Linda Petzold - Publications

Affiliations: 
University of California, Santa Barbara, Santa Barbara, CA, United States 
Area:
Systems Biology and Discovery Tools

162 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Wu TB, Wu S, Buoni M, Orfeo T, Brummel-Ziedins K, Cohen M, Petzold L. Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy. Annals of Biomedical Engineering. PMID 29675813 DOI: 10.1007/s10439-018-2031-9  1
2017 Carmona-Alcocer V, Abel JH, Sun TC, Petzold LR, Doyle FJ, Simms CL, Herzog ED. Ontogeny of circadian rhythms and synchrony in the suprachiasmatic nucleus. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. PMID 29054877 DOI: 10.1523/JNEUROSCI.2006-17.2017  0.8
2016 Abel JH, Drawert B, Hellander A, Petzold LR. GillesPy: A Python Package for Stochastic Model Building and Simulation. Ieee Life Sciences Letters. 2: 35-38. PMID 28630888 DOI: 10.1109/LLS.2017.2652448  0.52
2016 Drawert B, Hellander A, Bales B, Banerjee D, Bellesia G, Daigle BJ, Douglas G, Gu M, Gupta A, Hellander S, Horuk C, Nath D, Takkar A, Wu S, Lötstedt P, ... ... Petzold LR, et al. Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. Plos Computational Biology. 12: e1005220. PMID 27930676 DOI: 10.1371/journal.pcbi.1005220  0.72
2016 Zhang Y, Wu TB, Daigle BJ, Cohen M, Petzold L. Identification of disease states associated with coagulopathy in trauma. Bmc Medical Informatics and Decision Making. 16: 124. PMID 27658851 DOI: 10.1186/s12911-016-0360-x  0.6
2016 Abel JH, Meeker K, Granados-Fuentes D, St John PC, Wang TJ, Bales BB, Doyle FJ, Herzog ED, Petzold LR. Functional network inference of the suprachiasmatic nucleus. Proceedings of the National Academy of Sciences of the United States of America. PMID 27044085 DOI: 10.1073/pnas.1521178113  1
2016 Hellander S, Petzold L. Reaction rates for a generalized reaction-diffusion master equation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 93: 013307. PMID 26871190 DOI: 10.1103/PhysRevE.93.013307  1
2016 Zhang Y, Daigle BJ, Cohen M, Petzold L. A cure time model for joint prediction of outcome and time-to-outcome Proceedings - Ieee International Conference On Data Mining, Icdm. 2016: 1117-1122. DOI: 10.1109/ICDM.2015.14  1
2016 Lim RK, Petzold LR, Koç ÇK. Bitsliced high-performance AES-ECB on GPUs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9100: 125-133. DOI: 10.1007/978-3-662-49301-4_8  1
2015 Pourzanjani A, Herzog ED, Petzold LR. On the Inference of Functional Circadian Networks Using Granger Causality. Plos One. 10: e0137540. PMID 26413748 DOI: 10.1371/journal.pone.0137540  1
2015 Wu S, Fu J, Petzold LR. Adaptive deployment of model reductions for tau-leaping simulation. The Journal of Chemical Physics. 142: 204108. PMID 26026435 DOI: 10.1063/1.4921638  1
2015 Lawson MJ, Petzold L, Hellander A. Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 25833240 DOI: 10.1098/rsif.2015.0054  1
2015 Hellander S, Hellander A, Petzold L. Reaction rates for mesoscopic reaction-diffusion kinetics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 91: 023312. PMID 25768640 DOI: 10.1103/PhysRevE.91.023312  1
2015 Thakur GS, Daigle BJ, Dean KR, Zhang Y, Rodriguez-Fernandez M, Hammamieh R, Yang R, Jett M, Palma J, Petzold LR, Doyle FJ. Systems biology approach to understanding post-traumatic stress disorder. Molecular Biosystems. 11: 980-93. PMID 25627823 DOI: 10.1039/c4mb00404c  1
2015 Daigle BJ, Soltani M, Petzold LR, Singh A. Inferring single-cell gene expression mechanisms using stochastic simulation. Bioinformatics (Oxford, England). 31: 1428-35. PMID 25573914 DOI: 10.1093/bioinformatics/btv007  1
2015 Lim RK, Pro JW, Begley MR, Utz M, Petzold LR. High-performance simulation of fracture in idealized 'brick and mortar' composites using adaptive Monte Carlo minimization on the GPU International Journal of High Performance Computing Applications. 30: 186-199. DOI: 10.1177/1094342015593395  1
2015 Torshizi AD, Petzold L, Cohen M. Direct higher order fuzzy rule-based classification system: Application in mortality prediction Proceedings - 2015 Ieee International Conference On Bioinformatics and Biomedicine, Bibm 2015. 846-852. DOI: 10.1109/BIBM.2015.7359795  1
2015 Pro JW, Lim RK, Petzold LR, Utz M, Begley MR. The impact of stochastic microstructures on the macroscopic fracture properties of brick and mortar composites Extreme Mechanics Letters. 5: 1-9. DOI: 10.1016/j.eml.2015.09.001  0.36
