models in three-dimensional simulations of the interstellar medium (ISM). This allows us to study the role that chemistry plays in the thermal balance of a realistically-structured, turbulent ISM, as well as enabling us to generated detailed synthetic observations of important atomic or molecular tracers. However, one major constraint on the accuracy of these models is the accuracy with which the input chemical rate coefficients are known. Uncertainties in these chemical rate coefficients inevitably introduce uncertainties into the model predictions. In this talk, I will review some of the methods we can use to quantify these uncertainties and to identify the key reactions where improved chemical data is most urgently required. I will also discuss a few examples, ranging from the local ISM to the high-redshift universe.

A novel method to measure conspicuous facial pores using computer analysis of digital-camera-captured images: the effect of glycolic acid chemical peeling.

Science.gov (United States)

Kakudo, Natsuko; Kushida, Satoshi; Tanaka, Nobuko; Minakata, Tatsuya; Suzuki, Kenji; Kusumoto, Kenji

2011-11-01

Chemical peeling is becoming increasingly popular for skin rejuvenation in dermatological esthetic surgery. Conspicuous facial pores are one of the most frequently encountered skin problems in women of all ages. This study was performed to analyze the effectiveness of reducing conspicuous facial pores using glycolic acid chemical peeling (GACP) based on a novel computer analysis of digital-camera-captured images. GACP was performed a total of five times at 2-week intervals in 22 healthy women. Computerized image analysis of conspicuous, open, and darkened facial pores was performed using the Robo Skin Analyzer CS 50. The number of conspicuous facial pores decreased significantly in 19 (86%) of the 22 subjects, with a mean improvement rate of 34.6%. The number of open pores decreased significantly in 16 (72%) of the subjects, with a mean improvement rate of 11.0%. The number of darkened pores decreased significantly in 18 (81%) of the subjects, with a mean improvement rate of 34.3%. GACP significantly reduces the number of conspicuous facial pores. The Robo Skin Analyzer CS 50 is useful for the quantification and analysis of 'pore enlargement', a subtle finding in dermatological esthetic surgery. © 2011 John Wiley & Sons A/S.

A mathematical basis for plant patterning derived from physico-chemical phenomena.

Science.gov (United States)

Beleyur, Thejasvi; Abdul Kareem, Valiya Kadavu; Shaji, Anil; Prasad, Kalika

2013-04-01

The position of leaves and flowers along the stem axis generates a specific pattern, known as phyllotaxis. A growing body of evidence emerging from recent computational modeling and experimental studies suggests that regulators controlling phyllotaxis are chemical, e.g. the plant growth hormone auxin and its dynamic accumulation pattern by polar auxin transport, and physical, e.g. mechanical properties of the cell. Here we present comprehensive views on how chemical and physical properties of cells regulate the pattern of leaf initiation. We further compare different computational modeling studies to understand their scope in reproducing the observed patterns. Despite a plethora of experimental studies on phyllotaxis, understanding of molecular mechanisms of pattern initiation in plants remains fragmentary. Live imaging of growth dynamics and physicochemical properties at the shoot apex of mutants displaying stable changes from one pattern to another should provide mechanistic insights into organ initiation patterns. Copyright © 2013 WILEY Periodicals, Inc.

Conformational, structural, vibrational and quantum chemical analysis on 4-aminobenzohydrazide and 4-hydroxybenzohydrazide--a comparative study.

Science.gov (United States)

Arjunan, V; Jayaprakash, A; Carthigayan, K; Periandy, S; Mohan, S

2013-05-01

Experimental and theoretical quantum chemical studies were carried out on 4-hydroxybenzohydrazide (4HBH) and 4-aminobenzohydrazide (4ABH) using FTIR and FT-Raman spectral data. The structural characteristics and vibrational spectroscopic analysis were carried performed by quantum chemical methods with the hybrid exchange-correlation functional B3LYP using 6-31G(**), 6-311++G(**) and aug-cc-pVDZ basis sets. The most stable conformer of the title compounds have been determined from the analysis of potential energy surface. The stable molecular geometries, electronic and thermodynamic parameters, IR intensities, harmonic vibrational frequencies, depolarisation ratio and Raman intensities have been computed. Molecular electrostatic potential and frontier molecular orbitals were constructed to understand the electronic properties. The potential energy distributions (PEDs) were calculated to explain the mixing of fundamental modes. The theoretical geometrical parameters and the fundamental frequencies were compared with the experimental. The interactions of hydroxy and amino group substitutions on the characteristic vibrations of the ring and hydrazide group have been analysed. Copyright © 2013 Elsevier B.V. All rights reserved.

Computational study on the molecular inclusion of andrographolide by cyclodextrin

Science.gov (United States)

Zhou, Hongwei; Lai, Wai-Ping; Zhang, Zhiqiang; Li, Wai-Kee; Cheung, Hon-Yeung

2009-03-01

Due to the poor water solubility of andrographolide (andro), an inclusion technique has been developed to modify its physical and chemical properties so as to improve its bioavailability. In contrast with the immense experimental studies on the inclusion complexes of andro:cyclodextrin, no computational study has so far been carried out on this system. In this work, preliminary docking experiments with AutoDock were performed. Density Functional Theory (DFT) and Austin Model 1 (AM1) calculations upon the docking instances were applied to investigate the two possible modes of molecular inclusions between andro and x-cyclodextrin ( xCD, where x is α, β or γ). Atoms-in-Molecules (AIM) analysis based on the B3LYP/cc-pVDZ wavefunction was applied to verify the existence of the intermolecular hydrogen bonds. It was found that the most stable complex among the six possible inclusion complexes was the one formed between andro and βCD with andro's decalin ring moiety wrapped by CD at a ratio of 1:1. The hydrogen bonds between andro and CD were responsible for the stability of the inclusion complexes. The calculated data were found to be consistent with the experimental results. Thus, the results of this study can aid new drug design processes.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

Science.gov (United States)

Mankodi, T K; Bhandarkar, U V; Puranik, B P

2017-08-28

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N 2 +N 2 →N 2 +2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N 4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Energy conversion technology by chemical processes

Energy Technology Data Exchange (ETDEWEB)

Oh, I W; Yoon, K S; Cho, B W [Korea Inst. of Science and Technology, Seoul (Korea, Republic of); and others

1996-12-01

The sharp increase in energy usage according to the industry development has resulted in deficiency of energy resources and severe pollution problems. Therefore, development of the effective way of energy usage and energy resources of low pollution is needed. Development of the energy conversion technology by chemical processes is also indispensable, which will replace the pollutant-producing and inefficient mechanical energy conversion technologies. Energy conversion technology by chemical processes directly converts chemical energy to electrical one, or converts heat energy to chemical one followed by heat storage. The technology includes batteries, fuel cells, and energy storage system. The are still many problems on performance, safety, and manufacturing of the secondary battery which is highly demanded in electronics, communication, and computer industries. To overcome these problems, key components such as carbon electrode, metal oxide electrode, and solid polymer electrolyte are developed in this study, followed by the fabrication of the lithium secondary battery. Polymer electrolyte fuel cell, as an advanced power generating apparatus with high efficiency, no pollution, and no noise, has many applications such as zero-emission vehicles, on-site power plants, and military purposes. After fabricating the cell components and operating the single cells, the fundamental technologies in polymer electrolyte fuel cell are established in this study. Energy storage technology provides the safe and regular heat energy, irrespective of the change of the heat energy sources, adjusts time gap between consumption and supply, and upgrades and concentrates low grade heat energy. In this study, useful chemical reactions for efficient storage and transport are investigated and the chemical heat storage technology are developed. (author) 41 refs., 90 figs., 20 tabs.

Programmable chemical controllers made from DNA

Science.gov (United States)

Chen, Yuan-Jyue; Dalchau, Neil; Srinivas, Niranjan; Phillips, Andrew; Cardelli, Luca; Soloveichik, David; Seelig, Georg

2013-10-01

Biological organisms use complex molecular networks to navigate their environment and regulate their internal state. The development of synthetic systems with similar capabilities could lead to applications such as smart therapeutics or fabrication methods based on self-organization. To achieve this, molecular control circuits need to be engineered to perform integrated sensing, computation and actuation. Here we report a DNA-based technology for implementing the computational core of such controllers. We use the formalism of chemical reaction networks as a 'programming language' and our DNA architecture can, in principle, implement any behaviour that can be mathematically expressed as such. Unlike logic circuits, our formulation naturally allows complex signal processing of intrinsically analogue biological and chemical inputs. Controller components can be derived from biologically synthesized (plasmid) DNA, which reduces errors associated with chemically synthesized DNA. We implement several building-block reaction types and then combine them into a network that realizes, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents.

Computer Vision for High-Throughput Quantitative Phenotyping: A Case Study of Grapevine Downy Mildew Sporulation and Leaf Trichomes.

Science.gov (United States)

Divilov, Konstantin; Wiesner-Hanks, Tyr; Barba, Paola; Cadle-Davidson, Lance; Reisch, Bruce I

2017-12-01

Quantitative phenotyping of downy mildew sporulation is frequently used in plant breeding and genetic studies, as well as in studies focused on pathogen biology such as chemical efficacy trials. In these scenarios, phenotyping a large number of genotypes or treatments can be advantageous but is often limited by time and cost. We present a novel computational pipeline dedicated to estimating the percent area of downy mildew sporulation from images of inoculated grapevine leaf discs in a manner that is time and cost efficient. The pipeline was tested on images from leaf disc assay experiments involving two F 1 grapevine families, one that had glabrous leaves (Vitis rupestris B38 × 'Horizon' [RH]) and another that had leaf trichomes (Horizon × V. cinerea B9 [HC]). Correlations between computer vision and manual visual ratings reached 0.89 in the RH family and 0.43 in the HC family. Additionally, we were able to use the computer vision system prior to sporulation to measure the percent leaf trichome area. We estimate that an experienced rater scoring sporulation would spend at least 90% less time using the computer vision system compared with the manual visual method. This will allow more treatments to be phenotyped in order to better understand the genetic architecture of downy mildew resistance and of leaf trichome density. We anticipate that this computer vision system will find applications in other pathosystems or traits where responses can be imaged with sufficient contrast from the background.

Microprocessors in automatic chemical analysis

International Nuclear Information System (INIS)

Goujon de Beauvivier, M.; Perez, J.-J.

1979-01-01

Application of microprocessors to programming and computing of solutions chemical analysis by a sequential technique is examined. Safety, performances reliability are compared to other methods. An example is given on uranium titration by spectrophotometry [fr

Molecular models of zinc phthalocyanines: semi-empirical molecular orbital computations and physicochemical properties studied by molecular mechanics simulations

International Nuclear Information System (INIS)

Gantchev, Tsvetan G.; van Lier, Johan E.; Hunting, Darel J.

2005-01-01

To build 3D-molecular models of Zinc-phthalocyanines (ZnPc) and to study their diverse chemical and photosensitization properties, we performed quantum mechanical molecular orbital (MO) semi-empirical (AM1) computations of the ground, excited singlet and triplet states as well as free radical (ionic) species. RHF and UHF (open shell) geometry optimizations led to near-perfect symmetrical ZnPc. Predicted ionization potentials (IP), electron affinities (EA) and lowest electronic transitions of ZnPc are in good agreement with the published experimental and theoretical data. The computation-derived D 4h /D 2h -symmetry 3D-structures of ground and excited states and free radicals of ZnPc, together with the frontier orbital energies and Mulliken electron population analysis enabled us to build robust molecular models. These models were used to predict important chemical-reactivity entities such as global electronegativity (χ), hardness (η) and local softness based on Fukui-functions analysis. Examples of molecular mechanics (MM) applications of the 3D-molecular models are presented as approaches to evaluate solvation free energy (ΔG 0 ) solv and to estimate ground- and excited- state oxidation/reduction potentials as well as intermolecular interactions and stability of ground and excited state dimers (exciplexes) and radical ion-pairs

Study on Physical Properties and Chemical Composition of Some Myanmar Gems

International Nuclear Information System (INIS)

Kyaw Myint Htoo; Tun Khin; Sein Htoon

2004-05-01

Physical properties of some Myanmar gems were studied by using refractometer, dichroscope, polariscope, SG test, UV test and microscope. Then, chemical composition were investigated by XRF-technique. After that, gem identification, evaluation, colour improvement were studied according to these physical properties and chemical composition

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

... Journals; Journal of Chemical Sciences. Ashoka G Samuelson. Articles written in Journal of Chemical Sciences ... Issue 6 November 2012 pp 1343-1352. Computational tools for mechanistic discrimination in the reductive and metathesis coupling reactions mediated by titanium(IV) isopropoxide · Akshai Kumar Ashoka G ...

Scalable Computational Chemistry: New Developments and Applications

Energy Technology Data Exchange (ETDEWEB)

Alexeev, Yuri [Iowa State Univ., Ames, IA (United States)

2002-01-01

The computational part of the thesis is the investigation of titanium chloride (II) as a potential catalyst for the bis-silylation reaction of ethylene with hexaclorodisilane at different levels of theory. Bis-silylation is an important reaction for producing bis(silyl) compounds and new C-Si bonds, which can serve as monomers for silicon containing polymers and silicon carbides. Ab initio calculations on the steps involved in a proposed mechanism are presented. This choice of reactants allows them to study this reaction at reliable levels of theory without compromising accuracy. The calculations indicate that this is a highly exothermic barrierless reaction. The TiCl₂ catalyst removes a 50 kcal/mol activation energy barrier required for the reaction without the catalyst. The first step is interaction of TiCl₂ with ethylene to form an intermediate that is 60 kcal/mol below the energy of the reactants. This is the driving force for the entire reaction. Dynamic correlation plays a significant role because RHF calculations indicate that the net barrier for the catalyzed reaction is 50 kcal/mol. They conclude that divalent Ti has the potential to become an important industrial catalyst for silylation reactions. In the programming part of the thesis, parallelization of different quantum chemistry methods is presented. The parallelization of code is becoming important aspects of quantum chemistry code development. Two trends contribute to it: the overall desire to study large chemical systems and the desire to employ highly correlated methods which are usually computationally and memory expensive. In the presented distributed data algorithms computation is parallelized and the largest arrays are evenly distributed among CPUs. First, the parallelization of the Hartree-Fock self-consistent field (SCF) method is considered. SCF method is the most common starting point for more accurate calculations. The Fock build (sub step of SCF) from AO integrals is

pyJac: Analytical Jacobian generator for chemical kinetics

Science.gov (United States)

Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

2017-06-01

Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using py

Electro Thermal Chemical Gun Technology Study

National Research Council Canada - National Science Library

Diamond, P

1999-01-01

.... Michael Stroscio. Electro Thermal Chemical (ETC) gun technology refers to the use of plasma devices in place of traditional chemical ignitors to initiate the burning of high energy propellants in a controlled manner...

Trends in supercomputers and computational physics

International Nuclear Information System (INIS)

Bloch, T.

