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Meeting the Information Assurance Crisis in the U.S. Now

EDPACS 2006年第6期28卷 1-14页

作者： Corey Schou Deborah Frincke Charles Reynolds James Frost The Associate Dean of Information Systems Programs at Idaho State University (ISU) in Pocatello and the director of the Center for Decision Support. Currently he serves as the Chair of the National Colloquium on Information System Security Education. Schou also directs the ISU National Center of Excellence in Information Assurance Education and the ISU Technology Innovation Center. Contact Corey Schou one of the authors of this article and the Chair of the NCISSE by email at Schou@*** for help in finding additional ways to address the issues raised in this article. A member of the University of Idaho College of Engineering faculty. She graduated from the University of California at Davis. Frincke is the co-director and co-founder of the university's Center for Secure and Dependable Software (CSDS). She was the program chair for the 2nd International Workshop on Recent Advances in Intrusion Detection (RAID). A professor of Computer Science at the College of Integrated Science and Technology at James Madison University in Harrisonburg Virginia. He holds a Ph.D. in computer science from the University of Texas at Austin and a BA in philosophy from the University of Houston. Reynolds is the Director of Information System Security Education at James Madison University. Since 1997 Reynolds has led the development of the first remote Internet-based curriculum that leads to an M.S. degree in computer science with a concentration in information security. Thus far 160 students have completed this program. A professor of computer information systems at Idaho State University and the manager of its Simplot Decision Support Center.

T he only difference etween evolution and revolution is the speed at which each occurs.

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Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

arXiv

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arXiv 2023年

作者： Takaba, Kenichiro Pulido, Iván Behara, Pavan Kumar Cavender, Chapin E. Friedman, Anika J. Henry, Michael M. MacDermott-Opeskin, Hugo Iacovella, Christopher R. Nagle, Arnav M. Payne, Alexander Matthew Shirts, Michael R. Mobley, David L. Chodera, John D. Wang, Yuanqing Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Pharmaceuticals Research Center Advanced Drug Discovery Asahi Kasei Pharma Corporation Shizuoka410-2321 Japan Center for Neurotherapeutics Department of Pathology and Laboratory Medicine University of California IrvineCA92697 United States Skaggs School of Pharmacy and Pharmaceutical Sciences University of California 9500 Gilman Drive La Jolla San DiegoCA92093 United States Department of Chemical and Biological Engineering University of Colorado Boulder BoulderCO80309 United States Open Molecular Software Foundation DavisCA95618 United States Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Department of Pharmaceutical Sciences University of California IrvineCA92697 United States Tri-Institutional Ph.D. Program in Chemical Biology Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University New YorkNY10004 United States

The development of reliable and extensible molecular mechanics (MM) force fields—fast, empirical models characterizing the potential energy surface of molecular systems—is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, espaloma-0.3, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, espaloma-0.3 reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest. © 2023, CC BY.

关键词： Quantum chemistry

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THE CALLING(SM) NETWORK - A GLOBAL WIRELESS COMMUNICATION-SYSTEM

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INTERNATIONAL JOURNAL OF SATELLITE COMMUNICATIONS 1994年第1期12卷 45-61页

