Primary tabs

@journal{ghaffari2020
	author		= {Ghaffari, H., Grant, S. C., Petzold, L. R., and Harrington, M. G.},
	title		= {Regulation of CSF and Brain Tissue Sodium Levels by the Blood-CSF and Blood-Brain Barriers During Migraine},
	article		= {Front. Comput. Neurosci. 14:4},
	year		= {2020},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/fncom-14-00004.pdf},
	note		= {doi: 10.3389/fncom.2020.00004 | PMCID: PMC7010722},
}
@journal{zhao2019
	author		= {Zhao, Y., Guzman, E., Audouard, M., Cheng, Z., Hansma, P. K., Kosik, K. S., & Petzold, L.},
	title		= {A Deep Learning Framework for Classification of in vitro Multi-Electrode Array Recordings},
	article		= {Proceedings of the 2019 International Conference on Data Mining},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/mea_dl.pdf},
}
@journal{drawert2019
	author		= {Drawert, B., Jacob, B., Li, Z., Yi, T-M, & Petzold, L.},
	title		= {A Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) for Advection-Diffusion-Reaction Problems},
	article		= {J. Comp. Phys. 378, pp. 1-17.},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/hybrid_sdpd_and_ssa.pdf},
	note		= {doi: 10.1016/j.jcp.2018.10.043 | PMCID: PMC6481948},
}
@journal{mitchell2019
	author		= {Mitchell, B. A., Lauharatanahirun, N., Garcia, J. O., Wymbs, N., Grafton, S., Vettel, J. M., & Petzold, L. R.},
	title		= {A Minimum Free Energy Model of Motor Learning},
	article		= {Neural Computation 32, 1945-1963},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/neco_a_01219.pdf},
	note		= {doi: 10.1162/neco_a_01219 | PMID: 31393824},
}
@journal{ghaffari2019
	author		= {Ghaffari, H., Varner, J. D., & Petzold, L. R.},
	title		= {Analysis of the Role of Thrombomodulin in All-trans Retinoic Acid Treatment of Coagulation Disorders in Cancer Patients},
	article		= {Theoretical Biology and Medical Modelling 16(1):3},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/s12976-019-0099-z.pdf},
	note		= {doi: 10.1186/s12976-019-0099-z | PMCID: PMC6376718},
}
@journal{jang2019
	author		= {Jang, J., Han, D., Golkaram, M., Audouard, M., Liu, G., Bridges, D., Hellander, S., Chialastri, A., Dey, S. S.,  Petzold, L. R., & Kosik, K. S.},
	title		= {Control over single-cell distribution of G1 lengths by WNT governs pluripotency},
	article		= {PLoS Biol 17(9): e3000453.},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/journal.pbio_.3000453-2.pdf},
	note		= {doi: 10.1371/journal.pbio.3000453 | PMCID: PMC6782112},
}
@journal{alber2019
	author		= {Alber, M., Tepole, A. B., Cannon, W. R., De, S., Dura-Bernal, S., Garikipati, K., Karniadakis, G., Lytton, W. W., Perdikaris, P., Petzold, L., & Kuhl, E.},
	title		= {Integrating machine learning and multiscale modeling--perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences},
	article		= {npj Digital Medicine, 2:115},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/digmed19.pdf},
	note		= {doi: 10.1038/s41746-019-0193-y | PMCID: PMC6877584},
}
@journal{dean2019
	author		= {Dean, K. R., Hammamieh, R., Mellon, S. H., Abu-Amara, D., Flory, J. D., Guffanti, G., Wang, K., Daigle Jr., B. J., Gautam, A., Lee, I., Yang, R., Almli, L. M., Bersani, F. S., Chakraborty, N., Donohue, D., Kerley, K., Kim, T-K, Laska, E., Lee, M. Y., Lindqvist, D., Lori, A., Lu, L., Misganaw, B., Muhie, S., Newman, J., Price, N. D., Qin, S., Reus, V. I., Siegel, C., Somvanshi, P. R., Thakur, G. S., Zhou, Y., The PTSD Systems Biology Consortium, Hood, L., Ressler, K. J., Wolkowitz, O. M., Yehuda, R., Jett, M., Doyle III, F. J., & Marmar, C.},
	title		= {Multi-omic biomarker identification and validation for diagnosing warzone-related post-traumatic stress disorder},
	article		= {Mol Psychiatry (2019)},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ptsd.pdf},
	note		= {doi: 10.1038/s41380-019-0496-z | PMID: 31501510},
}
@journal{doering2019
	author		= {Doering, G. N.,  Sheehy, K. A., Lichtenstein, J. L. L., Drawert, B., Petzold, L. R., & Pruitt, J. N},
	title		= {Sources of Intraspecific Variation in the Collective Tempo and Synchrony of Ant Societies},
	article		= {Behavioral Ecology, 30:6, 1682-1690},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/arz135.pdf},
	note		= {doi: 10.1093/beheco/arz135},
}
@journal{drawert2019
	author		= {Drawert, B., Jacob, B., Li, Z., Yi, T-M, & Petzold, L.},
	title		= {Validation Data for a Hybrid Smoothed Dissipative Particle Dynamics (SDPD) Spatial Stochastic Simulation Algorithm (sSSA) Method},
	article		= {Data in Brief, 22, pp. 11-15.},
	year		= {2019},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1-s2.0-s2352340918314963-main.pdf},
	note		= {doi: 10.1016/j.dib.2018.11.103 | PMCID: PMC6293021},
}
@journal{bales2018
	author		= {Bales, B., Petzold, L., Goodlet, B. R., Lenthe, W. C., & Pollock, T. M.},
	title		= {Bayesian Inference of Elastic Properties with Resonant Ultrasound Spectroscopy},
	article		= {J. Acoust. Soc. Am., 143, pp. 71-83},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1.5017840.pdf},
	note		= {doi: 10.1121/1.5017840},
}
@journal{wu2018
	author		= {Wu, T. B., Wu, S., Buoni, M., Orfeo, T., Brummel-Ziedins, K., Cohen, M., & Petzold, L.},
	title		= {Computational Model for Hyperfibrinolytic Onset of Acute Traumatic Coagulopathy},
	article		= {Ann. Biomed. Eng. pp. 1-10},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/10.10072fs10439-018-2031-9.pdf},
	note		= {doi: 10.1007/s10439-018-2031-9 | PMID: 29675813},
}
@journal{pro2018
	author		= {Pro, J. W., Sehr, S., Lim, R. K., Petzold, L. R., & Begley, M. R.},
	title		= {Conditions controlling kink crack nucleation out of, and delamination along, a mixed-mode interface crack},
	article		= {J. Mech. Phys. Solids 121, 480-495.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1-s2.0-s0022509618303429-main.pdf},
	note		= {doi: 10.1016/j.jmps.2018.08.015},
}
@journal{mitchell2018
	author		= {Mitchell, B. A. & Petzold, L. R.},
	title		= {Control of Neural Systems at Multiple Scales Using Model-free, Deep Reinforcement Learning},
	article		= {Scientific Reports 8:10721},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/mitchell_et_al-2018-scientific_reports.pdf},
	note		= {doi:10.1038/s41598-018-29134-x | PMCID: PMC6048054},
}
@journal{goodlet2018
	author		= {Goodlet, B. R., Mills, L., Bales, B., Charpagne, M-A, Murray, S. P., Lenthe, W. C., Petzold, L., & Pollock, T.M.},
	title		= {Elastic Properties of Novel Co- and CoNi-Based Superalloys Determined through Bayesian Inference and Resonant Ultrasound Spectroscopy},
	article		= {Metall. and Mat. Trans. A},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/10.1007-s11661-018-4575-6.pdf},
	note		= {doi: 10.1007/s11661-018-4575-6},
}
@journal{pourzanjani2018
	author		= {Pourzanjani, A. A., Bales, B. B., Harrington, M., & Petzold, L. R.},
	title		= {Flexible Modeling of Alzheimer's Disease Progression with I-Splines},
	article		= {StanCon 2018 Proceedings.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stancon_alzheimers.pdf},
}
@journal{koupaee2018
	author		= {Koupaee, M., Zhang, Y., Wu, T. B., Cohen, M., & Petzold, L.},
	title		= {Identification of Disease States for Trauma Patients using Commonly Available Hospital Data},
	article		= {2018 IEEE 8th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/iccabs-koupaee.pdf},
}
@journal{ghaffari2018
	author		= {Ghaffari, H. & Petzold, L. R.},
	title		= {Identification of Influential Proteins in the Classical Retinoic Acid Signaling Pathway},
	article		= {Theoretical Biology and Medical Modelling, 15:16.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/s12976-018-0088-7.pdf},
	note		= {doi: 10.1186/s12976-018-0088-7 | PMCID: PMC6190658},
}
@journal{wilken2018
	author		= {Wilken, S. E., Saxena, M., Petzold, L. R., & O'Malley, M.A.},
	title		= {In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi},
	article		= {Processes 2018, 6, 7.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/fungi.pdf},
	note		= {doi: 10.3390/pr6010007},
}
@journal{banavar2018
	author		= {Banavar, S. P., Gomez, C., Trogdon, M., Petzold, L. R., Yi, T-M, & Campas, O.},
	title		= {Mechanical Feedback Coordinates Cell Wall Expansion and Assembly in Yeast Mating Morphogenesis},
	article		= {PLoS Comput. Biol. 14(1):e1005940},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/mechanical_feedback.pdf},
	note		= {doi: 10.1371/journal.pcbi.1005940 | PMCID: PMC5790295},
}
@journal{mcbride2018
	author		= {McBride, D. & Petzold, L.},
	title		= {Model-based Inference of a Directed Network of Circadian Neurons},
	article		= {J. Biological Rhythms, 33(5), 515-522},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/sage_paper_1.4.pdf},
	note		= {doi: 10.1177/0748730418790402 | PMID: 30084298},
}
@journal{camonaalocer2018
	author		= {Camona-Alocer, V., Abel, J. H., Sun, T. C., Petzold, L. R., Doyle III, F. J., Simms, C. L., & Herzog, E. D.},
	title		= {Ontogeny of Circadian Rhythms and Synchrony in the Suprachiasmatic Nucleus},
	article		= {J. Neurosci. 38(6): 1326-1334},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1326.full_.pdf},
	note		= {doi: 10.1523/JNEUROSCI.2006-17.2017 | PMCID: PMC5815340},
}
@journal{nowakowski2018
	author		= {Nowakowski, T. J., Rani, N., Golkaram, M., Zhou, H. R., Alvarado, B., Huch, K., West, J. A., Leyrat, A., Pollen, A. A., Kriegstein, A. R., Petzold, L. R., & Kosik, K. S.},
	title		= {Regulation of Cell-type-specific Transcriptomes by microRNA Networks During Human Brain Development},
	article		= {Nature Neuroscience 21, 1784–1792.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/nature_neuroscience_s41593-018-0265-3_0.pdf},
	note		= {doi: 10.1038/s41593-018-0265-3 | PMCID: PMC6312854},
}
@journal{pourzanjani2018
	author		= {Pourzanjani, A. A., Wu, T. B., Bales, B. B., & Petzold, L. R.},
	title		= {Relating Disparate Measures of Coagulapathy Using Unorthodox Data: A Hybrid Mechanistic-Statistical Approach},
	article		= {StanCon 2018 Proceedings.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stancon_coag_0.pdf},
}
@journal{rde2018
	author		= {Rüde, U., Willcox, K., McInnes, L. C., & DeSterck, H.},
	title		= {Research and Education in Computational Science and Engineering},
	article		= {SIAM Review, 60(3), 707-754.},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/siamcse.pdf},
}
@journal{trogdon2018
	author		= {Trogdon, M., Drawert, B., Gomez, C., Banavar, S. P., Yi, T-M., Campas, O., & Petzold, L. R.},
	title		= {The Effect of Cell Geometry on Polarization in Budding Yeast},
	article		= {PLoS Comput. Biol. 14(6):e1006241},
	year		= {2018},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/journal.pcbi_.1006241.pdf},
	note		= {doi: 10.1371/journal.pcbi.1006241 | PMCID: PMC6013239},
}
@journal{abel2017
	author		= {Abel, J., Drawert, B., Hellander, A. & Petzold, L. R.},
	title		= {GillesPy: A Python Package for Stochastic Model Building and Simulation},
	article		= {IEEE Life Sciences Letters, Vol. 2, No. 3, pp. 35-38.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/07843624_0.pdf},
	note		= {doi: 10.1109/LLS.2017.2652448 | PMCID: PMC5473341},
}
@journal{torshizi2017
	author		= {Torshizi, A. D. & Petzold, L. R.},
	title		= {Graph-based Semi-Supervised Learning with Genomic Data Integration Using Condition-Responsive Genes Applied to Phenotype Classification},
	article		= {J. Am. Med. Inform. Assoc. 25(1), 2018, 99-108.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ocx032.pdf},