1985-01-01

Today, scientists using numerical models explore the basic mechanisms of semiconductors, apply global circulation models to climatic and oceanographic problems, probe into the behaviour of galaxies and try to verify basic theories of matter, such as Quantum Chromo Dynamics by simulating the constitution of elementary particles. Chemists, crystallographers and molecular dynamics researchers develop models for chemical reactions, formation of crystals and try to deduce the chemical properties of molecules as a function of the shapes of their states. Chaotic systems are studied extensively in turbulence (combustion included) and the design of the next generation of controlled fusion devices relies heavily on computational physics. (orig./HSI)

ACToR Chemical Structure processing using Open Source ...

Science.gov (United States)

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

Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations

International Nuclear Information System (INIS)

Wu, Fuke; Tian, Tianhai; Rawlings, James B.; Yin, George

2016-01-01

The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in the work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.

Computer simulations of disordering kinetics in irradiated intermetallic compounds

International Nuclear Information System (INIS)

Spaczer, M.; Caro, A.; Victoria, M.; Diaz de la Rubia, T.

1994-01-01

Molecular-dynamics computer simulations of collision cascades in intermetallic Cu 3 Au, Ni 3 Al, and NiAl have been performed to study the nature of the disordering processes in the collision cascade. The choice of these systems was suggested by the quite accurate description of the thermodynamic properties obtained using embedded-atom-type potentials. Since melting occurs in the core of the cascades, interesting effects appear as a result of the superposition of the loss (and subsequent recovery) of the crystalline order and the evolution of the chemical order, both processes being developed on different time scales. In our previous simulations on Ni 3 Al and Cu 3 Au [T. Diaz de la Rubia, A. Caro, and M. Spaczer, Phys. Rev. B 47, 11 483 (1993)] we found a significant difference between the time evolution of the chemical short-range order (SRO) and the crystalline order in the cascade core for both alloys, namely the complete loss of the crystalline structure but only partial chemical disordering. Recent computer simulations in NiAl show the same phenomena. To understand these features we study the liquid phase of these three alloys and present simulation results concerning the dynamical melting of small samples, examining the atomic mobility, the relaxation time, and the saturation value of the chemical short-range order. An analytic model for the time evolution of the SRO is given

On Medium Chemical Reaction in Diffusion-Based Molecular Communication: a Two-Way Relaying Example

OpenAIRE

Farahnak-Ghazani, Maryam; Aminian, Gholamali; Mirmohseni, Mahtab; Gohari, Amin; Nasiri-Kenari, Masoumeh

2016-01-01

Chemical reactions are a prominent feature of molecular communication (MC) systems, with no direct parallels in wireless communications. While chemical reactions may be used inside the transmitter nodes, receiver nodes or the communication medium, we focus on its utility in the medium in this paper. Such chemical reactions can be used to perform computation over the medium as molecules diffuse and react with each other (physical-layer computation). We propose the use of chemical reactions for...

Programming in biomolecular computation

DEFF Research Database (Denmark)

Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

2011-01-01

Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem...... conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined...... by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways...

Writing Apprehension, Computer Anxiety and Telecomputing: A Pilot Study.

Science.gov (United States)

Harris, Judith; Grandgenett, Neal

1992-01-01

A study measured graduate students' writing apprehension and computer anxiety levels before and after using electronic mail, computer conferencing, and remote database searching facilities during an educational technology course. Results indicted postcourse computer anxiety levels significantly related to usage statistics. Precourse writing…

Numerical computation of space shuttle orbiter flow field

Science.gov (United States)

Tannehill, John C.

1988-01-01

A new parabolized Navier-Stokes (PNS) code has been developed to compute the hypersonic, viscous chemically reacting flow fields around 3-D bodies. The flow medium is assumed to be a multicomponent mixture of thermally perfect but calorically imperfect gases. The new PNS code solves the gas dynamic and species conservation equations in a coupled manner using a noniterative, implicit, approximately factored, finite difference algorithm. The space-marching method is made well-posed by special treatment of the streamwise pressure gradient term. The code has been used to compute hypersonic laminar flow of chemically reacting air over cones at angle of attack. The results of the computations are compared with the results of reacting boundary-layer computations and show excellent agreement.

Correlation study of chemical elements in phosphate ores

International Nuclear Information System (INIS)

Braganca, Maura Julia Camara da Silva

1999-07-01

Geological phenomena, 1) endogenous (volcanism, magmatic flow, metasomatism); 2) metamorphic (resultant of action of high temperature and pressure) and; 3) exogenous (intemperism, contamination) can modify the chemical composition of rocks soils. Thus, chemical elements with little mobility can be used as indicators of the previous geological situation before the occurrence of these phenomena and can sign the chemical composition of the initial formation. The elements with great mobility can already be used as indicators of the characteristic and intensity of the changes, can point out the influence factors and its space and time conditions. In this work the results of the study of phosphated samples ores coming from two alkaline-carbonatitic chimneys (Araxa and Catalao) and from a meta sedimentary rock (Patos de Minas), located phosphate rock deposit, are presented. The results were obtained using the instrumental neutron activation analysis, inductively coupled plasma-mass spectrometry (ICP-MS) and ICP-AES techniques. A comparison of the three types of samples ores, using chemical, crystallographic and statistical methods, shows that the Araxa and Catalao present some geochemical similarities and they are distinguished of Patos de Minas, despite its geographic proximity. (author)

Towards quantum chemistry on a quantum computer.

Science.gov (United States)

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

2010-02-01

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

Applied chemical engineering thermodynamics

CERN Document Server

Tassios, Dimitrios P

1993-01-01

Applied Chemical Engineering Thermodynamics provides the undergraduate and graduate student of chemical engineering with the basic knowledge, the methodology and the references he needs to apply it in industrial practice. Thus, in addition to the classical topics of the laws of thermodynamics,pure component and mixture thermodynamic properties as well as phase and chemical equilibria the reader will find: - history of thermodynamics - energy conservation - internmolecular forces and molecular thermodynamics - cubic equations of state - statistical mechanics. A great number of calculated problems with solutions and an appendix with numerous tables of numbers of practical importance are extremely helpful for applied calculations. The computer programs on the included disk help the student to become familiar with the typical methods used in industry for volumetric and vapor-liquid equilibria calculations.

Toxicity studies of drugs and chemicals in animals: An overview

Directory of Open Access Journals (Sweden)

S. Saganuwan

2017-12-01

Full Text Available Toxicity study is the investigation of either short or long-term toxic effects of a drug or chemical on animals. The toxicity is dose-dependent as asserted by Paracelsus over 500 years ago. However, short-term toxic effect is determined using median lethal dose (LD50 first introduced by Trevan in 1927 and revised many times. Presently there is a growing preponderance of rejection of scientific papers on acute toxicity study, simply because of the belief that in the current hazard and safety as-sessment of drugs and chemicals, LD50 values are no longer used. In view of this, literature search was carried out with a view to investigating the relevance of LD50 in development and assessment of drugs and chemicals. The findings revealed that in the past, many animals had been used for LD50 determination. OECD has reduced the number of test animals to 5–15 and presently it is further re-duced to 2–6. Acute toxicity study is being carried out in medicinal plants research and in the study of patent medicine. Although the application of LD50 has been drastically reduced, it is still applied and accepted in some parts of the world. Moreover, animals on which LD50 tests are conducted, should be allowed to die to see the end effect of the test drug or chemical because euthanisia of test animals may mask some toxicity signs of the test agents. Therefore, toxicity study of drugs and chemicals is a sci-entific process necessary for discovery and development of drugs as well as identification of potential toxicants.

Minimum Energy Pathways for Chemical Reactions

Science.gov (United States)

Walch, S. P.; Langhoff, S. R. (Technical Monitor)

1995-01-01

Computed potential energy surfaces are often required for computation of such parameters as rate constants as a function of temperature, product branching ratios, and other detailed properties. We have found that computation of the stationary points/reaction pathways using CASSCF/derivative methods, followed by use of the internally contracted CI method to obtain accurate energetics, gives useful results for a number of chemically important systems. The talk will focus on a number of applications to reactions leading to NOx and soot formation in hydrocarbon combustion.

Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

Directory of Open Access Journals (Sweden)

Mohammad Firoz Khan

2016-12-01

Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.

Reduced chemical kinetic mechanisms for NOx emission prediction in biomass combustion

DEFF Research Database (Denmark)

Houshfar, Ehsan; Skreiberg, Øyvind; Glarborg, Peter

2012-01-01

Because of the complex composition of biomass, the chemical mechanism contains many different species and therefore a large number of reactions. Although biomass gas‐phase combustion is fairly well researched and understood, the proposed mechanisms are still complex and need very long computational...... time and powerful hardware resources. A reduction of the mechanism for biomass volatile oxidation has therefore been performed to avoid these difficulties. The selected detailed mechanism in this study contains 81 species and 703 elementary reactions. Necessity analysis is used to determine which...... reactions and chemical species, that is, 35 species and 198 reactions, corresponding to 72% reduction in the number of reactions and, therefore, improving the computational time considerably. Yet, the model based on the reduced mechanism predicts correctly concentrations of NOx and CO that are essentially...

Integrating user studies into computer graphics-related courses.

Science.gov (United States)

Santos, B S; Dias, P; Silva, S; Ferreira, C; Madeira, J

2011-01-01

This paper presents computer graphics. Computer graphics and visualization are essentially about producing images for a target audience, be it the millions watching a new CG-animated movie or the small group of researchers trying to gain insight into the large amount of numerical data resulting from a scientific experiment. To ascertain the final images' effectiveness for their intended audience or the designed visualizations' accuracy and expressiveness, formal user studies are often essential. In human-computer interaction (HCI), such user studies play a similar fundamental role in evaluating the usability and applicability of interaction methods and metaphors for the various devices and software systems we use.

Challenging chemical concepts through charge density of molecules and crystals

International Nuclear Information System (INIS)

Gatti, Carlo

2013-01-01

Narrating my scientific career, I show in this paper how, starting as a computational and theoretical chemist, I got naturally involved with x-ray crystallographers because of the common interest in charge density and in the study of chemical bonds based on such an observable. The tools I devised and the conceptual developments I made to facilitate a profitable encounter between x-ray charge density and computational chemistry researchers are illustrated, with a special focus on the proposal and applications of the Source Function concept. (comment)

Preliminary study of chemical compositional data from Amazon ceramics

International Nuclear Information System (INIS)

Toyota, Rosimeiri G.; Munita, Casimiro S.; Luz, Fabio A.; Neves, Eduardo G.; Oliveira, Paulo M.S.

2005-01-01

Eighty seven ceramic samples from Acutuba, Lago Grande and Osvaldo archaeological sites located in the confluence of the rivers Negro and Solimoes were submitted to chemical analysis using instrumental neutron activation analysis to determine As, Ba, Ce, Co, Cr, Cs, Eu, Fe, Hf, K, La, Lu, Rb, Na, Nd, Sb, Sc, Sm, Ta, Tb, Th, Yb, Zn, and U. The database were studied using the Mahalanobis distance, and discriminant analysis. The results showed that the ceramics of each site differ from each other in chemical composition and that they form three different groups. Chemical classification of the ceramics suggests that vessels were made locally, as only ceramics from the same area show homogeneity of data. (author)

Chemical kinetic modeling of H{sub 2} applications

Energy Technology Data Exchange (ETDEWEB)

Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D. [Lawrence Livermore National Lab., CA (United States)] [and others

1995-09-01

Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamic computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.

Inventory Control: A Small Electronic Device for Studying Chemical Kinetics.

Science.gov (United States)

Perez-Rodriguez, A. L.; Calvo-Aguilar, J. L.

1984-01-01

Shows how the rate of reaction can be studied using a simple electronic device that overcomes the difficulty students encounter in solving the differential equations describing chemical equilibrium. The device, used in conjunction with an oscilloscope, supplies the voltages that represent the chemical variables that take part in the equilibrium.…

Viscous fingering and channeling in chemical enhanced oil recovery

Science.gov (United States)

Daripa, Prabir; Dutta, Sourav

2017-11-01

We have developed a hybrid numerical method based on discontinuous finite element method and modified method of characteristics to compute the multiphase multicomponent fluid flow in porous media in the context of chemical enhanced oil recovery. We use this method to study the effect of various chemical components on the viscous fingering and channeling in rectilinear and radial flow configurations. We will also discuss about the efficiency of various flooding schemes based on these understandings. Time permitting, we will discuss about the effect of variable injection rates in these practical setting. U.S. National Science Foundation Grant DMS-1522782.

Open Babel: An open chemical toolbox

Directory of Open Access Journals (Sweden)

O'Boyle Noel M

2011-10-01

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

Open Babel: An open chemical toolbox

Science.gov (United States)

2011-01-01

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

Computational/experimental studies of isolated, single component droplet combustion

Science.gov (United States)

Dryer, Frederick L.

1993-01-01

Isolated droplet combustion processes have been the subject of extensive experimental and theoretical investigations for nearly 40 years. The gross features of droplet burning are qualitatively embodied by simple theories and are relatively well understood. However, there remain significant aspects of droplet burning, particularly its dynamics, for which additional basic knowledge is needed for thorough interpretations and quantitative explanations of transient phenomena. Spherically-symmetric droplet combustion, which can only be approximated under conditions of both low Reynolds and Grashof numbers, represents the simplest geometrical configuration in which to study the coupled chemical/transport processes inherent within non-premixed flames. The research summarized here, concerns recent results on isolated, single component, droplet combustion under microgravity conditions, a program pursued jointly with F.A. Williams of the University of California, San Diego. The overall program involves developing and applying experimental methods to study the burning of isolated, single component droplets, in various atmospheres, primarily at atmospheric pressure and below, in both drop towers and aboard space-based platforms such as the Space Shuttle or Space Station. Both computational methods and asymptotic methods, the latter pursued mainly at UCSD, are used in developing the experimental test matrix, in analyzing results, and for extending theoretical understanding. Methanol, and the normal alkanes, n-heptane, and n-decane, have been selected as test fuels to study time-dependent droplet burning phenomena. The following sections summarizes the Princeton efforts on this program, describe work in progress, and briefly delineate future research directions.

Synthesis, structural characterization and quantum chemical studies of silicon-containing benzoic acid derivatives

Science.gov (United States)

Zaltariov, Mirela-Fernanda; Cojocaru, Corneliu; Shova, Sergiu; Sacarescu, Liviu; Cazacu, Maria

2016-09-01

The present paper is concerned with the synthesis and molecular structure investigation of two new benzoic acid derivatives having trimethylsilyl tails, 4-((trimethylsilyl)methoxy) and 4-(3-(trimethylsilyl)propoxy)benzoic acids. The structures of the novel compounds have been confirmed by X-ray crystallography, Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H and 13C NMR). The theoretical studies of molecules were conducted by using the quantum chemical methods, such as Density Functional Theory (DFT B3LYP/6-31 + G**), Hartree-Fock (HF/6-31 + G**) and semiempirical computations (PM3, PM6 and PM7). The optimized molecular geometries have been found to be in good agreement with experimental structures resulted from the X-ray diffraction. The maximum electronic absorption bands observed at 272-287 nm (UV-vis spectra) have been assigned to π → π* transitions, which were in reasonable agreement with the time dependent density functional theory (TD-DFT) calculations. The computed vibrational frequencies by DFT method were assigned and compared with the experimental FTIR spectra. The mapped electrostatic potentials revealed the reactive sites, which corroborated the observation of the dimer supramolecular structures formed in the crystals by hydrogen-bonding. The energies of frontier molecular orbitals (HOMO and LUMO), energy gap, dipole moment and molecular descriptors for the new compounds were calculated and discussed.