2015 Bhattacharjee K, Petzold L. Detecting opinions in a temporally evolving conversation on twitter Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9471: 82-97. DOI: 10.1007/978-3-319-27433-1_6  1
2014 Hellander A, Lawson MJ, Drawert B, Petzold L. Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting. Journal of Computational Physics. 266: 89-100. PMID 26865735 DOI: 10.1016/j.jcp.2014.02.004  1
2014 Fu J, Wu S, Li H, Petzold LR. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems. Journal of Computational Physics. 274: 524-549. PMID 26609185 DOI: 10.1016/j.jcp.2014.06.025  1
2014 Griesemer M, Young C, Robinson AS, Petzold L. BiP clustering facilitates protein folding in the endoplasmic reticulum. Plos Computational Biology. 10: e1003675. PMID 24991821 DOI: 10.1371/journal.pcbi.1003675  1
2014 Gillespie DT, Petzold LR, Seitaridou E. Validity conditions for stochastic chemical kinetics in diffusion-limited systems. The Journal of Chemical Physics. 140: 054111. PMID 24511926 DOI: 10.1063/1.4863990  1
2014 Sturrock M, Hellander A, Aldakheel S, Petzold L, Chaplain MA. The role of dimerisation and nuclear transport in the Hes1 gene regulatory network. Bulletin of Mathematical Biology. 76: 766-98. PMID 23686434 DOI: 10.1007/s11538-013-9842-5  1
2014 Bezzola A, Bales BB, Petzold LR, Alkire RC. Numerical scaling studies of kinetically-limited electrochemical nucleation and growth with accelerated stochastic simulations Journal of the Electrochemical Society. 161: E3001-E3008. DOI: 10.1149/2.001408jes  1
2014 Horuk CB, Douglas G, Gupta A, Krintz C, Abales B, Bellesia G, Drawert B, Wolski R, Petzold L, Hellander A. Automatic and portable cloud deployment for scientific simulations Proceedings of the 2014 International Conference On High Performance Computing and Simulation, Hpcs 2014. 374-381. DOI: 10.1109/HPCSim.2014.6903710  1
2014 Bezzola A, Bales BB, Alkire RC, Petzold LR. An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice Journal of Computational Physics. 256: 183-197. DOI: 10.1016/j.jcp.2013.08.053  1
2014 Bhattacharjee K, Petzold L. Probabilistic user-level opinion detection on online social networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8851: 309-325.  1
2014 Thakur GS, Daigle BJ, Petzold LR, Doyle FJ. A multivariate ensemble approach for identification of biomarkers: Application to breast cancer Ifac Proceedings Volumes (Ifac-Papersonline). 19: 809-814.  1
2013 An S, Harang R, Meeker K, Granados-Fuentes D, Tsai CA, Mazuski C, Kim J, Doyle FJ, Petzold LR, Herzog ED. A neuropeptide speeds circadian entrainment by reducing intercellular synchrony. Proceedings of the National Academy of Sciences of the United States of America. 110: E4355-61. PMID 24167276 DOI: 10.1073/pnas.1307088110  1
2013 Yang R, Daigle BJ, Muhie SY, Hammamieh R, Jett M, Petzold L, Doyle FJ. Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder. Bmc Systems Biology. 7: 80. PMID 23962043 DOI: 10.1186/1752-0509-7-80  1
2013 Lawson MJ, Drawert B, Khammash M, Petzold L, Yi TM. Spatial stochastic dynamics enable robust cell polarization. Plos Computational Biology. 9: e1003139. PMID 23935469 DOI: 10.1371/journal.pcbi.1003139  1
2013 Gillespie DT, Hellander A, Petzold LR. Perspective: Stochastic algorithms for chemical kinetics. The Journal of Chemical Physics. 138: 170901. PMID 23656106 DOI: 10.1063/1.4801941  1
2013 Kolpas A, Busch M, Li H, Couzin ID, Petzold L, Moehlis J. How the spatial position of individuals affects their influence on swarms: a numerical comparison of two popular swarm dynamics models. Plos One. 8: e58525. PMID 23555585 DOI: 10.1371/journal.pone.0058525  1
2013 Macropol K, Bogdanov P, Singh AK, Petzold L, Yan X. I act, therefore i judge: Network sentiment dynamics based on user activity change Proceedings of the 2013 Ieee/Acm International Conference On Advances in Social Networks Analysis and Mining, Asonam 2013. 396-402. DOI: 10.1145/2492517.2492623  1
2013 Fu J, Wu S, Petzold LR. Time dependent solution for acceleration of tau-leaping Journal of Computational Physics. 235: 446-457. DOI: 10.1016/j.jcp.2012.10.036  1