作者： TUCK, EF PATTERSON, DP STUART, JR LAWRENCE, MH Calling Communications Corporation. 1900 West Garvey Ave South. Suite 200 West Covina CA 91790 USA. Chairman of Calling Communications Corporation. He is also the Managing Director of Kinship Venture Management Inc. the general partner of Kinship Partners 11 and a General Partner of Boundary the general partner of The Boundary Fund. As a venture capitalist he has founded or participated in founding several telecommunications companies including Calling Communications Corporation Magellan Systems Corporation manufactures of Global Positioning System receivers Applied Digital Access manufacturer of DS-3 test access and network performance monitoring equipment Endgate Technology Corporation specialists in satellite phased array antennas and Poynting Systems Corporation. now a division of Reliance Corporation manufacturers of fibre optic transport equipment. He was a founder of Kebby Microwave Corporation where he invented the first solid-state. frequency-modulated commercial microwave link system. The company was acquired by ITT Corporation where he rose to the position of V.P. and Technical Director of ITT North America Telecommunications Inc. Subsequently he was V.P. of Marketing and Engineering at American Telecommunications Inc. (ATC). He was founding Director of American Telecom Inc. a joint venture between ATC and Fujitsu and has served on more than 20 boards of directors including those of three public companies. He has authored articles on microwave engineering and telephone signalling and was a contributor to Reference Data For Radio Engineers. He is a graduate of the University of Missouri at Rolla where he was later awarded an honorary Professional degree and serves on its Academy of Electrical Engineering. Mr Tuck is a Senior Member of the IEEE a Fellow of the Institution of Engineers (Australia) a Professional Member of the AIAA and a registered professional engineer in three states. More than 25 years of experience in the telecommunications industry where he has been responsibl

There is a very large demand for basic telephone service in developing nations, and remote parts of industrialized nations, which cannot be met by conventional wireline and cellular systems. This is the world's largest unserved market. We describe a system which uses recent advances in active phased arrays, fast-packet switching technology, adaptive routeing, and light spacecraft technology, in part based on the work of the Jet Propulsion Laboratory and on recently-declassified work done on the Strategic Defense Initiative, to make it possible to address this market with a global telephone network based on a large low-Earth-orbit constellation of identical satellites. A telephone utility can use such a network to provide the same modern basic and enhanced telephone services offered by telephone utilities in the urban centres of fully-industrialized nations. Economies of scale permit capital and operating costs per subscriber low enough to provide a service to all subscribers, regardless of location, at prices comparable to the same services in urban areas of industrialized nations, while generating operating profits great enough to attract the capital needed for its construction. The bandwidth needed to support the capacity needed to gain these economies of scale requires that the system use K(alpha)-band frequencies. This choice of frequencies places unusual constraints on the network design, and in particular forces the use of a large number of satellites. Global demand for basic and enhanced telephone service is great enough to support at least three networks of the size described herein. The volume of advanced components, and services such as launch services, required to construct and replace these networks is sufficient to propel certain industries to market leadership positions in the early 21st Century.

关键词： LOW EARTH ORBIT SATELLITE COMMUNICATIONS FAST PACKET SWITCHING EARTH FIXED CELLS ADAPTIVE ROUTEING LIGHT SPACECRAFT K(A) BAND PHASED-ARRAY ANTENNAS

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The Jimmie Hamilton Award

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Naval Engineers Journal 1971年第3期83卷 36-38页

作者： NACHTSHEIM, JOHN J. BALLOU, L. DENNIS John J. Nachtsheim:is currently the Deputy Assistant Administrator for Research & Development for the Maritime Administration. His duties are the planning coordinating organizing evaluating and directing of the R&D activities of MarAd. His past experiences include: Naval Architect for the Naval Ship Engineering Center 1959 Deputy Chief Design Engineer for the Puget Sound Naval Shipyard 1958 to 1959 and Naval Architect the former Bureau of Ships 1948 to 1958. His education is comprised of a B.S. degree from the Webb Institute of Naval Architecture an L.L.B. degree from the George Washington University Law School completion of the Advanced Management Program at Harvard University and current study of Transportation at the American University. He is a Registered Professional Engineer in the District of Columbia and a Member of the Bar in the District of Columbia and the State of Maryland. In addition to ASNE his other professional memberships include the Society of Naval Architects and Marine Engineers the Society of Aeronautical Weight Engineers and the Association of Senior Engineers of the Naval Ships Systems Command (Honorary). USN Commander L. Dennis Ballou: USN is the Head of the Engineering Service Office Naval Ship Engineering Center. He is involved in computer hardware and software services to support engineering design automatic data processing systems design work study and quality assurance. Prior to NavSec duty Commander Ballou served in various billets afloat and ashore: tours on the USS Skagit and Tang supervision of the USS Skipjack's first overhul construction of the USS Nathanael Greene and helping to establish the Polaris overhaul program. He is a graduate of the U.S. Naval Academy Officers' Submarine School and the Webb Institute of Naval Architecture. He holds BS and MS degrees in marine engineering and naval architecture respectively. He has also completed many graduate

