• The Numerical Solution of Initial Value Problems in Differential-Algebraic Equations, K.E. Brenan, S.L. Campbell, and L.R. Petzold1996, SIAM Classics Series
• Computer Methods for Ordinary Differential Equations and Differential-Algebraic Equations. Uri M. Ascher and Linda R. Petzold, 1998, SIAM

PAPERS

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• Oscillator Model Reduction Preserving the Phase Response: Application to the Circadian Clock, S. Taylor, F. Doyle and L. Petzold, submitted, 2008.
  
• Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit, H. Li and L. Petzold, submitted, 2007.
  
• A Top-Down Approach to Mechanistic Biological Modeling; Application to Single-Chain Antibody Folding, S. Hildebrandt, D. Raden, L. Petzold, A. S. Robinson, F. J. Doyle III, submitted, 2007.
  
• Slow Scale Tau-leaping Method, Y. Cao and L. Petzold, to appear, Computer Methods in Applied Mechanics and Engineering, 2008.
  
• Systems Analysis of the Insulin Signaling Pathway, E. C. Kwei, K. R. Sanft, L. R. Petzold and F. J. Doyle III, to appear, Proc. 17th IFAC World congress, Seoul, Korea, July 2008.
  
• Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs, R. Liu, T. Papagiannakopoulos, K. Puskar, S. Qi, F. Santiago, W. Clay, K. Lao, Y. Lee, S. Nelson, H. Kornblum, F. Doyle, L. Petzold, B. Shraiman,
• Parallel Simulation for a Fish Schooling Model on a General-Purpose Graphics Processing Unit, H. Li, A. Kolpas, L. Petzold and J. Moehlis, to appear, Concurrency and Computation: Practice and Experience, 2008.
  
• Effect of Reactant Size on 2D Discrete Stochastic Chemical Kinetics, S. Lampoudi, D. Gillespie, L. Petzold, submitted, 2007.
  
• Synchrony and Entrainment Properties of Robust Circadian Oscillators, N. Bagheri, S. Taylor, K. Meeker, L. Petzold and F. Doyle, Proc. FOSBE Conf., 2007.
  
• Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit, H. Li, L. Petzold, submitted, 2007.
  
• A Hybrid Multiscale Kinetic Monte Carlo Method for Simulation of Copper Electrodeposition, Z. Zheng, R. Stephens, R. Braatz, R. Alkire, L. Petzold, J. Comp. Phys. 227, 2008, pp. 5184-5199.
  
• A Stabilized Explicit Lagrange Multiplier Based Domain Decomposition Method for Parabolic Problems, Z. Zheng, B. Simeon, L. Petzold, J. Comp. Phys. 227, May 2008, pp. 5272-5285.
  
• Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems, H. Li, Y. Cao, L. Petzold and D. Gillespie, to appear, Biotechnology Progress, 2007.
  
• Computational Modeling of Chaperone Interactions in the Endoplasmic Reticulum of Saccharomyces Cerevisai, M. Griesemer, C. Young, D. Raden, F. Doyle III, A. Robinson and L. Petzold, FOSBE 2007 Conference Proceedings.
  
• Robust Timekeeping in Circadian Networks: From Genes to Cells, N. Bagheri, S. Taylor, K. Meeker, L. Petzold and F. Doyle III, FOSBE 2007 Conference Proceedings.
  
• Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network, S. Taylor, R. Gunawan, L. Petzold and Francis J. Doyle III, to appear, IEEE Trans. Circuits and Systems, 2007.
  
• A Framework for the Analysis of Second Order Projection Methods, Z. Zheng and L. Petzold, submitted, J. Comp. Phys., 2007.
  
• Effect of Reactant Size on Discrete Stochastic Chemical Kinetics, D. Gillespie, S. Lampoudi and L. Petzold,< J. Chem. Phys. 126(3), 034302-034302-9, 2007.
  
• The Adaptive Explicit-Implicit Tau-Leaping Method with Automatic Tau Selection, Y. Cao, D. Gillespie and L. Petzold, J. Chem. Phys. 126(22), pp. 224101-224101-9, 2007.
  
