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Papers

2005
consistency042.pdf Rathinam, M., Petzold, L, R., Cao, Y. & Gillespie, D. T. (2005). Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems. Multiscale Modeling and Simulation (SIAM) 4(3), 867-895.
sandiaconf05.pdf Meeker, K., Homescu, C., Petzold, L., El-Samad, H., Khammash, M., & Soderlind, G. (2005). Digital Filter Stepsize Control in DASPK and its Effect on Control Optimization Performance. Proc. Sandia Real-Time Optimization PDE Optimization Conf.
corrosion04.pdf Gray, J., Homescu, C., Petzold, L. R. & Alkire, R. C. J. (2005). Efficient Solution and Sensitivity Analysis of Partial Differential-Algebraic Equation Systems Modelling Corrosion Pit Initiation. Electrochem. Soc. 152(8).
reducedmodelpaper052.pdf Petzold, L. R. & Serban, R. (2005). Error Estimation for Reduced-Order Models of Dynamical Systems C. Homescu. 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.
MSSA042.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). Multiscale Stochastic Simulation Algorithm with Stochastic Partial Equilibrium Assumption for Chemically Reacting Systems. J. Comp. Phys. 206(2) pp. 395-411.
IFACC_HS_OPT04.pdf El Samad, H., Khammash, M., Homescu, C. & Petzold, L. (2005). Optimal Performance of the Heat-Shock Gene Regulatory Network. Proceedings 16th IFAC World Congress, held in Prague, Czech Republic, July
biophys052.pdf Gunawan, R., Cao, Y., Petzold, L. & Doyle, F. (2005). Sensitivity Analysis of Discrete Stochastic Systems. Biophys. J. 88:2530-2540
LBM042.pdf Zhu, L., Tretheway, D., Meinhart, C. & Petzold, L. (2005). Simulation of Fluid Slip at Hydrophobic Microchannel Walls by the Lattice Boltzmann Method. J. Comp. Phys. 202, pp. 181-195.
IJRNC05.pdf El Samad, H., Khammash, M., Petzold, L. & Gillespie, D. (2005). Stochastic Modeling of Gene Regulatory Networks. Int. J. Robust and Nonlinear Control, 15:691-711
ssSSA2.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). The Slow-Scale Stochastic Simulation Algorithm. J. Chem. Phys. 122(1), 014116-014166-18.
trapezoidal.pdf Cao, Y & Petzold, L. R. (2005). Trapezoidal Tau-Leaping Formula for the Stochastic Simulation of Biochemical Systems. Proc. of Foundations of Systems Biology in Engineering (FOSBE) Conf., pp. 149-152.
2004
condition_ode032.pdf Cao, Y. & Petzold, L. (2004). A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method. SIAM J. Scientific Computing 26(2), 359-374.
adjpde2.pdf Li, S. & Petzold, L. (2004). Adjoint Sensitivity Analysis for Time-Dependent Partial Differential Equations with Adaptive Mesh Refinement. Journal of Computational Physics 198(1), 310-325.
adjmatrix2.pdf Cao, Y. & Petzold, L. (2004). An Error Estimate for Matrix Equations. Applied Numerical Mathematics 50(3-4), 395-407.
kirstenMS04.pdf Meeker, K. (2004). Digital Filter Stepsize Control of DASPK and its Effect on Control Optimization Performance. M.S. thesis, Computer Science, UCSB.
optSSA042.pdf Cao, Y., Li, H. & Petzold, L. R. (2004). Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems. Journal of Chemical Physics 121 (9), 4059-4067
Nanotechabs2004.pdf Mathew, G., Mezic, I., Serban, R. & Petzold, L. (2004). Optimization of Mixing in an Active Micromixing Device. Nanotech04 Proceedings
IPDPS04.pdf Zhou, J., Zhu, L., Petzold, L. & Yang, T. (2004). Parallel Simulation of Fluid Slip in a Microchannel. Int. Parallel,Dist. Processing Symposium IPDPS04
fluidslip03.pdf Zhu, L., Tretheway, D., Petzold, L. & Meinhart, C. (2004). Simulation of Fluid Slip at 3D Hydrophobic Microchannel Walls by the Lattice Boltzmann Method. J. Comp. Phys. 202(1), 181-195.
nanotech04yanting.pdf Zhang, Y, T., Chen, H., Mezic, I., Meinhart, C. D., Petzold, L. & MacDonald, N. C. (2004). SOI Processing of a Ring Electrokinetic Chaotic Micromixer. Nanotech04 Proceedings
stochasticstability042.pdf Cao, Y., Petzold, L., Rathinam, M. & Gillespie, D. (2004). The Numerical Stability of Leaping Methods for Stochastic Simulation of Chemically Reacting Systems. J. Chem. Phys. 121(24), 12169-12178.