	note		= {doi: 10.1093/jamia/ocx032 | PMID: 28505320},
}
@journal{pourzanjani2017
	author		= {Pourzanjani, A. A., Jiang, R. M., & Petzold, L. R.},
	title		= {Improving the Identifiability of Neural Networks for Bayesian Inference},
	article		= {Proceedings of NIPS Workshop on Bayesian Deep Learning},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/nips_.pdf},
}
@journal{hellander2017
	author		= {Hellander, S., Hellander, A., & Petzold, L.},
	title		= {Mesoscopic-microscopic Spatial Stochastic Simulation with Automatic System Partitioning},
	article		= {J. Chem. Phys. 147, 234101.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1.5002773.pdf},
	note		= {doi: 10.1063/1.5002773 | PMCID: PMC5732015},
}
@journal{drawert2017
	author		= {Drawert, B., Thakore, N., Mitchell, B., Pioro, E., Ravits, J., & Petzold, L. R.},
	title		= {Modeling the Neuroanatomic Propagation of ALS in the Spinal Cord},
	article		= {AIP Conference Proceedings 1863, 500002},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/icnaam16_als_drawert_petzold.pdf},
	note		= {doi: 10.1063/1.4992656},
}
@journal{torshizi2017
	author		= {Torshizi, A. D., Petzold, L., & Cohen, M.},
	title		= {Multivariate Soft Repulsive System Identification for Constructing Rule-based Classification Systems: Application to Trauma Clinical Data},
	article		= {Neurocomputing 245, pp. 77-85.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1-s2.0-s0925231217305581-main.pdf},
}
@journal{hellander2017
	author		= {Hellander, S. & Petzold, L.},
	title		= {Reaction Rates for Reaction-Diffusion Kinetics on Unstructured Meshes},
	article		= {J. Chem. Phys. 146, 064101},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1.4975167.pdf},
	note		= {doi: 10.1063/1.4975167 | PMCID: PMC5303170},
}
@journal{bales2017
	author		= {Bales, B., Pollock, T., & Petzold, L.},
	title		= {Segmentation-Free Image Processing and Analysis of Precipitate Shapes in 2D and 3D},
	article		= {Modelling Simul. Mater. Sci. Eng. 25, 045009},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/bales_2017_modelling_simul._mater._sci._eng._25_045009.pdf},
}
@journal{torshizi2017
	author		= {Torshizi, A. D. & Petzold, L.},
	title		= {Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases},
	article		= {IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(3), 1028-1034.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/07887681.pdf},
	note		= {doi: 10.1109/TCBB.2017.2687925 | PMID: 28368826},
}
@journal{zhang2017
	author		= {Zhang, Y., Jiang, R., & Petzold, L.},
	title		= {Survival Topic Models for Predicting Outcomes for Trauma Patients},
	article		= {2017 IEEE 33rd International Conference on Data Engineering (ICDE)},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/main_1.pdf},
}
@journal{golkaram2017
	author		= {Golkaram, M., Jang, J., Hellander, S., Kosik, K. S., & Petzold, L. R.},
	title		= {The Role of Chromatin Density in Cell Population Heterogeneity during Stem Cell Differentiation},
	article		= {Scientific Reports, 7(1), 13307},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/scirep.pdf},
	note		= {doi:10.1038/s41598-017-13731-3 | PMCID: PMC5645312},
}
@journal{porzanjani2017
	author		= {Porzanjani, A., Wu, T. B., Jiang, R. M., Cohen, M. J., & Petzold, L. R.},
	title		= {Understanding Coagulopathy Using Multi-view Data in the Presence of Sub-Cohorts: A Hierarchical Subspace Approach},
	article		= {Proceedings of Machine Learning for Healthcare 2017, W&C Track Volume 68},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/understanding-coagulopathy-multi_6.pdf},
}
@journal{drawert2017
	author		= {Drawert, B., Griesemer, M., Petzold, L. R., Briggs, C. J.},
	title		= {Using Stochastic Epidemiological Models to Evaluate Conservation Strategies for Endangered Amphibians},
	article		= {J. R. Soc. Interface 14: 20170480},
	year		= {2017},
	note		= {Journal Version | doi: 10.1098/rsif.2017.0480 | PMCID: PMC5582134},
}
@journal{hammamieh2017
	author		= {Hammamieh, R., Chakraborty, N., Gautam, A., Muhie, S., Yang, R., Donohue, D., Kumar, R., Daigle, Jr., B. J., Zhang, Y., Amara, D. A., Miller, S-A., Srinivasan, S., Flory, J., Yehuda, R., Petzold, L., Wolkoxitz, O. M., Mellon, S. H., Hood, L., Doyle III, F. J., Marmar, C., & Jett, M.},
	title		= {Whole Genome DNA Methylation Status Associated with Clinical PTSD Measure of OIF/OEF Veterans},
	article		= {Transl. Psychiatry (2017) 7, e1169.},
	year		= {2017},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/tp2017129a.pdf},
	note		= {doi: 10.1038/tp.2017.129 | PMCID: PMC5538114},
}
@journal{drawert2016
	author		= {Drawert, B., Hellander, S., Trogdon, M., Yi, T-M, & Petzold, L.},
	title		= {A Framework for Discrete Stochastic Simulation on 3D Moving Boundary Domains},
	article		= {J. Chem. Phys., 145, 184113.},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1.4967338.pdf},
	note		= {doi:10.1063/1.4967338 | PMCID: PMC5116030},
}
@journal{lim2016
	author		= {Lim, R. K., Petzold, L. R., & Koc, C. K.},
	title		= {Bitsliced High-Performance AES-ECB on GPUs},
	article		= {LNCS 9100, pp. 125-133},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/aes_paper_0.pdf},
}
@journal{abel2016
	author		= {Abel, J. H., Meeker, K., Granados-Fuentes, D., St. John, P. C., Wang, T. J., Bales, B. B., Doyle III, F. J., Herzog, E. D., & Petzold L. R.},
	title		= {Functional Network Inference of the Suprachiasmatic Nucleus},
	article		= {Proceedings of the National Academy of Science.},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/pnas.pdf},
	note		= {doi:10.1073/pnas.1521178113 | PMCID: PMC4843423},
}
@journal{zhang2016
	author		= {Zhang, Y. Wu, T. B., Daigle, Jr., B. J., Cohen, M., & Petzold, L.},
	title		= {Identification of Disease States Associated with Coagulopathy in Trauma},
	article		= {BMC Medical Informatics and Decision Making, 16:124},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/art3a10.11862fs12911-016-0360-x.pdf},
	note		= {doi:10.1186/s12911-016-0360-x},
}
@journal{golkaram2016
	author		= {Golkaram, M., Hellander, S., Drawert, B., & Petzold, L. R.},
	title		= {Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion},
	article		= {PLoS Comput. Biol. 12(11):e1005122},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/pcbi.1005122.pdf},
	note		= {doi:10.1371/journal.pcbi.1005122 | PMCID: PMC5125560},
}
@journal{drawert2016
	author		= {Drawert, B., Trogdon, M., Toor, S., Petzold, L., & Hellander, A.},
	title		= {MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME},
	article		= {SIAM J. Sci. Comput., 38(3), C179-C202},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/15m1014784.pdf},
	note		= {doi:10.1137/15M1014784 | PMCID: PMC5302863},
}
@journal{hellander2016
	author		= {Hellander, S., & Petzold, L.},
	title		= {Reaction Rates for a Generalized Reaction-Diffusion Master Equation},
	article		= {Phys. Rev. E 93, 013307.},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/physreve.93.013307.pdf},
	note		= {doi: 10.1103/PhysRevE.93.013307  |  PMCID: PMC4854577},
}
@journal{drawert2016
	author		= {Drawert, B., Hellander, A., Bales, B., Banerjee, D., Bellesia, G., Daigle, Jr., B. J., Douglas, G., Gu, M., Gupta, A., Hellander, S., Horuk, C., Nath, D., Takkar, A., Wu, S., Lötstedt, P., Krintz, C., & Petzold, L. R.},
	title		= {Stochastic Simulation Service: Bridging the Gap Between the Compuational Expert and the Biologist},
	article		= {PLoS Comput. Biol. 12(12): e1005220},
	year		= {2016},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/journal.pcbi_.1005220.pdf},
	note		= {doi:10.1371/journal.pcbi.1005220 | PMCID: PMC5145134},
}
@journal{lawson2015
	author		= {Lawson, M. J., Petzold, L., & Hellander, A.},
	title		= {Accuracy of the Michaelis-Menten Approximation When Analysing Effects of Molecular Noise},
	article		= {J. R. Soc. Interface 12:20150054.},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/interface_latex.pdf},
	note		= {doi:10.1098/rsif.2015.0054 | PMCID: PMC4424680},
}
@journal{wu2015
	author		= {Wu, S., Fu, J., & Petzold, L. R.},
	title		= {Adaptive Deployment of Model Reductions for Tau-Leaping Simulation},
	article		= {J. Chem. Phys. 142, 204108},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1.4921638.pdf},
	note		= {doi:10.1063/1.4921638  |  PMCID: PMC4449353},
}
@inproceedings{bhattacharjee2015
	author		= {Bhattacharjee, K., & Petzold, L. (2015, December).},
	title		= {Detecting Opinions in a Temporally Evolving Conversation on Twitter},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/temporal_opdetection-2_1.pdf},
}
@inproceedings{doostparast2015
	author		= {Doostparast, A. Petzold, L., & Cohen, M. (2015, November).},
	title		= {Direct Higher Order Fuzzy Rule-based Classification System: Application in Mortality Prediction},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/b325.pdf},
}
@inproceedings{abel2015
	author		= {Abel, J. H., Drawert, B., Hellander, A., & Petzold, L. R. (2015, August).},
	title		= {GillesPy: A Python Package for Stochastic Model Building and Simulation},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/abel-gillespy-fosbe-vf.pdf},
}
@journal{pro2015
	author		= {Pro, J. W., Lim, R. K., Petzold, L. R., Utz, M., & Begley, M. R.},
	title		= {GPU-Based Simulations of Fracture in Idealized Brick and Mortar Composites},
	article		= {J. Mech. Phys. Solids 80, 68-85.},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/gpubasedsims.pdf},
	note		= {doi:10.1016/j.jmps.2015.03.011},
}
@journal{lim2015
	author		= {Lim, R. K., Pro, J. W., Begley, M. R., Utz, M., & Petzold, L. R.},
	title		= {High-performance Simulation of Fracture in Idealized "Brick and Mortar" Composites Using Adaptive Monte Carlo Minimization on the GPU},
	article		= {Int. J. High Perform. C. 1-14},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/international_journal_of_high_performance_computing_applications-2015-lim-1094342015593395.pdf},
	note		= {doi: 10.1177/1094342015593395},
}
@journal{daigle2015
	author		= {Daigle, Jr., B. J., Soltani, M., Petzold, L. R. & Singh, A.},
	title		= {Inferring Single-Cell Gene Expression Mechanisms Using Stochastic Simulation},
	article		= {Bioinformatics, 31(9), 2015, 1428-1435},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/daigle_2015.pdf},
	note		= {doi: 10.1093/bioinformatics/btv007 | PMCID: PMC4492418},
}
@journal{pourzanjani2015
	author		= {Pourzanjani, A., Herzog, E. D., & Petzold, L. R.},
	title		= {On the Inference of Functional Circadian Networks Using Granger Causality},
	article		= {PLoS ONE 10(9):e0137540},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/manuscript.pdf},
	note		= {doi: 10.1371/journal.pone.0137540  |  PMCID: PMC4586144},
}
@journal{hellander2015
	author		= {Hellander, S., Hellander, A., & Petzold, L.},
	title		= {Reaction Rates for Mesoscopic Reaction-Diffusion Kinetics},
	article		= {Phys. Rev. E 91, 023312.},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/physreve.91.023312.pdf},
	note		= {doi:10.1103/PhysRevE.91.023312  |  PMCID: PMC4854576},
}
@journal{thakur2015
	author		= {Thakur, G. S., Daigle Jr., B. J., Dean, K. R., Zhang, Y., Rodriguez-Fernandez, M., Hammamieh, R., Yang, R., Jett, M., Palma, J., Petzold, L. R., & Doyle III, F. J.},
	title		= {Systems Biology Approach to Understanding Post-Traumatic Stress Disorder},
	article		= {Mol. BioSyst., 2015, 11, 980.},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/thakur_etal_molbiosystems_2015.pdf},
