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186 Molecular dynamics and ligand based studies for the validation of potential inhibitors for SrtA againstBacillus anthracis

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Journal of Biomolecular Structure and Dynamics 2013年第SUPP 1期31卷 119-120页

作者： Sanjeev Kumar Singh[a][*] & Chandrabose Selvaraj[a] [a] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi 630003 India Phone: Phone: +91-4565-230725 Fax: Phone: +91-4565-230725

SrtA enzymes cleave the sorting signals of secreted proteins to form isopeptide (amide) bonds between the secreted proteins and peptidoglycan or polypeptides to function as the principal architects of theBacillus anthracis. Inhibition of SrtA can completely eradicate the growth ofB. anthracisdue to the lack of signals and so the SrtA is universally accepted as the drug target for all gram positive pathogens. Here, with the reported compounds, the pharmacophore-based virtual screening protocol has been used to obtain similar pharmacological property that derived new compounds to inhibit the SrtA structure. New compounds on AAAHR Pharmacophore hypothesis screening were treated with four phase of docking protocols with combined Glide-QPLD docking approach and charge accuracy variations were dominated by QM/MM approach. Finally, the compounds of 19941, 14704, 121962, 20137, and 19533 from binding db, Chembridge db, and Toslab were succeeded from the screening; these compounds are having better scoring, energy parameters, ADME physio/chemical properties, tendency to transfer the electrons between the protein–ligand interactions, and these compounds also predict having cell adhesion inhibitory activity. These screened compounds have better stability at active site loop regions with strong bonding interactions and these compounds on clinical trials will definitely emerge as better SrtA inhibitor against theB. anthracis.

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195In silicostudy on HIV-PRIs substructures to terminate proteolytic activity in HTLV

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Journal of Biomolecular Structure and Dynamics 2013年第SUPP 1期31卷 127页

作者： Poonam Singh[a][*] Sanjeev Kumar Singh[b] Chandrabose Selvaraj[b] & Rama Kant Singh[a] [a] Toxicology Division Central Drug Research Institute Lucknow 226 001 Uttar Pradesh India Phone: Phone: +91-522-2612411 Fax: Phone: +91-522-2612411 [b] Computer Aided Drug Design and Molecular Modeling Lab Department of Bioinformatics Alagappa University Karaikudi 630003 Tamilnadu India

Human T-lymphotropic virus (HTLV) is RNA retrovirus, which causes CD3 + and CD4 + T-cell type leukemia and demyelinating diseases, like tropical spastic myelopathy. The replicative stage of the virus is one of the critical stages for the development of the disease. At present, there are no approved therapeutic agents targeting HTLV. The HTLV mechanism of malignant cell growth in adult T-cell leukemia (ATL)/lymphoma, and the HTLV-PR has been an attractive target for anticancer drug design. In comparison with other retroviruses, HTLV also encodes protease (PR) enzyme which is essential for maturation. Both the HIV and HTLV proteases show high structural similarity but known inhibitors of HIV-PR are not able to inhibit the HTLV-PR, while comparing the binding pocket of both proteases, MET37 of HTLV shows repulsive role with known HIV inhibitors. Functional analysis of M37A mutation clearly shows that MET37 is highly important for the protease function. Available inhibitors were tested against the HTLV-PR binding pocket and failed to interact with MET37. Screening of similar libraries of known compounds provides better interactions with MET37 and further validation within vivoandin vitrostudies on these screened compounds will provide more strength in discovering potent inhibitor for HTLV-PR.

