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Papers

2007
Griesemer_FOSBE07.pdf Griesemer, M., Young, C., Raden, D., Doyle III, F., Robinson, A. & Petzold, L. (2007). Computational Modeling of Chaperone Interactions in the Endoplasmic Reticulum of Saccharomyces Cerevisai. FOSBE 2007 Conference Proceedings.
PlosOne07.pdf Liu, R., Papagiannakopoulos, T., Puskar, K., Qi, S., Santiago, F., Clay, W., Lao, K., Lee, Y., Nelson, S., Kornblum, H., Doyle, F., Petzold, L., Shraiman, B. & Kosik, K. (2007). Detection of a MicroRNA Signal in an In Vivo ExpressionSet of mRNAs. Plos One, Vol. 8, August 2007, e804
reactant_size06.pdf Gillespie, D., Lampoudi, S. & Petzold, L. (2007). Effect of Reactant Size on Discrete Stochastic Chemical Kinetics. J. Chem. Phys. 126(3), 034302-034302-9
controlofmixing06.pdf Mathew, G., Mezic, I., Grivopoulos, S., Vaidya, U. & Petzold, L. (2007). Optimal Control of Mixing in Stokes Fluid Flows. J. Fluid Mech. 580, pp. 261-281
Doyle_FOSBE07.pdf Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle III, F. (2007). Robust Timekeeping in Circadian Networks: From Genes to Cells. FOSBE 2007 Conference Proceedings.
stochastic_simulation_of_biochemical_systems_on_th.pdf Li, H. & Petzold, L. R. (2007). Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit.
FOSBE_proceedings07.pdf Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle, F. (2007). Synchrony and Entrainment Properties of Robust Circadian Oscillators. Proc. FOSBE Conf.
adaptivetau06.pdf Cao, Y., Gillespie, D. & Petzold, L. (2007). The Adaptive Explicit-Implicit Tau-Leaping Method with Automatic Tau Selection. J. Chem. Phys. 126(22), pp. 224101-224101-9, 2007.
ROMerror06.pdf Serban, R., Homescu, C. & Petzold, L. (2007). The Effect of Problem Perturbations on Nonlinear Dynamical Systems and their Reduced Order Models. SIAM J. Sci. Comput., Vol. 29, No. 6, pp. 2621-2643
2006
1.2166392.pdf Zheng, Z., Stroumpoulis, D., Parra, A., Petzold, L., & Tirrell, M. (2006). A Monte Carlo Simulation Study of Lipid Bilayer Formation on Hydrophilic Substrates from Vesicle Solutions. J. Chem. Phys. 124, 064904.
Lipid_Bilayer06.pdf Stroumpoulis, D., Parra, A., Petzold, L. & Tirrell, M. (2006). A Monte Carlo Simulation Study of Lipid Bilayer Formation on Hydrophilic Substrates from Vesicle Solutions Z. Zheng. J. Chem. Phys. 7
distributiondistance042.pdf Cao, Y. & Petzold, L. (2006). Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems. J. Comp. Phys. 212(1), pp. 6-24
NewTau052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2006). Efficient Stepsize Selection for the Tau-Leaping Method. J. Chem. Phys. 124, 044109-144109-11
ldm0513.pdf Li, H. & Petzold, L. (2006). Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems. Technical report
BookChapter06.pdf Book chapter by Gillespie, D. & Petzold, L. (2006). Numerical Simulation for Biochemical Kinetics. In System Modelling in Cellular Biology, Ed. Z. Szallasi, J. Stelling, V. Periwal MIT Press
rkcpmethod052.pdf Z. Zheng and L. Petzold (2006). Runge-Kutta-Chebyshev Projection Method. J. Comp. Phys. 219, 976-991
CCEpaper.pdf Petzold, L., Li, S., Cao, Y. & Serban, R. (2006). Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations. Computers, Chemical Engineering 30 30, pp. 1553-1559
CSE_undergrad_report06.pdf SIAM Working Group on CSE Undergraduate Education (2006). Undergraduate Computational Science and Engineering Education.
2005
multiscalemixing05.pdf Mathew, G., Mezic, I. & Petzold, L. (2005). A Multiscale Measure for Mixing. Physica D 211 (1-2): pp. 23-46.
EnzymSubstr052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction. J. Chem. Phys. 123(14), pp. 144917-144929
ModTau052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). Avoiding Negative Populations in Explicit Poisson Tau Leaping. J. Chem. Phys.123, pp. 054104-054112
nSSAComment.pdf Gillespie, D., Petzold, L. & Cao, Y. (2005). Comment on 'Nested Stochastic Simulation Algorithm for Chemical Kinetic Systems with Disparate Rates'. J. Chem. Phys. 126, pp. 137101-137101-4
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.

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