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ADVANCED AVIONICS ARCHITECTURE - THE NAVAIR STUDY

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NAVAL ENGINEERS JOURNAL 1994年第6期106卷 31-40页

作者： KATZ, RS JAHNKE, L JEWETT, CE Cdr. Larry Jahnke USN:is presently Head of the Architecture Branch of the Avionics Engineering division AIR-546 of the Naval Air Systems Command. Among his current responsibilities is to lead implementation activities of the NAVAIR Advanced Avionics Architecture study described in this paper. Cdr. Jahnke graduated from the University of Minnesota with a B.S. degree in aeronautical engineering and was commissioned in 1974. After flight training as a Naval flight officer he was assigned to Naval Air Station Barbers Point Hawaii where he served as Tactical Coordinator for P-3B aircraft. He was assigned to the Communications Directorate of the Joint Staff in 1990 where he participated in support of Desert Shield/Desert Storm and was part of the original cadre of officers responsible for the “C41 for the Warrior” concept. Cdr. Jahnke also has a Master of Science degree from the University of Southern California and is a 1990 graduate of the Industrial College of the Armed Forces. Cdr. Charles E. Jewett USN:is currently the Common Avionics Requirements Officer for Naval Aircraft Programs. He has served the Navy as an Aeronautical Engineering Duty Officer since 1982 with previous defense acquisition assignments as the Avionics Architecture and Engineering Branch Head Fighter/Attack Avionics systems Engineering Branch Head and A-12 Avionics Officer and A-6F Deputy Program Manager and the A-6 Avionics Officer. Cdr. Jewett entered the Navy as an Aviation Officer Candidate in 1971 receiving his commission and earning his wings as a Naval Flight Officer the same year. After graduating from the U.S. Naval Test Pilot School in 1976 he was assigned to the Strike Aircraft Test Directorate of the Naval Air Test Center where he participated in various electronic warfare electro-optics and software update evaluations for A-6 EA-6B and OV-10 aircraft. In Cdr. Jewett's previous assignment at NAVAIRSYSCOM he led a major Avionics Architecture Study (the subject of this paper) that surveyed cutting-edge avionics technol

To establish a planning basis for future avionics systems, the Naval Air systems Command (NAVAIR) conducted an avionics architecture investigation during 1992-1993, culminating in a final report published in August 1993. In the course of the study, U.S. Industry provided significant information to a NAVAIR avionics database for both technologies and systems integration methods. From the study emerged an implementation strategy to allow NAVAIR to develop effective avionics systems in the future that use commercial products and standards where applicable but also allow the ready use of new and emerging technologies. Recommended strategies concentrate on the development process, especially the use of sound systems engineering techniques and the maximum practical use of commercial standards and products. This paper reviews the methodology employed during the NAVAIR investigation, and presents the key findings and resulting implementation strategies. The paper concludes with a brief summary of current implementation plans at NAVAIR.

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RATIONALE FOR AN ADA software engineering ENVIRONMENT FOR NAVY MISSION CRITICAL APPLICATIONS

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NAVAL ENGINEERS JOURNAL 1984年第4期96卷 133-145页

