Daniel T Gillespie

Summary

Affiliation: Indiana University Purdue University Indianapolis
Country: USA

Publications

  1. ncbi Accelerated stochastic simulation of the stiff enzyme-substrate reaction
    Yang Cao
    Department of Computer Science, University of California, Santa Barbara, California 93106, USA
    J Chem Phys 123:144917. 2005
  2. ncbi Stochastic simulation of chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, Castaic, CA 91384, USA
    Annu Rev Phys Chem 58:35-55. 2007
  3. ncbi Deterministic limit of stochastic chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Phys Chem B 113:1640-4. 2009
  4. ncbi The subtle business of model reduction for stochastic chemical kinetics
    Dan T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Place, Castaic, California 91384, USA
    J Chem Phys 130:064103. 2009
  5. ncbi Refining the weighted stochastic simulation algorithm
    Dan T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Chem Phys 130:174103. 2009
  6. ncbi A diffusional bimolecular propensity function
    Daniel T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Chem Phys 131:164109. 2009
  7. ncbi Efficient step size selection for the tau-leaping simulation method
    Yang Cao
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
    J Chem Phys 124:044109. 2006
  8. ncbi Adaptive explicit-implicit tau-leaping method with automatic tau selection
    Yang Cao
    Department of Computer Science, 660 McBryde Hall, Virginia Tech, Blacksburg, Virginia 24061, USA
    J Chem Phys 126:224101. 2007
  9. ncbi Algorithms and software for stochastic simulation of biochemical reacting systems
    Hong Li
    Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, USA
    Biotechnol Prog 24:56-61. 2008

Collaborators

Detail Information

Publications9

  1. ncbi Accelerated stochastic simulation of the stiff enzyme-substrate reaction
    Yang Cao
    Department of Computer Science, University of California, Santa Barbara, California 93106, USA
    J Chem Phys 123:144917. 2005
    ..Finally, we explain the connection between this slow-scale SSA approach and the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] formula, which has long been used in deterministic chemical kinetics to describe the enzyme-substrate reaction...
  2. ncbi Stochastic simulation of chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, Castaic, CA 91384, USA
    Annu Rev Phys Chem 58:35-55. 2007
    ....
  3. ncbi Deterministic limit of stochastic chemical kinetics
    Daniel T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Phys Chem B 113:1640-4. 2009
    ....
  4. ncbi The subtle business of model reduction for stochastic chemical kinetics
    Dan T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Place, Castaic, California 91384, USA
    J Chem Phys 130:064103. 2009
    ....
  5. ncbi Refining the weighted stochastic simulation algorithm
    Dan T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Chem Phys 130:174103. 2009
    ..The paper also attempts to clarify some theoretical issues connected with the wSSA, including its connection to first passage time theory and its relation to the SSA...
  6. ncbi A diffusional bimolecular propensity function
    Daniel T Gillespie
    Dan T Gillespie Consulting, 30504 Cordoba Pl, Castaic, California 91384, USA
    J Chem Phys 131:164109. 2009
    ....
  7. ncbi Efficient step size selection for the tau-leaping simulation method
    Yang Cao
    Department of Computer Science, Virginia Tech, Blacksburg, Virginia 24061, USA
    J Chem Phys 124:044109. 2006
    ..This new tau-selection procedure is more accurate, easier to code, and faster to execute than the currently used procedure. The speedup in execution will be especially pronounced in systems that have many reaction channels...
  8. ncbi Adaptive explicit-implicit tau-leaping method with automatic tau selection
    Yang Cao
    Department of Computer Science, 660 McBryde Hall, Virginia Tech, Blacksburg, Virginia 24061, USA
    J Chem Phys 126:224101. 2007
    ..Numerical testing demonstrates the advantages of the adaptive method for stiff systems...
  9. ncbi Algorithms and software for stochastic simulation of biochemical reacting systems
    Hong Li
    Department of Computer Science, University of California Santa Barbara, Santa Barbara, California 93106, USA
    Biotechnol Prog 24:56-61. 2008
    ..In this manuscript, we briefly review the state of the art in discrete stochastic and multiscale algorithms for simulation of biochemical systems and we present the StochKit software toolkit...