	note		= {doi:10.1039/C4MB00404C  |  PMID: 25627823 [PubMed - in process]},
}
@journal{pro2015
	author		= {Pro, J. W., Lim, R. K., Petzold, L. R., Utz, M., & Begley, M. R.},
	title		= {The Impact of Stochastic Microstructures on the Macroscopic Fracture Properties of Brick and Mortar Composites},
	article		= {Extreme Mechanics Letters 5 (2015) 1-9},
	year		= {2015},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1-s2.0-s2352431615001054-main.pdf},
	note		= {DOI: 10.1016/j.eml.2015.09.001},
}
@journal{thakur2014
	author		= {Thakur, G., Daigle Jr., B., Petzold, L. R. & Doyle, F.},
	title		= {A Multivariate Ensemble Approach for Identification of Biomarkers: Application to Breast Cancer},
	article		= {Proceedings of the 19th IFAC World Congress.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IFAC14_2031_FI.pdf},
}
@journal{bezzola2014
	author		= {Bezzola, A., Bales, B. B., Alkire, R. C. & Petzold, L. R.},
	title		= {An Exact and Efficient First Passage Time Algorithm for Reaction-Diffusion Processes on a 2D-Lattice},
	article		= {J. Comp. Phys., 256, pp. 183-197.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ELFPT_main.pdf},
}
@journal{griesemer2014
	author		= {Griesemer, M., Young, C., Robinson, A. S. & Petzold, L. R.},
	title		= {BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum},
	article		= {PLoS Comput. Biol. 10(7): e1003675.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/BiPClustering.pdf},
	note		= {PMCID: PMC4081015},
}
@misc{zhang2014
	author		= {Zhang, Y., Daigle, Jr., B. J., Ferrigno, L., Cohen, M., & Petzold, L.},
	title		= {Data-Driven Mortality Prediction for Trauma Patients},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/main.pdf},
}
@journal{hellander2014
	author		= {Hellander, A., Lawson, M., Drawert, B. & Petzold, L.},
	title		= {Local Error Estimates for Adaptive Simulation of the Reaction-Diffusion Master Equation via Operator Splitting},
	article		= {J. Comp. Phys. 266, pp. 89-100.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/LocalError.pdf},
	note		= {doi:10.1016/j.jcp.2014.02.004 | PMCID: PMC4746020},
}
@journal{bezzola2014
	author		= {Bezzola, A., Bales, B. B., Petzold, L. R. & Alkire, R. C.},
	title		= {Numerical Scaling Studies of Kinetically-Limited Electrochemical Nucleation and Growth with Accelerated Stochastic Simulations},
	article		= {J. Electrochem. Soc. 161(8), E3001-E3008.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/NumericalScaling.pdf},
}
@journal{bhattacharjee2014
	author		= {Bhattacharjee, K. & Petzold, L. R.},
	title		= {Probabilistic User-level Opinion Detection on Online Social Networks},
	article		= {Proceedings of the International Conference on Social Informatics (SocInfo).},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/OpinionMining.pdf},
}
@journal{sturrock2014
	author		= {Sturrock, M., Hellander, A., Aldakheel, S., Petzold, L. R. & Chaplain, M. A. J.},
	title		= {The Role of Dimerisation and Nuclear Transport in the Hes1 Gene Regulatory Network},
	article		= {Bull. Math Biol. 76(4):766-98.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Hes1_dimerisation.pdf},
	note		= {PMCID: PMC3999905},
}
@journal{fu2014
	author		= {Fu, J., Wu, S., Li, H. & Petzold, L. R.},
	title		= {The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems},
	article		= {J. Comp. Phys. 274, pp. 524–549.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/TimeDependentPropensity.pdf},
	note		= {doi:10.1016/j.jcp.2014.06.025 | PMCID: PMC4655327},
}
@journal{gillespie2014
	author		= {Gillespie, D., Petzold, L. R. & Seitaridou, E.},
	title		= {Validity Conditions for Stochastic Chemical Kinetics in Diffusion-Limited Systems},
	article		= {J. Chem. Phys. 140, 054111.},
	year		= {2014},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Validity.pdf},
	note		= {© 2014 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version  |  PMCID: PMC3977787},
}
@journal{an2013
	author		= {An, S., Harang, R., Meeker, K., Granados-Fuentes, D., Tsai, C., Mazuski, C., Kim, J., Doyle III, F. J., Petzold, L. R. & Herzog, E. D.},
	title		= {A Neuropeptide Speeds Circadian Entrainment by Reducing Intercellular Synchrony},
	article		= {Proceedings of the National Academy of Sciences.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Neuropeptide.pdf},
	note		= {PMCID: PMC3832006},
}
@journal{yang2013
	author		= {Yang, R., Daigle, Jr., B. J., Muhie, S. Y., Hammamieh, R., Jett, M., Petzold, L. & Doyle III, F. J.},
	title		= {Core Modular Blood and Brain Biomarkers in Social Defeat Mouse Model for Post Traumatic Stress Disorder},
	article		= {BMC Systems Biology 2013, 7:80.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Mouse_Model.pdf},
	note		= {PMCID: PMC3751782},
}
@journal{kolpas2013
	author		= {Kolpas, A., Busch, M., Li, H., Couzin, I. D., Petzold, L. R. & Moehlis, J.},
	title		= {How the Spatial Position of Individuals Affects Their Influence on Swarms: A Numerical Comparison of Two Popular Swarm Dynamics Models},
	article		= {PLoS ONE 8(3): e58525.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Pub199-1.pdf},
	note		= {PMCID: PMC3605438},
}
@journal{macropol2013
	author		= {Macropol, K., Bogdanov, P., Singh, A. K., Petzold, L. R. & Yan, X.},
	title		= {I Act, Therefore I Judge: Network Sentiment Dynamics Based on User Activity Change},
	article		= {Proceedings of IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/I_Act.pdf},
}
@journal{gillespie2013
	author		= {Gillespie, D. T., Hellander, A. & Petzold, L. R.},
	title		= {Perspective: Stochastic Algorithms for Chemical Kinetics},
	article		= {J. Chem. Phys. 138, 170901.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Perspective.pdf},
	note		= {© 2013 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the authors and the American Institute of Physics. Journal Version  |  PMCID: PMC3656953},
}
@journal{lawson2013
	author		= {Lawson, M. J., Drawert, B., Khammash, M., Petzold, L. R. & Yi, T.},
	title		= {Spatial Stochastic Dynamics Enable Robust Cell Polarization},
	article		= {PLoS Comput. Biol. 9(7): e1003139.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Polarization.pdf},
	note		= {PMCID: PMC3723497},
}
@journal{fu2013
	author		= {Fu, J., Wu, S. & Petzold, L. R.},
	title		= {Time Dependent Solution for Acceleration of Tau-Leaping},
	article		= {J. Comp. Phys. 235, 446-457.},
	year		= {2013},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Time_Dependent.pdf},
	note		= {doi: 10.1016/j.jcp.2012.10.036},
}
@journal{stberg2012
	author		= {Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R.},
	title		= {Abstractions for Scaling eScience Applications to Distributed Computing Environments: A StratUm Integration Case Study in Molecular Systems Biology},
	article		= {Proceedings of Bioinformatics 2012, International Conference on Bioinformatics Models, Methods, and Algorithms.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/URDME_StratUm.pdf},
}
@journal{daigle2012
	author		= {Daigle, Jr., B. J., Roh, M. K., Petzold, L. R. & Niemi, J.},
	title		= {Accelerated Maximum Likelihood Parameter Estimation for Stochastic Biochemical Systems},
	article		= {BMC Bioinformatics 2012, 13:68.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Accelerated.pdf},
	note		= {doi: 10.1186/1471-2105-13-68 | PMCID: PMC3496601},
}
@journal{wu2012
	author		= {Wu, S., Fe, J., Li, H. & Petzold, L. R.},
	title		= {Automatic Identification of Model Reductions for Discrete Stochastic Simulation},
	article		= {J. Chem. Phys. 137(3), 034106.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Automatic_Id.pdf},
	note		= {doi: 10.1063/1.4733563 | PMID: 22830682},
}
@journal{yang2012
	author		= {Yang, R., Daigle Jr., B., Petzold, L. R. & Doyle III, F. J.},
	title		= {Core Module Biomarker Identification with Network Exploration for Breast Cancer Metastasis},
	article		= {BMC Bioinfomatics 13:12.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/COMBINER.pdf},
	note		= {doi: 10.1186/1471-2105-13-12 | PMCID: PMC3349569},
}
@journal{yang2012
	author		= {Yang, R., Daigle, Jr., B. J., Petzold, L. R. & Doyle III, F. J.},
	title		= {Core Module Network Construction for Breast Cancer Metastasis},
	article		= {Proceedings of the 10th World Congress on Intelligent Control and Automation, Beijing, China.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Core_module.pdf},
}
@journal{bunch2012
	author		= {Bunch, C., Drawert, B., Chohan, N., Krintz, C., Petzold, L. R. & Shams, K.},
	title		= {Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics},
	article		= {J. Grid Computing 10(1) 23-46},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Language_Runtime.pdf},
}
@journal{wallace2012
	author		= {Wallace, E., Gillespie, D. T., Sanft, K. R., & Petzold, L. R.},
	title		= {Linear Noise Approximation is Valid Over Limited Times for any Chemical System that is Sufficiently Large},
	article		= {IET Systems Biology 6(4) 102-115.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/06353000.pdf},
}
@journal{hellander2012
	author		= {Hellander, S., Hellander, A. & Petzold, L.},
	title		= {Reaction-diffusion Master Equation in the Microscopic Limit},
	article		= {Phys. Rev. E 85(4), 042901.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/physreve.85.042901.pdf},
	note		= {doi: 10.1103/PhysRevE.85.042901},
}
@journal{stberg2012
	author		= {Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R.},
	title		= {Reducing Complexity in Management of eScience Computations},
	article		= {Proceedings of CCGrid 2012, 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Reducing_MSGC.pdf},
	note		= {doi: 10.1109/CCGrid.2012.72},
}
@journal{griesemer2012
	author		= {Griesemer, M., Young, C., Robinson, A. & Petzold, L.},
	title		= {Spatial Localization of Chaperone Distribution in the Endoplasmic Reticulum of Yeast},
	article		= {IET Systems Biology 6(2):54-63.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Spatial_Local_Final.pdf},
	note		= {doi: 10.1049/iet-syb.2011.0006},
}
@journal{drawert2012
	author		= {Drawert, B., Engblom, S. & Hellander, A.},
	title		= {URDME: A Modular Framework for Stochastic Simulation of Reaction-Transport Processes in Complex Geometries},
	article		= {BMC Syst. Biol. 6:76.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/URDME_BMCsysbio.pdf},
	note		= {doi: 10.1186/1752-0509-6-76},
}
@journal{harang2012
	author		= {Harang, R., Bonnet, G. & Petzold, L. R.},
	title		= {WAVOS: a MATLAB Toolkit for Wavelet Analysis and Visualization of Oscillatory Systems},
	article		= {BMC Research Notes 5:163.},
	year		= {2012},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1756-0500-5-163.pdf},
	note		= {doi: 10.1186/1756-0500-5-163 | PMCID: PMC3353168},
}
@journal{daigle2011
	author		= {Daigle, B., Roh, M., Gillespie, D. & Petzold, L.},
	title		= {Automated Estimation of Rare Event Probabilities in Biochemical Systems},
	article		= {J. Chem. Phys. 134, 044110.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JCPSA61344044110_1.pdf},
	note		= {doi: 10.1063/1.3522769 | PMCID: PMC3045218},
}
@journal{abdurrahim2011
	author		= {Abdur-Rahim, J. A., Petzold, L. R., Grafton, S. T. & Doyle III, F. J.},
	title		= {Identifying Learning in a Visuomotor Skill},
	article		= {Transactions on Biomedical Engineering, Submitted},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/tbme_paper_020311.pdf},
}
@journal{sanft2011
	author		= {Sanft, K. R., Gillespie, D. T. & Petzold, L. R.},