HExpoChem: a systems biology resource to explore human exposure to chemicals

DEFF Research Database (Denmark)

Taboureau, Olivier; Jacobsen, Ulrik Plesner; Kalhauge, Christian Gram

2013-01-01

of computational biology approaches are needed to assess the health risks of chemical exposure. Here we present HExpoChem, a tool based on environmental chemicals and their bioactivities on human proteins with the objective of aiding the qualitative exploration of human exposure to chemicals. The chemical...

Modeling of turbulent chemical reaction

Science.gov (United States)

Chen, J.-Y.

1995-01-01

Viewgraphs are presented on modeling turbulent reacting flows, regimes of turbulent combustion, regimes of premixed and regimes of non-premixed turbulent combustion, chemical closure models, flamelet model, conditional moment closure (CMC), NO(x) emissions from turbulent H2 jet flames, probability density function (PDF), departures from chemical equilibrium, mixing models for PDF methods, comparison of predicted and measured H2O mass fractions in turbulent nonpremixed jet flames, experimental evidence of preferential diffusion in turbulent jet flames, and computation of turbulent reacting flows.

Moessbauer study of the chemical state of gold in gold ores

International Nuclear Information System (INIS)

Wagner, F.E.; Marion, P.H.; Regnard, J.-R.

1986-01-01

Information on the chemical state of gold in gold ores has been obtained by 197 Au Moessbauer spectroscopy in cases where the state of this element cannot be determined by such standard methods as optical or electron microscopy. Ore concentrates consisting mainly of pyrite or arsenopyrite and roasted ore and matte samples were studied. The results yielded directly the respective amounts of metallic and chemically bound gold. Unless the gold is metallic, its chemical state in the ores turns out to be different from that in the minerals studied so far as reference materials. The chemical processes taking place during various treatments of the ores, such as roasting or leaching, can also be followed by Moessbauer spectroscopy. It is hoped that Moessbauer spectroscopy will eventually facilitate the development of more efficient methods of gold extraction

Computational Studies of Positive and Negative Streamers in Bubbles Suspended in Distilled Water

KAUST Repository

Sharma, Ashish

2017-01-05

We perform computational studies of nanosecond streamers generated in helium bubbles immersed in distilled water under high pressure conditions. The model takes into account the presence of water vapor in the gas bubble for an accurate description of the chemical kinetics of the discharge. We apply positive and negative trigger voltages much higher than the breakdown voltage and study the dynamic characteristics of the resulting discharge. We observe that, for high positive trigger voltages, the streamer moves along the surface of the gas bubble during the initial stages of the discharge. We also find a considerable difference in the evolution of the streamer discharge for positive and negative trigger voltages with more uniform volumetric distribution of species in the streamer channel for negative trigger voltages due to formation of multiple streamers. We also observe that the presence of water vapor does not influence the breakdown voltage of the discharge but greatly affects the composition of dominant species in the trail of the streamer channel.

Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

Subseabed Disposal Project chemical response studies. Annual report, October 1982-September 1983

International Nuclear Information System (INIS)

Brush, L.H.

1985-10-01

Studies of the chemical response of deep-sea sediments to a subseabed repository for high-level radioactive waste continued during Fiscal Year 1983. Chemical Response Studies comprise Waste Package, Near-Field, and Far-Field Studies. This year, as in the past, investigators in the US Subseabed Disposal Project (SDP) carried out most of these chemical response experiments with red clay from the MPG 1 study location 1500 km north of Hawaii. The results of all studies carried out to date imply that oxidized red clay would form a highly effective barrier to radionuclides that form cationic species, but that anionic radionuclides would begin to escape from the sediment to the overlying water column on the order of thousands of years after emplacement. In Fiscal Year 1984, investigators in the US SDP will initiate chemical response studies with mildly reduced Atlantic clay- and carbonate-rich sediments in cooperation with the Sediment Barrier Task Group of the Organization for Economic Cooperation and Development - Nuclear Energy Agency Coordinated Program on the Assessment of the Subseabed Disposal of Radioactive Waste (Seabed Working Group). The objective of these US studies will be to quantify the chemical response of Atlantic sediments to a subseabed repository with a level of confidence similar to that for Pacific red clay

Study of plasma-chemical NO-containing gas flow for treatment of wounds and inflammatory processes.

Science.gov (United States)

Pekshev, Alexander V; Shekhter, Anatoly B; Vagapov, Andrey B; Sharapov, Nikolay A; Vanin, Anatoly F

2018-02-28

This work is aimed at exhaustive and detailed study of chemical, physical and physico-chemical characteristics of NO-containing gas flow (NO-CGF) generated by a plasma-chemical generator of Plason device, which has been used in medical practice for more than 15 years for effectively healing wound and inflammatory conditions with exogenous nitric oxide (NO-therapy). Data was obtained on spatial structure of the gas flow, and values of its local parameters in axial and radial directions, such as nitric oxide content, velocity, temperature and mass flow density of nitric oxide, providing altogether the effectiveness of treatment by the exogenous NO-therapy method, were determined experimentally and by computations. It was demonstrated that plasma-chemical synthesis of NO from atmospheric air in a low direct current (DC) arc provides a high mass flow of nitric oxide at the level of 1.6-1.8 mg/s, while in the area of impact of NO-CGF on the biological tissue, on its axis, NO content is 400-600 ppm, flow velocity about 5 m/s, nitric oxide mass flow density 0.25-0.40 mg/(s·cm 2 ), temperature 40-60 °C. Tendencies were determined for designing new devices for further experimental biological and medical research in the field of NO-therapy: lowering the temperature of NO-CGF to ambient temperature will enable variation, in experiments, of the affecting flow parameters in a wide range up to their maximum values: NO content up to 2000 ppm, velocity up to 20 m/s, nitric oxide mass flow density up to 2.5 mg/(s·cm 2 ). Copyright © 2017. Published by Elsevier Inc.

Open-Source Software in Computational Research: A Case Study

Directory of Open Access Journals (Sweden)

Sreekanth Pannala

2008-04-01

Full Text Available A case study of open-source (OS development of the computational research software MFIX, used for multiphase computational fluid dynamics simulations, is presented here. The verification and validation steps required for constructing modern computational software and the advantages of OS development in those steps are discussed. The infrastructure used for enabling the OS development of MFIX is described. The impact of OS development on computational research and education in gas-solids flow, as well as the dissemination of information to other areas such as geophysical and volcanology research, is demonstrated. This study shows that the advantages of OS development were realized in the case of MFIX: verification by many users, which enhances software quality; the use of software as a means for accumulating and exchanging information; the facilitation of peer review of the results of computational research.

Case Studies in Library Computer Systems.

Science.gov (United States)

Palmer, Richard Phillips

Twenty descriptive case studies of computer applications in a variety of libraries are presented in this book. Computerized circulation, serial and acquisition systems in public, high school, college, university and business libraries are included. Each of the studies discusses: 1) the environment in which the system operates, 2) the objectives of…

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Wang, Chao [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Xu, Zhijie [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Lai, Kevin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Physical and Computational Sciences Directorate; Whyatt, Greg [Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Energy and Environment Directorate; Marcy, Peter W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sun, Xin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Energy and Transportation Science Division

2017-10-24

Part 1 of this paper presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO₂) capture. In this study, to generate data for WWC model validation, CO₂ mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work can account for both chemical absorption and desorption of CO₂ in MEA. In addition, the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO₂ across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry's constant and gas diffusivity in the non-reacting nitrous oxide (N₂O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO₂ reaction rate constants after using the N₂O/CO₂ analogy method. Finally, the calibrated model can be used to predict the CO₂ mass transfer in a WWC for a wider range of operating conditions.

Hispanic women overcoming deterrents to computer science: A phenomenological study

Science.gov (United States)

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

Computer processing of dynamic scintigraphic studies

International Nuclear Information System (INIS)

Ullmann, V.

1985-01-01

The methods are discussed of the computer processing of dynamic scintigraphic studies which were developed, studied or implemented by the authors within research task no. 30-02-03 in nuclear medicine within the five year plan 1981 to 85. This was mainly the method of computer processing radionuclide angiography, phase radioventriculography, regional lung ventilation, dynamic sequential scintigraphy of kidneys and radionuclide uroflowmetry. The problems are discussed of the automatic definition of fields of interest, the methodology of absolute volumes of the heart chamber in radionuclide cardiology, the design and uses are described of the multipurpose dynamic phantom of heart activity for radionuclide angiocardiography and ventriculography developed within the said research task. All methods are documented with many figures showing typical clinical (normal and pathological) and phantom measurements. (V.U.)

[A computer-aided image diagnosis and study system].

Science.gov (United States)

Li, Zhangyong; Xie, Zhengxiang

2004-08-01

The revolution in information processing, particularly the digitizing of medicine, has changed the medical study, work and management. This paper reports a method to design a system for computer-aided image diagnosis and study. Combined with some good idea of graph-text system and picture archives communicate system (PACS), the system was realized and used for "prescription through computer", "managing images" and "reading images under computer and helping the diagnosis". Also typical examples were constructed in a database and used to teach the beginners. The system was developed by the visual developing tools based on object oriented programming (OOP) and was carried into operation on the Windows 9X platform. The system possesses friendly man-machine interface.

How to compute isomerization energies of organic molecules with quantum chemical methods.

Science.gov (United States)

Grimme, Stefan; Steinmetz, Marc; Korth, Martin

2007-03-16

The reaction energies for 34 typical organic isomerizations including oxygen and nitrogen heteroatoms are investigated with modern quantum chemical methods that have the perspective of also being applicable to large systems. The experimental reaction enthalpies are corrected for vibrational and thermal effects, and the thus derived "experimental" reaction energies are compared to corresponding theoretical data. A series of standard AO basis sets in combination with second-order perturbation theory (MP2, SCS-MP2), conventional density functionals (e.g., PBE, TPSS, B3-LYP, MPW1K, BMK), and new perturbative functionals (B2-PLYP, mPW2-PLYP) are tested. In three cases, obvious errors of the experimental values could be detected, and accurate coupled-cluster [CCSD(T)] reference values have been used instead. It is found that only triple-zeta quality AO basis sets provide results close enough to the basis set limit and that sets like the popular 6-31G(d) should be avoided in accurate work. Augmentation of small basis sets with diffuse functions has a notable effect in B3-LYP calculations that is attributed to intramolecular basis set superposition error and covers basic deficiencies of the functional. The new methods based on perturbation theory (SCS-MP2, X2-PLYP) are found to be clearly superior to many other approaches; that is, they provide mean absolute deviations of less than 1.2 kcal mol-1 and only a few (computational thermochemistry methods.

Studi Perbandingan Layanan Cloud Computing

Directory of Open Access Journals (Sweden)

Afdhal Afdhal

2014-03-01

Full Text Available In the past few years, cloud computing has became a dominant topic in the IT area. Cloud computing offers hardware, infrastructure, platform and applications without requiring end-users knowledge of the physical location and the configuration of providers who deliver the services. It has been a good solution to increase reliability, reduce computing cost, and make opportunities to IT industries to get more advantages. The purpose of this article is to present a better understanding of cloud delivery service, correlation and inter-dependency. This article compares and contrasts the different levels of delivery services and the development models, identify issues, and future directions on cloud computing. The end-users comprehension of cloud computing delivery service classification will equip them with knowledge to determine and decide which business model that will be chosen and adopted securely and comfortably. The last part of this article provides several recommendations for cloud computing service providers and end-users.

Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations for solvent-based carbon capture. Part 2: Chemical absorption across a wetted wall column: Original Research Article: Hierarchical calibration and validation framework of bench-scale computational fluid dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Wang, Chao [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Xu, Zhijie [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Lai, Kevin [Pacific Northwest National Laboratory, Physical and Computational Sciences Directorate, Richland WA; Whyatt, Greg [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland WA; Marcy, Peter W. [Los Alamos National Laboratory, Statistical Sciences Group, Los Alamos NM; Sun, Xin [Oak Ridge National Laboratory, Energy and Transportation Science Division, Oak Ridge TN

2017-10-24

The first part of this paper (Part 1) presents a numerical model for non-reactive physical mass transfer across a wetted wall column (WWC). In Part 2, we improved the existing computational fluid dynamics (CFD) model to simulate chemical absorption occurring in a WWC as a bench-scale study of solvent-based carbon dioxide (CO2) capture. To generate data for WWC model validation, CO2 mass transfer across a monoethanolamine (MEA) solvent was first measured on a WWC experimental apparatus. The numerical model developed in this work has the ability to account for both chemical absorption and desorption of CO2 in MEA. In addition, the overall mass transfer coefficient predicted using traditional/empirical correlations is conducted and compared with CFD prediction results for both steady and wavy falling films. A Bayesian statistical calibration algorithm is adopted to calibrate the reaction rate constants in chemical absorption/desorption of CO2 across a falling film of MEA. The posterior distributions of the two transport properties, i.e., Henry’s constant and gas diffusivity in the non-reacting nitrous oxide (N2O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO2 reaction rate constants after using the N2O/CO2 analogy method. The calibrated model can be used to predict the CO2 mass transfer in a WWC for a wider range of operating conditions.

Determination of chemical parameters for the Schlema-Alberoda uranium tailings pile migration case study

International Nuclear Information System (INIS)

Bryan, N.; Vopalka, D.; Benes, P.; Stamberg, K.; Doubravova, K.

2004-01-01

A central aim of environmental chemistry is to develop an understanding of processes at the microscopic level, and to develop speciation models to simulate that behaviour, which may be used with transport codes to predict the fate of pollutants on the field scale. In fact, one objective of this HUPA project is to develop a coupled chemical transport computer code, which includes the effects of humic substances, and then apply it to three field scale test cases: 1. a deep hypothetical repository in a salt formation; 2. a shallow, sandy hypothetical repository; 3. a large pile of uranium mine tailings. This work concerns the third case study (U-tailings), which is based upon a real U-tailings pile at Schlema-Alberoda, near Dresden, Saxony, Germany. Environmental problems are inherently complex, and even apparently simple systems, such as a single metal ion interacting with a 'single' surface may be extremely complex. There have been considerable advances in computing power over the last few decades, unfortunately, in order to make calculations solvable in a reasonable time, the models used to simulate the chemistry of the system must be as simple as possible. The interaction between uranium and humic substances has been studied previously. However, the details of the interaction of uranyl cations with the material of the pile have not been modelled. Therefore, the objective here is to develop a simple model of this interaction, ready to use in the migration case study. Experiments were performed at the Czech Technical University, Prague and the data modelled at the University of Manchester. (orig.)

