Frank Doyle  publication list
     
Patents
     
  T. Komulainen, S.-L. Jamsa-Jounela, System and Method for Controlling an Industrial Copper Solvent Extraction Process, disclosed March 20, 2007.
   
  F.J. Doyle III and L. Jovanovic, Method and Apparatus for Glucose Control and Insulin Dosing for Diabetics, U.S. Provisional Patent Application 60/571,243, submitted May 13, 2004. Full patent application submitted May 12, 2005.
     
Books
     
  M. Cassman, A. Arkin, F. Doyle, F. Katagiri, D. Lauffenburger, and C. Stokes, Systems Biology – International Research and Development, Springer, Dordrecht, 2007.
   
  F.J. Doyle III, R.K. Pearson, and B.A. Ogunnaike, Identification and Control of Process Systems Using Volterra Models, Springer-Verlag, New York, 2001.
     
  F.J. Doyle III, Process Control Modules – A Software Laboratory for Control Design, Prentice, New Jersey, 1999.
     
Archival Book Chapters
     
  S. Hildebrandt, N. Bagheri, R. Gunawan, H. Mirsky, J. Shoemaker, S. Taylor, L. Petzold, and F.J. Doyle III, “Systems Analysis for Systems Biology”, in Systems Biology, E. Liu, G. Nolan, and D. Lauffenburger, Editors, Academic Press, 2007.
     
  J. Shoemaker, R. Gunawan, and F.J. Doyle III, “Model-Based Optimal Experimental Design for Biological Systems”, in Methods in Molecular Biology: Caspase Signaling, J. Varner, Editor, Humana Press, 2007.
     
  J. Stelling, U. Sauer, F.J. Doyle III, and J. Doyle, “Complexity and Robustness of Cellular Systems”, in System Modeling in Cellular Biology, Z. Szallasi, V. Periwal and J. Stelling, Editors, MIT Press, 2005.
     
  R. Gunawan, K. Gadkar, and F.J. Doyle III, “Methods to Identify Cellular Architecture and Dynamics from Experimental Data”, in System Modeling in Cellular Biology, Z. Szallasi, V. Periwal and J. Stelling, Editors, MIT Press, 2005.
     
  N. Hernjak, F.J. Doyle III, B.A. Ogunnaike, and R.K. Pearson, “Chemical Process Characterization for Control Design”, in Integration of Design and Control, P. Seferlis and M. Georgiadis, Editors, Elsevier, 2004.
     
  F.J. Doyle III, M. Soroush, and C. Cordeiro, “Control of Product Quality in Polymerization Processes”, in Chemical Process Control VI: Assessment and Directions for Research, J. Rawlings, B. Ogunnaike, and J. Eaton, Editors, AIChE Symp. Series No. 326, Volume 98, 290-306, 2002.
     
  J. Schwaber, F.J. Doyle III and D. Zak, “Controlled Biological Processes and Computational Genomics”, in Chemical Process Control VI: Assessment and Directions for Research, J. Rawlings, B. Ogunnaike, and J. Eaton, Editors, AIChE Symp. Series No. 326, Volume 98, 75-80, 2002.
     
  F.J. Doyle III and P.A. Wisnewski, “Nonlinear Multi-rate MPC with Large Scale Fundamental Models: Application to a Continuous Pulp Digester”, in Nonlinear Model Predictive Control, F. Allgower and A. Zheng, Editors, Birkhaeuser, 2000.
     
  F.J. Doyle III, “Using the WWW to Teach Process Control in Engineering”, in Teaching with Technology: 50 Professors from 8 Universities Tell Their Stories, D. Brown, Editor, 2000.
     
  F.J. Doyle III, “Computational Issues in the Application of Model-based Control to the Pulp and Paper Industry”, in Fundamental Advances and Innovations in the Pulp and Paper Industry, B.N. Brogdon, Editor, 1999.
     
  F. Allgöwer and F.J. Doyle III, “Approximate I/O-Linearization of Nonlinear Systems”, in Nonlinear Model-based Control, R. Berber, Editor, 1998.
     
  F.J. Doyle III and F. Allgöwer, “Nonlinear Process Control: Which Way to the Promised Land?”, in Chemical Process Control V: Assessment and Future Directions, J. Kantor, C. Garcia, and B. Carnahan, Editors, AIChE Symp. Series No. 316, Volume 93, 1997.
     
  A. Aoyama, F.J. Doyle III and V. Venkatasubramanian, “Fuzzy Neural Network Techniques and their Application for Nonlinear Chemical Process Control”, in Fuzzy Theory Systems Techniques & Applications, C.T. Leondes, Editor, Academic Press, 1997.
     
  F.J. Doyle III and M.A. Henson, “Nonlinear Systems Theory”, in Nonlinear Process Control, M.A. Henson and D.E. Seborg, Editors, Prentice-Hall, 1997.
     
  F.J. Doyle III, M.A. Henson, B.A. Ogunnaike, J.S. Schwaber, and I. Rybak, “Neuronal Modeling of the Baroreceptor Reflex with Applications in Process Modeling and Control”, in Neural Networks for Control, D.L. Elliott, Editor, Springer Verlag, pp. 89-130, 1997.
     
  F.J. Doyle III, A.P. Packard, and M. Morari, “Robust Controller Design for a Nonlinear CSTR”, in Recent Advances in Robust Control, P. Dorato, Editor, IEEE Press, pp. 456-461, 1990.
     