	title		= {Legitimacy of the Stochastic Michaelis-Menten Approximation},
	article		= {IET Systems Biology, 5(1), 58-69.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stoch_2011.pdf},
	note		= {doi: 10.1049/iet-syb.2009.0057 },
}
@journal{wu2011
	author		= {Wu, S., Fu, J., Cao, Y. & Petzold, L.},
	title		= {Michaelis-Menten Speeds up Tau-leaping Under a Wide Range of Conditions},
	article		= {J. Chem. Phys. 134, 134112.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JCPSA613413134112_1.pdf},
	note		= {doi: 10.1063/1.3576123 | PMCID: PMC3087420},
}
@journal{roh2011
	author		= {Roh, M., Daigle Jr., B., Gillespie, D. & Petzold, L. R.},
	title		= {State-dependent Doubly Weighted Stochastic Simulation Algorithm for Automatic Characterization of Stochastic Biochemical Rare Events},
	article		= {J. Chem. Phys. 135(23):234108.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/sdwSSA_ver3.1.pdf},
	note		= {doi: 10.1063/1.3668100 | PMCID: PMC3264419},
}
@journal{sanft2011
	author		= {Sanft, K. R., Wu, S., Roh, M., Fu, J., Lim, R. K. & Petzold, L. R.},
	title		= {StochKit2: Software for Discrete Stochastic Simulation of Biochemical Systems with Events},
	article		= {Bioinformatics (2011) 27(17): 2457-2458.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/btr401.pdf},
	note		= {doi: 10.1093/bioinformatics/btr401 | PMCID: PMC3157925},
}
@journal{turner2011
	author		= {Turner, P. & Petzold, L., Co-Chairs, Shiflet, A., Vakalis, I., Jordan, K. & St. John, S., SIAM Working Group on CSE Undergraduate Education},
	title		= {Undergraduate Computational Science and Engineering Education},
	article		= {SIAM Review 53(3), 561-574.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SIREVCSE.pdf},
}
@journal{meeker2011
	author		= {Meeker, K., Harang, R., Webb, A. B., Welsh, D. K., Doyle III, F. J., Bonnet, G., Herzog, E. D. & Petzold, L. R.},
	title		= {Wavelet Measurement Suggests Cause of Period Instability in Mammalian Circadian Neurons},
	article		= {J. of Biological Rhythms 26(4):353-62.},
	year		= {2011},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JBRWavelet.pdf},
	note		= {doi: 10.1177/0748730411409863 | PMCID: PMC3472003},
}
@journal{buoni2010
	author		= {Buoni, M. & Petzold, L.},
	title		= {An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies},
	article		= {J. Comp. Phys. 229(2), pp. 379-398},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Buoni_2009_Journal-of-Computational-Physics.pdf},
	note		= {doi: 10.1016/j.jcp.2009.09.032},
}
@journal{hildebrandt2010
	author		= {Hildebrandt, S., Bagheri, N., Gunawan, R., Mirsky, H., Shoemaker, J., Taylor, S., Petzold, L., & Doyle III, F. J.},
	title		= {Chapter 10 Systems Analysis for Systems Biology},
	article		= {In: Systems Biomedicine (pp. 249–272). Elsevier},
	year		= {2010},
	note		= {Online Version},
}
@journal{luni2010
	author		= {Luni, C., Shoemaker, J., Sanft, K., Petzold, L., Doyle, F.},
	title		= {Confidence from Uncertainty - A Multi-Target Drug Screening Method from Robust Control Theory},
	article		= {BMC Systems Biology 4:161},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Pub178.pdf},
	note		= {doi: 10.1186/1752-0509-4-161 | PMCID: PMC3277951},
}
@journal{luni2010
	author		= {Luni, C., Sanft, K., Petzold, L., Doyle III, F.},
	title		= {Modelling of Detailed Insulin Receptor Kinetics Affects Sensitivity and Noise in the Downstream Signalling Pathway},
	article		= {DYCOPS2010, 9th IFAC Symposium on Dynamics and Control of Process Systems, Leuven, Belgium},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Luni_Dycops-1.pdf},
	note		= {doi: 10.3182/20100705-3-BE-2011.00054 },
}
@journal{roh2010
	author		= {Roh, M., Gillespie, D., Petzold, L.},
	title		= {State-Dependent Biasing Method for Importance Sampling in the Weighted Stochastic Simulation Algorithm},
	article		= {J. Chem. Phys. 133, p. 174106},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/wSSA_state-dependent-biasing_2010.pdf},
	note		= {doi: 10.1063/1.3493460 | PMCID: PMC3188645},
}
@journal{drawert2010
	author		= {Drawert, B., Lawson, M. J., Petzold, L. & Khammash, M.},
	title		= {The Diffusive Finite State Projection Algorithm for Efficient Simulation of the Stochastic Reaction-Diffusion Master Equation},
	article		= {J. Chem. Phys. 132(7), 074101 (12 pages)},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/DFSP.pdf},
	note		= {doi: 10.1063/1.3310809 | PMCID: PMC2905448},
}
@journal{taylor2010
	author		= {Taylor, S., Webb, A., Smith, K., Petzold, L., Doyle III, F.},
	title		= {Velocity Response Curves Support the Role of Continuous Entrainment in Circadian Clocks},
	article		= {J. Biological Rhythms 25(2):138-149},
	year		= {2010},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Pub173.pdf},
	note		= {doi: 10.1177/0748730409360949},
}
@journal{zheng2009
	author		= {Zheng, Z., Petzold, L. & Simeon, B.},
	title		= {A Framework for the Analysis of Second Order Projection Methods},
	article		= {Submitted},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/projection_methods.pdf},
}
@journal{simeon2009
	author		= {Simeon, B., Serban, R. & Petzold, L.},
	title		= {A Model of Macroscale Deformation and Microvibration in Skeletal Muscle Tissue},
	article		= {M2AN 43, pp. 805-823},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/simeonserbanpetzold.pdf},
}
@journal{gillespie2009
	author		= {Gillespie, D., Cao, Y., Sanft, K. & Petzold, L.},
	title		= {Abridging Chemical Reaction Networks: It's a Subtle Business},
	article		= {Proc. 2009 FOSBE Conference},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Gillespie_FOSBE.pdf},
}
@journal{buoni2009
	author		= {Buoni, M. & Petzold, L.},
	title		= {An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies},
	article		= {18th IMACS CONGRESS MODSIM},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/An_Algorithm.pdf},
}
@journal{lampoudi2009
	author		= {Lampoudi, S., Gillespie, D. & Petzold, L.},
	title		= {Effect of excluded volume on 2D discrete stochastic chemical kinetics},
	article		= {J. Comp. Phys. 228(10), pp. 3656-3668},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JCompPhys_122208.pdf},
}
@journal{li2009
	author		= {Li, H. & Petzold, L.},
	title		= {Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit},
	article		= {Int. J. of High Performance Computing Applications 24(2), pp. 107-116},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Pub161.pdf},
}
@journal{resat2009
	author		= {Resat, H., Petzold, L. & Pettigrew, M. F.},
	title		= {Kinetic Modeling of Biological Systems},
	article		= {Computational Systems Biology, Vol. 541, Jason McDermott et al. (eds.), Humana Press},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Kinetic_Modeling_of_Biological_Systems.pdf},
}
@journal{kwei2009
	author		= {Kwei, E., Shoemaker, J., Sanft, K., Petzold, L. & Doyle III, F.},
	title		= {Model-Based Therapeutic Target Discrimination using Stochastic Simulation and Robustness Analysis in an Insulin Signaling Pathway},
	article		= {Proc. 2009 FOSBE conference},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/FOSBE-IRPpaper.pdf},
}
@journal{griesemer2009
	author		= {Griesemer, M. B., Young, C. L., Raden, D., Doyle III, F. J., Robinson, A. S.  & Petzold, L. R.},
	title		= {Modeling the Impact of Spatial Localization of Protein Function in the Endoplasmic Reticulum of Yeast},
	article		= {Proc. 2009 FOSBE Conference},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Griesemer_FOSBE_09.pdf},
}
@journal{li2009
	author		= {Li, H., Kolpas, A., Petzold, L. & Moehlis, J.},
	title		= {Parallel Simulation for a Fish Schooling Model on a General-Purpose Graphics Processing Unit},
	article		= {Concurrency and Computation: Practice and Experience. 21(6), pp. 725-737.},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/FISH-GPU.pdf},
}
@journal{gillespie2009
	author		= {Gillespie, D. T., Roh, M. & Petzold, L, R.},
	title		= {Refining the Weighted Stochastic Simulation Algorithm},
	article		= {J. Chem. Phys. 130, p. 174103},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/WSSA.pdf},
}
@journal{lampoudi2009
	author		= {Lampoudi, S.,  Gillespie, D. & Petzold, L.},
	title		= {The Multinomial Simulation Algorithm for Discrete Stochastic Simulation of Reaction-Diffusion Systems},
	article		= {J. Chem. Phys. 130(9), pp. 094104-094104-26},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Multinomial081215.pdf},
}
@journal{gillespie2009
	author		= {Gillespie, D. T., Cao, Y., Sanft R. K. & Petzold, L, R.},
	title		= {The Subtle Business of Model Reduction for Stochastic Chemical Kinetics},
	article		= {J. Chem. Phys. 130, 064103 (12 pages)},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/GilCaoSanPet.pdf},
	note		= {PMCID: PMC2675560},
}
@journal{turner2009
	author		= {Turner, P., Petzold, L., Shiflet, A., Vakalis, I. & Jordan, K.},
	title		= {Undergraduate Computational Science and Engineering Education},
	article		= {Submitted},
	year		= {2009},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SIAMRevCSEug_article.pdf},
}
@journal{zheng2008
	author		= {Zheng, Z., Stephens, R., Braatz, R., Alkire, R. & Petzold, L.},
	title		= {A Hybrid Multiscale Kinetic Monte Carlo Method for Simulation of Copper Electrodeposition},
	article		= {J. Comp. Phys. 227, 2008, pp. 5184-5199},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/HMKMC07.pdf},
}
@journal{zheng2008
	author		= {Zheng, Z., Simeon, B. & Petzold, L.},
	title		= {A Stabilized Explicit Lagrange Multiplier Based Domain Decomposition Method for Parabolic Problems},
	article		= {J. Comp. Phys. 227, May 2008, pp. 5272-5285.},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/domain_decomposition07.pdf},
}
@journal{hildebrandt2008
	author		= {Hildebrandt, S., Raden, D., Petzold, L., Robinson, A, S., Doyle III, F. J.},
	title		= {A Top-Down Approach to Mechanistic Biological Modeling; Application to Single-Chain Antibody Folding},
	article		= {Biophysical Journal 95(8), pp. 3535-3558},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/hildebrandt07.pdf},
}
@journal{li2008
	author		= {Li, H., Cao, Y., Petzold, L. & Gillespie, D.},
	title		= {Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems},
	article		= {Biotechnology Progress 24(1), pp. 56-62},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Biotechnology_Progress07.pdf},
}
@journal{campbell2008
	author		= {Campbell, S. L., Linh, V. H., & Petzold, L. R.},
	title		= {Differential-algebraic equations},
	article		= {Scholarpedia, 3(8):2849},
	year		= {2008},
	note		= {doi: 10.4249/scholarpedia.2849},
}
@journal{taylor2008
	author		= {Taylor, S., Doyle, F., Petzold, L.},
	title		= {Oscillator Model Reduction Preserving the Phase Response: Application to the Circadian Clock},
	article		= {Biophysical Journal 95(4)},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Oscillator_Model_Reduction08.pdf},
}
@journal{taylor2008
	author		= {Taylor, S., Gunawan, R., Petzold, L. & Doyle III, F. J.},
	title		= {Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network},
	article		= {IEEE Trans. Automat. Contr. 53, pp. 177-188},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/pIPRC.pdf},
}
@journal{cao2008
	author		= {Cao, Y. & Petzold, L.},
	title		= {Slow Scale Tau-leaping Method},
	article		= {Computer Methods in Applied Mechanics and Engineering 197, pp. 3472-3479},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/slow_tauleaping.pdf},
}
@journal{bagheri2008