作者： PAIGE, KK CONVERSE, RA USN LCdr. Kathleen K. Paige USN:graduated with a BA from the University of New Hampshire in 1970. She received her commission from Officer Candidate School in April 1971 and performed her first tour of duty with VFP-63 NAS Miramar. LCdr. Paige then received her MS from the Naval Post Graduate School in June 1976 and returned to San Diego to serve as Head Support Software Division at the Fleet Combat Direction System Support Activity. In May 1981 she reported to NA VSEA (PMS-408) where she served initially as Chairman of the NAVMAT Software Engineering Environment Working Group. She has been assigned as Deputy AN/UYK-43 Acquisition Manager since October 1981. LCdr. Paige was designated a fully qualified Engineering Duty Officer in December 1983. Robert A. Converse:is presently the Acquisition Manager for the Ada Language System/Navy (ALS/N) for the Naval Sea Systems Command Tactical Embedded Computer Resources Project. As such he is responsible for the definition and development of the ALS/N to be provided as a Navy standard computer programming system for Navy mission critical applications. Mr. Converse received a Bachelor of Science degree in Physics from Wheaton College Wheaton II. He spent fourteen years with the Naval Underwater Systems Center Newport Rhode Island during which time he designed and developed the Fortran compiler for the Navy Standard AN/UYK-7 computer. Also during that period he received a Master of Science degree in Computer Science from the University of Rhode Island. His thesis for that degree was entitled “Optimization Techniques for the NUSC Fortran Cross-Compiler”. Mr. Converse started his involvement with the Ada program in 1975 with the initial “Strawman” requirements review. Subsequently he was named as the Navy Ada Distinguished Reviewer and was intimately involved in the selection and refinement of the Ada language as it evolved to become ANSI/MIL-STD-1815A.

The U.S. Navy introduced the use of digital computers in mission critical applications over a quarter of a century ago. Today, virtually every system in the current and planned Navy inventory makes extensive use of computer technology. Computers embedded in mission critical Navy systems are integral to our strategic and tactical defense capabilities. Thus, the military power of the U.S. Navy is inextricably tied to the use of programmable digital computers. The computer program is the essential element that embodies the system “intelligence”. In addition, it provides the flexibility to respond to changing threats and requirements. However, this very flexibility and capability poses a host of difficulties hindering full realization of the advantages. This paper describes the lessons learned about computer program development over the past twenty five years and discusses a software engineering process that addresses these lessons. It then describes how Ada and its related Ada programming Support and Run-Time Environments foster this software engineering process to improve computer program productivity and achieve greater system reliability and adaptibility. Finally, the paper discusses how the use of Ada and its environments can enhance the interoperability and transferability of computer programs among Navy projects and significantly reduce overall life cycle costs for Navy mission critical computer programs.

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EMI - THE ENEMY WITHIN

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NAVAL ENGINEERS JOURNAL 1992年第2期104卷 69-80页

作者： BARON, NT CEBULSKI, DR Neil T. Baronis currently the team leader for the combat system topside design work for amphibious assault auxiliary mine warfare and Coast Guard ships. He sits on the IEEE SCC-28 Committee for personnel radiation hazards and is extensively involved in the EM engineering initiative at NavSea. Mr. Baron has lectured at the MIT Summer Professional Series on the subject of electromagnetic interference. While attending Marquette University he started his career with the Navy as a coop student supporting personnel radiation hazard assessments. After graduating with a BS in bio-medical engineering he took an electronics engineer position in the Systems Electromagnetic Division. Since then he has lectured on Navy training films and has developed several software packages which have pushed the state-of-the-art in EMI assessment. Mr. Baron has prepared several reports and professional papers. He has worked on several professional committees and in February of 1991 was awarded the “Young Engineer of the Year Award” which was presented by the D.C. Council of Engineering and Architectural Societies. Donald R. Cebulskiis currently the head of the Topside Design Division in the Naval Sea Systems Command Weapons and Combat System Directorate. He graduated from the University of Michigan with a bachelor's degree in 1963 and a master's degree in 1977 both in naval architecture and marine engineering. He started his career in 1964 at the Bureau of Ships and joined the Aircraft Carrier Section of the Arrangements Branch in Hull Design. During the past 25 years he has included almost every naval ship type in his ship arrangement experience and in October of 1988 he transferred to the Topside Design and Integration Branch in the System Electromagnetics Division Sea 06. Mr. Cebulski has written several papers on ship arrangements computer aided design and ship topside design. He prepared and presented lectures at the MIT Professional Series on ship topside design and has served on many ASNE committees. He is currently the