Computational Exposure Science: An Emerging Discipline to ...

Science.gov (United States)

Background: Computational exposure science represents a frontier of environmental science that is emerging and quickly evolving.Objectives: In this commentary, we define this burgeoning discipline, describe a framework for implementation, and review some key ongoing research elements that are advancing the science with respect to exposure to chemicals in consumer products.Discussion: The fundamental elements of computational exposure science include the development of reliable, computationally efficient predictive exposure models; the identification, acquisition, and application of data to support and evaluate these models; and generation of improved methods for extrapolating across chemicals. We describe our efforts in each of these areas and provide examples that demonstrate both progress and potential.Conclusions: Computational exposure science, linked with comparable efforts in toxicology, is ushering in a new era of risk assessment that greatly expands our ability to evaluate chemical safety and sustainability and to protect public health. The National Exposure Research Laboratory’s (NERL’s) Human Exposure and Atmospheric Sciences Division (HEASD) conducts research in support of EPA’s mission to protect human health and the environment. HEASD’s research program supports Goal 1 (Clean Air) and Goal 4 (Healthy People) of EPA’s strategic plan. More specifically, our division conducts research to characterize the movement of pollutants from the source

Using the world-wide computer network, Internet, in chemical sciences

International Nuclear Information System (INIS)

Edvardsen, Oe.

1995-01-01

Modern computer and information technology has opened up many possibilities for communicating various types of information efficiently throughout the world. A non-technical introduction to some of the available resources on the computer network, Internet, is given in this paper. Hints on where to start exploring the Internet and how to obtain information are provided. Methods of communicating between scientists, how to access archives, and modern multi-media information systems are described. Several examples of services available to chemists are shown. (au) (26 refs.)

Aggregated Computational Toxicology Online Resource

Data.gov (United States)

U.S. Environmental Protection Agency — Aggregated Computational Toxicology Online Resource (AcTOR) is EPA's online aggregator of all the public sources of chemical toxicity data. ACToR aggregates data...

Case studies in intelligent computing achievements and trends

CERN Document Server

Issac, Biju

2014-01-01

Although the field of intelligent systems has grown rapidly in recent years, there has been a need for a book that supplies a timely and accessible understanding of this important technology. Filling this need, Case Studies in Intelligent Computing: Achievements and Trends provides an up-to-date introduction to intelligent systems.This edited book captures the state of the art in intelligent computing research through case studies that examine recent developments, developmental tools, programming, and approaches related to artificial intelligence (AI). The case studies illustrate successful ma

Computer Assisted Instruction in Special Education Three Case Studies

Directory of Open Access Journals (Sweden)

İbrahim DOĞAN

2015-09-01

Full Text Available The purpose of this study is to investigate the computer use of three students attending the special education center. Students have mental retardation, hearing problem and physical handicap respectively. The maximum variation sampling is used to select the type of handicap while the convenience sampling is used to select the participants. Three widely encountered handicap types in special education are chosen to select the study participants. The multiple holistic case study design is used in the study. Results of the study indicate that teachers in special education prefer to use educational games and drill and practice type of computers programs. Also it is found that over use of the animation, text and symbols cause cognitive overload on the student with mental retardation. Additionally, it is also discovered that the student with hearing problem learn words better when the computers are used in education as compared to the traditional method. Furthermore the student with physical handicap improved his fine muscle control abilities besides planned course objectives when computers are used in special education.

G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

Science.gov (United States)

Lee, Hui Sun; Im, Wonpil

2016-04-01

Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.

US QCD computational performance studies with PERI

International Nuclear Information System (INIS)

Zhang, Y; Fowler, R; Huck, K; Malony, A; Porterfield, A; Reed, D; Shende, S; Taylor, V; Wu, X

2007-01-01

We report on some of the interactions between two SciDAC projects: The National Computational Infrastructure for Lattice Gauge Theory (USQCD), and the Performance Engineering Research Institute (PERI). Many modern scientific programs consistently report the need for faster computational resources to maintain global competitiveness. However, as the size and complexity of emerging high end computing (HEC) systems continue to rise, achieving good performance on such systems is becoming ever more challenging. In order to take full advantage of the resources, it is crucial to understand the characteristics of relevant scientific applications and the systems these applications are running on. Using tools developed under PERI and by other performance measurement researchers, we studied the performance of two applications, MILC and Chroma, on several high performance computing systems at DOE laboratories. In the case of Chroma, we discuss how the use of C++ and modern software engineering and programming methods are driving the evolution of performance tools

Physical Chemistry Chemical Kinetics and Reaction Mechanism

CERN Document Server

Trimm, Harold H

2011-01-01

Physical chemistry covers diverse topics, from biochemistry to materials properties to the development of quantum computers. Physical chemistry applies physics and math to problems that interest chemists, biologists, and engineers. Physical chemists use theoretical constructs and mathematical computations to understand chemical properties and describe the behavior of molecular and condensed matter. Their work involves manipulations of data as well as materials. Physical chemistry entails extensive work with sophisticated instrumentation and equipment as well as state-of-the-art computers. This

Chemical graph-theoretic cluster expansions

International Nuclear Information System (INIS)

Klein, D.J.

1986-01-01

A general computationally amenable chemico-graph-theoretic cluster expansion method is suggested as a paradigm for incorporation of chemical structure concepts in a systematic manner. The cluster expansion approach is presented in a formalism general enough to cover a variety of empirical, semiempirical, and even ab initio applications. Formally such approaches for the utilization of chemical structure-related concepts may be viewed as discrete analogues of Taylor series expansions. The efficacy of the chemical structure concepts then is simply bound up in the rate of convergence of the cluster expansions. In many empirical applications, e.g., boiling points, chromatographic separation coefficients, and biological activities, this rate of convergence has been observed to be quite rapid. More note will be made here of quantum chemical applications. Relations to questions concerning size extensivity of energies and size consistency of wave functions are addressed

Study of phenol extraction from coke-chemical sources

Energy Technology Data Exchange (ETDEWEB)

Catana, E.; Mateescu, I.; Giurcaneanu, V.; Bota, T.

1990-09-01

The paper presents an experimental study of the phase equilibrium in the coke-chemical tarphenols-solvent system (NaOH) solution and (phenolate solution) implied in the extraction of the phenols from coke-chemical sources. The possibility of using the phenolate solution as an extraction agent, thus making possible the improvement of the specific consumption and also simplifying the problem of the corrosion and of the waste water at the same time is presented. The influence of the solvent tar mass ratio on the selectivity of the process is discussed, this criterion being considered for establishing the conditions of the extraction. 2 figs., 7 tabs., 13 refs.

Application of computational systems biology to explore environmental toxicity hazards

DEFF Research Database (Denmark)

Audouze, Karine Marie Laure; Grandjean, Philippe

2011-01-01

Background: Computer-based modeling is part of a new approach to predictive toxicology.Objectives: We investigated the usefulness of an integrated computational systems biology approach in a case study involving the isomers and metabolites of the pesticide dichlorodiphenyltrichloroethane (DDT......) to ascertain their possible links to relevant adverse effects.Methods: We extracted chemical-protein association networks for each DDT isomer and its metabolites using ChemProt, a disease chemical biology database that includes both binding and gene expression data, and we explored protein-protein interactions...... using a human interactome network. To identify associated dysfunctions and diseases, we integrated protein-disease annotations into the protein complexes using the Online Mendelian Inheritance in Man database and the Comparative Toxicogenomics Database.Results: We found 175 human proteins linked to p,p´-DDT...

Remedial action assessment system (RAAS) - A computer-based methodology for conducting feasibility studies

International Nuclear Information System (INIS)

Buelt, J.L.; Stottlemyre, J.A.; White, M.K.

1991-01-01

Because of the great complexity and number of potential waste sites facing the US Department of Energy (DOE) for potential cleanup, the DOE is supporting the development of a computer-based methodology to streamline the remedial investigation/feasibility study process required for DOE operable units. DOE operable units are generally more complex in nature because of the existence of multiple waste sites within many of the operable units and the presence of mixed radioactive and hazardous chemical wastes. Consequently, Pacific Northwest Laboratory (PNL) is developing the Remedial Action Assessment System (RAAS), which is aimed at screening, linking, and evaluating established technology process options in support of conducting feasibility studies under the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). It is also intended to do the same in support of corrective measures studies required by the Resource Conservation and Recovery Act (RCRA). One of the greatest attributes of the RAAS project is that the computer interface with the user is being designed to be friendly, intuitive, and interactive. Consequently, the user interface employs menus, windows, help features, and graphical information while RAAS is in operation. During operation, each technology process option is represented by an open-quotes objectclose quotes module. Object-oriented programming is then used to link these unit processes into remedial alternatives. In this way, various object modules representing technology process options can communicate so that a linked set of compatible processes form an appropriate remedial alternative. Once the remedial alternatives are formed, they can be evaluated in terms of effectiveness, implementability, and cost

Use of high performance computing to examine the effectiveness of aquifer remediation

International Nuclear Information System (INIS)

Tompson, A.F.B.; Ashby, S.F.; Falgout, R.D.; Smith, S.G.; Fogwell, T.W.; Loosmore, G.A.

1994-06-01

Large-scale simulation of fluid flow and chemical migration is being used to study the effectiveness of pump-and-treat restoration of a contaminated, saturated aquifer. A three-element approach focusing on geostatistical representations of heterogeneous aquifers, high-performance computing strategies for simulating flow, migration, and reaction processes in large three-dimensional systems, and highly-resolved simulations of flow and chemical migration in porous formations will be discussed. Results from a preliminary application of this approach to examine pumping behavior at a real, heterogeneous field site will be presented. Future activities will emphasize parallel computations in larger, dynamic, and nonlinear (two-phase) flow problems as well as improved interpretive methods for defining detailed material property distributions

Computational fluid dynamics simulation for chemical looping combustion of coal in a dual circulation fluidized bed

International Nuclear Information System (INIS)

Su, Mingze; Zhao, Haibo; Ma, Jinchen

2015-01-01

Highlights: • CFD simulation of a 5 kW_t_h CLC reactor of coal was conducted. • Gas leakage, flow pattern and combustion efficiency of the reactor was analyzed. • Optimal condition was achieved based on operation characteristics understanding. - Abstract: A dual circulation fluidized bed system is widely accepted for chemical looping combustion (CLC) for enriching CO_2 from the utilization of fossil fuels. Due to the limitations of the measurement, the details of multiphase reactive flows in the interconnected fluidized bed reactors are difficult to obtain. Computational Fluid Dynamics (CFD) simulation provides a promising method to understand the hydrodynamics, chemical reaction, and heat and mass transfers in CLC reactors, which are very important for the rational design, optimal operation, and scaling-up of the CLC system. In this work, a 5 kW_t_h coal-fired CLC dual circulation fluidized bed system, which was developed by our research group, was first simulated for understanding gas leakage, flow pattern and combustion efficiency. The simulation results achieved good agreement with the experimental measurements, which validates the simulation model. Subsequently, to improve the combustion efficiency, a new operation condition was simulated by increasing the reactor temperature and decreasing the coal feeding. An improvement in the combustion efficiency was attained, and the simulation results for the new operation condition were also validated by the experimental measurements in the same CLC combustor. All of the above processes demonstrated the validity and usefulness of the simulation results to improve the CLC reactor operation.

Aberration studies and computer algebra

International Nuclear Information System (INIS)

Hawkes, P.W.

1981-01-01

The labour of calculating expressions for aberration coefficients is considerably lightened if a computer algebra language is used to perform the various substitutions and expansions involved. After a brief discussion of matrix representations of aberration coefficients, a particular language, which has shown itself to be well adapted to particle optics, is described and applied to the study of high frequency cavity lenses. (orig.)

Insight into the structures and stabilities of Tc and Re DMSA complexes: A computational study

International Nuclear Information System (INIS)

Blanco González, Alejandro; Hernández Valdés, Daniel; García Fleitas, Ariel; Rodríguez Riera, Zalua; Jáuregui Haza, Ulises

2016-01-01

Meso-2,3-dimercaptosuccinic acid (DMSA) is used in nuclear medicine as ligand for preparation of radiopharmaceuticals for diagnostic and therapy. DMSA has been the subject of numerous investigations during the past three decades and new and significant information of the chemistry and pharmacology of DMSA complexes have emerged. In comparison to other ligands, the structure of some DMSA complexes is unclear up today. The structures and applications of DMSA complexes are strictly dependent on the chemical conditions of their preparation, especially pH and the ratio of components. A computational study of M-DMSA (M = Tc, Re) complexes has been performed using density functional theory. Different isomers for M(V) and M(III) complexes were study. The pH influence over ligand structures was taken into account and the solvent effect was evaluated using an implicit solvation model. The fully optimized complex syn-endo Re(V)-DMSA shows a geometry similar to the X-ray data and was used to validate the methodology. Moreover, new alternative structures for the renal agent 99mTc(III)-DMSA were proposed and computationally studied. For two complex structures, a larger stability respect to that proposed in the literature was obtained. Furthermore, Tc(V)-DMSA complexes are more stable than the Tc(III)-DMSA proposed structures. In general, Re complexes are more stables than the corresponding Tc ones. (author)

A constrained approach to multiscale stochastic simulation of chemically reacting systems

KAUST Repository

Cotter, Simon L.; Zygalakis, Konstantinos C.; Kevrekidis, Ioannis G.; Erban, Radek

2011-01-01

Stochastic simulation of coupled chemical reactions is often computationally intensive, especially if a chemical system contains reactions occurring on different time scales. In this paper, we introduce a multiscale methodology suitable to address

Climate-based archetypes for the environmental fate assessment of chemicals.

Science.gov (United States)

Ciuffo, Biagio; Sala, Serenella

2013-11-15

Emissions of chemicals have been on the rise for years, and their impacts are greatly influenced by spatial differentiation. Chemicals are usually emitted locally but their impact can be felt both locally and globally, due to their chemical properties and persistence. The variability of environmental parameters in the emission compartment may affect the chemicals' fate and the exposure at different orders of magnitude. The assessment of the environmental fate of chemicals and the inherent spatial differentiation requires the use of multimedia models at various levels of complexity (from a simple box model to complex computational and high-spatial-resolution models). The objective of these models is to support ecological and human health risk assessment, by reducing the uncertainty of chemical impact assessments. The parameterisation of spatially resolved multimedia models is usually based on scenarios of evaluative environments, or on geographical resolutions related to administrative boundaries (e.g. countries/continents) or landscape areas (e.g. watersheds, eco-regions). The choice of the most appropriate scale and scenario is important from a management perspective, as a balance should be reached between a simplified approach and computationally intensive multimedia models. In this paper, which aims to go beyond the more traditional approach based on scale/resolution (cell, country, and basin), we propose and assess climate-based archetypes for the impact assessment of chemicals released in air. We define the archetypes based on the main drivers of spatial variability, which we systematically identify by adopting global sensitivity analysis techniques. A case study that uses the high resolution multimedia model MAPPE (Multimedia Assessment of Pollutant Pathways in the Environment) is presented. Results of the analysis showed that suitable archetypes should be both climate- and chemical-specific, as different chemicals (or groups of them) have different traits

Vulnerability assessment of chemical industry facilities in South Korea based on the chemical accident history

Science.gov (United States)

Heo, S.; Lee, W. K.; Jong-Ryeul, S.; Kim, M. I.