• Optimal Control of Mixing in Stokes Fluid Flows, G. Mathew, I. Mezic, S. Grivopoulos, U. Vaidya and L. Petzold, J. Fluid Mech. 580, pp. 261-281, 2007.
  
• Comment on "Nested Stochastic Simulation Algorithm for Chemical Kinetic Systems with Disparate Rates" [J. Chem. Phys. 123, 194107 (2005)], D. Gillespie, L. Petzold and Y. Cao, J. Chem. Phys. 126, pp. 137101-137101-4 2007.
  
• An Efficient, Scalable Numerical Algorithm for the Simulation of Electrochemical Systems on Irregular Domains, M. Buoni and L. Petzold, to appear, J. Comp. Phys., 2007.
  
• Undergraduate Computational Science and Engineering Education, SIAM Working Group on CSE Undergraduate Education, 2006.
  
• Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations, L. Petzold, S. Li, Y. Cao and R. Serban, Computers and Chemical Engineering 30, pp. 1553-1559, 2006.
  
• Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems, H. Li and L. Petzold, technical report, 2006.
  
• Numerical Simulation for Biochemical Kinetics, book chapter by D. Gillespie and L. Petzold, in System Modelling in Cellular Biology, Ed. Z. Szallasi, J. Stelling and V. Periwal, MIT Press, 2006.
  