Publications
     
  M. Mercangoz and F.J. Doyle III, “Real-time Optimization of the Pulp Mill Benchmark Problem”, Comp. Chem. Eng, in press, 2007.
     
  M. Dokucu and F.J. Doyle III, “Batch-to-Batch Control of Characteristic Points on the PSD in Experimental Emulsion Polymerization”, AIChE J., accepted, 2008.
     
  N. Bagheri, S.R. Taylor, K. Meeker, L.R. Petzold, and F.J. Doyle III, “Synchrony and Entrainment Properties of Robust Circadian Oscillators”, Roy. Soc. Interface, accepted, 2008.
     
  R. Ramachandran, J.M.-H. Poon, C.F.W. Sanders, T. Glaser, I.T. Cameron, F.J. Doyle III, C.D. Immanuel, J.D. Litster, F. Stepanek, and F. Wang, “Experimental Studies on Distributions of Granule Size, Binder Content and Porosity in Batch Drum Granulation: Inferences on Process Modelling Requirements and Process Sensitivities”, Powder Tech., accepted, 2008.
     
  N. Bagheri, J. Stelling, and F.J. Doyle III, “Circadian Phase Resetting & Multiple Control Targets”, PLoS Comp. Biol., accepted, 2008.
     
  M. Percival, H. Zisser, L. Jovanovic, and F.J. Doyle III, “Closed-loop Control and Advisory Mode Evaluation of an Artificial b-Cell: Use of proportional-Integral-Derivative Equivalent Model-Based Controllers”, Diabetes Tech. Ther., submitted, 2008.
     
  H. Mirsky, R. Gunawan, S. Taylor, J. Stelling, and F.J. Doyle III, “Noise Propagation and Sensitivity in Mammalian Circadian Clocks”, PLoS Comp. Biol., submitted, 2008.
     
  T. Glaser, C.F.W. Sanders, F.Y. Wang, I.T. Cameron, J.D. Litster, J. M.-H. Poon, R. Ramachandran, C. Immanuel, and F.J. Doyle III, “Model Predictive Control of Continuous Drum Granulation”, J. Process Control, submitted, 2007.
     
  C.F.W. Sanders, M.J. Hounslow, and F.J. Doyle III, “Identification of Models for Control of Wet Granulation”, Powder Tech., submitted, 2007.
     
  S. Hildebrandt, D. Raden, A.S. Robinson and F.J. Doyle III, “A top-down approach to mechanistic biological modeling: application to the single-chain antibody folding pathway”, Biophys. J., submitted, 2007.
     
  S. Hildebrandt, D. Raden, A.S. Robinson and F.J. Doyle III, “Sensitivity Analysis Discriminates Between Ire1p Activation Regulation Models in S. cerevisiae”, Nature Molecular Systems Biology, submitted, 2007.
     
  P. Xu, D. Raden, C. Gelmi, S. Hildebrandt, B. Ogunnaike, F.J. Doyle III, and A.S. Robinson, “Genomic Analysis of the Cellular Response During Heterologous Protein Expression in Saccharomyces cerevisiae: using a Novel Probabilistic Framework”, Genome Biology, submitted, 2006.
     
  E. Dassau, B.A. Buckingham, Q.W. Bequette, and F.J. Doyle III, “Detection of a Meal Using Continuous Glucose Monitoring: Implications for an Artificial b-cell”, Diabetes Care, 31, 295-300, 2008.
     
  S. Taylor, R. Gunawan, L. Petzold, and F.J. Doyle III, “Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network”, IEEE Trans. Aut. Control-Special Issue, 53, 177-188, 2008.
     
  C. Palerm, H. Zisser, L. Jovanovic, and F.J. Doyle III, “A Run-to-Run Control Strategy to Adjust Basal Insulin Infusion Rates in Type 1 Diabetes”, J. Process Control, 18, 258-265, 2008.
     
  M.J. Park, F.W. Dahlquist, and F.J. Doyle III, “Simultaneous high gain and wide dynamic range in a model of bacterial chemotaxis”, IEEE Systems Biology, 1, 222-229, 2007.
     
  J. Poon, C.I. Immanuel, F.J. Doyle III, and J. Litster, “A Three-Dimensional Population Balance Model of Granulation with a Mechanistic Representation of the Nucleation and Aggregate Phenomena”, Chem. Eng. Sci., 63, 1315-1329, 2008.
     
  M. Pinto, C.I. Immanuel and F.J. Doyle III, “A Two-level Discretisation Algorithm for the Efficient Solution of Higher-Dimensional Population Balance Models”, Chem. Eng. Sci., 63, 1304-1314, 2008.
     
  M. Dokucu, M.-J. Park, and F.J. Doyle III, “Multi-rate Model Predictive Control of Particle Size Distribution in a Semibatch Emulsion Copolymerization Reactor”, J. Process Control, 18, 105-120, 2008.
     
  M. Dokucu, M.-J. Park, and F.J. Doyle III, “Reduced-order Methodologies for Feedback Control of Particle Size Distribution in Semi-batch Emulsion Copolymerization”, Chem. Eng. Sci., 63, 1230-1245, 2008.
     
  A. Liu, D. Welsh, C. Ho, H. Tran, E. Zhang,A. Priest, E. Buhr, O. Singer, K. Meeker, I. Verma, F.J. Doyle III, J. Takahashi, and S. Kay, “Intercellular Coupling Confers Robustness against Mutations in teh SCN Circadian Clock Network”, Cell, 129, 605-616, 2007.
     