2016-12-01

The use of chemical compounds are keep increasing because of their use in manufacturing industry. Chemical accident is growing as the consequence of the chemical use increment. Devastating damages from chemical accidents are far enough to aware people's cautious about the risk of the chemical accident. In South Korea, Gumi Hydrofluoric acid leaking accident triggered the importance of risk management and emphasized the preventing the accident over the damage reducing process after the accident occurs. Gumi accident encouraged the government data base construction relate to the chemical accident. As the result of this effort Chemical Safety-Clearing-house (CSC) have started to record the chemical accident information and damages according to the Harmful Chemical Substance Control Act (HCSC). CSC provide details information about the chemical accidents from 2002 to present. The detail informations are including title of company, address, business type, accident dates, accident types, accident chemical compounds, human damages inside of the chemical industry facilities, human damage outside of the chemical industry facilities, financial damages inside of the chemical industry facilities, and financial damages outside of the chemical industry facilities, environmental damages and response to the chemical accident. Collected the chemical accident history of South Korea from 2002 to 2015 and provide the spatial information to the each accident records based on their address. With the spatial information, compute the data on ArcGIS for the spatial-temporal analysis. The spatial-temporal information of chemical accident is organized by the chemical accident types, damages, and damages on environment and conduct the spatial proximity with local community and environmental receptors. Find the chemical accident vulnerable area of South Korea from 2002 to 2015 and add the vulnerable area of total period to examine the historically vulnerable area from the chemical accident in

Children as Educational Computer Game Designers: An Exploratory Study

Science.gov (United States)

Baytak, Ahmet; Land, Susan M.; Smith, Brian K.

2011-01-01

This study investigated how children designed computer games as artifacts that reflected their understanding of nutrition. Ten 5th grade students were asked to design computer games with the software "Game Maker" for the purpose of teaching 1st graders about nutrition. The results from the case study show that students were able to…

FORMING SCHOOLCHILD’S PERSONALITY IN COMPUTER STUDY LESSONS AT PRIMARY SCHOOL

Directory of Open Access Journals (Sweden)

Natalia Salan

2017-04-01

Full Text Available The influence of computer on the formation of primary schoolchildren’s personality and their implementing into learning activity are considered in the article. Based on the materials of state standards and the Law of Ukraine on Higher Education the concepts “computer”, “information culture” are defined, modern understanding of the concept “basics of computer literacy” is identified. The main task of school propaedeutic course in Computer Studies is defined. Interactive methods of activity are singled out. They are didactic games, designing, research, collaboration in pairs, and group interaction, etc. The essential characteristics of didactic game technologies are distinguished, the peculiarities of their use at primary school in Computer Study lessons are analyzed. Positive and negative aspects of using these technologies in Computer Study lessons are defined. The expediency of using game technologies while organizing students’ educational and cognitive activity in Computer Studies is substantiated. The idea to create a school course “Computer Studies at primary school” is caused by the wide introduction of computer technics into the educational system. Today’s schoolchild has to be able to use a computer as freely and easily as he can use a pen, a pencil or a ruler. That’s why it is advisable to start studying basics of Computer Studies at the primary school age. This course is intended for the pupils of the 2nd-4th forms. Firstly, it provides mastering practical skills of computer work and, secondly, it anticipates the development of children’s logical and algorithmic thinking styles. At these lessons students acquire practical skills to work with information on the computer. Having mastered the computer skills at primary school, children will be able to use it successfully in their work. In senior classes they will be able to realize acquired knowledge of the methods of work with information, ways of problem solving

Tools for studying dry-cured ham processing by using computed tomography.

Science.gov (United States)

Santos-Garcés, Eva; Muñoz, Israel; Gou, Pere; Sala, Xavier; Fulladosa, Elena

2012-01-11

An accurate knowledge and optimization of dry-cured ham elaboration processes could help to reduce operating costs and maximize product quality. The development of nondestructive tools to characterize chemical parameters such as salt and water contents and a(w) during processing is of special interest. In this paper, predictive models for salt content (R(2) = 0.960 and RMSECV = 0.393), water content (R(2) = 0.912 and RMSECV = 1.751), and a(w) (R(2) = 0.906 and RMSECV = 0.008), which comprise the whole elaboration process, were developed. These predictive models were used to develop analytical tools such as distribution diagrams, line profiles, and regions of interest (ROIs) from the acquired computed tomography (CT) scans. These CT analytical tools provided quantitative information on salt, water, and a(w) in terms of content but also distribution throughout the process. The information obtained was applied to two industrial case studies. The main drawback of the predictive models and CT analytical tools is the disturbance that fat produces in water content and a(w) predictions.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

Science.gov (United States)

Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

2014-03-11

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

Computer Series, 99: Bits and Pieces, 39.

Science.gov (United States)

Moore, John W., Ed.

1989-01-01

Presents five computer programs: (1) Accurate Numerical Solutions of the One-Dimensional Schrodinger Equation; (2) NMR Simulation and Interactive Drill/Interpretation; (3) A Simple Computer Program for the Calculation of 13C-NMR Chemical Shifts; (4) Constants of 1:1 Complexes from NMR or Spectrophotometric Measurements; and (5) Saturation…

Researchers study decontamination of chemical, biological warfare agents

OpenAIRE

Trulove, Susan

2007-01-01

The U.S. Army Research Office has awarded Virginia Tech a $680,000 grant over two years to build an instrument that can be used to study the chemistry of gases that will decompose both chemical and biological warfare agents on surfaces.

Study of bone microarchitecture abnormalities in mice through microct due to U and Th chemical contamination

International Nuclear Information System (INIS)

Taam, Pedro; Lopes, Ricardo Tadeu; Lima, Inaya

2009-01-01

The di calcium phosphate, widely used to manufacture fertilizers and animal ration, is extracted from rock minerals. Some of these rocks, as fluoroapatite and collophanite, had together with the calcium phosphate, traces of elements as Fe, F, Mg, Mn, Th and U. Most of these elements are considered to be proper additives for fertilizers and animal ration. In the same time, the presence of U and Th is inappropriate and potentially harmful. The risks posed are more than radioactive exposure, it is rather chemical contamination and its biological effects, since U and Th have strong chemical affinity with many substances present in live organisms, specially phosphorus. The effects of U and Th in bone microarchiteture are still unknown. The aim of this work was to study bone microarchiteture changes in mice fed with animal ration enriched with uranyl phosphate and thorium nitrate, both compounds present in the nuclear fuel cycle. At regular intervals(24, 72, 120 and 168 hours after beginning of the enriched feeding) subjects were sacrificed, blood and bone samples were collected and U and Th levels measured through wavelength dispersive X ray fluorescence (WDXRF). We present the data of U and Th blood level and microarchiteture evaluation through micro computed tomography (microCT) for each mice studied. The results showed that the intake of U and Th does indeed affect bone porosity. (author)

Study of bone microarchitecture abnormalities in mice through microct due to U and Th chemical contamination

Energy Technology Data Exchange (ETDEWEB)

Taam, Pedro; Lopes, Ricardo Tadeu, E-mail: taam@lin.ufrj.b, E-mail: ricardo@lin.ufrj.b [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Inst. Alberto Luiz Coimbra de Pos Graduacao e Pesquisa de Engenharia. Lab. de Instrumentacao Nuclear; Lima, Inaya, E-mail: inaya@lin.ufrj.b [Universidade do Estado do Rio de Janeiro (UERJ), Nova Friburgo, RJ (Brazil). Instituto Politecnico

2009-07-01

The di calcium phosphate, widely used to manufacture fertilizers and animal ration, is extracted from rock minerals. Some of these rocks, as fluoroapatite and collophanite, had together with the calcium phosphate, traces of elements as Fe, F, Mg, Mn, Th and U. Most of these elements are considered to be proper additives for fertilizers and animal ration. In the same time, the presence of U and Th is inappropriate and potentially harmful. The risks posed are more than radioactive exposure, it is rather chemical contamination and its biological effects, since U and Th have strong chemical affinity with many substances present in live organisms, specially phosphorus. The effects of U and Th in bone microarchiteture are still unknown. The aim of this work was to study bone microarchiteture changes in mice fed with animal ration enriched with uranyl phosphate and thorium nitrate, both compounds present in the nuclear fuel cycle. At regular intervals(24, 72, 120 and 168 hours after beginning of the enriched feeding) subjects were sacrificed, blood and bone samples were collected and U and Th levels measured through wavelength dispersive X ray fluorescence (WDXRF). We present the data of U and Th blood level and microarchiteture evaluation through micro computed tomography (microCT) for each mice studied. The results showed that the intake of U and Th does indeed affect bone porosity. (author)

Evaluation of a semi-automated computer algorithm for measuring total fat and visceral fat content in lambs undergoing in vivo whole body computed tomography.

Science.gov (United States)

Rosenblatt, Alana J; Scrivani, Peter V; Boisclair, Yves R; Reeves, Anthony P; Ramos-Nieves, Jose M; Xie, Yiting; Erb, Hollis N

2017-10-01

Computed tomography (CT) is a suitable tool for measuring body fat, since it is non-destructive and can be used to differentiate metabolically active visceral fat from total body fat. Whole body analysis of body fat is likely to be more accurate than single CT slice estimates of body fat. The aim of this study was to assess the agreement between semi-automated computer analysis of whole body volumetric CT data and conventional proximate (chemical) analysis of body fat in lambs. Data were collected prospectively from 12 lambs that underwent duplicate whole body CT, followed by slaughter and carcass analysis by dissection and chemical analysis. Agreement between methods for quantification of total and visceral fat was assessed by Bland-Altman plot analysis. The repeatability of CT was assessed for these measures using the mean difference of duplicated measures. When compared to chemical analysis, CT systematically underestimated total and visceral fat contents by more than 10% of the mean fat weight. Therefore, carcass analysis and semi-automated CT computer measurements were not interchangeable for quantifying body fat content without the use of a correction factor. CT acquisition was repeatable, with a mean difference of repeated measures being close to zero. Therefore, uncorrected whole body CT might have an application for assessment of relative changes in fat content, especially in growing lambs. Copyright © 2017 Elsevier Ltd. All rights reserved.

History of EPI Suite™ and future perspectives on chemical property estimation in US Toxic Substances Control Act new chemical risk assessments.

Science.gov (United States)

Card, Marcella L; Gomez-Alvarez, Vicente; Lee, Wen-Hsiung; Lynch, David G; Orentas, Nerija S; Lee, Mari Titcombe; Wong, Edmund M; Boethling, Robert S

2017-03-22

Chemical property estimation is a key component in many industrial, academic, and regulatory activities, including in the risk assessment associated with the approximately 1000 new chemical pre-manufacture notices the United States Environmental Protection Agency (US EPA) receives annually. The US EPA evaluates fate, exposure and toxicity under the 1976 Toxic Substances Control Act (amended by the 2016 Frank R. Lautenberg Chemical Safety for the 21 st Century Act), which does not require test data with new chemical applications. Though the submission of data is not required, the US EPA has, over the past 40 years, occasionally received chemical-specific data with pre-manufacture notices. The US EPA has been actively using this and publicly available data to develop and refine predictive computerized models, most of which are housed in EPI Suite™, to estimate chemical properties used in the risk assessment of new chemicals. The US EPA develops and uses models based on (quantitative) structure-activity relationships ([Q]SARs) to estimate critical parameters. As in any evolving field, (Q)SARs have experienced successes, suffered failures, and responded to emerging trends. Correlations of a chemical structure with its properties or biological activity were first demonstrated in the late 19 th century and today have been encapsulated in a myriad of quantitative and qualitative SARs. The development and proliferation of the personal computer in the late 20 th century gave rise to a quickly increasing number of property estimation models, and continually improved computing power and connectivity among researchers via the internet are enabling the development of increasingly complex models.

Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution

DEFF Research Database (Denmark)

Eriksen, Janus J.; Olsen, Jógvan Magnus H.; Aidas, Kestutis

2011-01-01

to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations......In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...

Harnessing the Department of Energy’s High-Performance Computing Expertise to Strengthen the U.S. Chemical Enterprise

Energy Technology Data Exchange (ETDEWEB)

Dixon, David A.; Dupuis, Michel; Garrett, Bruce C.; Neaton, Jeffrey B.; Plata, Charity; Tarr, Matthew A.; Tomb, Jean-Francois; Golab, Joseph T.

2012-01-17

High-performance computing (HPC) is one area where the DOE has developed extensive expertise and capability. However, this expertise currently is not properly shared with or used by the private sector to speed product development, enable industry to move rapidly into new areas, and improve product quality. Such use would lead to substantial competitive advantages in global markets and yield important economic returns for the United States. To stimulate the dissemination of DOE's HPC expertise, the Council for Chemical Research (CCR) and the DOE jointly held a workshop on this topic. Four important energy topic areas were chosen as the focus of the meeting: Biomass/Bioenergy, Catalytic Materials, Energy Storage, and Photovoltaics. Academic, industrial, and government experts in these topic areas participated in the workshop to identify industry needs, evaluate the current state of expertise, offer proposed actions and strategies, and forecast the expected benefits of implementing those strategies.

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

Science.gov (United States)

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

2012-05-21

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

The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer.

Directory of Open Access Journals (Sweden)

Lei Chen

Full Text Available Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer.

Trends of chemical monitoring in power stations

International Nuclear Information System (INIS)

Winkler, R.; Venz, H.

1983-01-01

Frequently, the state-of-the-art of chemical monitoring in power plants is still determined by conservative methods. A thorough rationalization requires not only modern analytical procedures, but also the consideration of chemically affected processes in complex process analyses and the combination of automatic analyzers with available process computers. Using some examples, ways of reducing monitoring efforts without impairing safety and economy of nuclear power plant operation are pointed out. (author)

Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

Science.gov (United States)

Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

2018-02-01

Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

Time-resolved resonance fluorescence spectroscopy for study of chemical reactions in laser-induced plasmas.

