International Nuclear Information System (INIS)
Kubo, Momoji; Ando, Minako; Sakahara, Satoshi; Jung, Changho; Seki, Kotaro; Kusagaya, Tomonori; Endou, Akira; Takami, Seiichi; Imamura, Akira; Miyamoto, Akira
2004-01-01
Recently, we have proposed a new concept called 'combinatorial computational chemistry' to realize a theoretical, high-throughput screening of catalysts and materials. We have already applied our combinatorial, computational-chemistry approach, mainly based on static first-principles calculations, to various catalysts and materials systems and its applicability to the catalysts and materials design was strongly confirmed. In order to realize more effective and efficient combinatorial, computational-chemistry screening, a high-speed, chemical-reaction-dynamics simulator based on quantum-chemical, molecular-dynamics method is essential. However, to the best of our knowledge, there is no chemical-reaction-dynamics simulator, which has an enough high-speed ability to perform a high-throughput screening. In the present study, we have succeeded in the development of a chemical-reaction-dynamics simulator based on our original, tight-binding, quantum-chemical, molecular-dynamics method, which is more than 5000 times faster than the regular first-principles, molecular-dynamics method. Moreover, its applicability and effectiveness to the atomistic clarification of the methanol-synthesis dynamics at reaction temperature were demonstrated
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.
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.
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...
Computing Equilibrium Chemical Compositions
Mcbride, Bonnie J.; Gordon, Sanford
1995-01-01
Chemical Equilibrium With Transport Properties, 1993 (CET93) computer program provides data on chemical-equilibrium compositions. Aids calculation of 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/PC is version of CET93 specifically designed to run within 640K memory limit of MS-DOS operating system. CET93/PC written in FORTRAN.
Computer simulation of chemical nucleation
International Nuclear Information System (INIS)
Turner, J.S.
1979-01-01
The problem of nucleation at chemical instabilities is investigated by means of microscopic computer simulation. The first-order transition of interest involves a new kind of nucleation arising from chemical transformations rather than physical forces. Here it is the chemical state of matter, and not matter itself, which is spatially localized to form the nucleus for transition between different chemical states. First, the concepts of chemical instability, nonequilibrium phase transition, and dissipative structure are reviewed briefly. Then recently developed methods of reactive molecular dynamics are used to study chemical nucleation in a simple model chemical reactions. Finally, the connection of these studies to nucleation and condensation processes involving physical and chemical interactions is explored. (orig.)
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
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
Farantos, Stavros C
2014-01-01
This brief presents numerical methods for describing and calculating invariant phase space structures, as well as solving the classical and quantum equations of motion for polyatomic molecules. Examples covered include simple model systems to realistic cases of molecules spectroscopically studied. Vibrationally excited and reacting molecules are nonlinear dynamical systems, and thus, nonlinear mechanics is the proper theory to elucidate molecular dynamics by investigating invariant structures in phase space. Intramolecular energy transfer, and the breaking and forming of a chemical bond have now found a rigorous explanation by studying phase space structures.
International Nuclear Information System (INIS)
Myeong, Hyeon Guk
1999-06-01
This book deals with computational fluid dynamics with basic and history of numerical fluid dynamics, introduction of finite volume method using one-dimensional heat conduction equation, solution of two-dimensional heat conduction equation, solution of Navier-Stokes equation, fluid with heat transport, turbulent flow and turbulent model, Navier-Stokes solution by generalized coordinate system such as coordinate conversion, conversion of basic equation, program and example of calculation, application of abnormal problem and high speed solution of numerical fluid dynamics.
Computational Systems Chemical Biology
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).
Essential Computational Fluid Dynamics
Zikanov, Oleg
2011-01-01
This book serves as a complete and self-contained introduction to the principles of Computational Fluid Dynamic (CFD) analysis. It is deliberately short (at approximately 300 pages) and can be used as a text for the first part of the course of applied CFD followed by a software tutorial. The main objectives of this non-traditional format are: 1) To introduce and explain, using simple examples where possible, the principles and methods of CFD analysis and to demystify the `black box’ of a CFD software tool, and 2) To provide a basic understanding of how CFD problems are set and
Computational fluid dynamic applications
Energy Technology Data Exchange (ETDEWEB)
Chang, S.-L.; Lottes, S. A.; Zhou, C. Q.
2000-04-03
The rapid advancement of computational capability including speed and memory size has prompted the wide use of computational fluid dynamics (CFD) codes to simulate complex flow systems. CFD simulations are used to study the operating problems encountered in system, to evaluate the impacts of operation/design parameters on the performance of a system, and to investigate novel design concepts. CFD codes are generally developed based on the conservation laws of mass, momentum, and energy that govern the characteristics of a flow. The governing equations are simplified and discretized for a selected computational grid system. Numerical methods are selected to simplify and calculate approximate flow properties. For turbulent, reacting, and multiphase flow systems the complex processes relating to these aspects of the flow, i.e., turbulent diffusion, combustion kinetics, interfacial drag and heat and mass transfer, etc., are described in mathematical models, based on a combination of fundamental physics and empirical data, that are incorporated into the code. CFD simulation has been applied to a large variety of practical and industrial scale flow systems.
International Nuclear Information System (INIS)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
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.
Computable Types for Dynamic Systems
P.J. Collins (Pieter); K. Ambos-Spies; B. Loewe; W. Merkle
2009-01-01
textabstractIn this paper, we develop a theory of computable types suitable for the study of dynamic systems in discrete and continuous time. The theory uses type-two effectivity as the underlying computational model, but we quickly develop a type system which can be manipulated abstractly, but for
Computing chemical organizations in biological networks.
Centler, Florian; Kaleta, Christoph; di Fenizio, Pietro Speroni; Dittrich, Peter
2008-07-15
Novel techniques are required to analyze computational models of intracellular processes as they increase steadily in size and complexity. The theory of chemical organizations has recently been introduced as such a technique that links the topology of biochemical reaction network models to their dynamical repertoire. The network is decomposed into algebraically closed and self-maintaining subnetworks called organizations. They form a hierarchy representing all feasible system states including all steady states. We present three algorithms to compute the hierarchy of organizations for network models provided in SBML format. Two of them compute the complete organization hierarchy, while the third one uses heuristics to obtain a subset of all organizations for large models. While the constructive approach computes the hierarchy starting from the smallest organization in a bottom-up fashion, the flux-based approach employs self-maintaining flux distributions to determine organizations. A runtime comparison on 16 different network models of natural systems showed that none of the two exhaustive algorithms is superior in all cases. Studying a 'genome-scale' network model with 762 species and 1193 reactions, we demonstrate how the organization hierarchy helps to uncover the model structure and allows to evaluate the model's quality, for example by detecting components and subsystems of the model whose maintenance is not explained by the model. All data and a Java implementation that plugs into the Systems Biology Workbench is available from http://www.minet.uni-jena.de/csb/prj/ot/tools.
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.
Computer Modelling of Dynamic Processes
Directory of Open Access Journals (Sweden)
B. Rybakin
2000-10-01
Full Text Available Results of numerical modeling of dynamic problems are summed in the article up. These problems are characteristic for various areas of human activity, in particular for problem solving in ecology. The following problems are considered in the present work: computer modeling of dynamic effects on elastic-plastic bodies, calculation and determination of performances of gas streams in gas cleaning equipment, modeling of biogas formation processes.
Computer Series, 3: Computer Graphics for Chemical Education.
Soltzberg, Leonard J.
1979-01-01
Surveys the current scene in computer graphics from the point of view of a chemistry educator. Discusses the scope of current applications of computer graphics in chemical education, and provides information about hardware and software systems to promote communication with vendors of computer graphics equipment. (HM)
Computational Fluid Dynamics in Ventilation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Allard, Francis; Awbi, Hazim B.
2008-01-01
Computational Fluid Dynamics in Ventilation Design is a new title in the is a new title in the REHVA guidebook series. The guidebook is written for people who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD...
Computational Approaches to Chemical Hazard Assessment
Luechtefeld, Thomas; Hartung, Thomas
2018-01-01
Summary Computational prediction of toxicity has reached new heights as a result of decades of growth in the magnitude and diversity of biological data. Public packages for statistics and machine learning make model creation faster. New theory in machine learning and cheminformatics enables integration of chemical structure, toxicogenomics, simulated and physical data in the prediction of chemical health hazards, and other toxicological information. Our earlier publications have characterized a toxicological dataset of unprecedented scale resulting from the European REACH legislation (Registration Evaluation Authorisation and Restriction of Chemicals). These publications dove into potential use cases for regulatory data and some models for exploiting this data. This article analyzes the options for the identification and categorization of chemicals, moves on to the derivation of descriptive features for chemicals, discusses different kinds of targets modeled in computational toxicology, and ends with a high-level perspective of the algorithms used to create computational toxicology models. PMID:29101769
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.
Principles of computational fluid dynamics
Wesseling, Pieter
2001-01-01
The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state-of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and ho...
Dynamic computing random access memory
International Nuclear Information System (INIS)
Traversa, F L; Bonani, F; Pershin, Y V; Di Ventra, M
2014-01-01
The present von Neumann computing paradigm involves a significant amount of information transfer between a central processing unit and memory, with concomitant limitations in the actual execution speed. However, it has been recently argued that a different form of computation, dubbed memcomputing (Di Ventra and Pershin 2013 Nat. Phys. 9 200–2) and inspired by the operation of our brain, can resolve the intrinsic limitations of present day architectures by allowing for computing and storing of information on the same physical platform. Here we show a simple and practical realization of memcomputing that utilizes easy-to-build memcapacitive systems. We name this architecture dynamic computing random access memory (DCRAM). We show that DCRAM provides massively-parallel and polymorphic digital logic, namely it allows for different logic operations with the same architecture, by varying only the control signals. In addition, by taking into account realistic parameters, its energy expenditures can be as low as a few fJ per operation. DCRAM is fully compatible with CMOS technology, can be realized with current fabrication facilities, and therefore can really serve as an alternative to the present computing technology. (paper)
Computational approach to large quantum dynamical problems
International Nuclear Information System (INIS)
Friesner, R.A.; Brunet, J.P.; Wyatt, R.E.; Leforestier, C.; Binkley, S.
1987-01-01
The organizational structure is described for a new program that permits computations on a variety of quantum mechanical problems in chemical dynamics and spectroscopy. Particular attention is devoted to developing and using algorithms that exploit the capabilities of current vector supercomputers. A key component in this procedure is the recursive transformation of the large sparse Hamiltonian matrix into a much smaller tridiagonal matrix. An application to time-dependent laser molecule energy transfer is presented. Rate of energy deposition in the multimode molecule for systematic variations in the molecular intermode coupling parameters is emphasized
molecular dynamics simulations and quantum chemical calculations
African Journals Online (AJOL)
ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.
Chemical emission rates from personal computers
DEFF Research Database (Denmark)
Nakagawa, T.; Wargocki, Pawel; Tanabe, S.
2003-01-01
Chemical emission measurements from different brands of personal computers (PCs) were conducted in a 1 m3 glass chamber. Eight PCs were tested individually. Each consisted of the same brand of PC tower and one of the 4 different brands of PC monitors. Within each brand both cathode-ray tube (CRT...
Computer Applications in Balancing Chemical Equations.
Kumar, David D.
2001-01-01
Discusses computer-based approaches to balancing chemical equations. Surveys 13 methods, 6 based on matrix, 2 interactive programs, 1 stand-alone system, 1 developed in algorithm in Basic, 1 based on design engineering, 1 written in HyperCard, and 1 prepared for the World Wide Web. (Contains 17 references.) (Author/YDS)
Principles of computational fluid dynamics
International Nuclear Information System (INIS)
Wesseling, P.
2001-01-01
The book is aimed at graduate students, researchers, engineers and physicists involved in flow computations. An up-to-date account is given of the present state- of-the-art of numerical methods employed in computational fluid dynamics. The underlying numerical principles are treated with a fair amount of detail, using elementary mathematical analysis. Attention is given to difficulties arising from geometric complexity of the flow domain and of nonuniform structured boundary-fitted grids. Uniform accuracy and efficiency for singular perturbation problems is studied, pointing the way to accurate computation of flows at high Reynolds number. Much attention is given to stability analysis, and useful stability conditions are provided, some of them new, for many numerical schemes used in practice. Unified methods for compressible and incompressible flows are discussed. Numerical analysis of the shallow-water equations is included. The theory of hyperbolic conservation laws is treated. Godunov's order barrier and how to overcome it by means of slope-limited schemes is discussed. An introduction is given to efficient iterative solution methods, using Krylov subspace and multigrid acceleration. Many pointers are given to recent literature, to help the reader to quickly reach the current research frontier. (orig.)
Computational methods for fluid dynamics
Ferziger, Joel H
2002-01-01
In its 3rd revised and extended edition the book offers an overview of the techniques used to solve problems in fluid mechanics on computers and describes in detail those most often used in practice. Included are advanced methods in computational fluid dynamics, like direct and large-eddy simulation of turbulence, multigrid methods, parallel computing, moving grids, structured, block-structured and unstructured boundary-fitted grids, free surface flows. The 3rd edition contains a new section dealing with grid quality and an extended description of discretization methods. The book shows common roots and basic principles for many different methods. The book also contains a great deal of practical advice for code developers and users, it is designed to be equally useful to beginners and experts. The issues of numerical accuracy, estimation and reduction of numerical errors are dealt with in detail, with many examples. A full-feature user-friendly demo-version of a commercial CFD software has been added, which ca...
Chemical kinetics and reaction dynamics
Houston, Paul L
2006-01-01
This text teaches the principles underlying modern chemical kinetics in a clear, direct fashion, using several examples to enhance basic understanding. It features solutions to selected problems, with separate sections and appendices that cover more technical applications.Each chapter is self-contained and features an introduction that identifies its basic goals, their significance, and a general plan for their achievement. This text's important aims are to demonstrate that the basic kinetic principles are essential to the solution of modern chemical problems, and to show how the underlying qu
Computational singular perturbation analysis of stochastic chemical systems with stiffness
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.
Chemical Dynamics at the Advanced Light Source
International Nuclear Information System (INIS)
Baer, T.; Berrah, N.; Fadley, C.; Moore, C.B.; Neumark, D.M.; Ng, C.Y.; Ruscic, B.; Smith, N.V.; Suits, A.G.; Wodtke, A.M.
1999-01-01
A day-long retreat was held January 15, 1999 to chart the future directions for chemical dynamics studies at the Advanced Light Source. This represents an important period for the Chemical Dynamics Beamline, as the hardware is well-developed, most of the initial experimental objectives have been realized and the mission is now to identify the future scientific priorities for the beamline and attract users of the highest caliber. To this end, we have developed a detailed scientific program for the near term; identified and prioritized the long range scientific opportunities, identified essential new hardware, and outlined an aggressive outreach program to involve the chemical physics community
Molecular computing: paths to chemical Turing machines.
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.
Dynamics of Information as Natural Computation
Directory of Open Access Journals (Sweden)
Gordana Dodig Crnkovic
2011-08-01
Full Text Available Processes considered rendering information dynamics have been studied, among others in: questions and answers, observations, communication, learning, belief revision, logical inference, game-theoretic interactions and computation. This article will put the computational approaches into a broader context of natural computation, where information dynamics is not only found in human communication and computational machinery but also in the entire nature. Information is understood as representing the world (reality as an informational web for a cognizing agent, while information dynamics (information processing, computation realizes physical laws through which all the changes of informational structures unfold. Computation as it appears in the natural world is more general than the human process of calculation modeled by the Turing machine. Natural computing is epitomized through the interactions of concurrent, in general asynchronous computational processes which are adequately represented by what Abramsky names “the second generation models of computation” [1] which we argue to be the most general representation of information dynamics.
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.
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.
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.
Chemical structure and dynamics. Annual report 1995
Energy Technology Data Exchange (ETDEWEB)
Colson, S.D.; McDowell, R.S.
1996-05-01
The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.
Chemical structure and dynamics: Annual report 1996
International Nuclear Information System (INIS)
Colson, S.D.; McDowell, R.S.
1997-03-01
The Chemical Structure and Dynamics (CS ampersand D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species
Annual Report 2000. Chemical Structure and Dynamics
Energy Technology Data Exchange (ETDEWEB)
Colson, Steven D.; McDowell, Robin S.
2001-04-15
This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.
Chemical structure and dynamics: Annual report 1996
Energy Technology Data Exchange (ETDEWEB)
Colson, S.D.; McDowell, R.S.
1997-03-01
The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.
Security Dynamics of Cloud Computing
Khan, Khaled M.
2009-01-01
This paper explores various dimensions of cloud computing security. It argues that security concerns of cloud computing need to be addressed from the perspective of individual stakeholder. Security focuses of cloud computing are essentially different in terms of its characteristics and business model. Conventional way of viewing as well as addressing security such as ‘bolting-in’ on the top of cloud computing may not work well. The paper attempts to portray the security spectrum necessary for...
DNA-Encoded Dynamic Combinatorial Chemical Libraries.
Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin
2015-06-26
Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Nanomotor dynamics in a chemically oscillating medium
Energy Technology Data Exchange (ETDEWEB)
Robertson, Bryan, E-mail: bryan.robertson@mail.utoronto.ca; Kapral, Raymond, E-mail: rkapral@chem.utoronto.ca [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)
2015-04-21
Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media.
Nanomotor dynamics in a chemically oscillating medium
International Nuclear Information System (INIS)
Robertson, Bryan; Kapral, Raymond
2015-01-01
Synthetic nanomotors powered by chemical reactions have potential uses as cargo transport vehicles in both in vivo and in vitro applications. In many situations, motors will have to operate in out-of-equilibrium complex chemically reacting media, which supply fuel to the motors and remove the products they produce. Using molecular simulation and mean-field theory, this paper describes some of the new features that arise when a chemically powered nanomotor, operating through a diffusiophoretic mechanism, moves in an environment that supports an oscillatory chemical reaction network. It is shown how oscillations in the concentrations in chemical species in the environment give rise to oscillatory motor dynamics. More importantly, since the catalytic reactions on the motor that are responsible for its propulsion couple to the bulk phase reaction network, the motor can change its local environment. This process can give rise to distinctive spatiotemporal structures in reaction-diffusion media that occur as a result of active motor motion. Such locally induced nonequilibrium structure will play an important role in applications that involve motor dynamics in complex chemical media
Fluid dynamics theory, computation, and numerical simulation
Pozrikidis, C
2001-01-01
Fluid Dynamics Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes Two distinguishing features of the discourse are solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty Matlab codes are presented and discussed for a broad...
Fluid Dynamics Theory, Computation, and Numerical Simulation
Pozrikidis, Constantine
2009-01-01
Fluid Dynamics: Theory, Computation, and Numerical Simulation is the only available book that extends the classical field of fluid dynamics into the realm of scientific computing in a way that is both comprehensive and accessible to the beginner. The theory of fluid dynamics, and the implementation of solution procedures into numerical algorithms, are discussed hand-in-hand and with reference to computer programming. This book is an accessible introduction to theoretical and computational fluid dynamics (CFD), written from a modern perspective that unifies theory and numerical practice. There are several additions and subject expansions in the Second Edition of Fluid Dynamics, including new Matlab and FORTRAN codes. Two distinguishing features of the discourse are: solution procedures and algorithms are developed immediately after problem formulations are presented, and numerical methods are introduced on a need-to-know basis and in increasing order of difficulty. Matlab codes are presented and discussed for ...
Nonlinear dynamics as an engine of computation.
Kia, Behnam; Lindner, John F; Ditto, William L
2017-03-06
Control of chaos teaches that control theory can tame the complex, random-like behaviour of chaotic systems. This alliance between control methods and physics-cybernetical physics-opens the door to many applications, including dynamics-based computing. In this article, we introduce nonlinear dynamics and its rich, sometimes chaotic behaviour as an engine of computation. We review our work that has demonstrated how to compute using nonlinear dynamics. Furthermore, we investigate the interrelationship between invariant measures of a dynamical system and its computing power to strengthen the bridge between physics and computation.This article is part of the themed issue 'Horizons of cybernetical physics'. © 2017 The Author(s).
Computational neuropharmacology: dynamical approaches in drug discovery.
Aradi, Ildiko; Erdi, Péter
2006-05-01
Computational approaches that adopt dynamical models are widely accepted in basic and clinical neuroscience research as indispensable tools with which to understand normal and pathological neuronal mechanisms. Although computer-aided techniques have been used in pharmaceutical research (e.g. in structure- and ligand-based drug design), the power of dynamical models has not yet been exploited in drug discovery. We suggest that dynamical system theory and computational neuroscience--integrated with well-established, conventional molecular and electrophysiological methods--offer a broad perspective in drug discovery and in the search for novel targets and strategies for the treatment of neurological and psychiatric diseases.
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.
Chemical Structure and Dynamics annual report 1997
International Nuclear Information System (INIS)
Colson, S.D.; McDowell, R.S.
1998-03-01
The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE's environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous
Chemical Structure and Dynamics annual report 1997
Energy Technology Data Exchange (ETDEWEB)
Colson, S.D.; McDowell, R.S.
1998-03-01
The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.
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 (CO_{2}) capture. In this study, to generate data for WWC model validation, CO_{2} 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 CO_{2} 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 CO_{2} 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 (N_{2}O)/MEA system obtained from Part 1 of this study, serves as priors for the calibration of CO_{2} reaction rate constants after using the N_{2}O/CO_{2} analogy method. Finally, the calibrated model can be used to predict the CO_{2} mass transfer in a WWC for a wider range of operating conditions.
Fluid dynamics computer programs for NERVA turbopump
Brunner, J. J.
1972-01-01
During the design of the NERVA turbopump, numerous computer programs were developed for the analyses of fluid dynamic problems within the machine. Program descriptions, example cases, users instructions, and listings for the majority of these programs are presented.
Fluid dynamics theory, computation, and numerical simulation
Pozrikidis, C
2017-01-01
This book provides an accessible introduction to the basic theory of fluid mechanics and computational fluid dynamics (CFD) from a modern perspective that unifies theory and numerical computation. Methods of scientific computing are introduced alongside with theoretical analysis and MATLAB® codes are presented and discussed for a broad range of topics: from interfacial shapes in hydrostatics, to vortex dynamics, to viscous flow, to turbulent flow, to panel methods for flow past airfoils. The third edition includes new topics, additional examples, solved and unsolved problems, and revised images. It adds more computational algorithms and MATLAB programs. It also incorporates discussion of the latest version of the fluid dynamics software library FDLIB, which is freely available online. FDLIB offers an extensive range of computer codes that demonstrate the implementation of elementary and advanced algorithms and provide an invaluable resource for research, teaching, classroom instruction, and self-study. This ...
Molecular dynamics simulation of a chemical reaction
International Nuclear Information System (INIS)
Gorecki, J.; Gryko, J.
1988-06-01
Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs
Hardware for dynamic quantum computing.
Ryan, Colm A; Johnson, Blake R; Ristè, Diego; Donovan, Brian; Ohki, Thomas A
2017-10-01
We describe the hardware, gateware, and software developed at Raytheon BBN Technologies for dynamic quantum information processing experiments on superconducting qubits. In dynamic experiments, real-time qubit state information is fed back or fed forward within a fraction of the qubits' coherence time to dynamically change the implemented sequence. The hardware presented here covers both control and readout of superconducting qubits. For readout, we created a custom signal processing gateware and software stack on commercial hardware to convert pulses in a heterodyne receiver into qubit state assignments with minimal latency, alongside data taking capability. For control, we developed custom hardware with gateware and software for pulse sequencing and steering information distribution that is capable of arbitrary control flow in a fraction of superconducting qubit coherence times. Both readout and control platforms make extensive use of field programmable gate arrays to enable tailored qubit control systems in a reconfigurable fabric suitable for iterative development.
A Computational Fluid Dynamics Algorithm on a Massively Parallel Computer
Jespersen, Dennis C.; Levit, Creon
1989-01-01
The discipline of computational fluid dynamics is demanding ever-increasing computational power to deal with complex fluid flow problems. We investigate the performance of a finite-difference computational fluid dynamics algorithm on a massively parallel computer, the Connection Machine. Of special interest is an implicit time-stepping algorithm; to obtain maximum performance from the Connection Machine, it is necessary to use a nonstandard algorithm to solve the linear systems that arise in the implicit algorithm. We find that the Connection Machine ran achieve very high computation rates on both explicit and implicit algorithms. The performance of the Connection Machine puts it in the same class as today's most powerful conventional supercomputers.
Chemical structure and dynamics. Annual report 1994
Energy Technology Data Exchange (ETDEWEB)
Colson, S.D.
1995-07-01
The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.
Annual Report 1998: Chemical Structure and Dynamics
Energy Technology Data Exchange (ETDEWEB)
SD Colson; RS McDowell
1999-05-10
The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).
The Dynamic Geometrisation of Computer Programming
Sinclair, Nathalie; Patterson, Margaret
2018-01-01
The goal of this paper is to explore dynamic geometry environments (DGE) as a type of computer programming language. Using projects created by secondary students in one particular DGE, we analyse the extent to which the various aspects of computational thinking--including both ways of doing things and particular concepts--were evident in their…
Dynamics and computation in functional shifts
Namikawa, Jun; Hashimoto, Takashi
2004-07-01
We introduce a new type of shift dynamics as an extended model of symbolic dynamics, and investigate the characteristics of shift spaces from the viewpoints of both dynamics and computation. This shift dynamics is called a functional shift, which is defined by a set of bi-infinite sequences of some functions on a set of symbols. To analyse the complexity of functional shifts, we measure them in terms of topological entropy, and locate their languages in the Chomsky hierarchy. Through this study, we argue that considering functional shifts from the viewpoints of both dynamics and computation gives us opposite results about the complexity of systems. We also describe a new class of shift spaces whose languages are not recursively enumerable.
Computational plasticity algorithm for particle dynamics simulations
Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.
2018-01-01
The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.
Modeling Computer Virus and Its Dynamics
Directory of Open Access Journals (Sweden)
Mei Peng
2013-01-01
Full Text Available Based on that the computer will be infected by infected computer and exposed computer, and some of the computers which are in suscepitible status and exposed status can get immunity by antivirus ability, a novel coumputer virus model is established. The dynamic behaviors of this model are investigated. First, the basic reproduction number R0, which is a threshold of the computer virus spreading in internet, is determined. Second, this model has a virus-free equilibrium P0, which means that the infected part of the computer disappears, and the virus dies out, and P0 is a globally asymptotically stable equilibrium if R01 then this model has only one viral equilibrium P*, which means that the computer persists at a constant endemic level, and P* is also globally asymptotically stable. Finally, some numerical examples are given to demonstrate the analytical results.
Three-Dimensional Computational Fluid Dynamics
Energy Technology Data Exchange (ETDEWEB)
Haworth, D.C.; O' Rourke, P.J.; Ranganathan, R.
1998-09-01
Computational fluid dynamics (CFD) is one discipline falling under the broad heading of computer-aided engineering (CAE). CAE, together with computer-aided design (CAD) and computer-aided manufacturing (CAM), comprise a mathematical-based approach to engineering product and process design, analysis and fabrication. In this overview of CFD for the design engineer, our purposes are three-fold: (1) to define the scope of CFD and motivate its utility for engineering, (2) to provide a basic technical foundation for CFD, and (3) to convey how CFD is incorporated into engineering product and process design.
Application of synchrotron radiation in chemical dynamics
International Nuclear Information System (INIS)
Heimann, P.; Koike, M.; Kung, A.H.; Ng, C.Y.; White, M.G.; Wodtke, A.
1993-05-01
In October 1992, funding was approved to begin construction of a beamline and two end stations to support chemical dynamics experiments at LBL's Advanced Light Source (ALS). This workshop was organized to develop specifications and plans and to select a working team to design and supervise the construction project. Target date for starting the experiments is January 1995. Conclusions of the workshop and representative experiments proposed in earlier workshops to form the basis for beamline plans and end-station designs are summarized in this report. 6 figs
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.
Evaluating amber force fields using computed NMR chemical shifts.
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.
Computational Fluid Dynamics and Room Air Movement
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2004-01-01
on the mass fraction transport equation. The importance of ?false? or numerical diffusion is also addressed in connection with the simple description of a supply opening. The different aspects of boundary conditions in the indoor environment as e.g. the simulation of Air Terminal Devices and the simulation......Nielsen, P.V. Computational Fluid Dynamics and Room Air Movement. Indoor Air, International Journal of Indoor Environment and Health, Vol. 14, Supplement 7, pp. 134-143, 2004. ABSTRACT Computational Fluid Dynamics (CFD) and new developments of CFD in the indoor environment as well as quality...... considerations are important elements in the study of energy consumption, thermal comfort and indoor air quality in buildings. The paper discusses the quality level of Computational Fluid Dynamics and the involved schemes (first, second and third order schemes) by the use of the Smith and Hutton problem...
An introduction to Computational Fluid Dynamics
DEFF Research Database (Denmark)
Sørensen, Lars Schiøtt
1999-01-01
CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building.......CFD is the shortname for Computational Fluid Dynamics and is a numerical method by means of which we can analyze systems containing fluids. For instance systems dealing with heat flow or smoke control systems acting when a fire occur in a building....
Computing Properties Of Chemical Mixtures At Equilibrium
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.
Traffic Dynamics of Computer Networks
Fekete, Attila
2008-10-01
Two important aspects of the Internet, namely the properties of its topology and the characteristics of its data traffic, have attracted growing attention of the physics community. My thesis has considered problems of both aspects. First I studied the stochastic behavior of TCP, the primary algorithm governing traffic in the current Internet, in an elementary network scenario consisting of a standalone infinite-sized buffer and an access link. The effect of the fast recovery and fast retransmission (FR/FR) algorithms is also considered. I showed that my model can be extended further to involve the effect of link propagation delay, characteristic of WAN. I continued my thesis with the investigation of finite-sized semi-bottleneck buffers, where packets can be dropped not only at the link, but also at the buffer. I demonstrated that the behavior of the system depends only on a certain combination of the parameters. Moreover, an analytic formula was derived that gives the ratio of packet loss rate at the buffer to the total packet loss rate. This formula makes it possible to treat buffer-losses as if they were link-losses. Finally, I studied computer networks from a structural perspective. I demonstrated through fluid simulations that the distribution of resources, specifically the link bandwidth, has a serious impact on the global performance of the network. Then I analyzed the distribution of edge betweenness in a growing scale-free tree under the condition that a local property, the in-degree of the "younger" node of an arbitrary edge, is known in order to find an optimum distribution of link capacity. The derived formula is exact even for finite-sized networks. I also calculated the conditional expectation of edge betweenness, rescaled for infinite networks.
Computational fluid dynamics a practical approach
Tu, Jiyuan; Liu, Chaoqun
2018-01-01
Computational Fluid Dynamics: A Practical Approach, Third Edition, is an introduction to CFD fundamentals and commercial CFD software to solve engineering problems. The book is designed for a wide variety of engineering students new to CFD, and for practicing engineers learning CFD for the first time. Combining an appropriate level of mathematical background, worked examples, computer screen shots, and step-by-step processes, this book walks the reader through modeling and computing, as well as interpreting CFD results. This new edition has been updated throughout, with new content and improved figures, examples and problems.
Graphics supercomputer for computational fluid dynamics research
Liaw, Goang S.
1994-11-01
The objective of this project is to purchase a state-of-the-art graphics supercomputer to improve the Computational Fluid Dynamics (CFD) research capability at Alabama A & M University (AAMU) and to support the Air Force research projects. A cutting-edge graphics supercomputer system, Onyx VTX, from Silicon Graphics Computer Systems (SGI), was purchased and installed. Other equipment including a desktop personal computer, PC-486 DX2 with a built-in 10-BaseT Ethernet card, a 10-BaseT hub, an Apple Laser Printer Select 360, and a notebook computer from Zenith were also purchased. A reading room has been converted to a research computer lab by adding some furniture and an air conditioning unit in order to provide an appropriate working environments for researchers and the purchase equipment. All the purchased equipment were successfully installed and are fully functional. Several research projects, including two existing Air Force projects, are being performed using these facilities.
Visualization of unsteady computational fluid dynamics
Haimes, Robert
1994-11-01
A brief summary of the computer environment used for calculating three dimensional unsteady Computational Fluid Dynamic (CFD) results is presented. This environment requires a super computer as well as massively parallel processors (MPP's) and clusters of workstations acting as a single MPP (by concurrently working on the same task) provide the required computational bandwidth for CFD calculations of transient problems. The cluster of reduced instruction set computers (RISC) is a recent advent based on the low cost and high performance that workstation vendors provide. The cluster, with the proper software can act as a multiple instruction/multiple data (MIMD) machine. A new set of software tools is being designed specifically to address visualizing 3D unsteady CFD results in these environments. Three user's manuals for the parallel version of Visual3, pV3, revision 1.00 make up the bulk of this report.
Domain of attraction computation for tumor dynamics
Doban, A.I.; Lazar, M.
2014-01-01
In this paper we propose the use of rational Lyapunov functions to estimate the domain of attraction of the tumor dormancy equilibrium of immune cells-malignant cells interaction dynamics. A procedure for computing rational Lyapunov functions is worked out, with focus on obtaining a meaningful
Engineering applications of computational fluid dynamics
Awang, Mokhtar
2015-01-01
This volume presents the results of Computational Fluid Dynamics (CFD) analysis that can be used for conceptual studies of product design, detail product development, process troubleshooting. It demonstrates the benefit of CFD modeling as a cost saving, timely, safe and easy to scale-up methodology.
Chemical memory reactions induced bursting dynamics in gene expression.
Tian, Tianhai
2013-01-01
Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.
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.)
Programming Unconventional Computers: Dynamics, Development, Self-Reference
Directory of Open Access Journals (Sweden)
Susan Stepney
2012-10-01
Full Text Available Classical computing has well-established formalisms for specifying, refining, composing, proving, and otherwise reasoning about computations. These formalisms have matured over the past 70 years or so. Unconventional Computing includes the use of novel kinds of substrates–from black holes and quantum effects, through to chemicals, biomolecules, even slime moulds–to perform computations that do not conform to the classical model. Although many of these unconventional substrates can be coerced into performing classical computation, this is not how they “naturally” compute. Our ability to exploit unconventional computing is partly hampered by a lack of corresponding programming formalisms: we need models for building, composing, and reasoning about programs that execute in these substrates. What might, say, a slime mould programming language look like? Here I outline some of the issues and properties of these unconventional substrates that need to be addressed to find “natural” approaches to programming them. Important concepts include embodied real values, processes and dynamical systems, generative systems and their meta-dynamics, and embodied self-reference.
Computational Methods in Stochastic Dynamics Volume 2
Stefanou, George; Papadopoulos, Vissarion
2013-01-01
The considerable influence of inherent uncertainties on structural behavior has led the engineering community to recognize the importance of a stochastic approach to structural problems. Issues related to uncertainty quantification and its influence on the reliability of the computational models are continuously gaining in significance. In particular, the problems of dynamic response analysis and reliability assessment of structures with uncertain system and excitation parameters have been the subject of continuous research over the last two decades as a result of the increasing availability of powerful computing resources and technology. This book is a follow up of a previous book with the same subject (ISBN 978-90-481-9986-0) and focuses on advanced computational methods and software tools which can highly assist in tackling complex problems in stochastic dynamic/seismic analysis and design of structures. The selected chapters are authored by some of the most active scholars in their respective areas and...
The use of computers for instruction in fluid dynamics
Watson, Val
1987-01-01
Applications for computers which improve instruction in fluid dynamics are examined. Computers can be used to illustrate three-dimensional flow fields and simple fluid dynamics mechanisms, to solve fluid dynamics problems, and for electronic sketching. The usefulness of computer applications is limited by computer speed, memory, and software and the clarity and field of view of the projected display. Proposed advances in personal computers which will address these limitations are discussed. Long range applications for computers in education are considered.
Colour in visualisation for computational fluid dynamics
Kinnear, D; Atherton, MA; Collins, MW; Dokhan, J; Karayiannis, TG
2006-01-01
Colour is used in computational fluid dynamic (CFD) simulations in two key ways. First it is used to visualise the geometry and allow the engineers to be confident that the model constructed is a good representation of the engineering situation. Once an analysis has been completed, colour is used in post-processing the data from the simulations to illustrate the complex fluid mechanic phenomena under investigation. This paper describes these two uses of colour and provides some examples to il...
Computational fluid dynamics in ventilation design
Allard, Francis; Awbi, Hazim B; Davidson, Lars; Schälin, Alois
2007-01-01
CFD-calculations have been rapidly developed to a powerful tool for the analysis of air pollution distribution in various spaces. However, the user of CFD-calculation should be aware of the basic principles of calculations and specifically the boundary conditions. Computational Fluid Dynamics (CFD) – in Ventilation Design models is written by a working group of highly qualified international experts representing research, consulting and design.
International Nuclear Information System (INIS)
Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M
2010-01-01
Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives
Arterioportal shunts on dynamic computed tomography
International Nuclear Information System (INIS)
Nakayama, T.; Hiyama, Y.; Ohnishi, K.; Tsuchiya, S.; Kohno, K.; Nakajima, Y.; Okuda, K.
1983-01-01
Thirty-two patients, 20 with hepatocelluar carcinoma and 12 with liver cirrhosis, were examined by dynamic computed tomography (CT) using intravenous bolus injection of contrast medium and by celiac angiography. Dynamic CT disclosed arterioportal shunting in four cases of hepatocellular carcinoma and in one of cirrhosis. In three of the former, the arterioportal shunt was adjacent to a mass lesion on CT, suggesting tumor invasion into the portal branch. In one with hepatocellular carcinoma, the shunt was remote from the mass. In the case with cirrhosis, there was no mass. In these last two cases, the shunt might have been caused by prior percutaneous needle puncture. In another case of hepatocellular carcinoma, celiac angiography but not CT demonstrated an arterioportal shunt. Thus, dynamic CT was diagnostic in five of six cases of arteriographically demonstrated arterioportal shunts
Computer-graphic visualization of dynamics
International Nuclear Information System (INIS)
Stewart, H.B.
