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Papers

2013
Polarization.pdf Lawson, M. J., Drawert, B., Khammash, M., Petzold, L. R. & Yi, T. (2013). Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. 9(7): e1003139.
Time_Dependent.pdf Fu, J., Wu, S. & Petzold, L. R. (2013). Time Dependent Solution for Acceleration of Tau-Leaping. J. Comp. Phys. 235, 446-457.
2012
URDME_StratUm.pdf Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R. (2012). Abstractions for Scaling eScience Applications to Distributed Computing Environments: A StratUm Integration Case Study in Molecular Systems Biology. Proceedings of Bioinformatics 2012, International Conference on Bioinformatics Models, Methods, and Algorithms.
Accelerated.pdf Daigle, Jr., B. J., Roh, M. K., Petzold, L. R. & Niemi, J. (2012). Accelerated Maximum Likelihood Parameter Estimation for Stochastic Biochemical Systems. BMC Bioinformatics 2012, 13:68.
Automatic_Id.pdf Wu, S., Fe, J., Li, H. & Petzold, L. R. (2012). Automatic Identification of Model Reductions for Discrete Stochastic Simulation. J. Chem. Phys. 137(3), 034106.
COMBINER.pdf Yang, R., Daigle Jr., B., Petzold, L. R. & Doyle III, F. J. (2012). Core Module Biomarker Identification with Network Exploration for Breast Cancer Metastasis. BMC Bioinfomatics 13:12.
Core_module.pdf Yang, R., Daigle, Jr., B. J., Petzold, L. R. & Doyle III, F. J. (2012). Core Module Network Construction for Breast Cancer Metastasis. Proceedings of the 10th World Congress on Intelligent Control and Automation, Beijing, China.
Language_Runtime.pdf Bunch, C., Drawert, B., Chohan, N., Krintz, C., Petzold, L. R. & Shams, K. (2012). Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics. J. Grid Computing 10(1) 23-46
06353000.pdf Wallace, E., Gillespie, D. T., Sanft, K. R., & Petzold, L. R. (2012). Linear Noise Approximation is Valid Over Limited Times for any Chemical System that is Sufficiently Large. IET Systems Biology 6(4) 102-115.
physreve.85.042901.pdf Hellander, S., Hellander, A. & Petzold, L. (2012). Reaction-diffusion Master Equation in the Microscopic Limit. Phys. Rev. E 85(4), 042901.
Reducing_MSGC.pdf Östberg, P., Hellander, A., Drawert, B., Elmroth, E., Holmgren, S. & Petzold, L. R. (2012). Reducing Complexity in Management of eScience Computations. Proceedings of CCGrid 2012, 12th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.
Spatial_Local_Final.pdf Griesemer, M., Young, C., Robinson, A. & Petzold, L. (2012). Spatial Localization of Chaperone Distribution in the Endoplasmic Reticulum of Yeast. IET Systems Biology 6(2):54-63.
URDME_BMCsysbio.pdf Drawert, B., Engblom, S. & Hellander, A. (2012). URDME: A Modular Framework for Stochastic Simulation of Reaction-Transport Processes in Complex Geometries. BMC Syst. Biol. 6:76.
1756-0500-5-163.pdf Harang, R., Bonnet, G. & Petzold, L. R. (2012). WAVOS: a MATLAB Toolkit for Wavelet Analysis and Visualization of Oscillatory Systems. BMC Research Notes 5:163.
2011
JCPSA61344044110_1.pdf Daigle, B., Roh, M., Gillespie, D. & Petzold, L. (2011). Automated Estimation of Rare Event Probabilities in Biochemical Systems. J. Chem. Phys. 134, 044110.
tbme_paper_020311.pdf Abdur-Rahim, J. A., Petzold, L. R., Grafton, S. T. & Doyle III, F. J. (2011). Identifying Learning in a Visuomotor Skill. Transactions on Biomedical Engineering, Submitted
stoch_2011.pdf Sanft, K. R., Gillespie, D. T. & Petzold, L. R. (2011). Legitimacy of the Stochastic Michaelis-Menten Approximation. IET Systems Biology, 5(1), 58-69.
JCPSA613413134112_1.pdf Wu, S., Fu, J., Cao, Y. & Petzold, L. (2011). Michaelis-Menten Speeds up Tau-leaping Under a Wide Range of Conditions. J. Chem. Phys. 134, 134112.
sdwSSA_ver3.1.pdf Roh, M., Daigle Jr., B., Gillespie, D. & Petzold, L. R. (2011). State-dependent Doubly Weighted Stochastic Simulation Algorithm for Automatic Characterization of Stochastic Biochemical Rare Events. J. Chem. Phys. 135(23):234108.
btr401.pdf Sanft, K. R., Wu, S., Roh, M., Fu, J., Lim, R. K. & Petzold, L. R. (2011). StochKit2: Software for Discrete Stochastic Simulation of Biochemical Systems with Events. Bioinformatics (2011) 27(17): 2457-2458.