Electromagnetic interference (EMI) is one of the major contributors to mission degradation in our fleet today due to the increase in population and sensitivity of both topside and below deck electronic systems. Sensitive combat systems designed to counter intelligent and deceptive targets can be confused by the complex intra-ship EM environment. This can cause identification failure or losing "track" of a hostile or incoming missile or even engaging "friendly targets." Topside design and integration efforts have been used to reduce EMI, but this is not the total solution to the problem. A program of total ship and system EMI assessment and control must be implemented. This program must exploit electromagnetic compatibility (EMC) optimization in electronic circuit design and take advantage of and (in some cases) direct topside shapes and structures to control the propagation of desired and undesired EM energy. Positive and active control of EM design characteristics are absolutely required before optimum combat system effectiveness can be realized. This paper will describe the current topside design process, EMC improvements being made, and how the process is being integrated into, and is dependent upon, the ship design process. It will give examples of some of the major mission degrading EMI problems in the fleet today and how past problems were solved with existing EM analysis programs. It will also discuss the control of EM energy in new design through the use of techniques being developed such as ray tracing and ray casting. The paper projects where the challenges lie for future topside and EM engineering designers and describes how the equipment technology transfer process must be better integrated to meet the challenge of effective EMI control.

关键词： Signal Interference

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25th Annual Computational Neuroscience Meeting CNS-2016, Seogwipo City, South Korea, July 2-7, 2016 Abstracts

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BMC NEUROSCIENCE 2016年第1期17卷 1-112页

作者： [Anonymous] Computational Neurobiology Laboratory The Salk Institute for Biological Studies San Diego USA UNIC CNRS Gif sur Yvette France The European Institute for Theoretical Neuroscience (EITN) Paris France ATR Computational Neuroscience Laboratories Kyoto Japan Krembil Research Institute University Health Network Toronto Canada Department of Physiology University of Toronto Toronto Canada Department of Medicine (Neurology) University of Toronto Toronto Canada Department of Physics University of New Hampshire Durham USA Department of Neurophysiology Nencki Institute of Experimental Biology Warsaw Poland Department of Theory Wigner Research Centre for Physics of the Hungarian Academy of Sciences Budapest Hungary Department of Mathematical Sciences KAIST Daejoen Republic of Korea Department of Mathematics University of Houston Houston USA Department of Biochemistry & Cell Biology and Institute of Biosciences and Bioengineering Rice University Houston USA Department of Biology and Biochemistry University of Houston Houston USA Grupo de Neurocomputación Biológica Dpto. de Ingeniería Informática Escuela Politécnica Superior Universidad Autónoma de Madrid Madrid Spain Department of Biological Sciences University of Southern California Los Angeles USA Center for Neuroscience Korea Institute of Science and Technology Seoul South Korea Department of Neurology Albert Einstein College of Medicine Bronx USA Center for Neuroscience KIST Seoul South Korea Department of Neuroscience University of Science and Technology Daejon South Korea Systems Neuroscience Group QIMR Berghofer Medical Research Institute Herston Australia Department of Psychology Yonsei University Seoul South Korea Department of Psychiatry Kyung Hee University Hospital at Gangdong Seoul South Korea Department of Psychiatry Veterans Administration Boston Healthcare System and Harvard Medical School Brockton USA Department of Electrical and Electronic Engineering The University of Melbourne Parkvil