1986-01-01
As engineered systems become increasingly sophisticated and complex, questions of efficiency, reliability, and safety demand the application of more powerful methods of analysis. One indication of this is the accelerating trend away from purely static or quasi-steady system modeling toward models that include essentially dynamic behavior. It is here that the qualitative ideas of nonlinear dynamics, dealing as they do with the most typical behavior in real dynamical systems, can be expected to play an increasingly prominent role. As part of a continuing investigation of the most important low-order differential equations, an interactive computer graphics environment has been created for the study of systems in three-dimensional phase space. This environment makes available the basic control of both numerical simulation and graphic visualization by a specially designed menu system. A key ingredient in this environment is the possibility of graphic communication not only from machine to man, but also from man to machine. Thus to specify the starting point for a numerical integration, for example, the user points to a location in phase space on the screen of the graphics terminal (using crosshairs or a mouse and cursor), bypassing the necessity to give numerical values of the phase-space coordinates. By devising a flexible computer interface which implements conceptual approaches to phase-space analysis of dynamical systems, significant advances in understanding of prototypical differential equations have been achieved
Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.
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.
Quantum dynamics of fast chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Light, J.C. [Univ. of Chicago, IL (United States)
1993-12-01
The aims of this research are to explore, develop, and apply theoretical methods for the evaluation of the dynamics of gas phase collision processes, primarily chemical reactions. The primary theoretical tools developed for this work have been quantum scattering theory, both in time dependent and time independent forms. Over the past several years, the authors have developed and applied methods for the direct quantum evaluation of thermal rate constants, applying these to the evaluation of the hydrogen isotopic exchange reactions, applied wave packet propagation techniques to the dissociation of Rydberg H{sub 3}, incorporated optical potentials into the evaluation of thermal rate constants, evaluated the use of optical potentials for state-to-state reaction probability evaluations, and, most recently, have developed quantum approaches for electronically non-adiabatic reactions which may be applied to simplify calculations of reactive, but electronically adiabatic systems. Evaluation of the thermal rate constants and the dissociation of H{sub 3} were reported last year, and have now been published.
Computational chemical product design problems under property uncertainties
DEFF Research Database (Denmark)
Frutiger, Jerome; Cignitti, Stefano; Abildskov, Jens
2017-01-01
Three different strategies of how to combine computational chemical product design with Monte Carlo based methods for uncertainty analysis of chemical properties are outlined. One method consists of a computer-aided molecular design (CAMD) solution and a post-processing property uncertainty...... fluid design. While the higher end of the uncertainty range of the process model output is similar for the best performing fluids, the lower end of the uncertainty range differs largely....
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
Directory of Open Access Journals (Sweden)
Trambouze P.
2006-11-01
Full Text Available Computational Fluid Dynamics (CFD and its applications have developed quite rapidly during the last ten years. This fast growing hybrid branch of Mechanics and Mathematics is certainly to be considered as a potentially useful and efficient tool in the field of Chemical Engineering and more specifically in the area of Chemical Reaction Engineering (CRE. The difficulties in this new approach stems from the consequence of the complexity of the mechanims to be simulated simultaneously : fluid dynamics, chemical reactions and physical aspects of each system considered. Another difficulty comes from the numerical treatment of the equations for the final model, resulting in very sophisticated and diversified mathematical treatments. The types of chemical reactors to be considered for potential performance improvements when applying CFD as a new tool for their design are numerous ; two broad classes of problem have be identified as relevant to this new approach :(a Systems involving fast chemical reactions, with characteristic times of the same order of magnitude as the characteristic time scales of turbulence. In-line mixing equipment should preferably be studied for this type of reactions. (b Multiphase systems, whose scaling-up still has to be performed with great difficulty and, more often than not, according to empirical procedures based on very simplified models. When looking at the various types of systems found in practice, it appears that gas-liquid and fluid-solid systems should be considered first. However, basic knowledge is still missing concerning the physical behaviour of these systems, especially for the coalescence of bubbles and the momentum transfer between gas and solid. Specific research should be done in order to get this missing information. Presently there are a certain number of existing CFD software packages available commercially or developed by various research laboratories. This is certainly an interesting starting point
Computational fluid dynamics in fire engineering theory, modelling and practice
Yuen, Kwok Kit
2009-01-01
Fire and combustion presents a significant engineering challenge to mechanical, civil and dedicated fire engineers, as well as specialists in the process and chemical, safety, buildings and structural fields. We are reminded of the tragic outcomes of 'untenable' fire disasters such as at King's Cross underground station or Switzerland's St Gotthard tunnel. In these and many other cases, computational fluid dynamics (CFD) is at the forefront of active research into unravelling the probable causes of fires and helping to design structures and systems to ensure that they are less likely in the f
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.)
BALANCER: A Computer Program for Balancing Chemical Equations.
Jones, R. David; Schwab, A. Paul
1989-01-01
Describes the theory and operation of a computer program which was written to balance chemical equations. Software consists of a compiled file of 46K for use under MS-DOS 2.0 or later on IBM PC or compatible computers. Additional specifications of courseware and availability information are included. (Author/RT)
Dynamical Models for Computer Viruses Propagation
Directory of Open Access Journals (Sweden)
José R. C. Piqueira
2008-01-01
Full Text Available Nowadays, digital computer systems and networks are the main engineering tools, being used in planning, design, operation, and control of all sizes of building, transportation, machinery, business, and life maintaining devices. Consequently, computer viruses became one of the most important sources of uncertainty, contributing to decrease the reliability of vital activities. A lot of antivirus programs have been developed, but they are limited to detecting and removing infections, based on previous knowledge of the virus code. In spite of having good adaptation capability, these programs work just as vaccines against diseases and are not able to prevent new infections based on the network state. Here, a trial on modeling computer viruses propagation dynamics relates it to other notable events occurring in the network permitting to establish preventive policies in the network management. Data from three different viruses are collected in the Internet and two different identification techniques, autoregressive and Fourier analyses, are applied showing that it is possible to forecast the dynamics of a new virus propagation by using the data collected from other viruses that formerly infected the network.
Semiclassical methods in chemical reaction dynamics
International Nuclear Information System (INIS)
Keshavamurthy, S.
1994-12-01
Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems
Semiclassical methods in chemical reaction dynamics
Energy Technology Data Exchange (ETDEWEB)
Keshavamurthy, Srihari [Univ. of California, Berkeley, CA (United States)
1994-12-01
Semiclassical approximations, simple as well as rigorous, are formulated in order to be able to describe gas phase chemical reactions in large systems. We formulate a simple but accurate semiclassical model for incorporating multidimensional tunneling in classical trajectory simulations. This model is based on the existence of locally conserved actions around the saddle point region on a multidimensional potential energy surface. Using classical perturbation theory and monitoring the imaginary action as a function of time along a classical trajectory we calculate state-specific unimolecular decay rates for a model two dimensional potential with coupling. Results are in good comparison with exact quantum results for the potential over a wide range of coupling constants. We propose a new semiclassical hybrid method to calculate state-to-state S-matrix elements for bimolecular reactive scattering. The accuracy of the Van Vleck-Gutzwiller propagator and the short time dynamics of the system make this method self-consistent and accurate. We also go beyond the stationary phase approximation by doing the resulting integrals exactly (numerically). As a result, classically forbidden probabilties are calculated with purely real time classical trajectories within this approach. Application to the one dimensional Eckart barrier demonstrates the accuracy of this approach. Successful application of the semiclassical hybrid approach to collinear reactive scattering is prevented by the phenomenon of chaotic scattering. The modified Filinov approach to evaluating the integrals is discussed, but application to collinear systems requires a more careful analysis. In three and higher dimensional scattering systems, chaotic scattering is suppressed and hence the accuracy and usefulness of the semiclassical method should be tested for such systems.
The dynamic micro computed tomography at SSRF
Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.
2018-05-01
Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.
Dynamic X-ray computed tomography
International Nuclear Information System (INIS)
Grangeat, P.
2003-01-01
Paper Dynamic computed tomography (CT) imaging aims at reconstructing image sequences where the dynamic nature of the living human body is of primary interest. Main concerned applications are image-guided interventional procedures, functional studies and cardiac imaging. The introduction of ultra-fast rotating gantries along with multi-row detectors and in near future area detectors allows a huge progress toward the imaging of moving organs with low-contrast resolution. This paper gives an overview of the different concepts used in dynamic CT. A new reconstruction algorithm based on a voxel-specific dynamic evolution compensation is also presented. It provides four-dimensional image sequences with accurate spatio-temporal information, where each frame is reconstructed using a long-scan acquisition mode on several half-turns. In the same time, this technique permits to reduce the dose delivered per rotation while keeping the same signal to noise ratio for every frame using an adaptive motion-compensated temporal averaging. Results are illustrated on simulated data. (authors)
High performance computations using dynamical nucleation theory
International Nuclear Information System (INIS)
Windus, T L; Crosby, L D; Kathmann, S M
2008-01-01
Chemists continue to explore the use of very large computations to perform simulations that describe the molecular level physics of critical challenges in science. In this paper, we describe the Dynamical Nucleation Theory Monte Carlo (DNTMC) model - a model for determining molecular scale nucleation rate constants - and its parallel capabilities. The potential for bottlenecks and the challenges to running on future petascale or larger resources are delineated. A 'master-slave' solution is proposed to scale to the petascale and will be developed in the NWChem software. In addition, mathematical and data analysis challenges are described
A network dynamics approach to chemical reaction networks
van der Schaft, Abraham; Rao, S.; Jayawardhana, B.
2016-01-01
A treatment of chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a
Zonal methods and computational fluid dynamics
International Nuclear Information System (INIS)
Atta, E.H.
1985-01-01
Recent advances in developing numerical algorithms for solving fluid flow problems, and the continuing improvement in the speed and storage of large scale computers have made it feasible to compute the flow field about complex and realistic configurations. Current solution methods involve the use of a hierarchy of mathematical models ranging from the linearized potential equation to the Navier Stokes equations. Because of the increasing complexity of both the geometries and flowfields encountered in practical fluid flow simulation, there is a growing emphasis in computational fluid dynamics on the use of zonal methods. A zonal method is one that subdivides the total flow region into interconnected smaller regions or zones. The flow solutions in these zones are then patched together to establish the global flow field solution. Zonal methods are primarily used either to limit the complexity of the governing flow equations to a localized region or to alleviate the grid generation problems about geometrically complex and multicomponent configurations. This paper surveys the application of zonal methods for solving the flow field about two and three-dimensional configurations. Various factors affecting their accuracy and ease of implementation are also discussed. From the presented review it is concluded that zonal methods promise to be very effective for computing complex flowfields and configurations. Currently there are increasing efforts to improve their efficiency, versatility, and accuracy
Direct modeling for computational fluid dynamics
Xu, Kun
2015-06-01
All fluid dynamic equations are valid under their modeling scales, such as the particle mean free path and mean collision time scale of the Boltzmann equation and the hydrodynamic scale of the Navier-Stokes (NS) equations. The current computational fluid dynamics (CFD) focuses on the numerical solution of partial differential equations (PDEs), and its aim is to get the accurate solution of these governing equations. Under such a CFD practice, it is hard to develop a unified scheme that covers flow physics from kinetic to hydrodynamic scales continuously because there is no such governing equation which could make a smooth transition from the Boltzmann to the NS modeling. The study of fluid dynamics needs to go beyond the traditional numerical partial differential equations. The emerging engineering applications, such as air-vehicle design for near-space flight and flow and heat transfer in micro-devices, do require further expansion of the concept of gas dynamics to a larger domain of physical reality, rather than the traditional distinguishable governing equations. At the current stage, the non-equilibrium flow physics has not yet been well explored or clearly understood due to the lack of appropriate tools. Unfortunately, under the current numerical PDE approach, it is hard to develop such a meaningful tool due to the absence of valid PDEs. In order to construct multiscale and multiphysics simulation methods similar to the modeling process of constructing the Boltzmann or the NS governing equations, the development of a numerical algorithm should be based on the first principle of physical modeling. In this paper, instead of following the traditional numerical PDE path, we introduce direct modeling as a principle for CFD algorithm development. Since all computations are conducted in a discretized space with limited cell resolution, the flow physics to be modeled has to be done in the mesh size and time step scales. Here, the CFD is more or less a direct
Chemical Dynamics, Molecular Energetics, and Kinetics at the Synchrotron
International Nuclear Information System (INIS)
Leone, Stephen R.; Ahmed, Musahid; Wilson, Kevin R.
2010-01-01
Scientists at the Chemical Dynamics Beamline of the Advanced Light Source in Berkeley are continuously reinventing synchrotron investigations of physical chemistry and chemical physics with vacuum ultraviolet light. One of the unique aspects of a synchrotron for chemical physics research is the widely tunable vacuum ultraviolet light that permits threshold ionization of large molecules with minimal fragmentation. This provides novel opportunities to assess molecular energetics and reaction mechanisms, even beyond simple gas phase molecules. In this perspective, significant new directions utilizing the capabilities at the Chemical Dynamics Beamline are presented, along with an outlook for future synchrotron and free electron laser science in chemical dynamics. Among the established and emerging fields of investigations are cluster and biological molecule spectroscopy and structure, combustion flame chemistry mechanisms, radical kinetics and product isomer dynamics, aerosol heterogeneous chemistry, planetary and interstellar chemistry, and secondary neutral ion-beam desorption imaging of biological matter and materials chemistry.
Computed potential energy surfaces for chemical reactions
Walch, Stephen P.
1988-01-01
The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.
Computational Fluid Dynamics in Ventilation Design
DEFF Research Database (Denmark)
Nielsen, Peter V.
2008-01-01
This paper is based on the new REHVA Guidebook Computational Fluid Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people....... The guidebook introduces rules for good quality prediction work, and it is the purpose of the guidebook to improve the technical level of CFD work in ventilation.......This paper is based on the new REHVA Guidebook Computational Fluid Dynamics in Ventilation Design (Nielsen et al. 2007) written by Peter V. Nielsen, Francis(Nielsen 2007) written by Peter V. Nielsen, Francis Allard, Hazim B. Awbi, Lars Davidson and Alois Schälin. The guidebook is made for people...... who need to use and discuss results based on CFD predictions, and it gives insight into the subject for those who are not used to work with CFD. The guidebook is also written for people working with CFD who have to be more aware of how this numerical method is applied in the area of ventilation...
Introduction to computational mass transfer with applications to chemical engineering
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...
Computational Analyses of Complex Flows with Chemical Reactions
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
A computational approach to chemical etiologies of diabetes
DEFF Research Database (Denmark)
Audouze, Karine Marie Laure; Brunak, Søren; Grandjean, Philippe
2013-01-01
Computational meta-analysis can link environmental chemicals to genes and proteins involved in human diseases, thereby elucidating possible etiologies and pathogeneses of non-communicable diseases. We used an integrated computational systems biology approach to examine possible pathogenetic...... linkages in type 2 diabetes (T2D) through genome-wide associations, disease similarities, and published empirical evidence. Ten environmental chemicals were found to be potentially linked to T2D, the highest scores were observed for arsenic, 2,3,7,8-tetrachlorodibenzo-p-dioxin, hexachlorobenzene...
Computational prediction of chemical reactions: current status and outlook.
Engkvist, Ola; Norrby, Per-Ola; Selmi, Nidhal; Lam, Yu-Hong; Peng, Zhengwei; Sherer, Edward C; Amberg, Willi; Erhard, Thomas; Smyth, Lynette A
2018-06-01
Over the past few decades, various computational methods have become increasingly important for discovering and developing novel drugs. Computational prediction of chemical reactions is a key part of an efficient drug discovery process. In this review, we discuss important parts of this field, with a focus on utilizing reaction data to build predictive models, the existing programs for synthesis prediction, and usage of quantum mechanics and molecular mechanics (QM/MM) to explore chemical reactions. We also outline potential future developments with an emphasis on pre-competitive collaboration opportunities. Copyright © 2018 Elsevier Ltd. All rights reserved.
Verification and validation in computational fluid dynamics
Oberkampf, William L.; Trucano, Timothy G.
2002-04-01
Verification and validation (V&V) are the primary means to assess accuracy and reliability in computational simulations. This paper presents an extensive review of the literature in V&V in computational fluid dynamics (CFD), discusses methods and procedures for assessing V&V, and develops a number of extensions to existing ideas. The review of the development of V&V terminology and methodology points out the contributions from members of the operations research, statistics, and CFD communities. Fundamental issues in V&V are addressed, such as code verification versus solution verification, model validation versus solution validation, the distinction between error and uncertainty, conceptual sources of error and uncertainty, and the relationship between validation and prediction. The fundamental strategy of verification is the identification and quantification of errors in the computational model and its solution. In verification activities, the accuracy of a computational solution is primarily measured relative to two types of highly accurate solutions: analytical solutions and highly accurate numerical solutions. Methods for determining the accuracy of numerical solutions are presented and the importance of software testing during verification activities is emphasized. The fundamental strategy of validation is to assess how accurately the computational results compare with the experimental data, with quantified error and uncertainty estimates for both. This strategy employs a hierarchical methodology that segregates and simplifies the physical and coupling phenomena involved in the complex engineering system of interest. A hypersonic cruise missile is used as an example of how this hierarchical structure is formulated. The discussion of validation assessment also encompasses a number of other important topics. A set of guidelines is proposed for designing and conducting validation experiments, supported by an explanation of how validation experiments are different
Foreign Language Translation of Chemical Nomenclature by Computer
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
Artificial Intelligence In Computational Fluid Dynamics
Vogel, Alison Andrews
1991-01-01
Paper compares four first-generation artificial-intelligence (Al) software systems for computational fluid dynamics. Includes: Expert Cooling Fan Design System (EXFAN), PAN AIR Knowledge System (PAKS), grid-adaptation program MITOSIS, and Expert Zonal Grid Generation (EZGrid). Focuses on knowledge-based ("expert") software systems. Analyzes intended tasks, kinds of knowledge possessed, magnitude of effort required to codify knowledge, how quickly constructed, performances, and return on investment. On basis of comparison, concludes Al most successful when applied to well-formulated problems solved by classifying or selecting preenumerated solutions. In contrast, application of Al to poorly understood or poorly formulated problems generally results in long development time and large investment of effort, with no guarantee of success.
Computational modeling of intraocular gas dynamics
International Nuclear Information System (INIS)
Noohi, P; Abdekhodaie, M J; Cheng, Y L
2015-01-01
The purpose of this study was to develop a computational model to simulate the dynamics of intraocular gas behavior in pneumatic retinopexy (PR) procedure. The presented model predicted intraocular gas volume at any time and determined the tolerance angle within which a patient can maneuver and still gas completely covers the tear(s). Computational fluid dynamics calculations were conducted to describe PR procedure. The geometrical model was constructed based on the rabbit and human eye dimensions. SF_6 in the form of pure and diluted with air was considered as the injected gas. The presented results indicated that the composition of the injected gas affected the gas absorption rate and gas volume. After injection of pure SF_6, the bubble expanded to 2.3 times of its initial volume during the first 23 h, but when diluted SF_6 was used, no significant expansion was observed. Also, head positioning for the treatment of retinal tear influenced the rate of gas absorption. Moreover, the determined tolerance angle depended on the bubble and tear size. More bubble expansion and smaller retinal tear caused greater tolerance angle. For example, after 23 h, for the tear size of 2 mm the tolerance angle of using pure SF_6 is 1.4 times more than that of using diluted SF_6 with 80% air. Composition of the injected gas and conditions of the tear in PR may dramatically affect the gas absorption rate and gas volume. Quantifying these effects helps to predict the tolerance angle and improve treatment efficiency. (paper)
Chemical Dynamics Studies of Reactions in Solids
National Research Council Canada - National Science Library
Thompson, Donald O
1998-01-01
... the properties inherent in high-energy high-density materials. This research lays the groundwork for that by providing the theoretical and computational methods as well as accurate molecular and crystal models for important types of energetic systems...
Special Issue on Theoretical Chemistry/Chemical Dynamics
Indian Academy of Sciences (India)
2017-07-02
Jul 2, 2017 ... This month's issue of the Journal of Chemical Sciences honours Professor Charusita Chakravarty, who has made immeasurable contributions to theoretical chemistry and chemical dynamics. The editors Biman Bagchi (FASc, FNA, FTWAS; Indian Institute of Science, Bangalore, India), David Clary (FRS; ...
Experiences on dynamic simulation software in chemical engineering education
DEFF Research Database (Denmark)
Komulainen, Tiina M.; Enemark-rasmussen, Rasmus; Sin, Gürkan
2012-01-01
Commercial process simulators are increasing interest in the chemical engineer education. In this paper, the use of commercial dynamic simulation software, D-SPICE® and K-Spice®, for three different chemical engineering courses is described and discussed. The courses cover the following topics...
Computational Fluid Dynamics Modeling of Bacillus anthracis ...
Journal Article Three-dimensional computational fluid dynamics and Lagrangian particle deposition models were developed to compare the deposition of aerosolized Bacillus anthracis spores in the respiratory airways of a human with that of the rabbit, a species commonly used in the study of anthrax disease. The respiratory airway geometries for each species were derived from computed tomography (CT) or µCT images. Both models encompassed airways that extended from the external nose to the lung with a total of 272 outlets in the human model and 2878 outlets in the rabbit model. All simulations of spore deposition were conducted under transient, inhalation-exhalation breathing conditions using average species-specific minute volumes. Four different exposure scenarios were modeled in the rabbit based upon experimental inhalation studies. For comparison, human simulations were conducted at the highest exposure concentration used during the rabbit experimental exposures. Results demonstrated that regional spore deposition patterns were sensitive to airway geometry and ventilation profiles. Despite the complex airway geometries in the rabbit nose, higher spore deposition efficiency was predicted in the upper conducting airways of the human at the same air concentration of anthrax spores. This greater deposition of spores in the upper airways in the human resulted in lower penetration and deposition in the tracheobronchial airways and the deep lung than that predict
Computer simulation of dynamic processes on accelerators
International Nuclear Information System (INIS)
Kol'ga, V.V.
1979-01-01
The problems of computer numerical investigation of motion of accelerated particles in accelerators and storages, an effect of different accelerator systems on the motion, determination of optimal characteristics of accelerated charged particle beams are considered. Various simulation representations are discussed which describe the accelerated particle dynamics, such as the enlarged particle method, the representation where a great number of discrete particle is substituted for a field of continuously distributed space charge, the method based on determination of averaged beam characteristics. The procedure is described of numerical studies involving the basic problems, viz. calculation of closed orbits, establishment of stability regions, investigation of resonance propagation determination of the phase stability region, evaluation of the space charge effect the problem of beam extraction. It is shown that most of such problems are reduced to solution of the Cauchy problem using a computer. The ballistic method which is applied to solution of the boundary value problem of beam extraction is considered. It is shown that introduction into the equation under study of additional members with the small positive regularization parameter is a general idea of the methods for regularization of noncorrect problems [ru
Computer integrated manufacturing in the chemical industry : Theory & practice
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.
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...
Computer program determines chemical composition of physical system at equilibrium
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.
Molecular dynamics simulations and quantum chemical calculations ...
African Journals Online (AJOL)
Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...
Symbolic mathematical computing: orbital dynamics and application to accelerators
International Nuclear Information System (INIS)
Fateman, R.
1986-01-01
Computer-assisted symbolic mathematical computation has become increasingly useful in applied mathematics. A brief introduction to such capabilitites and some examples related to orbital dynamics and accelerator physics are presented. (author)
Introduction to computational mass transfer with applications to chemical engineering
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...
Chemical reaction dynamics using the Advanced Light Source
International Nuclear Information System (INIS)
Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.
1995-01-01
The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10(sup 16) photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source
Chemical reaction dynamics using the Advanced Light Source
International Nuclear Information System (INIS)
Yang, X.; Blank, D.A.; Heimann, P.A.; Lee, Y.T.; Suits, A.G.; Lin, J.; Wodtke, A.M.
1995-09-01
The recently commissioned Advanced Light Source (ALS) at Berkeley provides a high brightness, tunable VUV light source for chemical dynamics studies. A dedicated chemical dynamics beamline has been built at the ALS for studies of fundamental chemical processes. High flux (10 16 photon/s with 2% bandwidth) VUV synchrotron radiation from 5 to 30 eV can be obtained from the beamline, whose source is the U8/10 undulator. Three endstations will be in operation for studies ranging from crossed beam reaction dynamics and photodissociation to high resolution photoionization dynamics and spectroscopy. A rotatable source crossed molecular beam apparatus (endstation one) has been established for unimolecular and bimolecular reactive scattering studies. Photodissociation of methylamine and ozone were carried out using VUV synchrotron radiation as the ionization detection technique at this endstation. Results show the advantages of the new endstation using VUV ionization as the detection scheme over similar machines using electron bombardment as the ionization source
Energy Technology Data Exchange (ETDEWEB)
Tully, John C. [Yale Univ., New Haven, CT (United States)
2017-06-10
Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opens up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.
Computational fluid dynamics modelling in cardiovascular medicine.
Morris, Paul D; Narracott, Andrew; von Tengg-Kobligk, Hendrik; Silva Soto, Daniel Alejandro; Hsiao, Sarah; Lungu, Angela; Evans, Paul; Bressloff, Neil W; Lawford, Patricia V; Hose, D Rodney; Gunn, Julian P
2016-01-01
This paper reviews the methods, benefits and challenges associated with the adoption and translation of computational fluid dynamics (CFD) modelling within cardiovascular medicine. CFD, a specialist area of mathematics and a branch of fluid mechanics, is used routinely in a diverse range of safety-critical engineering systems, which increasingly is being applied to the cardiovascular system. By facilitating rapid, economical, low-risk prototyping, CFD modelling has already revolutionised research and development of devices such as stents, valve prostheses, and ventricular assist devices. Combined with cardiovascular imaging, CFD simulation enables detailed characterisation of complex physiological pressure and flow fields and the computation of metrics which cannot be directly measured, for example, wall shear stress. CFD models are now being translated into clinical tools for physicians to use across the spectrum of coronary, valvular, congenital, myocardial and peripheral vascular diseases. CFD modelling is apposite for minimally-invasive patient assessment. Patient-specific (incorporating data unique to the individual) and multi-scale (combining models of different length- and time-scales) modelling enables individualised risk prediction and virtual treatment planning. This represents a significant departure from traditional dependence upon registry-based, population-averaged data. Model integration is progressively moving towards 'digital patient' or 'virtual physiological human' representations. When combined with population-scale numerical models, these models have the potential to reduce the cost, time and risk associated with clinical trials. The adoption of CFD modelling signals a new era in cardiovascular medicine. While potentially highly beneficial, a number of academic and commercial groups are addressing the associated methodological, regulatory, education- and service-related challenges. Published by the BMJ Publishing Group Limited. For permission
Cluster dynamics transcending chemical dynamics toward nuclear fusion.
Heidenreich, Andreas; Jortner, Joshua; Last, Isidore
2006-07-11
Ultrafast cluster dynamics encompasses femtosecond nuclear dynamics, attosecond electron dynamics, and electron-nuclear dynamics in ultraintense laser fields (peak intensities 10(15)-10(20) W.cm(-2)). Extreme cluster multielectron ionization produces highly charged cluster ions, e.g., (C(4+)(D(+))(4))(n) and (D(+)I(22+))(n) at I(M) = 10(18) W.cm(-2), that undergo Coulomb explosion (CE) with the production of high-energy (5 keV to 1 MeV) ions, which can trigger nuclear reactions in an assembly of exploding clusters. The laser intensity and the cluster size dependence of the dynamics and energetics of CE of (D(2))(n), (HT)(n), (CD(4))(n), (DI)(n), (CD(3)I)(n), and (CH(3)I)(n) clusters were explored by electrostatic models and molecular dynamics simulations, quantifying energetic driving effects, and kinematic run-over effects. The optimization of table-top dd nuclear fusion driven by CE of deuterium containing heteroclusters is realized for light-heavy heteroclusters of the largest size, which allows for the prevalence of cluster vertical ionization at the highest intensity of the laser field. We demonstrate a 7-orders-of-magnitude enhancement of the yield of dd nuclear fusion driven by CE of light-heavy heteroclusters as compared with (D(2))(n) clusters of the same size. Prospective applications for the attainment of table-top nucleosynthesis reactions, e.g., (12)C(P,gamma)(13)N driven by CE of (CH(3)I)(n) clusters, were explored.
Study of blast wave overpressures using the computational fluid dynamics
Directory of Open Access Journals (Sweden)
M. L. COSTA NETO
Full Text Available ABSTRACT The threats of bomb attacks by criminal organizations and accidental events involving chemical explosives are a danger to the people and buildings. Due the severity of these issues and the need of data required for a safety design, more research is required about explosions and shock waves. This paper presents an assessment of blast wave overpressures using a computational fluid dynamics software. Analyses of phenomena as reflection of shock waves and channeling effects were done and a comparison between numerical results and analytical predictions has been executed, based on the simulation on several models. The results suggest that the common analytical predictions aren’t accurate enough for an overpressure analysis in small stand-off distances and that poorly designed buildings may increase the shock wave overpressures due multiple blast wave reflections, increasing the destructive potential of the explosions.
Partial chemical equilibrium in fluid dynamics
International Nuclear Information System (INIS)
Ramshaw, J.D.
1980-01-01
An analysis is given for the flow of a multicomponent fluid in which an arbitrary number of chemical reactions may occur, some of which are in equilibrium while the others proceed kinetically. The primitive equations describing this situation are inconvenient to use because the progress rates omega-dot/sub s/ for the equilibrium reactions are determined implicitly by the associated equilibrium constraint conditions. Two alternative equivalent equation systems that are more pleasant to deal with are derived. In the first system, the omega-dot/sub s/ are eliminated by replacing the transport equations for the chemical species involved in the equilibrium reactions with transport equations for the basic components of which these species are composed. The second system retains the usual species transport equations, but eliminates the nonlinear algebraic equilibrium constraint conditions by deriving an explicit expression for the omega-dot/sub s/. Both systems are specialized to the case of an ideal gas mixture. Considerations involved in solving these equation systems numerically are discussed briefly
CFDLIB05, Computational Fluid Dynamics Library
International Nuclear Information System (INIS)
Kashiwa, B.A.; Padial, N.T.; Rauenzahn, R.M.; VanderHeyden, W.B.
2007-01-01
1 - Description of program or function: CFDLib05 is the Los Alamos Computational Fluid Dynamics Library. This is a collection of hydro-codes using a common data structure and a common numerical method, for problems ranging from single-field, incompressible flow, to multi-species, multi-field, compressible flow. The data structure is multi-block, with a so-called structured grid in each block. The numerical method is a Finite-Volume scheme employing a state vector that is fully cell-centered. This means that the integral form of the conversation laws is solved on the physical domain that is represented by a mesh of control volumes. The typical control volume is an arbitrary quadrilateral in 2D and an arbitrary hexahedron in 3D. The Finite-Volume scheme is for time-unsteady flow and remains well coupled by means of time and space centered fluxes; if a steady state solution is required, the problem is integrated forward in time until the user is satisfied that the state is stationary. 2 - Methods: Cells-centered Implicit Continuous-fluid Eulerian (ICE) method
Computational social dynamic modeling of group recruitment.
Energy Technology Data Exchange (ETDEWEB)
Berry, Nina M.; Lee, Marinna; Pickett, Marc; Turnley, Jessica Glicken (Sandia National Laboratories, Albuquerque, NM); Smrcka, Julianne D. (Sandia National Laboratories, Albuquerque, NM); Ko, Teresa H.; Moy, Timothy David (Sandia National Laboratories, Albuquerque, NM); Wu, Benjamin C.
2004-01-01
The Seldon software toolkit combines concepts from agent-based modeling and social science to create a computationally social dynamic model for group recruitment. The underlying recruitment model is based on a unique three-level hybrid agent-based architecture that contains simple agents (level one), abstract agents (level two), and cognitive agents (level three). This uniqueness of this architecture begins with abstract agents that permit the model to include social concepts (gang) or institutional concepts (school) into a typical software simulation environment. The future addition of cognitive agents to the recruitment model will provide a unique entity that does not exist in any agent-based modeling toolkits to date. We use social networks to provide an integrated mesh within and between the different levels. This Java based toolkit is used to analyze different social concepts based on initialization input from the user. The input alters a set of parameters used to influence the values associated with the simple agents, abstract agents, and the interactions (simple agent-simple agent or simple agent-abstract agent) between these entities. The results of phase-1 Seldon toolkit provide insight into how certain social concepts apply to different scenario development for inner city gang recruitment.
Computational fluid dynamics principles and applications
Blazek, J
2005-01-01
Computational Fluid Dynamics (CFD) is an important design tool in engineering and also a substantial research tool in various physical sciences as well as in biology. The objective of this book is to provide university students with a solid foundation for understanding the numerical methods employed in today's CFD and to familiarise them with modern CFD codes by hands-on experience. It is also intended for engineers and scientists starting to work in the field of CFD or for those who apply CFD codes. Due to the detailed index, the text can serve as a reference handbook too. Each chapter includes an extensive bibliography, which provides an excellent basis for further studies. The accompanying companion website contains the sources of 1-D and 2-D Euler and Navier-Stokes flow solvers (structured and unstructured) as well as of grid generators. Provided are also tools for Von Neumann stability analysis of 1-D model equations. Finally, the companion website includes the source code of a dedicated visualisation so...
Computational fluid dynamics in ventilation: Practical approach
Fontaine, J. R.
The potential of computation fluid dynamics (CFD) for conceiving ventilation systems is shown through the simulation of five practical cases. The following examples are considered: capture of pollutants on a surface treating tank equipped with a unilateral suction slot in the presence of a disturbing air draft opposed to suction; dispersion of solid aerosols inside fume cupboards; performances comparison of two general ventilation systems in a silkscreen printing workshop; ventilation of a large open painting area; and oil fog removal inside a mechanical engineering workshop. Whereas the two first problems are analyzed through two dimensional numerical simulations, the three other cases require three dimensional modeling. For the surface treating tank case, numerical results are compared to laboratory experiment data. All simulations are carried out using EOL, a CFD software specially devised to deal with air quality problems in industrial ventilated premises. It contains many analysis tools to interpret the results in terms familiar to the industrial hygienist. Much experimental work has been engaged to validate the predictions of EOL for ventilation flows.
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.
Computer Programme for the Dynamic Analysis of Tall Regular ...
African Journals Online (AJOL)
The traditional method of dynamic analysis of tall rigid frames assumes the shear frame model. Models that allow joint rotations with/without the inclusion of the column axial loads give improved results but pose much more computational difficulty. In this work a computer program Natfrequency that determines the dynamic ...
HTTR plant dynamic simulation using a hybrid computer
International Nuclear Information System (INIS)
Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.
1990-01-01
A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)
Annual Report 2000. Chemical Structure and Dynamics; FINAL
International Nuclear Information System (INIS)
Colson, Steve D; McDowell, Rod S
2001-01-01
This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS and D) program is meeting the need for a fundamental, molecular-level understanding by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and (3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems
Dynamics of chemical equilibrium of hadronic matter close to Tc
International Nuclear Information System (INIS)
Noronha-Hostler, J.; Beitel, M.; Greiner, C.; Shovkovy, I.
2010-01-01
Quick chemical equilibration times of hadrons (specifically, pp-bar, KK-bar, ΛΛ-bar, and ΩΩ-bar pairs) within a hadron gas are explained dynamically using Hagedorn states, which drive particles into equilibrium close to the critical temperature. Within this scheme, we use master equations and derive various analytical estimates for the chemical equilibration times. We compare our model to recent lattice results and find that for both T c =176 MeV and T c =196 MeV, the hadrons can reach chemical equilibrium almost immediately, well before the chemical freeze-out temperatures found in thermal fits for a hadron gas without Hagedorn states. Furthermore, the ratios p/π, K/π, Λ/π, and Ω/π match experimental values well in our dynamical scenario.
NATO Advanced Study Institute on Advances in Chemical Reaction Dynamics
Capellos, Christos
1986-01-01
This book contains the formal lectures and contributed papers presented at the NATO Advanced Study Institute on. the Advances in Chemical Reaction Dynamics. The meeting convened at the city of Iraklion, Crete, Greece on 25 August 1985 and continued to 7 September 1985. The material presented describes the fundamental and recent advances in experimental and theoretical aspects of, reaction dynamics. A large section is devoted to electronically excited states, ionic species, and free radicals, relevant to chemical sys tems. In addition recent advances in gas phase polymerization, formation of clusters, and energy release processes in energetic materials were presented. Selected papers deal with topics such as the dynamics of electric field effects in low polar solutions, high electric field perturbations and relaxation of dipole equilibria, correlation in picosecond/laser pulse scattering, and applications to fast reaction dynamics. Picosecond transient Raman spectroscopy which has been used for the elucidati...
Dynamic leaching test of personal computer components.
Li, Yadong; Richardson, Jay B; Niu, Xiaojun; Jackson, Ollie J; Laster, Jeremy D; Walker, Aaron K
2009-11-15
A dynamic leaching test (DLT) was developed and used to evaluate the leaching of toxic substances for electronic waste in the environment. The major components in personal computers (PCs) including motherboards, hard disc drives, floppy disc drives, and compact disc drives were tested. The tests lasted for 2 years for motherboards and 1.5 year for the disc drives. The extraction fluids for the standard toxicity characteristic leaching procedure (TCLP) and synthetic precipitation leaching procedure (SPLP) were used as the DLT leaching solutions. A total of 18 elements including Ag, Al, As, Au, Ba, Be, Cd, Cr, Cu, Fe, Ga, Ni, Pd, Pb, Sb, Se, Sn, and Zn were analyzed in the DLT leachates. Only Al, Cu, Fe, Ni, Pb, and Zn were commonly found in the DLT leachates of the PC components. Their leaching levels were much higher in TCLP extraction fluid than in SPLP extraction fluid. The toxic heavy metal Pb was found to continuously leach out of the components over the entire test periods. The cumulative amounts of Pb leached out of the motherboards in TCLP extraction fluid reached 2.0 g per motherboard over the 2-year test period, and that in SPLP extraction fluid were 75-90% less. The leaching rates or levels of Pb were largely affected by the content of galvanized steel in the PC components. The higher was the steel content, the lower the Pb leaching rate would be. The findings suggest that the obsolete PCs disposed of in landfills or discarded in the environment continuously release Pb for years when subjected to landfill leachate or rains.
