Publications

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Petzold L, Buoni M.  2007.  An efficient, scalable numerical algorithm for the simulation of electrochemical systems on irregular domains. JOURNAL OF COMPUTATIONAL PHYSICS. 225:2320-2332.
Petzold L, Drawert B, Khammash M, Yi T-M, Lawson MJ.  2013.  Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLOS COMPUTATIONAL BIOLOGY. 9
Petzold L, Bhattacharjee K.  2015.  Detecting Opinions in a Temporally Evolving Conversation on Twitter. Lecture Notes in Computer Science. 9471:82-97.
Petzold LR, Cao Y, Gillespie DT.  2006.  Efficient step size selection for the tau-leaping simulation method. JOURNAL OF CHEMICAL PHYSICS. 124
Petzold L, Meinhart CD, Mezic I, Zhang YT, Chen H, MacDonald NC.  2004.  SOI processing of a ring electrokinetic chaotic micromixer. :292-295.
Petzold LR, Fu J, Li H, Wu S.  2014.  The time dependent propensity function for acceleration of spatial stochastic simulation of reaction-diffusion systems. JOURNAL OF COMPUTATIONAL PHYSICS. 274:524-549.
Petzold L, Zheng Z.  2006.  Runge-Kutta-Chebyshev projection method. JOURNAL OF COMPUTATIONAL PHYSICS. 219:976-991.
Petzold L, Zhu WJ.  1999.  Model reduction for chemical kinetics: An optimization approach. AICHE JOURNAL. 45:869-886.
Petzold L, Li ST, Cao Y.  2002.  Adjoint sensitivity analysis for differential-algebraic equations: algorithms and software. JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS. 149:171-191.
Petzold LR, Cao Y, Li H, Gillespie DT.  2008.  Algorithms and software for stochastic simulation of biochemical reacting systems. BIOTECHNOLOGY PROGRESS. 24:56-61.
Petzold LR, Cao Y, Gillespie DT.  2005.  Accelerated stochastic simulation of the stiff enzyme-substrate reaction. JOURNAL OF CHEMICAL PHYSICS. 123
Petzold L, Bales B, Pollock T.  2017.  Segmentation-free image processing and analysis of precipitate shapes in 2D and 3D. MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING. 25
Petzold L, Hellander S, Hellander A.  2015.  Reaction rates for mesoscopic reaction-diffusion kinetics. PHYSICAL REVIEW E. 91
Petzold L, Cao Y.  2006.  Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems. JOURNAL OF COMPUTATIONAL PHYSICS. 212:6-24.
Petzold LR, Bales BB, Alkire RC, Bezzola A.  2014.  An exact and efficient first passage time algorithm for reaction diffusion processes on a 2D-lattice. JOURNAL OF COMPUTATIONAL PHYSICS. 256:183-197.
Petzold L, Drawert B, Khammash M, Lawson MJ.  2010.  The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. JOURNAL OF CHEMICAL PHYSICS. 132
Petzold L, Hellander S.  2017.  Reaction rates for reaction-diffusion kinetics on unstructured meshes. JOURNAL OF CHEMICAL PHYSICS. 146
Petzold L, Raha S, Yen J.  1998.  A time integration algorithm for flexible mechanism dynamics: The DAE alpha-method. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING. 158:341-355.
Petzold L, Cao Y.  2008.  Slow-scale tau-leaping method. COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING. 197:3472-3479.
Petzold L, Bhattacharjee K.  2016.  What Drives Consumer Choices? Mining Aspects and Opinions on Large Scale Review Data using Distributed Representation of Words International Conference on Data Mining Workshops. :908-915.
Petzold L, Li ST.  2004.  Adjoint sensitivity analysis for time-dependent partial differential equations with adaptive mesh refinement. JOURNAL OF COMPUTATIONAL PHYSICS. 198:310-325.
Petzold L, Li H, Moehlis J, Kolpas A.  2009.  Parallel simulation for a fish schooling model on a general-purpose graphics processing unit. CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE. 21:725-737.
Petzold L, Hellander S.  2016.  Reaction rates for a generalized reaction-diffusion master equation. PHYSICAL REVIEW E. 93
Petzold L, Cao Y, Li S, Serban R.  2003.  ADJOINT SENSITIVITY ANALYSIS FOR DIFFERENTIAL-ALGEBRAIC EQUATIONS: THE ADJOINT DAE SYSTEM AND ITS NUMERICAL SOLUTION. SIAM JOURNAL ON SCIENTIFIC COMPUTING. 24:1076-1089.
Petzold L, Li H, Cao Y.  2004.  Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. JOURNAL OF CHEMICAL PHYSICS. 121:4059-4067.

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