SIREVCSE.pdf Turner, P. & Petzold, L., Co-Chairs, Shiflet, A., Vakalis, I., Jordan, K. & St. John, S., SIAM Working Group on CSE Undergraduate Education (2011). Undergraduate Computational Science and Engineering Education. SIAM Review 53(3), 561-574.
JBRWavelet.pdf Meeker, K., Harang, R., Webb, A. B., Welsh, D. K., Doyle III, F. J., Bonnet, G., Herzog, E. D. & Petzold, L. R. (2011). Wavelet Measurement Suggests Cause of Period Instability in Mammalian Circadian Neurons. J. of Biological Rhythms 26(4):353-62.
2010
Buoni_2009_Journal-of-Computational-Physics.pdf Buoni, M. & Petzold, L. (2010). An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies. J. Comp. Phys. 229(2), pp. 379-398
Hildebrandt, S., Bagheri, N., Gunawan, R., Mirsky, H., Shoemaker, J., Taylor, S., Petzold, L., & Doyle III, F. J. (2010). Chapter 10 Systems Analysis for Systems Biology. In: Systems Biomedicine (pp. 249–272). Elsevier
Pub178.pdf Luni, C., Shoemaker, J., Sanft, K., Petzold, L., Doyle, F. (2010). Confidence from Uncertainty - A Multi-Target Drug Screening Method from Robust Control Theory. BMC Systems Biology 4:161
Luni_Dycops-1.pdf Luni, C., Sanft, K., Petzold, L., Doyle III, F. (2010). Modelling of Detailed Insulin Receptor Kinetics Affects Sensitivity and Noise in the Downstream Signalling Pathway. DYCOPS2010, 9th IFAC Symposium on Dynamics and Control of Process Systems, Leuven, Belgium
wSSA_state-dependent-biasing_2010.pdf Roh, M., Gillespie, D., Petzold, L. (2010). State-Dependent Biasing Method for Importance Sampling in the Weighted Stochastic Simulation Algorithm. J. Chem. Phys. 133, p. 174106
DFSP.pdf Drawert, B., Lawson, M. J., Petzold, L. & Khammash, M. (2010). The Diffusive Finite State Projection Algorithm for Efficient Simulation of the Stochastic Reaction-Diffusion Master Equation. J. Chem. Phys. 132(7), 074101 (12 pages)
Pub173.pdf Taylor, S., Webb, A., Smith, K., Petzold, L., Doyle III, F. (2010). Velocity Response Curves Support the Role of Continuous Entrainment in Circadian Clocks. J. Biological Rhythms 25(2):138-149
2009
projection_methods.pdf Zheng, Z., Petzold, L. & Simeon, B. (2009). A Framework for the Analysis of Second Order Projection Methods. Submitted
simeonserbanpetzold.pdf Simeon, B., Serban, R. & Petzold, L. (2009). A Model of Macroscale Deformation and Microvibration in Skeletal Muscle Tissue. M2AN 43, pp. 805-823
Gillespie_FOSBE.pdf Gillespie, D., Cao, Y., Sanft, K. & Petzold, L. (2009). Abridging Chemical Reaction Networks: It's a Subtle Business. Proc. 2009 FOSBE Conference
An_Algorithm.pdf Buoni, M. & Petzold, L. (2009). An Algorithm for Simulation of Electrochemical Systems with Surface-Bulk Coupling Strategies. 18th IMACS CONGRESS MODSIM
JCompPhys_122208.pdf Lampoudi, S., Gillespie, D. & Petzold, L. (2009). Effect of excluded volume on 2D discrete stochastic chemical kinetics. J. Comp. Phys. 228(10), pp. 3656-3668
Pub161.pdf Li, H. & Petzold, L. (2009). Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit. Int. J. of High Performance Computing Applications 24(2), pp. 107-116
Kinetic_Modeling_of_Biological_Systems.pdf Resat, H., Petzold, L. & Pettigrew, M. F. (2009). Kinetic Modeling of Biological Systems. Computational Systems Biology, Vol. 541, Jason McDermott et al. (eds.), Humana Press
FOSBE-IRPpaper.pdf Kwei, E., Shoemaker, J., Sanft, K., Petzold, L. & Doyle III, F. (2009). Model-Based Therapeutic Target Discrimination using Stochastic Simulation and Robustness Analysis in an Insulin Signaling Pathway. Proc. 2009 FOSBE conference
Griesemer_FOSBE_09.pdf Griesemer, M. B., Young, C. L., Raden, D., Doyle III, F. J., Robinson, A. S. & Petzold, L. R. (2009). Modeling the Impact of Spatial Localization of Protein Function in the Endoplasmic Reticulum of Yeast. Proc. 2009 FOSBE Conference
FISH-GPU.pdf Li, H., Kolpas, A., Petzold, L. & Moehlis, J. (2009). Parallel Simulation for a Fish Schooling Model on a General-Purpose Graphics Processing Unit. Concurrency and Computation: Practice and Experience. 21(6), pp. 725-737.
