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DNASUN: A package of computer programs for the biotechnology laboratory

Bioinformatics 1995年第3期11卷 331-335页

作者： Mironov, A.A. Alexandrov, N.N. Bogodarova, N.Yu. Grigorjev, A. Lebedev, V.F. Lunovskaya, L.V. Truchan, M.E. Pevzner, P.A. Laboratory of Mathematical Methods National Center for Biotechnology NIIGENETIKA Moscow 113545 Russian Federation National Cancer Institute Frederick MD 21702 United States Imperial Cancer Research Fund London WC2A 3PX 44 Lincoln's Inn Fields United Kingdom Department of Computer Science and Engineering Pennsylvania State University University Park PA 16802 United States

The paper describes a new software package DNASUN developed for supporting gene engineering laboratories. The package provides a user-friendly interface for experimental researches and supports the traditional nucleotide/protein sequence analysis as well as physical mapping, sequencing, plasmid manipulations, optimal oligonucleotide probe selection and other common molecular biology procedures. © 1995 Oxford University Press.

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PARALLEL AND DISTRIBUTED TLM COMPUTATION WITH SIGNAL-PROCESSING FOR ELECTROMAGNETIC-FIELD MODELING

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INTERNATIONAL JOURNAL OF NUMERICAL MODELLING-ELECTRONIC NETWORKS DEVICES AND FIELDS 1995年第3-4期8卷 169-185页

作者： SO, PPM ESWARAPPA, C HOEFER, WJR NSERC/MPR Teltech Research Chair in RF Engineering Department of Electrical and Computer Engineering University of Victoria Victoria British Columbia V8W 3P6 Canada Poman So received his B.Sc. degree in computer science and physics from the University of Toronto Toronto Onatario Canada in 1985. He obtained his B.A. Sc. and M.A.Sc. degrees in electrical engineering (summa cum laude) from the University of Ottawa Ottawa Ontario Canada in 1987 and 1989 respectively. Mr So was a research engineer in the University of Ottawa from January 1989 to October 1991 his research interests included CAD techniques of microwave circuits and numerical methods for electromagnetic wave modelling. He specialized in the development of electromagnetic engineering CAD software and successfully implemented a number of electromagnetic wave simulators based on the two-dimensional and three-dimensional transmission-line matrix methods. From August 1990 to February 1991 he accompanied Professor W. J. R. Hoefer to Rome Italy and Sophia Antiopolas France. During that time he implemented a parallel version of the 3D-TLM simulator for the CM-2 Connection Machine using C-Star and X Windows Library. He is a research engineer and a Ph.D. student at the University of Victoria Victoria British Columbia Canada. He ported the 2D- and 3D-TLM simulators to DECmpp 1200 massively parallel computer using MPL C and C++. He also combined OSA90/hope a commercially available microwave CAD program with a 2D-TLM simulation module for geometry optimization using the Datapipe technique of OSA90/hope. Recently he has developed a distributed client-server computing technique for the TLM method this technique could accelerate the TLM simulation by more than an order of magnitude. Channabasappa Eswarappa received the M.Tech. degree in electrical engineering from the Indian Institute of Technology Kanpur India in 1983 and Ph. D. degree from the University of Ottawa Canada in 1990. He worked as an Assistant Executive Engineer and later as

This paper describes the implementation of transmission-line matrix (TLM) method algorithms on a massively parallel computer (DECmpp 12000), the technique of distributed computing in the UNIX environment, and the combination of TLM analysis with Prony's method as well as with autoregressive moving average (ARMA) digital signal processing for electromagnetic field modelling. By combining these advanced computation techniques, typical electromagnetic field modelling of microwave structures by TLM analysis can be accelerated by a few orders of magnitude.