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Conceptual design of compliant mechanisms using level set method

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中国高等学校学术文摘·机械工程 2006年第2期1卷 131-145页

作者： Shi-kui CHEN Michael Yu WANG Computational Modeling and Design Laboratory Department of Automation and Computer-Aided EngineeringThe Chinese University of Hong KongShatinN.T.Hong KongChina

We propose a level set method-based framework for the conceptual design of compliant *** this method,the compliant mechanism design problem is recast as an infinite dimensional optimization problem,where the design variable is the geometric shape of the compliant mechanism and the goal is to find a suitable shape in the admissible design space so that the objective functional can reach a *** geometric shape of the compliant mechanism is represented as the zero level set of a one-higher dimensional level set function,and the dynamic variations of the shape are governed by the Hamilton-Jacobi partial differential *** application of level set methods endows the optimization process with the particular quality that topological changes of the boundary,such as merging or splitting,can be handled in a natural *** making a connection between the velocity field in the Hamilton-Jacobi partial differential equation with the shape gradient of the objective functional,we go further to transform the optimization problem into that of finding a steady-state solution of the partial differential *** the above-mentioned methodological issues,some numerical examples together with prototypes are presented to validate the performance of the method.

关键词： compliant mechanisms conceptual design level set methods shape gradient Hamilton- Jacobi PDE

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Developing a prototype concurrent design tool for composite topside structures

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NAVAL ENGINEERS JOURNAL 1997年第3期109卷 279-290页

作者： Dirlik, S Hambric, S Azarm, S Marquardt, M Hellman, A Bartlett, S Castelli, V Steve Dirlik:began his career at the Naval Surface Warfare Center Carderock Division in 1981 as an aerospace engineer co-op student. He completed his bachelor of science degree in aeropace and ocean engineering from Virginia Polytechnic Institute and State University in 1985 and his master of science degree in aerospace engineering from the University of Maryland in 1990. Mr. Dirlik recently completed a master of science program in applied physics at The Johns Hopins University and currently works in the Radar Cross Section and Target Physics Branch of the Signatures Directorate at the Naval Surface Warfare Center Corderoke Division. He has worked on Navy low observable programs since 1990. Stephen Hambric:is a research associate at the Applied Research Laboratory at The Pennsylvania State University. He received his B. S. and M.S. degree in mechanical engineering from Virginia Polytechnic Institute and State University and his D. Sc. in mechnical engineering from the George Washington University. He has worked on several computer aided multidiscikplinary design and optimization projects over the years including an automated propeller design system and a structural acoustic optimization capability. Dr. Shpour Azarm:is currently working as an associate professor with the Design and Manufacturing Group of the Department of Mechanical Engineering at the University of maryland at College Park. Dr Azarm's expertise is in the areas of optimization-based designed and concurrent design and optimization of multidisciplinary systems. He was a consultant at Black & Decker Corporation (summer 1996) and worked as a Navy senior summer faculty fellow (summer 1995) and a NASA summer faculty fellow (summer 1994). He was a visiting scientist at NASA Langley Research Center for Multidisciplinary Analysis and Applied Structural Optimzatiom at the University of Siegen in Germany (spring 1992) and the Design Institute of the Technical University of Denmark (summer 1990). Dr Azarm was an associate technical editor of the ASME Jour

A prototype concurrent engineering tool has been developed for the preliminary design of composite topside structures for modern navy warships. This tool, named GELS for the Concurrent Engineering of Layered Structures, provides designers with an immediate assessment of the impacts of their decisions on several disciplines which are important to the performance of a modern naval topside structure, including electromagnetic interference effects (EMI), radar cross section (RCS), structural integrity, cost, and weight. Preliminary analysis modules in each of these disciplines are integrated to operate from a common set of design variables and a common materials database. Performance in each discipline and an overall fitness function for the concept are then evaluated. A graphical user interface (GUI) is used to define requirements and to display the results from the technical analysis modules. Optimization techniques, including feasible sequential quadratic programming (FSQP) and exhaustive search are used to modify the design variables to satisfy all requirements simultaneously. The development of this tool, the technical modules, and their integration are discussed noting the decisions and compromises required to develop and integrate the modules into a prototype conceptual design tool.