WSSA.pdf Gillespie, D. T., Roh, M. & Petzold, L, R. (2009). Refining the Weighted Stochastic Simulation Algorithm. J. Chem. Phys. 130, p. 174103
Multinomial081215.pdf Lampoudi, S., Gillespie, D. & Petzold, L. (2009). The Multinomial Simulation Algorithm for Discrete Stochastic Simulation of Reaction-Diffusion Systems. J. Chem. Phys. 130(9), pp. 094104-094104-26
GilCaoSanPet.pdf Gillespie, D. T., Cao, Y., Sanft R. K. & Petzold, L, R. (2009). The Subtle Business of Model Reduction for Stochastic Chemical Kinetics. J. Chem. Phys. 130, 064103 (12 pages)
SIAMRevCSEug_article.pdf Turner, P., Petzold, L., Shiflet, A., Vakalis, I. & Jordan, K. (2009). Undergraduate Computational Science and Engineering Education. Submitted
2008
HMKMC07.pdf Zheng, Z., Stephens, R., Braatz, R., Alkire, R. & Petzold, L. (2008). A Hybrid Multiscale Kinetic Monte Carlo Method for Simulation of Copper Electrodeposition. J. Comp. Phys. 227, 2008, pp. 5184-5199
domain_decomposition07.pdf Zheng, Z., Simeon, B. & Petzold, L. (2008). A Stabilized Explicit Lagrange Multiplier Based Domain Decomposition Method for Parabolic Problems. J. Comp. Phys. 227, May 2008, pp. 5272-5285.
hildebrandt07.pdf Hildebrandt, S., Raden, D., Petzold, L., Robinson, A, S., Doyle III, F. J. (2008). A Top-Down Approach to Mechanistic Biological Modeling; Application to Single-Chain Antibody Folding. Biophysical Journal 95(8), pp. 3535-3558
Biotechnology_Progress07.pdf Li, H., Cao, Y., Petzold, L. & Gillespie, D. (2008). Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems. Biotechnology Progress 24(1), pp. 56-62
Campbell, S. L., Linh, V. H., & Petzold, L. R. (2008). Differential-algebraic equations. Scholarpedia, 3(8):2849
Oscillator_Model_Reduction08.pdf Taylor, S., Doyle, F., Petzold, L. (2008). Oscillator Model Reduction Preserving the Phase Response: Application to the Circadian Clock. Biophysical Journal 95(4)
pIPRC.pdf Taylor, S., Gunawan, R., Petzold, L. & Doyle III, F. J. (2008). Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. IEEE Trans. Automat. Contr. 53, pp. 177-188
slow_tauleaping.pdf Cao, Y. & Petzold, L. (2008). Slow Scale Tau-leaping Method. Computer Methods in Applied Mechanics and Engineering 197, pp. 3472-3479
Interface_08.pdf Bagheri, N., Taylor, S, R., Meeker, K., Petzold, L. R. & Doyle III, F, J. (2008). Synchrony and Entrainment Properties of Robust Circadian Oscillators. J. Royal Society Interface 6 (5), pp. S17-S28
Insulin_Signaling08.pdf Kwei, E, C., Sanft, K. R., Petzold, L, R., Doyle III, F. J. (2008). Systems Analysis of the Insulin Signaling Pathway. Proc. 17th IFAC World Congress, Seoul, Korea, July
2007
projection_2D06.pdf Buoni, M. & Petzold, L. (2007). An Efficient, Scalable Numerical Algorithm for the Simulation of Electrochemical Systems on Irregular Domains: Full Technical Details. J. Comp. Phys. 225(2), pp. 2320-2332
Griesemer_FOSBE07.pdf Griesemer, M., Young, C., Raden, D., Doyle III, F., Robinson, A. & Petzold, L. (2007). Computational Modeling of Chaperone Interactions in the Endoplasmic Reticulum of Saccharomyces Cerevisai. FOSBE 2007 Conference Proceedings.