  N. Bagheri, J. Stelling and F.J. Doyle III, “Circadian Phase Entrainment via Nonlinear Model Predictive Control”, Intl. J. Robust and Nonlinear Control, 17, 1555-1571, 2007.
     
  C. Palerm, H. Zisser, W. Bevier, L. Jovanovic, and F.J. Doyle III “Prandial Insulin Dosing Using Run-to-Run Control: Application of Clinical Data and Medical Expertise to Define a Suitable Performance Metric”, Diabetes Care, 30, 1131-1136, 2007 .
     
  M.A. Pinto, C.D. Immanuel, and F.J. Doyle III, “A Feasible Solution Technique for Higher-Dimensional Population Balance Models”, Comp. Chem. Eng, 31, 1242-1256, 2007.
     
  R. Gunawan and F.J. Doyle III, “Phase Sensitivity Analysis of Circadian Rhythm Entrainment”, J. Biol. Rhythms, 22, 180-194, 2007.
     
  R. Kronauer, G. Gunzelmann, H. Van Dongen, F.J. Doyle III, and E. Klerman, ”Uncovering Physiologic Mechanisms of Circadian Rhythms and Sleep/Wake Regulation through Mathematical Modeling ”, J. Biol. Rhythms, 22, 233-245, 2007.
     
  W. Bevier, H. Zisser, C. Palerm, D. Finan, D. Seborg, F.J. Doyle III, A. Wollitzer, L. Jovanovic, “Calculating the Insulin to Carbohydrate Ratio Using The Hyperinsulinemic-Euglycemic Clamp – A Novel Use for a Proven Technique”, Diabetes Metabolism Research & Reviews, 23, 472-478, 2007.
     
  N. Bagheri, J. Stelling and F.J. Doyle III, “Quantitative Performance Metrics for Robustness in Circadian Rhythms”, Bioinformatics, 23, 358-364, 2007.
     
  T.L. To, M.A. Henson, E.D. Herzog, and F.J. Doyle III, “A Molecular Model for Intercellular Synchronization in the Mammalian Circadian Clock”, Biophys. J., 92, 3792-3803, 2007.
     
  N. Padhiyar, A. Gupta, A. Gautam, S. Bhartiya, F.J. Doyle III, S. Dash, and S. Gaikwad, “Nonlinear Inferential Control of Kappa Number At Multiple Locations in A Continuous Pulp Digester”, J. Process Control, 16, 1037-1053, 2006.
     
  C. Palerm, H. Zisser, L. Jovanovic, and F.J. Doyle III, “A Run-to-Run Framework for Prandial Insulin Dosing: Handling Real-life Uncertainty”, Int. J. Robust Nonlinear Control, 17, 1194-1213, 2007 .
     
  M.N. Zeilinger, E.M. Farre, S.R. Taylor, S.A. Kay, and F.J. Doyle III, “A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9”, Nature Molecular Systems Biology, 2, 1-13, 2006. (doi:10.1038/msb4100101)
     
  R. Gunawan and F.J. Doyle III, “Isochron-based Phase Response Analysis of Circadian Rhythms”, Biophys. J., 91, 2131-2141, 2006.
     
  F.J. Doyle III, R. Gunawan, N. Bagheri, H. Mirsky, and T.L. To, “Circadin Rhythm: A Natural Robust, Multi-Scale Control System”, Comp. Chem. Eng., 30, 1700-1711, 2006.
     
  P. Dua, F.J. Doyle III, and E. Pistikopoulos, “Model Based Blood Glucose Control for Type 1 Diabetes via Parametric Programming”, IEEE Trans. Biomed. Eng., 53, 1478-1491, 2005.
     
  F. J. Doyle III and J. Stelling, ‘Systems Interface Biology”, J. Royal Soc. Interface, 3, 603-616, 2006.
     
  K. Gadkar, R. Mahadevan, and F.J. Doyle III, “Optimal Genetic Manipulations in Batch Bioreactor Control”, Automatica, 42, 1723-1733, 2006.
     
  M. Mercangoz and F.J. Doyle III, “Control Challenges in the Pulp and Paper Industry”, Control Systems Magazine, August, 30-39, 2006.
     
  M. Cassman, A. Arkin, F. Katagiri, D. Lauffenburger, F.J. Doyle III, and C.L. Stokes, “Barriers to progress in systems biology” (Commentary), Nature, 438, 1079, 2006.
     
  R.S. Parker, F.J. Doyle III, and M.A. Henson, “Integrating Biological Systems in the Process Dynamics and Control Curriculum”, Chem. Eng. Educ., 181-188, 2006.
     
  D. Raden, S. Hildebrandt, P. Xu, E. Bell, F.J. Doyle III and A.S. Robinson, “Analysis of Cellular Response to Protein Overexpression”, IEE Systems Biology, 152, 285-289, 2005.
     
  S. Bhartiya, N. Chaudhary, K.V. Venkatesh, and F.J. Doyle III, “Multiple Feedback Loop Motif in Regulatory Networks Reveals a Design Paradigm for Robust Regulation of Processes in Series”, J. Royal Soc. Interface, 3, 383-391, 2005.
     
