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» A stochastic particle-based biological system simulator
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SIAMAM
2000
81views more  SIAMAM 2000»
14 years 9 months ago
Electrodiffusion Model of Rectangular Current Pulses in Ionic Channels of Cellular Membranes
A simplified electrodiffusion model for rectangular current pulses in ionic channels of biological membranes is presented. Numerical simulations and a dynamical systems analysis of...
Carl L. Gardner, Joseph W. Jerome, Robert S. Eisen...
CIBCB
2006
IEEE
15 years 3 months ago
A Stochastic model to estimate the time taken for Protein-Ligand Docking
Abstract— Quantum mechanics and molecular dynamic simulation provide important insights into structural configurations and molecular interaction data today. To extend this atomi...
Preetam Ghosh, Samik Ghosh, Kalyan Basu, Sajal K. ...
ENTCS
2006
155views more  ENTCS 2006»
14 years 9 months ago
Biomolecular Agents as Multi-behavioural Concurrent Objects
In recent years, there has been increasing interest in computational models of biological systems based on various calculi of communicating processes, such as the stochastic pi-ca...
Denys Duchier, Céline Kuttler
RECOMB
2007
Springer
15 years 9 months ago
Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions
Abstract. Given the substantial computational requirements of stochastic simulation, approximation is essential for efficient analysis of any realistic biochemical system. This pap...
Hiroyuki Kuwahara, Chris J. Myers
CORR
2010
Springer
174views Education» more  CORR 2010»
14 years 9 months ago
Hybrid Numerical Solution of the Chemical Master Equation
We present a numerical approximation technique for the analysis of continuous-time Markov chains that describe networks of biochemical reactions and play an important role in the ...
Thomas A. Henzinger, Maria Mateescu, Linar Mikeev,...