2012 Wallace EW, Gillespie DT, Sanft KR, Petzold LR. Linear noise approximation is valid over limited times for any chemical system that is sufficiently large. Iet Systems Biology. 6: 102-15. PMID 23039691 DOI: 10.1049/iet-syb.2011.0038  1
2012 Wu S, Fu J, Li H, Petzold L. Automatic identification of model reductions for discrete stochastic simulation. The Journal of Chemical Physics. 137: 034106. PMID 22830682 DOI: 10.1063/1.4733563  1
2012 Hellander S, Hellander A, Petzold L. Reaction-diffusion master equation in the microscopic limit. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 042901. PMID 22680526 DOI: 10.1103/PhysRevE.85.042901  1
2012 Daigle BJ, Roh MK, Petzold LR, Niemi J. Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. Bmc Bioinformatics. 13: 68. PMID 22548918 DOI: 10.1186/1471-2105-13-68  1
2012 Griesemer M, Young C, Robinson A, Petzold L. Spatial localisation of chaperone distribution in the endoplasmic reticulum of yeast Iet Systems Biology. 6: 54-63. PMID 22519358 DOI: 10.1049/iet-syb.2011.0006  1
2012 Harang R, Bonnet G, Petzold LR. WAVOS: a MATLAB toolkit for wavelet analysis and visualization of oscillatory systems. Bmc Research Notes. 5: 163. PMID 22448897 DOI: 10.1186/1756-0500-5-163  1
2012 Yang R, Daigle BJ, Petzold LR, Doyle FJ. Core module biomarker identification with network exploration for breast cancer metastasis. Bmc Bioinformatics. 13: 12. PMID 22257533 DOI: 10.1186/1471-2105-13-12  1
2012 Yang R, Daigle BJ, Petzold LR, Doyle FJ. Core module network construction for breast cancer metastasis Proceedings of the World Congress On Intelligent Control and Automation (Wcica). 5083-5089. DOI: 10.1109/WCICA.2012.6359441  1
2012 Petzold L, Krintz C. Stochastic simulation service: Towards an integrated development environment for modeling and simulation of stochastic biochemical systems Proceedings - 2012 Sc Companion: High Performance Computing, Networking Storage and Analysis, Scc 2012. 2303-2324. DOI: 10.1109/SC.Companion.2012.360  1
2012 Östberg PO, Hellander A, Drawert B, Elmroth E, Holmgren S, Petzold L. Reducing complexity in management of escience computations Proceedings - 12th Ieee/Acm International Symposium On Cluster, Cloud and Grid Computing, Ccgrid 2012. 845-852. DOI: 10.1109/CCGrid.2012.72  1
2012 Bunch C, Drawert B, Chohan N, Krintz C, Petzold L, Shams K. Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics Journal of Grid Computing. 10: 23-46. DOI: 10.1007/s10723-012-9213-8  1
2012 Östberg PO, Hellander A, Drawert B, Elmroth E, Holmgren S, Petzold L. Abstractions for scaling escience applications to distributed computing environments: A StratUm integration case study in molecular systems biology Bioinformatics 2012 - Proceedings of the International Conference On Bioinformatics Models, Methods and Algorithms. 290-294.  1
2011 Roh MK, Daigle BJ, Gillespie DT, Petzold LR. State-dependent doubly weighted stochastic simulation algorithm for automatic characterization of stochastic biochemical rare events. The Journal of Chemical Physics. 135: 234108. PMID 22191865 DOI: 10.1063/1.3668100  1
2011 Meeker K, Harang R, Webb AB, Welsh DK, Doyle FJ, Bonnet G, Herzog ED, Petzold LR. Wavelet measurement suggests cause of period instability in mammalian circadian neurons. Journal of Biological Rhythms. 26: 353-62. PMID 21775294 DOI: 10.1177/0748730411409863  1
2011 Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR. StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics (Oxford, England). 27: 2457-8. PMID 21727139 DOI: 10.1093/bioinformatics/btr401  1
2011 Wu S, Fu J, Cao Y, Petzold L. Michaelis-Menten speeds up tau-leaping under a wide range of conditions. The Journal of Chemical Physics. 134: 134112. PMID 21476748 DOI: 10.1063/1.3576123  1
2011 Daigle BJ, Roh MK, Gillespie DT, Petzold LR. Automated estimation of rare event probabilities in biochemical systems. The Journal of Chemical Physics. 134: 044110. PMID 21280690 DOI: 10.1063/1.3522769  1
2011 Sanft KR, Gillespie DT, Petzold LR. Legitimacy of the stochastic Michaelis-Menten approximation. Iet Systems Biology. 5: 58. PMID 21261403 DOI: 10.1049/iet-syb.2009.0057  1
2011 Turner P, Petzold L, Shiflet A, Vakalis I, Jordan K, St. John S. Undergraduate computational science and engineering education Siam Review. 53: 561-574. DOI: 10.1137/07070406X  1