  M.J. Park, M.T. Dokucu, and F.J. Doyle III, “Modeling and Sensitivity Analysis of Particle Size Distribution and Chain Length Distribution in a Semibatch Emulsion Copolymerization Reactor”, Macromol. Theory Simul., 14, 474-490, 2005.
     
  K. Gadkar, R. Gunawan, and F.J. Doyle III, “Iterative Approach to Model Identification of Biological Networks”, BMC Bioinformatics, 6, 155-175, 2005.
     
  C. Owens, H. Zisser, L. Jovanovic, B. Srinivasan, D. Bonvin, and F.J. Doyle III, “Run-to-Run Control of Blood Glucose Concentrations for People with Type 1 Diabetes Mellitus”, IEEE Trans. Biomed. Eng., 53, 996-1005, 2006.
     
  P. Xu, D. Raden, F.J. Doyle III, and A.S. Robinson, “Analysis of Unfolded Protein Response During Single-Chain Antibody Expression in Saccaromyces cerevisiae Reveals During Roles for BiP and PDI in folding”, Metabolic Eng., 7, 269-279, 2005.
     
  D. Saffer and F.J. Doyle III, “Efficient Model Predictive Control for Cross Directional Control of a Paper Machine”, Ind. Eng. Chem. Res., 44, 2134-2144, 2005.
     
  K. Gadkar, J. Varner, and F.J. Doyle III, “Model Identification of Signal Transduction Networks from Data Using a State Regulator Problem”, IEE Systems Biology, 2, 17-30, 2005.
     
  C. Immanuel and F.J. Doyle III, “Solution Technique for a Multi-Dimensional Population Balance Model Describing Granulation Processes”, Powder Technology, 156, 213-225, 2005.
     
  R. Gunawan, Y. Cao, L. Petzold, and F.J. Doyle III, “Sensitivity Analysis of Discrete Stochastic Systems”, Biophys. J., 88, 2530-2540, 2005.
     
  H. Zisser, L. Jovanovic, F. Doyle III, P. Ospina, and C. Owens, “Run-to-Run Control of Meal-Related Insulin Dosing”, Diabetes Tech. & Ther., 7, 48-57, 2005.
     
  P. DuFour, S. Bhartiya, P. Dhurjati, and F.J. Doyle III, “Neural Network-based Software Sensor: Training Set Design and Application to a Continuous Pulp Digester”, Control Eng. Practice, 13, 135-143, 2005.
     
  N. Hernjak and F.J. Doyle III, “Glucose Control Design Using Nonlinearity Assessment Techniques”, AIChE J., 51, 544-554, 2005.
     
  D. Zak, R. Vadigepalli, G. Gonye, F.J. Doyle III, J. Schwaber, and B. Ogunnaike, “Unconventional Systems Analysis Problems in Molecular Biology: A Case Study in Genetic Regulatory Network Modeling”, Comp. Chem. Eng., 29, 547-563, 2005.
     
  D. Zak, J. Stelling, and F.J. Doyle III, “Sensitivity Analysis of Oscillatory (Bio)Chemical Systems”, Comp. Chem. Eng., 29, 663-673, 2005.
     
  D. Saffer, J.J. Castro-Velez, F.J. Doyle III, “A Variable Time Delay Compensator for Multivariable Linear Processes”, J. Process Control, 15, 215-222, 2005.
     
  S.T. Junker, R.W. Birkmire, and F.J. Doyle III, “Mass and Heat Transfer Modeling of a Physical Vapor Deposition Effusion Source”, AIChE J., 51, 878-894, 2005.
     
  J. Stelling, U. Sauer, Z. Szallasi, F.J. Doyle III, and J. Doyle, “Robustness of Cellular Functions”, Cell, 118, 675-685, 2004.
     
  D. Saffer and F.J. Doyle III, “Analysis of Linear Programming in Model Predictive Control”, Comp. Chem. Eng., 28, 2749-2763, 2004.
     
  Y.Wang and F.J. Doyle III, “Reachability Analysis of Particle Size Distribution in Semi-batch Emulsion Polymerization”, AIChE J., 50, 3049-3059, 2004.
     
  A. Kremling, S. Fischer, F.J. Doyle III, K. Gadkar, T. Sauter, E. Bullinger, F. Allgower, and E.D. Gilles, “A Benchmark for Methods in Reverse Engineering and Model Discrimination: Problem Formulation and Solutions”, Genome Res., 14, 1773-1785, 2004.
     
  M.J. Park, D. Dokocu, and F.J. Doyle III, “Regulation of Emulsion PSD to Optimal Trajectory Using PLS Model-based Predictive Control “, Ind. Eng. Chem. Res., 43, 7227-7237, 2004.
     
  K. Gadkar, F.J. Doyle III, J.S. Edwards and R. Mahadevan, “Estimating Optimal Profiles of Genetic Alterations using Constraint-based Models”, Biotech. Bioeng., 89, 243-251, 2004.
     
  D. Feather, D. Harrell, R. Lieberman, and F.J. Doyle III, “Hybrid Approach to Polymer Grade Transition”, AIChE J., 50, 2502-2513, 2004.
     
  S. Bhartiya and F.J. Doyle III, “Mathematical Model Predictions of Plugging Phenomenon in an Industrial Single Vessel Pulp Digester”, Ind. Eng. Chem. Res., 43, 5225-5232, 2004.
     
  J. Stelling, E.D. Gilles, and F.J. Doyle III, “Robustness Properties of Circadian Clock Architectures”, Proc. Natl. Acad. Sci. USA, 101, 13210-13215, 2004.
     