Science.gov (United States)

Liu, Lei; Deng, Leimin; Fan, Lisha; Huang, Xi; Lu, Yao; Shen, Xiaokang; Jiang, Lan; Silvain, Jean-François; Lu, Yongfeng

2017-10-30

Identification of chemical intermediates and study of chemical reaction pathways and mechanisms in laser-induced plasmas are important for laser-ablated applications. Laser-induced breakdown spectroscopy (LIBS), as a promising spectroscopic technique, is efficient for elemental analyses but can only provide limited information about chemical products in laser-induced plasmas. In this work, time-resolved resonance fluorescence spectroscopy was studied as a promising tool for the study of chemical reactions in laser-induced plasmas. Resonance fluorescence excitation of diatomic aluminum monoxide (AlO) and triatomic dialuminum monoxide (Al 2 O) was used to identify these chemical intermediates. Time-resolved fluorescence spectra of AlO and Al 2 O were used to observe the temporal evolution in laser-induced Al plasmas and to study their formation in the Al-O 2 chemistry in air.

Study on chemical reactivity control of liquid sodium. Research program

International Nuclear Information System (INIS)

Saito, Jun-ichi; Ara, Kuniaki; Sugiyama, Ken-ichiro; Kitagawa, Hiroshi; Oka, Nobuki; Yoshioka, Naoki

2007-01-01

Liquid sodium has the excellent properties as coolant of the fast breeder reactor (FBR). On the other hand, it reacts high with water and oxygen. So an innovative technology to suppress the reactivity is desired. The purpose of this study is to control the chemical reactivity of liquid sodium by dispersing the nanometer-size metallic particles (we call them Nano-particles) into liquid sodium. We focus on the atomic interaction between Nano-particles and sodium atoms. And we try to apply it to suppress the chemical reactivity of liquid sodium. Liquid sodium dispersing Nano-particles is named 'Nano-fluid'. Research programs of this study are the Nano-particles production, the evaluation of reactivity suppression of liquid sodium and the feasibility study to FBR plant. In this paper, the research programs and status are described. The important factors for particle production were understood. In order to evaluate the chemical reactivity of Nano-fluid the research programs were planned. The feasibility of the application of Nano-fluid to the coolant of FBR plant was evaluated preliminarily from the viewpoint of design and operation. (author)

Spacelab experiment computer study. Volume 1: Executive summary (presentation)

Science.gov (United States)

Lewis, J. L.; Hodges, B. C.; Christy, J. O.

1976-01-01

A quantitative cost for various Spacelab flight hardware configurations is provided along with varied software development options. A cost analysis of Spacelab computer hardware and software is presented. The cost study is discussed based on utilization of a central experiment computer with optional auxillary equipment. Groundrules and assumptions used in deriving the costing methods for all options in the Spacelab experiment study are presented. The groundrules and assumptions, are analysed and the options along with their cost considerations, are discussed. It is concluded that Spacelab program cost for software development and maintenance is independent of experimental hardware and software options, that distributed standard computer concept simplifies software integration without a significant increase in cost, and that decisions on flight computer hardware configurations should not be made until payload selection for a given mission and a detailed analysis of the mission requirements are completed.

Discovery and Computational Rationalization of Diminishing Alternation in [n]Dendralenes.

Science.gov (United States)

Saglam, Mehmet F; Fallon, Thomas; Paddon-Row, Michael N; Sherburn, Michael S

2016-01-27

The [n]dendralenes are a family of acyclic hydrocarbons which, by virtue of their ability to rapidly generate structural complexity, have attracted significant recent synthetic attention. [3]Dendralene through [8]dendralene have been previously prepared but no higher member of the family has been reported to date. Here, we describe the first chemical syntheses of the "higher" dendralenes, [9]dendralene through [12]dendralene. We also report a detailed investigation into the spectroscopic properties and chemical reactivity of the complete family of fundamental hydrocarbons, [3]dendralene to [12]dendralene. These studies reveal the first case of diminishing alternation in behavior in a series of related structures. We also report a comprehensive series of computational studies, which trace this dampening oscillatory effect in both spectroscopic measurements and chemical reactivity to conformational preferences.

Algebraic computing program for studying the gauge theory

International Nuclear Information System (INIS)

Zet, G.

2005-01-01

An algebraic computing program running on Maple V platform is presented. The program is devoted to the study of the gauge theory with an internal Lie group as local symmetry. The physical quantities (gauge potentials, strength tensors, dual tensors etc.) are introduced either as equations in terms of previous defined quantities (tensors), or by manual entry of the component values. The components of the strength tensor and of its dual are obtained with respect to a given metric of the space-time used for describing the gauge theory. We choose a Minkowski space-time endowed with spherical symmetry and give some example of algebraic computing that are adequate for studying electroweak or gravitational interactions. The field equations are also obtained and their solutions are determined using the DEtools facilities of the Maple V computing program. (author)

An analysis of the CSNI/GREST core concrete interaction chemical thermodynamic benchmark exercise using the MPEC2 computer code

International Nuclear Information System (INIS)

Muramatsu, Ken; Kondo, Yasuhiko; Uchida, Masaaki; Soda, Kunihisa

1989-01-01

Fission product (EP) release during a core concrete interaction (CCI) is an important factor of the uncertainty associated with a source term estimation for an LWR severe accident. An analysis was made on the CCI Chemical Thermodynamic Benchmark Exercise organized by OECD/NEA/CSNI Group of Experts on Source Terms (GREST) for investigating the uncertainty in thermodynamic modeling for CCI. The benchmark exercise was to calculate the equilibrium FP vapor pressure for given system of temperature, pressure, and debris composition. The benchmark consisted of two parts, A and B. Part A was a simplified problem intended to test the numerical techniques. In part B, the participants were requested to use their own best estimate thermodynamic data base to examine the variability of the results due to the difference in thermodynamic data base. JAERI participated in this benchmark exercise with use of the MPEC2 code. Chemical thermodynamic data base needed for analysis of Part B was taken from the VENESA code. This report describes the computer code used, inputs to the code, and results from the calculation by JAERI. The present calculation indicates that the FP vapor pressure depends strongly on temperature and Oxygen potential in core debris and the pattern of dependency may be different for different FP elements. (author)

Improved inhalation technology for setting safe exposure levels for workplace chemicals

Science.gov (United States)

Stuart, Bruce O.

1993-01-01

Threshold Limit Values recommended as allowable air concentrations of a chemical in the workplace are often based upon a no-observable-effect-level (NOEL) determined by experimental inhalation studies using rodents. A 'safe level' for human exposure must then be estimated by the use of generalized safety factors in attempts to extrapolate from experimental rodents to man. The recent development of chemical-specific physiologically-based toxicokinetics makes use of measured physiological, biochemical, and metabolic parameters to construct a validated model that is able to 'scale-up' rodent response data to predict the behavior of the chemical in man. This procedure is made possible by recent advances in personal computer software and the emergence of appropriate biological data, and provides an analytical tool for much more reliable risk evaluation and airborne chemical exposure level setting for humans.

Physico-chemical studies of radiation effects in cells: Final report

International Nuclear Information System (INIS)

Powers, E.L.

1987-03-01

The career of Dr. E.L. Powers, a pioneer in the development of radiobiology, is reviewed. His initial research involved the effects of radiation and certain chemicals on Paramecium, associated ultrastructural studies on protozoan cells, responses of Rickettsia and bacteriophage to irradiation, and the development of techniques for studying bacterial spores. These efforts established the basic radiation biology of the spore and its importance in understanding the effects of free radicals, oxygen, and water. His recent research extended work on the dry spore to the very wet spore and to other selected chemical systems in aqueous suspension. 126 refs., 2 figs

Modelling of Mass Transfer Phenomena in Chemical and Biochemical Reactor Systems using Computational Fluid Dynamics

DEFF Research Database (Denmark)

Larsson, Hilde Kristina

the velocity and pressure distributions in a fluid. CFD also enables the modelling of several fluids simultaneously, e.g. gas bubbles in a liquid, as well as the presence of turbulence and dissolved chemicals in a fluid, and many other phenomena. This makes CFD an appreciated tool for studying flow structures......, mixing, and other mass transfer phenomena in chemical and biochemical reactor systems. In this project, four selected case studies are investigated in order to explore the capabilities of CFD. The selected cases are a 1 ml stirred microbioreactor, an 8 ml magnetically stirred reactor, a Rushton impeller...... and an ion-exchange reaction are also modelled and compared to experimental data. The thesis includes a comprehensive overview of the fundamentals behind a CFD software, as well as a more detailed review of the fluid dynamic phenomena investigated in this project. The momentum and continuity equations...

Studi Perbandingan Layanan Cloud Computing

OpenAIRE

Afdhal, Afdhal

2013-01-01

In the past few years, cloud computing has became a dominant topic in the IT area. Cloud computing offers hardware, infrastructure, platform and applications without requiring end-users knowledge of the physical location and the configuration of providers who deliver the services. It has been a good solution to increase reliability, reduce computing cost, and make opportunities to IT industries to get more advantages. The purpose of this article is to present a better understanding of cloud d...

Programming in biomolecular computation

DEFF Research Database (Denmark)

Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

2010-01-01

in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level......., by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete...

Hydro-chemical study of the evolution of interstellar pre-biotic molecules during the collapse of molecular clouds

International Nuclear Information System (INIS)

Majumdar, Liton; Das, Ankan; Chakrabarti, Sandip K.; Chakrabarti, Sonali

2012-01-01

One of the stumbling blocks for studying the evolution of interstellar molecules is the lack of adequate knowledge about the rate coefficients of various reactions which take place in the interstellar medium and molecular clouds. Some theoretical models of rate coefficients do exist in the literature for computing abundances of complex pre-biotic molecules. So far these have been used to study the abundances of these molecules in space. However, in order to obtain more accurate final compositions in these media, we have calculated the rate coefficients for the formation of some of the most important interstellar pre-biotic molecules by using quantum chemical theory. We use these rates inside our hydro-chemical model to examine the chemical evolution and final abundances of pre-biotic species during the collapsing phase of a proto-star. We find that a significant amount of various pre-biotic molecules could be produced during the collapse phase of a proto-star. We thoroughly study the formation of these molecules via successive neutral-neutral and radical-radical/radical-molecular reactions. We present the time evolution of the chemical species with an emphasis on how the production of these molecules varies with the depth of a cloud. We compare the formation of adenine in interstellar space using our rate-coefficients and using those obtained from existing theoretical models. Formation routes of the pre-biotic molecules are found to be highly dependent on the abundances of the reactive species and the rate coefficients involved in the reactions. The presence of grains strongly affects the abundances of the gas phase species. We also carry out a comparative study between different pathways available for the synthesis of adenine, alanine, glycine and other molecules considered in our network. Despite the huge abundances of the neutral reactive species, production of adenine is found to be strongly dominated by the radical-radical/radical-molecular reaction pathways

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

Science.gov (United States)

Nguyen, Q N; Bauschlicher, C W; Myers, D L; Jacobson, N S; Opila, E J

2017-12-14

Gaseous titanium hydroxide and oxyhydroxide species were studied with quantum chemical methods. The results are used in conjunction with an experimental transpiration study of titanium dioxide (TiO 2 ) in water vapor-containing environments at elevated temperatures to provide a thermodynamic description of the Ti(OH) 4 (g) and TiO(OH) 2 (g) species. The geometry and harmonic vibrational frequencies of these species were computed using the coupled-cluster singles and doubles method with a perturbative correction for connected triple substitutions [CCSD(T)]. For the OH bending and rotation, the B3LYP density functional theory was used to compute corrections to the harmonic approximations. These results were combined to determine the enthalpy of formation. Experimentally, the transpiration method was used with water contents from 0 to 76 mol % in oxygen or argon carrier gases for 20-250 h exposure times at 1473-1673 K. Results indicate that oxygen is not a key contributor to volatilization, and the primary reaction for volatilization in this temperature range is TiO 2 (s) + H 2 O(g) = TiO(OH) 2 (g). Data were analyzed with both the second and third law methods using the thermal functions derived from the theoretical calculations. The third law enthalpy of formation at 298.15 K for TiO(OH) 2 (g) at 298 K was -838.9 ± 6.5 kJ/mol, which compares favorably to the theoretical calculation of -838.7 ± 25 kJ/mol. We recommend the experimentally derived third law enthalpy of formation at 298.15 K for TiO(OH) 2 , the computed entropy of 320.67 J/mol·K, and the computed heat capacity [149.192 + (-0.02539)T + (8.28697 × 10 -6 )T 2 + (-15614.05)/T + (-5.2182 × 10 -11 )/T 2 ] J/mol-K, where T is the temperature in K.

Acoustic wave propagation in fluids with coupled chemical reactions

International Nuclear Information System (INIS)

Margulies, T.S.; Schwarz, W.H.

1984-08-01

This investigation presents a hydroacoustic theory which accounts for sound absorption and dispersion in a multicomponent mixture of reacting fluids (assuming a set of first-order acoustic equations without diffusion) such that several coupled reactions can occur simultaneously. General results are obtained in the form of a biquadratic characteristic equation (called the Kirchhoff-Langevin equation) for the complex propagation variable chi = - (α + iω/c) in which α is the attenuation coefficient, c is the phase speed of the progressive wave and ω is the angular frequency. Computer simulations of sound absorption spectra have been made for three different chemical systems, each comprised of two-step chemical reactions using physico-chemical data available in the literature. The chemical systems studied include: (1) water-dioxane, (2) aqueous solutions of glycine and (3) cobalt polyphosphate mixtures. Explicit comparisons are made between the exact biquadratic characteristic solution and the approximate equation (sometimes referred to as a Debye equation) previously applied to interpret the experimental data for the chemical reaction contribution to the absorption versus frequency. The relative chemical reaction and classical viscothermal contributions to the sound absorption are also presented. Several discrepancies that can arise when estimating thermodynamic data (chemical reaction heats or volume changes) for multistep chemical reaction systems when making dilute solution or constant density assumptions are discussed

Chemical Risk Evaluation: A Case Study in an Automotive Air Conditioner Production Facility

Directory of Open Access Journals (Sweden)

Tengku Hanidza T.I.

2010-01-01

Full Text Available There has been limited knowledge on worker’s exposure to chemicals used in the automotive industries. The purpose of this study is to assess chemical risk and to determine the adequacy of the existing control measures to reduce chemical exposure. A cross sectional survey was conducted in a factory involving installation and servicing of automotive air conditioner units. Qualitative exposure assessment was carried out following the Malaysian Chemical Health Risk Assessment Manual (CHRA. There were 180 employees, 156 workers worked in the production line, which constitutes six work units Tube fin pressed, Brazing, Welding, Final assembly, Piping and Kit II. From the chemical risk evaluation for each work unit, 26 chemical compounds were used. Most of the chemicals were irritants (eye and skin and some were asphyxiants and sensitizers. Based on the work assignment, 93 out of 180 (51.67% of the workers were exposed to chemicals. The highest numbers of workers exposed to chemicals were from the Brazing section (22.22% while the Final Assembly section was the lowest (1.67%. Health survey among the workers showed occurrence of eye irritation, skin irritation, and respiratory irritation, symptoms usually associated with chemical exposure. Using a risk rating matrix, several work process were identified as having ‘significant risk’. For these areas, the workers are at risk of adverse health effects since chemical exposure is not adequately controlled. This study recommends corrective actions be taken in order to control the level of exposure and to provide a safe work environment for workers.