关键词： Mathematical models

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Distributed automation control using broadcasting networks

Distributed automation control using broadcasting networks

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International Conference on Industrial Electronics, Control and Instrumentation

作者： I. Lobl P. Morel Department of Microengineering Laboratory of Methods and Techniques for Assembly Swiss Federal Institute of Technology Lausanne Switzerland Department of Computer Science Laboratory of Industrial Computing Swiss Federal Institute of Technology Lausanne Switzerland

Assembly stations, also known as cells, is a generalised term denoting the place where one of the operations is carried out in the sequence needed to assemble a product. As each station is in general dedicated to a specific operation for a specific product, it is uncommon to find two instances of the same station. Stations are custom designed and expensive. The authors have developed standard modular assembly station components that one just has to "plug together to operate". The authors present in this paper an original solution using the LAN system from LonWorks. This solution is at present operational on real production and test cells.< >

关键词： Automation Distributed control Automatic control Broadcasting Assembly Standards development Field buses Laboratories Local area networks Production

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3-D EDGE ELEMENT ANALYSIS OF DIELECTRIC-LOADED RESONANT CAVITIES

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INTERNATIONAL JOURNAL OF NUMERICAL MODELLING-ELECTRONIC NETWORKS DEVICES AND FIELDS 1994年第1期7卷 35-41页

作者： ZHU, ZL DAVIES, JB FERNANDEZ, FA Department of Electronic and Electrical Engineering University College London WC1E 7JE U.K. On leave from the Department of Radio Electronics Peking University Beijing 100871 People's Republic of China. Le-zhu Zhou was born in Guizhou China in 1944. He received the B.S. degree in Physics and M.S. degree in Electronics from Peking University Beijing China in 1968 and 1981 respectively. Since 1981 he has been on the staff of the Department of Radio-Electronics of Peking University. In 1983 he was appointed as a Lecturer. In 1989 he became an Associate Professor. Since September 1991 he has been doing research as an Academic Visitor at the Department of Electronic and Electrical Engineering of University College London. He has been engaged in the electromagnetic field theory and its application. Recently his research interest has been in the computer modelling of optical and microwave structures by using edge element methods. J. Brian Davies was born in Liverpool England in 1932. He received the B.A. degree in mathematics in 1955 from Jesus College Cambridge England. He received the M.Sc. degree in mathematics the Ph.D. degree in mathematical physics and the D.Sc. (Eng) degree in engineering in 1957 1960 and 1980 respectively from the University of London England. From 1955 to 1963 he worked at the Mullard Research Laboratories Salford Surrey England except for two years spent at University College London. In 1963 he joined the academic staff of the Department of Electrical Engineering University of Sheffield England. Since 1967 he has been on the staff at University College London where he is now Professor of Electrical Engineering. From 1971 to 1972 he was Visiting Scientist at the National Bureau of Standards Boulder CO. In 1983 he was a Visitor at the Department of Engineering Science University of Oxford England. From 1988 to 1989 he was a Visiting Professor at the University of Colorado Boulder CO. His research interests have included microwave and optical aspects of electr

The eigenmodes in electromagnetic cavities, loaded with arbitrarily shaped dielectric materials, are computed by the edge element method. The computation shows that the well known 'spurious modes' no longer appear. Formulae are given and verified so that the number of zero eigenvalues, which come from del x H = 0, may be accurately predicted. Formulae for the order and density of the global matrices are given for a rectangular cavity regularly divided into bricks and tetrahedra, allowing an associated comparison between the contrasting edge and nodal element formulations. Comparison of the computed results with available theoretical and previously published data show the edge element approach to be a robust, accurate and effective method.

关键词： Dielectric waveguides

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Nondifferentiable design optimization problems with application to control engineering

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Optimization 1992年第1期25卷 83-90页

作者： Venkov, G.I. Krushev, N.I. Technical University of Sofia Dept. of Numerical Methods and Analysis Institute of Applied Mathematics and Computer Science Bulgaria

The problems and algorithms in question are applied to the parameter design of automatic control systems. The generality of (1-1) permits the definition of a wide range of constraints in the time and frequency domains, as well as on the eigenvalues and singular values of the system matrices. The designer can set up and satisfy direct requirements to the form of the output reaction, the locus of the return difference, the frequency characteristics, the degree of stability etc. Examples and graphics illustrate the characteristic features of the methods discussed. The algorithms are implemented in a software system for vector optimization developed by the authors. © 1992 Gordon and Breach science Publishers S.A.