  M.J. Park and F.J. Doyle III, “Nonlinear Model Order Reduction and Control of Particle Size Distribution in a Semibatch Vinyl Acetate/Butyl Acrylate Emulsion Copolymerization Reactor”, Korean J. Chem. Eng., 21, 168-176, 2004.
     
  D. Zak, R.K. Pearson, R. Vadigepalli, G. Gonye, J. Schwaber, and F.J. Doyle III, “Continuous Time Identification of Gene Expression Models”, Omics, 7, 373-386, 2003.
     
  S.T. Junker, R.W. Birkmire, and F.J. Doyle III, “Manufacture of Thin Film Solar Cells: Modeling and Control of Cu(InGa)Se2 Physical Vapor Deposition onto a Moving Substrate”, Ind. Eng. Chem. Res., 43, 566-576, 2004.
     
  J. Castro-Velez, and F.J. Doyle III, “A Pulp Mill Benchmark Problem for Control: Application of Plantwide Control Design”, J. Process Control, 14, 329-347, 2004.
     
  S. BenAmor, F.J. Doyle III, and R. McFarlane, “Polymer Grade Transition Control Using Advanced Real-time Optimization Software”, J. Process Control, 14, 349-364, 2004.
     
  J. Castro-Velez, and F.J. Doyle III, “A Pulp Mill Benchmark Problem for Control: Problem Description”, J. Process Control, 14, 17-29, 2004.
     
  C. Immanuel, and F.J. Doyle III, “A Hierarchical Strategy for Control of Particle Size Distribution Using Multi-Objective Optimization”, AIChE J., 49, 2383-2399, 2003.
     
  N. Hernjak, and F.J. Doyle III, “Correlation of Process Nonlinearity with Closed-loop Disturbance Rejection”, Ind. & Eng. Chem. Res., 42, 4611-4619, 2003.
   
  D. Zak, G. Gonye, J. Schwaber, and F.J. Doyle III, “Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights from an Identifiability Analysis of an In Silico Network”, Genome Research, 13, 2396-2405, 2003.
     
  K.G. Gadkar, F.J. Doyle III, T.C. Crowley, and J. Varner, “Cybernetic Model Predictive Control of a Continuous Bioreactor with Cell Recycle”, Biotech. Progress, 19, 1487-1497, 2003.
     
  C. Immanuel, T.J. Crowley, C.F. Cordeiro, and F.J. Doyle III, “Evolution of Multimodeal Particle Size Distribution in Vinyl Acetate/Butyl Acrylate Emulsion Co-Polymerizations”, J.Poly. Sci. Part A: Polymer Chemistry, 41, 2232-2249, 2003.
     
  C. Immanuel, and F.J. Doyle III, “Computationally Efficient Solution of Population Balance Models Incorporating Nucleation, Growth, and Coagulation”, Chem. Eng. Sci., 58, 3681-3698, 2003.
     
  C. Immanuel, C.F. Cordeiro, S.S. Sundaram, and F.J. Doyle III, “Particle Size Distribution Model for Emulsion Co-polymerization Under Steric Stabilization”, AIChE J, 49, 1392-1404, 2002.
     
  R. Mahadevan, and F.J. Doyle III, “Efficient Optimization Approaches to Nonlinear Model Predictive Control”, Int. Journal Robust Nonlinear Control, 13, 309-329, 2003.
   
  E.S. Meadows, T.J. Crowley, C.D. Immanuel, and F.J. Doyle III, “Non-isothermal Modeling and Sensitivity Studies for Batch and Semi-batch Emulsion Polymerization of Styrene”, Ind. Eng. Chem. Res., 42, 555-567, 2003.
     
  R. Vadigepalli and F.J. Doyle III, “A Distributed State Estimation and Control Algorithm for Plantwide Processes”, IEEE Trans. Control Sys. Tech., 11, 119-127, 2003.
     
  R. Vadigepalli and F.J. Doyle III, “Structural Analysis of Large Scale Systems for Distributed State Estimation and Control Applications”, Control Eng. Practice, 11, 895-905, 2003.
     
  F.J. Doyle III, C. Harrison, and T. Crowley, “Hybrid Model-based Approach to Batch-to-Batch Control of Particle Size Distribution in Emulsion Polymerization”, Comp. Chem. Eng., 27, 1153-1163, 2003.
     
  K.J. Kauffman, E.M. Pridgen, F.J. Doyle III, P.S. Dhurjati, and A.S. Robinson, “Decreased Protein Expression and Intermittent Recoveries in BiP Levels Result from Cellular Stress during Heterologous Protein Expression in Saccharomyces cerivisiae”, Biotech. Progress, 18, 942-950, 2002.
     
  R. Mahadevan, J.S. Edwards, and F.J. Doyle III, “Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli”, Biophysical Journal, 83, 1331-1340, 2002.
     
  D.R. Saffer II and F.J. Doyle III, “Closed-loop Identification with MPC for an Industrial Scale CD Control Problem”, IEE Proceedings on Control Theory and Application, Special Edition on CD Control, 149, 448-456, 2002.
     
 

C. Immanuel and F.J. Doyle III, "Open-loop Control of Particle Size Distribution in Semi-Batch Emulsion Copolymerization Using a Genetic Algorithm", Chem. Eng. Sci., 57, 4415-4427, 2002.
     