AIR INGRESS ANALYSIS: COMPUTATIONAL FLUID DYNAMIC MODELS
Energy Technology Data Exchange (ETDEWEB)
Chang H. Oh; Eung S. Kim; Richard Schultz; Hans Gougar; David Petti; Hyung S. Kang
2010-08-01
The Idaho National Laboratory (INL), under the auspices of the U.S. Department of Energy, is performing research and development that focuses on key phenomena important during potential scenarios that may occur in very high temperature reactors (VHTRs). Phenomena Identification and Ranking Studies to date have ranked an air ingress event, following on the heels of a VHTR depressurization, as important with regard to core safety. Consequently, the development of advanced air ingress-related models and verification and validation data are a very high priority. Following a loss of coolant and system depressurization incident, air will enter the core of the High Temperature Gas Cooled Reactor through the break, possibly causing oxidation of the in-the core and reflector graphite structure. Simple core and plant models indicate that, under certain circumstances, the oxidation may proceed at an elevated rate with additional heat generated from the oxidation reaction itself. Under postulated conditions of fluid flow and temperature, excessive degradation of the lower plenum graphite can lead to a loss of structural support. Excessive oxidation of core graphite can also lead to the release of fission products into the confinement, which could be detrimental to a reactor safety. Computational fluid dynamic model developed in this study will improve our understanding of this phenomenon. This paper presents two-dimensional and three-dimensional CFD results for the quantitative assessment of the air ingress phenomena. A portion of results of the density-driven stratified flow in the inlet pipe will be compared with results of the experimental results.
A network dynamics approach to chemical reaction networks
van der Schaft, A. J.; Rao, S.; Jayawardhana, B.
2016-04-01
A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.
Dynamic computed tomography findings in cerebrovascular diseases
International Nuclear Information System (INIS)
Araki, Yutaka; Tomoda, Kaname; Kariya, Mitsumasa; Mori, Shigeru; Mitomo, Masanori.
1988-01-01
Dynamic CT was performed with 41 patients with the clinically diagnosed cerebrovascular diseases. A visual evaluation based on the dynamic CT images classified six patterns of brain parenchymal enhancement, especially four patterns of which could only be detected by dynamic CT technique. Dynamic CT was proved of great value in detecting regional cerebral tissue filled by collaterals in retrograde fashion because of the occlusion of main arteries, namely brain tissue perfusion of internal carotid occlusion disease and moyamoya disease was best understood by dynamic CT with adequate resolution. (author)
Quantum Computation and Quantum Spin Dynamics
Raedt, Hans De; Michielsen, Kristel; Hams, Anthony; Miyashita, Seiji; Saito, Keiji
2001-01-01
We analyze the stability of quantum computations on physically realizable quantum computers by simulating quantum spin models representing quantum computer hardware. Examples of logically identical implementations of the controlled-NOT operation are used to demonstrate that the results of a quantum
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
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.
Review of computational fluid dynamics applications in biotechnology processes.
Sharma, C; Malhotra, D; Rathore, A S
2011-01-01
Computational fluid dynamics (CFD) is well established as a tool of choice for solving problems that involve one or more of the following phenomena: flow of fluids, heat transfer,mass transfer, and chemical reaction. Unit operations that are commonly utilized in biotechnology processes are often complex and as such would greatly benefit from application of CFD. The thirst for deeper process and product understanding that has arisen out of initiatives such as quality by design provides further impetus toward usefulness of CFD for problems that may otherwise require extensive experimentation. Not surprisingly, there has been increasing interest in applying CFD toward a variety of applications in biotechnology processing in the last decade. In this article, we will review applications in the major unit operations involved with processing of biotechnology products. These include fermentation,centrifugation, chromatography, ultrafiltration, microfiltration, and freeze drying. We feel that the future applications of CFD in biotechnology processing will focus on establishing CFD as a tool of choice for providing process understanding that can be then used to guide more efficient and effective experimentation. This article puts special emphasis on the work done in the last 10 years. © 2011 American Institute of Chemical Engineers
Computational fluid dynamics on a massively parallel computer
Jespersen, Dennis C.; Levit, Creon
1989-01-01
A finite difference code was implemented for the compressible Navier-Stokes equations on the Connection Machine, a massively parallel computer. The code is based on the ARC2D/ARC3D program and uses the implicit factored algorithm of Beam and Warming. The codes uses odd-even elimination to solve linear systems. Timings and computation rates are given for the code, and a comparison is made with a Cray XMP.
Fractal sets generated by chemical reactions discrete chaotic dynamics
International Nuclear Information System (INIS)
Gontar, V.; Grechko, O.
2007-01-01
Fractal sets composed by the parameters values of difference equations derived from chemical reactions discrete chaotic dynamics (DCD) and corresponding to the sequences of symmetrical patterns were obtained in this work. Examples of fractal sets with the corresponding symmetrical patterns have been presented
Control of chemical dynamics by lasers: theoretical considerations.
Kondorskiy, Alexey; Nanbu, Shinkoh; Teranishi, Yoshiaki; Nakamura, Hiroki
2010-06-03
Theoretical ideas are proposed for laser control of chemical dynamics. There are the following three elementary processes in chemical dynamics: (i) motion of the wave packet on a single adiabatic potential energy surface, (ii) excitation/de-excitation or pump/dump of wave packet, and (iii) nonadiabatic transitions at conical intersections of potential energy surfaces. A variety of chemical dynamics can be controlled, if we can control these three elementary processes as we desire. For (i) we have formulated the semiclassical guided optimal control theory, which can be applied to multidimensional real systems. The quadratic or periodic frequency chirping method can achieve process (ii) with high efficiency close to 100%. Concerning process (iii) mentioned above, the directed momentum method, in which a predetermined momentum vector is given to the initial wave packet, makes it possible to enhance the desired transitions at conical intersections. In addition to these three processes, the intriguing phenomenon of complete reflection in the nonadiabatic-tunneling-type of potential curve crossing can also be used to control a certain class of chemical dynamics. The basic ideas and theoretical formulations are provided for the above-mentioned processes. To demonstrate the effectiveness of these controlling methods, numerical examples are shown by taking the following processes: (a) vibrational photoisomerization of HCN, (b) selective and complete excitation of the fine structure levels of K and Cs atoms, (c) photoconversion of cyclohexadiene to hexatriene, and (d) photodissociation of OHCl to O + HCl.
Chemical dynamics in the gas phase: Time-dependent quantum mechanics of chemical reactions
Energy Technology Data Exchange (ETDEWEB)
Gray, S.K. [Argonne National Laboratory, IL (United States)
1993-12-01
A major goal of this research is to obtain an understanding of the molecular reaction dynamics of three and four atom chemical reactions using numerically accurate quantum dynamics. This work involves: (i) the development and/or improvement of accurate quantum mechanical methods for the calculation and analysis of the properties of chemical reactions (e.g., rate constants and product distributions), and (ii) the determination of accurate dynamical results for selected chemical systems, which allow one to compare directly with experiment, determine the reliability of the underlying potential energy surfaces, and test the validity of approximate theories. This research emphasizes the use of recently developed time-dependent quantum mechanical methods, i.e. wave packet methods.
In Silico Dynamics: computer simulation in a Virtual Embryo ...
Abstract: Utilizing cell biological information to predict higher order biological processes is a significant challenge in predictive toxicology. This is especially true for highly dynamical systems such as the embryo where morphogenesis, growth and differentiation require precisely orchestrated interactions between diverse cell populations. In patterning the embryo, genetic signals setup spatial information that cells then translate into a coordinated biological response. This can be modeled as ‘biowiring diagrams’ representing genetic signals and responses. Because the hallmark of multicellular organization resides in the ability of cells to interact with one another via well-conserved signaling pathways, multiscale computational (in silico) models that enable these interactions provide a platform to translate cellular-molecular lesions perturbations into higher order predictions. Just as ‘the Cell’ is the fundamental unit of biology so too should it be the computational unit (‘Agent’) for modeling embryogenesis. As such, we constructed multicellular agent-based models (ABM) with ‘CompuCell3D’ (www.compucell3d.org) to simulate kinematics of complex cell signaling networks and enable critical tissue events for use in predictive toxicology. Seeding the ABMs with HTS/HCS data from ToxCast demonstrated the potential to predict, quantitatively, the higher order impacts of chemical disruption at the cellular or biochemical level. This is demonstrate
Molecular dynamics simulations of solutions at constant chemical potential
Perego, C.; Salvalaglio, M.; Parrinello, M.
2015-04-01
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.
Solving Dynamic Battlespace Movement Problems Using Dynamic Distributed Computer Networks
National Research Council Canada - National Science Library
Bradford, Robert
2000-01-01
.... The thesis designs a system using this architecture that invokes operations research network optimization algorithms to solve problems involving movement of people and equipment over dynamic road networks...
DYNSIR; A dynamic simulator for the chemical process
International Nuclear Information System (INIS)
Park, Hyun Soo; Yoo, Jae Hyung; Byeon, Kee Hoh; Park, Jeong Hwa; Park, Seong Won
1990-03-01
A program code for dynamic simulation of arbitrary chemical process, called DYNSIR, is developed. The code can simulate rather arbitrary arrangements of individual chemical processing units whose models are described by ordinary differential equations. The code structure to handle input/output, memory and data management, numerical interactive or predetermined changes in parameter values during the simulation. Individual model is easy to maintain since the modular approach is used. The integration routine is highly effective because of the development of algorithm for modular integration method using the cubic spline. DYNSIR's data structures are not the index but the pointer structure. This pointer structure allows the dynamic memory allocation for the memory management. The dynamic memory allocation methods is to minimize the amount of memories and to overcome the limitation of the number of variables to be used. Finally, it includes various functions, such as the input preprocessor, the effective error processing, and plotting and reporting routines. (author)
COMPUTER SUPPORT SYSTEMS FOR ESTIMATING CHEMICAL TOXICITY: PRESENT CAPABILITIES AND FUTURE TRENDS
Computer Support Systems for Estimating Chemical Toxicity: Present Capabilities and Future Trends A wide variety of computer-based artificial intelligence (AI) and decision support systems exist currently to aid in the assessment of toxicity for environmental chemicals. T...
Computational and experimental investigation of dynamic shock reflection phenomena
CSIR Research Space (South Africa)
Naidoo, K
2007-07-01
Full Text Available wedge are used to analyse dynamic flow field phenomena and response of the triple point below and within the dual solution domain. Computed, unsteady pressure traces on the reflection plane are also analysed...
Directory of Open Access Journals (Sweden)
Juan P. Marcolongo
2018-03-01
Full Text Available In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU, that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.
2018-03-01
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
Deep Learning with Dynamic Computation Graphs
Looks, Moshe; Herreshoff, Marcello; Hutchins, DeLesley; Norvig, Peter
2017-01-01
Neural networks that compute over graph structures are a natural fit for problems in a variety of domains, including natural language (parse trees) and cheminformatics (molecular graphs). However, since the computation graph has a different shape and size for every input, such networks do not directly support batched training or inference. They are also difficult to implement in popular deep learning libraries, which are based on static data-flow graphs. We introduce a technique called dynami...
Computer architecture evaluation for structural dynamics computations: Project summary
Standley, Hilda M.
1989-01-01
The intent of the proposed effort is the examination of the impact of the elements of parallel architectures on the performance realized in a parallel computation. To this end, three major projects are developed: a language for the expression of high level parallelism, a statistical technique for the synthesis of multicomputer interconnection networks based upon performance prediction, and a queueing model for the analysis of shared memory hierarchies.
Computational modeling of turn-taking dynamics in spoken conversations
Chowdhury, Shammur Absar
2017-01-01
The study of human interaction dynamics has been at the center for multiple research disciplines in- cluding computer and social sciences, conversational analysis and psychology, for over decades. Recent interest has been shown with the aim of designing computational models to improve human-machine interaction system as well as support humans in their decision-making process. Turn-taking is one of the key aspects of conversational dynamics in dyadic conversations and is an integral part of hu...
Characterizing chemical systems with on-line computers and graphics
International Nuclear Information System (INIS)
Frazer, J.W.; Rigdon, L.P.; Brand, H.R.; Pomernacki, C.L.
1979-01-01
Incorporating computers and graphics on-line to chemical experiments and processes opens up new opportunities for the study and control of complex systems. Systems having many variables can be characterized even when the variable interactions are nonlinear, and the system cannot a priori be represented by numerical methods and models. That is, large sets of accurate data can be rapidly acquired, then modeling and graphic techniques can be used to obtain partial interpretation plus design of further experimentation. The experimenter can thus comparatively quickly iterate between experimentation and modeling to obtain a final solution. We have designed and characterized a versatile computer-controlled apparatus for chemical research, which incorporates on-line instrumentation and graphics. It can be used to determine the mechanism of enzyme-induced reactions or to optimize analytical methods. The apparatus can also be operated as a pilot plant to design control strategies. On-line graphics were used to display conventional plots used by biochemists and three-dimensional response-surface plots
A computer investigation of chemically mediated detachment in bacterial biofilms.
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.
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.
Unsteady computational fluid dynamics in aeronautics
Tucker, P G
2014-01-01
The field of Large Eddy Simulation (LES) and hybrids is a vibrant research area. This book runs through all the potential unsteady modelling fidelity ranges, from low-order to LES. The latter is probably the highest fidelity for practical aerospace systems modelling. Cutting edge new frontiers are defined. One example of a pressing environmental concern is noise. For the accurate prediction of this, unsteady modelling is needed. Hence computational aeroacoustics is explored. It is also emerging that there is a critical need for coupled simulations. Hence, this area is also considered and the tensions of utilizing such simulations with the already expensive LES. This work has relevance to the general field of CFD and LES and to a wide variety of non-aerospace aerodynamic systems (e.g. cars, submarines, ships, electronics, buildings). Topics treated include unsteady flow techniques; LES and hybrids; general numerical methods; computational aeroacoustics; computational aeroelasticity; coupled simulations and...
Prospects for Computational Fluid Dynamics in Room Air Contaminant Control
DEFF Research Database (Denmark)
Nielsen, Peter V.
The fluid dynamics research is strongly influenced by the increasing computer power which has been available for the last decades. This development is obvious from the curve in figure 1 which shows the computation cost as a function of years. It is obvious that the cost for a given job will decre...
Computational fluid dynamics for sport simulation
2009-01-01
All over the world sport plays a prominent role in society: as a leisure activity for many, as an ingredient of culture, as a business and as a matter of national prestige in such major events as the World Cup in soccer or the Olympic Games. Hence, it is not surprising that science has entered the realm of sports, and, in particular, that computer simulation has become highly relevant in recent years. This is explored in this book by choosing five different sports as examples, demonstrating that computational science and engineering (CSE) can make essential contributions to research on sports topics on both the fundamental level and, eventually, by supporting athletes’ performance.
Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks
Pyle, Ryan; Rosenbaum, Robert
2017-01-01
Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.
Spatiotemporal Dynamics and Reliable Computations in Recurrent Spiking Neural Networks.
Pyle, Ryan; Rosenbaum, Robert
2017-01-06
Randomly connected networks of excitatory and inhibitory spiking neurons provide a parsimonious model of neural variability, but are notoriously unreliable for performing computations. We show that this difficulty is overcome by incorporating the well-documented dependence of connection probability on distance. Spatially extended spiking networks exhibit symmetry-breaking bifurcations and generate spatiotemporal patterns that can be trained to perform dynamical computations under a reservoir computing framework.
Self-study manual for introduction to computational fluid dynamics
Nabatov, Andrey
2017-01-01
Computational Fluid Dynamics (CFD) is the branch of Fluid Mechanics and Computational Physics that plays a decent role in modern Mechanical Engineering Design process due to such advantages as relatively low cost of simulation comparing with conduction of real experiment, an opportunity to easily correct the design of a prototype prior to manufacturing of the final product and a wide range of application: mixing, acoustics, cooling and aerodynamics. This makes CFD particularly and Computation...
Computational Fluid Dynamics and Ventilation Airflow
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm
2014-01-01
the principle behind CFD, the development in numerical schemes and computer size since the 1970s. Special attention is given to the selection of the correct governing equations, to the understanding of low turbulent flow, to the selection of turbulence models, and to addressing situations with more steady...
Computer simulation of multiple dynamic photorefractive gratings
DEFF Research Database (Denmark)
Buchhave, Preben
1998-01-01
The benefits of a direct visualization of space-charge grating buildup are described. The visualization is carried out by a simple repetitive computer program, which simulates the basic processes in the band-transport model and displays the result graphically or in the form of numerical data. The...
Computing in Large-Scale Dynamic Systems
Pruteanu, A.S.
2013-01-01
Software applications developed for large-scale systems have always been difficult to de- velop due to problems caused by the large number of computing devices involved. Above a certain network size (roughly one hundred), necessary services such as code updating, topol- ogy discovery and data
Statistical properties of dynamical systems – Simulation and abstract computation
International Nuclear Information System (INIS)
Galatolo, Stefano; Hoyrup, Mathieu; Rojas, Cristóbal
2012-01-01
Highlights: ► A survey on results about computation and computability on the statistical properties of dynamical systems. ► Computability and non-computability results for invariant measures. ► A short proof for the computability of the convergence speed of ergodic averages. ► A kind of “constructive” version of the pointwise ergodic theorem. - Abstract: We survey an area of recent development, relating dynamics to theoretical computer science. We discuss some aspects of the theoretical simulation and computation of the long term behavior of dynamical systems. We will focus on the statistical limiting behavior and invariant measures. We present a general method allowing the algorithmic approximation at any given accuracy of invariant measures. The method can be applied in many interesting cases, as we shall explain. On the other hand, we exhibit some examples where the algorithmic approximation of invariant measures is not possible. We also explain how it is possible to compute the speed of convergence of ergodic averages (when the system is known exactly) and how this entails the computation of arbitrarily good approximations of points of the space having typical statistical behaviour (a sort of constructive version of the pointwise ergodic theorem).
Neural Computations in a Dynamical System with Multiple Time Scales.
Mi, Yuanyuan; Lin, Xiaohan; Wu, Si
2016-01-01
Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions.
A simple nonlinear dynamical computing device
International Nuclear Information System (INIS)
Miliotis, Abraham; Murali, K.; Sinha, Sudeshna; Ditto, William L.; Spano, Mark L.
2009-01-01
We propose and characterize an iterated map whose nonlinearity has a simple (i.e., minimal) electronic implementation. We then demonstrate explicitly how all the different fundamental logic gates can be implemented and morphed using this nonlinearity. These gates provide the full set of gates necessary to construct a general-purpose, reconfigurable computing device. As an example of how such chaotic computing devices can be exploited, we use an array of these maps to encode data and to process information. Each map can store one of M items, where M is variable and can be large. This nonlinear hardware stores data naturally in different bases or alphabets. We also show how this method of storing information can serve as a preprocessing tool for exact or inexact pattern-matching searches.
Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.
Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles
2016-05-03
Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.
Dynamics of prebiotic RNA reproduction illuminated by chemical game theory
Yeates, Jessica A. M.; Hilbe, Christian; Zwick, Martin; Nowak, Martin A.; Lehman, Niles
2016-01-01
Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock–paper–scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. PMID:27091972
Robot-Arm Dynamic Control by Computer
Bejczy, Antal K.; Tarn, Tzyh J.; Chen, Yilong J.
1987-01-01
Feedforward and feedback schemes linearize responses to control inputs. Method for control of robot arm based on computed nonlinear feedback and state tranformations to linearize system and decouple robot end-effector motions along each of cartesian axes augmented with optimal scheme for correction of errors in workspace. Major new feature of control method is: optimal error-correction loop directly operates on task level and not on joint-servocontrol level.
Exponential rise of dynamical complexity in quantum computing through projections.
Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya
2014-10-10
The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
2013-03-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.; Allen, J.W.; Green, W.H.
2013-01-01
We present RPMDrate, a computer program for the calculation of gas phase bimolecular reaction rate coefficients using the ring polymer molecular dynamics (RPMD) method. The RPMD rate coefficient is calculated using the Bennett-Chandler method as a product of a static (centroid density quantum transition state theory (QTST) rate) and a dynamic (ring polymer transmission coefficient) factor. The computational procedure is general and can be used to treat bimolecular polyatomic reactions of any complexity in their full dimensionality. The program has been tested for the H+H2, H+CH 4, OH+CH4 and H+C2H6 reactions. © 2012 Elsevier B.V. All rights reserved.
Fluid dynamics applications of the Illiac IV computer
Maccormack, R. W.; Stevens, K. G., Jr.
1976-01-01
The Illiac IV is a parallel-structure computer with computing power an order of magnitude greater than that of conventional computers. It can be used for experimental tasks in fluid dynamics which can be simulated more economically, for simulating flows that cannot be studied by experiment, and for combining computer and experimental simulations. The architecture of Illiac IV is described, and the use of its parallel operation is demonstrated on the example of its solution of the one-dimensional wave equation. For fluid dynamics problems, a special FORTRAN-like vector programming language was devised, called CFD language. Two applications are described in detail: (1) the determination of the flowfield around the space shuttle, and (2) the computation of transonic turbulent separated flow past a thick biconvex airfoil.
A future for computational fluid dynamics at CERN
Battistin, M
2005-01-01
Computational Fluid Dynamics (CFD) is an analysis of fluid flow, heat transfer and associated phenomena in physical systems using computers. CFD has been used at CERN since 1993 by the TS-CV group, to solve thermo-fluid related problems, particularly during the development, design and construction phases of the LHC experiments. Computer models based on CFD techniques can be employed to reduce the effort required for prototype testing, saving not only time and money but offering possibilities of additional investigations and design optimisation. The development of a more efficient support team at CERN depends on to two important factors: available computing power and experienced engineers. Available computer power IS the limiting resource of CFD. Only the recent increase of computer power had allowed important high tech and industrial applications. Computer Grid is already now (OpenLab at CERN) and will be more so in the future natural environment for CFD science. At CERN, CFD activities have been developed by...
Method for the deconvolution of incompletely resolved CARS spectra in chemical dynamics experiments
International Nuclear Information System (INIS)
Anda, A.A.; Phillips, D.L.; Valentini, J.J.
1986-01-01
We describe a method for deconvoluting incompletely resolved CARS spectra to obtain quantum state population distributions. No particular form for the rotational and vibrational state distribution is assumed, the population of each quantum state is treated as an independent quantity. This method of analysis differs from previously developed approaches for the deconvolution of CARS spectra, all of which assume that the population distribution is Boltzmann, and thus are limited to the analysis of CARS spectra taken under conditions of thermal equilibrium. The method of analysis reported here has been developed to deconvolute CARS spectra of photofragments and chemical reaction products obtained in chemical dynamics experiments under nonequilibrium conditions. The deconvolution procedure has been incorporated into a computer code. The application of that code to the deconvolution of CARS spectra obtained for samples at thermal equilibrium and not at thermal equilibrium is reported. The method is accurate and computationally efficient
Overview of Computational Fluid Dynamics (CFD) simulation of stirred vessel
International Nuclear Information System (INIS)
Mohd Rizal Mamat; Azraf Azman; Anwar Abdul Rahman; Noraishah Othman
2010-01-01
Stirred vessel is one of many widely used equipment in industrial process and chemical industry. The design of stirred vessel typically follows a certain standard chemical engineering practice that may also involve empirical data acquired from experiments. However the design may still take a different route which is computational engineering simulation and analysis. CFD has been identified as one of the possible tools for such purposes. CFD enables the flow fields variables such as velocity, temperature and pressure in the whole computational domain to be obtained and as such it presents an advantage over the experimental setup. (author)
Computer simulation of confined liquid crystal dynamics
International Nuclear Information System (INIS)
Webster, R.E.
2001-11-01
Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)
Computer simulation of confined liquid crystal dynamics
Energy Technology Data Exchange (ETDEWEB)
Webster, R.E
2001-11-01
Results are presented from a series of simulations undertaken to determine whether dynamic processes observed in device-scale liquid crystal cells confined between aligning substrates can be simulated in a molecular system using parallel molecular dynamics of the Gay-Berne model. In a nematic cell, on removal of an aligning field, initial near-surface director relaxation can induce flow, termed 'backflow' in the liquid. This, in turn, can cause director rotation, termed 'orientational kickback', in the centre of the cell. Simulations are performed of the relaxation in nematic systems confined between substrates with a common alignment on removal of an aligning field. Results show /that relaxation timescales of medium sized systems are accessible. Following this, simulations are performed of relaxation in hybrid aligned nematic systems, where each surface induces a different alignment. Flow patterns associated with director reorientation are observed. The damped oscillatory nature of the relaxation process suggests that the behaviour of these systems is dominated by orientational elastic forces and that the observed director motion and flow do not correspond to the macroscopic processes of backflow and kickback. Chevron structures can occur in confined smectic cells which develop two domains of equal and opposite layer tilt on cooling. Layer lilting is thought to be caused by a need to reconcile a mismatch between bulk and surface smectic layer spacing. Here, simulations are performed of the formation of structures in confined smectic systems where layer tilt is induced by an imposed surface pretilt. Results show that bookshelf, chevron and tilled layer structures are observable in a confined Gay-Berne system. The formation and stability of the chevron structure are shown to be influenced by surface slip. (author)
Energy Technology Data Exchange (ETDEWEB)
Cramer, Christopher J. [Univ. of Minnesota, Minneapolis, MN (United States)
2017-11-12
Charge transfer and charge transport in photoactivated systems are fundamental processes that underlie solar energy capture, solar energy conversion, and photoactivated catalysis, both organometallic and enzymatic. We developed methods, algorithms, and software tools needed for reliable treatment of the underlying physics for charge transfer and charge transport, an undertaking with broad applicability to the goals of the fundamental-interaction component of the Department of Energy Office of Basic Energy Sciences and the exascale initiative of the Office of Advanced Scientific Computing Research.
Interface between computational fluid dynamics (CFD) and plant analysis computer codes
International Nuclear Information System (INIS)
Coffield, R.D.; Dunckhorst, F.F.; Tomlinson, E.T.; Welch, J.W.
1993-01-01
Computational fluid dynamics (CFD) can provide valuable input to the development of advanced plant analysis computer codes. The types of interfacing discussed in this paper will directly contribute to modeling and accuracy improvements throughout the plant system and should result in significant reduction of design conservatisms that have been applied to such analyses in the past
Fluid dynamics parallel computer development at NASA Langley Research Center
Townsend, James C.; Zang, Thomas A.; Dwoyer, Douglas L.
1987-01-01
To accomplish more detailed simulations of highly complex flows, such as the transition to turbulence, fluid dynamics research requires computers much more powerful than any available today. Only parallel processing on multiple-processor computers offers hope for achieving the required effective speeds. Looking ahead to the use of these machines, the fluid dynamicist faces three issues: algorithm development for near-term parallel computers, architecture development for future computer power increases, and assessment of possible advantages of special purpose designs. Two projects at NASA Langley address these issues. Software development and algorithm exploration is being done on the FLEX/32 Parallel Processing Research Computer. New architecture features are being explored in the special purpose hardware design of the Navier-Stokes Computer. These projects are complementary and are producing promising results.
Computational fluid dynamic modelling of cavitation
Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.
1993-01-01
Models in sheet cavitation in cryogenic fluids are developed for use in Euler and Navier-Stokes codes. The models are based upon earlier potential-flow models but enable the cavity inception point, length, and shape to be determined as part of the computation. In the present paper, numerical solutions are compared with experimental measurements for both pressure distribution and cavity length. Comparisons between models are also presented. The CFD model provides a relatively simple modification to an existing code to enable cavitation performance predictions to be included. The analysis also has the added ability of incorporating thermodynamic effects of cryogenic fluids into the analysis. Extensions of the current two-dimensional steady state analysis to three-dimensions and/or time-dependent flows are, in principle, straightforward although geometrical issues become more complicated. Linearized models, however offer promise of providing effective cavitation modeling in three-dimensions. This analysis presents good potential for improved understanding of many phenomena associated with cavity flows.
Computational Fluid and Particle Dynamics in the Human Respiratory System
Tu, Jiyuan; Ahmadi, Goodarz
2013-01-01
Traditional research methodologies in the human respiratory system have always been challenging due to their invasive nature. Recent advances in medical imaging and computational fluid dynamics (CFD) have accelerated this research. This book compiles and details recent advances in the modelling of the respiratory system for researchers, engineers, scientists, and health practitioners. It breaks down the complexities of this field and provides both students and scientists with an introduction and starting point to the physiology of the respiratory system, fluid dynamics and advanced CFD modeling tools. In addition to a brief introduction to the physics of the respiratory system and an overview of computational methods, the book contains best-practice guidelines for establishing high-quality computational models and simulations. Inspiration for new simulations can be gained through innovative case studies as well as hands-on practice using pre-made computational code. Last but not least, students and researcher...
Dynamics and Control of Chemical Reactors-Selectively Surveyed
DEFF Research Database (Denmark)
Jørgensen, S. B.; Jensen, N.
1989-01-01
The chemical reactor or bioreactor is physically at a central position in a process, and often with a decisive role on the overall technical and economical performance. Even though application of feedback control on reactors is gaining momentum and on-line optimization has been implemented....... For bioreactors the theory and practice of reactor design, dynamics and control have to be adapted to the peculiarities of the biological catalysts. Enzymes, the protein catalysts, are the simplest ones, which have many common features with chemical catalysts. The living cells are much more complex, these growing...... in industry, many reactor control problems are still left unsolved or only partly solved using open loop strategies where disturbance rejection and model inaccuracies have to be handled through manual reactor control and feedback control of raw material preprocessing and product purification operations...
Ramasesha, Krupa; De Marco, Luigi; Horning, Andrew D; Mandal, Aritra; Tokmakoff, Andrei
2012-04-07
We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.
Computational fluid dynamics modelling of displacement natural ventilation.
Ji, Yingchun
2005-01-01
Natural ventilation is widely recognised as contributing towards low-energy building design. The requirement to reduce energy usage in new buildings has rejuvenated interest in natural ventilation. This thesis deals with computer modelling of natural displacement ventilation driven either by buoyancy or buoyancy combined with wind forces. Two benchmarks have been developed using computational fluid dynamics (CFD) in order to evaluate the accuracy with which CFD is able to mo...
Forward and adjoint sensitivity computation of chaotic dynamical systems
Energy Technology Data Exchange (ETDEWEB)
Wang, Qiqi, E-mail: qiqi@mit.edu [Department of Aeronautics and Astronautics, MIT, 77 Mass Ave., Cambridge, MA 02139 (United States)
2013-02-15
This paper describes a forward algorithm and an adjoint algorithm for computing sensitivity derivatives in chaotic dynamical systems, such as the Lorenz attractor. The algorithms compute the derivative of long time averaged “statistical” quantities to infinitesimal perturbations of the system parameters. The algorithms are demonstrated on the Lorenz attractor. We show that sensitivity derivatives of statistical quantities can be accurately estimated using a single, short trajectory (over a time interval of 20) on the Lorenz attractor.
Modeling dynamics of biological and chemical components of aquatic ecosystems
International Nuclear Information System (INIS)
Lassiter, R.R.
1975-05-01
To provide capability to model aquatic ecosystems or their subsystems as needed for particular research goals, a modeling strategy was developed. Submodels of several processes common to aquatic ecosystems were developed or adapted from previously existing ones. Included are submodels for photosynthesis as a function of light and depth, biological growth rates as a function of temperature, dynamic chemical equilibrium, feeding and growth, and various types of losses to biological populations. These submodels may be used as modules in the construction of models of subsystems or ecosystems. A preliminary model for the nitrogen cycle subsystem was developed using the modeling strategy and applicable submodels. (U.S.)
Chemical elements dynamic in the fermentation process of ethanol producing
International Nuclear Information System (INIS)
Nepomuceno, N.; Nadai Fernandes, E.A. de; Bacchi, M.A.
1994-01-01
This paper provides useful information about the dynamics of chemical elements analysed by instrumental neutron activation analysis (INAA) and, found in the various segments of the fermentation process of producing ethanol from sugar cane. For this, a mass balance of Ce, Co, Cs, Eu, Fe, Hf, La, Sc, Sm, and Th, terrigenous elements, as well as Br, K, Rb, and Zn, sugar cane plant elements, has been demonstrated for the fermentation vats in industrial conditions of ethanol production. (author). 10 refs, 4 figs, 1 tab
DYNSYL: a general-purpose dynamic simulator for chemical processes
International Nuclear Information System (INIS)
Patterson, G.K.; Rozsa, R.B.
1978-01-01
Lawrence Livermore Laboratory is conducting a safeguards program for the Nuclear Regulatory Commission. The goal of the Material Control Project of this program is to evaluate material control and accounting (MCA) methods in plants that handle special nuclear material (SNM). To this end we designed and implemented the dynamic chemical plant simulation program DYNSYL. This program can be used to generate process data or to provide estimates of process performance; it simulates both steady-state and dynamic behavior. The MCA methods that may have to be evaluated range from sophisticated on-line material trackers such as Kalman filter estimators, to relatively simple material balance procedures. This report describes the overall structure of DYNSYL and includes some example problems. The code is still in the experimental stage and revision is continuing
Dynamics of dissipative systems and computational physics
International Nuclear Information System (INIS)
Adam, Gh.; Scutaru, H.; Ixaru, L.; Adam, S.; Rizea, M.; Stefanescu, E.; Mihalache, D.; Mazilu, D.; Crasovan, L.
2002-01-01
During the first year of research activity in the frame of this project there have been investigated two main topics: I. Dynamics of systems of fermions in complex dissipative media; II. Solitons with topologic charge in dissipative systems. An essential problem of the quantum information systems is the controllability and observability of the quantum states, generally described by Lindblad's master equation with phenomenological coefficients. In its usual form, this equation describes a decay of the mean-values, but not necessarily the expected decaying transitions. The basic and very difficult problem of a dissipative quantum theory is to project the evolution of the total system (the system of interest + the environment) on the space of the system of interest. In this case, one obtains a quantum master equation where the system evolution is described by two terms: 1) a Hamiltonian term for the processes with energy conservation, and 2) a non-Hamiltonian term with coefficients depending on the dissipative coupling. That means that a master equation is based on some approximations enabling the replacement of the operators of the dissipative environment with average value coefficients. It is often assumed that the evolution operators of the dissipative system define a semigroup, not a group as in the case of an isolated system. In this framework, Lindblad obtained a quantum master equation in agreement with all the quantum-mechanical principles. However, the Lindblad master equation was unable to secure a correct description of the decaying states. To do that, one has to take into account the transition operators between the system eigenstates with appropriate coefficients. Within this investigation, we have obtained an equation obeying to this requirement, giving the ρ(t) time derivative in terms of creation-annihilation operators of the single-particle states |i>, and λ ij , representing the dissipative coefficients, the microscopic expressions of which are
Neural Computations in a Dynamical System with Multiple Time Scales
Directory of Open Access Journals (Sweden)
Yuanyuan Mi
2016-09-01
Full Text Available Neural systems display rich short-term dynamics at various levels, e.g., spike-frequencyadaptation (SFA at single neurons, and short-term facilitation (STF and depression (STDat neuronal synapses. These dynamical features typically covers a broad range of time scalesand exhibit large diversity in different brain regions. It remains unclear what the computationalbenefit for the brain to have such variability in short-term dynamics is. In this study, we proposethat the brain can exploit such dynamical features to implement multiple seemingly contradictorycomputations in a single neural circuit. To demonstrate this idea, we use continuous attractorneural network (CANN as a working model and include STF, SFA and STD with increasing timeconstants in their dynamics. Three computational tasks are considered, which are persistent activity,adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, andhence cannot be implemented by a single dynamical feature or any combination with similar timeconstants. However, with properly coordinated STF, SFA and STD, we show that the network isable to implement the three computational tasks concurrently. We hope this study will shed lighton the understanding of how the brain orchestrates its rich dynamics at various levels to realizediverse cognitive functions.
Computational fluid dynamics simulations of light water reactor flows
International Nuclear Information System (INIS)
Tzanos, C.P.; Weber, D.P.
1999-01-01
Advances in computational fluid dynamics (CFD), turbulence simulation, and parallel computing have made feasible the development of three-dimensional (3-D) single-phase and two-phase flow CFD codes that can simulate fluid flow and heat transfer in realistic reactor geometries with significantly reduced reliance, especially in single phase, on empirical correlations. The objective of this work was to assess the predictive power and computational efficiency of a CFD code in the analysis of a challenging single-phase light water reactor problem, as well as to identify areas where further improvements are needed
Computational Psychometrics for Modeling System Dynamics during Stressful Disasters
Directory of Open Access Journals (Sweden)
Pietro Cipresso
2017-08-01
Full Text Available Disasters can be very stressful events. However, computational models of stress require data that might be very difficult to collect during disasters. Moreover, personal experiences are not repeatable, so it is not possible to collect bottom-up information when building a coherent model. To overcome these problems, we propose the use of computational models and virtual reality integration to recreate disaster situations, while examining possible dynamics in order to understand human behavior and relative consequences. By providing realistic parameters associated with disaster situations, computational scientists can work more closely with emergency responders to improve the quality of interventions in the future.
Dynamic computer simulation of the Fort St. Vrain steam turbines
International Nuclear Information System (INIS)
Conklin, J.C.
1983-01-01
A computer simulation is described for the dynamic response of the Fort St. Vrain nuclear reactor regenerative intermediate- and low-pressure steam turbines. The fundamental computer-modeling assumptions for the turbines and feedwater heaters are developed. A turbine heat balance specifying steam and feedwater conditions at a given generator load and the volumes of the feedwater heaters are all that are necessary as descriptive input parameters. Actual plant data for a generator load reduction from 100 to 50% power (which occurred as part of a plant transient on November 9, 1981) are compared with computer-generated predictions, with reasonably good agreement
Morphing-Based Shape Optimization in Computational Fluid Dynamics
Rousseau, Yannick; Men'Shov, Igor; Nakamura, Yoshiaki
In this paper, a Morphing-based Shape Optimization (MbSO) technique is presented for solving Optimum-Shape Design (OSD) problems in Computational Fluid Dynamics (CFD). The proposed method couples Free-Form Deformation (FFD) and Evolutionary Computation, and, as its name suggests, relies on the morphing of shape and computational domain, rather than direct shape parameterization. Advantages of the FFD approach compared to traditional parameterization are first discussed. Then, examples of shape and grid deformations by FFD are presented. Finally, the MbSO approach is illustrated and applied through an example: the design of an airfoil for a future Mars exploration airplane.