PlosOne07.pdf Liu, R., Papagiannakopoulos, T., Puskar, K., Qi, S., Santiago, F., Clay, W., Lao, K., Lee, Y., Nelson, S., Kornblum, H., Doyle, F., Petzold, L., Shraiman, B. & Kosik, K. (2007). Detection of a MicroRNA Signal in an In Vivo ExpressionSet of mRNAs. Plos One, Vol. 8, August 2007, e804
reactant_size06.pdf Gillespie, D., Lampoudi, S. & Petzold, L. (2007). Effect of Reactant Size on Discrete Stochastic Chemical Kinetics. J. Chem. Phys. 126(3), 034302-034302-9
controlofmixing06.pdf Mathew, G., Mezic, I., Grivopoulos, S., Vaidya, U. & Petzold, L. (2007). Optimal Control of Mixing in Stokes Fluid Flows. J. Fluid Mech. 580, pp. 261-281
Doyle_FOSBE07.pdf Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle III, F. (2007). Robust Timekeeping in Circadian Networks: From Genes to Cells. FOSBE 2007 Conference Proceedings.
stochastic_simulation_of_biochemical_systems_on_th.pdf Li, H. & Petzold, L. R. (2007). Stochastic Simulation of Biochemical Systems on the Graphics Processing Unit.
FOSBE_proceedings07.pdf Bagheri, N., Taylor, S., Meeker, K., Petzold, L. & Doyle, F. (2007). Synchrony and Entrainment Properties of Robust Circadian Oscillators. Proc. FOSBE Conf.
adaptivetau06.pdf Cao, Y., Gillespie, D. & Petzold, L. (2007). The Adaptive Explicit-Implicit Tau-Leaping Method with Automatic Tau Selection. J. Chem. Phys. 126(22), pp. 224101-224101-9, 2007.
ROMerror06.pdf Serban, R., Homescu, C. & Petzold, L. (2007). The Effect of Problem Perturbations on Nonlinear Dynamical Systems and their Reduced Order Models. SIAM J. Sci. Comput., Vol. 29, No. 6, pp. 2621-2643
2006
Lipid_Bilayer06.pdf Stroumpoulis, D., Parra, A., Petzold, L. & Tirrell, M. (2006). A Monte Carlo Simulation Study of Lipid Bilayer Formation on Hydrophilic Substrates from Vesicle Solutions Z. Zheng. J. Chem. Phys. 7
distributiondistance042.pdf Cao, Y. & Petzold, L. (2006). Accuracy Limitations and the Measurement of Errors in the Stochastic Simulation of Chemically Reacting Systems. J. Comp. Phys. 212(1), pp. 6-24
NewTau052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2006). Efficient Stepsize Selection for the Tau-Leaping Method. J. Chem. Phys. 124, 044109-144109-11
ldm0513.pdf Li, H. & Petzold, L. (2006). Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems. Technical report
BookChapter06.pdf Book chapter by Gillespie, D. & Petzold, L. (2006). Numerical Simulation for Biochemical Kinetics. In System Modelling in Cellular Biology, Ed. Z. Szallasi, J. Stelling, V. Periwal MIT Press
rkcpmethod052.pdf Z. Zheng and L. Petzold (2006). Runge-Kutta-Chebyshev Projection Method. J. Comp. Phys. 219, 976-991
CCEpaper.pdf Petzold, L., Li, S., Cao, Y. & Serban, R. (2006). Sensitivity Analysis of Differential-Algebraic Equations and Partial Differential Equations. Computers, Chemical Engineering 30 30, pp. 1553-1559
CSE_undergrad_report06.pdf SIAM Working Group on CSE Undergraduate Education (2006). Undergraduate Computational Science and Engineering Education.
2005
multiscalemixing05.pdf Mathew, G., Mezic, I. & Petzold, L. (2005). A Multiscale Measure for Mixing. Physica D 211 (1-2): pp. 23-46.
EnzymSubstr052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). Accelerated Stochastic Simulation of the Stiff Enzyme-Substrate Reaction. J. Chem. Phys. 123(14), pp. 144917-144929
ModTau052.pdf Cao, Y., Gillespie, D. & Petzold, L. (2005). Avoiding Negative Populations in Explicit Poisson Tau Leaping. J. Chem. Phys.123, pp. 054104-054112
nSSAComment.pdf Gillespie, D., Petzold, L. & Cao, Y. (2005). Comment on 'Nested Stochastic Simulation Algorithm for Chemical Kinetic Systems with Disparate Rates'. J. Chem. Phys. 126, pp. 137101-137101-4

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