  R. Mahadevan and F.J. Doyle III, “Control-relevant Scheduling of Polymer Grade Transitions”, AIChE J., 48, 1754-1764, 2002.
     
 

C.D. Immanuel, C.F. Cordeiro, E.S. Meadows, T.J. Crowley, and F.J. Doyle III, “Modeling of Particle Size Distribution in Emulsion Co-polymerization: Comparison with Experimental Data and Parametric Sensitivity Studies”, Comp. Chem. Eng., 26, 1133-1152, 2002.
     
 

A. Mahoney, D. Ramkrishna, and F.J. Doyle III, “Inverse Problems in Population Balances: Particle Growth and Nucleation from Dynamic Data”, AIChE J., 48, 981-900, 2002.
     
 

J. Castro and F.J. Doyle III, “Mill-wide Control of a Pulp Process.”, Ind. Eng. Chem. Res., 41, 1310-1320, 2002.
     
 

D. Saffer, F.J. Doyle III, A. Rigopoulos, and P.A. Wisnewski, “MPC Study for a Dual Headbox CD Control Problem”, Pulp & Paper Canada, 102, 97-101, 2001.
     
 

E.P. Gatzke and F.J. Doyle III, “Model Predictive Control of a Granulation System Using Soft Output Constraints and Prioritized Control Objectives”, Powder Technology, 121, 149-158, 2001.
     
 

E. Gatzke and F.J. Doyle III, “Use of Multiple Models and Qualitative Constraints for on-line Moving-horizon Disturbance Estimation and Fault Diagnosis”, J. Process Control, 12, 339-352, 2002.
     
 

R. Vadigepalli, F.J. Doyle III, and J.S. Schwaber, “Analysis and Neuronal Modeling of the Nonlinear Characteristics of a Local Cardiac Reflex in the Rat”, Neural Computation, 13, 2239- 2271, 2001.
     
 

R.S. Parker, F.J. Doyle III, and N.A. Peppas, ”The Intravenous Route to Blood Glucose Control”, IEEE Eng. Med. Biology, Jan/Feb, 65-73, 2001.
   
R. Mahadevan, S.K. Agrawal, and F.J. Doyle III, “Differential Flatness based nonlinear predictive control of fed-batch bioreactors.” Control Engineering Practice, 9, 889-899, 2001.
   
  R.S. Parker and F.J. Doyle III, “Control-relevant Modeling in Drug Delivery”, Adv. Drug Delivery Reviews, 48, 211-228, 2001.
   
  F.J. Doyle III, L. Puig, and F. Kayihan, “Grade Transition Modeling in Continuous Pulp Digester for Reaction Profile Control”, Pulp & Paper Canada, 102, 56-59, 2001.
   
  J. Castro, F.J. Doyle III, and T.A. Kendi, “Mathematical Model for the Simulation and Control of Rotary Lime Kilns”, Pulp & Paper Canada, 102, 48-51, 2001.
   
  R.S. Parker, D. Heemstra, F.J. Doyle III, R.K. Pearson, and B.A. Ogunnaike, “ The Identification of Nonlinear Models for Process Control Using Tailored “Plant-Friendly” Input Sequences ”, J. Process Control, 11, 237-250, 2001.
   
  R.S. Parker and F.J. Doyle III, “Optimal Control of a Continuous Bioreactor Using an Empirical Nonlinear Model”, Ind. & Eng. Chem. Res., 40, 1939-1951, 2001.
   
R.Vadigepalli, E.P. Gatzke, and F.J. Doyle III, “Robust Control of a Multivariable Experimental Four-Tank System.”, Ind. Eng. Chem. Res., 40, 1916-1927, 2001.
   
  P. Wisnewski and F.J. Doyle III, “Model-based Predictive Control Studies for a Continuous Pulp Digester”, IEEE Trans. Control Sys. Tech., 9, 435-444, 2001.
   
E.P. Gatzke, E.S. Meadows, C. Wang, and F.J. Doyle III, “Model Based Control of a Four- Tank System”, Comp. Chem. Eng., 24, 1503-1509, 2000.
   
  R.S. Parker, J. Ward, F.J. Doyle III, and N.A. Peppas, “Robust Glucose Control in Diabetes Using a Physiological Model”, AIChE J., 46, 2537-2549, 2000.
   
  L.S. Balasubramhanya and F.J. Doyle III, “Nonlinear Model-based Control of a Batch Reactive Distillation Column”, J. Process Control, 10, 209-218, 2000.
   
A. Kayihan and F.J. Doyle III, “Friction Compensation for a process control valve ”, Control Eng. Practice, 8, 799-812, 2000.
   
  T. Crowley, E.S. Meadows, A. Kostoulas, and F.J. Doyle III, “Control of Particle Size Distribution in Semibatch Emulsion Polymerization by Surfactant Addition”, J. Process Control, 10, 419-432, 2000.
   
  K. Podual, F.J. Doyle III, and N.A. Peppas, “Glucose Sensitivity of Glucose-Oxidase- containing Cationic Copolymer Hydrogels Having Poly(ethylene glycol) Grafts”, J. Controlled Release, 67, 9-17, 2000.
   
  K. Podual, F.J. Doyle III, and N.A. Peppas, “Preparation and Dynamic Response of Cationic Copolymer Hydrogels Containing Glucose Oxidase, Polymer, 41, 3975-3983, 2000.
   
