Publications

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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 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 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 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
Petzold L, Hellander S, Hellander A.  2012.  Reaction-diffusion master equation in the microscopic limit. PHYSICAL REVIEW E. 85
Petzold L, Krintz C.  2012.  Stochastic Simulation Service: Towards an Integrated Development Environment for Modeling and Simulation of Stochastic Biochemical Systems. :2303-2324.
Petzold LR, Serban R, Homescu C.  2007.  Error estimation for reduced-order models of dynamical systems. SIAM REVIEW. 49:277-299.
Petzold L, Bhattacharjee K.  2014.  Probabilistic User-Level Opinion Detection on Online Social Networks. Lecture Notes in Computer Science. 8851:309-325.
Petzold L, Gunawan R, Doyle FJ, Cao Y.  2005.  Sensitivity analysis of discrete stochastic systems. BIOPHYSICAL JOURNAL. 88:2530-2540.
Petzold L, Li ST, Zhu WJ.  2000.  Sensitivity analysis of differential-algebraic equations: A comparison of methods on a special problem. APPLIED NUMERICAL MATHEMATICS. 32:161-174.
Petzold L, Li ST.  2000.  Software and algorithms for sensitivity analysis of large-scale differential algebraic systems. JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS. 125:131-145.
Petzold LR, Simeon B, Serban R.  2009.  A MODEL OF MACROSCALE DEFORMATION AND MICROVIBRATION IN SKELETAL MUSCLE TISSUE. ESAIM-MATHEMATICAL MODELLING AND NUMERICAL ANALYSIS-MODELISATION MATHEMATIQUE ET ANALYSE NUMERIQUE. 43:805-823.

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