• A Monte Carlo Simulation Study of Lipid Bilayer Formation on Hydrophilic Substrates from Vesicle Solutions
  Z. Zheng, D. Stroumpoulis, A. Parra, L. Petzold and M. Tirrell, J. Chem. Phys. 7, 2006.
• Efficient Stepsize Selection for the Tau-Leaping Method
  Y. Cao, D. Gillespie and L. Petzold, J. Chem. Phys. 124, 044109-144109-11, 2006.
• Stochastic Modeling of Gene Regulatory Networks
  H. El Samad, M. Khammash, L. Petzold and D. Gillespie, Int. J. Robust and Nonlinear Control, 15:691-711, 2005.
• Avoiding Negative Populations in Explicit Tau Leaping
  Y. Cao, D. Gillespie and L. Petzold, J. Chem. Phys.123, pp. 054104-054112, 2005.
• Runge-Kutta Chebyshev Projection Method
  Z. Zheng and L. Petzold, J. Comp. Phys. 219, 976-991, 2006.
• Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction
  Y. Cao, D. Gillespie and L. Petzold, J. Chem. Phys. 123(14), pp. 144917-144929, 2005.
• Sensitivity Analysis of Discrete Stochastic Systems
  R. Gunawan, Y. Cao, L. Petzold and F. Doyle, Biophys. J. 88:2530-2540, 2005.
• The Effect of Problem Perturbations on Nonlinear Dynamical Systems and their Reduced Order Models
  R. Serban, C. Homescu and L. Petzold, SIAM J. Sci. Comput., Vol. 29, No. 6, pp. 2621-2643, 2007.
• Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems
  Y. Cao and L. Petzold, J. Comp. Phys. 212(1), pp. 6-24, 2006.
• Optimal Performance of the Heat-Shock Gene Regulatory Network
  H. El Samad, M. Khammash, C. Homescu and L. Petzold, Proceedings 16th IFAC World Congress, held in Prague, Czech Republic, July 2005.
• Digital Filter Stepsize Control of DASPK and its Effect on Control Optimization Performance
  Kirsten Meeker, M.S. thesis, Computer Science, UCSB, 2004.
• Efficient Solution and Sensitivity Analysis of Partial Differential-Algebraic Equation Systems Modelling Corrosion Pit Initiation
  J. Gray, C. Homescu, L. R. Petzold, R. C. Alkire, J. Electrochem. Soc. 152(8), 2005.
• Digital Filter Stepsize Control in DASPK and its Effect on Control Optimization Performance
  K. Meeker, C. Homescu, L. Petzold, H. El-Samad, M. Khammash and G. Soderlind, Proc.Sandia Real-Time Optimization PDE Optimization Conf. 2005.
• The Numerical Stability of Leaping Methods for Stochastic Simulation of Chemically Reacting Systems
  Y. Cao, L. Petzold, M. Rathinam and D. Gillespie, J. Chem. Phys. 121(24), 12169-12178, 2004.
• A Multiscale Measure for Mixing
  G. Mathew, I. Mezic and L. Petzold, Physica D 211 (1-2): pp. 23-46, 2005.
• The Slow-Scale Stochastic Simulation Algorithm
  Y. Cao, D. Gillespie, L. Petzold, J. Chem. Phys. 122(1), 014116-014166-18, 2005.
• Simulation of Fluid Slip at Hydrophobic Microchannel Walls by the Lattice Boltzmann Method
  L. Zhu, D. Tretheway, C. Meinhart, L. Petzold, J. Comp. Phys. 202, pp. 181-195, 2005.
• Multiscale Stochastic Simulation Algorithm with Stochastic Partial Equilibrium Assumption for Chemically Reacting Systems
  Y. Cao, D. Gillespie, L. Petzold, J. Comp. Phys. 206(2) 2005, pp. 395-411.
• Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems
  Y. Cao, H. Li, L. R. Petzold, Journal of Chemical Physics 121 (9), 4059-4067, 2004.
• Consistency and Stability of Tau Leaping Schemes for Chemical Reaction Systems
  M. Rathinam, L. R. Petzold, Y. Cao, D. T. Gillespie, Multiscale Modeling and Simulation (SIAM) 4(3), 867-895, 2005.
• Error Estimation for Reduced Order Models of Dynamical Systems
  C. Homescu, L. R. Petzold and R. Serban, SIAM J. Numer. Anal. 43, pp. 1693-1714, 2005. Also, selected to appear in the SIGEST section of SIAM Review 49(2), pp. 277-299.
• Error Estimation for Reduced Order Models of Dynamical Systems
  C. Homescu, L. R. Petzold and R. Serban, LLNL Technical Report, 2003.
• Optimization of Mixing in an Active Micromixing Device a Ring Electrokinetic Chaotic Micromixer
  G. Mathew, I. Mezic, R. Serban and L. Petzold, to appear, Nanotech04.
• SOI Processing of a Ring Electrokinetic Chaotic Micromixer