Applied Computational Fluid Dynamics at NASA Ames Research Center
Holst, Terry L.; Kwak, Dochan (Technical Monitor)
1994-01-01
The field of Computational Fluid Dynamics (CFD) has advanced to the point where it can now be used for many applications in fluid mechanics research and aerospace vehicle design. A few applications being explored at NASA Ames Research Center will be presented and discussed. The examples presented will range in speed from hypersonic to low speed incompressible flow applications. Most of the results will be from numerical solutions of the Navier-Stokes or Euler equations in three space dimensions for general geometry applications. Computational results will be used to highlight the presentation as appropriate. Advances in computational facilities including those associated with NASA's CAS (Computational Aerosciences) Project of the Federal HPCC (High Performance Computing and Communications) Program will be discussed. Finally, opportunities for future research will be presented and discussed. All material will be taken from non-sensitive, previously-published and widely-disseminated work.
Computational fluid dynamics (CFD) simulation of hot air flow ...
African Journals Online (AJOL)
Computational Fluid Dynamics simulation of air flow distribution, air velocity and pressure field pattern as it will affect moisture transient in a cabinet tray dryer is performed using SolidWorks Flow Simulation (SWFS) 2014 SP 4.0 program. The model used for the drying process in this experiment was designed with Solid ...
Computational Fluid Dynamics and Building Energy Performance Simulation
DEFF Research Database (Denmark)
Nielsen, Peter V.; Tryggvason, Tryggvi
An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...
Modelling Emission from Building Materials with Computational Fluid Dynamics
DEFF Research Database (Denmark)
Topp, Claus; Nielsen, Peter V.; Heiselberg, Per
This paper presents a numerical model that by means of computational fluid dynamics (CFD) is capable of dealing with both pollutant transport across the boundary layer and internal diffusion in the source without prior knowledge of which is the limiting process. The model provides the concentration...
On Computational Fluid Dynamics Tools in Architectural Design
DEFF Research Database (Denmark)
Kirkegaard, Poul Henning; Hougaard, Mads; Stærdahl, Jesper Winther
engineering computational fluid dynamics (CFD) simulation program ANSYS CFX and a CFD based representative program RealFlow are investigated. These two programs represent two types of CFD based tools available for use during phases of an architectural design process. However, as outlined in two case studies...
Dynamic enhanced computed tomographic findings of a perirenal capillary hemangioma
Energy Technology Data Exchange (ETDEWEB)
Lee, Jung Min; Kim, Sang Won; Kim, Hyun Cheol; Yang, Dal Mo; Ryu, Jung Kyu; Lim, Sung Jig [Kyung Hee University Hospital at Gangdong, Seoul (Korea, Republic of)
2016-05-15
Hemangiomas are benign mesenchymal neoplasms that rarely occur in the kidney and perirenal space. Perirenal hemangiomas can mimic the appearance of exophytic renal cell carcinoma or various retroperitoneal tumors. We report a case of perirenal hemangioma detected by dynamic enhanced computed tomography in a 43-year-old female.
Body dynamics and hydrodynamics of swimming larvae: a computational study
Li, G.; Müller, U.K.; Leeuwen, van J.L.; Liu, H.
2012-01-01
To understand the mechanics of fish swimming, we need to know the forces exerted by the fluid and how these forces affect the motion of the fish. To this end, we developed a 3-D computational approach that integrates hydrodynamics and body dynamics. This study quantifies the flow around a swimming
A Parameter Estimation Method for Dynamic Computational Cognitive Models
Thilakarathne, D.J.
2015-01-01
A dynamic computational cognitive model can be used to explore a selected complex cognitive phenomenon by providing some features or patterns over time. More specifically, it can be used to simulate, analyse and explain the behaviour of such a cognitive phenomenon. It generates output data in the
Privacy context model for dynamic privacy adaptation in ubiquitous computing
Schaub, Florian; Koenings, Bastian; Dietzel, Stefan; Weber, M.; Kargl, Frank
Ubiquitous computing is characterized by the merger of physical and virtual worlds as physical artifacts gain digital sensing, processing, and communication capabilities. Maintaining an appropriate level of privacy in the face of such complex and often highly dynamic systems is challenging. We argue
Dynamics of number systems computation with arbitrary precision
Kurka, Petr
2016-01-01
This book is a source of valuable and useful information on the topics of dynamics of number systems and scientific computation with arbitrary precision. It is addressed to scholars, scientists and engineers, and graduate students. The treatment is elementary and self-contained with relevance both for theory and applications. The basic prerequisite of the book is linear algebra and matrix calculus. .
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.
Computed Potential Energy Surfaces and Minimum Energy Pathways for Chemical Reactions
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.
Structure and dynamics of amorphous polymers: computer simulations compared to experiment and theory
International Nuclear Information System (INIS)
Paul, Wolfgang; Smith, Grant D
2004-01-01
This contribution considers recent developments in the computer modelling of amorphous polymeric materials. Progress in our capabilities to build models for the computer simulation of polymers from the detailed atomistic scale up to coarse-grained mesoscopic models, together with the ever-improving performance of computers, have led to important insights from computer simulations into the structural and dynamic properties of amorphous polymers. Structurally, chain connectivity introduces a range of length scales from that of the chemical bond to the radius of gyration of the polymer chain covering 2-4 orders of magnitude. Dynamically, this range of length scales translates into an even larger range of time scales observable in relaxation processes in amorphous polymers ranging from about 10 -13 to 10 -3 s or even to 10 3 s when glass dynamics is concerned. There is currently no single simulation technique that is able to describe all these length and time scales efficiently. On large length and time scales basic topology and entropy become the governing properties and this fact can be exploited using computer simulations of coarse-grained polymer models to study universal aspects of the structure and dynamics of amorphous polymers. On the largest length and time scales chain connectivity is the dominating factor leading to the strong increase in longest relaxation times described within the reptation theory of polymer melt dynamics. Recently, many of the universal aspects of this behaviour have been further elucidated by computer simulations of coarse-grained polymer models. On short length scales the detailed chemistry and energetics of the polymer are important, and one has to be able to capture them correctly using chemically realistic modelling of specific polymers, even when the aim is to extract generic physical behaviour exhibited by the specific chemistry. Detailed studies of chemically realistic models highlight the central importance of torsional dynamics
Laboratory of Chemical Physics
Federal Laboratory Consortium — Current research in the Laboratory of Chemical Physics is primarily concerned with experimental, theoretical, and computational problems in the structure, dynamics,...
Towards Dynamic Remote Data Auditing in Computational Clouds
Khurram Khan, Muhammad; Anuar, Nor Badrul
2014-01-01
Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA) techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server. PMID:25121114
Towards Dynamic Remote Data Auditing in Computational Clouds
Directory of Open Access Journals (Sweden)
Mehdi Sookhak
2014-01-01
Full Text Available Cloud computing is a significant shift of computational paradigm where computing as a utility and storing data remotely have a great potential. Enterprise and businesses are now more interested in outsourcing their data to the cloud to lessen the burden of local data storage and maintenance. However, the outsourced data and the computation outcomes are not continuously trustworthy due to the lack of control and physical possession of the data owners. To better streamline this issue, researchers have now focused on designing remote data auditing (RDA techniques. The majority of these techniques, however, are only applicable for static archive data and are not subject to audit the dynamically updated outsourced data. We propose an effectual RDA technique based on algebraic signature properties for cloud storage system and also present a new data structure capable of efficiently supporting dynamic data operations like append, insert, modify, and delete. Moreover, this data structure empowers our method to be applicable for large-scale data with minimum computation cost. The comparative analysis with the state-of-the-art RDA schemes shows that the proposed scheme is secure and highly efficient in terms of the computation and communication overhead on the auditor and server.
SD-CAS: Spin Dynamics by Computer Algebra System.
Filip, Xenia; Filip, Claudiu
2010-11-01
A computer algebra tool for describing the Liouville-space quantum evolution of nuclear 1/2-spins is introduced and implemented within a computational framework named Spin Dynamics by Computer Algebra System (SD-CAS). A distinctive feature compared with numerical and previous computer algebra approaches to solving spin dynamics problems results from the fact that no matrix representation for spin operators is used in SD-CAS, which determines a full symbolic character to the performed computations. Spin correlations are stored in SD-CAS as four-entry nested lists of which size increases linearly with the number of spins into the system and are easily mapped into analytical expressions in terms of spin operator products. For the so defined SD-CAS spin correlations a set of specialized functions and procedures is introduced that are essential for implementing basic spin algebra operations, such as the spin operator products, commutators, and scalar products. They provide results in an abstract algebraic form: specific procedures to quantitatively evaluate such symbolic expressions with respect to the involved spin interaction parameters and experimental conditions are also discussed. Although the main focus in the present work is on laying the foundation for spin dynamics symbolic computation in NMR based on a non-matrix formalism, practical aspects are also considered throughout the theoretical development process. In particular, specific SD-CAS routines have been implemented using the YACAS computer algebra package (http://yacas.sourceforge.net), and their functionality was demonstrated on a few illustrative examples. Copyright © 2010 Elsevier Inc. All rights reserved.
Development of real-time visualization system for Computational Fluid Dynamics on parallel computers
International Nuclear Information System (INIS)
Muramatsu, Kazuhiro; Otani, Takayuki; Matsumoto, Hideki; Takei, Toshifumi; Doi, Shun
1998-03-01
A real-time visualization system for computational fluid dynamics in a network connecting between a parallel computing server and the client terminal was developed. Using the system, a user can visualize the results of a CFD (Computational Fluid Dynamics) simulation on the parallel computer as a client terminal during the actual computation on a server. Using GUI (Graphical User Interface) on the client terminal, to user is also able to change parameters of the analysis and visualization during the real-time of the calculation. The system carries out both of CFD simulation and generation of a pixel image data on the parallel computer, and compresses the data. Therefore, the amount of data from the parallel computer to the client is so small in comparison with no compression that the user can enjoy the swift image appearance comfortably. Parallelization of image data generation is based on Owner Computation Rule. GUI on the client is built on Java applet. A real-time visualization is thus possible on the client PC only if Web browser is implemented on it. (author)
Thorp, Scott A.
1992-01-01
This presentation will discuss the development of a NASA Geometry Exchange Specification for transferring aerodynamic surface geometry between LeRC systems and grid generation software used for computational fluid dynamics research. The proposed specification is based on a subset of the Initial Graphics Exchange Specification (IGES). The presentation will include discussion of how the NASA-IGES standard will accommodate improved computer aided design inspection methods and reverse engineering techniques currently being developed. The presentation is in viewgraph format.
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.
Rapid computation of chemical equilibrium composition - An application to hydrocarbon combustion
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.
Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.
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)
Developments of multibody system dynamics: computer simulations and experiments
International Nuclear Information System (INIS)
Yoo, Wan-Suk; Kim, Kee-Nam; Kim, Hyun-Woo; Sohn, Jeong-Hyun
2007-01-01
It is an exceptional success when multibody dynamics researchers Multibody System Dynamics journal one of the most highly ranked journals in the last 10 years. In the inaugural issue, Professor Schiehlen wrote an interesting article explaining the roots and perspectives of multibody system dynamics. Professor Shabana also wrote an interesting article to review developments in flexible multibody dynamics. The application possibilities of multibody system dynamics have grown wider and deeper, with many application examples being introduced with multibody techniques in the past 10 years. In this paper, the development of multibody dynamics is briefly reviewed and several applications of multibody dynamics are described according to the author's research results. Simulation examples are compared to physical experiments, which show reasonableness and accuracy of the multibody formulation applied to real problems. Computer simulations using the absolute nodal coordinate formulation (ANCF) were also compared to physical experiments; therefore, the validity of ANCF for large-displacement and large-deformation problems was shown. Physical experiments for large deformation problems include beam, plate, chain, and strip. Other research topics currently being carried out in the author's laboratory are also briefly explained
Computer Vision Based Measurement of Wildfire Smoke Dynamics
Directory of Open Access Journals (Sweden)
BUGARIC, M.
2015-02-01
Full Text Available This article presents a novel method for measurement of wildfire smoke dynamics based on computer vision and augmented reality techniques. The aspect of smoke dynamics is an important feature in video smoke detection that could distinguish smoke from visually similar phenomena. However, most of the existing smoke detection systems are not capable of measuring the real-world size of the detected smoke regions. Using computer vision and GIS-based augmented reality, we measure the real dimensions of smoke plumes, and observe the change in size over time. The measurements are performed on offline video data with known camera parameters and location. The observed data is analyzed in order to create a classifier that could be used to eliminate certain categories of false alarms induced by phenomena with different dynamics than smoke. We carried out an offline evaluation where we measured the improvement in the detection process achieved using the proposed smoke dynamics characteristics. The results show a significant increase in algorithm performance, especially in terms of reducing false alarms rate. From this it follows that the proposed method for measurement of smoke dynamics could be used to improve existing smoke detection algorithms, or taken into account when designing new ones.
Techniques for animation of CFD results. [computational fluid dynamics
Horowitz, Jay; Hanson, Jeffery C.
1992-01-01
Video animation is becoming increasingly vital to the computational fluid dynamics researcher, not just for presentation, but for recording and comparing dynamic visualizations that are beyond the current capabilities of even the most powerful graphic workstation. To meet these needs, Lewis Research Center has recently established a facility to provide users with easy access to advanced video animation capabilities. However, producing animation that is both visually effective and scientifically accurate involves various technological and aesthetic considerations that must be understood both by the researcher and those supporting the visualization process. These considerations include: scan conversion, color conversion, and spatial ambiguities.
Parallel algorithms and architecture for computation of manipulator forward dynamics
Fijany, Amir; Bejczy, Antal K.
1989-01-01
Parallel computation of manipulator forward dynamics is investigated. Considering three classes of algorithms for the solution of the problem, that is, the O(n), the O(n exp 2), and the O(n exp 3) algorithms, parallelism in the problem is analyzed. It is shown that the problem belongs to the class of NC and that the time and processors bounds are of O(log2/2n) and O(n exp 4), respectively. However, the fastest stable parallel algorithms achieve the computation time of O(n) and can be derived by parallelization of the O(n exp 3) serial algorithms. Parallel computation of the O(n exp 3) algorithms requires the development of parallel algorithms for a set of fundamentally different problems, that is, the Newton-Euler formulation, the computation of the inertia matrix, decomposition of the symmetric, positive definite matrix, and the solution of triangular systems. Parallel algorithms for this set of problems are developed which can be efficiently implemented on a unique architecture, a triangular array of n(n+2)/2 processors with a simple nearest-neighbor interconnection. This architecture is particularly suitable for VLSI and WSI implementations. The developed parallel algorithm, compared to the best serial O(n) algorithm, achieves an asymptotic speedup of more than two orders-of-magnitude in the computation the forward dynamics.
Dynamic integration of remote cloud resources into local computing clusters
Energy Technology Data Exchange (ETDEWEB)
Fleig, Georg; Erli, Guenther; Giffels, Manuel; Hauth, Thomas; Quast, Guenter; Schnepf, Matthias [Institut fuer Experimentelle Kernphysik, Karlsruher Institut fuer Technologie (Germany)
2016-07-01
In modern high-energy physics (HEP) experiments enormous amounts of data are analyzed and simulated. Traditionally dedicated HEP computing centers are built or extended to meet this steadily increasing demand for computing resources. Nowadays it is more reasonable and more flexible to utilize computing power at remote data centers providing regular cloud services to users as they can be operated in a more efficient manner. This approach uses virtualization and allows the HEP community to run virtual machines containing a dedicated operating system and transparent access to the required software stack on almost any cloud site. The dynamic management of virtual machines depending on the demand for computing power is essential for cost efficient operation and sharing of resources with other communities. For this purpose the EKP developed the on-demand cloud manager ROCED for dynamic instantiation and integration of virtualized worker nodes into the institute's computing cluster. This contribution will report on the concept of our cloud manager and the implementation utilizing a remote OpenStack cloud site and a shared HPC center (bwForCluster located in Freiburg).
Computer codes for beam dynamics analysis of cyclotronlike accelerators
Smirnov, V.
2017-12-01
Computer codes suitable for the study of beam dynamics in cyclotronlike (classical and isochronous cyclotrons, synchrocyclotrons, and fixed field alternating gradient) accelerators are reviewed. Computer modeling of cyclotron segments, such as the central zone, acceleration region, and extraction system is considered. The author does not claim to give a full and detailed description of the methods and algorithms used in the codes. Special attention is paid to the codes already proven and confirmed at the existing accelerating facilities. The description of the programs prepared in the worldwide known accelerator centers is provided. The basic features of the programs available to users and limitations of their applicability are described.
Multitasking the code ARC3D. [for computational fluid dynamics
Barton, John T.; Hsiung, Christopher C.
1986-01-01
The CRAY multitasking system was developed in order to utilize all four processors and sharply reduce the wall clock run time. This paper describes the techniques used to modify the computational fluid dynamics code ARC3D for this run and analyzes the achieved speedup. The ARC3D code solves either the Euler or thin-layer N-S equations using an implicit approximate factorization scheme. Results indicate that multitask processing can be used to achieve wall clock speedup factors of over three times, depending on the nature of the program code being used. Multitasking appears to be particularly advantageous for large-memory problems running on multiple CPU computers.
Operational computer graphics in the flight dynamics environment
Jeletic, James F.
1989-01-01
Over the past five years, the Flight Dynamics Division of the National Aeronautics and Space Administration's (NASA's) Goddard Space Flight Center has incorporated computer graphics technology into its operational environment. In an attempt to increase the effectiveness and productivity of the Division, computer graphics software systems have been developed that display spacecraft tracking and telemetry data in 2-d and 3-d graphic formats that are more comprehensible than the alphanumeric tables of the past. These systems vary in functionality from real-time mission monitoring system, to mission planning utilities, to system development tools. Here, the capabilities and architecture of these systems are discussed.
A rapid method for the computation of equilibrium chemical composition of air to 15000 K
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.
Direct single-molecule dynamic detection of chemical reactions.
Guan, Jianxin; Jia, Chuancheng; Li, Yanwei; Liu, Zitong; Wang, Jinying; Yang, Zhongyue; Gu, Chunhui; Su, Dingkai; Houk, Kendall N; Zhang, Deqing; Guo, Xuefeng
2018-02-01
Single-molecule detection can reveal time trajectories and reaction pathways of individual intermediates/transition states in chemical reactions and biological processes, which is of fundamental importance to elucidate their intrinsic mechanisms. We present a reliable, label-free single-molecule approach that allows us to directly explore the dynamic process of basic chemical reactions at the single-event level by using stable graphene-molecule single-molecule junctions. These junctions are constructed by covalently connecting a single molecule with a 9-fluorenone center to nanogapped graphene electrodes. For the first time, real-time single-molecule electrical measurements unambiguously show reproducible large-amplitude two-level fluctuations that are highly dependent on solvent environments in a nucleophilic addition reaction of hydroxylamine to a carbonyl group. Both theoretical simulations and ensemble experiments prove that this observation originates from the reversible transition between the reactant and a new intermediate state within a time scale of a few microseconds. These investigations open up a new route that is able to be immediately applied to probe fast single-molecule physics or biophysics with high time resolution, making an important contribution to broad fields beyond reaction chemistry.
2009-01-01
At the 19th Annual Conference on Parallel Computational Fluid Dynamics held in Antalya, Turkey, in May 2007, the most recent developments and implementations of large-scale and grid computing were presented. This book, comprised of the invited and selected papers of this conference, details those advances, which are of particular interest to CFD and CFD-related communities. It also offers the results related to applications of various scientific and engineering problems involving flows and flow-related topics. Intended for CFD researchers and graduate students, this book is a state-of-the-art presentation of the relevant methodology and implementation techniques of large-scale computing.
Gentzsch, Wolfgang
1986-01-01
The GAMM Committee for Numerical Methods in Fluid Mechanics organizes workshops which should bring together experts of a narrow field of computational fluid dynamics (CFD) to exchange ideas and experiences in order to speed-up the development in this field. In this sense it was suggested that a workshop should treat the solution of CFD problems on vector computers. Thus we organized a workshop with the title "The efficient use of vector computers with emphasis on computational fluid dynamics". The workshop took place at the Computing Centre of the University of Karlsruhe, March 13-15,1985. The participation had been restricted to 22 people of 7 countries. 18 papers have been presented. In the announcement of the workshop we wrote: "Fluid mechanics has actively stimulated the development of superfast vector computers like the CRAY's or CYBER 205. Now these computers on their turn stimulate the development of new algorithms which result in a high degree of vectorization (sca1ar/vectorized execution-time). But w...
Combining dynamical decoupling with fault-tolerant quantum computation
International Nuclear Information System (INIS)
Ng, Hui Khoon; Preskill, John; Lidar, Daniel A.
2011-01-01
We study how dynamical decoupling (DD) pulse sequences can improve the reliability of quantum computers. We prove upper bounds on the accuracy of DD-protected quantum gates and derive sufficient conditions for DD-protected gates to outperform unprotected gates. Under suitable conditions, fault-tolerant quantum circuits constructed from DD-protected gates can tolerate stronger noise and have a lower overhead cost than fault-tolerant circuits constructed from unprotected gates. Our accuracy estimates depend on the dynamics of the bath that couples to the quantum computer and can be expressed either in terms of the operator norm of the bath's Hamiltonian or in terms of the power spectrum of bath correlations; we explain in particular how the performance of recursively generated concatenated pulse sequences can be analyzed from either viewpoint. Our results apply to Hamiltonian noise models with limited spatial correlations.
Automatic differentiation tools in the dynamic simulation of chemical engineering processes
Directory of Open Access Journals (Sweden)
Castro M.C.
2000-01-01
Full Text Available Automatic Differentiation is a relatively recent technique developed for the differentiation of functions applicable directly to the source code to compute the function written in standard programming languages. That technique permits the automatization of the differentiation step, crucial for dynamic simulation and optimization of processes. The values for the derivatives obtained with AD are exact (to roundoff. The theoretical exactness of the AD comes from the fact that it uses the same rules of differentiation as in differential calculus, but these rules are applied to an algorithmic specification of the function rather than to a formula. The main purpose of this contribution is to discuss the impact of Automatic Differentiation in the field of dynamic simulation of chemical engineering processes. The influence of the differentiation technique on the behavior of the integration code, the performance of the generated code and the incorporation of AD tools in consistent initialization tools are discussed from the viewpoint of dynamic simulation of typical models in chemical engineering.
Recent Development in Rigorous Computational Methods in Dynamical Systems
Arai, Zin; Kokubu, Hiroshi; Pilarczyk, Paweł
2009-01-01
We highlight selected results of recent development in the area of rigorous computations which use interval arithmetic to analyse dynamical systems. We describe general ideas and selected details of different ways of approach and we provide specific sample applications to illustrate the effectiveness of these methods. The emphasis is put on a topological approach, which combined with rigorous calculations provides a broad range of new methods that yield mathematically rel...
Quality control of computational fluid dynamics in indoor environments
DEFF Research Database (Denmark)
Sørensen, Dan Nørtoft; Nielsen, P. V.
2003-01-01
Computational fluid dynamics (CFD) is used routinely to predict air movement and distributions of temperature and concentrations in indoor environments. Modelling and numerical errors are inherent in such studies and must be considered when the results are presented. Here, we discuss modelling as...... the quality of CFD calculations, as well as guidelines for the minimum information that should accompany all CFD-related publications to enable a scientific judgment of the quality of the study....
A semiautomated computer-interactive dynamic impact testing system
International Nuclear Information System (INIS)
Alexander, D.J.; Nanstad, R.K.; Corwin, W.R.; Hutton, J.T.
1989-01-01
A computer-assisted semiautomated system has been developed for testing a variety of specimen types under dynamic impact conditions. The primary use of this system is for the testing of Charpy specimens. Full-, half-, and third-size specimens have been tested, both in the lab and remotely in a hot cell for irradiated specimens. Specimens are loaded into a transfer device which moves the specimen into a chamber, where a hot air gun is used to heat the specimen, or cold nitrogen gas is used for cooling, as required. The specimen is then quickly transferred from the furnace to the anvils and then broken. This system incorporates an instrumented tup to determine the change in voltage during the fracture process. These data are analyzed by the computer system after the test is complete. The voltage-time trace is recorded with a digital oscilloscope, transferred to the computer, and analyzed. The analysis program incorporates several unique features. It interacts with the operator and identifies the maximum voltage during the test, the amount of rapid fracture during the test (if any), and the end of the fracture process. The program then calculates the area to maximum voltage and the total area under the voltage-time curve. The data acquisition and analysis part of the system can also be used to conduct other dynamic testing. Dynamic tear and precracked specimens can be tested with an instrumented tup and analyzed in a similar manner. 3 refs., 7 figs
Dynamic computed tomography scanning of benign bone lesions: Preliminary results
International Nuclear Information System (INIS)
Levine, E.; Neff, J.R.
1983-01-01
The majority of benign bone lesions can be evaluated adequately using conventional radiologic techniques. However, it is not always possible to differentiate reliably between different types of benign bone lesions on the basis of plain film appearances alone. Dynamic computed tomography (CT) scanning provides a means for further characterizing such lesions by assessing their degree of vascularity. Thus, it may help in distinguishing an osteoid osteoma, which has a hypervascular nidus, from a Brodie's abscess, which is avascular. Dynamic CT scanning may also help in the differentiation between a fluid-containing simple bone cyst, which is avascular, and other solid or semi-solid benign bone lesions which slow varying degrees of vascularity. However, because of the additional irradiation involved, dynamic CT scanning should be reserved for evaluation of selected patients with benign bone lesions in whom the plain film findings are not definitive and in whom the CT findings may have a significant influence on management. (orig.)
Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
Directory of Open Access Journals (Sweden)
Dario Gioia
2017-11-01
Full Text Available Molecular docking is the methodology of choice for studying in silico protein-ligand binding and for prioritizing compounds to discover new lead candidates. Traditional docking simulations suffer from major limitations, mostly related to the static or semi-flexible treatment of ligands and targets. They also neglect solvation and entropic effects, which strongly limits their predictive power. During the last decade, methods based on full atomistic molecular dynamics (MD have emerged as a valid alternative for simulating macromolecular complexes. In principle, compared to traditional docking, MD allows the full exploration of drug-target recognition and binding from both the mechanistic and energetic points of view (dynamic docking. Binding and unbinding kinetic constants can also be determined. While dynamic docking is still too computationally expensive to be routinely used in fast-paced drug discovery programs, the advent of faster computing architectures and advanced simulation methodologies are changing this scenario. It is feasible that dynamic docking will replace static docking approaches in the near future, leading to a major paradigm shift in in silico drug discovery. Against this background, we review the key achievements that have paved the way for this progress.
Developing Computer Model-Based Assessment of Chemical Reasoning: A Feasibility Study
Liu, Xiufeng; Waight, Noemi; Gregorius, Roberto; Smith, Erica; Park, Mihwa
2012-01-01
This paper reports a feasibility study on developing computer model-based assessments of chemical reasoning at the high school level. Computer models are flash and NetLogo environments to make simultaneously available three domains in chemistry: macroscopic, submicroscopic, and symbolic. Students interact with computer models to answer assessment…
Analysis of forward and inverse problems in chemical dynamics and spectroscopy
Energy Technology Data Exchange (ETDEWEB)
Rabitz, H. [Princeton Univ., NJ (United States)
1993-12-01
The overall scope of this research concerns the development and application of forward and inverse analysis tools for problems in chemical dynamics and chemical kinetics. The chemical dynamics work is specifically associated with relating features in potential surfaces and resultant dynamical behavior. The analogous inverse research aims to provide stable algorithms for extracting potential surfaces from laboratory data. In the case of chemical kinetics, the focus is on the development of systematic means to reduce the complexity of chemical kinetic models. Recent progress in these directions is summarized below.
Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations
DEFF Research Database (Denmark)
Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E
2017-01-01
Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...
Computational complexity of symbolic dynamics at the onset of chaos
Lakdawala, Porus
1996-05-01
In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behavior of cellular automata, that the computational basis for modeling this region is the universal Turing machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.
The Challenge '88 Project: Interfacing of Chemical Instruments to Computers.
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…
SCREENING CHEMICALS FOR ESTROGEN RECEPTOR BIOACTIVITY USING A COMPUTATIONAL MODEL
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...
EXAFS characterization of supported metal catalysts in chemically dynamic environments
International Nuclear Information System (INIS)
Robota, H.J.
1991-01-01
Characterization of catalysts focuses on the identification of an active site responsible for accelerating desirable chemical reactions. The identification, characterization, and selective modification of such sites is fundamental to the development of structure-function relationships. Unfortunately, this goal is far from realized in nearly all catalysts, and particularly in catalysts comprised of small supported metal particles. X-ray absorption spectroscopy (XAS) has had a dramatic effect on our understanding of supported metal particles in their resting state. However, the performance of a catalyst can not be assessed from such simple resting state measurements. Among the factors which influence catalyst performance are the exact catalyst composition, including the support and any modifiers; particle size; catalyst finishing and pretreatment conditions; pressure, composition, and temperature of the operating environment; time. Gaining an understanding of how the structure of a catalytic site can change with such an array of variables requires that we begin to develop measurement methods which are effective under chemically dynamic conditions. Ideally, it should be possible to obtain a full X-ray absorption spectrum of each element thought to have a causal relationship with observed catalyst properties. From these spectra, we can optimally extract only a relatively limited amount of information which we must then piece together with information derived from other characterization methods and intuition to arrive at a hypothetical structure of the operating catalyst. Information about crystallinity, homogeneity, and general disorder can be obtained from the Debye-Waller factor. Finally, through analogy with known compounds, the electronic structure of the active atoms can be inferred from near edge absorption features
Computed tomography of hepatocellular carcinoma: Usefulness of dynamic CT
Energy Technology Data Exchange (ETDEWEB)
Takemoto, Kazumasa; Inoue, Yuichi; Matsuoka, Toshiyuki; Nakatsuka, Haruki; Oda, Junro [Osaka City Univ. (Japan). Faculty of Medicine
1983-04-01
Dynamic computed tomography (CT) scans in 65 hepatocellular carcinomas were analyzed and compared to plain and drip infusion contrast CT scans of those. Scans were obtained before, 10, 30, and 50 seconds after an intravenous bolus injection of 50ml 65% Angiografin. By this method, 49 hepatomas had moderate to marked enhancement at the arterial phase while the enhancement of normal liver parenchyma was only slight at the arterial phase and peaked at the portal phase. Compared to a drip infusion contrast CT, a dynamic CT had advantages to detect an isodense hepatoma in 4 and daughter tumors in 16 both of which were not appreciated by a plain and a drip infusion contrast CT. The tumor extension was also better delineated by a dynamic CT because a part of hepatoma had an isodense area. An arterio-portal shunt was visualized in one. Tumor thrombus in the portal vein was clearly demonstrated in 6 at the portal phase of a dynamic CT. Since a dynamic CT is convenient to perform without any special program or soft wear and gives us very useful information, we believe that it should be routinely employed as a part of a liver CT examination.
The quantum dynamics of electronically nonadiabatic chemical reactions
Truhlar, Donald G.
1993-01-01
Considerable progress was achieved on the quantum mechanical treatment of electronically nonadiabatic collisions involving energy transfer and chemical reaction in the collision of an electronically excited atom with a molecule. In the first step, a new diabatic representation for the coupled potential energy surfaces was created. A two-state diabatic representation was developed which was designed to realistically reproduce the two lowest adiabatic states of the valence bond model and also to have the following three desirable features: (1) it is more economical to evaluate; (2) it is more portable; and (3) all spline fits are replaced by analytic functions. The new representation consists of a set of two coupled diabatic potential energy surfaces plus a coupling surface. It is suitable for dynamics calculations on both the electronic quenching and reaction processes in collisions of Na(3p2p) with H2. The new two-state representation was obtained by a three-step process from a modified eight-state diatomics-in-molecules (DIM) representation of Blais. The second step required the development of new dynamical methods. A formalism was developed for treating reactions with very general basis functions including electronically excited states. Our formalism is based on the generalized Newton, scattered wave, and outgoing wave variational principles that were used previously for reactive collisions on a single potential energy surface, and it incorporates three new features: (1) the basis functions include electronic degrees of freedom, as required to treat reactions involving electronic excitation and two or more coupled potential energy surfaces; (2) the primitive electronic basis is assumed to be diabatic, and it is not assumed that it diagonalizes the electronic Hamiltonian even asymptotically; and (3) contracted basis functions for vibrational-rotational-orbital degrees of freedom are included in a very general way, similar to previous prescriptions for locally
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.
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.
Computational Fluid Dynamics (CFD) Technology Programme 1995- 1999
Energy Technology Data Exchange (ETDEWEB)
Haekkinen, R.J.; Hirsch, C.; Krause, E.; Kytoemaa, H.K. [eds.
1997-12-31
The report is a mid-term evaluation of the Computational Fluid Dynamics (CFD) Technology Programme started by Technology Development Centre Finland (TEKES) in 1995 as a five-year initiative to be concluded in 1999. The main goal of the programme is to increase the know-how and application of CFD in Finnish industry, to coordinate and thus provide a better basis for co-operation between national CFD activities and encouraging research laboratories and industry to establish co-operation with the international CFD community. The projects of the programme focus on the following areas: (1) studies of modeling the physics and dynamics of the behaviour of fluid material, (2) expressing the physical models in a numerical mode and developing a computer codes, (3) evaluating and testing current physical models and developing new ones, (4) developing new numerical algorithms, solvers, and pre- and post-processing software, and (5) applying the new computational tools to problems relevant to their ultimate industrial use. The report consists of two sections. The first considers issues concerning the whole programme and the second reviews each project
Energy Technology Data Exchange (ETDEWEB)
Jardini, Andre L.; Bineli, Aulus R.R.; Viadana, Adriana M.; Maciel, Maria Regina Wolf; Maciel Filho, Rubens [State University of Campinas (UNICAMP), SP (Brazil). School of Chemical Engineering; Medina, Lilian C.; Gomes, Alexandre de O. [PETROBRAS S.A., Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Barros, Ricardo S. [University Foundation Jose Bonifacio (FUJB), Rio de Janeiro, RJ (Brazil)
2008-07-01
In this paper, the design of microreactor with microfluidics channels has been carried out in Computer Aided Design Software (CAD) and constructed in rapid prototyping system to be used in chemical reaction processing of the heavy oil fractions. The flow pattern properties of microreactor (fluid dynamics, mixing behavior) have been considered through CFD (computational fluid dynamics) simulations. CFD calculations are also used to study the design and specification of new microreactor developments. The potential advantages of using a microreactor include better control of reaction conditions, improved safety and portability. A more detailed crude assay of the raw national oil, whose importance was evidenced by PETROBRAS/CENPES allows establishing the optimum strategies and processing conditions, aiming at a maximum utilization of the heavy oil fractions, towards valuable products. These residues are able to be processed in microreactor, in which conventional process like as hydrotreating, catalytic and thermal cracking may be carried out in a much more intensified fashion. The whole process development involves a prior thermal study to define the possible operating conditions for a particular task, the microreactor design through computational fluid dynamics and construction using rapid prototyping. This gives high flexibility for process development, shorter time, and costumer/task oriented process/product development. (author)
Predicting Chemical Toxicity from Proteomics and Computational Chemistry
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
Dynamic computed tomography for the diagnosis of microadenoma, (2)
International Nuclear Information System (INIS)
Tsuchiya, Toshiaki; Andou, Kazuo; Ito, Jusuke; Kuroki, Sumio; Yokoyama, Motoharu; Tanaka, Ryuichi.
1987-01-01
Dynamic computed tomography was used to study 19 patients with hormone-secreting microadenomas: 10 prolactin-secreting, 5 growth-hormone-secreting, and 4 adrenocorticotropic-hormone-secreting. A distorted and displaced tuft indicates a mass effect mainly on the opposite side. A mid-situated tuft with a disproportionately small size compared with the size of the anterior lobe indicates a mass effect mainly in the midportion. An area into which a high density at the tuft definitely spreads indicates a normal anterior lobe; an area in which less increase in the density than in the former area is observed indicates an abnormal mass. In the time-density curve, the former area represents the vascular pattern or the hypervascular extravasation pattern, while the latter area represents the extravasation of the contrast material in a hypovascular tissue. Only eight microadenomas appeared as a less enhanced mass. The rest of the cases exhibited adenomas isodense to the normal pituitary gland. A dynamic CT scan was particularly useful in the diagnosis of isodense adenomas. In these isodense adenomas, the dynamic CT scan facilitated the identification of an adenoma as a relatively less enhanced area than the normal gland. The extent of a normal pituitary gland could also be identified by means of dynamic CT. In three of the 11 isodense microadenomas, the conventional diagnostic criteria, such as infundibulum displacement, abnormal height and upward convexity of a pituitary-microadenoma complex, and changes in the sellar floor, were not encountered. A dynamic CT scan, however, enabled us to diagnose the localization of microadenomas in two of these three cases. In 18 of the 19 microadenomas, dynamic CT findings as to the localization of a microadenoma and the normal pituitary gland correlated well with the surgical findings. (J.P.N.)
SciDAC advances and applications in computational beam dynamics
International Nuclear Information System (INIS)
Ryne, R; Abell, D; Adelmann, A; Amundson, J; Bohn, C; Cary, J; Colella, P; Dechow, D; Decyk, V; Dragt, A; Gerber, R; Habib, S; Higdon, D; Katsouleas, T; Ma, K-L; McCorquodale, P; Mihalcea, D; Mitchell, C; Mori, W; Mottershead, C T; Neri, F; Pogorelov, I; Qiang, J; Samulyak, R; Serafini, D; Shalf, J; Siegerist, C; Spentzouris, P; Stoltz, P; Terzic, B; Venturini, M; Walstrom, P
2005-01-01
SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators-which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook-are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design calculations that were once thought impossible are now carried routinely, and new challenging and important calculations are within reach. SciDAC accelerator modeling codes are being used to get the most science out of existing facilities, to produce optimal designs for future facilities, and to explore advanced accelerator concepts that may hold the key to qualitatively new ways of accelerating charged particle beams. In this paper we present highlights from the SciDAC Accelerator Science and Technology (AST) project Beam Dynamics focus area in regard to algorithm development, software development, and applications
SciDAC Advances and Applications in Computational Beam Dynamics
International Nuclear Information System (INIS)
Ryne, R.; Abell, D.; Adelmann, A.; Amundson, J.; Bohn, C.; Cary, J.; Colella, P.; Dechow, D.; Decyk, V.; Dragt, A.; Gerber, R.; Habib, S.; Higdon, D.; Katsouleas, T.; Ma, K.-L.; McCorquodale, P.; Mihalcea, D.; Mitchell, C.; Mori, W.; Mottershead, C.T.; Neri, F.; Pogorelov, I.; Qiang, J.; Samulyak, R.; Serafini, D.; Shalf, J.; Siegerist, C.; Spentzouris, P.; Stoltz, P.; Terzic, B.; Venturini, M.; Walstrom, P.