Computer Facilitated Mathematical Methods in Chemical Engineering--Similarity Solution

Science.gov (United States)

Subramanian, Venkat R.

2006-01-01

High-performance computers coupled with highly efficient numerical schemes and user-friendly software packages have helped instructors to teach numerical solutions and analysis of various nonlinear models more efficiently in the classroom. One of the main objectives of a model is to provide insight about the system of interest. Analytical…

Does computer use affect the incidence of distal arm pain? A one-year prospective study using objective measures of computer use

DEFF Research Database (Denmark)

Mikkelsen, S.; Lassen, C. F.; Vilstrup, Imogen

2012-01-01

PURPOSE: To study how objectively recorded mouse and keyboard activity affects distal arm pain among computer workers. METHODS: Computer activities were recorded among 2,146 computer workers. For 52 weeks mouse and keyboard time, sustained activity, speed and micropauses were recorded with a soft......PURPOSE: To study how objectively recorded mouse and keyboard activity affects distal arm pain among computer workers. METHODS: Computer activities were recorded among 2,146 computer workers. For 52 weeks mouse and keyboard time, sustained activity, speed and micropauses were recorded...... with a software program installed on the participants' computers. Participants reported weekly pain scores via the software program for elbow, forearm and wrist/hand as well as in a questionnaire at baseline and 1-year follow up. Associations between pain development and computer work were examined for three pain...... were not risk factors for acute pain, nor did they modify the effects of mouse or keyboard time. Computer usage parameters were not associated with prolonged or chronic pain. A major limitation of the study was low keyboard times. CONCLUSION: Computer work was not related to the development...

Identification of Chemical Toxicity Using Ontology Information of Chemicals

Directory of Open Access Journals (Sweden)

Zhanpeng Jiang

2015-01-01

Full Text Available With the advance of the combinatorial chemistry, a large number of synthetic compounds have surged. However, we have limited knowledge about them. On the other hand, the speed of designing new drugs is very slow. One of the key causes is the unacceptable toxicities of chemicals. If one can correctly identify the toxicity of chemicals, the unsuitable chemicals can be discarded in early stage, thereby accelerating the study of new drugs and reducing the R&D costs. In this study, a new prediction method was built for identification of chemical toxicities, which was based on ontology information of chemicals. By comparing to a previous method, our method is quite effective. We hope that the proposed method may give new insights to study chemical toxicity and other attributes of chemicals.

LCA of Chemicals and Chemical Products

DEFF Research Database (Denmark)

Fantke, Peter; Ernstoff, Alexi

2018-01-01

This chapter focuses on the application of Life Cycle Assessment (LCA) to evaluate the environmental performance of chemicals as well as of products and processes where chemicals play a key role. The life cycle stages of chemical products, such as pharmaceuticals drugs or plant protection products......, are discussed and differentiated into extraction of abiotic and biotic raw materials, chemical synthesis and processing, material processing, product manufacturing, professional or consumer product use, and finally end-of-life . LCA is discussed in relation to other chemicals management frameworks and concepts...... including risk assessment , green and sustainable chemistry , and chemical alternatives assessment. A large number of LCA studies focus on contrasting different feedstocks or chemical synthesis processes, thereby often conducting a cradle to (factory) gate assessment. While typically a large share...

Endocrine Disruptor Screening Program (EDSP) Universe of Chemicals and General Validation Principles

Science.gov (United States)

This document was developed by the EPA to provide guidance to staff and managers regarding the EDSP universe of chemicals and general validation principles for consideration of computational toxicology tools for chemical prioritization.

Computational study of a High Pressure Turbine Nozzle/Blade Interaction

Science.gov (United States)

Kopriva, James; Laskowski, Gregory; Sheikhi, Reza

2015-11-01

A downstream high pressure turbine blade has been designed for this study to be coupled with the upstream uncooled nozzle of Arts and Rouvroit [1992]. The computational domain is first held to a pitch-line section that includes no centrifugal forces (linear sliding-mesh). The stage geometry is intended to study the fundamental nozzle/blade interaction in a computationally cost efficient manner. Blade/Nozzle count of 2:1 is designed to maintain computational periodic boundary conditions for the coupled problem. Next the geometry is extended to a fully 3D domain with endwalls to understand the impact of secondary flow structures. A set of systematic computational studies are presented to understand the impact of turbulence on the nozzle and down-stream blade boundary layer development, resulting heat transfer, and downstream wake mixing in the absence of cooling. Doing so will provide a much better understanding of stage mixing losses and wall heat transfer which, in turn, can allow for improved engine performance. Computational studies are performed using WALE (Wale Adapted Local Eddy), IDDES (Improved Delayed Detached Eddy Simulation), SST (Shear Stress Transport) models in Fluent.

CHEMSIMUL: A simulator for chemical kinetics

DEFF Research Database (Denmark)

Kirkegaard, P.; Bjergbakke, E.

1999-01-01

CHEMSIMUL is a computer program system for numerical simulation of chemical reaction systems. It can be used for modeling complex kinetics in many contexts, in particular radiolytic processes. It contains a translator module and a module for solving theresulting coupled nonlinear ordinary...

Chemical characterization, leach, and adsorption studies of solidified low-level wastes

International Nuclear Information System (INIS)

Walter, M.B.; Serne, R.J.; Jones, T.L.; McLaurine, S.B.

1986-12-01

Laboratory and field leaching experiments are beig conducted by Pacific Northwest Laboratory (PNL) to investigate the performance of solidified low-level nuclear waste in a typical, arid, near-surface disposal site. Under PNL's Special Waste Form Lysimeters-Arid Program, a field test facility was constructed to monitor the leaching of commercial solidified waste. Laboratory experiments were conducted to investigate the leaching and adsorption characteristics of the waste forms in contact with soil. Liquid radioactive wastes solidified in cement, vinyl ester-styrene, and bitumen were obtained from commercial boiling water and pressurized water reactors, and buried in a field leaching facility on the Hanford site in southeastern Washington State. Batch leaching, soil column adsorption, and soil/waste form column experiments were conducted in the laboratory, using small-scale cement waste forms and Hanford site ground water. The purpose of these experiments is to evaluate the ability of laboratory leaching tests to predict leaching under actual field conditions and to determine which mechanisms (i.e., diffusion, solubility, adsorption) actually control the concentration of radionuclides in the soil surrounding the waste form. Chemical and radionuclide analyses performed on samples collected from the field and laboratory experiments indicate strong adsorption of /sup 134,137/Cs and 85 Sr onto the Hanford site sediment. Small amounts of 60 Co are leached from the waste forms as very mobile species. Some 60 Co migrated through the soil at the same rate as water. Chemical constituents present in the reactor waste streams also found at elevated levels in the field and laboratory leachates include sodium, sulfate, magnesium, and nitrate. Plausible solid phases that could be controlling some of the chemical and radionuclide concentrations in the leachate were identified using the MINTEQ geochemical computer code

Mathematical challenges from theoretical/computational chemistry

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-12-31

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

Quantum chemical evaluation for the stability of liquid sodium containing titanium nanoparticles

International Nuclear Information System (INIS)

Suzuki, Ai; Inaba, Kenji; Ishizawa, Yukie; Miura, Ryuji; Hatakeyama, Nozomu; Miyamoto, Akira; Saito, Jun-ichi; Ara, Kuniaki

2015-01-01

Recently, liquid sodium containing titanium nanoparticles (LSnanop) have attracted considerable attention. In this study, suspension state of Ti nanoparticle in liquid sodium was quantum chemically evaluated. The atomic interaction between Ti nanoparticles and sodium atoms in the liquid sodium medium was investigated. There were some literatures which gained quantum chemical insight into a nanoparticle with the surrounding sodium atom. However, liquid sodium medium itself together with a Ti nanoparticle under the realistic temperature has not yet been investigated theoretically. To overcome the problem of conventional theoretical method, we applied computationally low-load Tight Binding Quantum Chemical Molecular Dynamics (TB-QCMD) calculation method to investigate the suspension state of the Ti nanoparticle in liquid sodium metal. (author)

XRD, vibrational spectra and quantum chemical studies of an anticancer drug: 6-Mercaptopurine.

Science.gov (United States)

Kumar, S Suresh; Athimoolam, S; Sridhar, B

2015-07-05

The single crystal of the hydrated anticancer drug, 6-Mercaptopurine (6-MP), has been grown by slow evaporation technique under room temperature. The structure was determined by single crystal X-ray diffraction. The vibrational spectral analysis was carried out using Laser Raman and FT-IR spectroscopy in the range of 3300-100 and 4000-400 cm(-1). The single crystal X-ray studies shows that the crystal packing is dominated by N-H⋯O and O-H⋯N classical hydrogen bonds leading to a hydrogen bonded ensemble. This classical hydrogen bonds were further connected through O-H⋯S hydrogen bond to form two primary ring R4(4)(16) and R4(4)(12) motifs. These two primary ring motifs are interlinked with each other to build a ladder like structure. These ladders are connected through N-H⋯N hydrogen bond along c-axis of the unit cell through chain C(5) motifs. Further, the strength of the hydrogen bonds is studied through vibrational spectral measurements. The shifting of bands due to the intermolecular interactions was also analyzed in the solid crystalline state. Geometrical optimizations of the drug molecule were done by Density Functional Theory (DFT) using the B3LYP function and Hartree-Fock (HF) level with 6-311++G(d,p) basis set. The optimized molecular geometry and computed vibrational spectra are compared with experimental results which show significant agreement. The natural bond orbital (NBO) analysis was carried out to interpret hyperconjugative interaction and intramolecular charge transfer (ICT). The chemical hardness, electro-negativity and chemical potential of the molecule are carried out by HOMO-LUMO plot. In which, the frontier orbitals has lower band gap value indicating the possible pharmaceutical activity of the molecule. Copyright © 2015 Elsevier B.V. All rights reserved.

Computational problems in engineering

CERN Document Server

Mladenov, Valeri

2014-01-01

This book provides readers with modern computational techniques for solving variety of problems from electrical, mechanical, civil and chemical engineering. Mathematical methods are presented in a unified manner, so they can be applied consistently to problems in applied electromagnetics, strength of materials, fluid mechanics, heat and mass transfer, environmental engineering, biomedical engineering, signal processing, automatic control and more.   • Features contributions from distinguished researchers on significant aspects of current numerical methods and computational mathematics; • Presents actual results and innovative methods that provide numerical solutions, while minimizing computing times; • Includes new and advanced methods and modern variations of known techniques that can solve difficult scientific problems efficiently.  

Computational study of the combustion and atmospheric decomposition of 2-methylfuran

KAUST Repository

Davis, Alexander C.

2013-08-22

There is a growing interest in alkylfurans as potential biofuels. Recent work has highlighted the need for further study of the atmospheric oxidation mechanism of 2-methylfuran (2MF). This study utilizes the high level composite computational methods, G4 and CBS-QB3, to determine the bond dissociation energies for the C-H bond in 2MF and the reaction enthalpies and barrier heights of several of the known possible initiation reaction pathways. This study also investigates the possible subsequent low temperature reaction pathways following the addition of OH and then O2 onto the 2MF ring. The placement of the OH and O2 on the ring, either cis or trans to each other, dictates the viability of subsequent reactions. Of particular interest is the observation that 1,4 H-migrations that abstract the hydrogen bound to the same carbon as the OH have abnormally low barrier height. This dramatic decrease puts the reaction barrier lower than concerted eliminations and 6-membered ring Waddington-type reactions. In addition, a novel reaction type, described as a Waddington concerted elimination, is reported herein. This reaction, when viable, is generally more favorable than other reactions. The results presented here are of interest to combustion modelers and atmospheric chemists, particularly those working on aromatic hydrocarbons and systems with conjugated double bonds. © 2013 American Chemical Society.

A Grid-Based Cyber Infrastructure for High Performance Chemical Dynamics Simulations

Directory of Open Access Journals (Sweden)

Khadka Prashant

2008-10-01

Full Text Available Chemical dynamics simulation is an effective means to study atomic level motions of molecules, collections of molecules, liquids, surfaces, interfaces of materials, and chemical reactions. To make chemical dynamics simulations globally accessible to a broad range of users, recently a cyber infrastructure was developed that provides an online portal to VENUS, a popular chemical dynamics simulation program package, to allow people to submit simulation jobs that will be executed on the web server machine. In this paper, we report new developments of the cyber infrastructure for the improvement of its quality of service by dispatching the submitted simulations jobs from the web server machine onto a cluster of workstations for execution, and by adding an animation tool, which is optimized for animating the simulation results. The separation of the server machine from the simulation-running machine improves the service quality by increasing the capacity to serve more requests simultaneously with even reduced web response time, and allows the execution of large scale, time-consuming simulation jobs on the powerful workstation cluster. With the addition of an animation tool, the cyber infrastructure automatically converts, upon the selection of the user, some simulation results into an animation file that can be viewed on usual web browsers without requiring installation of any special software on the user computer. Since animation is essential for understanding the results of chemical dynamics simulations, this animation capacity provides a better way for understanding simulation details of the chemical dynamics. By combining computing resources at locations under different administrative controls, this cyber infrastructure constitutes a grid environment providing physically and administratively distributed functionalities through a single easy-to-use online portal

Studies of radiation and chemical toxicity. Progress report

International Nuclear Information System (INIS)

1986-01-01

Annual report for the Studies of Radiation and Chemical Toxicity Program at the University of Rochester is presented. Progress is reported on four projects: Neurobehavorial Toxicity of Organometallic Fuel Additives, Mechanisms of Permanent and Delayed Pathologic Effects of Ionizing Radiation, Solid State Radiation Chemistry of the DNA Backbone, and Pulmonary Biochemistry

Modelling stratospheric chemistry in a global three-dimensional chemical transport model

Energy Technology Data Exchange (ETDEWEB)

Rummukainen, M [Finnish Meteorological Inst., Sodankylae (Finland). Sodankylae Observatory

1996-12-31

Numerical modelling of atmospheric chemistry aims to increase the understanding of the characteristics, the behavior and the evolution of atmospheric composition. These topics are of utmost importance in the study of climate change. The multitude of gases and particulates making up the atmosphere and the complicated interactions between them affect radiation transfer, atmospheric dynamics, and the impacts of anthropogenic and natural emissions. Chemical processes are fundamental factors in global warming, ozone depletion and atmospheric pollution problems in general. Much of the prevailing work on modelling stratospheric chemistry has so far been done with 1- and 2-dimensional models. Carrying an extensive chemistry parameterisation in a model with high spatial and temporal resolution is computationally heavy. Today, computers are becoming powerful enough to allow going over to 3-dimensional models. In order to concentrate on the chemistry, many Chemical Transport Models (CTM) are still run off-line, i.e. with precalculated and archived meteorology and radiation. In chemistry simulations, the archived values drive the model forward in time, without interacting with the chemical evolution. This is an approach that has been adopted in stratospheric chemistry modelling studies at the Finnish Meteorological Institute. In collaboration with the University of Oslo, a development project was initiated in 1993 to prepare a stratospheric chemistry parameterisation, fit for global 3-dimensional modelling. This article presents the parameterisation approach. Selected results are shown from basic photochemical simulations

Modelling stratospheric chemistry in a global three-dimensional chemical transport model

Energy Technology Data Exchange (ETDEWEB)

Rummukainen, M. [Finnish Meteorological Inst., Sodankylae (Finland). Sodankylae Observatory

1995-12-31

Numerical modelling of atmospheric chemistry aims to increase the understanding of the characteristics, the behavior and the evolution of atmospheric composition. These topics are of utmost importance in the study of climate change. The multitude of gases and particulates making up the atmosphere and the complicated interactions between them affect radiation transfer, atmospheric dynamics, and the impacts of anthropogenic and natural emissions. Chemical processes are fundamental factors in global warming, ozone depletion and atmospheric pollution problems in general. Much of the prevailing work on modelling stratospheric chemistry has so far been done with 1- and 2-dimensional models. Carrying an extensive chemistry parameterisation in a model with high spatial and temporal resolution is computationally heavy. Today, computers are becoming powerful enough to allow going over to 3-dimensional models. In order to concentrate on the chemistry, many Chemical Transport Models (CTM) are still run off-line, i.e. with precalculated and archived meteorology and radiation. In chemistry simulations, the archived values drive the model forward in time, without interacting with the chemical evolution. This is an approach that has been adopted in stratospheric chemistry modelling studies at the Finnish Meteorological Institute. In collaboration with the University of Oslo, a development project was initiated in 1993 to prepare a stratospheric chemistry parameterisation, fit for global 3-dimensional modelling. This article presents the parameterisation approach. Selected results are shown from basic photochemical simulations

Computational methods in metabolic engineering for strain design.