  Y. T. Zhang, H. Chen, I. Mezic, C. D. Meinhart, L. Petzold and N. C. MacDonald, Nanotech04.
• Parallel Simulation of Fluid Slip in a Microchannel
  J. Zhou, L. Zhu, L. Petzold and T. Yang, Int. Parallel and Dist. Processing Symposium, IPDPS04.
• Simulation of Fluid Slip at 3D Hydrophobic Microchannel Walls by the Lattice Boltzmann Method
  L. Zhu, D. Tretheway, L. Petzold and C. Meinhart, submitted, J. Comput. Phys.
• Numerical Simulation of an Electroosmotic Micromixer
  H. Chen, Y. Zhang, I. Mezic, C. Meinhart and L. Petzold, Proceedings of IMECE'2003, 2003 ASME International Mechanical Engineering Congress and Exosition, Washington, D. C., Nov. 15-21, 2003.
• Update Wizardry: Automatically Generating Update and Import Wizards for Evolving XML-encoded GUIs
  A. Strelzoff and L. Petzold, to appear, 18th Annual ACM SIGPLAN Conference on Object Oriented Programming, Systems, Languages and Applications, 2003.
• Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation
  J. Gray, C. Homescu, L. Petzold and R. Alkire, Abstract, to be presented at 204th Meeting of The Electrochemical Society in Orlando, FL, October 12-October 16, 2003.
• Adaptive Numerical Methods for Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations
  L. Petzold, Y. Cao, S. Li and R. Serban, Proceedings, Workshop on Modelling and Simulation in Chemical Engineering, Coimbra, Portugal, 2003.
• A Multiscale Measure for Mixing and its Applications
  G. Mathew, I. Mezic, L. Petzold, to appear, IEEE Conf. on Decision and Control, 2003.
• Decision Tree Organization Organization for GUI Generation
  A. Strelzoff, L. Petzold, Proceedings, 28th Annual IEEE/NASA Software Engineering Workshop, Dec 2-4 2003, Greenbelt Maryland.
• Revision Recognition for Scientific Computing: Theory and Application
  A. Strelzoff, L. Petzold, Proceedings, SEKE03, Fifteenth International Conference on Software Engineering and Knowledge Engineering, 2003.
• Deriving User Interface Requirements from Densly Interleaved Scientific Computing Applications
  A. Strelzoff, L. Petzold, Proceedings, 18th IEEE International Conference on Automated Software Engineering, Oct. 6-10, 2003.
• Stiffness in Stochastic Chemically Reacting Systems: The Implicit Tau-Leaping Method
  M. Rathinam, L. Petzold, D. Gillespie, J. Chemical Physics 119 (24), 12784-12794, 2003.
• Improved Leap-Size Selection for Accelerated Stochastic Simulation
  D. Gillespie and L. Petzold, J. Chemical Physics 119 (2003), pp. 8229-8234.
• A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method
  Y. Cao and L. Petzold, SIAM J. Scientific Computing 26(2), 359-374, 2004.
• An Error Estimate for Matrix Equations
  Y. Cao and L. Petzold, Applied Numerical Mathematics 50(3-4), 395-407, 2004.
• Examination of the Slip Boundary Condition by Micro-PIV and Lattice Boltzmann Simulations
  D. Tretheway, L. Zhu, L. Petzold and C. Meinhart, Proceedings of IMECE'2002, 2002 ASME International Mechanical Engineering Congress and Exosition, New Orleans, Louisiana, Nov. 17-22, 2002.
• Computational Techniques for Quantification and Optimization of Mixing in Microfluidic Devices
  G. Mathew, L. Petzold and R. Serban, submitted, Journal of Computational Physics.
• Adjoint Sensitivity Analysis for Time-Dependent Partial Differential Equations with Adaptive Mesh Refinement
  S. Li and L. Petzold, Journal of Computational P Description of DASPKADJOINT: An Adjoint Sensitivity Solver for Differential-Algebraic Equations
  S. Li and L. Petzold, Technical Report.
• Adaptive Algorithms for Optimal Control of Time-Dependent Partial Differential-Algebraic Equation Systems
  R. Serban, S. Li and L. Petzold, Int. J. Num. Methods in Engineering 57(10) (2003), 1457-1469.
• A New Look at Proper Orthogonal Decomposition
  M. Rathinam and L. Petzold, SIAM J. Num. Anal. 41 (5) (2003), 1893-1925.
• Dynamic Iteration using Reduced Order Models: A Method for Simulation of Large Scale Modular Systems