2010 Luni C, Shoemaker JE, Sanft KR, Petzold LR, Doyle FJ. Confidence from uncertainty--a multi-target drug screening method from robust control theory. Bmc Systems Biology. 4: 161. PMID 21106087 DOI: 10.1186/1752-0509-4-161  1
2010 Roh MK, Gillespie DT, Petzold LR. State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm. The Journal of Chemical Physics. 133: 174106. PMID 21054005 DOI: 10.1063/1.3493460  1
2010 Taylor SR, Webb AB, Smith KS, Petzold LR, Doyle FJ. Velocity response curves support the role of continuous entrainment in circadian clocks. Journal of Biological Rhythms. 25: 138-49. PMID 20348465 DOI: 10.1177/0748730409360949  1
2010 Drawert B, Lawson MJ, Petzold L, Khammash M. The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. The Journal of Chemical Physics. 132: 074101. PMID 20170209 DOI: 10.1063/1.3310809  1
2010 Luni C, Sanft KR, Petzold LR, Doyle FJ. Modelling of detailed insulin receptor kinetics affects sensitivity and noise in the downstream signalling pathway Ifac Proceedings Volumes (Ifac-Papersonline). 9: 326-331. DOI: 10.3182/20100705-3-BE-2011.0059  1
2010 Li H, Petzold L. Efficient parallelization of the stochastic simulation algorithm for chemically reacting systems on the graphics processing unit International Journal of High Performance Computing Applications. 24: 107-116. DOI: 10.1177/1094342009106066  1
2010 Buoni M, Petzold L. An algorithm for simulation of electrochemical systems with surface-bulk coupling strategies Journal of Computational Physics. 229: 379-398. DOI: 10.1016/j.jcp.2009.09.032  1
2010 Hildebrandt S, Bagheri N, Gunawan R, Mirsky H, Shoemaker J, Taylor S, Petzold L, Doyle FJ. Systems Analysis for Systems Biology Systems Biomedicine. 249-272. DOI: 10.1016/B978-0-12-372550-9.00010-9  1
2010 Petzold L, Minnich D, Kreschel T, Peisker D. Effect of microstructure on mechanical properties of a thin-walled cast duplex steel Steel Research International. 81: 482-488. DOI: 10.1002/srin.201000004  1
2009 Gillespie DT, Roh M, Petzold LR. Refining the weighted stochastic simulation algorithm. The Journal of Chemical Physics. 130: 174103. PMID 19425765 DOI: 10.1063/1.3116791  1
2009 Resat H, Petzold L, Pettigrew MF. Kinetic modeling of biological systems. Methods in Molecular Biology (Clifton, N.J.). 541: 311-35. PMID 19381542 DOI: 10.1007/978-1-59745-243-4_14  1
2009 Lampoudi S, Gillespie DT, Petzold LR. Effect of excluded volume on 2D discrete stochastic chemical kinetics. Journal of Computational Physics. 228: 3656-3668. PMID 19360139 DOI: 10.1016/j.jcp.2009.02.002  1
2009 Lampoudi S, Gillespie DT, Petzold LR. The multinomial simulation algorithm for discrete stochastic simulation of reaction-diffusion systems. The Journal of Chemical Physics. 130: 094104. PMID 19275393 DOI: 10.1063/1.3074302  1
2009 Gillespie DT, Cao Y, Sanft KR, Petzold LR. The subtle business of model reduction for stochastic chemical kinetics. The Journal of Chemical Physics. 130: 064103. PMID 19222263 DOI: 10.1063/1.3072704  1
2009 Li H, Kolpas A, Petzold L, Moehlis J. Parallel simulation for a fish schooling model on a general-purpose graphics processing unit Concurrency Computation Practice and Experience. 21: 725-737. DOI: 10.1002/cpe.1330  1
2008 Cao Y, Petzold L. Slow Scale Tau-leaping Method. Computer Methods in Applied Mechanics and Engineering. 197: 3472-3479. PMID 19794828 DOI: 10.1016/j.cma.2008.02.024  1
2008 Taylor SR, Gunawan R, Petzold LR, Doyle FJ. Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. Ieee Transactions On Automatic Control. 53: 177-188. PMID 19593456 DOI: 10.1109/TAC.2007.911364  1
2008 Hildebrandt S, Raden D, Petzold L, Robinson AS, Doyle FJ. A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway. Biophysical Journal. 95: 3535-58. PMID 18641066 DOI: 10.1529/biophysj.107.125039  1
2008 Taylor SR, Doyle FJ, Petzold LR. Oscillator model reduction preserving the phase response: application to the circadian clock. Biophysical Journal. 95: 1658-73. PMID 18487303 DOI: 10.1529/biophysj.107.128678  1
2008 Bagheri N, Taylor SR, Meeker K, Petzold LR, Doyle FJ. Synchrony and entrainment properties of robust circadian oscillators. Journal of the Royal Society, Interface / the Royal Society. 5: S17-28. PMID 18426774 DOI: 10.1098/rsif.2008.0045.focus  1