2005-01-01
SciDAC has had a major impact on computational beam dynamics and the design of particle accelerators. Particle accelerators--which account for half of the facilities in the DOE Office of Science Facilities for the Future of Science 20 Year Outlook--are crucial for US scientific, industrial, and economic competitiveness. Thanks to SciDAC, accelerator design calculations that were once thought impossible are now carried routinely, and new challenging and important calculations are within reach. SciDAC accelerator modeling codes are being used to get the most science out of existing facilities, to produce optimal designs for future facilities, and to explore advanced accelerator concepts that may hold the key to qualitatively new ways of accelerating charged particle beams. In this poster we present highlights from the SciDAC Accelerator Science and Technology (AST) project Beam Dynamics focus area in regard to algorithm development, software development, and applications
Adaptive Dynamic Process Scheduling on Distributed Memory Parallel Computers
Directory of Open Access Journals (Sweden)
Wei Shu
1994-01-01
Full Text Available One of the challenges in programming distributed memory parallel machines is deciding how to allocate work to processors. This problem is particularly important for computations with unpredictable dynamic behaviors or irregular structures. We present a scheme for dynamic scheduling of medium-grained processes that is useful in this context. The adaptive contracting within neighborhood (ACWN is a dynamic, distributed, load-dependent, and scalable scheme. It deals with dynamic and unpredictable creation of processes and adapts to different systems. The scheme is described and contrasted with two other schemes that have been proposed in this context, namely the randomized allocation and the gradient model. The performance of the three schemes on an Intel iPSC/2 hypercube is presented and analyzed. The experimental results show that even though the ACWN algorithm incurs somewhat larger overhead than the randomized allocation, it achieves better performance in most cases due to its adaptiveness. Its feature of quickly spreading the work helps it outperform the gradient model in performance and scalability.
Dynamic computer simulations of electrophoresis: three decades of active research.
Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A
2009-06-01
Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.
A Symbolic and Graphical Computer Representation of Dynamical Systems
Gould, Laurence I.
2005-04-01
AUTONO is a Macsyma/Maxima program, designed at the University of Hartford, for solving autonomous systems of differential equations as well as for relating Lagrangians and Hamiltonians to their associated dynamical equations. AUTONO can be used in a number of fields to decipher a variety of complex dynamical systems with ease, producing their Lagrangian and Hamiltonian equations in seconds. These equations can then be incorporated into VisSim, a modeling and simulation program, which yields graphical representations of motion in a given system through easily chosen input parameters. The program, along with the VisSim differential-equations graphical package, allows for resolution and easy understanding of complex problems in a relatively short time; thus enabling quicker and more advanced computing of dynamical systems on any number of platforms---from a network of sensors on a space probe, to the behavior of neural networks, to the effects of an electromagnetic field on components in a dynamical system. A flowchart of AUTONO, along with some simple applications and VisSim output, will be shown.
Data Point Averaging for Computational Fluid Dynamics Data
Norman, Jr., David (Inventor)
2016-01-01
A system and method for generating fluid flow parameter data for use in aerodynamic heating analysis. Computational fluid dynamics data is generated for a number of points in an area on a surface to be analyzed. Sub-areas corresponding to areas of the surface for which an aerodynamic heating analysis is to be performed are identified. A computer system automatically determines a sub-set of the number of points corresponding to each of the number of sub-areas and determines a value for each of the number of sub-areas using the data for the sub-set of points corresponding to each of the number of sub-areas. The value is determined as an average of the data for the sub-set of points corresponding to each of the number of sub-areas. The resulting parameter values then may be used to perform an aerodynamic heating analysis.
Distributed interactive graphics applications in computational fluid dynamics
International Nuclear Information System (INIS)
Rogers, S.E.; Buning, P.G.; Merritt, F.J.
1987-01-01
Implementation of two distributed graphics programs used in computational fluid dynamics is discussed. Both programs are interactive in nature. They run on a CRAY-2 supercomputer and use a Silicon Graphics Iris workstation as the front-end machine. The hardware and supporting software are from the Numerical Aerodynamic Simulation project. The supercomputer does all numerically intensive work and the workstation, as the front-end machine, allows the user to perform real-time interactive transformations on the displayed data. The first program was written as a distributed program that computes particle traces for fluid flow solutions existing on the supercomputer. The second is an older post-processing and plotting program modified to run in a distributed mode. Both programs have realized a large increase in speed over that obtained using a single machine. By using these programs, one can learn quickly about complex features of a three-dimensional flow field. Some color results are presented
Fast reactor safety and computational thermo-fluid dynamics approaches
International Nuclear Information System (INIS)
Ninokata, Hisashi; Shimizu, Takeshi
1993-01-01
This article provides a brief description of the safety principle on which liquid metal cooled fast breeder reactors (LMFBRs) is based and the roles of computations in the safety practices. A number of thermohydraulics models have been developed to date that successfully describe several of the important types of fluids and materials motion encountered in the analysis of postulated accidents in LMFBRs. Most of these models use a mixture of implicit and explicit numerical solution techniques in solving a set of conservation equations formulated in Eulerian coordinates, with special techniques included to specific situations. Typical computational thermo-fluid dynamics approaches are discussed in particular areas of analyses of the physical phenomena relevant to the fuel subassembly thermohydraulics design and that involve describing the motion of molten materials in the core over a large scale. (orig.)
Cardioplegia heat exchanger design modelling using computational fluid dynamics.
van Driel, M R
2000-11-01
A new cardioplegia heat exchanger has been developed by Sorin Biomedica. A three-dimensional computer-aided design (CAD) model was optimized using computational fluid dynamics (CFD) modelling. CFD optimization techniques have commonly been applied to velocity flow field analysis, but CFD analysis was also used in this study to predict the heat exchange performance of the design before prototype fabrication. The iterative results of the optimization and the actual heat exchange performance of the final configuration are presented in this paper. Based on the behaviour of this model, both the water and blood fluid flow paths of the heat exchanger were optimized. The simulation predicted superior heat exchange performance using an optimal amount of energy exchange surface area, reducing the total contact surface area, the device priming volume and the material costs. Experimental results confirm the empirical results predicted by the CFD analysis.
Application of a distributed network in computational fluid dynamic simulations
Deshpande, Manish; Feng, Jinzhang; Merkle, Charles L.; Deshpande, Ashish
1994-01-01
A general-purpose 3-D, incompressible Navier-Stokes algorithm is implemented on a network of concurrently operating workstations using parallel virtual machine (PVM) and compared with its performance on a CRAY Y-MP and on an Intel iPSC/860. The problem is relatively computationally intensive, and has a communication structure based primarily on nearest-neighbor communication, making it ideally suited to message passing. Such problems are frequently encountered in computational fluid dynamics (CDF), and their solution is increasingly in demand. The communication structure is explicitly coded in the implementation to fully exploit the regularity in message passing in order to produce a near-optimal solution. Results are presented for various grid sizes using up to eight processors.
Parallel computing and molecular dynamics of biological membranes
International Nuclear Information System (INIS)
La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.
1998-01-01
In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)
Computational model of lightness perception in high dynamic range imaging
Krawczyk, Grzegorz; Myszkowski, Karol; Seidel, Hans-Peter
2006-02-01
An anchoring theory of lightness perception by Gilchrist et al. [1999] explains many characteristics of human visual system such as lightness constancy and its spectacular failures which are important in the perception of images. The principal concept of this theory is the perception of complex scenes in terms of groups of consistent areas (frameworks). Such areas, following the gestalt theorists, are defined by the regions of common illumination. The key aspect of the image perception is the estimation of lightness within each framework through the anchoring to the luminance perceived as white, followed by the computation of the global lightness. In this paper we provide a computational model for automatic decomposition of HDR images into frameworks. We derive a tone mapping operator which predicts lightness perception of the real world scenes and aims at its accurate reproduction on low dynamic range displays. Furthermore, such a decomposition into frameworks opens new grounds for local image analysis in view of human perception.
2011-08-09
heterogeneous computing concept advertised recently as the paradigm capable of delivering exascale flop rates by the end of the decade. In this framework...and Lamb. Page 10 of 10 UNCLASSIFIED [3] Skaugen, K., Petascale to Exascale : Extending Intel’s HPC Commitment: http://download.intel.com
Computer studies of multiple-quantum spin dynamics
Energy Technology Data Exchange (ETDEWEB)
Murdoch, J.B.
1982-11-01
The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment.
Modeling fires in adjacent ship compartments with computational fluid dynamics
International Nuclear Information System (INIS)
Wix, S.D.; Cole, J.K.; Koski, J.A.
1998-01-01
This paper presents an analysis of the thermal effects on radioactive (RAM) transportation pack ages with a fire in an adjacent compartment. An assumption for this analysis is that the adjacent hold fire is some sort of engine room fire. Computational fluid dynamics (CFD) analysis tools were used to perform the analysis in order to include convective heat transfer effects. The analysis results were compared to experimental data gathered in a series of tests on the United States Coast Guard ship Mayo Lykes located at Mobile, Alabama. (authors)
MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps
Directory of Open Access Journals (Sweden)
Paolo Ruggerone
2013-02-01
Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.
Computer studies of multiple-quantum spin dynamics
International Nuclear Information System (INIS)
Murdoch, J.B.
1982-11-01
The excitation and detection of multiple-quantum (MQ) transitions in Fourier transform NMR spectroscopy is an interesting problem in the quantum mechanical dynamics of spin systems as well as an important new technique for investigation of molecular structure. In particular, multiple-quantum spectroscopy can be used to simplify overly complex spectra or to separate the various interactions between a nucleus and its environment. The emphasis of this work is on computer simulation of spin-system evolution to better relate theory and experiment
Torque converter transient characteristics prediction using computational fluid dynamics
International Nuclear Information System (INIS)
Yamaguchi, T; Tanaka, K
2012-01-01
The objective of this research is to investigate the transient torque converter performance used in an automobile. A new technique in computational fluid dynamics is introduced, which includes the inertia of the turbine in a three dimensional simulation of the torque converter during a launch condition. The simulation results are compared to experimental test data with good agreement across the range of data. In addition, the simulated flow structure inside the torque converter is visualized and compared to results from a steady-state calculation.
Robust dynamical decoupling for quantum computing and quantum memory.
Souza, Alexandre M; Alvarez, Gonzalo A; Suter, Dieter
2011-06-17
Dynamical decoupling (DD) is a popular technique for protecting qubits from the environment. However, unless special care is taken, experimental errors in the control pulses used in this technique can destroy the quantum information instead of preserving it. Here, we investigate techniques for making DD sequences robust against different types of experimental errors while retaining good decoupling efficiency in a fluctuating environment. We present experimental data from solid-state nuclear spin qubits and introduce a new DD sequence that is suitable for quantum computing and quantum memory.
Approaching multiphase flows from the perspective of computational fluid dynamics
International Nuclear Information System (INIS)
Banas, A.O.
1992-01-01
Thermalhydraulic simulation methodologies based on subchannel and porous-medium concepts are briefly reviewed and contrasted with the general approach of Computational Fluid Dynamics (CFD). An outline of the advanced CFD methods for single-phase turbulent flows is followed by a short discussion of the unified formulation of averaged equations for turbulent and multiphase flows. Some of the recent applications of CFD at Chalk River Laboratories are discussed, and the complementary role of CFD with regard to the established thermalhydraulic methods of analysis is indicated. (author). 8 refs
Symposium on computational fluid dynamics: technology and applications
International Nuclear Information System (INIS)
1988-01-01
A symposium on the technology and applications of computational fluid dynamics (CFD) was held in Pretoria from 21-23 Nov 1988. The following aspects were covered: multilevel adaptive methods and multigrid solvers in CFD, a symbolic processing approach to CFD, interplay between CFD and analytical approximations, CFD on a transfer array, the application of CFD in high speed aerodynamics, numerical simulation of laminar blood flow, two-phase flow modelling in nuclear accident analysis, and the finite difference scheme for the numerical solution of fluid flow
Computational Fluid Dynamics of Choanoﬂagellate Filter-Feeding
DEFF Research Database (Denmark)
Asadzadeh, Seyed Saeed; Walther, Jens Honore; Nielsen, Lasse Tor
Choanoﬂagellates are unicellular aquatic organisms with a single ﬂagellum that drives a feeding current through a funnel-shaped collar ﬁlter on which bacteria-sized prey are caught. Using computational ﬂuid dynamics (CFD) we model the beating ﬂagellum and the complex ﬁlter ﬂow of the choanoﬂagell...... to suggest a radically diﬀerent ﬁltration mechanism that requires a ﬂagellar vane (sheet), and addition of a wide vane in our CFD model allows us to correctly predict the observed clearance rate....
Dynamic stability calculations for power grids employing a parallel computer
Energy Technology Data Exchange (ETDEWEB)
Schmidt, K
1982-06-01
The aim of dynamic contingency calculations in power systems is to estimate the effects of assumed disturbances, such as loss of generation. Due to the large dimensions of the problem these simulations require considerable computing time and costs, to the effect that they are at present only used in a planning state but not for routine checks in power control stations. In view of the homogeneity of the problem, where a multitude of equal generator models, having different parameters, are to be integrated simultaneously, the use of a parallel computer looks very attractive. The results of this study employing a prototype parallel computer (SMS 201) are presented. It consists of up to 128 equal microcomputers bus-connected to a control computer. Each of the modules is programmed to simulate a node of the power grid. Generators with their associated control are represented by models of 13 states each. Passive nodes are complemented by 'phantom'-generators, so that the whole power grid is homogenous, thus removing the need for load-flow-iterations. Programming of microcomputers is essentially performed in FORTRAN.
Computer Facilitated Mathematical Methods in Chemical Engineering--Similarity Solution
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…
Chemical industrial areas and their dynamic danger behaviour
Reniers, Genserik L L; Audenaert, Amaryllis; Dullaert, W.; Soudan, K.
2007-01-01
Chemical industrial areas or so-called chemical clusters consist of various companies situated next to each other. Such areas are composed of hundreds of chemical installations exhibiting danger to a certain degree for initiating or continuing knock-on effects. In this paper, a methodology to model
Chiu, Mei-Hung; Chou, Chin-Cheng; Liu, Chia-Ju
2002-01-01
Investigates students' mental models of chemical equilibrium using dynamic science assessments. Reports that students at various levels have misconceptions about chemical equilibrium. Involves 10th grade students (n=30) in the study doing a series of hands-on chemical experiments. Focuses on the process of constructing mental models, dynamic…
A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry
Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew
2012-01-01
In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…
Issues in computational fluid dynamics code verification and validation
Energy Technology Data Exchange (ETDEWEB)
Oberkampf, W.L.; Blottner, F.G.
1997-09-01
A broad range of mathematical modeling errors of fluid flow physics and numerical approximation errors are addressed in computational fluid dynamics (CFD). It is strongly believed that if CFD is to have a major impact on the design of engineering hardware and flight systems, the level of confidence in complex simulations must substantially improve. To better understand the present limitations of CFD simulations, a wide variety of physical modeling, discretization, and solution errors are identified and discussed. Here, discretization and solution errors refer to all errors caused by conversion of the original partial differential, or integral, conservation equations representing the physical process, to algebraic equations and their solution on a computer. The impact of boundary conditions on the solution of the partial differential equations and their discrete representation will also be discussed. Throughout the article, clear distinctions are made between the analytical mathematical models of fluid dynamics and the numerical models. Lax`s Equivalence Theorem and its frailties in practical CFD solutions are pointed out. Distinctions are also made between the existence and uniqueness of solutions to the partial differential equations as opposed to the discrete equations. Two techniques are briefly discussed for the detection and quantification of certain types of discretization and grid resolution errors.
Nano-Modeling and Computation in Bio and Brain Dynamics
Directory of Open Access Journals (Sweden)
Paolo Di Sia
2016-04-01
Full Text Available The study of brain dynamics currently utilizes the new features of nanobiotechnology and bioengineering. New geometric and analytical approaches appear very promising in all scientific areas, particularly in the study of brain processes. Efforts to engage in deep comprehension lead to a change in the inner brain parameters, in order to mimic the external transformation by the proper use of sensors and effectors. This paper highlights some crossing research areas of natural computing, nanotechnology, and brain modeling and considers two interesting theoretical approaches related to brain dynamics: (a the memory in neural network, not as a passive element for storing information, but integrated in the neural parameters as synaptic conductances; and (b a new transport model based on analytical expressions of the most important transport parameters, which works from sub-pico-level to macro-level, able both to understand existing data and to give new predictions. Complex biological systems are highly dependent on the context, which suggests a “more nature-oriented” computational philosophy.
Computational Fluid Dynamics Analysis of High Injection Pressure Blended Biodiesel
Khalid, Amir; Jaat, Norrizam; Faisal Hushim, Mohd; Manshoor, Bukhari; Zaman, Izzuddin; Sapit, Azwan; Razali, Azahari
2017-08-01
Biodiesel have great potential for substitution with petrol fuel for the purpose of achieving clean energy production and emission reduction. Among the methods that can control the combustion properties, controlling of the fuel injection conditions is one of the successful methods. The purpose of this study is to investigate the effect of high injection pressure of biodiesel blends on spray characteristics using Computational Fluid Dynamics (CFD). Injection pressure was observed at 220 MPa, 250 MPa and 280 MPa. The ambient temperature was kept held at 1050 K and ambient pressure 8 MPa in order to simulate the effect of boost pressure or turbo charger during combustion process. Computational Fluid Dynamics were used to investigate the spray characteristics of biodiesel blends such as spray penetration length, spray angle and mixture formation of fuel-air mixing. The results shows that increases of injection pressure, wider spray angle is produced by biodiesel blends and diesel fuel. The injection pressure strongly affects the mixture formation, characteristics of fuel spray, longer spray penetration length thus promotes the fuel and air mixing.
A hybrid computer simulation of reactor spatial dynamics
International Nuclear Information System (INIS)
Hinds, H.W.
1977-08-01
The partial differential equations describing the one-speed spatial dynamics of thermal neutron reactors were converted to a set of ordinary differential equations, using finite-difference approximations for the spatial derivatives. The variables were then normalized to a steady-state reference condition in a novel manner, to yield an equation set particularly suitable for implementation on a hybrid computer. One Applied Dynamics AD/FIVE analog-computer console is capable of solving, all in parallel, up to 30 simultaneous differential equations. This corresponds roughly to eight reactor nodes, each with two active delayed-neutron groups. To improve accuracy, an increase in the number of nodes is usually required. Using the Hsu-Howe multiplexing technique, an 8-node, one-dimensional module was switched back and forth between the left and right halves of the reactor, to simulate a 16-node model, also in one dimension. These two versions (8 or 16 nodes) of the model were tested on benchmark problems of the loss-of-coolant type, which were also solved using the digital code FORSIM, with two energy groups and 26 nodes. Good agreement was obtained between the two solution techniques. (author)
National Research Council Canada - National Science Library
Edge, Harris
1999-01-01
...), computational fluid dynamics (CFD) 6 project. Under the project, a proven zonal Navier-Stokes solver was rewritten for scalable parallel performance on both shared memory and distributed memory high performance computers...
High performance computer code for molecular dynamics simulations
International Nuclear Information System (INIS)
Levay, I.; Toekesi, K.
2007-01-01
Complete text of publication follows. Molecular Dynamics (MD) simulation is a widely used technique for modeling complicated physical phenomena. Since 2005 we are developing a MD simulations code for PC computers. The computer code is written in C++ object oriented programming language. The aim of our work is twofold: a) to develop a fast computer code for the study of random walk of guest atoms in Be crystal, b) 3 dimensional (3D) visualization of the particles motion. In this case we mimic the motion of the guest atoms in the crystal (diffusion-type motion), and the motion of atoms in the crystallattice (crystal deformation). Nowadays, it is common to use Graphics Devices in intensive computational problems. There are several ways to use this extreme processing performance, but never before was so easy to programming these devices as now. The CUDA (Compute Unified Device) Architecture introduced by nVidia Corporation in 2007 is a very useful for every processor hungry application. A Unified-architecture GPU include 96-128, or more stream processors, so the raw calculation performance is 576(!) GFLOPS. It is ten times faster, than the fastest dual Core CPU [Fig.1]. Our improved MD simulation software uses this new technology, which speed up our software and the code run 10 times faster in the critical calculation code segment. Although the GPU is a very powerful tool, it has a strongly paralleled structure. It means, that we have to create an algorithm, which works on several processors without deadlock. Our code currently uses 256 threads, shared and constant on-chip memory, instead of global memory, which is 100 times slower than others. It is possible to implement the total algorithm on GPU, therefore we do not need to download and upload the data in every iteration. On behalf of maximal throughput, every thread run with the same instructions
A Computational Fluid Dynamic Model for a Novel Flash Ironmaking Process
Perez-Fontes, Silvia E.; Sohn, Hong Yong; Olivas-Martinez, Miguel
A computational fluid dynamic model for a novel flash ironmaking process based on the direct gaseous reduction of iron oxide concentrates is presented. The model solves the three-dimensional governing equations including both gas-phase and gas-solid reaction kinetics. The turbulence-chemistry interaction in the gas-phase is modeled by the eddy dissipation concept incorporating chemical kinetics. The particle cloud model is used to track the particle phase in a Lagrangian framework. A nucleation and growth kinetics rate expression is adopted to calculate the reduction rate of magnetite concentrate particles. Benchmark experiments reported in the literature for a nonreacting swirling gas jet and a nonpremixed hydrogen jet flame were simulated for validation. The model predictions showed good agreement with measurements in terms of gas velocity, gas temperature and species concentrations. The relevance of the computational model for the analysis of a bench reactor operation and the design of an industrial-pilot plant is discussed.
Computational fluid dynamics applied to flows in an internal combustion engine
Griffin, M. D.; Diwakar, R.; Anderson, J. D., Jr.; Jones, E.
1978-01-01
The reported investigation is a continuation of studies conducted by Diwakar et al. (1976) and Griffin et al. (1976), who reported the first computational fluid dynamic results for the two-dimensional flowfield for all four strokes of a reciprocating internal combustion (IC) engine cycle. An analysis of rectangular and cylindrical three-dimensional engine models is performed. The working fluid is assumed to be inviscid air of constant specific heats. Calculations are carried out of a four-stroke IC engine flowfield wherein detailed finite-rate chemical combustion of a gasoline-air mixture is included. The calculations remain basically inviscid, except that in some instances thermal conduction is included to allow a more realistic model of the localized sparking of the mixture. All the results of the investigation are obtained by means of an explicity time-dependent finite-difference technique, using a high-speed digital computer.
A paradigm for modeling and computation of gas dynamics
Xu, Kun; Liu, Chang
2017-02-01
In the continuum flow regime, the Navier-Stokes (NS) equations are usually used for the description of gas dynamics. On the other hand, the Boltzmann equation is applied for the rarefied flow. These two equations are based on distinguishable modeling scales for flow physics. Fortunately, due to the scale separation, i.e., the hydrodynamic and kinetic ones, both the Navier-Stokes equations and the Boltzmann equation are applicable in their respective domains. However, in real science and engineering applications, they may not have such a distinctive scale separation. For example, around a hypersonic flying vehicle, the flow physics at different regions may correspond to different regimes, where the local Knudsen number can be changed significantly in several orders of magnitude. With a variation of flow physics, theoretically a continuous governing equation from the kinetic Boltzmann modeling to the hydrodynamic Navier-Stokes dynamics should be used for its efficient description. However, due to the difficulties of a direct modeling of flow physics in the scale between the kinetic and hydrodynamic ones, there is basically no reliable theory or valid governing equations to cover the whole transition regime, except resolving flow physics always down to the mean free path scale, such as the direct Boltzmann solver and the Direct Simulation Monte Carlo (DSMC) method. In fact, it is an unresolved problem about the exact scale for the validity of the NS equations, especially in the small Reynolds number cases. The computational fluid dynamics (CFD) is usually based on the numerical solution of partial differential equations (PDEs), and it targets on the recovering of the exact solution of the PDEs as mesh size and time step converging to zero. This methodology can be hardly applied to solve the multiple scale problem efficiently because there is no such a complete PDE for flow physics through a continuous variation of scales. For the non-equilibrium flow study, the direct
Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement
Srinivas, Niranjan
Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry. In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive. Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for
Modeling Behavior Dynamics using Computational Psychometrics within Virtual Worlds
Directory of Open Access Journals (Sweden)
Pietro eCipresso
2015-11-01
Full Text Available In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video and audio and an advanced technique (Virtual Reality to manipulate experimental settings. The second step concerns the measurement of behavior in one, two or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.
Modeling behavior dynamics using computational psychometrics within virtual worlds.
Cipresso, Pietro
2015-01-01
In case of fire in a building, how will people behave in the crowd? The behavior of each individual affects the behavior of others and, conversely, each one behaves considering the crowd as a whole and the individual others. In this article, I propose a three-step method to explore a brand new way to study behavior dynamics. The first step relies on the creation of specific situations with standard techniques (such as mental imagery, text, video, and audio) and an advanced technique [Virtual Reality (VR)] to manipulate experimental settings. The second step concerns the measurement of behavior in one, two, or many individuals focusing on parameters extractions to provide information about the behavior dynamics. Finally, the third step, which uses the parameters collected and measured in the previous two steps in order to simulate possible scenarios to forecast through computational models, understand, and explain behavior dynamics at the social level. An experimental study was also included to demonstrate the three-step method and a possible scenario.
Cepstrum analysis and applications to computational fluid dynamic solutions
Meadows, Kristine R.
1990-04-01
A novel approach to the problem of spurious reflections introduced by artificial boundary conditions in computational fluid dynamic (CFD) solutions is proposed. Instead of attempting to derive non-reflecting boundary conditions, the approach is to accept the fact that spurious reflections occur, but to remove these reflections with cepstrum analysis, a signal processing technique which has been successfully used to remove echoes from experimental data. First, the theory of the cepstrum method is presented. This includes presentation of two types of cepstra: The Power Cepstrum and the Complex Cepstrum. The definitions of the cepstrum methods are applied theoretically and numerically to the analytical solution of sinusoidal plane wave propagation in a duct. One-D and 3-D time dependent solutions to the Euler equations are computed, and hard-wall conditions are prescribed at the numerical boundaries. The cepstrum method is applied, and the reflections from the boundaries are removed from the solutions. One-D and 3-D solutions are computed with so called nonreflecting boundary conditions, and these solutions are compared to those obtained by prescribing hard wall conditions and processing with the cepstrum.
Energy Conservation Using Dynamic Voltage Frequency Scaling for Computational Cloud
Directory of Open Access Journals (Sweden)
A. Paulin Florence
2016-01-01
Full Text Available Cloud computing is a new technology which supports resource sharing on a “Pay as you go” basis around the world. It provides various services such as SaaS, IaaS, and PaaS. Computation is a part of IaaS and the entire computational requests are to be served efficiently with optimal power utilization in the cloud. Recently, various algorithms are developed to reduce power consumption and even Dynamic Voltage and Frequency Scaling (DVFS scheme is also used in this perspective. In this paper we have devised methodology which analyzes the behavior of the given cloud request and identifies the associated type of algorithm. Once the type of algorithm is identified, using their asymptotic notations, its time complexity is calculated. Using best fit strategy the appropriate host is identified and the incoming job is allocated to the victimized host. Using the measured time complexity the required clock frequency of the host is measured. According to that CPU frequency is scaled up or down using DVFS scheme, enabling energy to be saved up to 55% of total Watts consumption.
High-Performance Java Codes for Computational Fluid Dynamics
Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)
2001-01-01
The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.
High-Precision Computation: Mathematical Physics and Dynamics
International Nuclear Information System (INIS)
Bailey, D.H.; Barrio, R.; Borwein, J.M.
2010-01-01
At the present time, IEEE 64-bit oating-point arithmetic is suficiently accurate for most scientic applications. However, for a rapidly growing body of important scientic computing applications, a higher level of numeric precision is required. Such calculations are facilitated by high-precision software packages that include high-level language translation modules to minimize the conversion e ort. This pa- per presents a survey of recent applications of these techniques and provides someanalysis of their numerical requirements. These applications include supernova simulations, climate modeling, planetary orbit calculations, Coulomb n-body atomic systems, studies of the one structure constant, scattering amplitudes of quarks, glu- ons and bosons, nonlinear oscillator theory, experimental mathematics, evaluation of orthogonal polynomials, numerical integration of ODEs, computation of periodic orbits, studies of the splitting of separatrices, detection of strange nonchaotic at- tractors, Ising theory, quantum held theory, and discrete dynamical systems. We conclude that high-precision arithmetic facilities are now an indispensable compo- nent of a modern large-scale scientic computing environment.
High-Precision Computation: Mathematical Physics and Dynamics
Energy Technology Data Exchange (ETDEWEB)
Bailey, D. H.; Barrio, R.; Borwein, J. M.
2010-04-01
At the present time, IEEE 64-bit oating-point arithmetic is suficiently accurate for most scientic applications. However, for a rapidly growing body of important scientic computing applications, a higher level of numeric precision is required. Such calculations are facilitated by high-precision software packages that include high-level language translation modules to minimize the conversion e ort. This pa- per presents a survey of recent applications of these techniques and provides someanalysis of their numerical requirements. These applications include supernova simulations, climate modeling, planetary orbit calculations, Coulomb n-body atomic systems, studies of the one structure constant, scattering amplitudes of quarks, glu- ons and bosons, nonlinear oscillator theory, experimental mathematics, evaluation of orthogonal polynomials, numerical integration of ODEs, computation of periodic orbits, studies of the splitting of separatrices, detection of strange nonchaotic at- tractors, Ising theory, quantum held theory, and discrete dynamical systems. We conclude that high-precision arithmetic facilities are now an indispensable compo- nent of a modern large-scale scientic computing environment.
Secure Dynamic access control scheme of PHR in cloud computing.
Chen, Tzer-Shyong; Liu, Chia-Hui; Chen, Tzer-Long; Chen, Chin-Sheng; Bau, Jian-Guo; Lin, Tzu-Ching
2012-12-01
With the development of information technology and medical technology, medical information has been developed from traditional paper records into electronic medical records, which have now been widely applied. The new-style medical information exchange system "personal health records (PHR)" is gradually developed. PHR is a kind of health records maintained and recorded by individuals. An ideal personal health record could integrate personal medical information from different sources and provide complete and correct personal health and medical summary through the Internet or portable media under the requirements of security and privacy. A lot of personal health records are being utilized. The patient-centered PHR information exchange system allows the public autonomously maintain and manage personal health records. Such management is convenient for storing, accessing, and sharing personal medical records. With the emergence of Cloud computing, PHR service has been transferred to storing data into Cloud servers that the resources could be flexibly utilized and the operation cost can be reduced. Nevertheless, patients would face privacy problem when storing PHR data into Cloud. Besides, it requires a secure protection scheme to encrypt the medical records of each patient for storing PHR into Cloud server. In the encryption process, it would be a challenge to achieve accurately accessing to medical records and corresponding to flexibility and efficiency. A new PHR access control scheme under Cloud computing environments is proposed in this study. With Lagrange interpolation polynomial to establish a secure and effective PHR information access scheme, it allows to accurately access to PHR with security and is suitable for enormous multi-users. Moreover, this scheme also dynamically supports multi-users in Cloud computing environments with personal privacy and offers legal authorities to access to PHR. From security and effectiveness analyses, the proposed PHR access
Quinoa - Adaptive Computational Fluid Dynamics, 0.2
Energy Technology Data Exchange (ETDEWEB)
2017-09-22
Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter, an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh
Computational Fluid Dynamics and Building Energy Performance Simulation
DEFF Research Database (Denmark)
Nielsen, Peter Vilhelm; Tryggvason, T.
1998-01-01
An interconnection between a building energy performance simulation program and a Computational Fluid Dynamics program (CFD) for room air distribution will be introduced for improvement of the predictions of both the energy consumption and the indoor environment. The building energy performance...... simulation program requires a detailed description of the energy flow in the air movement which can be obtained by a CFD program. The paper describes an energy consumption calculation in a large building, where the building energy simulation program is modified by CFD predictions of the flow between three...... zones connected by open areas with pressure and buoyancy driven air flow. The two programs are interconnected in an iterative procedure. The paper shows also an evaluation of the air quality in the main area of the buildings based on CFD predictions. It is shown that an interconnection between a CFD...
Computational Fluid Dynamics (CFD) simulations of a Heisenberg Vortex Tube
Bunge, Carl; Sitaraman, Hariswaran; Leachman, Jake
2017-11-01
A 3D Computational Fluid Dynamics (CFD) simulation of a Heisenberg Vortex Tube (HVT) is performed to estimate cooling potential with cryogenic hydrogen. The main mechanism driving operation of the vortex tube is the use of fluid power for enthalpy streaming in a highly turbulent swirl in a dual-outlet tube. This enthalpy streaming creates a temperature separation between the outer and inner regions of the flow. Use of a catalyst on the peripheral wall of the centrifuge enables endothermic conversion of para-ortho hydrogen to aid primary cooling. A κ- ɛ turbulence model is used with a cryogenic, non-ideal equation of state, and para-orthohydrogen species evolution. The simulations are validated with experiments and strategies for parametric optimization of this device are presented.
Modeling centrifugal cell washers using computational fluid dynamics.
Kellet, Beth E; Han, Binbing; Dandy, David S; Wickramasinghe, S Ranil
2004-11-01
Reinfusion of shed blood during surgery could avoid the need for blood transfusions. Prior to reinfusion of the red blood cells, the shed blood must be washed in order to remove leukocytes, platelets, and other contaminants. Further, the hematocrit of the washed blood must be increased. The feasibility of using computational fluid dynamics (CFD) to guide the design of better centrifuges for processing shed blood is explored here. The velocity field within a centrifuge bowl and the rate of protein removal from the shed blood has been studied. The results obtained indicate that CFD could help screen preliminary centrifuge bowl designs, thus reducing the number of initial experimental tests required when developing new centrifuge bowls. Although the focus of this work is on washing shed blood, the methods developed here are applicable to the design of centrifuge bowls for other blood-processing applications.
Improving coal flotation recovery using computational fluid dynamics
Energy Technology Data Exchange (ETDEWEB)
Peter Koh [CSIRO Minerals (Australia)
2009-06-15
This work involves using the latest advances in computational fluid dynamics (CFD) to increase understanding of the hydrodynamics in coal flotation and to identify any opportunities to improve design and operation of both the Microcel column and Jameson cell. The CSIRO CFD model incorporates micro-processes from cell hydrodynamics that affect particle-bubble attachments and detachments. CFD simulation results include the liquid velocities, turbulent dissipation rates, gas hold-up, particle-bubble attachment rates and detachment rates. This work has demonstrated that CFD modelling is a cost effective means of developing an understanding of particle-bubble attachments and detachments, and can be used to identify and test potential cell or process modifications.
Simulation of Tailrace Hydrodynamics Using Computational Fluid Dynamics Models
Energy Technology Data Exchange (ETDEWEB)
Cook, Christopher B.; Richmond, Marshall C.
2001-05-01
This report investigates the feasibility of using computational fluid dynamics (CFD) tools to investigate hydrodynamic flow fields surrounding the tailrace zone below large hydraulic structures. Previous and ongoing studies using CFD tools to simulate gradually varied flow with multiple constituents and forebay/intake hydrodynamics have shown that CFD tools can provide valuable information for hydraulic and biological evaluation of fish passage near hydraulic structures. These studies however are incapable of simulating the rapidly varying flow fields that involving breakup of the free-surface, such as those through and below high flow outfalls and spillways. Although the use of CFD tools for these types of flow are still an active area of research, initial applications discussed in this report show that these tools are capable of simulating the primary features of these highly transient flow fields.
Qweak Data Analysis for Target Modeling Using Computational Fluid Dynamics
Moore, Michael; Covrig, Silviu
2015-04-01
The 2.5 kW liquid hydrogen (LH2) target used in the Qweak parity violation experiment is the highest power LH2 target in the world and the first to be designed with Computational Fluid Dynamics (CFD) at Jefferson Lab. The Qweak experiment determined the weak charge of the proton by measuring the parity-violating elastic scattering asymmetry of longitudinally polarized electrons from unpolarized liquid hydrogen at small momentum transfer (Q2 = 0 . 025 GeV2). This target met the design goals of bench-marked with the Qweak target data. This work is an essential ingredient in future designs of very high power low noise targets like MOLLER (5 kW, target noise asymmetry contribution < 25 ppm) and MESA (4.5 kW).
Computational Fluid Dynamics Analysis of an Evaporative Cooling System
Directory of Open Access Journals (Sweden)
Kapilan N.
2016-11-01
Full Text Available The use of chlorofluorocarbon based refrigerants in the air-conditioning system increases the global warming and causes the climate change. The climate change is expected to present a number of challenges for the built environment and an evaporative cooling system is one of the simplest and environmentally friendly cooling system. The evaporative cooling system is most widely used in summer and in rural and urban areas of India for human comfort. In evaporative cooling system, the addition of water into air reduces the temperature of the air as the energy needed to evaporate the water is taken from the air. Computational fluid dynamics is a numerical analysis and was used to analyse the evaporative cooling system. The CFD results are matches with the experimental results.
Lightweight computational steering of very large scale molecular dynamics simulations
International Nuclear Information System (INIS)
Beazley, D.M.
1996-01-01
We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages
Uncertainty quantification in computational fluid dynamics and aircraft engines
Montomoli, Francesco; D'Ammaro, Antonio; Massini, Michela; Salvadori, Simone
2015-01-01
This book introduces novel design techniques developed to increase the safety of aircraft engines. The authors demonstrate how the application of uncertainty methods can overcome problems in the accurate prediction of engine lift, caused by manufacturing error. This in turn ameliorates the difficulty of achieving required safety margins imposed by limits in current design and manufacturing methods. This text shows that even state-of-the-art computational fluid dynamics (CFD) are not able to predict the same performance measured in experiments; CFD methods assume idealised geometries but ideal geometries do not exist, cannot be manufactured and their performance differs from real-world ones. By applying geometrical variations of a few microns, the agreement with experiments improves dramatically, but unfortunately the manufacturing errors in engines or in experiments are unknown. In order to overcome this limitation, uncertainty quantification considers the probability density functions of manufacturing errors...