  M. Rathinam and L. Petzold, SIAM J. Num. Anal. 40(4) (2003), 1446-1474.
• A Subspace Error Estimate for Linear Systems
  Y. Cao and L. Petzold, SIAM J. Mat. Anal. Appl. 24 (2003), pp. 787-801.
• Graduate Education in Computational Science and Engineering
  SIAM Working Group on CSE Education (L. Petzold, chair), SIAM Review 43 (1), (2001), pp. 163-177.
• An Adaptive Moving Mesh Method with Static Rezoning for Partial Differential Equations
  J. M. Hyman, S. Li and L. Petzold, Computers and Mathematics with Applications 46 (2003), 1511-1524.
• Solution Adapted Mesh Refinement and Sensitivity Analysis for Parabolic Partial Differential Equation Systems
  S. Li, L. Petzold and J. M. Hyman, Lecture Notes in Computational Science and Engineering 30, Springer-Verlag, Heidelberg, 2003.
• Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and its Numerical Solution
  Y. Cao, S. Li, L. R. Petzold, and R. Serban, SIAM J. Sci. Comput. 24(3) (2003), 1076-1089,.
• Adjoint Sensitivity Analysis for Differential-Algebraic Equations: Algorithms and Software
  Y. Cao, S. Li and L. R. Petzold, J. Comp. Appl. Math. 149 (2002), 171-192.
• An Iterative Method for Simulation of Large Scale Modular Systems using Reduced Order Models
  M. Rathinam and L. R. Petzold, Proc. IEEE Control and Decision Conference, Sydney, Australia, December 2000.
• Sensitivity Analysis and Design Optimization of Differential-Algebraic Equation Systems
  L. Petzold, R. Serban, S. Li, S. Raha and Y. Cao, Proc. NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion
• Efficient Computation of Sensitivities for Ordinary Differential Equation Boundary Value Problems
  R. Serban and L.R. Petzold, SIAM J. Num. Analysis 40(1), pp. 220-232.
• Constraint Partitioning for Stability in Path-Constrained Dynamic Optimization Problems
  S. Raha and L.R. Petzold, SIAM J. Sci. Comput. 22(6), pp. 2051-2074.
• Constraint Partitioning for Structure in Path-Constrained Dynamic Optimization Problems
  S. Raha and L.R. Petzold, Applied Numerical Mathematics 39, 2002, pp. 65-.
• A Numerical Study of Transient Ignition in a Counterflow Nonpremixed Methane-Air Flame Using Adaptive Time Integration
  H. G. Im, L. L. Raja, R. J. Kee and L.R. Petzold, Combust. Sci. and Tech. 158 (2000), pp. 341-363.
• COOPT - A Software Package for Optimal Control of Large-Scale Differential-Algebraic Equation Systems
  R. Serban and L.R. Petzold, J. Math. and Computers in Simulation 56 (2) (2001), pp. 187-204
• Halo Orbit Mission Correction Maneuvers Using Optimal Control
  R. Serban, W.S. Koon, M. Lo, J. Marsden, L.R. Petzold, S.D. Ross, and R. Wilson, Vol 38(4), pp. 571-583, 2002
• A Problem Solving Environment for Dynamic Optimization of Partial Differential-Algebraic Equation Systems
  L.R. Petzold, R. Serban, S. Li, S. Raha, and A. Strelzoff, 16th IMACS World Congress, Lausanne, Switzerland, 2000
• Optimal Control for Halo Orbit Missions
  R. Serban, W.S. Koon, M. Lo, J. Marsden, L.R. Petzold, S.D. Ross, and R. Wilson, Proc. IFAC Workshop on Lagrangian and Hamiltonian Methods for Nonlinear Control, Princeton, NJ, 2000
• Computational Algorithm for Dynamic Optimization of Chemical Vapor Deposition Processes in Stagnation Flow Reactors
  L.L. Raja, R.J. Kee, R. Serban, and L.R. Petzold, Journal of the Electrochemical Society, Vol. 147(7), 2718-2726, 2000
• Dynamic Optimization of Chemically Reacting Stagnation Flows
  L.L. Raja, R.J. Kee, R. Serban, and L.R. Petzold, Fundamental Gas-phase and Surface Chemistry of Vapor-Phase Materials Synthesis, Eds. M.D. Allendorf, M.R. Zachariah, L. Mountziaris, and A.H. McDaniel, Electrochem. Soc. Proc. Series 98-23, p.340-351, 1999
• An SQP Method for the Optimal Control of Large-Scale Dynamical Systems
  Philip Gill, Laurent Jay, Michael Leonard, Linda Petzold and Vivek Sharma, J. Comp. Appl. Math. 120 (2000), pp. 197-213.
• COOPT - Control and Optimization of Dynamic Systems: Users' Guide