A1 Functional advantages of cell-type heterogeneity in neural circuits Tatyana O. Sharpee A2 Mesoscopic modeling of propagating waves in visual cortex Alain Destexhe A3 Dynamics and biomarkers of mental disorders Mitsuo Kawato F1 Precise recruitment of spiking output at theta frequencies requires dendritic h-channels in multi-compartment models of oriens-lacunosum/moleculare hippocampal interneurons Vladislav Sekulić, Frances K. Skinner F2 Kernel methods in reconstruction of current sources from extracellular potentials for single cells and the whole brains Daniel K. Wójcik, Chaitanya Chintaluri, Dorottya Cserpán, Zoltán Somogyvári F3 The synchronized periods depend on intracellular transcriptional repression mechanisms in circadian clocks. Jae Kyoung Kim, Zachary P. Kilpatrick, Matthew R. Bennett, Kresimir Josić O1 Assessing irregularity and coordination of spiking-bursting rhythms in central pattern generators Irene Elices, David Arroyo, Rafael Levi, Francisco B. Rodriguez, Pablo Varona O2 Regulation of top-down processing by cortically-projecting parvalbumin positive neurons in basal forebrain Eunjin Hwang, Bowon Kim, Hio-Been Han, Tae Kim, James T. McKenna, Ritchie E. Brown, Robert W. McCarley, Jee Hyun Choi O3 Modeling auditory stream segregation, build-up and bistability James Rankin, Pamela Osborn Popp, John Rinzel O4 Strong competition between tonotopic neural ensembles explains pitch-related dynamics of auditory cortex evoked fields Alejandro Tabas, André Rupp, Emili Balaguer-Ballester O5 A simple model of retinal response to multi-electrode stimulation Matias I. Maturana, David B. Grayden, Shaun L. Cloherty, Tatiana Kameneva, Michael R. Ibbotson, Hamish Meffin O6 Noise correlations in V4 area correlate with behavioral performance in visual discrimination task Veronika Koren, Timm Lochmann, Valentin Dragoi, Klaus Obermayer O7 Input-location dependent gain modulation in cerebellar nucleus neurons Maria Psarrou, Maria Schilstra, Neil Davey, Benjamin Torben-Ni

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Solid‐liquid interface of an inductively heated metal sphere

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European Transactions on Electrical Power 1993年第6期3卷 407-414页

作者： Bex, H. Greuel, K. Prof. Dr.-Ing. Hans Bex (1937) VDE VDI IEEE is head of the department of High-Frequency Techniques at the Fachhochschule of Aachen Germany. He received his degrees at the Technical University of Aachen Germany in 1965 and 1969. From 1965 to 1980 he was with the Philips Research Laboratories in Aachen as a research scientist where he was engaged in research on lumped element circulators YIG-filters linear and non-linear microstrip circuits for microwave subsystems. Since 1981 he has been a professor for high-frequency techniques at the Fachhoch-schule Aachen Germany teaching electromagnetics and microwaves. His areas of interest include microwave and millimeter wave integrated circuits and devices non-linear analysis techniques device modelling planar transmission line modelling and electromagnetic field theory applied to isotropic and anisotropic materials. (FH Aachen Abteilung fur Theoretische Nachrichtentechnik und Hochstfrequenztechnik. Eupener Str. 70 D-52066 Aachen T + 492 41/60 09 21 08 Fax + 49 241/60 09 21 91) Dipl.-Ing. Karl Greuel (1960) VDE studied Electrical Engineering at the FH Aachen Germany and got his degree there in 1988. After his study he designed software for industry-furnaces with stored-program controllers at the Otto Junker GmbH. Since 1990 he works at the Datus GmbH for electrical information-systems in software development. (Datus GmbH Abteilung Software-Entwicklung Tempelhofer Str. 4-6 D-52068 Aachen T +49241/1 6802-0 Fax + 492 41/168 02-80)

In this paper inductive melting in a metal sphere is investigated, whereby the temperature dependence of the sample 's most important material parameters is considered. The solid‐liquid interface in the sphere is determined in consideration of heat conduction. The melting process takes place in a vacuum with zero gravity under the influence of a homogeneous, magnetic alternating field. For the numerical solution of the heat conduction equation, homogeneous, isotropic conditions are assumed in discrete toroidal volumes. This approach simplifies, at the same time, the use of Maxwell's equations. Using the method of finite differences, the procedure yields not only the spatial location of the solid‐liquid interface but also the corresponding time and absorbed active power as a function of frequency, radius of the sphere and intensity of the exciting field. And not least, the total required melting time for melting the sphere can be determined. Copyright © 1993 John Wiley & Sons, Ltd.

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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