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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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for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations
Qualitative Simulation
 Artificial Intelligence
, 2001
"... Qualitative simulation predicts the set of possible behaviors... ..."
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Cited by 513 (31 self)
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Qualitative simulation predicts the set of possible behaviors...
Large steps in cloth simulation
 SIGGRAPH 98 Conference Proceedings
, 1998
"... The bottleneck in most cloth simulation systems is that time steps must be small to avoid numerical instability. This paper describes a cloth simulation system that can stably take large time steps. The simulation system couples a new technique for enforcing constraints on individual cloth particle ..."
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Cited by 578 (5 self)
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particles with an implicit integration method. The simulator models cloth as a triangular mesh, with internal cloth forces derived using a simple continuum formulation that supports modeling operations such as local anisotropic stretch or compression; a unified treatment of damping forces is included
Discrete Choice Methods with Simulation
, 2002
"... This book describes the new generation of discrete choice methods, focusing on the many advances that are made possible by simulation. Researchers use these statistical methods to examine the choices that consumers, households, firms, and other agents make. Each of the major models is covered: logi ..."
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Cited by 1277 (20 self)
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This book describes the new generation of discrete choice methods, focusing on the many advances that are made possible by simulation. Researchers use these statistical methods to examine the choices that consumers, households, firms, and other agents make. Each of the major models is covered
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
Ptolemy: A Framework for Simulating and Prototyping Heterogeneous Systems
, 1992
"... Ptolemy is an environment for simulation and prototyping of heterogeneous systems. It uses modern objectoriented software technology (C++) to model each subsystem in a natural and efficient manner, and to integrate these subsystems into a whole. Ptolemy encompasses practically all aspects of design ..."
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Cited by 569 (90 self)
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Ptolemy is an environment for simulation and prototyping of heterogeneous systems. It uses modern objectoriented software technology (C++) to model each subsystem in a natural and efficient manner, and to integrate these subsystems into a whole. Ptolemy encompasses practically all aspects
A Fast Algorithm for Particle Simulations
, 1987
"... this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions a ..."
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Cited by 1145 (19 self)
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this paper to the case where the potential (or force) at a point is a sum of pairwise An algorithm is presented for the rapid evaluation of the potential and force fields in systems involving large numbers of particles interactions. More specifically, we consider potentials of whose interactions are Coulombic or gravitational in nature. For a the form system of N particles, an amount of work of the order O(N 2 ) has traditionally been required to evaluate all pairwise interactions, un F5F far 1 (F near 1F external ), less some approximation or truncation method is used. The algorithm of the present paper requires an amount of work proportional to N to evaluate all interactions to within roundoff error, making it where F near (when present) is a rapidly decaying potential con
An introduction to disk drive modeling
 IEEE Computer
, 1994
"... Much research in I/O systems is based on disk drive simulation models, but how good are they? An accurate simulation model should emphasize the performancecritical areas. ..."
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Cited by 494 (15 self)
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Much research in I/O systems is based on disk drive simulation models, but how good are they? An accurate simulation model should emphasize the performancecritical areas.
TOSSIM: Accurate and Scalable Simulation of Entire TinyOS Applications
, 2003
"... Accurate and scalable simulation has historically been a key enabling factor for systems research. We present TOSSIM, a simulator for TinyOS wireless sensor networks. By exploiting the sensor network domain and TinyOS’s design, TOSSIM can capture network behavior at a high fidelity while scaling to ..."
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Cited by 765 (18 self)
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Accurate and scalable simulation has historically been a key enabling factor for systems research. We present TOSSIM, a simulator for TinyOS wireless sensor networks. By exploiting the sensor network domain and TinyOS’s design, TOSSIM can capture network behavior at a high fidelity while scaling
Flocks, herds, and schools: a distributed behavioral model
 Computer Graphics
, 1987
"... The aggregate motion of a flock of birds, a herd of land animals, or a school of fish is a beautiful and familiar part of the natural world. But this type of complex motion is rarely seen in computer animation. This paper explores an approach based on simulation as an alternative to scripting the pa ..."
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Cited by 1293 (5 self)
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the paths of each bird individually. The simulated flock is an elaboration of a particle system, with the simulated birds being the particles. The aggregate motion of the simulated flock is created by a distributed behavioral model much like that at work in a natural flock; the birds choose their own course
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