2008 Li H, Cao Y, Petzold LR, Gillespie DT. Algorithms and software for stochastic simulation of biochemical reacting systems. Biotechnology Progress. 24: 56-61. PMID 17894470 DOI: 10.1021/bp070255h  1
2008 Kwei E, Sanft K, Petzold L, Doyle F. Systems analysis of the insulin signaling pathway Ifac Proceedings Volumes (Ifac-Papersonline). 17. DOI: 10.3182/20080706-5-KR-1001.3822  1
2008 Zheng Z, Simeon B, Petzold L. A stabilized explicit Lagrange multiplier based domain decomposition method for parabolic problems Journal of Computational Physics. 227: 5272-5285. DOI: 10.1016/j.jcp.2008.01.057  1
2008 Zheng Z, Stephens RM, Braatz RD, Alkire RC, Petzold LR. A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition Journal of Computational Physics. 227: 5184-5199. DOI: 10.1016/j.jcp.2008.01.056  1
2008 Kwei EC, Sanft KR, Shoemaker JE, Petzold LR, Doyle FJ. Stochastic simulation and systems analysis of insulin-stimulated GLUT4 translocation Aiche Annual Meeting, Conference Proceedings 1
2007 Liu T, Papagiannakopoulos T, Puskar K, Qi S, Santiago F, Clay W, Lao K, Lee Y, Nelson SF, Kornblum HI, Doyle F, Petzold L, Shraiman B, Kosik KS. Detection of a microRNA signal in an in vivo expression set of mRNAs. Plos One. 2: e804. PMID 17726534 DOI: 10.1371/journal.pone.0000804  1
2007 Cao Y, Gillespie DT, Petzold LR. Adaptive explicit-implicit tau-leaping method with automatic tau selection. The Journal of Chemical Physics. 126: 224101. PMID 17581038 DOI: 10.1063/1.2745299  1
2007 Gillespie DT, Petzold LR, Cao Y. Comment on "nested stochastic simulation algorithm for chemical kinetic systems with disparate rates" [J. Chem. Phys. 123, 194107 (2005)]. The Journal of Chemical Physics. 126: 137101; discussion 1. PMID 17430072 DOI: 10.1063/1.2567036  1
2007 Gillespie DT, Lampoudi S, Petzold LR. Effect of reactant size on discrete stochastic chemical kinetics. The Journal of Chemical Physics. 126: 034302. PMID 17249866 DOI: 10.1063/1.2424461  1
2007 Homescu C, Petzold LR, Serban R. Error estimation for reduced-order models of dynamical systems Siam Review. 49: 277-299. DOI: 10.1137/070684392  1
2007 Serban R, Homescu C, Petzold LR. The effect of problem perturbations on nonlinear dynamical systems and their reduced-order models Siam Journal On Scientific Computing. 29: 2621-2643. DOI: 10.1137/050625278  1
2007 Mathew G, Mezić I, Grivopoulos S, Vaidya U, Petzold L. Optimal control of mixing in Stokes fluid flows Journal of Fluid Mechanics. 580: 261-281. DOI: 10.1017/S0022112007005332  1
2007 Buoni M, Petzold L. An efficient, scalable numerical algorithm for the simulation of electrochemical systems on irregular domains Journal of Computational Physics. 225: 2320-2332. DOI: 10.1016/j.jcp.2007.03.025  1
2006 Zheng Z, Stroumpoulis D, Parra A, Petzold L, Tirrell M. A Monte Carlo simulation study of lipid bilayer formation on hydrophilic substrates from vesicle solutions. The Journal of Chemical Physics. 124: 64904. PMID 16483241 DOI: 10.1063/1.2166392  1
2006 Cao Y, Gillespie DT, Petzold LR. Efficient step size selection for the tau-leaping simulation method. The Journal of Chemical Physics. 124: 044109. PMID 16460151 DOI: 10.1063/1.2159468  1
2006 Zheng Z, Petzold L. Runge-Kutta-Chebyshev projection method Journal of Computational Physics. 219: 976-991. DOI: 10.1016/j.jcp.2006.07.005  1
2006 Cao Y, Petzold L. Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems Journal of Computational Physics. 212: 6-24. DOI: 10.1016/j.jcp.2005.06.012  1
2006 Petzold L, Li S, Cao Y, Serban R. Sensitivity analysis of differential-algebraic equations and partial differential equations Computers and Chemical Engineering. 30: 1553-1559. DOI: 10.1016/j.compchemeng.2006.05.015  1
2005 Cao Y, Gillespie DT, Petzold LR. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. The Journal of Chemical Physics. 123: 144917. PMID 16238434 DOI: 10.1063/1.2052596  1
2005 Cao Y, Gillespie DT, Petzold LR. Avoiding negative populations in explicit Poisson tau-leaping. The Journal of Chemical Physics. 123: 054104. PMID 16108628 DOI: 10.1063/1.1992473  1
2005 Gunawan R, Cao Y, Petzold L, Doyle FJ. Sensitivity analysis of discrete stochastic systems. Biophysical Journal. 88: 2530-40. PMID 15695639 DOI: 10.1529/biophysj.104.053405  1
2005 Cao Y, Gillespie DT, Petzold LR. The slow-scale stochastic simulation algorithm. The Journal of Chemical Physics. 122: 14116. PMID 15638651 DOI: 10.1063/1.1824902  1