关键词： Warships

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Influence of human engineering on manning levels and human performance on ships

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NAVAL ENGINEERS JOURNAL 1997年第5期109卷 67-76页

作者： Anderson, DE Oberman, FR Malone, TB Baker, CC David E. Anderson:has a bachelor of science degree in environmental engineering from Florida Technological University and a master's degree in environmental engineering from the University of Central Florida. He is a graduate of the Naval Sea Systems Command's Engineer-In-Training (EIT) Program. Mr. Anderson was instrumental in introducing the collective protection system (CPS) in the U.S. Navy developing the initial forward-fit package for the USS Gunston Hall and the engineering change proposal (ECP) for the USS Wasp. In 1990 he joined the Human Systems Integration (HSI) Division (SEA 55W5) where he was task leader for auxiliary ships. He is currently the HSI manager for the future technology variant of the SeaLift ship and the future carrier. Association of Scientists and Engineers 33rdAnnual Technical Symposium 26 April 1996. Fred R. Oberman:has B.A. and M.A. degrees from the University of Chicago and Loyola University (experimental psychology) and an M.S. degree in industrial engineering and operations research from Virginia Polytechnic Institute (VPI). He has more than 30 years experience in HSI management planning research analysis design and testing in government and private sector positions. He is currently responsible for NavSea HSI generic research and tool development efforts. He is responsible for Human Engineering Specifications and Standards (Commercial Hypertext) and is the NavSea 03D7 representative on HSI in Performance Specifications and for integration of HSI within Integrated Logistic Support (ILS). He has served as DoD HSI SubTAG chair and member of the Simulation and Modeling Test and Evaluation Display and Control Systems Human Computer Interaction Specifications and Standards and Systems Design Sub Tags as a member of the Society of Naval Architects and Marine Engineers (SNAME) Systems Safety Panel and a member of NATO RSG 14 on man-machine analysis. Thomas B. Malone: CHFEP received a Ph.D. in experimental psychology from Fordham University in 1964. He is president of Carlow

The objectives of Human Engineering (HE) are generally viewed as increasing human performance, reducing human error, enhancing personnel and equipment safety, and reducing training and related personnel costs. There are other benefits that are thoroughly consistent with the direction of the Navy of the future, chief among these is reduction of required numbers of personnel to operate and maintain Navy ships. The Naval Research Advisory Committee (NRAC) report on Man-Machine Technology in the Navy estimated that one of the benefits from increased application of man-machine technology to Navy ship design is personnel reduction as well as improving system availability, effectiveness, and safety The objective of this paper is to discuss aspects of the human engineering design of ships and systems that affect manning requirements, and impact human-performance and safety The paper will also discuss how the application of human engineering leads to improved performance, and crew safety, and reduced workload, all of which influence manning levels. Finally, the paper presents a discussion of tools and case studies of good human engineering design practices which reduce manning.

关键词： Human engineering

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USING VIRTUAL ENVIRONMENTS IN THE design OF SHIPS

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NAVAL ENGINEERS JOURNAL 1994年第3期106卷 91-106页

作者： JONS, OP RYAN, JC JONES, GW Otto P. Jons:received a Diplom Ing. in shipbuilding from the Technical University of Hanover W. Germany and an MS in naval architecture and marine engineering from MIT. He then joined Litton Ship Systems where he was responsible for the preliminary design of the DD-963 hull structure and then for ship system integration as manager LHA ship systems engineering department. From 1972 to 1974 he was the principal research scientist at Hydronautics. In 1974 as technical director he helped establish the Crystal City office of Designers and Planners. Mr. Jons was one of the co-founders of Advanced Marine Enterprises Inc. in 1976 where he serves as corporate vice president engineering. J. Christopher Ryan:earned his bachelors and masters degrees in naval architecture from Webb Institute and MIT respectively. He spent three years at the advanced marine technology division of Litton Industries working on the DD-963 class ship design and related computer aided design projects. He subsequently went to the Navy Department concentrating on early stage design of surface combatants for twelve years including work on the FFG-7 Sea Control Ship CSGN and CVV aircraft carrier projects. He then shifted focus and became the Technical Director for the Computer Supported Design Program in NavSea for five years. Mr. Ryan has served in several supervisory positions within the Ship Design Group in NavSea since that time. He is currently the director of the future ship concepts division. Gary W. Jones:graduated from the University of Tennessee in 1971 with a BS in mechanical engineering and followed up with graduate work at George Washington University and the University of Maryland. Mr. Jones was with the Naval Sea Systems Command from 1971 until 1988 where he was a naval architect in the submarine section of the hull form design division. In 1988 he was detailed to the Defense Advanced Research Projects Agency (DARPA) where he became the program manager for the advanced submarine technology program's hydrodynamic hydroac