关键词： control engineering design optimization Non-differentiable optimization

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COMPARISON OF DOWNHOLE AND SURFACE SAMPLING FOR THE DETERMINATION OF VOLATILE ORGANIC-COMPOUNDS (VOCS) IN GROUND-WATER

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GROUND WATER MONITORING AND REMEDIATION 1992年第1期12卷 126-133页

作者： ROSEN, ME PANKOW, JF GIBS, J IMBRIGIOTTA, TE Michael E. Rosen received his B.A. in chemistry from the State University of New York at Binghamton in 1981 and a Ph.D. in environmental science and engineering from the Oregon Graduate Institute in 1988. His research interests include trace environmental analysis of organic compounds. He is now manager of the Voluntary Cleanup Section of the Oregon Department of Environmental Quality (Environmental Cleanup Division 811 S.W. 6th Ave. Portland OR 97204) where he is working to develop streamlined procedures and processes for the investigation and cleanup of hazardous substance sites. James F. Pankow is professor and chairman of the Department of Environmental Science and Engineering at the Oregon Graduate Institute (Oregon Graduate Institute of Science and Technology Department of Environmental Science and Engineering 19600 N.W. von Neumann Dr. Beaverton OR 97006–1999). He received his B.A. in chemistry in 1973 from the State University of New York in Binghamton and his Ph.D. in environmental engineering science from the California Institute of Technology in Pasadena California in 1979. His group is involved in the study of the physical and chemical processes affecting the behavior of organic and inorganic chemicals in the environment. This work includes the development and application of sensitive analytical methods for the determination of trace organic contaminants in ground water systems. Jacob Gibs is an environmental engineer with the U.S. Geological Survey Water Resources Division (810 Bear Tavern Rd. Ste. 207 West Trenton NJ 08628). He received a B.S. in mechanical engineering in 1968 an M.S. in environmental engineering in 1975 and a Ph.D. in environmental engineering in 1983 all from Drexel University Philadelphia Pennsylvania. He is currently project chief of a study on representative sampling of ground water for trace levels of organic compounds. His research interests include evaluating ground water sampling techniques and devices for purgeable organic compounds design of sampling

The relative precision and accuracy of sampling and analysis methods for the determination of trace concentrations of volatile organic compounds (VOCs) in ground water were compared. Samples were collected from a well containing nanogram-per-liter (ng/L) to microgram-per-liter (mu-g/L) levels of VOCs. A Keck helical rotor submersible pump was used to collect samples at the surface for analysis by purge and trap (P&T) and for analysis by adsorption/thermal desorption (ATD). Downhole samples were collected by passing water through an ATD cartridge. Although slight spontaneous bubble outgassing occurred when the water was brought to the surface, the relative precisions and comparabilities of the surface and downhole methods were generally found to be equivalent from a statistical point of view. A main conclusion of this study is that bringing sample water to the surface for placement in VOC vials (and subsequent analysis by P&T) can be done reliably under many circumstances. However, care must still be taken to prevent adsorption losses and cross contamination. Samples subject to strong bubble outgassing will need to be handled in a special fashion (e.g., by downhole ATD) to minimize volatilization losses. Additionally, the higher sensitivity of the ATD method allows lower detection limits than are possible with P&T. For example, several compounds present at the ng/L level could be determined with confidence by ATD, but not by P&T.