2005 Gray JR, Homescu C, Petzold LR, Alkire RC. Efficient solution and sensitivity analysis of partial differential- algebraic equation systems application to corrosion pit initiation Journal of the Electrochemical Society. 152: B277-B285. DOI: 10.1149/1.1940807  1
2005 Cao Y, Petzold L. A posteriori error estimation and global error control for ordinary differential equations by the adjoint method Siam Journal On Scientific Computing. 26: 359-374. DOI: 10.1137/S1064827503420969  1
2005 Rathinam M, Petzold LR, Cao Y, Gillespie DT. Consistency and stability of tau-leaping schemes for chemical reaction systems Multiscale Modeling and Simulation. 4: 867-895. DOI: 10.1137/040603206  1
2005 Mathew G, Mezić I, Petzold L. A multiscale measure for mixing Physica D: Nonlinear Phenomena. 211: 23-46. DOI: 10.1016/j.physd.2005.07.017  1
2005 Cao Y, Gillespie D, Petzold L. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems Journal of Computational Physics. 206: 395-411. DOI: 10.1016/j.jcp.2004.12.014  1
2005 Zhu L, Tretheway D, Petzold L, Meinhart C. Simulation of fluid slip at 3D hydrophobic microchannel walls by the lattice Boltzmann method Journal of Computational Physics. 202: 181-195. DOI: 10.1016/j.jcp.2004.07.004  1
2005 El Samad H, Khammash M, Petzold L, Gillespie D. Stochastic modelling of gene regulatory networks International Journal of Robust and Nonlinear Control. 15: 691-711. DOI: 10.1002/rnc.1018  1
2005 El Samad H, Khammash M, Homescu C, Petzold L. Optimal performance of the heat-shock gene regulatory network Ifac Proceedings Volumes (Ifac-Papersonline). 16: 19-24.  1
2004 Cao Y, Petzold LR, Rathinam M, Gillespie DT. The numerical stability of leaping methods for stochastic simulation of chemically reacting systems. The Journal of Chemical Physics. 121: 12169-78. PMID 15606235 DOI: 10.1063/1.1823412  1
2004 Cao Y, Li H, Petzold L. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. The Journal of Chemical Physics. 121: 4059-67. PMID 15332951 DOI: 10.1063/1.1778376  1
2004 Li S, Petzold L. Adjoint sensitivity analysis for time-dependent partial differential equations with adaptive mesh refinement Journal of Computational Physics. 198: 310-325. DOI: 10.1016/j.jcp.2003.01.001  1
2004 Cao Y, Petzold L. An error estimate for matrix equations Applied Numerical Mathematics. 50: 395-407. DOI: 10.1016/j.apnum.2004.01.002  1
2004 Zhou J, Zhu L, Petzold L, Yang T. Parallel simulation of fluid slip in a microchannel Proceedings - International Parallel and Distributed Processing Symposium, Ipdps 2004 (Abstracts and Cd-Rom). 18: 581-590.  1
2004 Gunawan R, Cao Y, Petzold L, Doyle FJ. Sensitivity analysis of discrete stochastic biological systems Aiche Annual Meeting, Conference Proceedings. 8559-8567.  1
2004 Zhang YT, Chen H, Mezic I, Meinhart CD, Petzold L, MacDonald NC. SOI processing of a ring electrokinetic chaotic micromixer 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 292-295.  1
2004 Mathew G, Mezic I, Serban R, Petzold L. Optimization of mixing in an active micromixing device 2004 Nsti Nanotechnology Conference and Trade Show - Nsti Nanotech 2004. 1: 300-303.  1
2003 Cao Y, Li S, Petzold L, Serban R. Adjoint sensitivity analysis for differential-algebraic equations: The adjoint DAE system and its numerical solution Siam Journal On Scientific Computing. 24: 1076-1089. DOI: 10.1137/S1064827501380630  1
2003 Cao Y, Petzold L. A subspace error estimate for linear systems Siam Journal On Matrix Analysis and Applications. 24: 787-801. DOI: 10.1137/S0895479801390649  1
2003 Rathinam M, Petzold LR. A new look at proper orthogonal decomposition Siam Journal On Numerical Analysis. 41: 1893-1925. DOI: 10.1137/S0036142901389049  1
2003 Chen H, Zhang Y, Mezic I, Meinhart C, Petzold L. Numerical simulation of an electroosmotic micromixer American Society of Mechanical Engineers, Fluids Engineering Division (Publication) Fed. 259: 653-658. DOI: 10.1115/IMECE2003-55017  1
2003 Rathinam M, Petzold LR, Cao Y, Gillespie DT. Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method Journal of Chemical Physics. 119: 12784-12794. DOI: 10.1063/1.1627296  1
2003 Gillespie DT, Petzold LR. Improved lead-size selection for accelerated stochastic simulation Journal of Chemical Physics. 119: 8229-8234. DOI: 10.1063/1.1613254  1