Simulating Smoke Filling in Big Halls by Computational Fluid Dynamics
Directory of Open Access Journals (Sweden)
W. K. Chow
2011-01-01
Full Text Available Many tall halls of big space volume were built and, to be built in many construction projects in the Far East, particularly Mainland China, Hong Kong, and Taiwan. Smoke is identified to be the key hazard to handle. Consequently, smoke exhaust systems are specified in the fire code in those areas. An update on applying Computational Fluid Dynamics (CFD in smoke exhaust design will be presented in this paper. Key points to note in CFD simulations on smoke filling due to a fire in a big hall will be discussed. Mathematical aspects concerning of discretization of partial differential equations and algorithms for solving the velocity-pressure linked equations are briefly outlined. Results predicted by CFD with different free boundary conditions are compared with those on room fire tests. Standards on grid size, relaxation factors, convergence criteria, and false diffusion should be set up for numerical experiments with CFD.
FAST - A multiprocessed environment for visualization of computational fluid dynamics
International Nuclear Information System (INIS)
Bancroft, G.V.; Merritt, F.J.; Plessel, T.C.; Kelaita, P.G.; Mccabe, R.K.
1991-01-01
The paper presents the Flow Analysis Software Toolset (FAST) to be used for fluid-mechanics analysis. The design criteria for FAST including the minimization of the data path in the computational fluid-dynamics (CFD) process, consistent user interface, extensible software architecture, modularization, and the isolation of three-dimensional tasks from the application programmer are outlined. Each separate process communicates through the FAST Hub, while other modules such as FAST Central, NAS file input, CFD calculator, surface extractor and renderer, titler, tracer, and isolev might work together to generate the scene. An interprocess communication package making it possible for FAST to operate as a modular environment where resources could be shared among different machines as well as a single host is discussed. 20 refs
Computational Fluid Dynamics of Choanoflagellate Filter-Feeding
Asadzadeh, Seyed Saeed; Walther, Jens; Nielsen, Lasse Tore; Kiorboe, Thomas; Dolger, Julia; Andersen, Anders
2017-11-01
Choanoflagellates are unicellular aquatic organisms with a single flagellum that drives a feeding current through a funnel-shaped collar filter on which bacteria-sized prey are caught. Using computational fluid dynamics (CFD) we model the beating flagellum and the complex filter flow of the choanoflagellate Diaphanoeca grandis. Our CFD simulations based on the current understanding of the morphology underestimate the experimentally observed clearance rate by more than an order of magnitude: The beating flagellum is simply unable to draw enough water through the fine filter. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), and addition of a wide vane in our CFD model allows us to correctly predict the observed clearance rate.
Mapping flow distortion on oceanographic platforms using computational fluid dynamics
Directory of Open Access Journals (Sweden)
N. O'Sullivan
2013-10-01
Full Text Available Wind speed measurements over the ocean on ships or buoys are affected by flow distortion from the platform and by the anemometer itself. This can lead to errors in direct measurements and the derived parametrisations. Here we computational fluid dynamics (CFD to simulate the errors in wind speed measurements caused by flow distortion on the RV Celtic Explorer. Numerical measurements were obtained from the finite-volume CFD code OpenFOAM, which was used to simulate the velocity fields. This was done over a range of orientations in the test domain from −60 to +60° in increments of 10°. The simulation was also set up for a range of velocities, ranging from 5 to 25 m s−1 in increments of 0.5 m s−1. The numerical analysis showed close agreement to experimental measurements.
Helicopter fuselage drag - combined computational fluid dynamics and experimental studies
Batrakov, A.; Kusyumov, A.; Mikhailov, S.; Pakhov, V.; Sungatullin, A.; Valeev, M.; Zherekhov, V.; Barakos, G.
2015-06-01
In this paper, wind tunnel experiments are combined with Computational Fluid Dynamics (CFD) aiming to analyze the aerodynamics of realistic fuselage configurations. A development model of the ANSAT aircraft and an early model of the AKTAI light helicopter were employed. Both models were tested at the subsonic wind tunnel of KNRTU-KAI for a range of Reynolds numbers and pitch and yaw angles. The force balance measurements were complemented by particle image velocimetry (PIV) investigations for the cases where the experimental force measurements showed substantial unsteadiness. The CFD results were found to be in fair agreement with the test data and revealed some flow separation at the rear of the fuselages. Once confidence on the CFD method was established, further modifications were introduced to the ANSAT-like fuselage model to demonstrate drag reduction via small shape changes.
A Dynamic Bayesian Approach to Computational Laban Shape Quality Analysis
Directory of Open Access Journals (Sweden)
Dilip Swaminathan
2009-01-01
kinesiology. LMA (especially Effort/Shape emphasizes how internal feelings and intentions govern the patterning of movement throughout the whole body. As we argue, a complex understanding of intention via LMA is necessary for human-computer interaction to become embodied in ways that resemble interaction in the physical world. We thus introduce a novel, flexible Bayesian fusion approach for identifying LMA Shape qualities from raw motion capture data in real time. The method uses a dynamic Bayesian network (DBN to fuse movement features across the body and across time and as we discuss can be readily adapted for low-cost video. It has delivered excellent performance in preliminary studies comprising improvisatory movements. Our approach has been incorporated in Response, a mixed-reality environment where users interact via natural, full-body human movement and enhance their bodily-kinesthetic awareness through immersive sound and light feedback, with applications to kinesiology training, Parkinson's patient rehabilitation, interactive dance, and many other areas.
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.
Moving finite elements: A continuously adaptive method for computational fluid dynamics
International Nuclear Information System (INIS)
Glasser, A.H.; Miller, K.; Carlson, N.
1991-01-01
Moving Finite Elements (MFE), a recently developed method for computational fluid dynamics, promises major advances in the ability of computers to model the complex behavior of liquids, gases, and plasmas. Applications of computational fluid dynamics occur in a wide range of scientifically and technologically important fields. Examples include meteorology, oceanography, global climate modeling, magnetic and inertial fusion energy research, semiconductor fabrication, biophysics, automobile and aircraft design, industrial fluid processing, chemical engineering, and combustion research. The improvements made possible by the new method could thus have substantial economic impact. Moving Finite Elements is a moving node adaptive grid method which has a tendency to pack the grid finely in regions where it is most needed at each time and to leave it coarse elsewhere. It does so in a manner which is simple and automatic, and does not require a large amount of human ingenuity to apply it to each particular problem. At the same time, it often allows the time step to be large enough to advance a moving shock by many shock thicknesses in a single time step, moving the grid smoothly with the solution and minimizing the number of time steps required for the whole problem. For 2D problems (two spatial variables) the grid is composed of irregularly shaped and irregularly connected triangles which are very flexible in their ability to adapt to the evolving solution. While other adaptive grid methods have been developed which share some of these desirable properties, this is the only method which combines them all. In many cases, the method can save orders of magnitude of computing time, equivalent to several generations of advancing computer hardware
Unsteady computational fluid dynamics in front crawl swimming.
Samson, Mathias; Bernard, Anthony; Monnet, Tony; Lacouture, Patrick; David, Laurent
2017-05-01
The development of codes and power calculations currently allows the simulation of increasingly complex flows, especially in the turbulent regime. Swimming research should benefit from these technological advances to try to better understand the dynamic mechanisms involved in swimming. An unsteady Computational Fluid Dynamics (CFD) study is conducted in crawl, in order to analyse the propulsive forces generated by the hand and forearm. The k-ω SST turbulence model and an overset grid method have been used. The main objectives are to analyse the evolution of the hand-forearm propulsive forces and to explain this relative to the arm kinematics parameters. In order to validate our simulation model, the calculated forces and pressures were compared with several other experimental and numerical studies. A good agreement is found between our results and those of other studies. The hand is the segment that generates the most propulsive forces during the aquatic stroke. As the pressure component is the main source of force, the orientation of the hand-forearm in the absolute coordinate system is an important kinematic parameter in the swimming performance. The propulsive forces are biggest when the angles of attack are high. CFD appears as a very valuable tool to better analyze the mechanisms of swimming performance and offers some promising developments, especially for optimizing the performance from a parametric study.
Efficient Parallel Kernel Solvers for Computational Fluid Dynamics Applications
Sun, Xian-He
1997-01-01
Distributed-memory parallel computers dominate today's parallel computing arena. These machines, such as Intel Paragon, IBM SP2, and Cray Origin2OO, have successfully delivered high performance computing power for solving some of the so-called "grand-challenge" problems. Despite initial success, parallel machines have not been widely accepted in production engineering environments due to the complexity of parallel programming. On a parallel computing system, a task has to be partitioned and distributed appropriately among processors to reduce communication cost and to attain load balance. More importantly, even with careful partitioning and mapping, the performance of an algorithm may still be unsatisfactory, since conventional sequential algorithms may be serial in nature and may not be implemented efficiently on parallel machines. In many cases, new algorithms have to be introduced to increase parallel performance. In order to achieve optimal performance, in addition to partitioning and mapping, a careful performance study should be conducted for a given application to find a good algorithm-machine combination. This process, however, is usually painful and elusive. The goal of this project is to design and develop efficient parallel algorithms for highly accurate Computational Fluid Dynamics (CFD) simulations and other engineering applications. The work plan is 1) developing highly accurate parallel numerical algorithms, 2) conduct preliminary testing to verify the effectiveness and potential of these algorithms, 3) incorporate newly developed algorithms into actual simulation packages. The work plan has well achieved. Two highly accurate, efficient Poisson solvers have been developed and tested based on two different approaches: (1) Adopting a mathematical geometry which has a better capacity to describe the fluid, (2) Using compact scheme to gain high order accuracy in numerical discretization. The previously developed Parallel Diagonal Dominant (PDD) algorithm
Class of reconstructed discontinuous Galerkin methods in computational fluid dynamics
International Nuclear Information System (INIS)
Luo, Hong; Xia, Yidong; Nourgaliev, Robert
2011-01-01
A class of reconstructed discontinuous Galerkin (DG) methods is presented to solve compressible flow problems on arbitrary grids. The idea is to combine the efficiency of the reconstruction methods in finite volume methods and the accuracy of the DG methods to obtain a better numerical algorithm in computational fluid dynamics. The beauty of the resulting reconstructed discontinuous Galerkin (RDG) methods is that they provide a unified formulation for both finite volume and DG methods, and contain both classical finite volume and standard DG methods as two special cases of the RDG methods, and thus allow for a direct efficiency comparison. Both Green-Gauss and least-squares reconstruction methods and a least-squares recovery method are presented to obtain a quadratic polynomial representation of the underlying linear discontinuous Galerkin solution on each cell via a so-called in-cell reconstruction process. The devised in-cell reconstruction is aimed to augment the accuracy of the discontinuous Galerkin method by increasing the order of the underlying polynomial solution. These three reconstructed discontinuous Galerkin methods are used to compute a variety of compressible flow problems on arbitrary meshes to assess their accuracy. The numerical experiments demonstrate that all three reconstructed discontinuous Galerkin methods can significantly improve the accuracy of the underlying second-order DG method, although the least-squares reconstructed DG method provides the best performance in terms of both accuracy, efficiency, and robustness. (author)
Algorithms for computational fluid dynamics n parallel processors
International Nuclear Information System (INIS)
Van de Velde, E.F.
1986-01-01
A study of parallel algorithms for the numerical solution of partial differential equations arising in computational fluid dynamics is presented. The actual implementation on parallel processors of shared and nonshared memory design is discussed. The performance of these algorithms is analyzed in terms of machine efficiency, communication time, bottlenecks and software development costs. For elliptic equations, a parallel preconditioned conjugate gradient method is described, which has been used to solve pressure equations discretized with high order finite elements on irregular grids. A parallel full multigrid method and a parallel fast Poisson solver are also presented. Hyperbolic conservation laws were discretized with parallel versions of finite difference methods like the Lax-Wendroff scheme and with the Random Choice method. Techniques are developed for comparing the behavior of an algorithm on different architectures as a function of problem size and local computational effort. Effective use of these advanced architecture machines requires the use of machine dependent programming. It is shown that the portability problems can be minimized by introducing high level operations on vectors and matrices structured into program libraries
Benchmarking Computational Fluid Dynamics for Application to PWR Fuel
International Nuclear Information System (INIS)
Smith, L.D. III; Conner, M.E.; Liu, B.; Dzodzo, B.; Paramonov, D.V.; Beasley, D.E.; Langford, H.M.; Holloway, M.V.
2002-01-01
The present study demonstrates a process used to develop confidence in Computational Fluid Dynamics (CFD) as a tool to investigate flow and temperature distributions in a PWR fuel bundle. The velocity and temperature fields produced by a mixing spacer grid of a PWR fuel assembly are quite complex. Before using CFD to evaluate these flow fields, a rigorous benchmarking effort should be performed to ensure that reasonable results are obtained. Westinghouse has developed a method to quantitatively benchmark CFD tools against data at conditions representative of the PWR. Several measurements in a 5 x 5 rod bundle were performed. Lateral flow-field testing employed visualization techniques and Particle Image Velocimetry (PIV). Heat transfer testing involved measurements of the single-phase heat transfer coefficient downstream of the spacer grid. These test results were used to compare with CFD predictions. Among the parameters optimized in the CFD models based on this comparison with data include computational mesh, turbulence model, and boundary conditions. As an outcome of this effort, a methodology was developed for CFD modeling that provides confidence in the numerical results. (authors)
Computer simulations of liquid crystals: Defects, deformations and dynamics
Billeter, Jeffrey Lee
1999-11-01
Computer simulations play an increasingly important role in investigating fundamental issues in the physics of liquid crystals. Presented here are the results of three projects which utilize the unique power of simulations to probe questions which neither theory nor experiment can adequately answer. Throughout, we use the (generalized) Gay-Berne model, a widely-used phenomenological potential which captures the essential features of the anisotropic mesogen shapes and interactions. First, we used a Molecular Dynamics simulation with 65536 Gay-Berne particles to study the behaviors of topological defects in a quench from the isotropic to the nematic phase. Twist disclination loops were the dominant defects, and we saw evidence for dynamical scaling. We observed the loops separating, combining and collapsing, and we also observed numerous non-singular type-1 lines which appeared to be intimately involved with many of the loop processes. Second, we used a Molecular Dynamics simulation of a sphere embedded in a system of 2048 Gay-Berne particles to study the effects of radial anchoring of the molecules at the sphere's surface. A saturn ring defect configuration was observed, and the ring caused a driven sphere (modelling the falling ball experiment) to experience an increased resistance as it moved through the nematic. Deviations from a linear relationship between the driving force and the terminal speed are attributed to distortions of the saturn ring which we observed. The existence of the saturn ring confirms theoretical predictions for small spheres. Finally, we constructed a model for wedge-shaped molecules and used a linear response approach in a Monte Carlo simulation to investigate the flexoelectric behavior of a system of 256 such wedges. Novel potential models as well as novel analytical and visualization techniques were developed for these projects. Once again, the emphasis throughout was to investigate questions which simulations alone can adequately answer.
Evaluation of intracerebral hematoma resorption dynamics with computed tomography
International Nuclear Information System (INIS)
Strzesniewski, P.; Lasek, W.; Serafin, Z.; Ksiazkiewicz, B.; Wanat-Slupska, E.
2004-01-01
High mortality and severe grade of disability observed in patients after intracerebral hemorrhage provide efforts to improve diagnostics and therapy of the hemorrhagic cerebral stroke. An aim of this paper was an evaluation of blood resorption dynamics in patients with intracerebral hematoma, performed with computed tomography of the head and an analysis of clinical significance of this process. An examined group included 133 patients with intracerebral hematoma proven by a CT exam. In 97 patients resorption of the hematoma was measured, based on control scans taken on 15 th and 30 th day on average. Volume of the hemorrhagic foci was measured as well as the width of ventricles and the displacement of medial structures. The mean hematoma volume reached 11,59 ml after 15 days, and 3,16 m after 30 days (average decrease of the volume 0,67 ml/day). There was a significant difference in the rate of resorption between the first (0-15 days) and the second (15-30 days) observation period - 0,78 and 0,62 ml/day respectively. The dynamics of the process was dependent on volume and localization of the hematoma and independent of the grade of displacement and compression of the ventricles. The calculated mean rate of the hematomas resorption enables to schedule control examinations precisely. The significant differences of the dynamics of blood resorption depending on hematomas size and the independence of compression and displacement of ventricular system suggest, that the most important factor in therapeutic decision-making should be a clinical status of the patient. (author)
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.
International Nuclear Information System (INIS)
Lv Chen; Wang Xiaojing; Agalya, Govindasamy; Koyama, Michihisa; Kubo, Momoji; Miyamoto, Akira
2005-01-01
The clarification of the excited states dynamics on TiO 2 surface is important subject for the design of the highly active photocatalysts. In the present study, we applied our novel tight-binding quantum chemical molecular dynamics method to the investigation on the photocatalytic oxidation dynamics of acetone by photogenerated OH radicals on the hydrated anatase TiO 2 surface. The elucidated photocatalytic reaction mechanism strongly supports the previous experimental proposal and finally the effectiveness of our new approach for the clarification of the photocatalytic reaction dynamics employing the large simulation model was confirmed
Ma, Zhanshan (Sam)
In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three
1975-12-01
Frequency domain computer programs developed or acquired by TSC for the analysis of rail vehicle dynamics are described in two volumes. Volume I defines the general analytical capabilities required for computer programs applicable to single rail vehi...
An Automated High Aspect Ratio Mesher for Computational Fluid Dynamics, Phase II
National Aeronautics and Space Administration — Computational fluid dynamics (CFD) simulations are routinely used while designing, analyzing, and optimizing air- and spacecraft. An important component of CFD...
National Research Council Canada - National Science Library
Faragher, John
2004-01-01
... conservatism to allow for them. This report examines the feasibility of using a probabilistic approach for modelling the component temperatures in an engine using CFD (Computational Fluid Dynamics).
Novel scheme to compute chemical potentials of chain molecules on a lattice
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.
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.
Evidence for Dynamic Chemical Kinetics at Individual Molecular Ruthenium Catalysts.
Easter, Quinn T; Blum, Suzanne A
2018-02-05
Catalytic cycles are typically depicted as possessing time-invariant steps with fixed rates. Yet the true behavior of individual catalysts with respect to time is unknown, hidden by the ensemble averaging inherent to bulk measurements. Evidence is presented for variable chemical kinetics at individual catalysts, with a focus on ring-opening metathesis polymerization catalyzed by the second-generation Grubbs' ruthenium catalyst. Fluorescence microscopy is used to probe the chemical kinetics of the reaction because the technique possesses sufficient sensitivity for the detection of single chemical reactions. Insertion reactions in submicron regions likely occur at groups of many (not single) catalysts, yet not so many that their unique kinetic behavior is ensemble averaged. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment
Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.
2008-01-01
A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…
Some Matrix Iterations for Computing Generalized Inverses and Balancing Chemical Equations
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 ...
Design of multi-phase dynamic chemical networks
Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.
2017-08-01
Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.
Computational fluid dynamic modeling of fluidized-bed polymerization reactors
Energy Technology Data Exchange (ETDEWEB)
Rokkam, Ram [Iowa State Univ., Ames, IA (United States)
2012-01-01
Polyethylene is one of the most widely used plastics, and over 60 million tons are produced worldwide every year. Polyethylene is obtained by the catalytic polymerization of ethylene in gas and liquid phase reactors. The gas phase processes are more advantageous, and use fluidized-bed reactors for production of polyethylene. Since they operate so close to the melting point of the polymer, agglomeration is an operational concern in all slurry and gas polymerization processes. Electrostatics and hot spot formation are the main factors that contribute to agglomeration in gas-phase processes. Electrostatic charges in gas phase polymerization fluidized bed reactors are known to influence the bed hydrodynamics, particle elutriation, bubble size, bubble shape etc. Accumulation of electrostatic charges in the fluidized-bed can lead to operational issues. In this work a first-principles electrostatic model is developed and coupled with a multi-fluid computational fluid dynamic (CFD) model to understand the effect of electrostatics on the dynamics of a fluidized-bed. The multi-fluid CFD model for gas-particle flow is based on the kinetic theory of granular flows closures. The electrostatic model is developed based on a fixed, size-dependent charge for each type of particle (catalyst, polymer, polymer fines) phase. The combined CFD model is first verified using simple test cases, validated with experiments and applied to a pilot-scale polymerization fluidized-bed reactor. The CFD model reproduced qualitative trends in particle segregation and entrainment due to electrostatic charges observed in experiments. For the scale up of fluidized bed reactor, filtered models are developed and implemented on pilot scale reactor.
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...
Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.
2005-01-01
A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-08
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.
International Nuclear Information System (INIS)
Zhou, Chenn
2008-01-01
Pulverized coal injection (PCI) into the blast furnace (BF) has been recognized as an effective way to decrease the coke and total energy consumption along with minimization of environmental impacts. However, increasing the amount of coal injected into the BF is currently limited by the lack of knowledge of some issues related to the process. It is therefore important to understand the complex physical and chemical phenomena in the PCI process. Due to the difficulty in attaining trus BF measurements, Computational fluid dynamics (CFD) modeling has been identified as a useful technology to provide such knowledge. CFD simulation is powerful for providing detailed information on flow properties and performing parametric studies for process design and optimization. In this project, comprehensive 3-D CFD models have been developed to simulate the PCI process under actual furnace conditions. These models provide raceway size and flow property distributions. The results have provided guidance for optimizing the PCI process
Computed Potential Energy Surfaces and Minimum Energy Pathway for Chemical Reactions
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.
Design of airborne wind turbine and computational fluid dynamics analysis
Anbreen, Faiqa
Wind energy is a promising alternative to the depleting non-renewable sources. The height of the wind turbines becomes a constraint to their efficiency. Airborne wind turbine can reach much higher altitudes and produce higher power due to high wind velocity and energy density. The focus of this thesis is to design a shrouded airborne wind turbine, capable to generate 70 kW to propel a leisure boat with a capacity of 8-10 passengers. The idea of designing an airborne turbine is to take the advantage of higher velocities in the atmosphere. The Solidworks model has been analyzed numerically using Computational Fluid Dynamics (CFD) software StarCCM+. The Unsteady Reynolds Averaged Navier Stokes Simulation (URANS) with K-epsilon turbulence model has been selected, to study the physical properties of the flow, with emphasis on the performance of the turbine and the increase in air velocity at the throat. The analysis has been done using two ambient velocities of 12 m/s and 6 m/s. At 12 m/s inlet velocity, the velocity of air at the turbine has been recorded as 16 m/s. The power generated by the turbine is 61 kW. At inlet velocity of 6 m/s, the velocity of air at turbine increased to 10 m/s. The power generated by turbine is 25 kW.
Dynamic computed tomography for the evaluation of cerebrovascular disease
Energy Technology Data Exchange (ETDEWEB)
Terada, Tomoaki; Nishiguchi, Takashi; Hyotani, Genhachi; Miyamoto, Kazuki; Hayashi, Seiji; Komai, Norihiko [Wakayama Medical Coll. (Japan); Nakamura, Yoshinari; Moriwaki, Hiroshi
1991-10-01
Dynamic computed tomography (DCT) was evaluated as a diagnostic indicator for chronic supratentorial ischemia in 50 cases with or without minor neurological deficits. Peak height (PH, the maximum value of the gamma fitted curve), peak time (PT, the time to PH from the start of DCT), transit time (TT, the time between the first and second inflection points of the gamma fitted curve), and their functional maps were analyzed. Cerebral angiography was then performed in all cases to identify stenotic or occlusive vascular lesions in major cerebral arteries. DCT clearly detected 12 of 13 occlusions of the internal carotid artery (ICA) or middle cerebral artery (MCA), although one ICA occlusion was masked by the contralateral MCA occlusion. However, DCT detected only severe ICA or MCA stenosis (more than 90%). Probably, stenotic lesions of less than 90% did not cause detectable hemodynamic compromise. DCT using PH, PT, and TT functional maps is a useful diagnostic method for hemodynamic changes in ischemic cerebrovascular disease, althogh bilateral lesions and less stenotic lesions (<90%) are difficult to detect. (author).
Improving flow distribution in influent channels using computational fluid dynamics.
Park, No-Suk; Yoon, Sukmin; Jeong, Woochang; Lee, Seungjae
2016-10-01
Although the flow distribution in an influent channel where the inflow is split into each treatment process in a wastewater treatment plant greatly affects the efficiency of the process, and a weir is the typical structure for the flow distribution, to the authors' knowledge, there is a paucity of research on the flow distribution in an open channel with a weir. In this study, the influent channel of a real-scale wastewater treatment plant was used, installing a suppressed rectangular weir that has a horizontal crest to cross the full channel width. The flow distribution in the influent channel was analyzed using a validated computational fluid dynamics model to investigate (1) the comparison of single-phase and two-phase simulation, (2) the improved procedure of the prototype channel, and (3) the effect of the inflow rate on flow distribution. The results show that two-phase simulation is more reliable due to the description of the free-surface fluctuations. It should first be considered for improving flow distribution to prevent a short-circuit flow, and the difference in the kinetic energy with the inflow rate makes flow distribution trends different. The authors believe that this case study is helpful for improving flow distribution in an influent channel.
Introducing Computational Fluid Dynamics Simulation into Olfactory Display
Ishida, Hiroshi; Yoshida, Hitoshi; Nakamoto, Takamichi
An olfactory display is a device that delivers various odors to the user's nose. It can be used to add special effects to movies and games by releasing odors relevant to the scenes shown on the screen. In order to provide high-presence olfactory stimuli to the users, the display must be able to generate realistic odors with appropriate concentrations in a timely manner together with visual and audio playbacks. In this paper, we propose to use computational fluid dynamics (CFD) simulations in conjunction with the olfactory display. Odor molecules released from their source are transported mainly by turbulent flow, and their behavior can be extremely complicated even in a simple indoor environment. In the proposed system, a CFD solver is employed to calculate the airflow field and the odor dispersal in the given environment. An odor blender is used to generate the odor with the concentration determined based on the calculated odor distribution. Experimental results on presenting odor stimuli synchronously with movie clips show the effectiveness of the proposed system.
Computational fluid dynamics (CFD) studies of a miniaturized dissolution system.
Frenning, G; Ahnfelt, E; Sjögren, E; Lennernäs, H
2017-04-15
Dissolution testing is an important tool that has applications ranging from fundamental studies of drug-release mechanisms to quality control of the final product. The rate of release of the drug from the delivery system is known to be affected by hydrodynamics. In this study we used computational fluid dynamics to simulate and investigate the hydrodynamics in a novel miniaturized dissolution method for parenteral formulations. The dissolution method is based on a rotating disc system and uses a rotating sample reservoir which is separated from the remaining dissolution medium by a nylon screen. Sample reservoirs of two sizes were investigated (SR6 and SR8) and the hydrodynamic studies were performed at rotation rates of 100, 200 and 400rpm. The overall fluid flow was similar for all investigated cases, with a lateral upward spiraling motion and central downward motion in the form of a vortex to and through the screen. The simulations indicated that the exchange of dissolution medium between the sample reservoir and the remaining release medium was rapid for typical screens, for which almost complete mixing would be expected to occur within less than one minute at 400rpm. The local hydrodynamic conditions in the sample reservoirs depended on their size; SR8 appeared to be relatively more affected than SR6 by the resistance to liquid flow resulting from the screen. Copyright © 2017 Elsevier B.V. All rights reserved.
Computational studies of beam dynamics in the ETA gun
International Nuclear Information System (INIS)
Paul, A.C.; Neil, V.K.
1979-03-01
A new general purpose computer code call EBQ, has been written to simulate the beam dynamics of the ETA, find its beam emittance and evaluate effects of changes in the electrode positions and external magnetic fields. The original calculations of the ETA were made with EGUN and yielded considerable insight into the operation of the device in the non-relativistic regime. The EBQ code was written specifically to attend to the special problems associated with high current relativistic beam propagation in axially symmetric machines possessing external 2-dimensional electric and magnetic fields. The coherent electric and magnetic self-fields of the beam must be calculated accurately. Special care has been used in the relativistic regime where a high degree of cancellation occurs between the self-magnetic and self electric forces of the beam. Additionally, EBQ can handle equally well non-relativistic problems involving multiple ion species where the space charge from each must be included in its mutual effect on the others. Such problems arise in the design of ion sources where different charge and mass states are present
Computational fluid dynamics for turbomachinery internal air systems.
Chew, John W; Hills, Nicholas J
2007-10-15
Considerable progress in development and application of computational fluid dynamics (CFD) for aeroengine internal flow systems has been made in recent years. CFD is regularly used in industry for assessment of air systems, and the performance of CFD for basic axisymmetric rotor/rotor and stator/rotor disc cavities with radial throughflow is largely understood and documented. Incorporation of three-dimensional geometrical features and calculation of unsteady flows are becoming commonplace. Automation of CFD, coupling with thermal models of the solid components, and extension of CFD models to include both air system and main gas path flows are current areas of development. CFD is also being used as a research tool to investigate a number of flow phenomena that are not yet fully understood. These include buoyancy-affected flows in rotating cavities, rim seal flows and mixed air/oil flows. Large eddy simulation has shown considerable promise for the buoyancy-driven flows and its use for air system flows is expected to expand in the future.
Computational Fluid Dynamics Analysis of Flexible Duct Junction Box Design
Energy Technology Data Exchange (ETDEWEB)
Beach, Robert [IBACOS Inc., Pittsburgh, PA (United States); Prahl, Duncan [IBACOS Inc., Pittsburgh, PA (United States); Lange, Rich [IBACOS Inc., Pittsburgh, PA (United States)
2013-12-01
IBACOS explored the relationships between pressure and physical configurations of flexible duct junction boxes by using computational fluid dynamics (CFD) simulations to predict individual box parameters and total system pressure, thereby ensuring improved HVAC performance. Current Air Conditioning Contractors of America (ACCA) guidance (Group 11, Appendix 3, ACCA Manual D, Rutkowski 2009) allows for unconstrained variation in the number of takeoffs, box sizes, and takeoff locations. The only variables currently used in selecting an equivalent length (EL) are velocity of air in the duct and friction rate, given the first takeoff is located at least twice its diameter away from the inlet. This condition does not account for other factors impacting pressure loss across these types of fittings. For each simulation, the IBACOS team converted pressure loss within a box to an EL to compare variation in ACCA Manual D guidance to the simulated variation. IBACOS chose cases to represent flows reasonably correlating to flows typically encountered in the field and analyzed differences in total pressure due to increases in number and location of takeoffs, box dimensions, and velocity of air, and whether an entrance fitting is included. The team also calculated additional balancing losses for all cases due to discrepancies between intended outlet flows and natural flow splits created by the fitting. In certain asymmetrical cases, the balancing losses were significantly higher than symmetrical cases where the natural splits were close to the targets. Thus, IBACOS has shown additional design constraints that can ensure better system performance.
Incorporating Computer-Aided Software in the Undergraduate Chemical Engineering Core Courses
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…
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...
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...
International Nuclear Information System (INIS)
Adamatzky, Andrew; Lacy Costello, Benjamin de
2003-01-01
A reaction-diffusion chemical computer in this context is a planar uniform chemical reactor, where data and results of a computation are represented by concentration profiles of reactants and the computation itself is implemented via the spreading and interaction of diffusive and phase waves. This class of chemical computers are efficient at solving problems with a 'natural' parallelism where data sets are decomposable onto a large number of geographically neighboring domains which are then processed in parallel. Typical problems of this type include image processing, geometrical transformations and optimisation. When chemical based devices are used to solve such problems questions regarding their reproducible, efficiency and the accuracy of their computations arise. In addition to these questions what are the limitations of reaction-diffusion chemical processors--what type of problems cannot currently and are unlikely ever to be solved? To answer the questions we study how a Voronoi diagram is constructed and how it is inverted in a planar chemical processor. We demonstrate that a Voronoi diagram is computed only partially in the chemical processor. We also prove that given a specific Voronoi diagram it is impossible to reconstruct the planar set (from which diagram was computed) in the reaction-diffusion chemical processor. In the Letter we open the first ever line of enquiry into the computational inability of reaction-diffusion chemical computers
Computational Methods to Assess the Production Potential of Bio-Based Chemicals.
Campodonico, Miguel A; Sukumara, Sumesh; Feist, Adam M; Herrgård, Markus J
2018-01-01
Elevated costs and long implementation times of bio-based processes for producing chemicals represent a bottleneck for moving to a bio-based economy. A prospective analysis able to elucidate economically and technically feasible product targets at early research phases is mandatory. Computational tools can be implemented to explore the biological and technical spectrum of feasibility, while constraining the operational space for desired chemicals. In this chapter, two different computational tools for assessing potential for bio-based production of chemicals from different perspectives 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.
Directory of Open Access Journals (Sweden)
Marquis Crose
2017-02-01
Full Text Available This work focuses on the development of a multiscale computational fluid dynamics (CFD simulation framework with application to plasma-enhanced chemical vapor deposition of thin film solar cells. A macroscopic, CFD model is proposed which is capable of accurately reproducing plasma chemistry and transport phenomena within a 2D axisymmetric reactor geometry. Additionally, the complex interactions that take place on the surface of a-Si:H thin films are coupled with the CFD simulation using a novel kinetic Monte Carlo scheme which describes the thin film growth, leading to a multiscale CFD model. Due to the significant computational challenges imposed by this multiscale CFD model, a parallel computation strategy is presented which allows for reduced processing time via the discretization of both the gas-phase mesh and microscopic thin film growth processes. Finally, the multiscale CFD model has been applied to the PECVD process at industrially relevant operating conditions revealing non-uniformities greater than 20% in the growth rate of amorphous silicon films across the radius of the wafer.
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...
ClassyFire: automated chemical classification with a comprehensive, computable taxonomy.
Djoumbou Feunang, Yannick; Eisner, Roman; Knox, Craig; Chepelev, Leonid; Hastings, Janna; Owen, Gareth; Fahy, Eoin; Steinbeck, Christoph; Subramanian, Shankar; Bolton, Evan; Greiner, Russell; Wishart, David S
2016-01-01
Scientists have long been driven by the desire to describe, organize, classify, and compare objects using taxonomies and/or ontologies. In contrast to biology, geology, and many other scientific disciplines, the world of chemistry still lacks a standardized chemical ontology or taxonomy. Several attempts at chemical classification have been made; but they have mostly been limited to either manual, or semi-automated proof-of-principle applications. This is regrettable as comprehensive chemical classification and description tools could not only improve our understanding of chemistry but also improve the linkage between chemistry and many other fields. For instance, the chemical classification of a compound could help predict its metabolic fate in humans, its druggability or potential hazards associated with it, among others. However, the sheer number (tens of millions of compounds) and complexity of chemical structures is such that any manual classification effort would prove to be near impossible. We have developed a comprehensive, flexible, and computable, purely structure-based chemical taxonomy (ChemOnt), along with a computer program (ClassyFire) that uses only chemical structures and structural features to automatically assign all known chemical compounds to a taxonomy consisting of >4800 different categories. This new chemical taxonomy consists of up to 11 different levels (Kingdom, SuperClass, Class, SubClass, etc.) with each of the categories defined by unambiguous, computable structural rules. Furthermore each category is named using a consensus-based nomenclature and described (in English) based on the characteristic common structural properties of the compounds it contains. The ClassyFire webserver is freely accessible at http://classyfire.wishartlab.com/. Moreover, a Ruby API version is available at https://bitbucket.org/wishartlab/classyfire_api, which provides programmatic access to the ClassyFire server and database. ClassyFire has been used to
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.
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...
Williams, R. W. (Compiler)
1996-01-01
The purpose of the workshop was to discuss experimental and computational fluid dynamic activities in rocket propulsion and launch vehicles. The workshop was an open meeting for government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.
Dynamics of the chemical composition of rainwater throughout Hurricane Irene
Directory of Open Access Journals (Sweden)
K. M. Mullaugh
2013-03-01
Full Text Available Sequential sampling of rainwater from Hurricane Irene was carried out in Wilmington, NC, USA on 26 and 27 August 2011. Eleven samples were analyzed for pH, major ions (Cl−, NO3−, SO42−, Na+, K+, Mg2+, Ca2+, NH4+, dissolved organic carbon (DOC and hydrogen peroxide (H2O2. Hurricane Irene contributed 16% of the total rainwater and 18% of the total chloride wet deposition received in Wilmington NC during all of 2011. This work highlights the main physical factors influencing the chemical composition of tropical storm rainwater: wind speed, wind direction, back trajectory and vertical mixing, time of day and total rain volume. Samples collected early in the storm, when winds blew out of the east, contained dissolved components indicative of marine sources (salts from sea spray and low DOC. The sea-salt components in the samples had two maxima in concentration during the storm the first of which occurred before the volume of rain had sufficiently washed out sea salt from the atmosphere and the second when back trajectories showed large volumes of marine surface air were lifted. As the storm progressed and winds shifted to a westerly direction, the chemical composition of the rainwater became characteristic of terrestrial storms (high DOC and NH4+ and low sea salt. This work demonstrates that tropical storms are not only responsible for significant wet deposition of marine components to land, but terrestrial components can also become entrained in rainwater, which can then be delivered to coastal waters via wet deposition. This study also underscores why analysis of one composite sample can lead to an incomplete interpretation of the factors that influence the chemically divergent analytes in rainwater during extreme weather events.
Time-resolved imaging of purely valence-electron dynamics during a chemical reaction
DEFF Research Database (Denmark)
Hockett, Paul; Bisgaard, Christer Z.; Clarkin, Owen J.
2011-01-01
Chemical reactions are manifestations of the dynamics of molecular valence electrons and their couplings to atomic motions. Emerging methods in attosecond science can probe purely electronic dynamics in atomic and molecular systems(1-6). By contrast, time-resolved structural-dynamics methods...... such as electron(7-10) or X-ray diffraction(11) and X-ray absorption(12) yield complementary information about the atomic motions. Time-resolved methods that are directly sensitive to both valence-electron dynamics and atomic motions include photoelectron spectroscopy(13-15) and high-harmonic generation(16......,17): in both cases, this sensitivity derives from the ionization-matrix element(18,19). Here we demonstrate a time-resolved molecular-frame photoelectron-angular-distribution (TRMFPAD) method for imaging the purely valence-electron dynamics during a chemical reaction. Specifically, the TRMFPADs measured during...