	author		= {Bagheri, N., Taylor, S, R., Meeker, K., Petzold, L. R. & Doyle III, F, J.},
	title		= {Synchrony and Entrainment Properties of Robust Circadian Oscillators},
	article		= {J. Royal Society Interface 6 (5), pp. S17-S28},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Interface_08.pdf},
}
@journal{kwei2008
	author		= {Kwei, E, C., Sanft, K. R., Petzold, L, R., Doyle III, F. J.},
	title		= {Systems Analysis of the Insulin Signaling Pathway},
	article		= {Proc. 17th IFAC World Congress, Seoul, Korea, July},
	year		= {2008},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Insulin_Signaling08.pdf},
}
@journal{buoni2007
	author		= {Buoni, M. & Petzold, L.},
	title		= {An Efficient, Scalable Numerical Algorithm for the Simulation of Electrochemical Systems on Irregular Domains: Full Technical Details},
	article		= {J. Comp. Phys. 225(2), pp. 2320-2332},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/projection_2D06.pdf},
}
@journal{griesemer2007
	author		= {Griesemer, M., Young, C., Raden, D., Doyle III, F., Robinson, A. & Petzold, L.},
	title		= {Computational Modeling of Chaperone Interactions in the Endoplasmic Reticulum of Saccharomyces Cerevisai},
	article		= {FOSBE 2007 Conference Proceedings.},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Griesemer_FOSBE07.pdf},
}
@journal{liu2007
	author		= {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.},
	title		= {Detection of a MicroRNA Signal in an In Vivo ExpressionSet of mRNAs},
	article		= {Plos One, Vol. 8, August 2007, e804},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/PlosOne07.pdf},
}
@journal{gillespie2007
	author		= {Gillespie, D., Lampoudi, S. & Petzold, L.},
	title		= {Effect of Reactant Size on Discrete Stochastic Chemical Kinetics},
	article		= {J. Chem. Phys. 126(3), 034302-034302-9},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/reactant_size06.pdf},
}
@journal{mathew2007
	author		= {Mathew, G., Mezic, I., Grivopoulos, S., Vaidya, U. & Petzold, L.},
	title		= {Optimal Control of Mixing in Stokes Fluid Flows},
	article		= {J. Fluid Mech. 580, pp. 261-281},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/controlofmixing06.pdf},
}
@journal{bagheri2007
	author		= {Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle III, F.},
	title		= {Robust Timekeeping in Circadian Networks: From Genes to Cells},
	article		= {FOSBE 2007 Conference Proceedings.},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Doyle_FOSBE07.pdf},
}
@journal{li2007
	author		= {Li, H. & Petzold, L. R.},
	title		= {Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stochastic_simulation_of_biochemical_systems_on_th.pdf},
}
@journal{bagheri2007
	author		= {Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle, F.},
	title		= {Synchrony and Entrainment Properties of Robust Circadian Oscillators},
	article		= {Proc. FOSBE Conf.},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/FOSBE_proceedings07.pdf},
}
@journal{cao2007
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {The Adaptive Explicit-Implicit Tau-Leaping Method with Automatic Tau Selection},
	article		= {J. Chem. Phys. 126(22), pp. 224101-224101-9, 2007.},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adaptivetau06.pdf},
}
@journal{serban2007
	author		= {Serban, R., Homescu, C. & Petzold, L.},
	title		= {The Effect of Problem Perturbations on Nonlinear Dynamical Systems and their Reduced Order Models},
	article		= {SIAM J. Sci. Comput., Vol. 29, No. 6, pp. 2621-2643},
	year		= {2007},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ROMerror06.pdf},
}
@journal{stroumpoulis2006
	author		= {Stroumpoulis, D., Parra, A., Petzold, L. & Tirrell, M.},
	title		= {A Monte Carlo Simulation Study of Lipid Bilayer Formation on Hydrophilic Substrates from Vesicle Solutions Z. Zheng},
	article		= {J. Chem. Phys. 7},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Lipid_Bilayer06.pdf},
}
@journal{cao2006
	author		= {Cao, Y. & Petzold, L.},
	title		= {Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems},
	article		= {J. Comp. Phys. 212(1), pp. 6-24},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/distributiondistance042.pdf},
}
@journal{cao2006
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {Efficient Stepsize Selection for the Tau-Leaping Method},
	article		= {J. Chem. Phys. 124, 044109-144109-11},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/NewTau052.pdf},
}
@journal{li2006
	author		= {Li, H. & Petzold, L.},
	title		= {Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems},
	article		= {Technical report},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ldm0513.pdf},
}
@journal{book2006
	author		= {Book chapter by Gillespie, D. & Petzold, L.},
	title		= {Numerical Simulation for Biochemical Kinetics},
	article		= {In System Modelling in Cellular Biology, Ed. Z. Szallasi, J. Stelling, V. Periwal MIT Press},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/BookChapter06.pdf},
}
@journal{z2006
	author		= {Z. Zheng and L. Petzold},
	title		= {Runge-Kutta-Chebyshev Projection Method},
	article		= {J. Comp. Phys. 219, 976-991},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/rkcpmethod052.pdf},
}
@journal{petzold2006
	author		= {Petzold, L., Li, S., Cao, Y. & Serban, R.},
	title		= {Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations},
	article		= {Computers, Chemical Engineering 30 30, pp. 1553-1559},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CCEpaper.pdf},
}
@journal{siam2006
	author		= {SIAM Working Group on CSE Undergraduate Education},
	title		= {Undergraduate Computational Science and Engineering Education},
	year		= {2006},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CSE_undergrad_report06.pdf},
}
@journal{mathew2005
	author		= {Mathew, G., Mezic, I. & Petzold, L.},
	title		= {A Multiscale Measure for Mixing},
	article		= {Physica D 211 (1-2): pp. 23-46.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/multiscalemixing05.pdf},
}
@journal{cao2005
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction},
	article		= {J. Chem. Phys. 123(14), pp. 144917-144929},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/EnzymSubstr052.pdf},
}
@journal{cao2005
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {Avoiding Negative Populations in Explicit Poisson Tau Leaping},
	article		= {J. Chem. Phys.123, pp. 054104-054112},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ModTau052.pdf},
}
@journal{gillespie2005
	author		= {Gillespie, D., Petzold, L. & Cao, Y.},
	title		= {Comment on 'Nested Stochastic Simulation Algorithm for Chemical Kinetic Systems with Disparate Rates'},
	article		= {J. Chem. Phys. 126, pp. 137101-137101-4},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/nSSAComment.pdf},
}
@journal{rathinam2005
	author		= {Rathinam, M., Petzold, L, R., Cao, Y. & Gillespie, D. T.},
	title		= {Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems},
	article		= {Multiscale Modeling and Simulation (SIAM) 4(3), 867-895.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/consistency042.pdf},
}
@journal{meeker2005
	author		= {Meeker, K., Homescu, C., Petzold, L., El-Samad, H., Khammash, M., & Soderlind, G.},
	title		= {Digital Filter Stepsize Control in DASPK and its Effect on Control Optimization Performance},
	article		= {Proc. Sandia Real-Time Optimization PDE Optimization Conf.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/sandiaconf05.pdf},
}
@journal{gray2005
	author		= {Gray, J., Homescu, C., Petzold, L. R. & Alkire, R. C. J.},
	title		= {Efficient Solution and Sensitivity Analysis of Partial Differential-Algebraic Equation Systems Modelling Corrosion Pit Initiation},
	article		= {Electrochem. Soc. 152(8).},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/corrosion04.pdf},
}
@journal{petzold2005
	author		= {Petzold, L. R. & Serban, R.},
	title		= {Error Estimation for Reduced-Order Models of Dynamical Systems C. Homescu},
	article		= {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.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/reducedmodelpaper052.pdf},
}
@journal{cao2005
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {Multiscale Stochastic Simulation Algorithm with Stochastic Partial Equilibrium Assumption for Chemically Reacting Systems},
	article		= {J. Comp. Phys. 206(2) pp. 395-411.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/MSSA042.pdf},
}
@journal{el2005
	author		= {El Samad, H., Khammash, M., Homescu, C. & Petzold, L.},
	title		= {Optimal Performance of the Heat-Shock Gene Regulatory Network},
	article		= {Proceedings 16th IFAC World Congress, held in Prague, Czech Republic, July},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IFACC_HS_OPT04.pdf},
}
@journal{gunawan2005
	author		= {Gunawan, R., Cao, Y., Petzold, L. & Doyle, F.},
	title		= {Sensitivity Analysis of Discrete Stochastic Systems},
	article		= {Biophys. J. 88:2530-2540},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/biophys052.pdf},
}
@journal{zhu2005
	author		= {Zhu, L., Tretheway, D., Meinhart, C. & Petzold, L.},
	title		= {Simulation of Fluid Slip at Hydrophobic Microchannel Walls by the Lattice Boltzmann Method},
	article		= {J. Comp. Phys. 202, pp. 181-195.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/LBM042.pdf},
}
@journal{el2005
	author		= {El Samad, H., Khammash, M., Petzold, L. & Gillespie, D.},
	title		= {Stochastic Modeling of Gene Regulatory Networks},
	article		= {Int. J. Robust and Nonlinear Control, 15:691-711},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IJRNC05.pdf},
}
@journal{cao2005
	author		= {Cao, Y., Gillespie, D. & Petzold, L.},
	title		= {The Slow-Scale Stochastic Simulation Algorithm},
	article		= {J. Chem. Phys. 122(1), 014116-014166-18.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ssSSA2.pdf},
}
@journal{cao2005
	author		= {Cao, Y & Petzold, L. R.},
	title		= {Trapezoidal Tau-Leaping Formula for the Stochastic Simulation of Biochemical Systems},
	article		= {Proc. of Foundations of Systems Biology in Engineering (FOSBE) Conf., pp. 149-152.},
	year		= {2005},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/trapezoidal.pdf},
}
@journal{cao2004
	author		= {Cao, Y. & Petzold, L.},
	title		= {A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method},
	article		= {SIAM J. Scientific Computing 26(2), 359-374.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/condition_ode032.pdf},
}
@journal{li2004
	author		= {Li, S. & Petzold, L.},
	title		= {Adjoint Sensitivity Analysis for Time-Dependent Partial Differential Equations with Adaptive Mesh Refinement},
	article		= {Journal of Computational Physics 198(1), 310-325.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adjpde2.pdf},
}
@journal{cao2004
	author		= {Cao, Y. & Petzold, L.},
	title		= {An Error Estimate for Matrix Equations},
	article		= {Applied Numerical Mathematics 50(3-4), 395-407.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adjmatrix2.pdf},
}
@journal{meeker2004
	author		= {Meeker, K.},
	title		= {Digital Filter Stepsize Control of DASPK and its Effect on Control Optimization Performance},
	article		= {M.S. thesis, Computer Science, UCSB.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/kirstenMS04.pdf},
}
@journal{cao2004
	author		= {Cao, Y., Li, H. & Petzold, L. R.},
	title		= {Efficient Formulation of the Stochastic Simulation Algorithm for Chemically Reacting Systems},