  K. Podual, F.J. Doyle III, and N.A. Peppas, “Dynamic Behavior of Glucose-Oxidase- containing Microparticles of Poly(ethylene glycol)-grafted Cationic Hydrogels in an Environment of Changing pH”, Biomaterials, 21, 1439-1450, 2000.
   
  E. Gatzke, R. Vadigepalli, E.S. Meadows, and F.J. Doyle III, “Experiences with an Experimental Project in a Graduate Control Course” Chem. Eng. Education, 33, 270-275, 1999.
   
  Z. Cheng, T.L. Powley, J.S. Schwaber, and F.J. Doyle III, “Projections of the Dorsal Motor Nucleus of the Vagus to Cardiac of Rat Atria: An Anterograde Tracing Study”, J. Comp. Neurology, 410, 320-341, 1999.
   
  F.J. Doyle III and F. Kayihan “Reaction Profile Control of the Continuous Pulp Digester”, Chem. Eng. Sci., 54, 2679-2688, 1999.
   
  F.J. Doyle III, “An Anti-Windup Input-Output Linearization Scheme for SISO Systems”, J. Process Control, 9, 213-220, 1999.
   
  P. Dave, J.F. Pekny and F.J. Doyle III, “Customization strategies for the solution of linear programming problems arising from large scale model predictive control of a paper machine”, J. Proc. Control, 9, 385-396, 1999.
   
  F.J. Doyle III, R.S. Parker, and E.P. Gatzke, “Practical Case Studies for Undergraduate Process Dynamics and Control Using the Process Control Modules (PCM)”, Comp. Appl. Eng. Educ., 6, 181-191, 1999.
   
  R.S. Parker, F.J. Doyle III, and N.A. Peppas, “A Model-based Algorithm for Blood Glucose Control in Type I Diabetic Patients”, IEEE Trans. Biomed. Eng., 46, 148-157, 1999.
   
  F.J. Doyle III, “Nonlinear Inferential Control for Process Applications”, J. Proc. Control, 8, 339-353, 1998.
   
  P.A. Wisnewski and F.J. Doyle III, “Control Structure Selection and Model Predictive Control of the Weyerhaeuser Digester Problem”, J. Proc. Control, 8, 487-495, 1998.
   
  T.A. Kendi and F.J. Doyle III, “Nonlinear Internal Model Control for Systems with Measured Disturbances and Input Constraints”, Ind. & Eng. Chem. Res., 37, 489-505, 1998.
   
  H.S. Kwatra, F.J. Doyle III, and J.S. Schwaber, “Dynamic Gain Scheduled Process Control”, Chem. Eng. Sci., 53, 2675-2690, 1998.
   
  Z. Cheng, T.L. Powley, J.S. Schwaber, F.J. Doyle III, “A Laser Confocal Microscopic Study of Vagal Afferent Innervation of Rat Aortic Arch: Chemoreceptors as well as Baroreceptors”, J. Aut. Nerv. Sys., 67, 1-14, 1998.
   
  F.J. Doyle III, J.F. Pekny, G.V. Reklaitis, and V. Venkatasubramanian, “A Graduate Course in Computer Integrated Process Operations”, Comp. Chem. Eng., 21, S255-259, 1997.
   
  F.J. Doyle III, J.F. Pekny, P. Dave, and S. Bose, “Specialized Programming Methods in the Model Predictive Control of large Scale Systems”, Comp. Chem. Eng., 21, S847-852, 1997.
   
  P.A. Wisnewski, F.J. Doyle III, and F. Kayihan, “Fundamental Continuous Pulp Digester Model for Simulation and Control”, AIChE J., 43, 3175-3192, 1997.
   
  C.M. Hassan, F.J. Doyle III, and N.A. Peppas, “Dynamic Behavior of Glucose-Responsive Poly(methacrylic acid-g-ethylene glycol) Hydrogels”, Macromolecules, 30, 6166-6173, 1997.
   
  T. Kendi and F.J. Doyle III, “An Anti-Windup Scheme for Multivariable Nonlinear Systems”, J. Process Control, 7, 329-343, 1997.
   
  B. Maner and F.J. Doyle III, “Polymerization Reactor Control Using Auto regressive-Plus Volterra-Based MPC”, AIChE J., 43, 1763-1784, 1997.
   
  P.A. Wisnewski, F.J. Doyle III, and C. J. Primus, “Measurement Selection Issues for the Model Predictive Control of a Kamyr Digester”, Can. Pulp Paper, 98, T233-236, 1997.
   
  F.J. Doyle III, J.F. Pekny, P. Dave, S. Bose, “Specialized Programming Methods in the Model Predictive Control of Large Scale Systems”, Comp. Chem. Eng., 21, S847-S852, 1997.
   
  F.J. Doyle III, J.F. Pekny, G.V. Reklaitis, V. Venkatasubramanian, “A Graduate Course in Computer Integrated Process Operations”, Comp. Chem. Eng., 21, S255-S260, 1997.
   
  A.J. Stack and F.J. Doyle III, “The Optimal Control Structure: An Approach to Measuring Control-Law Nonlinearity”, Comp. Chem. Eng., 21, 1009-1019, 1997.
   
  A. Shaw and F.J. Doyle III, “Multivariable Nonlinear Control Applications for a High Purity Distillation Column Using a Recurrent Dynamic Neuron Model”, J. Process Control, 7, 255-268, 1997.
   