2003
CDC03.pdf Mathew, G., Mezic, I. & Petzold, L. (2003). A Multiscale Measure for Mixing and its Applications. IEEE Conf. on Decision,Control.
pod.pdf M. Rathinam M. & Petzold, L. (2003). A New Look at Proper Orthogonal Decomposition. SIAM J. Num. Anal. 41 (5), 1893-1925.
adjlinear.pdf Cao, Y. & Petzold, L. (2003). A Subspace Error Estimate for Linear Systems. SIAM J. Mat. Anal. Appl. 24, pp. 787-801.
AMpaper.pdf Serban, R., Li, S. & Petzold, L. (2003). Adaptive Algorithms for Optimal Control of Time-Dependent Partial Differential-Algebraic Equation Systems. Int. J. Num. Methods in Engineering 57(10), 1457-1469.
portugal03.pdf Petzold, L., Cao, Y., Li, S. & Serban, R. (2003). Adaptive Numerical Methods for Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations. Proceedings, Workshop on Modelling, Simulation in Chemical Engineering
adjointI01.pdf Cao, Y., Li, S., Petzold, L. R. & Serban, R. (2003). Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and its Numerical Solution. SIAM J. Sci. Comput. 24(3), 1076-1089,.
ecs03.pdf Gray, J., Homescu, C., Petzold, L. & Alkire, R. (2003). Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation. Abstract, presented at 204th Meeting of The Electrochemical Society in Orlando, FL, October 12-October 16.
mmsr.pdf Hyman, J, M., Li, S. & Petzold, L. (2003). An Adaptive Moving Mesh Method with Static Rezoning for Partial Differential Equations. Computers and Mathematics with Applications 46, 1511-1524.
Strelzoff_A_sew28.pdf Strelzoff, A. & Petzold, L. (2003). Decision Tree Organization for GUI Generation. Proceedings, 28th Annual IEEE/NASA Software Engineering Workshop, Dec 2-4 Greenbelt Maryland.
adpdd03.pdf Strelzoff, A. & Petzold, L. (2003). Deriving User Interface Requirements from Densly Interleaved Scientific Computing Applications. Proceedings,18th IEEE International Conferenceon Automated Software Engineering, Oct. 6-10.
daspkad.pdf Li, S. & Petzold, L. (2003). Description of DASPKADJOINT: An Adjoint Sensitivity Solver for Differential-Algebraic Equations. Technical Report.
dirm.pdf M. Rathinam M. & Petzold, L. (2003). Dynamic Iteration using Reduced Order Models: A Method for Simulation of Large Scale Modular Systems. SIAM J. Num. Anal. 40(4), 1446-1474.
PODtechreport03.pdf Homescu, C., Petzold, L. R., & Serban, R. (2003). Error Estimation for Reduced Order Models of Dynamical Systems . LLNL Technical Report.
leapsizeselection03.pdf Gillespie, D. & Petzold, L. (2003). Improved Leap-Size Selection for Accelerated Stochastic Simulation. J. Chemical Physics 119, pp. 8229-8234.
IMECE2003-55017.pdf Chen, H., Zhang, Y., Mezic, I., Meinhart, C. & Petzold, L. (2003). Numerical Simulation of an Electroosmotic Micromixer. Proceedings of IMECE '03, 2003 ASME International Mechanical Engineering Congress and Exosition, Washington, D. C., Nov. 15-21
SEKE03.pdf Strelzoff, A. & Petzold, L. (2003). Revision Recognition for Scientific Computing: Theory and Application. Proceedings, SEKE03, Fifteenth International Conference on Software Engineeringand Knowledge Engineering.
amr2dimp.pdf Li, S., Petzold, L. & Hyman, J. M. (2003). Solution Adapted Mesh Refinement and Sensitivity Analysis for Parabolic Partial Differential Equation Systems. Lecture Notes in Computational Science and Engineering 30, Springer-Verlag, Heidelberg.
stiffness03.pdf Rathinam, M., Petzold, L., & Gillespie, D. (2003). Stiffness in Stochastic Chemically Reacting Systems: The Implicit Tau-Leaping Method. J. Chemical Physics 119 (24), 12784-12794.