Computer Vision for the Solar Dynamics Observatory (SDO)
Martens, P. C. H.; Attrill, G. D. R.; Davey, A. R.; Engell, A.; Farid, S.; Grigis, P. C.; Kasper, J.; Korreck, K.; Saar, S. H.; Savcheva, A.; Su, Y.; Testa, P.; Wills-Davey, M.; Bernasconi, P. N.; Raouafi, N.-E.; Delouille, V. A.; Hochedez, J. F.; Cirtain, J. W.; Deforest, C. E.; Angryk, R. A.; de Moortel, I.; Wiegelmann, T.; Georgoulis, M. K.; McAteer, R. T. J.; Timmons, R. P.
2012-01-01
In Fall 2008 NASA selected a large international consortium to produce a comprehensive automated feature-recognition system for the Solar Dynamics Observatory (SDO). The SDO data that we consider are all of the Atmospheric Imaging Assembly (AIA) images plus surface magnetic-field images from the Helioseismic and Magnetic Imager (HMI). We produce robust, very efficient, professionally coded software modules that can keep up with the SDO data stream and detect, trace, and analyze numerous phenomena, including flares, sigmoids, filaments, coronal dimmings, polarity inversion lines, sunspots, X-ray bright points, active regions, coronal holes, EIT waves, coronal mass ejections (CMEs), coronal oscillations, and jets. We also track the emergence and evolution of magnetic elements down to the smallest detectable features and will provide at least four full-disk, nonlinear, force-free magnetic field extrapolations per day. The detection of CMEs and filaments is accomplished with Solar and Heliospheric Observatory (SOHO)/ Large Angle and Spectrometric Coronagraph (LASCO) and ground-based Hα data, respectively. A completely new software element is a trainable feature-detection module based on a generalized image-classification algorithm. Such a trainable module can be used to find features that have not yet been discovered (as, for example, sigmoids were in the pre- Yohkoh era). Our codes will produce entries in the Heliophysics Events Knowledgebase (HEK) as well as produce complete catalogs for results that are too numerous for inclusion in the HEK, such as the X-ray bright-point metadata. This will permit users to locate data on individual events as well as carry out statistical studies on large numbers of events, using the interface provided by the Virtual Solar Observatory. The operations concept for our computer vision system is that the data will be analyzed in near real time as soon as they arrive at the SDO Joint Science Operations Center and have undergone basic
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
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...
A full computation-relevant topological dynamics classification of elementary cellular automata.
Schüle, Martin; Stoop, Ruedi
2012-12-01
Cellular automata are both computational and dynamical systems. We give a complete classification of the dynamic behaviour of elementary cellular automata (ECA) in terms of fundamental dynamic system notions such as sensitivity and chaoticity. The "complex" ECA emerge to be sensitive, but not chaotic and not eventually weakly periodic. Based on this classification, we conjecture that elementary cellular automata capable of carrying out complex computations, such as needed for Turing-universality, are at the "edge of chaos."
Computational Fluid Dynamics Model for Saltstone Vault 4 Vapor Space
International Nuclear Information System (INIS)
Lee, Si Young
2005-01-01
Computational fluid dynamics (CFD) methods have been used to estimate the flow patterns for vapor space inside the Saltstone Vault No.4 under different operating scenarios. The purpose of this work is to examine the gas motions inside the vapor space under the current vault configurations. A CFD model took three-dimensional transient momentum-energy coupled approach for the vapor space domain of the vault. The modeling calculations were based on prototypic vault geometry and expected normal operating conditions as defined by Waste Solidification Engineering. The modeling analysis was focused on the air flow patterns near the ventilated corner zones of the vapor space inside the Saltstone vault. The turbulence behavior and natural convection mechanism used in the present model were benchmarked against the literature information and theoretical results. The verified model was applied to the Saltstone vault geometry for the transient assessment of the air flow patterns inside the vapor space of the vault region using the boundary conditions as provided by the customer. The present model considered two cases for the estimations of the flow patterns within the vapor space. One is the reference baseline case. The other is for the negative temperature gradient between the roof inner and top grout surface temperatures intended for the potential bounding condition. The flow patterns of the vapor space calculated by the CFD model demonstrate that the ambient air comes into the vapor space of the vault through the lower-end ventilation hole, and it gets heated up by the Benard-cell type circulation before leaving the vault via the higher-end ventilation hole. The calculated results are consistent with the literature information
Energy Technology Data Exchange (ETDEWEB)
Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)
2015-01-15
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.
In silico toxicology: computational methods for the prediction of chemical toxicity
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
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.
An Educational Approach to Computationally Modeling Dynamical Systems
Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl
2009-01-01
Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…
Decomposition and Cross-Product-Based Method for Computing the Dynamic Equation of Robots
Directory of Open Access Journals (Sweden)
Ching-Long Shih
2012-08-01
Full Text Available This paper aims to demonstrate a clear relationship between Lagrange equations and Newton-Euler equations regarding computational methods for robot dynamics, from which we derive a systematic method for using either symbolic or on-line numerical computations. Based on the decomposition approach and cross-product operation, a computing method for robot dynamics can be easily developed. The advantages of this computing framework are that: it can be used for both symbolic and on-line numeric computation purposes, and it can also be applied to biped systems, as well as some simple closed-chain robot systems.
A Simple Method for Dynamic Scheduling in a Heterogeneous Computing System
Žumer, Viljem; Brest, Janez
2002-01-01
A simple method for the dynamic scheduling on a heterogeneous computing system is proposed in this paper. It was implemented to minimize the parallel program execution time. The proposed method decomposes the program workload into computationally homogeneous subtasks, which may be of the different size, depending on the current load of each machine in a heterogeneous computing system.
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.
Analytical, Computational Fluid Dynamics and Flight Dynamics of Coandă MAV
Djojodihardjo, H.; Ahmed, RI
2016-11-01
The paper establishes the basic working relationships among various relevant variables and parameters governing the aerodynamics forces and performance measures of Coandă MAV in hover and translatory motion. With such motivation, capitalizing on the basic fundamental principles, the Fluid Dynamics and Flight Mechanics of semi-spherical Coandă MAV configurations are revisited and analyzed as a baseline. To gain better understanding on the principle of Coandă MAV lift generation, a mathematical model for a spherical Coandă MAV is developed and analyzed from first physical principles. To gain further insight into the prevailing flow field around a Coandă MAV, as well as to verify the theoretical prediction presented in the work, a computational fluid dynamic CFD simulation for a Coandă MAV generic model are elaborated using commercial software FLUENT®. In addition, the equation of motion for translatory motion of Coandă MAV is elaborated. The mathematical model and derived performance measures are shown to be capable in describing the physical phenomena of the flow field of the semi-spherical Coandă MAV. The relationships between the relevant parameters of the mathematical model of the Coandă MAV to the forces acting on it are elaborated subsequently.
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....
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...
Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.
2004-01-01
A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.
International Nuclear Information System (INIS)
Taguchi, K; Okada, J; Nomura, Y; Tamura, K
2012-01-01
In this paper, chemically etched fiber probe was proposed for laser trapping and manipulation of cells. We fabricated tapered fiber probe by dynamic chemical etching technique. Three-Dimensional optical trap of a yeast cell dispersed in water solution could be formed by the fiber tip with 17deg tip. Optical forces were sufficient to move the yeast cell for trapping and manipulation. From these experimental results, it was found that our proposed tapered fiber tip was a promising tool for cell isolation.
LION: A dynamic computer model for the low-latitude ionosphere
Directory of Open Access Journals (Sweden)
J. A. Bittencourt
2007-11-01
Full Text Available A realistic fully time-dependent computer model, denominated LION (Low-latitude Ionospheric model, that simulates the dynamic behavior of the low-latitude ionosphere is presented. The time evolution and spatial distribution of the ionospheric particle densities and velocities are computed by numerically solving the time-dependent, coupled, nonlinear system of continuity and momentum equations for the ions O^{+}, O_{2}^{+}, NO^{+}, N_{2}^{+} and N^{+}, taking into account photoionization of the atmospheric species by the solar extreme ultraviolet radiation, chemical and ionic production and loss reactions, and plasma transport processes, including the ionospheric effects of thermospheric neutral winds, plasma diffusion and electromagnetic E×B plasma drifts. The Earth's magnetic field is represented by a tilted centered magnetic dipole. This set of coupled nonlinear equations is solved along a given magnetic field line in a Lagrangian frame of reference moving vertically, in the magnetic meridian plane, with the electromagnetic E×B plasma drift velocity. The spatial and time distribution of the thermospheric neutral wind velocities and the pattern of the electromagnetic drifts are taken as known quantities, given through specified analytical or empirical models. The model simulation results are presented in the form of computer-generated color maps and reproduce the typical ionization distribution and time evolution normally observed in the low-latitude ionosphere, including details of the equatorial Appleton anomaly dynamics. The specific effects on the ionosphere due to changes in the thermospheric neutral winds and the electromagnetic plasma drifts can be investigated using different wind and drift models, including the important longitudinal effects associated with magnetic declination dependence and latitudinal separation between geographic and
LION: A dynamic computer model for the low-latitude ionosphere
Directory of Open Access Journals (Sweden)
J. A. Bittencourt
2007-11-01
Full Text Available A realistic fully time-dependent computer model, denominated LION (Low-latitude Ionospheric model, that simulates the dynamic behavior of the low-latitude ionosphere is presented. The time evolution and spatial distribution of the ionospheric particle densities and velocities are computed by numerically solving the time-dependent, coupled, nonlinear system of continuity and momentum equations for the ions O+, O2+, NO+, N2+ and N+, taking into account photoionization of the atmospheric species by the solar extreme ultraviolet radiation, chemical and ionic production and loss reactions, and plasma transport processes, including the ionospheric effects of thermospheric neutral winds, plasma diffusion and electromagnetic E×B plasma drifts. The Earth's magnetic field is represented by a tilted centered magnetic dipole. This set of coupled nonlinear equations is solved along a given magnetic field line in a Lagrangian frame of reference moving vertically, in the magnetic meridian plane, with the electromagnetic E×B plasma drift velocity. The spatial and time distribution of the thermospheric neutral wind velocities and the pattern of the electromagnetic drifts are taken as known quantities, given through specified analytical or empirical models. The model simulation results are presented in the form of computer-generated color maps and reproduce the typical ionization distribution and time evolution normally observed in the low-latitude ionosphere, including details of the equatorial Appleton anomaly dynamics. The specific effects on the ionosphere due to changes in the thermospheric neutral winds and the electromagnetic plasma drifts can be investigated using different wind and drift models, including the important longitudinal effects associated with magnetic declination dependence and latitudinal separation between geographic and geomagnetic equators. The model runs in a normal personal computer (PC and generates color maps illustrating the
Dynamical constraints and adiabatic invariants in chemical reactions.
Lorquet, J C
2007-08-23
For long-range electrostatic potentials and, more generally, when the topography of the potential energy surface is locally simple, the reaction path coordinate is adiabatically separable from the perpendicular degrees of freedom. For the ion-permanent dipole and ion-quadrupole interactions, the Poisson bracket of the adiabatic invariant decreases with the interfragment distance more rapidly than the electrostatic potential. The smaller the translational momentum, the moment of inertia of the neutral fragment, and the dipole or quadrupole moments are, the more reliable the adiabatic approximation is, as expected from the usual argumentation. Closed-form expressions for an effective one-dimensional potential in an adiabatic Hamiltonian are given. Connection with a model where the decoupling is exact is obtained in the limit of an infinitely heavy dipole. The dynamics is also constrained by adiabatic invariance for a harmonic valley about a curved reaction path, as shown by the reaction path Hamiltonian method. The maximum entropy method reveals that, as a result of the invariance properties of the entropy, constraints whose validity has been demonstrated locally only subsist in all parts of phase space. However, their form varies continuously, and they are not necessarily expressed in simple terms as they are in the asymptotic region. Therefore, although the influence of adiabatic invariance has been demonstrated at asymptotically large values of the reaction coordinate only, it persists in more interesting ranges.
Chemical kinetic insights into the ignition dynamics of n-hexane
Tingas, Alexandros
2017-10-13
Normal alkanes constitute a significant fraction of transportation fuels, and are the primary drivers of ignition processes in gasoline and diesel fuels. Low temperature ignition of n-alkanes is driven by a complex sequence of oxidation reactions, for which detailed mechanisms are still being developed. The current study explores the dynamics of low-temperature ignition of n-hexane/air mixtures, and identifies chemical pathways that characterize the combustion process. Two chemical kinetic mechanisms were selected as a comparative study in order to better understand the role of specific reaction sequences in ignition dynamics: one mechanism including a new third sequential O2 addition reaction pathways (recently proposed by Wang et al. 2017), while the other without (Zhang et al. 2015). The analysis is conducted by applying tools generated from the computational singular perturbation (CSP) approach to two distinct ignition phenomena: constant volume and compression ignition. In both cases, the role of the third sequential O2 addition reactions proves to be significant, although it is found to be much more pronounced in the constant volume cases compared to the HCCI. In particular, in the constant volume ignition case, reactions present in the third sequential O2 addition reaction pathways (e.g., KDHP → products + OH) contribute significantly to the explosivity of the mixture; when accounted for along with reactions P(OOH)2 + O2 → OOP(OOH)2 and OOP(OOH)2 → KDHP + OH, they decrease ignition delay time of the mixture by up to 40%. Under HCCI conditions, in the first-stage ignition, the third-O2 addition reactions contribute to the process, although their role decays with time and becomes negligible at the end of the first stage. The second ignition stage is dominated almost exclusively by hydrogen-related chemistry.
Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics
Linder, Mats; Johansson, Adam Johannes; Olsson, Tjelvar S. G.; Liebeschuetz, John; Brinck, Tore
2012-09-01
A novel computational Diels-Alderase design, based on a relatively rare form of carboxylesterase from Geobacillus stearothermophilus, is presented and theoretically evaluated. The structure was found by mining the PDB for a suitable oxyanion hole-containing structure, followed by a combinatorial approach to find suitable substrates and rational mutations. Four lead designs were selected and thoroughly modeled to obtain realistic estimates of substrate binding and prearrangement. Molecular dynamics simulations and DFT calculations were used to optimize and estimate binding affinity and activation energies. A large quantum chemical model was used to capture the salient interactions in the crucial transition state (TS). Our quantitative estimation of kinetic parameters was validated against four experimentally characterized Diels-Alderases with good results. The final designs in this work are predicted to have rate enhancements of ≈103-106 and high predicted proficiencies. This work emphasizes the importance of considering protein dynamics in the design approach, and provides a quantitative estimate of the how the TS stabilization observed in most de novo and redesigned enzymes is decreased compared to a minimal, `ideal' model. The presented design is highly interesting for further optimization and applications since it is based on a thermophilic enzyme ( T opt = 70 °C).
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.
Energy Technology Data Exchange (ETDEWEB)
Joshi, Abhinaya; Lou, Xinsheng; Neuschaefer, Carl; Chaudry, Majid; Quinn, Joseph
2012-07-31
This document provides the results of the project through September 2009. The Phase I project has recently been extended from September 2009 to March 2011. The project extension will begin work on Chemical Looping (CL) Prototype modeling and advanced control design exploration in preparation for a scale-up phase. The results to date include: successful development of dual loop chemical looping process models and dynamic simulation software tools, development and test of several advanced control concepts and applications for Chemical Looping transport control and investigation of several sensor concepts and establishment of two feasible sensor candidates recommended for further prototype development and controls integration. There are three sections in this summary and conclusions. Section 1 presents the project scope and objectives. Section 2 highlights the detailed accomplishments by project task area. Section 3 provides conclusions to date and recommendations for future work.
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....
Williams, R. W. (Compiler)
1996-01-01
This conference publication includes various abstracts and presentations given at the 13th Workshop for Computational Fluid Dynamic Applications in Rocket Propulsion and Launch Vehicle Technology held at the George C. Marshall Space Flight Center April 25-27 1995. The purpose of the workshop was to discuss experimental and computational fluid dynamic activities in rocket propulsion and launch vehicles. The workshop was an open meeting for government, industry, and academia. A broad number of topics were discussed including computational fluid dynamic methodology, liquid and solid rocket propulsion, turbomachinery, combustion, heat transfer, and grid generation.
Modelling the WWER-type reactor dynamics using a hybrid computer. Part 1
International Nuclear Information System (INIS)
Karpeta, C.
Results of simulation studies into reactor and steam generator dynamics of a WWER type power plant are presented. Spatial kinetics of the reactor core is described by a nodal approximation to diffusion equations, xenon poisoning equations and heat transfer equations. The simulation of the reactor model dynamics was performed on a hybrid computer. Models of both a horizontal and a vertical steam generator were developed. The dynamics was investigated over a large range of power by computing the transients on a digital computer. (author)
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.
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.
Savoir Fluide. A newsletter on computational hydraulics and fluid dynamics
International Nuclear Information System (INIS)
1997-01-01
This newsletter reports on computational works performed by the National Laboratory of Hydraulics (LNH) from Electricite de France (EdF). Two papers were selected which concern the simulation of the Paluel nuclear power plant plume and the computation of particles and droplets inside a cooling tower. (J.S.)
Applications of automatic differentiation in computational fluid dynamics
Green, Lawrence L.; Carle, A.; Bischof, C.; Haigler, Kara J.; Newman, Perry A.
1994-01-01
Automatic differentiation (AD) is a powerful computational method that provides for computing exact sensitivity derivatives (SD) from existing computer programs for multidisciplinary design optimization (MDO) or in sensitivity analysis. A pre-compiler AD tool for FORTRAN programs called ADIFOR has been developed. The ADIFOR tool has been easily and quickly applied by NASA Langley researchers to assess the feasibility and computational impact of AD in MDO with several different FORTRAN programs. These include a state-of-the-art three dimensional multigrid Navier-Stokes flow solver for wings or aircraft configurations in transonic turbulent flow. With ADIFOR the user specifies sets of independent and dependent variables with an existing computer code. ADIFOR then traces the dependency path throughout the code, applies the chain rule to formulate derivative expressions, and generates new code to compute the required SD matrix. The resulting codes have been verified to compute exact non-geometric and geometric SD for a variety of cases. in less time than is required to compute the SD matrix using centered divided differences.
Guidelines for Computing Longitudinal Dynamic Stability Characteristics of a Subsonic Transport
Thompson, Joseph R.; Frank, Neal T.; Murphy, Patrick C.
2010-01-01
A systematic study is presented to guide the selection of a numerical solution strategy for URANS computation of a subsonic transport configuration undergoing simulated forced oscillation about its pitch axis. Forced oscillation is central to the prevalent wind tunnel methodology for quantifying aircraft dynamic stability derivatives from force and moment coefficients, which is the ultimate goal for the computational simulations. Extensive computations are performed that lead in key insights of the critical numerical parameters affecting solution convergence. A preliminary linear harmonic analysis is included to demonstrate the potential of extracting dynamic stability derivatives from computational solutions.
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.
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...
The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.
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.
Czech Academy of Sciences Publication Activity Database
Herman, Zdeněk
2015-01-01
Roč. 378, FEB 2015 (2015), s. 113-126 ISSN 1387-3806 Institutional support: RVO:61388955 Keywords : Multiply-charged ions * Dynamics of chemical reactions * Beam scattering Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.183, year: 2015
In Silico Dynamics: computer simulation in a Virtual Embryo (SOT)
Abstract: Utilizing cell biological information to predict higher order biological processes is a significant challenge in predictive toxicology. This is especially true for highly dynamical systems such as the embryo where morphogenesis, growth and differentiation require preci...
Implementation of Keystroke Dynamics for Authentication in Computer Systems
Directory of Open Access Journals (Sweden)
S. V. Skuratov
2010-06-01
Full Text Available Implementation of keystroke dynamics in multifactor authentication systems is described in the article. Original access control system based on totality of matchers is presented. Testing results and useful recommendations are also adduced.
Computational Fluid Dynamic (CFD) Analysis of a Generic Missile With Grid Fins
National Research Council Canada - National Science Library
DeSpirito, James
2000-01-01
This report presents the results of a study demonstrating an approach for using viscous computational fluid dynamic simulations to calculate the flow field and aerodynamic coefficients for a missile with grid fin...
National Research Council Canada - National Science Library
Hisley, Dixie
1999-01-01
.... The goals of this report are: (1) to investigate the performance of message passing and loop level parallelization techniques, as they were implemented in the computational fluid dynamics (CFD...
Computer Processing and Display of Positron Scintigrams and Dynamic Function Curves
Energy Technology Data Exchange (ETDEWEB)
Wilensky, S.; Ashare, A. B.; Pizer, S. M.; Hoop, B. Jr.; Brownell, G. L. [Massachusetts General Hospital, Boston, MA (United States)
1969-01-15
A computer processing and display system for handling radioisotope data is described. The system has been used to upgrade and display brain scans and to process dynamic function curves. The hardware and software are described, and results are presented. (author)
Computational Fluid Dynamics of Whole-Body Aircraft
Agarwal, Ramesh
1999-01-01
The current state of the art in computational aerodynamics for whole-body aircraft flowfield simulations is described. Recent advances in geometry modeling, surface and volume grid generation, and flow simulation algorithms have led to accurate flowfield predictions for increasingly complex and realistic configurations. As a result, computational aerodynamics has emerged as a crucial enabling technology for the design and development of flight vehicles. Examples illustrating the current capability for the prediction of transport and fighter aircraft flowfields are presented. Unfortunately, accurate modeling of turbulence remains a major difficulty in the analysis of viscosity-dominated flows. In the future, inverse design methods, multidisciplinary design optimization methods, artificial intelligence technology, and massively parallel computer technology will be incorporated into computational aerodynamics, opening up greater opportunities for improved product design at substantially reduced costs.
International Nuclear Information System (INIS)
Itai, Y.; Moss, A.A.; Goldberg, H.I.
1982-01-01
Dynamic computed tomography of hepatic tumors revealed a transient attenuation difference of the liver in a lobar or segmental distribution in three cases. The difference was most prominent during the hepatogram phase. It was attributed to siphonage of arterial blood by hepatic tumors in two cases, while an increase of arterial flow induced by portal vein occlusion was inferred in the other case. Results indicate dynamic computed tomography will be usful in analysis of geometrical hemodynamics
Directory of Open Access Journals (Sweden)
Songzhu Mei
2012-09-01
Full Text Available Cloud computing bring a tremendous complexity to information security. Remote attestation can be used to establish trust relationship in cloud. TBVMM is designed to extend the existing chain of trust into the software layers to support dynamic remote attestation for cloud computing. TBVMM uses Bayesian network and Kalman filter to solve the dynamicity of the trusted relationship. It is proposed to fill the trust gap between the infrastructure and upper software stacks.
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
International Nuclear Information System (INIS)
Nichols, B.D.; Mueller, C.; Necker, G.A.; Travis, J.R.; Spore, J.W.; Lam, K.L.; Royl, P.; Redlinger, R.; Wilson, T.L.
1998-01-01
Los Alamos National Laboratory (LANL) and Forschungszentrum Karlsruhe (FzK) are developing GASFLOW, a three-dimensional (3D) fluid dynamics field code as a best-estimate tool to characterize local phenomena within a flow field. Examples of 3D phenomena include circulation patterns; flow stratification; hydrogen distribution mixing and stratification; combustion and flame propagation; effects of noncondensable gas distribution on local condensation and evaporation; and aerosol entrainment, transport, and deposition. An analysis with GASFLOW will result in a prediction of the gas composition and discrete particle distribution in space and time throughout the facility and the resulting pressure and temperature loadings on the walls and internal structures with or without combustion. A major application of GASFLOW is for predicting the transport, mixing, and combustion of hydrogen and other gases in nuclear reactor containments and other facilities. It has been applied to situations involving transporting and distributing combustible gas mixtures. It has been used to study gas dynamic behavior (1) in low-speed, buoyancy-driven flows, as well as sonic flows or diffusion dominated flows; and (2) during chemically reacting flows, including deflagrations. The effects of controlling such mixtures by safety systems can be analyzed. The code version described in this manual is designated GASFLOW 2.1, which combines previous versions of the United States Nuclear Regulatory Commission code HMS (for Hydrogen Mixing Studies) and the Department of Energy and FzK versions of GASFLOW. The code was written in standard Fortran 90. This manual comprises three volumes. Volume I describes the governing physical equations and computational model. Volume II describes how to use the code to set up a model geometry, specify gas species and material properties, define initial and boundary conditions, and specify different outputs, especially graphical displays. Sample problems are included
Directory of Open Access Journals (Sweden)
Yik Siang Pang
2018-01-01
Full Text Available This paper presents a Computational Fluid Dynamics (CFD study of a natural gas combustion burner focusing on the effect of combustion, thermal radiation and turbulence models on the temperature and chemical species concentration fields. The combustion was modelled using the finite rate/eddy dissipation (FR/EDM and partially premixed flame models. Detailed chemistry kinetics CHEMKIN GRI-MECH 3.0 consisting of 325 reactions was employed to model the methane combustion. Discrete ordinates (DO and spherical harmonics (P1 model were employed to predict the thermal radiation. The gas absorption coefficient dependence on the wavelength is resolved by the weighted-sum-of-gray-gases model (WSGGM. Turbulence flow was simulated using Reynolds-averaged Navier-Stokes (RANS based models. The findings showed that a combination of partially premixed flame, P1 and standard k-ε (SKE gave the most accurate prediction with an average deviation of around 7.8% of combustion temperature and 15.5% for reactant composition (methane and oxygen. The results show the multi-step chemistry in the partially premixed model is more accurate than the two-step FR/EDM. Meanwhile, inclusion of thermal radiation has a minor effect on the heat transfer and species concentration. SKE turbulence model yielded better prediction compared to the realizable k-ε (RKE and renormalized k-ε (RNG. The CFD simulation presented in this work may serve as a useful tool to evaluate a performance of a natural gas combustor. Copyright © 2018 BCREC Group. All rights reserved Received: 26th July 2017; Revised: 9th October 2017; Accepted: 30th October 2017; Available online: 22nd January 2018; Published regularly: 2nd April 2018 How to Cite: Pang, Y.S., Law, W.P., Pung, K.Q., Gimbun, J. (2018. A Computational Fluid Dynamics Study of Turbulence, Radiation, and Combustion Models for Natural Gas Combustion Burner. Bulletin of Chemical Reaction Engineering & Catalysis, 13 (1: 155-169 (doi:10.9767/bcrec
Development of a dynamic computational model of social cognitive theory.
Riley, William T; Martin, Cesar A; Rivera, Daniel E; Hekler, Eric B; Adams, Marc A; Buman, Matthew P; Pavel, Misha; King, Abby C
2016-12-01
Social cognitive theory (SCT) is among the most influential theories of behavior change and has been used as the conceptual basis of health behavior interventions for smoking cessation, weight management, and other health behaviors. SCT and other behavior theories were developed primarily to explain differences between individuals, but explanatory theories of within-person behavioral variability are increasingly needed as new technologies allow for intensive longitudinal measures and interventions adapted from these inputs. These within-person explanatory theoretical applications can be modeled as dynamical systems. SCT constructs, such as reciprocal determinism, are inherently dynamical in nature, but SCT has not been modeled as a dynamical system. This paper describes the development of a dynamical system model of SCT using fluid analogies and control systems principles drawn from engineering. Simulations of this model were performed to assess if the model performed as predicted based on theory and empirical studies of SCT. This initial model generates precise and testable quantitative predictions for future intensive longitudinal research. Dynamic modeling approaches provide a rigorous method for advancing health behavior theory development and refinement and for guiding the development of more potent and efficient interventions.
Dynamic defense and network randomization for computer systems
Chavez, Adrian R.; Stout, William M. S.; Hamlet, Jason R.; Lee, Erik James; Martin, Mitchell Tyler
2018-05-29
The various technologies presented herein relate to determining a network attack is taking place, and further to adjust one or more network parameters such that the network becomes dynamically configured. A plurality of machine learning algorithms are configured to recognize an active attack pattern. Notification of the attack can be generated, and knowledge gained from the detected attack pattern can be utilized to improve the knowledge of the algorithms to detect a subsequent attack vector(s). Further, network settings and application communications can be dynamically randomized, wherein artificial diversity converts control systems into moving targets that help mitigate the early reconnaissance stages of an attack. An attack(s) based upon a known static address(es) of a critical infrastructure network device(s) can be mitigated by the dynamic randomization. Network parameters that can be randomized include IP addresses, application port numbers, paths data packets navigate through the network, application randomization, etc.
Dynamics of Charged Particulate Systems Modeling, Theory and Computation
Zohdi, Tarek I
2012-01-01
The objective of this monograph is to provide a concise introduction to the dynamics of systems comprised of charged small-scale particles. Flowing, small-scale, particles ("particulates'') are ubiquitous in industrial processes and in the natural sciences. Applications include electrostatic copiers, inkjet printers, powder coating machines, etc., and a variety of manufacturing processes. Due to their small-scale size, external electromagnetic fields can be utilized to manipulate and control charged particulates in industrial processes in order to achieve results that are not possible by purely mechanical means alone. A unique feature of small-scale particulate flows is that they exhibit a strong sensitivity to interparticle near-field forces, leading to nonstandard particulate dynamics, agglomeration and cluster formation, which can strongly affect manufactured product quality. This monograph also provides an introduction to the mathematically-related topic of the dynamics of swarms of interacting objects, ...
Exploiting short-term memory in soft body dynamics as a computational resource.
Nakajima, K; Li, T; Hauser, H; Pfeifer, R
2014-11-06
Soft materials are not only highly deformable, but they also possess rich and diverse body dynamics. Soft body dynamics exhibit a variety of properties, including nonlinearity, elasticity and potentially infinitely many degrees of freedom. Here, we demonstrate that such soft body dynamics can be employed to conduct certain types of computation. Using body dynamics generated from a soft silicone arm, we show that they can be exploited to emulate functions that require memory and to embed robust closed-loop control into the arm. Our results suggest that soft body dynamics have a short-term memory and can serve as a computational resource. This finding paves the way towards exploiting passive body dynamics for control of a large class of underactuated systems. © 2014 The Author(s) Published by the Royal Society. All rights reserved.
Esophageal varices in cirrhotics on dynamic computed tomography
Energy Technology Data Exchange (ETDEWEB)
Miyazaki, Masaru; Takahashi, Osamu; Shimura, Tadanori
1985-07-01
Dynamic CT was performed on fifteen cirrhotics. The cirrhotics with esophageal varices were compared with those without esophageal varices in regard to the enhanced capacity of the liver and the spleen and the declining ratio of the spleen following the enhancement. Both the liver and the spleen in cirrhotics were enhanced less than non-cirrhotics, especially in those with esophageal varices (p<0.01). Splenic declining ratio following splenic enhancement clearly distinguish cirrhotics with esophageal varices from those without esophageal varices (p<0.01). These parameters on dynamic CT could be useful for the diagnosis of portal hypertension in cirrhotics.
Protected quantum computing: interleaving gate operations with dynamical decoupling sequences.
Zhang, Jingfu; Souza, Alexandre M; Brandao, Frederico Dias; Suter, Dieter
2014-02-07
Implementing precise operations on quantum systems is one of the biggest challenges for building quantum devices in a noisy environment. Dynamical decoupling attenuates the destructive effect of the environmental noise, but so far, it has been used primarily in the context of quantum memories. Here, we experimentally demonstrate a general scheme for combining dynamical decoupling with quantum logical gate operations using the example of an electron-spin qubit of a single nitrogen-vacancy center in diamond. We achieve process fidelities >98% for gate times that are 2 orders of magnitude longer than the unprotected dephasing time T2.
Comparison of Langevin dynamics and direct energy barrier computation
International Nuclear Information System (INIS)
Dittrich, Rok; Schrefl, Thomas; Thiaville, Andre; Miltat, Jacques; Tsiantos, Vassilios; Fidler, Josef
2004-01-01
Two complementary methods to study thermal effects in micromagnetics are compared. On short time scales Langevin dynamics gives insight in the thermally activated dynamics. For longer time scales the 'nudged elastic band' method is applied. The method calculates a highly probable thermal switching path between two local energy minima of a micromagnetic system. Comparing the predicted thermal transition rates between ground states in small softmagnetic elements up to a size of 90x90x4.5 nm 3 gives good agreement of the methods
Material Cycles and Chemicals: Dynamic Material Flow Analysis of Contaminants in Paper Recycling
DEFF Research Database (Denmark)
Pivnenko, Kostyantyn; Laner, David; Astrup, Thomas Fruergaard
2016-01-01
material source-segregation and collection was the least effective strategy for reducing chemical contamination, if the overall recycling rates should be maintained at the current level (approximately 70% for Europe). The study provides a consistent approach for evaluating contaminant levels in material......This study provides a systematic approach for assessment of contaminants in materials for recycling. Paper recycling is used as an illustrative example. Three selected chemicals, bisphenol A (BPA), diethylhexyl phthalate (DEHP) and mineral oil hydrocarbons (MOHs), are evaluated within the paper...... cycle. The approach combines static material flow analysis (MFA) with dynamic material and substance flow modeling. The results indicate that phasing out of chemicals is the most effective measure for reducing chemical contamination. However, this scenario was also associated with a considerable lag...
International Nuclear Information System (INIS)
Fay, P.J.; Ray, J.R.; Wolf, R.J.
1994-01-01
We present a new, nondestructive, method for determining chemical potentials in Monte Carlo and molecular dynamics simulations. The method estimates a value for the chemical potential such that one has a balance between fictitious successful creation and destruction trials in which the Monte Carlo method is used to determine success or failure of the creation/destruction attempts; we thus call the method a detailed balance method. The method allows one to obtain estimates of the chemical potential for a given species in any closed ensemble simulation; the closed ensemble is paired with a ''natural'' open ensemble for the purpose of obtaining creation and destruction probabilities. We present results for the Lennard-Jones system and also for an embedded atom model of liquid palladium, and compare to previous results in the literature for these two systems. We are able to obtain an accurate estimate of the chemical potential for the Lennard-Jones system at higher densities than reported in the literature
The effect of dynamic workstations on the performance of various computer and office-based tasks
Burford, E.M.; Botter, J.; Commissaris, D.; Könemann, R.; Hiemstra-Van Mastrigt, S.; Ellegast, R.P.
2013-01-01
The effect of different workstations, conventional and dynamic, on different types of performance measures for several different office and computer based task was investigated in this research paper. The two dynamic workstations assessed were the Lifespan Treadmill Desk and the RightAngle
Dynamic Scaffolding of Socially Regulated Learning in a Computer-Based Learning Environment
Molenaar, Inge; Roda, Claudia; van Boxtel, Carla; Sleegers, Peter
2012-01-01
The aim of this study is to test the effects of dynamically scaffolding social regulation of middle school students working in a computer-based learning environment. Dyads in the scaffolding condition (N=56) are supported with computer-generated scaffolds and students in the control condition (N=54) do not receive scaffolds. The scaffolds are…
Dynamic Scaffolding of Socially Regulated Learning in a Computer-Based Learning Environment
Molenaar, I.; Roda, Claudia; van Boxtel, Carla A.M.; Sleegers, P.J.C.
2012-01-01
The aim of this study is to test the effects of dynamically scaffolding social regulation of middle school students working in a computer-based learning environment. Dyads in the scaffolding condition (N = 56) are supported with computer-generated scaffolds and students in the control condition (N =
Formal Analysis of Dynamics Within Philosophy of Mind by Computer Simulation
Bosse, T.; Schut, M.C.; Treur, J.
2009-01-01
Computer simulations can be useful tools to support philosophers in validating their theories, especially when these theories concern phenomena showing nontrivial dynamics. Such theories are usually informal, whilst for computer simulation a formally described model is needed. In this paper, a
A dynamical-systems approach for computing ice-affected streamflow
Holtschlag, David J.
1996-01-01
A dynamical-systems approach was developed and evaluated for computing ice-affected streamflow. The approach provides for dynamic simulation and parameter estimation of site-specific equations relating ice effects to routinely measured environmental variables. Comparison indicates that results from the dynamical-systems approach ranked higher than results from 11 analytical methods previously investigated on the basis of accuracy and feasibility criteria. Additional research will likely lead to further improvements in the approach.
Czech Academy of Sciences Publication Activity Database
Brennan, J.K.; Lísal, Martin; Gubbins, K.E.; Rice, B.M.
2004-01-01
Roč. 70, č. 6 (2004), 0611031-0611034 ISSN 1063-651X R&D Projects: GA ČR GA203/03/1588 Grant - others:NSF(US) CTS-0211792 Institutional research plan: CEZ:AV0Z4072921 Keywords : reacting systems * simulation * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.352, year: 2004
Liu, Jie; Guo, Liang; Jiang, Jiping; Jiang, Dexun; Wang, Peng
2018-04-13
Aiming to minimize the damage caused by river chemical spills, efficient emergency material allocation is critical for an actual emergency rescue decision-making in a quick response. In this study, an emergency material allocation framework based on time-varying supply-demand constraint is developed to allocate emergency material, minimize the emergency response time, and satisfy the dynamic emergency material requirements in post-accident phases dealing with river chemical spills. In this study, the theoretically critical emergency response time is firstly obtained for the emergency material allocation system to select a series of appropriate emergency material warehouses as potential supportive centers. Then, an enumeration method is applied to identify the practically critical emergency response time, the optimum emergency material allocation and replenishment scheme. Finally, the developed framework is applied to a computational experiment based on south-to-north water transfer project in China. The results illustrate that the proposed methodology is a simple and flexible tool for appropriately allocating emergency material to satisfy time-dynamic demands during emergency decision-making. Therefore, the decision-makers can identify an appropriate emergency material allocation scheme in a balance between time-effective and cost-effective objectives under the different emergency pollution conditions.
Energy Technology Data Exchange (ETDEWEB)
Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.
2017-02-03
Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.
