Publications

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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, Hellander S.  2017.  Reaction rates for reaction-diffusion kinetics on unstructured meshes. JOURNAL OF CHEMICAL PHYSICS. 146
Petzold L, Robinson ASkaja, Doyle, III FJ, Raden D, Hildebrandt S.  2008.  A top-down approach to mechanistic biological modeling: Application to the single-chain antibody folding pathway. BIOPHYSICAL JOURNAL. 95:3535-3558.
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, 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.
Petzold L, Hellander A, Lawson MJ.  2015.  Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise. Journal of the Royal Society Interface. 12
Petzold L, Meinhart C, Zhu LD, Tretheway D.  2005.  Simulation of fluid slip at 3D hydrophobic microchannel walls by the lattice Boltzmann method. JOURNAL OF COMPUTATIONAL PHYSICS. 202:181-195.
Petzold LR, Cao Y, Gillespie DT.  2005.  Avoiding negative populations in explicit Poisson tau-leaping. JOURNAL OF CHEMICAL PHYSICS. 123
Petzold L, Gillespie D, Cao Y.  2005.  Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems. JOURNAL OF COMPUTATIONAL PHYSICS. 206:395-411.
Petzold LR, Bales BB, Alkire RC, Bezzola A.  2014.  Numerical Scaling Studies of Kinetically-Limited Electrochemical Nucleation and Growth with Accelerated Stochastic Simulations. JOURNAL OF THE ELECTROCHEMICAL SOCIETY. 161:E3001-E3008.
Petzold L, Zhang Y, Jiang R.  2017.  Survival Topic Models for Predicting Outcomes for Trauma Patients. IEEE International Conference on Data Engineering. :1497-1504.
Petzold L, Gunawan R, Doyle FJ, Cao Y.  2005.  Sensitivity analysis of discrete stochastic systems. BIOPHYSICAL JOURNAL. 88:2530-2540.
Petzold LR, Hellander A, Gillespie DT.  2013.  Perspective: Stochastic algorithms for chemical kinetics. JOURNAL OF CHEMICAL PHYSICS. 138
Petzold L, Cohen M, Torshizi ADoostparas.  2017.  Multivariate soft repulsive system identification for constructing rule-based classification systems: Application to trauma clinical data. NEUROCOMPUTING. 245:77-85.
Petzold L, Buoni M.  2010.  An algorithm for simulation of electrochemical systems with surface-bulk coupling strategies. JOURNAL OF COMPUTATIONAL PHYSICS. 229:379-398.
Petzold LR, Pourzanjani A, Herzog ED.  2015.  On the Inference of Functional Circadian Networks Using Granger Causality. PLOS ONE. 10
Petzold L, Cao Y.  2004.  A posteriori error estimation and global error control for ordinary differential equations by the adjoint method. SIAM JOURNAL ON SCIENTIFIC COMPUTING. 26:359-374.
Petzold L, Cao Y, Li S, Serban R.  2006.  Sensitivity analysis of differential-algebraic equations and partial differential equations. COMPUTERS & CHEMICAL ENGINEERING. 30:1553-1559.
Petzold L, Drawert B, Trogdon M, Hellander S, Yi T-M.  2016.  A framework for discrete stochastic simulation on 3D moving boundary domains. JOURNAL OF CHEMICAL PHYSICS. 145

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