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COMPARATIVE STRUCTURAL LIFE ASSESSMENT OF PATROL BOAT BOTTOM PLATING

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NAVAL ENGINEERS JOURNAL 1990年第3期102卷 253-262页

作者： AYYUB, BM WHITE, GJ BELLWRIGHT, TF PURCELL, ES Bilal M. Ayyub:is currently an associate professor of civil engineering at the University of Maryland. He received his B.S. degree in civil engineering from the University of Kuwait in 1980. He completed both his M.S. (1981) and Ph.D. (1983) in civil engineering at the Georgia Institute of Technology. Dr. Ayyub has an extensive background in risk-based analysis. He is engaged in research work involving structural reliability marine structures and mathematical modeling using the theories of probability statistics and fuzzy sets. His research work has been sponsored by the National Transportation Safety Board National Science Foundation U.S. Coast Guard Department of Defense State of Maryland and University of Maryland. He is the author of more than 100 publications in national and international journals conference proceedings and reports. Dr. Ayyub was a recipient of the ASNE “Jimmie” Hamilton Award for 1985 the ASCE “Outstanding Research Oriented Paper” in theJournal of Water Resources Planning and Managementfor 1987 and Edmund Friedman Young Engineer Award for Professional Achievement from ASCE for 1989. Gregory J. White:is an associate professor of naval architecture at the U.S. Naval Academy. He received his B.S. degreein engineering mechanics from Vanderbilt University in 1975 an M.E. degree in naval architecture from the University of California Berkeley in 1981 and a Ph.D. in civil engineering (structures) from the University of Maryland in 1986. Dr. White served on active duty with the U.S. Navy from 1975 to 1979 as a junior officer in the engineering and operations departments of Pacific Fleet destroyers. Prior to coming to the Naval Academy he worked at Mare Island Naval Shipyard in the scientific code and in the R&D division of Exxon International company's Tanker Department. Dr. White is the author of more than two dozen technical articles and reports and is one of the U.S. representatives to the International Ship and Offshore Structures Congress (ISSC). His research interests lie in t

The estimation of an absolute life expectancy of a structure is a complex process and the results are expected to have relatively large levels of uncertainty. In this study, a comparative analysis is undertaken between two different patrol boats. This is an approach which results in a higher confidence level because certain factors common to both boats can be eliminated by assuming them to be at constant normal levels. The study is limited to the critical forward bottom plating and takes into account the differences in material, plate dimensions, operational profile, structure and loading of the two vessels. Two failure modes, plastic plate deformation and fatigue, are considered, and a novel approach to plate wastage is included. Many factors affect the structural life of a vessel. They include structural type, operational profile, structural details, loads, inspection and maintenance, design methods, safety factors, corrosion, and environmental factors. There are three types of uncertainty associated with these factors; namely, physical randomness, statistical uncertainties, and model uncertainties. The method described is designed to address these uncertainties. The objective of the paper is to present the reliability-based structural life assessment method, and then to use it to evaluate and compare the structural performance of the forward bottom plating of the two patrol boats. The results of the evaluation are presented in the form of graphs and tables in order to facilitate the comparative evaluation. The method is performed within a computer-based format which allows parametric sensitivity analysis of several variables including the size of the plating panel, thickness, operational profile and loading. The sensitivity of the structural life expectancy of the forward bottom plating to variations in these parameters is evaluated.

关键词： Naval Vessels

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Analysis of artificial viscosity effects on reacting flows using a spectral multidomain technique

Analysis of artificial viscosity effects on reacting flows u...

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作者： Macaraeg, Michéle G. Streett, Craig L. Hussaini, M.Y. NASA Langley Research Center HamptonVA United States Institute for Computer Applications in Science and Engineering HamptonVA United States Computational Methods Branch Theoretical Aerodynamics Branch

Standard techniques used to model chemically reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least two computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. Present-day upwind schemes, which may be nonoscillatory and monotonic, are inherently dissipative, so that artificial viscosity exists in their fundamental formulation. In this study, the effects of imposing an artificial thickness on a calculated shock is investigated. The present study incorporates a nonequilibrium chemistry model for air into a multidomain spectral Navier-Stokes calculation. The computation follows the chemical kinetics and flow kinematics of a gas passing through a fully resolved viscous shock wave at hypersonic Mach numbers. Because no artificial viscosity, either added or inherent, is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features is determined. © 1987 American institute of Aeronautics and Astronautics, Inc. No copyright is

关键词： Chemical stability

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ESTIMATION OF STRUCTURAL SERVICE LIFE OF SHIPS

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NAVAL ENGINEERS JOURNAL 1989年第3期101卷 156-166页