Science.gov (United States)

Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L

2015-08-01

Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms. Copyright © 2015 Elsevier Ltd. All rights reserved.

A study of chemical equilibrium of tri-component mixtures of hydrogen isotopes

International Nuclear Information System (INIS)

Cristescu, Ioana; Cristescu, I.; Peculea, M.

1998-01-01

In this paper we present a model for computing the equilibrium constants for chemical reactions between hydrogen's isotopes as function of temperature. The equilibrium constants were expressed with the aid of Gibbs potential and the partition function of the mixture. We assessed the partition function for hydrogen's isotopes having in view that some nuclei are fermions and other bosons. As results we plotted the values of equilibrium constants as function of temperature. Knowing these values we determined the deuterium distribution on species (for mixture H 2 -HD-D 2 ) as function of total deuterium concentration and the tritium distribution on species (for mixtures D 2 -DT-T 2 and H 2 -HT-T 2 ) as function of total tritium concentration. (authors)

Computer-aided modeling for efficient and innovative product-process engineering

DEFF Research Database (Denmark)

Heitzig, Martina

Model-based computer aided product-process engineering has attained increased importance in a number of industries, including pharmaceuticals, petrochemicals, fine chemicals, polymers, biotechnology, food, energy and water. This trend is set to continue due to the substantial benefits computer...... in chemical and biochemical engineering have been solved to illustrate the application of the generic modelling methodology, the computeraided modelling framework and the developed software tool.......-aided methods provide. The key prerequisite of computer-aided productprocess engineering is however the availability of models of different types, forms and application modes. The development of the models required for the systems under investigation tends to be a challenging, time-consuming and therefore cost...

Non-allergic cutaneous reactions in airborne chemical sensitivity--a population based study.

Science.gov (United States)

Berg, Nikolaj Drimer; Linneberg, Allan; Thyssen, Jacob Pontoppidan; Dirksen, Asger; Elberling, Jesper

2011-06-01

Multiple chemical sensitivity (MCS) is characterised by adverse effects due to exposure to low levels of chemical substances. The aetiology is unknown, but chemical related respiratory symptoms have been found associated with positive patch test. The purpose of this study was to investigate the relationship between cutaneous reactions from patch testing and self-reported severity of chemical sensitivity to common airborne chemicals. A total of 3460 individuals participating in a general health examination, Health 2006, were patch tested with allergens from the European standard series and screened for chemical sensitivity with a standardised questionnaire dividing the participants into four severity groups of chemical sensitivity. Both allergic and non-allergic cutaneous reactions--defined as irritative, follicular, or doubtful allergic reactions--were analysed in relationship with severity of chemical sensitivity. Associations were controlled for the possible confounding effects of sex, age, asthma, eczema, atopic dermatitis, psychological and social factors, and smoking habits. In unadjusted analyses we found associations between allergic and non-allergic cutaneous reactions on patch testing and the two most severe groups of self-reported sensitivity to airborne chemicals. When adjusting for confounding, associations were weakened, and only non-allergic cutaneous reactions were significantly associated with individuals most severely affected by inhalation of airborne chemicals (odds ratio = 2.5, p = 0.006). Our results suggest that individuals with self-reported chemical sensitivity show increased non-allergic cutaneous reactions based on day 2 readings of patch tests. Copyright © 2011 Elsevier GmbH. All rights reserved.

Sensitivity and uncertainty studies of the CRAC2 computer code

International Nuclear Information System (INIS)

Kocher, D.C.; Ward, R.C.; Killough, G.G.; Dunning, D.E. Jr.; Hicks, B.B.; Hosker, R.P. Jr.; Ku, J.Y.; Rao, K.S.

1985-05-01

This report presents a study of the sensitivity of early fatalities, early injuries, latent cancer fatalities, and economic costs for hypothetical nuclear reactor accidents as predicted by the CRAC2 computer code (CRAC = Calculation of Reactor Accident Consequences) to uncertainties in selected models and parameters used in the code. The sources of uncertainty that were investigated in the CRAC2 sensitivity studies include (1) the model for plume rise, (2) the model for wet deposition, (3) the procedure for meteorological bin-sampling involving the selection of weather sequences that contain rain, (4) the dose conversion factors for inhalation as they are affected by uncertainties in the physical and chemical form of the released radionuclides, (5) the weathering half-time for external ground-surface exposure, and (6) the transfer coefficients for estimating exposures via terrestrial foodchain pathways. The sensitivity studies were performed for selected radionuclide releases, hourly meteorological data, land-use data, a fixed non-uniform population distribution, a single evacuation model, and various release heights and sensible heat rates. Two important general conclusions from the sensitivity and uncertainty studies are as follows: (1) The large effects on predicted early fatalities and early injuries that were observed in some of the sensitivity studies apparently are due in part to the presence of thresholds in the dose-response models. Thus, the observed sensitivities depend in part on the magnitude of the radionuclide releases. (2) Some of the effects on predicted early fatalities and early injuries that were observed in the sensitivity studies were comparable to effects that were due only to the selection of different sets of weather sequences in bin-sampling runs. 47 figs., 50 tabs

Factors associated with chemical burns in Zhejiang province, China: An epidemiological study

Directory of Open Access Journals (Sweden)

Jiang Rui M

2011-09-01

Full Text Available Abstract Background Work-related burns are common among occupational injuries. Zhejiang Province is an industrial area with a high incidence of chemical burns. We aimed to survey epidemiological features of chemical burns in Zhejiang province to determine associated factors and acquire data for developing a strategy to prevent and treat chemical burns. Methods Questionnaires were developed, reviewed and validated by experts, and sent to 25 hospitals in Zhejiang province to prospectively collect data of 492 chemical burn patients admitted during one year from Sept. 1, 2008 to Aug. 31, 2009. Questions included victims' characteristics and general condition, injury location, causes of accident, causative chemicals, total body surface area burn, concomitant injuries, employee safety training, and awareness level of protective measures. Surveys were completed for each of burn patients by burn department personnel who interviewed the hospitalized patients. Results In this study, 417 victims (87.61% got chemical burn at work, of which 355 victims (74.58% worked in private or individual enterprises. Most frequent chemicals involved were hydrofluoric acid and sulfuric acid. Main causes of chemical injury accidents were inappropriate operation of equipment or handling of chemicals and absence of or failure to use effective individual protection. Conclusions Most chemical burns are preventable occupational injuries that can be attributed to inappropriate operation of equipment or handling of chemicals, lack of employee awareness about appropriate action and lack of effective protective equipment and training. Emphasis on safety education and protection for workers may help protect workers and prevent chemical burns.

Does computer use affect the incidence of distal arm pain? A one-year prospective study using objective measures of computer use

DEFF Research Database (Denmark)

Mikkelsen, Sigurd; Lassen, Christina Funch; Vilstrup, Imogen

2012-01-01

PURPOSE: To study how objectively recorded mouse and keyboard activity affects distal arm pain among computer workers. METHODS: Computer activities were recorded among 2,146 computer workers. For 52 weeks mouse and keyboard time, sustained activity, speed and micropauses were recorded with a soft......PURPOSE: To study how objectively recorded mouse and keyboard activity affects distal arm pain among computer workers. METHODS: Computer activities were recorded among 2,146 computer workers. For 52 weeks mouse and keyboard time, sustained activity, speed and micropauses were recorded...... with a software program installed on the participants' computers. Participants reported weekly pain scores via the software program for elbow, forearm and wrist/hand as well as in a questionnaire at baseline and 1-year follow up. Associations between pain development and computer work were examined for three pain...... were not risk factors for acute pain, nor did they modify the effects of mouse or keyboard time. Computer usage parameters were not associated with prolonged or chronic pain. A major limitation of the study was low keyboard times. CONCLUSION: Computer work was not related to the development...

Computer aided drug design

Science.gov (United States)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

A unified algorithm for predicting partition coefficients for PBPK modeling of drugs and environmental chemicals

International Nuclear Information System (INIS)

Peyret, Thomas; Poulin, Patrick; Krishnan, Kannan

2010-01-01

The algorithms in the literature focusing to predict tissue:blood PC (P tb ) for environmental chemicals and tissue:plasma PC based on total (K p ) or unbound concentration (K pu ) for drugs differ in their consideration of binding to hemoglobin, plasma proteins and charged phospholipids. The objective of the present study was to develop a unified algorithm such that P tb , K p and K pu for both drugs and environmental chemicals could be predicted. The development of the unified algorithm was accomplished by integrating all mechanistic algorithms previously published to compute the PCs. Furthermore, the algorithm was structured in such a way as to facilitate predictions of the distribution of organic compounds at the macro (i.e. whole tissue) and micro (i.e. cells and fluids) levels. The resulting unified algorithm was applied to compute the rat P tb , K p or K pu of muscle (n = 174), liver (n = 139) and adipose tissue (n = 141) for acidic, neutral, zwitterionic and basic drugs as well as ketones, acetate esters, alcohols, aliphatic hydrocarbons, aromatic hydrocarbons and ethers. The unified algorithm reproduced adequately the values predicted previously by the published algorithms for a total of 142 drugs and chemicals. The sensitivity analysis demonstrated the relative importance of the various compound properties reflective of specific mechanistic determinants relevant to prediction of PC values of drugs and environmental chemicals. Overall, the present unified algorithm uniquely facilitates the computation of macro and micro level PCs for developing organ and cellular-level PBPK models for both chemicals and drugs.

Challenges to studying the health effects of early life environmental chemical exposures on children's health.

Science.gov (United States)

Braun, Joseph M; Gray, Kimberly

2017-12-01

Epidemiological studies play an important role in quantifying how early life environmental chemical exposures influence the risk of childhood diseases. These studies face at least four major challenges that can produce noise when trying to identify signals of associations between chemical exposure and childhood health. Challenges include accurately estimating chemical exposure, confounding from causes of both exposure and disease, identifying periods of heightened vulnerability to chemical exposures, and determining the effects of chemical mixtures. We provide recommendations that will aid in identifying these signals with more precision.

Effects of chemical equilibrium on turbine engine performance for various fuels and combustor temperatures

Science.gov (United States)

Tran, Donald H.; Snyder, Christopher A.

1992-01-01

A study was performed to quantify the differences in turbine engine performance with and without the chemical dissociation effects for various fuel types over a range of combustor temperatures. Both turbojet and turbofan engines were studied with hydrocarbon fuels and cryogenic, nonhydrocarbon fuels. Results of the study indicate that accuracy of engine performance decreases when nonhydrocarbon fuels are used, especially at high temperatures where chemical dissociation becomes more significant. For instance, the deviation in net thrust for liquid hydrogen fuel can become as high as 20 percent at 4160 R. This study reveals that computer central processing unit (CPU) time increases significantly when dissociation effects are included in the cycle analysis.

[Study on the chemical constituents of Buddleja purdomii].

Science.gov (United States)

Zhang, Yinghua; Li, Chong; Zhang, Chengzhong; Tao, Baoquan

2005-11-01

To study the chemical constituents of Buddleja purdomii W. W Smith. The constituents were isolated and purified by various chromatographic methods and structurally identified by spectral analysis. 4 compounds were obtained as cryptomeridiol (I), aucubin (II), galactilol (III), daucosterol (IV). All these compounds are obtained from this plant for the first time.

NASA Computational Case Study: The Flight of Friendship 7

Science.gov (United States)

Simpson, David G.

2012-01-01

In this case study, we learn how to compute the position of an Earth-orbiting spacecraft as a function of time. As an exercise, we compute the position of John Glenn's Mercury spacecraft Friendship 7 as it orbited the Earth during the third flight of NASA's Mercury program.

Computational Approaches to the Chemical Equilibrium Constant in Protein-ligand Binding.

Science.gov (United States)

Montalvo-Acosta, Joel José; Cecchini, Marco

2016-12-01

The physiological role played by protein-ligand recognition has motivated the development of several computational approaches to the ligand binding affinity. Some of them, termed rigorous, have a strong theoretical foundation but involve too much computation to be generally useful. Some others alleviate the computational burden by introducing strong approximations and/or empirical calibrations, which also limit their general use. Most importantly, there is no straightforward correlation between the predictive power and the level of approximation introduced. Here, we present a general framework for the quantitative interpretation of protein-ligand binding based on statistical mechanics. Within this framework, we re-derive self-consistently the fundamental equations of some popular approaches to the binding constant and pinpoint the inherent approximations. Our analysis represents a first step towards the development of variants with optimum accuracy/efficiency ratio for each stage of the drug discovery pipeline. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Elucidating reaction mechanisms on quantum computers

Science.gov (United States)

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

2017-01-01

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

Elucidating reaction mechanisms on quantum computers

Science.gov (United States)

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

2017-07-01

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

Elucidating reaction mechanisms on quantum computers.

Science.gov (United States)

Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

2017-07-18

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.