A major contributor to the expense and length of time to design, build, and test new systems has been the need to build and test hardware prototypes to determine their effectiveness in meeting operational requirements. Recent and dramatic advances in computer simulation technologies hold forth the promise of revolutionizing design and acquisition strategies by providing the means to validate end users' requirements prior to hardware construction. By designing and operationally testing virtual prototypes in a virtual environment, these technologies will soon offer naval architects the ability to build and launch ships in computer-based cyberspace in lieu of the shipbuilder's ways. The authors of this paper provide the background for these developments, explore the significance and ramifications of these technologies to the current process of ship and system design, outline challenges lying ahead, and present their vision and recommendations for future development.

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AN EFFICIENT SCHEME FOR SIMULATING LARGE, PASSIVE MICROSTRIP LAYOUTS

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INTERNATIONAL JOURNAL OF MICROWAVE AND MILLIMETER-WAVE computer-aided ENGINEERING 1992年第4期2卷 253-260页

作者： WU, DI MIMICAD Center Department of Electrical and Computer Engineering University of Colorado Boulder Colorado 80309 From 1980–1983 She was a Member of Technical Staff at Bell Laboratories AT&T Indianpolis. Indian where she was engaged in the study of radio frequency interference. From 1987-1988 she was with the National Institute of Standards and Technology working in the area of field characterization and measurment. Since 1989. she has been a member of the research faculty with the Center for Microwave Computer-Aided Design atthe University of Colorado. Presently she is also the President of Boulder Microwave Technologies Inc. a firm specializing in the development of computer-aided design tools and methodologies for electromagnetics. Her research intetest include CAD antenna radiation scattering and numerical modeling. Dr. Wu is an associate member of URSI Commission B.

An efficient algorithm is presented here for simulating large, passive, microstrip layouts using a circle of influence approach with a full-wave/integral-equation-based numerical solver. The procedure involves dividing the circuit into standard subcomponents or blocks and assigning a circle of influence for each block. Relying on physical intuition, the computation of the couplings between blocks is then limited to those that fall within the circle. By adjusting the circle size, different orders of parasitic coupling can be included in the simulation process. Local junction effects from the individual blocks and the parasitic couplings between blocks that are in close physical proximity can always be taken into account. aided by a newly developed graphical user interface, the tradeoff between computational efficiency and accuracy is examined by varying the diameter of the circle of influence. Data are presented to illustrate the effectiveness of this new approach.

关键词： Microstrip Devices

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REASONING ON THE LOCATION OF COMPONENTS FOR ASSEMBLY PACKAGING

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JOURNAL OF MECHANICAL design 1991年第4期113卷 402-407页

作者： KIM, JJ GOSSARD, DC T. J. Watson Research Center Interactive Geometric Modeling IBM Research Division Yorktown NY 10598 Computer-Aided Design Laboratory Department of Mechanical Engineering Massachusetts Institute of Technology Cambridge MA 02139

The process of locating components in an available space while satisfying spatial relationships among the components is called packaging. The task requires extensive spatial reasoning about geometric shapes. It is a generic design task common to many domains. It is also very time-consuming, especially as machines become more compact and complex. This paper describes progress toward automation of the packaging problem. An approach is proposed to determine the optimal locations of components in an assembly from spatial relationships between the components. The approach utilizes a novel combination of optimization and solid modeling techniques.

关键词： Machinery Optimization Solid modeling Packaging design Shapes Manufacturing

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An algorithm for discrete event logic simulation on distributed systems

An algorithm for discrete event logic simulation on distribu...