Dynamic computed tomography for the diagnosis of pituitary microadenoma, 2
International Nuclear Information System (INIS)
Tsuchiya, Toshiaki
1992-01-01
The purpose of this paper is to establish the diagnostic criteria on microadenoma by dynamic CT. Dynamic CT was studied in 19 patients with hormone-secreting microadenomas. There were 10 prolactin-secreting, 5 growth-hormone-secreting, and 4 adrenocorticotropic-hormone-secreting adenomas. The following diagnostic criteria on microadenomas were concluded by analyzing dynamic CT on 19 microadenomas, in which histology, location and extension of the tumor were verified by surgery and postoperative CT. The tuft distorted and displaced indicates a mass effect mainly in the opposite side. The mid-situated tuft with a disproportionately small size compared with a size of the anterior lobe indicates a mass effect mainly in the midportion. The area, into which a high density at the tuft definitely spreads, presents the normal anterior lobe. The area, in which less increase in density than the former area is observed, indicates an abnormal mass. In the time-density curve, the former area represents the vascular pattern or the hypervascular extravasation pattern, while the latter area represents extravasation of contrast material in a hypovascular tissue. Only eight microadenomas were presented as a less enhanced mass. The rest of the cases exhibited adenomas isodense to the normal pituitary gland. Dynamic CT was useful particularly in the diagnosis of isodense adenomas. (author)
Dynamical Trust and Reputation Computation Model for B2C E-Commerce
Bo Tian; Kecheng Liu; Yuanzhong Chen
2015-01-01
Trust is one of the most important factors that influence the successful application of network service environments, such as e-commerce, wireless sensor networks, and online social networks. Computation models associated with trust and reputation have been paid special attention in both computer societies and service science in recent years. In this paper, a dynamical computation model of reputation for B2C e-commerce is proposed. Firstly, conceptions associated with trust and reputation are...
Spatiotemporal chaos in the dynamics of buoyantly and diffusively unstable chemical fronts
Baroni, M. P. M. A.; Guéron, E.; De Wit, A.
2012-03-01
Nonlinear dynamics resulting from the interplay between diffusive and buoyancy-driven Rayleigh-Taylor (RT) instabilities of autocatalytic traveling fronts are analyzed numerically for various values of the relevant parameters. These are the Rayleigh numbers of the reactant A and autocatalytic product B solutions as well as the ratio D =DB/DA between the diffusion coefficients of the two key chemical species. The interplay between the coarsening dynamics characteristic of the RT instability and the constant short wavelength modulation of the diffusive instability can lead in some regimes to complex dynamics dominated by irregular succession of birth and death of fingers. By using spectral entropy measurements, we characterize the transition between order and spatial disorder in this system. The analysis of the power spectrum and autocorrelation function, moreover, identifies similarities between the various spatial patterns. The contribution of the diffusive instability to the complex dynamics is discussed.
Application of GPU to computational multiphase fluid dynamics
International Nuclear Information System (INIS)
Nagatake, T; Kunugi, T
2010-01-01
The MARS (Multi-interfaces Advection and Reconstruction Solver) [1] is one of the surface volume tracking methods for multi-phase flows. Nowadays, the performance of GPU (Graphics Processing Unit) is much higher than the CPU (Central Processing Unit). In this study, the GPU was applied to the MARS in order to accelerate the computation of multi-phase flows (GPU-MARS), and the performance of the GPU-MARS was discussed. From the performance of the interface tracking method for the analyses of one-directional advection problem, it is found that the computing time of GPU(single GTX280) was around 4 times faster than that of the CPU (Xeon 5040, 4 threads parallelized). From the performance of Poisson Solver by using the algorithm developed in this study, it is found that the performance of the GPU showed around 30 times faster than that of the CPU. Finally, it is confirmed that the GPU showed the large acceleration of the fluid flow computation (GPU-MARS) compared to the CPU. However, it is also found that the double-precision computation of the GPU must perform with very high precision.
Transient computational homogenization for heterogeneous materials under dynamic excitation
Pham, N.K.H.; Kouznetsova, V.; Geers, M.G.D.
2013-01-01
This paper presents a novel transient computational homogenization procedure that is suitable for the modelling of the evolution in space and in time of materials with non-steady state microstructure, such as metamaterials. This transient scheme is an extension of the classical (first-order)
Computational fluid dynamics simulations and validations of results
CSIR Research Space (South Africa)
Sitek, MA
2013-09-01
Full Text Available Wind flow influence on a high-rise building is analyzed. The research covers full-scale tests, wind-tunnel experiments and numerical simulations. In the present paper computational model used in simulations is described and the results, which were...
Groves, Curtis Edward
2014-01-01
Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional "validation by test only" mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions. Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in "Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations". This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics
Groves, Curtis Edward
2014-01-01
Spacecraft thermal protection systems are at risk of being damaged due to airflow produced from Environmental Control Systems. There are inherent uncertainties and errors associated with using Computational Fluid Dynamics to predict the airflow field around a spacecraft from the Environmental Control System. This paper describes an approach to quantify the uncertainty in using Computational Fluid Dynamics to predict airflow speeds around an encapsulated spacecraft without the use of test data. Quantifying the uncertainty in analytical predictions is imperative to the success of any simulation-based product. The method could provide an alternative to traditional validation by test only mentality. This method could be extended to other disciplines and has potential to provide uncertainty for any numerical simulation, thus lowering the cost of performing these verifications while increasing the confidence in those predictions.Spacecraft requirements can include a maximum airflow speed to protect delicate instruments during ground processing. Computational Fluid Dynamics can be used to verify these requirements; however, the model must be validated by test data. This research includes the following three objectives and methods. Objective one is develop, model, and perform a Computational Fluid Dynamics analysis of three (3) generic, non-proprietary, environmental control systems and spacecraft configurations. Several commercially available and open source solvers have the capability to model the turbulent, highly three-dimensional, incompressible flow regime. The proposed method uses FLUENT, STARCCM+, and OPENFOAM. Objective two is to perform an uncertainty analysis of the Computational Fluid Dynamics model using the methodology found in Comprehensive Approach to Verification and Validation of Computational Fluid Dynamics Simulations. This method requires three separate grids and solutions, which quantify the error bars around Computational Fluid Dynamics predictions
On the sighting of unicorns: A variational approach to computing invariant sets in dynamical systems
Junge, Oliver; Kevrekidis, Ioannis G.
2017-06-01
We propose to compute approximations to invariant sets in dynamical systems by minimizing an appropriate distance between a suitably selected finite set of points and its image under the dynamics. We demonstrate, through computational experiments, that this approach can successfully converge to approximations of (maximal) invariant sets of arbitrary topology, dimension, and stability, such as, e.g., saddle type invariant sets with complicated dynamics. We further propose to extend this approach by adding a Lennard-Jones type potential term to the objective function, which yields more evenly distributed approximating finite point sets, and illustrate the procedure through corresponding numerical experiments.
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)
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.
3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography
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
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.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Vashishta, Priya; Kalia, Rajiv
2005-01-01
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
Computer simulation of population dynamics inside the urban environment
Andreev, A. S.; Inovenkov, I. N.; Echkina, E. Yu.; Nefedov, V. V.; Ponomarenko, L. S.; Tikhomirov, V. V.
2017-12-01
In this paper using a mathematical model of the so-called “space-dynamic” approach we investigate the problem of development and temporal dynamics of different urban population groups. For simplicity we consider an interaction of only two population groups inside a single urban area with axial symmetry. This problem can be described qualitatively by a system of two non-stationary nonlinear differential equations of the diffusion type with boundary conditions of the third type. The results of numerical simulations show that with a suitable choice of the diffusion coefficients and interaction functions between different population groups we can receive different scenarios of population dynamics: from complete displacement of one population group by another (originally more “aggressive”) to the “peaceful” situation of co-existence of them together.
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.
Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R
2014-10-14
The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a
Image communication scheme based on dynamic visual cryptography and computer generated holography
Palevicius, Paulius; Ragulskis, Minvydas
2015-01-01
Computer generated holograms are often exploited to implement optical encryption schemes. This paper proposes the integration of dynamic visual cryptography (an optical technique based on the interplay of visual cryptography and time-averaging geometric moiré) with Gerchberg-Saxton algorithm. A stochastic moiré grating is used to embed the secret into a single cover image. The secret can be visually decoded by a naked eye if only the amplitude of harmonic oscillations corresponds to an accurately preselected value. The proposed visual image encryption scheme is based on computer generated holography, optical time-averaging moiré and principles of dynamic visual cryptography. Dynamic visual cryptography is used both for the initial encryption of the secret image and for the final decryption. Phase data of the encrypted image are computed by using Gerchberg-Saxton algorithm. The optical image is decrypted using the computationally reconstructed field of amplitudes.
Energy Technology Data Exchange (ETDEWEB)
Battaglia, Francine [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Agblevor, Foster [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Klein, Michael [Univ. of Delaware, Newark, DE (United States); Sheikhi, Reza [Northeastern Univ., Boston, MA (United States)
2015-12-31
A collaborative effort involving experiments, kinetic modeling, and computational fluid dynamics (CFD) was used to understand co-gasification of coal-biomass mixtures. The overall goal of the work was to determine the key reactive properties for coal-biomass mixed fuels. Sub-bituminous coal was mixed with biomass feedstocks to determine the fluidization and gasification characteristics of hybrid poplar wood, switchgrass and corn stover. It was found that corn stover and poplar wood were the best feedstocks to use with coal. The novel approach of this project was the use of a red mud catalyst to improve gasification and lower gasification temperatures. An important results was the reduction of agglomeration of the biomass using the catalyst. An outcome of this work was the characterization of the chemical kinetics and reaction mechanisms of the co-gasification fuels, and the development of a set of models that can be integrated into other modeling environments. The multiphase flow code, MFIX, was used to simulate and predict the hydrodynamics and co-gasification, and results were validated with the experiments. The reaction kinetics modeling was used to develop a smaller set of reactions for tractable CFD calculations that represented the experiments. Finally, an efficient tool was developed, MCHARS, and coupled with MFIX to efficiently simulate the complex reaction kinetics.
Nomura, Ken-Ichi; Kalia, Rajiv K; Nakano, Aiichiro; Vashishta, Priya; van Duin, Adri C T; Goddard, William A
2007-10-05
Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive force-field molecular dynamics (ReaxFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillion-atom ReaxFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front.
Using Amazon's Elastic Compute Cloud to scale CMS' compute hardware dynamically.
Melo, Andrew Malone
2011-01-01
Large international scientific collaborations such as the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider have traditionally addressed their data reduction and analysis needs by building and maintaining dedicated computational infrastructure. Emerging cloud-computing services such as Amazon's Elastic Compute Cloud (EC2) offer short-term CPU and storage resources with costs based on usage. These services allow experiments to purchase computing resources as needed, without significant prior planning and without long term investments in facilities and their management. We have demonstrated that services such as EC2 can successfully be integrated into the production-computing model of CMS, and find that they work very well as worker nodes. The cost-structure and transient nature of EC2 services makes them inappropriate for some CMS production services and functions. We also found that the resources are not truely on-demand as limits and caps on usage are imposed. Our trial workflows allow us t...
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
Optically intraconnected computer employing dynamically reconfigurable holographic optical element
Bergman, Larry A. (Inventor)
1992-01-01
An optically intraconnected computer and a reconfigurable holographic optical element employed therein. The basic computer comprises a memory for holding a sequence of instructions to be executed; logic for accessing the instructions in sequence; logic for determining for each the instruction the function to be performed and the effective address thereof; a plurality of individual elements on a common support substrate optimized to perform certain logical sequences employed in executing the instructions; and, element selection logic connected to the logic determining the function to be performed for each the instruction for determining the class of each function and for causing the instruction to be executed by those the elements which perform those associated the logical sequences affecting the instruction execution in an optimum manner. In the optically intraconnected version, the element selection logic is adapted for transmitting and switching signals to the elements optically.
Computational Modelling of Piston Ring Dynamics in 3D
Directory of Open Access Journals (Sweden)
Dlugoš Jozef
2014-12-01
Full Text Available Advanced computational models of a piston assembly based on the level of virtual prototypes require a detailed description of piston ring behaviour. Considering these requirements, the piston rings operate in regimes that cannot, in general, be simplified into an axisymmetric model. The piston and the cylinder liner do not have a perfect round shape, mainly due to machining tolerances and external thermo-mechanical loads. If the ring cannot follow the liner deformations, a local loss of contact occurs resulting in blow-by and increased consumption of lubricant oil in the engine. Current computational models are unable to implement such effects. The paper focuses on the development of a flexible 3D piston ring model based on the Timoshenko beam theory using the multibody system (MBS. The MBS model is compared to the finite element method (FEM solution.
Dynamic grid refinement for partial differential equations on parallel computers
International Nuclear Information System (INIS)
Mccormick, S.; Quinlan, D.
1989-01-01
The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids to provide adaptive resolution and fast solution of PDEs. An asynchronous version of FAC, called AFAC, that completely eliminates the bottleneck to parallelism is presented. This paper describes the advantage that this algorithm has in adaptive refinement for moving singularities on multiprocessor computers. This work is applicable to the parallel solution of two- and three-dimensional shock tracking problems. 6 refs
Computing the optimal path in stochastic dynamical systems
International Nuclear Information System (INIS)
Bauver, Martha; Forgoston, Eric; Billings, Lora
2016-01-01
In stochastic systems, one is often interested in finding the optimal path that maximizes the probability of escape from a metastable state or of switching between metastable states. Even for simple systems, it may be impossible to find an analytic form of the optimal path, and in high-dimensional systems, this is almost always the case. In this article, we formulate a constructive methodology that is used to compute the optimal path numerically. The method utilizes finite-time Lyapunov exponents, statistical selection criteria, and a Newton-based iterative minimizing scheme. The method is applied to four examples. The first example is a two-dimensional system that describes a single population with internal noise. This model has an analytical solution for the optimal path. The numerical solution found using our computational method agrees well with the analytical result. The second example is a more complicated four-dimensional system where our numerical method must be used to find the optimal path. The third example, although a seemingly simple two-dimensional system, demonstrates the success of our method in finding the optimal path where other numerical methods are known to fail. In the fourth example, the optimal path lies in six-dimensional space and demonstrates the power of our method in computing paths in higher-dimensional spaces.
Hybrid computing using a neural network with dynamic external memory.
Graves, Alex; Wayne, Greg; Reynolds, Malcolm; Harley, Tim; Danihelka, Ivo; Grabska-Barwińska, Agnieszka; Colmenarejo, Sergio Gómez; Grefenstette, Edward; Ramalho, Tiago; Agapiou, John; Badia, Adrià Puigdomènech; Hermann, Karl Moritz; Zwols, Yori; Ostrovski, Georg; Cain, Adam; King, Helen; Summerfield, Christopher; Blunsom, Phil; Kavukcuoglu, Koray; Hassabis, Demis
2016-10-27
Artificial neural networks are remarkably adept at sensory processing, sequence learning and reinforcement learning, but are limited in their ability to represent variables and data structures and to store data over long timescales, owing to the lack of an external memory. Here we introduce a machine learning model called a differentiable neural computer (DNC), which consists of a neural network that can read from and write to an external memory matrix, analogous to the random-access memory in a conventional computer. Like a conventional computer, it can use its memory to represent and manipulate complex data structures, but, like a neural network, it can learn to do so from data. When trained with supervised learning, we demonstrate that a DNC can successfully answer synthetic questions designed to emulate reasoning and inference problems in natural language. We show that it can learn tasks such as finding the shortest path between specified points and inferring the missing links in randomly generated graphs, and then generalize these tasks to specific graphs such as transport networks and family trees. When trained with reinforcement learning, a DNC can complete a moving blocks puzzle in which changing goals are specified by sequences of symbols. Taken together, our results demonstrate that DNCs have the capacity to solve complex, structured tasks that are inaccessible to neural networks without external read-write memory.
Bittracher, Andreas; Koltai, Péter; Klus, Stefan; Banisch, Ralf; Dellnitz, Michael; Schütte, Christof
2018-01-01
We consider complex dynamical systems showing metastable behavior, but no local separation of fast and slow time scales. The article raises the question of whether such systems exhibit a low-dimensional manifold supporting its effective dynamics. For answering this question, we aim at finding nonlinear coordinates, called reaction coordinates, such that the projection of the dynamics onto these coordinates preserves the dominant time scales of the dynamics. We show that, based on a specific reducibility property, the existence of good low-dimensional reaction coordinates preserving the dominant time scales is guaranteed. Based on this theoretical framework, we develop and test a novel numerical approach for computing good reaction coordinates. The proposed algorithmic approach is fully local and thus not prone to the curse of dimension with respect to the state space of the dynamics. Hence, it is a promising method for data-based model reduction of complex dynamical systems such as molecular dynamics.
Using Amazon's Elastic Compute Cloud to dynamically scale CMS computational resources
International Nuclear Information System (INIS)
Evans, D; Fisk, I; Holzman, B; Pordes, R; Tiradani, A; Melo, A; Sheldon, P; Metson, S
2011-01-01
Large international scientific collaborations such as the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider have traditionally addressed their data reduction and analysis needs by building and maintaining dedicated computational infrastructure. Emerging cloud computing services such as Amazon's Elastic Compute Cloud (EC2) offer short-term CPU and storage resources with costs based on usage. These services allow experiments to purchase computing resources as needed, without significant prior planning and without long term investments in facilities and their management. We have demonstrated that services such as EC2 can successfully be integrated into the production-computing model of CMS, and find that they work very well as worker nodes. The cost-structure and transient nature of EC2 services makes them inappropriate for some CMS production services and functions. We also found that the resources are not truely 'on-demand' as limits and caps on usage are imposed. Our trial workflows allow us to make a cost comparison between EC2 resources and dedicated CMS resources at a University, and conclude that it is most cost effective to purchase dedicated resources for the 'base-line' needs of experiments such as CMS. However, if the ability to use cloud computing resources is built into an experiment's software framework before demand requires their use, cloud computing resources make sense for bursting during times when spikes in usage are required.
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…
Energy Technology Data Exchange (ETDEWEB)
Pointer, William David [ORNL
2017-08-01
The objective of this effort is to establish a strategy and process for generation of suitable computational mesh for computational fluid dynamics simulations of departure from nucleate boiling in a 5 by 5 fuel rod assembly held in place by PWR mixing vane spacer grids. This mesh generation process will support ongoing efforts to develop, demonstrate and validate advanced multi-phase computational fluid dynamics methods that enable more robust identification of dryout conditions and DNB occurrence.Building upon prior efforts and experience, multiple computational meshes were developed using the native mesh generation capabilities of the commercial CFD code STAR-CCM+. These meshes were used to simulate two test cases from the Westinghouse 5 by 5 rod bundle facility. The sensitivity of predicted quantities of interest to the mesh resolution was then established using two evaluation methods, the Grid Convergence Index method and the Least Squares method. This evaluation suggests that the Least Squares method can reliably establish the uncertainty associated with local parameters such as vector velocity components at a point in the domain or surface averaged quantities such as outlet velocity magnitude. However, neither method is suitable for characterization of uncertainty in global extrema such as peak fuel surface temperature, primarily because such parameters are not necessarily associated with a fixed point in space. This shortcoming is significant because the current generation algorithm for identification of DNB event conditions relies on identification of such global extrema. Ongoing efforts to identify DNB based on local surface conditions will address this challenge
Dynamic computed tomography for the diagnosis of microadenoma, (1)
International Nuclear Information System (INIS)
Tsuchiya, Toshiaki; Andoh, Kazuo; Ito, Jyusuke
1987-01-01
A dynamic CT scan was used to study 20 normal pituitary glands. Eight were examined by means of a coronal dynamic CT scan, and 12, by means of an axial dynamic CT scan. In the anterior lobe, initially the secondary capillary bed (called the ''tuft'' by Bonneville) appeared as a high-density area located in the midline, beneath the upper surface of the anterior lobe. Subsequently, the high-density area located in the secondary capillary bed spread centrifugally into the anterior lobe. Finally, the entire anterior lobe became a homogeneous high-density area. Three patterns of the time-density curve were observed in the anterior lobe. Type 1, observed in the midline, beneath the upper surface of the anterior lobe, was a vascular pattern. It corresponded to the tuft topographically. Compared with the other venous system, the peak of Type 1 was somewhat delayed. This is attributable to the slower circulation in the hypophyseal portal system. Type 2, observed just below the tuft, represented the extravasation of the contrast material in a highly vascular tissue (hypervascular extravasation pattern). Type 3, observed at the bottom of the anterior lobe, represented the extravasation of the contrast material in a less vascular tissue (oligovascular extravasation pattern). The anterior lobe has no blood-brain barrier, and the sinusoid vessels are abundant in the following order: the upper surface of the anterior lobe, the area below the tuft, and the bottom of the anterior lobe. Taking these two facts into account, Type 1 (vascular pattern) is considered to be due to the abundant vascularity of the secondary capillary bed. Type 2 (hypervascular extravasation pattern) results from the extravasation of the contrast material at the site of highly vascular tissue without any blood-brain barrier. Type 3 (oligovascular extravasation pattern) seems to indicate the extravasation of the contrast material at the site of less vascular tissue without any blood-brain barrier. (J.P.N.)
Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.
Directory of Open Access Journals (Sweden)
Ferdinandus
Full Text Available This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing. A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.
Dynamics of the stochastic low concentration trimolecular oscillatory chemical system with jumps
Wei, Yongchang; Yang, Qigui
2018-06-01
This paper is devoted to discern long time dynamics through the stochastic low concentration trimolecular oscillatory chemical system with jumps. By Lyapunov technique, this system is proved to have a unique global positive solution, and the asymptotic stability in mean square of such model is further established. Moreover, the existence of random attractor and Lyapunov exponents are obtained for the stochastic homeomorphism flow generated by the corresponding global positive solution. And some numerical simulations are given to illustrate the presented results.
Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.
Ferdinandus; Arai, Satoshi; Ishiwata, Shin'ichi; Suzuki, Madoka; Sato, Hirotaka
2015-01-01
This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action) and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing). A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.
Yürekli, Yılmaz; Alsoy Altınkaya, Sacide
2011-01-01
Immobilized urease has been used for direct removal of urea from aqueous solution and as biological sensing material in the preparation of urea biosensors. The former application is carried out under dynamic condition using ultrafiltration membrane either in tubular form or in flat sheet, while the latter is used in static condition. In this study, the performance of chemically immobilized urease on poly(acrylonitrile-co-sodium methallyl sulfonate) ultrafiltration membrane was determined unde...
Stabilization of computational procedures for constrained dynamical systems
Park, K. C.; Chiou, J. C.
1988-01-01
A new stabilization method of treating constraints in multibody dynamical systems is presented. By tailoring a penalty form of the constraint equations, the method achieves stabilization without artificial damping and yields a companion matrix differential equation for the constraint forces; hence, the constraint forces are obtained by integrating the companion differential equation for the constraint forces in time. A principal feature of the method is that the errors committed in each constraint condition decay with its corresponding characteristic time scale associated with its constraint force. Numerical experiments indicate that the method yields a marked improvement over existing techniques.
Dynamic Programming and Graph Algorithms in Computer Vision*
Felzenszwalb, Pedro F.; Zabih, Ramin
2013-01-01
Optimization is a powerful paradigm for expressing and solving problems in a wide range of areas, and has been successfully applied to many vision problems. Discrete optimization techniques are especially interesting, since by carefully exploiting problem structure they often provide non-trivial guarantees concerning solution quality. In this paper we briefly review dynamic programming and graph algorithms, and discuss representative examples of how these discrete optimization techniques have been applied to some classical vision problems. We focus on the low-level vision problem of stereo; the mid-level problem of interactive object segmentation; and the high-level problem of model-based recognition. PMID:20660950
Molecular dynamics computer simulations based on NMR data
International Nuclear Information System (INIS)
Vlieg, J. de.
1989-01-01
In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs
Understanding the Offender/Environment Dynamic for Computer Crimes
DEFF Research Database (Denmark)
Willison, Robert Andrew
2005-01-01
practices by possiblyhighlighting new areas for safeguard implementation. To help facilitate a greaterunderstanding of the offender/environment dynamic, this paper assesses the feasibilityof applying criminological theory to the IS security context. More specifically, threetheories are advanced, which focus...... on the offender's behaviour in a criminal setting. Drawing on an account of the Barings Bank collapse, events highlighted in the casestudy are used to assess whether concepts central to the theories are supported by thedata. It is noted that while one of the theories is to be found wanting in terms ofconceptual...
Handling membership dynamicity in service composition for ubiquitous computing
DEFF Research Database (Denmark)
Brønsted, Jeppe Rørbæk; Hansen, Klaus Marius
2008-01-01
. A proposed solution is to use a service oriented architecture and implement applications as composite services. As long as the set of services that constitute the composite is static, traditional techniques can be used to specify the composite. In this paper we show how the PalCom service composition...... language can be extended to support service composites with dynamic membership and present a decentralized implementation. Preliminary user studies indicate that the extensions are easily understandable and simulations of application scenarios show that the performance of the implementation is appropriate...
Aligator: A computational tool for optimizing total chemical synthesis of large proteins.
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.
Status of computational fluid dynamics in the United States
International Nuclear Information System (INIS)
Kutler, P.; Steger, J.L.; Bailey, F.R.
1987-01-01
CFD-related progress in U.S. aerospace industries and research institutions is evaluated with respect to methods employed, their applications, and the computer technologies employed in their implementation. Goals for subsonic CFD are primarily aimed at greater fuel efficiency; those of supersonic CFD involve the achievement of high sustained cruise efficiency. Transatmospheric/hypersonic vehicles are noted to have recently become important concerns for CFD efforts. Attention is given to aspects of discretization, Euler and Navier-Stokes general purpose codes, zonal equation methods, internal and external flows, and the impact of supercomputers and their networks in advancing the state-of-the-art. 91 references
International Nuclear Information System (INIS)
Janecky, D.R.
1988-01-01
A computational modeling code (EQPSreverse arrowS) has been developed to examine sulfur isotopic distribution pathways coupled with calculations of chemical mass transfer pathways. A post processor approach to EQ6 calculations was chosen so that a variety of isotopic pathways could be examined for each reaction pathway. Two types of major bounding conditions were implemented: (1) equilibrium isotopic exchange between sulfate and sulfide species or exchange only accompanying chemical reduction and oxidation events, and (2) existence or lack of isotopic exchange between solution species and precipitated minerals, parallel to the open and closed chemical system formulations of chemical mass transfer modeling codes. All of the chemical data necessary to explicitly calculate isotopic distribution pathways is generated by most mass transfer modeling codes and can be input to the EQPS code. Routines are built in to directly handle EQ6 tabular files. Chemical reaction models of seafloor hydrothermal vent processes and accompanying sulfur isotopic distribution pathways illustrate the capabilities of coupling EQPSreverse arrowS with EQ6 calculations, including the extent of differences that can exist due to the isotopic bounding condition assumptions described above. 11 refs., 2 figs
Dynamic angle selection in X-ray computed tomography
Energy Technology Data Exchange (ETDEWEB)
Dabravolski, Andrei, E-mail: andrei.dabravolski@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Batenburg, Kees Joost, E-mail: joost.batenburg@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica (CWI), Science Park 123, 1098 XG Amsterdam (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk (Belgium)
2014-04-01
Highlights: • We propose the dynamic angle selection algorithm for CT scanning. • The approach is based on the concept of information gain over a set of solutions. • Projection angles are selected based on the already available projection data. • The approach can lead to more accurate results from fewer projections. - Abstract: In X-ray tomography, a number of radiographs (projections) are recorded from which a tomogram is then reconstructed. Conventionally, these projections are acquired equiangularly, resulting in an unbiased sampling of the Radon space. However, especially in case when only a limited number of projections can be acquired, the selection of the angles has a large impact on the quality of the reconstructed image. In this paper, a dynamic algorithm is proposed, in which new projection angles are selected by maximizing the information gain about the object, given the set of possible new angles. Experiments show that this approach can select projection angles for which the accuracy of the reconstructed image is significantly higher compared to the standard angle selections schemes.
Hardware for dynamic quantum computing experiments: Part I
Johnson, Blake; Ryan, Colm; Riste, Diego; Donovan, Brian; Ohki, Thomas
Static, pre-defined control sequences routinely achieve high-fidelity operation on superconducting quantum processors. Efforts toward dynamic experiments depending on real-time information have mostly proceeded through hardware duplication and triggers, requiring a combinatorial explosion in the number of channels. We provide a hardware efficient solution to dynamic control with a complete platform of specialized FPGA-based control and readout electronics; these components enable arbitrary control flow, low-latency feedback and/or feedforward, and scale far beyond single-qubit control and measurement. We will introduce the BBN Arbitrary Pulse Sequencer 2 (APS2) control system and the X6 QDSP readout platform. The BBN APS2 features: a sequencer built around implementing short quantum gates, a sequence cache to allow long sequences with branching structures, subroutines for code re-use, and a trigger distribution module to capture and distribute steering information. The X6 QDSP features a single-stage DSP pipeline that combines demodulation with arbitrary integration kernels, and multiple taps to inspect data flow for debugging and calibration. We will show system performance when putting it all together, including a latency budget for feedforward operations. This research was funded by the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), through the Army Research Office Contract No. W911NF-10-1-0324.
Validation of enhanced and dynamic computed tomography for cerebral ischemia
Energy Technology Data Exchange (ETDEWEB)
Ono, Kenichiro; Arimoto, Hirohiko; Wada, Kojiro; Takahara, Takashi; Shirotani, Toshiki; Shimizu, Akira [Japan Self-Defense Forces Central Hospital, Tokyo (Japan); Hatanaka, Kosuke [Japan Self-Defense Forces Medical School, Tokyo (Japan)
2003-03-01
This paper shows the usefulness of enhanced and dynamic CT for ischemic stroke patients. Sixteen patients with disturbance of consciousness or neurological sign who did not have low-density area on plain CT were selected for this study. We performed enhanced CT sequentially. Enhanced CT image, time-density curve and functional image were compared with final infarcted area and occlusion level of cerebral artery. Three patients whose enhanced CT images showed obvious laterality had occlusion of internal carotid (IC) or horizontal portion of middle cerebral artery (M1). Four of five patients whose functional image and time density curve revealed abnormal region had ischemia because of more peripheral vessel occlusion or IC stenosis. Others with no abnormality on all images had lacunar infarction or did not have infarction finally. Occlusion of cerebral artery proximal portion could be diagnosed only with enhanced CT images. If selected slice was fit to the lesion, more distant level of ischemic area could be determined 100% by time-density curve and functional image. This examination takes only about ten minutes without transferring the patient. Enhanced CT and dynamic scan is useful tool to determine the diagnosis and management for ischemic stroke patients. (author)
Dynamic angle selection in X-ray computed tomography
International Nuclear Information System (INIS)
Dabravolski, Andrei; Batenburg, Kees Joost; Sijbers, Jan
2014-01-01
Highlights: • We propose the dynamic angle selection algorithm for CT scanning. • The approach is based on the concept of information gain over a set of solutions. • Projection angles are selected based on the already available projection data. • The approach can lead to more accurate results from fewer projections. - Abstract: In X-ray tomography, a number of radiographs (projections) are recorded from which a tomogram is then reconstructed. Conventionally, these projections are acquired equiangularly, resulting in an unbiased sampling of the Radon space. However, especially in case when only a limited number of projections can be acquired, the selection of the angles has a large impact on the quality of the reconstructed image. In this paper, a dynamic algorithm is proposed, in which new projection angles are selected by maximizing the information gain about the object, given the set of possible new angles. Experiments show that this approach can select projection angles for which the accuracy of the reconstructed image is significantly higher compared to the standard angle selections schemes
Utility of dynamic computed tomography in diffuse liver diseases
International Nuclear Information System (INIS)
Fujikawa, Koichi; Inagawa, Akira; Yokoyama, Tatsushi; Iwamoto, Toshiyuki; Katayama, Hiroshi; Mori, Masaki; Ito, Katsuhide; Katsuta, Shizutomo.
1985-01-01
We tested the diagnostic abilities of dynamic CT in diffuse liver diseases. The material includes 23 cases of chronic active hepatitis (CAH), 32 cases of liver cirrhosis (LC) and 15 cases with normal liver. For each case, time-density curve was obtained from the right lobe of the liver. To allow numerical evaluation of the curve, gamma variate fit techniques were employed. Changes in the curves were analyzed by comparing three parameters-rise time (RT), decay time (DT) and corrected first moment (MC)-derived from two coefficients of the fitting equation. Values of three parameters increased with the severity of the diseases reflecting prolonged curves with delayed peak and gradual downslope in damaged livers. MC values showed most significant correlation with the degree of the diseases. High MC value (>95) were associated with 30 cases of LC and 3 cases of CHA, and moderate MC value (70< MC<=95) with 19 cases of CAH and 2 controls, and low MC value (<=70) with 15 controls and a case of CAH. We conclude that dynamic CT time-density study with gamma variate fitting is useful in the differential diagnosis of the diffuse liver diseases. (author)
Individual renal function study using dynamic computed tomography
International Nuclear Information System (INIS)
Fukuda, Yutaka; Kiya, Keiichi; Suzuki, Yoshiharu
1990-01-01
Dynamic CT scans of individual kindneys were obtained after an intravenous bolus injection of contrast agent. Time-density curves measured from the renal cortex, medulla and pelvis revealed the changes in density produced by the contrast agent reflecting the differential phase of renal function. Renal cortical density increased rapidly after bolus administration and then renal medullary and pelvic density increased continuously. In analyzing time-density curve, the cortico-medullary junction time, which is the time when the cortical and medullary curves cross was 57±8 seconds in patients with normal renal function. The cortico-medullary junction time was delayed in patient with decreased glomerular filtration rate. The cortico-pelvic junction time, which is the time when the cortical and pelvic curves cross was 104±33 seconds in patients with normal renal function. The cortico-pelvic junction time was delayed in patients with declined urinary concentrating capacity. In patients with unilateral renal agenesis and patients who were treated surgically by ureteral sprits, the relationship between individual renal functions and these junction times was examined. As a result of study there were inversely significant correlations between C-M junction time and unilateral GFR and between C-P junction time and urinary concentrating capacity. These studies indicate that dynamic CT scanning is an effective way that individual renal function can be monitored and evaluated. (author)
Validation of enhanced and dynamic computed tomography for cerebral ischemia
International Nuclear Information System (INIS)
Ono, Kenichiro; Arimoto, Hirohiko; Wada, Kojiro; Takahara, Takashi; Shirotani, Toshiki; Shimizu, Akira; Hatanaka, Kosuke
2003-01-01
This paper shows the usefulness of enhanced and dynamic CT for ischemic stroke patients. Sixteen patients with disturbance of consciousness or neurological sign who did not have low-density area on plain CT were selected for this study. We performed enhanced CT sequentially. Enhanced CT image, time-density curve and functional image were compared with final infarcted area and occlusion level of cerebral artery. Three patients whose enhanced CT images showed obvious laterality had occlusion of internal carotid (IC) or horizontal portion of middle cerebral artery (M1). Four of five patients whose functional image and time density curve revealed abnormal region had ischemia because of more peripheral vessel occlusion or IC stenosis. Others with no abnormality on all images had lacunar infarction or did not have infarction finally. Occlusion of cerebral artery proximal portion could be diagnosed only with enhanced CT images. If selected slice was fit to the lesion, more distant level of ischemic area could be determined 100% by time-density curve and functional image. This examination takes only about ten minutes without transferring the patient. Enhanced CT and dynamic scan is useful tool to determine the diagnosis and management for ischemic stroke patients. (author)
Do, Khanh
2015-10-22
In the quest to improve the performance of organic bulk-heterojunction solar cells, many recent efforts have focused on developing molecular and polymer alternatives to commonly used fullerene acceptors. Here, molecular dynamics simulations are used to investigate polymer-molecule blends comprised of the polymer donor poly(3-hexylthiophene) (P3HT) with a series of acceptors based on trialkylsilylethynyl-substituted pentacene. A matrix of nine pentacene derivatives, consisting of systematic chemical variation both in the nature of the alkyl groups and electron-withdrawing moieties appended to the acene, is used to draw connections between the chemical structure of the acene acceptor and the nanoscale properties of the polymer-molecule blend. These connections include polymer and molecular diffusivity, donor-acceptor packing and interfacial (contact) area, and miscibility. The results point to the very significant role that seemingly modest changes in chemical structure play during the formation of polymer-molecule blend morphologies.
Do, Khanh; Risko, Chad; Anthony, John E; Amassian, Aram; Bredas, Jean-Luc
2015-01-01
In the quest to improve the performance of organic bulk-heterojunction solar cells, many recent efforts have focused on developing molecular and polymer alternatives to commonly used fullerene acceptors. Here, molecular dynamics simulations are used to investigate polymer-molecule blends comprised of the polymer donor poly(3-hexylthiophene) (P3HT) with a series of acceptors based on trialkylsilylethynyl-substituted pentacene. A matrix of nine pentacene derivatives, consisting of systematic chemical variation both in the nature of the alkyl groups and electron-withdrawing moieties appended to the acene, is used to draw connections between the chemical structure of the acene acceptor and the nanoscale properties of the polymer-molecule blend. These connections include polymer and molecular diffusivity, donor-acceptor packing and interfacial (contact) area, and miscibility. The results point to the very significant role that seemingly modest changes in chemical structure play during the formation of polymer-molecule blend morphologies.
Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai
2018-06-13
An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.
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
Verifying Stability of Dynamic Soft-Computing Systems
Wen, Wu; Napolitano, Marcello; Callahan, John
1997-01-01
Soft computing is a general term for algorithms that learn from human knowledge and mimic human skills. Example of such algorithms are fuzzy inference systems and neural networks. Many applications, especially in control engineering, have demonstrated their appropriateness in building intelligent systems that are flexible and robust. Although recent research have shown that certain class of neuro-fuzzy controllers can be proven bounded and stable, they are implementation dependent and difficult to apply to the design and validation process. Many practitioners adopt the trial and error approach for system validation or resort to exhaustive testing using prototypes. In this paper, we describe our on-going research towards establishing necessary theoretic foundation as well as building practical tools for the verification and validation of soft-computing systems. A unified model for general neuro-fuzzy system is adopted. Classic non-linear system control theory and recent results of its applications to neuro-fuzzy systems are incorporated and applied to the unified model. It is hoped that general tools can be developed to help the designer to visualize and manipulate the regions of stability and boundedness, much the same way Bode plots and Root locus plots have helped conventional control design and validation.
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
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