OOPSLA03.pdf Strelzoff, A. & Petzold, L. (2003). Update Wizardry: Automatically Generating Update and Import Wizards for Evolving XML-encoded GUIs. 18th Annual ACM SIGPLAN Conference on Object Oriented Programming, Systems, Languages and Applications.
2002
adjointII01.pdf Cao, Y., Li, S. & Petzold, L. R. (2002). Adjoint Sensitivity Analysis for Differential-Algebraic Equations: Algorithms and Software. J. Comp. Appl. Math. 149, 171-192.
MixPaper.pdf Mathew, G., Petzold, L. & Serban, R. (2002). Computational Techniques for Quantification and Optimization of Mixing in Microfluidic Devices. Technical Report
SNA000220.pdf Serban, R. & Petzold, L. R. (2002). Efficient Computation of Sensitivities for Ordinary Differential Equation Boundary Value Problems. SIAM J. Num. Analysis, 40(1), 220-232.
CMA432002.pdf Mao, G. & Petzold, L. R. (2002). Efficient Integration over Discontinuities for Differential-Algebraic Systems. Computers and Mathematics with Applications 43, 65-79.
IMECE2002-33704.pdf Tretheway, D., Zhu, L., Petzold, L. & Meinhart, C. (2002). Examination of the Slip Boundary Condition by Micro-PIV and Lattice Boltzmann Simulations. Proceedings of IMECE'2002, 2002 ASME International Mechanical Engineering Congress and Exosition, New Orleans, Louisiana, Nov. 17-22
SerEtAl00.pdf Serban, R., Koon, W. S., Lo, M., Marsden, J., Petzold, L. R., Ros, S. D. & Wilson, R. (2002). Halo Orbit Mission Correction Maneuvers Using Optimal Control. Vol 38(4), pp. 571-583
attitude.pdf Petzold, L. (2002). Math, with an Attitude. Proceedings of The Olga Taussky Todd Celebration of Careers in Mathematics. Tallahassee, FL.
2001
RahaPetz00b.pdf Raha, S. & Petzold, L. R. (2001). Constraint Partitioning for Stability in Path-Constrained Dynamic Optimization Problems. SIAM J. Sci. Comput. 22(6), pp. 2051-2074.
RahaPetz00a.pdf Raha, S. & Petzold, L. R. (2001). Constraint Partitioning for Structure in Path-Constrained Dynamic Optimization Problems. Applied Numerical Mathematics, 39, 105-126.
SerPetz00.pdf Serban, R. & Petzold, L. R. (2001). COOPT - A Software Package for Optimal Control of Large-Scale Differential-Algebraic Equation Systems. J. Math. and Computers in Simulation 56 (2), pp. 187-204
Ser01.pdf Serban, R. (2001). COOPT - Control and Optimization of Dynamic Systems: Users' Guide. UCSB Technical Report
SIAMcsepaper.pdf SIAM Working Group on CSE Education (L. Petzold chair) (2001). Graduate Education in Computational Science and Engineering. SIAM Review 43 (1), pp. 163-177.
PD1542001.pdf Venkatesh, P. K., Petzold, L. R., Carr, R. W., Cohen, M. H. & Dean, A. M. (2001). Variational Optimisation by the Solution of a Series of Hamilton-Jacobi Equations. Physica D 154, 15-25.
2000
Im_et_al_CST.pdf Im, H. G., Raja, L. L., Kee, R. J. & Petzold, L. R. (2000). A Numerical Study of Transient Ignition in a Counterflow Nonpremixed Methane-Air Flame Using Adaptive Time Integration. Combust. Sci. and Tech. 158
PetzEtAl00a.pdf Petzold, L. R., Serban, R., Li, S., Raha, S. & Strelzoff, A. (2000). A Problem Solving Environment for Dynamic Optimization of Partial Differential-Algebraic Equation Systems. 16th IMACS World Congress, Lausanne, Switzerland
cdc2000.pdf Rathinam, M. & Petzold, L. R. (2000). An Iterative Method for Simulation of Large Scale Modular Systems using Reduced Order Models. Proc. IEEE Control and Decision Conference, Sydney, Australia, December
an_sqp_method.pdf GIll, P., Jay, L., Leonard, M., Petzold, L. R. & Sharma, V. (2000). An SQP Method for the Optimal Control of Large-Scale Dynamical Systems. J. Comp. Appl. Math. 120, pp. 197-213.