	article		= {Journal of Chemical Physics 121 (9), 4059-4067},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/optSSA042.pdf},
}
@journal{mathew2004
	author		= {Mathew, G., Mezic, I., Serban, R. & Petzold, L.},
	title		= {Optimization of Mixing in an Active Micromixing Device},
	article		= {Nanotech04 Proceedings},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Nanotechabs2004.pdf},
}
@journal{zhou2004
	author		= {Zhou, J., Zhu, L., Petzold, L. & Yang, T.},
	title		= {Parallel Simulation of Fluid Slip in a Microchannel},
	article		= {Int. Parallel,Dist. Processing Symposium IPDPS04},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IPDPS04.pdf},
}
@journal{zhu2004
	author		= {Zhu, L., Tretheway, D., Petzold, L. & Meinhart, C.},
	title		= {Simulation of Fluid Slip at 3D Hydrophobic Microchannel Walls by the Lattice Boltzmann Method},
	article		= {J. Comp. Phys. 202(1), 181-195.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/fluidslip03.pdf},
}
@journal{zhang2004
	author		= {Zhang, Y, T., Chen, H., Mezic, I., Meinhart, C. D., Petzold, L. & MacDonald, N. C.},
	title		= {SOI Processing of a Ring Electrokinetic Chaotic Micromixer},
	article		= {Nanotech04 Proceedings},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/nanotech04yanting.pdf},
}
@journal{cao2004
	author		= {Cao, Y., Petzold, L., Rathinam, M. & Gillespie, D.},
	title		= {The Numerical Stability of Leaping Methods for Stochastic Simulation of Chemically Reacting Systems},
	article		= {J. Chem. Phys. 121(24), 12169-12178.},
	year		= {2004},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stochasticstability042.pdf},
}
@journal{mathew2003
	author		= {Mathew, G., Mezic, I. & Petzold, L.},
	title		= {A Multiscale Measure for Mixing and its Applications},
	article		= {IEEE Conf. on Decision,Control.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CDC03.pdf},
}
@journal{m2003
	author		= {M. Rathinam M. & Petzold, L.},
	title		= {A New Look at Proper Orthogonal Decomposition},
	article		= {SIAM J. Num. Anal.  41 (5), 1893-1925.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/pod.pdf},
}
@journal{cao2003
	author		= {Cao, Y. & Petzold, L.},
	title		= {A Subspace Error Estimate for Linear Systems},
	article		= {SIAM J. Mat. Anal. Appl. 24, pp. 787-801.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adjlinear.pdf},
}
@journal{serban2003
	author		= {Serban, R., Li, S. & Petzold, L.},
	title		= {Adaptive Algorithms for Optimal Control of Time-Dependent Partial Differential-Algebraic Equation Systems},
	article		= {Int. J. Num. Methods in Engineering 57(10), 1457-1469.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/AMpaper.pdf},
}
@journal{petzold2003
	author		= {Petzold, L., Cao, Y., Li, S. & Serban, R.},
	title		= {Adaptive Numerical Methods for Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations},
	article		= {Proceedings, Workshop on Modelling, Simulation in Chemical Engineering},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/portugal03.pdf},
}
@journal{cao2003
	author		= {Cao, Y., Li, S., Petzold, L. R. & Serban, R.},
	title		= {Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and its Numerical Solution},
	article		= {SIAM J. Sci. Comput. 24(3), 1076-1089,.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adjointI01.pdf},
}
@journal{gray2003
	author		= {Gray, J., Homescu, C., Petzold, L. & Alkire, R.},
	title		= {Algorithms and Computing Architectures for Solving Differential-Algebraic Equation Systems Typically Encountered in Models of Corrosion Pit Initiation},
	article		= {Abstract, presented at 204th Meeting of The Electrochemical Society in Orlando, FL, October 12-October 16.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ecs03.pdf},
}
@journal{hyman2003
	author		= {Hyman, J, M., Li, S. & Petzold, L.},
	title		= {An Adaptive Moving Mesh Method with Static Rezoning for Partial Differential Equations},
	article		= {Computers and Mathematics with Applications 46, 1511-1524.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/mmsr.pdf},
}
@journal{strelzoff2003
	author		= {Strelzoff, A. & Petzold, L.},
	title		= {Decision Tree Organization for GUI Generation},
	article		= {Proceedings, 28th Annual IEEE/NASA Software Engineering Workshop, Dec 2-4 Greenbelt Maryland.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Strelzoff_A_sew28.pdf},
}
@journal{strelzoff2003
	author		= {Strelzoff, A. & Petzold, L.},
	title		= {Deriving User Interface Requirements from Densly Interleaved Scientific Computing Applications},
	article		= {Proceedings,18th IEEE International Conferenceon Automated Software Engineering, Oct. 6-10.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adpdd03.pdf},
}
@journal{li2003
	author		= {Li, S. & Petzold, L.},
	title		= {Description of DASPKADJOINT: An Adjoint Sensitivity Solver for Differential-Algebraic Equations},
	article		= {Technical Report.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/daspkad.pdf},
}
@journal{m2003
	author		= {M. Rathinam M. & Petzold, L.},
	title		= {Dynamic Iteration using Reduced Order Models: A Method for Simulation of Large Scale Modular Systems},
	article		= {SIAM J. Num. Anal. 40(4), 1446-1474.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/dirm.pdf},
}
@journal{homescu2003
	author		= {Homescu, C., Petzold, L. R., & Serban, R.},
	title		= {Error Estimation for Reduced Order Models of Dynamical Systems },
	article		= {LLNL Technical Report.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/PODtechreport03.pdf},
}
@journal{gillespie2003
	author		= {Gillespie, D. & Petzold, L.},
	title		= {Improved Leap-Size Selection for Accelerated Stochastic Simulation},
	article		= {J. Chemical Physics 119, pp. 8229-8234.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/leapsizeselection03.pdf},
}
@journal{chen2003
	author		= {Chen, H., Zhang, Y., Mezic, I., Meinhart, C. & Petzold, L.},
	title		= {Numerical Simulation of an Electroosmotic Micromixer},
	article		= {Proceedings of IMECE '03, 2003 ASME International Mechanical Engineering Congress and Exosition, Washington, D. C., Nov. 15-21},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IMECE2003-55017.pdf},
}
@journal{strelzoff2003
	author		= {Strelzoff, A. & Petzold, L.},
	title		= {Revision Recognition for Scientific Computing: Theory and Application},
	article		= {Proceedings, SEKE03, Fifteenth International Conference on Software Engineeringand Knowledge Engineering.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SEKE03.pdf},
}
@journal{li2003
	author		= {Li, S., Petzold, L. & Hyman, J. M.},
	title		= {Solution Adapted Mesh Refinement and Sensitivity Analysis for Parabolic Partial Differential Equation Systems},
	article		= {Lecture Notes in Computational Science and Engineering 30, Springer-Verlag, Heidelberg.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/amr2dimp.pdf},
}
@journal{rathinam2003
	author		= {Rathinam, M., Petzold, L., & Gillespie, D.},
	title		= {Stiffness in Stochastic Chemically Reacting Systems: The Implicit Tau-Leaping Method},
	article		= {J. Chemical Physics  119 (24), 12784-12794.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/stiffness03.pdf},
}
@journal{strelzoff2003
	author		= {Strelzoff, A. & Petzold, L.},
	title		= {Update Wizardry: Automatically Generating Update and Import Wizards for Evolving XML-encoded GUIs},
	article		= {18th Annual ACM SIGPLAN Conference on Object Oriented Programming, Systems, Languages and Applications.},
	year		= {2003},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/OOPSLA03.pdf},
}
@journal{cao2002
	author		= {Cao, Y., Li, S. & Petzold, L. R.},
	title		= {Adjoint Sensitivity Analysis for Differential-Algebraic Equations: Algorithms and Software},
	article		= {J. Comp. Appl. Math. 149, 171-192.},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/adjointII01.pdf},
}
@journal{mathew2002
	author		= {Mathew, G., Petzold, L. & Serban, R.},
	title		= {Computational Techniques for Quantification and Optimization of Mixing in Microfluidic Devices},
	article		= {Technical Report},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/MixPaper.pdf},
}
@journal{serban2002
	author		= {Serban, R. & Petzold, L. R.},
	title		= {Efficient Computation of Sensitivities for Ordinary Differential Equation Boundary Value Problems},
	article		= {SIAM J. Num. Analysis, 40(1), 220-232.},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000220.pdf},
}
@journal{mao2002
	author		= {Mao, G. & Petzold, L. R.},
	title		= {Efficient Integration over Discontinuities for Differential-Algebraic Systems},
	article		= {Computers and Mathematics with Applications 43, 65-79.},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CMA432002.pdf},
}
@journal{tretheway2002
	author		= {Tretheway, D., Zhu, L., Petzold, L. & Meinhart, C.},
	title		= {Examination of the Slip Boundary Condition by Micro-PIV and Lattice Boltzmann Simulations},
	article		= {Proceedings of IMECE'2002, 2002 ASME International Mechanical Engineering Congress and Exosition, New Orleans, Louisiana, Nov. 17-22},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/IMECE2002-33704.pdf},
}
@journal{serban2002
	author		= {Serban, R., Koon, W. S., Lo, M., Marsden, J., Petzold, L. R., Ros, S. D. & Wilson, R.},
	title		= {Halo Orbit Mission Correction Maneuvers Using Optimal Control},
	article		= {Vol 38(4), pp. 571-583},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SerEtAl00.pdf},
}
@journal{petzold2002
	author		= {Petzold, L.},
	title		= {Math, with an Attitude},
	article		= {Proceedings of The Olga Taussky Todd Celebration of Careers in Mathematics. Tallahassee, FL.},
	year		= {2002},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/attitude.pdf},
}
@journal{raha2001
	author		= {Raha, S. & Petzold, L. R.},
	title		= {Constraint Partitioning for Stability in Path-Constrained Dynamic Optimization Problems},
	article		= {SIAM J. Sci. Comput.  22(6), pp. 2051-2074.},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/RahaPetz00b.pdf},
}
@journal{raha2001
	author		= {Raha, S. & Petzold, L. R.},
	title		= {Constraint Partitioning for Structure in Path-Constrained Dynamic Optimization Problems},
	article		= {Applied Numerical Mathematics, 39, 105-126.},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/RahaPetz00a.pdf},
}
@journal{serban2001
	author		= {Serban, R. & Petzold, L. R.},
	title		= {COOPT - A Software Package for Optimal Control of Large-Scale Differential-Algebraic Equation Systems},
	article		= {J. Math. and Computers in Simulation 56 (2), pp. 187-204},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SerPetz00.pdf},
}
@journal{serban2001
	author		= {Serban, R.},
	title		= {COOPT - Control and Optimization of Dynamic Systems: Users' Guide},
	article		= {UCSB Technical Report},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Ser01.pdf},
}
@journal{siam2001
	author		= {SIAM Working Group on CSE Education (L. Petzold chair)},
	title		= {Graduate Education in Computational Science and Engineering},
	article		= {SIAM Review 43 (1), pp. 163-177.},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SIAMcsepaper.pdf},
}
@journal{venkatesh2001
	author		= {Venkatesh, P. K., Petzold, L. R., Carr, R. W., Cohen, M. H. & Dean, A. M.},
	title		= {Variational Optimisation by the Solution of a Series of Hamilton-Jacobi Equations},
	article		= {Physica D 154, 15-25.},
	year		= {2001},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/PD1542001.pdf},
}
@journal{im2000