2003 Hyman JM, Li S, Petzold LR. An adaptive moving mesh method with static rezoning for partial differential equations Computers and Mathematics With Applications. 46: 1511-1524. DOI: 10.1016/S0898-1221(03)90187-8  1
2003 Serban R, Li S, Petzold LR. Adaptive algorithms for optimal control of time-dependent partial differential-algebraic equation systems International Journal For Numerical Methods in Engineering. 57: 1457-1469. DOI: 10.1002/nme.786  1
2003 Mathew G, Mezić I, Petzold L. A Multiscale Measure for Mixing and its Applications Proceedings of the Ieee Conference On Decision and Control. 3: 2314-2321.  1
2002 Rathinam M, Petzold LR. Dynamic iteration using reduced order models: A method for simulation of large scale modular systems Siam Journal On Numerical Analysis. 40: 1446-1474. DOI: 10.1137/S0036142901390494  1
2002 Serban R, Petzold LR. Efficient computation of sensitivities for ordinary differential equation boundary value problems Siam Journal On Numerical Analysis. 40: 220-232. DOI: 10.1137/S0036142900376870  1
2002 Mao G, Petzold LR. Efficient integration over discontinuities for differential-algebraic systems Computers and Mathematics With Applications. 43: 65-79. DOI: 10.1016/S0898-1221(01)00272-3  1
2002 Cao Y, Li S, Petzold L. Adjoint sensitivity analysis for differential-algebraic equations: Algorithms and software Journal of Computational and Applied Mathematics. 149: 171-191. DOI: 10.1016/S0377-0427(02)00528-9  1
2002 Serban R, Koon WS, Lo MW, Marsden JE, Petzold LR, Ross SD, Wilson RS. Halo orbit mission correction maneuvers using optimal control Automatica. 38: 571-583. DOI: 10.1016/S0005-1098(01)00279-5  1
2002 Tretheway DC, Zhu L, Petzold L, Meinhart CD. Examination of the slip boundary condition by μ-PIV and lattice Boltzmann simulations American Society of Mechanical Engineers, Electronic and Photonic Packaging, Epp. 2: 551-556.  1
2002 Tretheway DC, Zhu L, Petzold L, Meinhart CD. Examination of the slip boundary condition by μ-PIV and lattice Boltzmann simulations American Society of Mechanical Engineers, Electronic and Photonic Packaging, Epp. 2: 551-556.  1
2001 Raha S, Petzold LR. Constraint partitioning for stability in path-constrained dynamic optimization problems Siam Journal On Scientific Computing. 22: 2051-2074. DOI: 10.1137/S1064827500372390  1
2001 Petzold LR. Graduate education in computational science and engineering Siam Review. 43: 163-177. DOI: 10.1137/S0036144500379745  1
2001 Taha T, Mac Hyman J, Petzold L, Schiesser W. Mathematics and Computers in Simulation: Foreword Mathematics and Computers in Simulation. 56: 113. DOI: 10.1016/S0378-4754(01)00303-2  1
2001 Serban R, Petzold LR. COOPT - A software package for optimal control of large-scale differential-algebraic equation systems Mathematics and Computers in Simulation. 56: 187-203. DOI: 10.1016/S0378-4754(01)00289-0  1
2001 Raha S, Petzold LR. Constraint partitioning for structure in path-constrained dynamic optimization problems Applied Numerical Mathematics. 39: 105-126. DOI: 10.1016/S0168-9274(01)00055-1  1
2001 Venkatesh PK, Petzold LR, Carr RW, Cohen MH, Dean AM. Variational optimisation by the solution of a series of Hamilton-Jacobi equations Physica D: Nonlinear Phenomena. 154: 15-25. DOI: 10.1016/S0167-2789(01)00222-6  1
2000 Raja LL, Kee RJ, Serban R, Petzold LR. Computational algorithm for dynamic optimization of chemical vapor deposition processes in stagnation flow reactors Journal of the Electrochemical Society. 147: 2718-2726. DOI: 10.1149/1.1393595  1
2000 Li S, Petzold L. Software and algorithms for sensitivity analysis of large-scale differential algebraic systems Journal of Computational and Applied Mathematics. 125: 131-145. DOI: 10.1016/S0377-0427(00)00464-7  1
2000 Gill PE, Jay LO, Leonard MW, Petzold LR, Sharma V. An SQP method for the optimal control of large-scale dynamical systems Journal of Computational and Applied Mathematics. 120: 197-213. DOI: 10.1016/S0377-0427(00)00310-1  1
2000 Im HG, Raja LL, Kee RJ, Petzold LR. A numerical study of transient ignition in a counterflow nonpremixed methane-air flame using adaptive time integration Combustion Science and Technology. 158: 341-363.  1