作者： AYYUB, BM WHITE, GJ PURCELL, ES P.E. Bilal M. Ayyub:is currently an associate professor of civil engineering at the University of Maryland. He received his B.S. degree in civil engineering from the University of Kuwait in 1980. He completed both his M.S. (1981) and Ph.D. (1983) in civil engineering at the Georgia Institute of Technology. Dr. Ayyub has an extensive background in risk-based analysis and design simulation and construction engineering. He is engaged in research work involving structural reliability bridges marine structures and mathematical modeling using the theories of probability statistics and fuzzy sets. His research work is sponsored by the National Transportation Safety Board the National Science Foundation the U.S. Coast Guard the State of Maryland and the University of Maryland. Dr. Ayyub is a member of ASNE the American Society of Civil Engineers (ASCE) the American Concrete Institute (ACI) the Committee on Forensic Engineering of ASCE and the Committee on Structural Safety of ACI. He is the author of more than three dozen publications in national and international journals conference proceedings and reports. Dr. Ayyub received the ASNE “Jimmie” Hamilton Award for 1985 and the ASCE “Outstanding Research Oriented Paper” in the Journal of Water Resources Planning and Management for 1987. Gregory J. White:is an associate professor of naval architecture at the U.S. Naval Academy. He received his B.S. degree in engineering mechanics from Vanderbilt University in 1975 an M.E. degree in naval architecture from the University of California Berkeley in 1981 and a Ph.D. in civil engineering (structures) from the University of Maryland in 1986. Dr. White served on active duty with the U.S. Navy from 1975 to 1979 as a junior officer in the engineering and operations departments of Pacific Fleet destroyers. Prior to coming to the Naval Academy he worked at Mare Island Naval Shipyard in the scientific code and in the R&D division of Exxon International Company's Tanker Department. Dr. White is a lieutenant commande

A methodology for the structural life assessment of a ship's structure is suggested. The methodology is based on probabilistic analysis using reliability concepts and the statistics of extremes. In this approach, the estimation of structural life expectancy is based on selected failure modes. All possible failure modes of the ship must be investigated and the most likely paths to structural failure identified. For the purpose of illustration two failure modes are considered in this study. They are plate plastic deformation and fatigue cracking. Structural life based on these two failure modes is determined for an example vessel. The methodology determines the probability of failure of the ship's structural components according to the identified failure modes as a function of time. The results can be interpreted as the cumulative probability distribution function (CDF) of structural life. Due to the unknown level of statistical correlation between failure modes, limits or bounds on the CDF of the structural life are established. The limits correspond to the extreme cases of fully correlated and independent failure modes. The CDFs of structural life are determined for two inspection strategies; namely, inspection every year and inspection every two years with a warranty inspection at the end of the first year. The meaning of the results for the case investigated in this study is that, for example, given an inspection strategy of two years and a desired life of 15 years, there is a 72% chance that the vessel will not experience enough partial damage‘ in the failure modes identified to constitute reaching the “end of structural life” as defined.

关键词： Ships

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Numerical experiments on subcritical transition mechanisms

Numerical experiments on subcritical transition mechanisms

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AlAA 23rd Aerospace sciences Meeting, 1985

作者： Zang, Thomas A. Hussaini, M. Yousuff Computational Methods Branch High-speed Aerodynamics Division NASA Langley Research Center HamptonVA United States Institute for Computer Applications in Science and Engineering NASA Langley Research Center HamptonVA United States

A spectral algorithm for simulating three-dimensional, incompressible, parallel shear flows is described. It applies to the channel, to the parallel boundary layer, and to other shear flows with one wall-bounded and two periodic directions. Simulations performed for the channel identify the one nonlinear interaction which is crucial to the secondary instability. Moreover, it is shown that subharmonic instability ensues for Reynolds numbers as low as 1500. Simulations performed for the heated water boundary layer reveal the operation of the secondary instability in this controlled flow. © 1985, American institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

关键词： Boundary layers

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