	author		= {Im, H. G., Raja, L. L., Kee, R. J. & Petzold, L. R.},
	title		= {A Numerical Study of Transient Ignition in a Counterflow Nonpremixed Methane-Air Flame Using Adaptive Time Integration},
	article		= {Combust. Sci. and Tech. 158},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Im_et_al_CST.pdf},
}
@journal{petzold2000
	author		= {Petzold, L. R., Serban, R., Li, S., Raha, S. & Strelzoff, A.},
	title		= {A Problem Solving Environment for Dynamic Optimization of Partial Differential-Algebraic Equation Systems},
	article		= {16th IMACS World Congress, Lausanne, Switzerland},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/PetzEtAl00a.pdf},
}
@journal{rathinam2000
	author		= {Rathinam, M. & Petzold, L. R.},
	title		= {An Iterative Method for Simulation of Large Scale Modular Systems using Reduced Order Models},
	article		= {Proc. IEEE Control and Decision Conference, Sydney, Australia, December},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/cdc2000.pdf},
}
@journal{gill2000
	author		= {GIll, P., Jay, L., Leonard, M., Petzold, L. R. & Sharma, V.},
	title		= {An SQP Method for the Optimal Control of Large-Scale Dynamical Systems},
	article		= {J. Comp. Appl. Math. 120, pp. 197-213.},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/an_sqp_method.pdf},
}
@journal{raja2000
	author		= {Raja, L. L., Kee, R. J., Serban, R. & Petzold, L. R.},
	title		= {Computational Algorithm for Dynamic Optimization of Chemical Vapor Deposition Processes in Stagnation Flow Reactors},
	article		= {Journal of the Electrochemical Society, Vol. 147(7), 2718-2726},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/RajaEtAl00.pdf},
}
@journal{serban2000
	author		= {Serban, R., Koon, W. S., Lo, M., Marsden, J., Petzold, L. R., Ross, S. D. & Wilson, R.},
	title		= {Optimal Control for Halo Orbit Missions},
	article		= {Proc. IFAC Workshop on Lagrangian,Hamiltonian Methods for Nonlinear Control, Princeton, NJ},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Optimal_Control.pdf},
}
@journal{petzold2000
	author		= {Petzold, L., Serban, R., Li, S., Raha, S. & Cao, Y.},
	title		= {Sensitivity Analysis and Design Optimization of Differential-Algebraic Equation Systems},
	article		= {Proc. NATO Advanced Research Workshop on Computational Aspects of Nonlinear Structural Systems with Large Rigid Body Motion},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Poland00.pdf},
}
@journal{li2000
	author		= {Li, S., Petzold, L. R. & Zhu, W.},
	title		= {Sensitivity Analysis of Differential-Algebraic Equations: A Comparison of Methods on a Special Problem},
	article		= {Applied Numerical Mathematics 32, pp. 161-174.},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Sensitivity_Analysis.pdf},
}
@journal{li2000
	author		= {Li, S. & Petzold, L. R.},
	title		= {Software and Algorithms for Sensitivity Analysis of Large-Scale Differential-Algebraic Systems},
	article		= {J. Comp. Appl. Math. 125, pp. 131-145},
	year		= {2000},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Software_and_algorithms1.pdf},
}
@journal{li1999
	author		= {Li, S. & Petzold, L. R.},
	title		= {Design of New DASPK for Sensitivity Analysis},
	article		= {UCSB Technical Report.},
	year		= {1999},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/LiPetz99.ps},
}
@journal{raja1999
	author		= {Raja, L. L., Kee, R. J., Serban, R. & Petzold, L. R.},
	title		= {Dynamic Optimization of Chemically Reacting Stagnation Flows},
	article		= {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},
	year		= {1999},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/RajaEtAl99.pdf},
}
@journal{zhu1999
	author		= {Zhu, W. & Petzold, L. R.},
	title		= {Model Reduction for Chemical Kinetics: An Optimization Approach},
	article		= {AIChE Journal, pp. 869-886},
	year		= {1999},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Model_Reduction_Zhu.pdf},
}
@journal{zhu1999
	author		= {Zhu, W. & Petzold, L. R.},
	title		= {Parallel Sensitivity Analysis for DAEs with Many Parameters},
	article		= {Concurrency: Practice and Experience, 11(10), 571-585},
	year		= {1999},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CPE11101999.pdf},
}
@journal{yen1998
	author		= {Yen, J., Petzold, L. R. & Raha, S.},
	title		= {A Time Integration Algorithm for Flexible Mechanism Dynamics: The DAE-Alpha Method},
	article		= {Computer Methods in Applied Mechanics, Engineering 158, pp. 341-355},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/DAE_Alpha_98.pdf},
}
@journal{yen1998
	author		= {Yen, J. & Petzold, L. R.},
	title		= {An Efficient Newton-Type Iteration for the Numerical Solution of Highly Oscillatory Constrained Multibody Dynamic Systems},
	article		= {SIAM J. Sci. Comput. 19, 1513-1534},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Newton_98.pdf},
}
@journal{zhu1998
	author		= {Zhu, W. & Petzold, L. R.},
	title		= {Asymptotic Stability of Hessenberg Delay Differential-Algebraic Equations of Retarded or Neutral Type},
	article		= {Applied Numerical Mathematics 27, pp. 309-325},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/HessenbergDelay_1998_ANM.pdf},
}
@journal{brown1998
	author		= {Brown, P., Hindmarsh, A. & Petzold, L. R.},
	title		= {Consistent Initial Condition Calculation For Differential-Algebraic Systems},
	article		= {SIAM J. Sci. Comput., 19(5), 1495-1512.},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE001495.pdf},
}
@journal{moore1998
	author		= {Moore, P. K., Petzold, L. R., & Ren, Y.},
	title		= {Regularization of Index-1 Differential-Algebraic Equations with Rank-Deficient Constraints},
	article		= {Computers Math. Applic., 35(5), 43-61},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/1-s2.0-s0898122198000042-main.pdf},
}
@journal{raja1998
	author		= {Raja, L. L., Kee, R. J. & Petzold, L. R.},
	title		= {Simulation of the Transient, Compressible, Gas-Dynamic Behavior of Catalytic-Combustion Ignition in Stagnation Flows},
	article		= {Twenty-Seventh Symposium (International) on Combustion/The Combustion Institute, 2249-2257},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/TCI1998.pdf},
}
@journal{li1998
	author		= {Li, S., Petzold, L. & Ren Y.},
	title		= {Stability of Moving Mesh Systems of Partial Differential Equations},
	article		= {SIAM J. Sci. Comput., 20(2), 719-738},
	year		= {1998},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/s1064827596302011.pdf},
}
@journal{zhu1997
	author		= {Zhu, W. & Petzold, L. R.},
	title		= {Asymptotic Stability of Linear Delay Differential Algebraic Equations and Numerical Methods},
	article		= {Applied Numerical Mathematics 24, pp. 247-264},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/LinearDelayPaper_1997_ANM.pdf},
}
@journal{li1997
	author		= {Li, S. & Petzold, L.},
	title		= {Moving Mesh Methods with Upwinding Schemes for Time-Dependent PDEs},
	article		= {J. Computational Phys. 131, 368-377.},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/LiPetz97.pdf},
}
@journal{petzold1997
	author		= {Petzold, L., Rosen, J. B., Gill, P. E., Jay, L. O., & Park K.},
	title		= {Numerical Optimal Control of Parabolic PDEs using DASOPT},
	article		= {In: Biegler L.T., Coleman T.F., Conn A.R., Santosa F.N. (eds) Large-Scale Optimization with Applications. The IMA Volumes in Mathematics and its Applications, vol 93. Springer, New York, NY.},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/978-1-4612-1960-6_12.pdf},
}
@journal{petzold1997
	author		= {Petzold, L. R., Jay, L. & Yen, J.},
	title		= {Numerical Solution of Highly Oscillatory Ordinary Differential Equations},
	article		= {Acta Numerica 6, pp. 437-484},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Numerical_Solution1.pdf},
}
@journal{petzold1997
	author		= {Petzold, L. R., Ren, Y. & Maly, T.},
	title		= {Regularization of Higher-Index Differential-Algebraic Equations with Rank-Deficient Constraints},
	article		= {SIAM J. Sci. Comput., 18(3), 753-774.},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE000753.pdf},
}
@journal{knapp1997
	author		= {Knapp, D. M., Barocas, V. H., Moon, A. G., Yoo, K., Petzold, L. R. & Tranquillo, R. T.},
	title		= {Rheology of Reconstituted Type I Collagen Gel in Confined Compression},
	article		= {J. Rheol., 41(5), 971-993.},
	year		= {1997},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JOR000971.pdf},
}
@journal{ashby1996
	author		= {Ashby, S. F., Lee, S. L., Petzold, L. R., Saylor, P. E. & Seidel E.},
	title		= {Computing Space-time Curvature via Differential-Algebraic Equations},
	article		= {Applied Numerical Mathematics 20, 221-234.},
	year		= {1996},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/sdarticle.pdf},
}
@journal{maly1996
	author		= {Maly, T. & Petzold, L. R.},
	title		= {Numerical Methods and Software for Sensitivity Analysis of Differential Algebraic Equations},
	article		= {Applied Numerical Mathematics 20, 57-79.},
	year		= {1996},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/MalyPetz96.pdf},
}
@journal{hindmarsh1995
	author		= {Hindmarsh, A. C. & Petzold, L. R.},
	title		= {Algorithms and Software for Ordinary Differential Equations and Differential-Algebraic Equations, Part II: Higher-Order Methods and Software Packages},
	article		= {Computers in Physics, 9(2), 148-155.},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CIP921995.pdf},
}
@journal{yen1995
	author		= {Yen, J. & Petzold, L. R.},
	title		= {Convergence of the Iterative Methods for Coordinate Splitting Formulation in Multibody Dynamics},
	article		= {Technical Report},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/convergence_of_the_iterative_methods_for_coordinat.pdf},
}
@journal{van1995
	author		= {Van Keken, P. E., Yuen, D. A. & Petzold, L. R.},
	title		= {DASPK: A New High Order and Adaptive Time-Integration Technique with Applications to Mantle Convection with Strongly Temperature and Pressure-Dependent Rheology},
	article		= {Geophys. Astrophys. Fluid Dynamics 80, 57-74.},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/DASPK.pdf},
}
@journal{jay1995
	author		= {Jay, L. O. & Petzold, L. R.},
	title		= {Highly Oscillatory Systems and Periodic Stability},
	article		= {Technical Report},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Highly_Oscillatory.pdf},
}
@journal{yen1995
	author		= {Yen, J. & Petzold, L. R.},
	title		= {Numerical Solution of Nonlinear Oscillatory Multibody Dynamic Systems},
	article		= {Proc. of 16th Numerical Analysis Conference, University of Dundee.},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/numerical_solution_of_nonlinear.pdf},
}
@journal{maier1995
	author		= {Maier, R. S., Petzold, L. R. & Rath, W.},
	title		= {Parallel Solution of Large-Scale Differential-Algebraic Systems},
	article		= {Concurrency: Practice and Experience, 7(8), 795-822.},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CPE781995.pdf},
}
@journal{ascher1995
	author		= {Ascher, U. & Petzold, L.},
	title		= {The Numerical Solution of Delay-Differential-Algebraic Equations of Retarded and Neutral Type},
	article		= {SIAM J. on Numerical Analysis 32, 1635-1657},
	year		= {1995},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/delay95.pdf},
}
@journal{moore1994
	author		= {Moore, P. K. & Petzold, L. R.},
	title		= {A Stepsize Control Strategy for Stiff Systems of Ordinary Differential Equations},
	article		= {Applied Numerical Mathematics 15, 449-463.},
	year		= {1994},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ANM151994.pdf},
