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Statistical mechanics of complex networks
 Rev. Mod. Phys
"... Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical links. While traditionally these systems were modeled as ra ..."
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Cited by 2083 (10 self)
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as random graphs, it is increasingly recognized that the topology and evolution of real
Modeling and simulation of genetic regulatory systems: A literature review
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
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Cited by 729 (15 self)
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DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools
A New Kind of Science
, 2002
"... “Somebody says, ‘You know, you people always say that space is continuous. How do you know when you get to a small enough dimension that there really are enough points in between, that it isn’t just a lot of dots separated by little distances? ’ Or they say, ‘You know those quantum mechanical amplit ..."
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Cited by 850 (0 self)
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“Somebody says, ‘You know, you people always say that space is continuous. How do you know when you get to a small enough dimension that there really are enough points in between, that it isn’t just a lot of dots separated by little distances? ’ Or they say, ‘You know those quantum mechanical amplitudes you told me about, they’re so complicated and absurd, what makes you think those are right? Maybe they aren’t right. ’ Such remarks are obvious and are perfectly clear to anybody who is working on this problem. It does not do any good to point this out.” —Richard Feynman [1, p.161]
Statecharts: A Visual Formalism For Complex Systems
, 1987
"... We present a broad extension of the conventional formalism of state machines and state diagrams, that is relevant to the specification and design of complex discreteevent systems, such as multicomputer realtime systems, communication protocols and digital control units. Our diagrams, which we cal ..."
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Cited by 2683 (56 self)
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We present a broad extension of the conventional formalism of state machines and state diagrams, that is relevant to the specification and design of complex discreteevent systems, such as multicomputer realtime systems, communication protocols and digital control units. Our diagrams, which we call statecharts, extend conventional statetransition diagrams with essentially three olements, dealing, respectively, with the notions of hierarchy, concurrency and communication. These transform the language of state diagrams into a highly structured' and economical description language. Statecharts are thus compact and expressivesmall diagrams can express complex behavioras well as compositional and modular. When coupled with the capabilities of computerized graphics, statecharts enable viewing the description at different levels of detail, and make even very large specifications manageable and comprehensible. In fact, we intend to demonstrate here that statecharts counter many of the objections raised against conventional state diagrams, and thus appear to render specification by diagrams an attractive and plausible approach. Statecharts can be used either as a standalone behavioral description or as part of a more general design methodology that deals also with the system's other aspects, such as functional decomposition and dataflow specification. We also discuss some practical experience that was gained over the last three years in applying the statechart formalism to the specification of a particularly complex system.
Planning Algorithms
, 2004
"... This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning, planning ..."
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Cited by 1108 (51 self)
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This book presents a unified treatment of many different kinds of planning algorithms. The subject lies at the crossroads between robotics, control theory, artificial intelligence, algorithms, and computer graphics. The particular subjects covered include motion planning, discrete planning, planning under uncertainty, sensorbased planning, visibility, decisiontheoretic planning, game theory, information spaces, reinforcement learning, nonlinear systems, trajectory planning, nonholonomic planning, and kinodynamic planning.
Simulating Physics with Computers
 SIAM Journal on Computing
, 1982
"... A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. ..."
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Cited by 601 (1 self)
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A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time of at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. This paper considers factoring integers and finding discrete logarithms, two problems which are generally thought to be hard on a classical computer and have been used as the basis of several proposed cryptosystems. Efficient randomized algorithms are given for these two problems on a hypothetical quantum computer. These algorithms take a number of steps polynomial in the input size, e.g., the number of digits of the integer to be factored. AMS subject classifications: 82P10, 11Y05, 68Q10. 1 Introduction One of the first results in the mathematics of computation, which underlies the subsequent development of much of theoretical computer science, was the distinction between computable and ...
Community detection in graphs
, 2009
"... The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of th ..."
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Cited by 801 (1 self)
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The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such
The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models
 Bioinformatics
, 2003
"... ..."
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