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IEEE Region 10 International Conference TENCON

作者： S. Sundaram T.S. Mohan L.M. Patnaik Computer Aided Design Laboratory Indian Institute of Technology Bangalore India Knoirkdgr Based Computer System Laboratory Supercomputer Education and Research Centre Indian Institute of Technology Bangalore India Department of Compritei Scienceand Automation Indian Institute of Technology Bangalore India

Increase in the complexity of VLSI digital circuit design demands faster logic simulation techniques than those currently available. One of the ways of speeding up existing logic Simulation Agorithms is by exploiting the inherent parallelism of the sequential version. In this paper, we explore the possibility of mapping an event driven logic simulation algorithm onto a cluster of processors interconnected by an ethernet. The set of events at any simulation time. step is partitionecl by the Master Task (running on the host processor) anlong the Worker Tasks(running of the other processor's). The partitioning scheme ensures a balanced load. Each Worker Task determines the fanout, elementts, evaluates them independently and comes up with the new event list which is passed onto the Master Task. After receiving the event lists from all the workers, the Master Task increments the simulation time step, computes the new event list partition for the next simulation cycle. We have implemented this distributed logic simulation algorithm on a set of 8 VAXstations using CT - a package for distributed programming. The paper concludes with a note on the speedup figures obtained on the ISCAS benchmark circuits.

关键词： Discrete event simulation Circuit simulation Computational modeling Packaging Delay Partitioning algorithms Runtime Logic circuits Distributed computing Very large scale integration

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ROLE OF SIMULATION IN RAPID PROTOTYPING FOR CONCEPT DEVELOPMENT

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NAVAL ENGINEERS JOURNAL 1991年第3期103卷 204-211页

作者： KING, JF BARTON, DE J. Fred King:is the manager of the Advanced Technology Department for Unisys in Reston Virginia. He earned his Ph.D. in mathematics from the University of Houston in 1977. He has been principal investigator of research projects in knowledge engineering pattern recognition and heuristic problem-solving. Efforts include the development of a multi-temporal multispectral classifier for identifying graincrops using LANDSAT satellite imagery data for NASA. Also as a member of the research team for a NCI study with Baylor College of Medicine and NASA he helped develop techniques for detection of carcinoma using multispectral microphotometer scans of lung tissue. He established and became technical director of the AI Laboratory for Ford Aerospace where he developed expert scheduling modeling and knowledge acquisition systems for NASA. Since joining Unisys in 1985 he has led the development of object-oriented programming environments blackboard architectures data fusion techniques using neural networks and intelligent data base systems. Douglas E. Barton:is manager of Logistics Information Systems for Unisys in Reston Virginia. He earned his B.A. degree in computer science from the College of William and Mary in 1978 and did postgraduate work in London as a Drapers Company scholar. Since joining Unisys in 1981 his work has concentrated on program management and software engineering of large scale data base management systems and design and implementation of knowledge-based systems in planning and logistics. As chairman of the Logistics Data Subcommittee of the National Security Industrial Association (NSIA) he led an industry initiative which examined concepts in knowledge-based systems in military logistics. His responsibilities also include evaluation development and tailoring of software engineering standards and procedures for data base and knowledge-based systems. He is currently program manager of the Navigation Information Management System which provides support to the Fleet Ballistic Missile Progr

A valuable technique during concept development is rapid prototyping of software for key design components. This approach is particularly useful when the optimum design approach is not readily apparent or several known alternatives need to be rapidly evaluated. A problem inherent in rapid prototyping is the lack of a "target system" with which to interface. Some alternatives are to develop test driver libraries, integrate the prototype with an existing working simulator, or build one for the specific problem. This paper presents a unique approach to concept development using rapid prototyping for concept development and scenario-based simulation for concept verification. The rapid prototyping environment, derived from artificial intelligence technology, is based on a blackboard architecture. The rapid prototype simulation capability is provided through an object-oriented modeling environment. It is shown how both simulation and blackboard technologies are used collectively to rapidly gain insight into a tenacious problem. A specific example will be discussed where this approach was used to evolve the logic of a mission controller for an autonomous underwater vehicle.

关键词： Military Engineering

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