}
@journal{yen1994
	author		= {Yen, J. & Petzold, L. R.},
	title		= {On the Numerical Solution of Constrained Multibody Dynamic Systems},
	article		= {Technical Report},
	year		= {1994},
}
@journal{ascher1993
	author		= {Ascher, U. M. & Petzold, L. R.},
	title		= {Stability of Computational Methods for Constrained Dynamics Systems},
	article		= {SIAM J. Sci. Comput., 14(1), 95-120.},
	year		= {1993},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE000095.pdf},
}
@journal{ascher1993
	author		= {Ascher, U. M., Chin, H., Petzold, L. R. & Reich, S.},
	title		= {Stabilization of Constrained Mechanical Systems with DAEs and Invariant Manifolds},
	article		= {Technical Report},
	year		= {1993},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Stabilization071993.pdf},
}
@journal{brown1993
	author		= {Brown, P. N., Hindmarsh, A. C. & Petzold, L. R.},
	title		= {Using Krylov Methods in the Solutions of Large-Scale Differential-Algebraic Systems},
	article		= {Technical Report},
	year		= {1993},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/Krylov051993.pdf},
}
@journal{petzold1992
	author		= {Petzold, L. R.},
	title		= {Numerical Solution of Differential-Algebraic Equations in Mechanical Systems Simulation},
	article		= {Physica D 60, 269-279.},
	year		= {1992},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/PD601992.pdf},
}
@journal{petzold1992
	author		= {Petzold, L. R. & Potra, F. A.},
	title		= {ODAE Methods for the Numerical Solution of Euler-Lagrange Equations},
	article		= {Applied Numerical Mathematics 10, 397-413.},
	year		= {1992},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ANM101992.pdf},
}
@journal{ascher1992
	author		= {Ascher, U. M. & Petzold, L. R.},
	title		= {Projected Collocation for Higher-Order Higher-Index Differential-Algebraic Equations},
	article		= {Journal of Computational and Applied Mathematics 43, 243-259.},
	year		= {1992},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/JCAM431992.pdf},
}
@journal{leimkuhler1991
	author		= {Leimkuhler, B., Petzold, L. R. & Gear, C. W.},
	title		= {Approximation Methods for the Consistent Initialization of Differential-Algebraic Equations},
	article		= {SIAM J. Numer. Anal., 28(1), 205-226.},
	year		= {1991},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000205.pdf},
}
@journal{ascher1991
	author		= {Ascher, U. M. & Petzold, L. R.},
	title		= {Projected Implicit Runge-Kutta Methods for Differential-Algebraic Equations},
	article		= {SIAM J. Numer. Anal., 28(4), 1097-1120.},
	year		= {1991},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA001097.pdf},
}
@journal{ascher1990
	author		= {Ascher, U. M. & Petzold, L. R.},
	title		= {Numerical Methods for Boundary Value Problems in Differential-Algebraic Equations},
	article		= {Proceedings from the AIChE National Meeting. Chicago, IL.},
	year		= {1990},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl091990.pdf},
}
@journal{burrage1990
	author		= {Burrage, K. & Petzold, L. R.},
	title		= {On Order Reduction for Runge-Kutta Methods Applied to Differential/Algebraic Systems and to Stiff Systems of ODEs},
	article		= {SIAM J. Numer. Anal., 27(2), 447-456.},
	year		= {1990},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000447.pdf},
}
@journal{petzold1989
	author		= {Petzold, L.},
	title		= {Methods and Software for Differential-Algebraic Systems},
	article		= {Proceedings from the NATO Advanced Research Workshop in Real-Time Integration Methods for Mechanical System Simulation. Snowbird, UT},
	year		= {1989},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl061989.pdf},
}
@journal{petzold1989
	author		= {Petzold, L. R.},
	title		= {Numerical Methods for Differential-Algebraic Equations Current Status and Future Directions},
	article		= {Proceedings from the Conference on Computational Ordinary Differential Equations. London, England.},
	year		= {1989},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl071989.pdf},
}
@journal{clark1989
	author		= {Clark, K. D. & Petzold, L. R.},
	title		= {Numerical Solutions of Boundary Value Problems in Differential-Algebraic Systems},
	article		= {SIAM J. Sci. Stat. Comput., 10(5), 915-936.},
	year		= {1989},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE000915.pdf},
}
@journal{petzold1989
	author		= {Petzold, L. R.},
	title		= {Recent Developments in the Numerical Solution of Differential/Algebraic Systems},
	article		= {Computer Methods in Applied Mechanics and Engineering 75, 77-89. [Also appeared in (1990) Lectures in Applied Mathematics, 25, 177-190.]},
	year		= {1989},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/CMAME75.pdf},
}
@journal{brenan1989
	author		= {Brenan, K. E. & Petzold, L. R.},
	title		= {The Numerical Solution of Higher Index Differential/Algebraic Equations by Implicit Methods},
	article		= {SIAM J. Numer. Anal., 26(4), 976-996.},
	year		= {1989},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000976.pdf},
}
@journal{petzold1988
	author		= {Petzold, L. R.},
	title		= {An Adaptive Moving Grid Method for One-Dimensional Systems of Partial Differential Equations and its Numerical Solution},
	article		= {Proceedings from the Workshop on Adaptive Methods for Partial Differential Equations. Troy, NY},
	year		= {1988},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl101988.pdf},
}
@journal{hindmarsh1988
	author		= {Hindmarsh, A. C. & Petzold, L. R.},
	title		= {Numerical Methods for Solving Ordinary Differential Equations and Differential/Algebraic Equations},
	article		= {Energy and Technology Review, LLNL, September 1988},
	year		= {1988},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl1988.pdf},
}
@journal{petzold1987
	author		= {Petzold, L. R.},
	title		= {Adaptive Moving Grid Strategies for One-Dimensional Systems of Partial Differential Equations},
	article		= {Proceedings from the Sixth IMACS International Symposium on Computer Methods for Partial Differential Equations. Lehigh, PA},
	year		= {1987},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/llnl021987.pdf},
}
@journal{petzold1987
	author		= {Petzold, L. R.},
	title		= {Observations on an Adaptive Moving Grid Method for One-Dimensional Systems of Partial Differential Equations},
	article		= {Applied Numerical Mathematics 3, 347-360.},
	year		= {1987},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ANM31987.pdf},
}
@journal{kee1986
	author		= {Kee, R. J. & Petzold, L. R.},
	title		= {A Differential/Algebraic Equations Formulation of the Method-of-Lines Solution of Partial Differential Equations},
	article		= {Sandia Report},
	year		= {1986},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SAND868893.pdf},
}
@journal{ltstedt1986
	author		= {Lötstedt, P. & Petzold, L. R.},
	title		= {Numerical Solution of Nonlinear Differential Equations with Algebraic Constraints I: Convergence Results for Backward Differentiation Formulas},
	article		= {Mathematics of Computation, 46(174), 491-516.},
	year		= {1986},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/MC46174.pdf},
}
@journal{petzold1986
	author		= {Petzold, L. R. & Lötstedt, P.},
	title		= {Numerical Solution of Nonlinear Differential Equations with Algebraic Constraints II: Practical Implications},
	article		= {SIAM J. Sci. Stat. Comput., 7(3), 720-733.},
	year		= {1986},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE000720.pdf},
}
@journal{petzold1986
	author		= {Petzold, L. R.},
	title		= {Order Results for Implicit Runge-Kutta Methods Applied to Differential/Algebraic Systems},
	article		= {SIAM J. Numer. Anal., 23(4), 837-852.},
	year		= {1986},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000837.pdf},
}
@journal{kee1985
	author		= {Kee, R. J., Petzold, L. R., Smooke, M. D., & Grcar, J. F.},
	title		= {Implicit Methods in Combustion and Chemical Kinetics Modeling},
	article		= {Multiple Time Scales, 113-144},
	year		= {1985},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/kee_petzold.pdf},
}
@journal{lafarge1984
	author		= {LaFarge, R. A. and Petzold, L. R.},
	title		= {An Exponentially Fitted Adams Method of Numerical Integration},
	article		= {Journal of Guidance, Control, and Dynamics, 7(3), 380-383},
	year		= {1984},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/j._guidance.pdf},
	note		= {doi:10.2514/3.56369},
}
@journal{gear1984
	author		= {Gear, C. W. & Petzold, L. R.},
	title		= {ODE Methods for the Solution of Differential/Algebraic Systems},
	article		= {SIAM J. Num. Anal., 21(4), 716-728.},
	year		= {1984},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/ODE_Methods.pdf},
}
@journal{petzold1983
	author		= {Petzold, L. R.},
	title		= {Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations},
	article		= {SIAM J. Sci. Stat. Comput., 4(1), 136-148.},
	year		= {1983},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SCE000136.pdf},
}
@journal{campbell1983
	author		= {Campbell, S. L. & Petzold, L. R.},
	title		= {Canonical Forms and Solvable Singular Systems of Differential Equations},
	article		= {SIAM J. Alg. Disc. Meth., (4)4, 517-521.},
	year		= {1983},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/0604051.pdf},
}
@journal{gear1983
	author		= {Gear, C. W. & Petzold, L. R.},
	title		= {Differential/Algebraic Systems and Matrix Pencils},
	article		= {In: Kågström B., Ruhe A. (eds) Matrix Pencils. Lecture Notes in Mathematics, vol 973. Springer, Berlin, Heidelberg},
	year		= {1983},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/differential_algebraic_systems_and_matric_pencils.pdf},
}
@journal{gear1983
	author		= {Gear, C. W., & Petzold, L. R.},
	title		= {Singular Implicit Ordinary Differential Equations and Constraints},
	article		= {In: Numerical Methods. Lecture Notes in Mathematics, 1005. Berlin, Heidelberg, Springer.},
	year		= {1983},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/10.1007-bfb0112529.pdf},
}
@journal{petzold1982
	author		= {Petzold, L, R.},
	title		= {A Description of DASSL: A Differential/Algebraic System Solver},
	article		= {Proc. IMACS World Congress},
	year		= {1982},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/DASSL.pdf},
}
@journal{petzold1982
	author		= {Petzold, L. R.},
	title		= {Differential/Algebraic Equations are not ODEs},
	article		= {SIAM J. Sci. Stat. Comput., 3(3), 367-384.},
	year		= {1982},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/DAEs_not_ODEs.pdf},
}
@journal{lafarge1982
	author		= {LaFarge, R. A., & Petzold, L.},
	title		= {EFAM (Exponentially Fitted Adams Methods): A Numerical Integrator for Artillery Shells},
	article		= {Proceedings from the AIAA 9th Atmospheric Flight Mechanics Conference. San Diego, CA.},
	year		= {1982},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/efam.pdf},
}
@journal{petzold1981
	author		= {Petzold, L. R.},
	title		= {An Efficient Numerical Method for Highly Oscillatory Ordinary Differential Equations},
	article		= {SIAM J. Numer. Anal., 18(3), 455-479.},
	year		= {1981},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/SNA000455.pdf},
	note		= {doi:10.1137/0718030},
}
@journal{gear1981
	author		= {Gear, C. W., Hsu, H. H., & Petzold, L.},
	title		= {Differential-Algebraic Equations Revisited},
	article		= {Proceedings from the meeting on Numerical Methods for Solving Stiff Initial Value Problems. Oberwolfach, Germany.},
	year		= {1981},
	url		= {https://cse.cs.ucsb.edu/sites/default/files/publications/revisited.pdf},
}