RajaEtAl00.pdf Raja, L. L., Kee, R. J., Serban, R. & Petzold, L. R. (2000). Computational Algorithm for Dynamic Optimization of Chemical Vapor Deposition Processes in Stagnation Flow Reactors. Journal of the Electrochemical Society, Vol. 147(7), 2718-2726
Optimal_Control.pdf Serban, R., Koon, W. S., Lo, M., Marsden, J., Petzold, L. R., Ross, S. D. & Wilson, R. (2000). Optimal Control for Halo Orbit Missions. Proc. IFAC Workshop on Lagrangian,Hamiltonian Methods for Nonlinear Control, Princeton, NJ
Poland00.pdf Petzold, L., Serban, R., Li, S., Raha, S. & Cao, Y. (2000). Sensitivity Analysis and Design Optimization of Differential-Algebraic Equation Systems. Proc. NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion
Sensitivity_Analysis.pdf Li, S., Petzold, L. R. & Zhu, W. (2000). Sensitivity Analysis of Differential-Algebraic Equations: A Comparison of Methods on a Special Problem. Applied Numerical Mathematics 32, pp. 161-174.
Software_and_algorithms1.pdf Li, S. & Petzold, L. R. (2000). Software and Algorithms for Sensitivity Analysis of Large-Scale Differential-Algebraic Systems. J. Comp. Appl. Math. 125, pp. 131-145
1999
LiPetz99.ps Li, S. & Petzold, L. R. (1999). Design of New DASPK for Sensitivity Analysis. UCSB Technical Report.
RajaEtAl99.pdf Raja, L. L., Kee, R. J., Serban, R. & Petzold, L. R. (1999). Dynamic Optimization of Chemically Reacting Stagnation Flows. Fundamental Gas-phase, 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
Model_Reduction_Zhu.pdf Zhu, W. & Petzold, L. R. (1999). Model Reduction for Chemical Kinetics: An Optimization Approach. AIChE Journal, pp. 869-886
CPE11101999.pdf Zhu, W. & Petzold, L. R. (1999). Parallel Sensitivity Analysis for DAEs with Many Parameters. Concurrency: Practice and Experience, 11(10), 571-585
1998
DAE_Alpha_98.pdf Yen, J., Petzold, L. R. & Raha, S. (1998). A Time Integration Algorithm for Flexible Mechanism Dynamics: The DAE-Alpha Method. Computer Methods in Applied Mechanics, Engineering 158, pp. 341-355
Newton_98.pdf Yen, J. & Petzold, L. R. (1998). An Efficient Newton-Type Iteration for the Numerical Solution of Highly Oscillatory Constrained Multibody Dynamic Systems. SIAM J. Sci. Comput. 19, 1513-1534
HessenbergDelay_1998_ANM.pdf Zhu, W. & Petzold, L. R. (1998). Asymptotic Stability of Hessenberg Delay Differential-Algebraic Equations of Retarded or Neutral Type. Applied Numerical Mathematics 27, pp. 309-325
SCE001495.pdf Brown, P., Hindmarsh, A. & Petzold, L. R. (1998). Consistent Initial Condition Calculation For Differential-Algebraic Systems. SIAM J. Sci. Comput., 19(5), 1495-1512.
1-s2.0-s0898122198000042-main.pdf Moore, P. K., Petzold, L. R., & Ren, Y. (1998). Regularization of Index-1 Differential-Algebraic Equations with Rank-Deficient Constraints. Computers Math. Applic., 35(5), 43-61
TCI1998.pdf Raja, L. L., Kee, R. J. & Petzold, L. R. (1998). Simulation of the Transient, Compressible, Gas-Dynamic Behavior of Catalytic-Combustion Ignition in Stagnation Flows. Twenty-Seventh Symposium (International) on Combustion/The Combustion Institute, 2249-2257
s1064827596302011.pdf Li, S., Petzold, L. & Ren Y. (1998). Stability of Moving Mesh Systems of Partial Differential Equations. SIAM J. Sci. Comput., 20(2), 719-738
1997
LinearDelayPaper_1997_ANM.pdf Zhu, W. & Petzold, L. R. (1997). Asymptotic Stability of Linear Delay Differential Algebraic Equations and Numerical Methods. Applied Numerical Mathematics 24, pp. 247-264
LiPetz97.pdf Li, S. & Petzold, L. (1997). Moving Mesh Methods with Upwinding Schemes for Time-Dependent PDEs. J. Computational Phys. 131, 368-377.

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