  Radu Serban, UCSB Technical Report, 2001.
• Design of New DASPK for Sensitivity Analysis
  Shengtai Li and Linda Petzold, UCSB Technical Report, 1999.
• Model Reduction for Chemical Kinetics: An Optimization Approach
  Wenjie Zhu and Linda Petzold, AIChE Journal, pp. 869-886, 1999. [ appendix with details on the original and reduced mechanisms]
• Parallel Sensitivity Analysis for DAEs with Many Parameters
  Wenjie Zhu and Linda Petzold, Concurrency: Practice and Experience 11, pp. 571-585, 1999.
• Sensitivity Analysis of Differential-Algebraic Equations: A Comparison of Methods on a Special Problem
  Shengtai Li, Linda Petzold and Wenjie Zhu, Applied Numerical Mathematics 32 (2000), pp. 161-174.
• Software and Algorithms for Sensitivity Analysis of Large-Scale Differential-Algebraic Systems
  S. Li and L.R. Petzold, to appear, J. Comp. Appl. Math.
• A Time Integration Algorithm for Flexible Mechanism Dynamics : The DAE-Alpha Method
  Jeng Yen, Linda Petzold, and Soumyendu Raha, Computer Methods in Applied Mechanics and Engineering, 158 , pp 341-355, 1998.
• Asymptotic Stability of Hessenberg Delay Differential-Algebraic Equations of Retarded or Neutral Type
  Wenjie Zhu and Linda Petzold, Applied Numerical Mathematics 27, pp. 309-325, 1998.
• Consistent Initial Condition Calculation For Differential - Algebraic Systems
  Peter Brown, Alan Hindmarsh and Linda Petzold, SIAM J. Sci. Comput. 19, 1495-1512, 1998.
• An Efficient Newton-Type Iteration for the Numerical Solution of Highly Oscillatory Constrained Multibody Dynamic Systems
  J. Yen and L. R. Petzold, SIAM J. Sci. Comput. 19, 1513-1534, 1998.
• Asymptotic Stability of Linear Delay Differential Algebraic Equations and Numerical Methods
  Wenjie Zhu and Linda Petzold, Applied Numerical Mathematics 24, pp. 247-264, 1997.
• Numerical Solution of Highly Oscillatory Ordinary Differential Equations
  Linda Petzold, Laurent Jay and Jeng Yen, Acta Numerica 6, pages 437-484, 1997.
• Moving Mesh Methods with Upwinding Schemes for Time-Dependent PDEs
  S. Li, L. Petzold, J. Computational Phys. 131, 368-377, 1997.
• Regularization of Index-One Differential-Algebraic Equations with Rank-Deficient Constraints
  P.K. Moore, Linda R Petzold and Yuhe Ren, to appear, Computers and Mathematics with Applications, 1997.
• Numerical Methods and Software for Sensitivity Analysis of Differential Algebraic Equations
  Timothy Maly and Linda Petzold, Applied Numerical Mathematics 20, 57-79, 1996.
• Computing Space-time Curvature via Differential- Algebraic Equations
  S F Ashby, S L Lee, L R Petzold, P E Saylor, and E Seidel, Applied Numerical Mathematics 20, 221-234, 1996.
• Stability of Moving Mesh Systems of Partial Differential Equations
  S. Li, L. Petzold, Y. Ren, to appear, SIAM J. Sci. Comput., 1996.
• Numerical Optimal Control of Parabolic PDEs using DASOPT
  L. Petzold, J. B. Rosen, P. E. Gill, L. O. Jay and K. Park, Proc. IMA Workshop on Large-Scale Optimization, 1996.
• Highly Oscillatory Systems and Periodic Stability
  Laurent O Jay and Linda Petzold, May 1995
• .The Numerical Solution of Delay-Differential-Algebraic Equations of Retarded and Neutral Type, U. Ascher and L. Petzold, SIAM J. on Numerical Analysis 32, (1995), 1635-1657.
  
• Convergence of the Iterative Methods for Coordinate Splitting Formulation in Multibody Dynamics
  Jeng Yen and Linda Petzold, July 1995
• Numerical Solution of Nonlinear Oscillatory Multibody Dynamic Systems
  J. Yen and L. R. Petzold, Proc. of 16th Numerical Analysis Conference, University of Dundee, 1995.
• On the Numerical Solution of Constrained Multibody Dynamic Systems
  J. Yen and L. R. Petzold, 1994.
• Canonical Forms and Solvable Singular Systems of Differential Equations, S. L. Campbell and L. R. Petzold, SIAM J. Alg. Disc. Meth. (4)4, 1983, pp. 517-521
  
• Differential/Algebraic Equations are not ODEs, L. R. Petzold, SIAM J. Sci. Stat. Comput. (3), 1982, pp. 367-384