2000 Rathinam M, Petzold LR. An iterative method for simulation of large scale modular systems using reduced order models Proceedings of the Ieee Conference On Decision and Control. 5: 4630-4635.  1
1999 Li S, Petzold L, Zhu W. Sensitivity analysis of differential-algebraic equations: A comparison of methods on a special problem Applied Numerical Mathematics. 32: 161-174. DOI: 10.1016/S0168-9274(99)00020-3  1
1999 Zhu W, Petzold L. Parallel sensitivity analysis for DAEs with many parameters Concurrency Practice and Experience. 11: 571-585. DOI: 10.1002/(SICI)1096-9128(19990825)11:10<571::AID-CPE440>3.0.CO;2-#  1
1999 Petzold L, Zhu W. Model reduction for chemical kinetics: An optimization approach Aiche Journal. 45: 869-886.  1
1998 Brown PN, Hindmarsh AC, Petzold LR. Consistent initial condition calculation for differential-algebraic systems Siam Journal On Scientific Computing. 19: 1495-1512.  1
1998 Yen J, Petzold LR. An efficient Newton-type iteration for the numerical solution of highly oscillatory constrained multibody dynamic systems Siam Journal On Scientific Computing. 19: 1513-1534.  1
1998 Zhu W, Petzold LR. Asymptotic stability of Hessenberg delay differential-algebraic equations of retarded or neutral type Applied Numerical Mathematics. 27: 309-325.  1
1998 Yen J, Petzold L, Raha S. A time integration algorithm for flexible mechanism dynamics: The DAE α-method Computer Methods in Applied Mechanics and Engineering. 158: 341-355.  1
1998 Moore PK, Petzold LR, Ren Y. Regularization of index-1 differential-algebraic equations with rank-deficient constraints Computers and Mathematics With Applications. 35: 43-61.  1
1997 Müller S, Hutter KJ, Bley T, Petzold L, Babel W. Dynamics of yeast cell states during proliferation and non proliferation periods in a brewing reactor monitored by multidimensional flow cytometry Bioprocess Engineering. 17: 287-293. DOI: 10.1007/s004490050387  1
1997 Li S, Petzold L. Moving mesh methods with upwinding schemes for time-dependent PDEs Journal of Computational Physics. 131: 368-377. DOI: 10.1006/jcph.1996.5611  1
1997 Knapp DM, Barocas VH, Moon AG, Yoo K, Petzold LR, Tranquillo RT. Rheology of reconstituted type I collagen gel in confined compression Journal of Rheology. 41: 971-993.  1
1997 Zhu W, Petzold LR. Asymptotic stability of linear delay differential-algebraic equations and numerical methods Applied Numerical Mathematics. 24: 247-264.  1
1997 Petzold LR, Ren Y, Maly T. Regularization of higher-index differential-algebraic equations with rank-deficient constraints Siam Journal On Scientific Computing. 18: 753-774.  1
1996 Ashby SF, Lee SL, Petzold LR, Saylor PE, Seidel E. Computing spacetime curvature via differential algebraic equations Applied Numerical Mathematics. 20: 221-234.  1
1996 Maly T, Petzold LR. Numerical methods and software for sensitivity analysis of differential-algebraic systems Applied Numerical Mathematics. 20: 57-79.  1
1995 Ascher UM, Chin H, Petzold LR, Reich S. Stabilization of Constrained Mechanical Systems with DAEs and Invariant Manifolds Mechanics of Structures and Machines. 23: 135-157. DOI: 10.1080/08905459508905232  1
1995 Van Keken PE, Yuen DA, Petzold LR. DASPK: a new high order and adaptive time-integration technique with applications to mantle convection with strongly temperature- and pressure-dependent rheology Geophysical & Astrophysical Fluid Dynamics. 80: 57-74.  1
1995 Maier RS, Petzold LR, Rath W. Parallel solution of large-scale differential-algebraic systems Concurrency Practice and Experience. 7: 795-822.  1
1994 Moore PK, Petzold LR. A stepsize control strategy for stiff systems of ordinary differential equations Applied Numerical Mathematics. 15: 449-463. DOI: 10.1016/0168-9274(94)00042-5  1
1992 Ascher UM, Petzold LR. Projected collocation for higher-order higher-index differential-algebraic equations Journal of Computational and Applied Mathematics. 43: 243-259. DOI: 10.1016/0377-0427(92)90269-4  1
1992 Petzold LR, Potra FA. ODAE methods for the numerical solution of Euler-Lagrange equations Applied Numerical Mathematics. 10: 397-413. DOI: 10.1016/0168-9274(92)90059-M  1
1992 Petzold LR. Numerical solution of differential-algebraic equations in mechanical systems simulation Physica D: Nonlinear Phenomena. 60: 269-279. DOI: 10.1016/0167-2789(92)90243-G  1
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