  Z. Cheng, T.L. Powley, J.S. Schwaber, F.J. Doyle III, “Vagal Afferent Innervation of the Atria of the Rat Heart Reconstructed with Confocal Microscopy”, J. Comp. Neurology, 381, 1-17, 1997.
   
  P. Dave, D. Willig, G. Kudva, J. Pekny, and F.J. Doyle III, “LP Methods in MPC of Large-Scale Systems: Applicaton to Paper-Machine CD Control ”, AIChE J., 43, 1016-1031, 1997.
   
  L.S. Balasubramhanya and F.J. Doyle III, “Nonlinear Control of a High-Purity Distillation Column Using a Traveling-Wave Model”, AIChE J., 43, 703-714, 1997.
   
  A.J. Stack and F.J. Doyle III, “Application of a Control-law Nonlinearity Measure to Chemical Reactor Analysis”, AIChE J., 43, 425-447, 1997.
   
  H. Kwatra, F.J. Doyle III, J.S. Schwaber, and I. Rybak, “A Neuro-mimetic Dynamic Scheduling Algorithm for Control: Analysis and Applications”, Neural Computation, 9, 479- 502, 1997.
   
  A.M. Shaw, F.J. Doyle III, and J.S. Schwaber, “A Dynamic Neural Network Approach to Nonlinear Process Modeling”, Comp. Chem. Eng., 21, 371-385, 1997.
   
  F.J. Doyle III, T.A. Kendi, and V. Venkatasubramanian, “PCM: A MATLAB-Based Set of Modules for Undergraduate Process Control”, Comp. Appl. Eng. Ed., 4, 179-190, 1996.
   
  R.B. McLain, M.J. Kurtz, M.A. Henson, and F.J. Doyle III, “Habituating Control for Nonsquare Nonlinear Processes”, Ind. Eng. Chem. Res., 35, 4067-4077, 1996.
   
  F.J. Doyle III, H.M. Budman, and M. Morari, “'Linearizing' Controller Design for a Packed-Bed Reactor Using a Low-Order Wave Propagation Model", Ind. & Eng. Chem. Res., 35, 3567-3580, 1996.
   
  R.K. Pearson, B.A. Ogunnaike, and F.J. Doyle III, “Identification of Structurally Constrained Second-Order Volterra Models”, IEEE Trans. Signal Processing, 44, 2837-2846, 1996.
   
  B. Maner, F.J. Doyle III, B.A. Ogunnaike, and R.K. Pearson, “Nonlinear Model Predictive Control of a Stimulated Multivariable Polymerization Reactor Using Second-Order Volterra Models”, Automatica, 32, 1285-1302, 1996.
   
  P.A. Wisnewski and F.J. Doyle III, “A Reduced Model Approach to Estimation and Control of a Kamyr Digester”, Comp. Chem. Eng., 20, S1053-S1058, 1996.
   
  T.A. Kendi and F.J. Doyle III, “Nonlinear Control of a Fluidized Bed Reactor Using Approximate Feedback Linearization”, Ind. & Eng. Chem. Res., 35, 746-757, 1996.
   
  A. Aoyama, F.J. Doyle III, and V. Venkatasubramanian, “Fuzzy Neural Network Approach for Nonlinear Process Control”, AIChE Symp. Ser., 312, 369-373, 1996.
   
  A. Aoyama, F.J. Doyle III, and V. Venkatasubramanian, “Control-Affine Neural Network Approach for Nonlinear Non-Minimum-Phase Process Control”, J. Process Control, 6, 17-26, 1996.
   
  M.H. Bassett, P. Dave, F.J. Doyle III, G.K. Kudva, J.F. Pekny, G.V. Reklaitis, S. Sub- rahmanyam, D.L. Miller and M.G. Zentner, “Perspectives on Model Based Integration of Process Operations”, Comp. Chem. Eng., 20, 821-844, 1996.
   
  A. Aoyama, F.J. Doyle III, and V. Venkatasubramanian, “Control-Affine Fuzzy Neural Network Approach for Nonlinear Process Control”, J. Process Control, 5, 375-386, 1995.
   
  A. Aoyama, F.J. Doyle III, and V. Venkatasubramanian, “A Fuzzy Neural-Network Approach for Nonlinear Process Control”, Eng. Appls. of AI, 8, 483-498, 1995.
   
  F.J. Doyle III, F. Allgöwer, and M. Morari, “A Normal Form Approach to Approximate Input-Output Linearization for Maximum ”, IEEE Trans. Aut. Control, 41, 305-309, 1996.
   
  F.J. Doyle III and J. Hobgood, “Input-Output Linearization Using Approximate Process Models ”, J. Process Control, 5, 263-275, 1995.
   
  F.J. Doyle III, T.A. Ogunnaike, and R.K. Pearson, “Nonlinear Model-Based Control Using Second-Order Volterra Models”, Automatica, 31, 697-714, 1995.
   
  M.A. Henson, B.A. Ogunnaike, J.S. Schwaber, and F.J. Doyle III, “The Baroreceptor Reflex: A Biological Control System with Applications in Chemical Process Control”, Ind. & Eng. Chem. Res., 33, 2453-2466, 1994.
   
  R. Shinnar, F.J. Doyle III, H.M. Budman, and M. Morari, “Design Considerations for Tubular Reactors with Highly Exothermic Reactions”, AIChE J., 38, No. 11, 1729-1743, 1992.
   
  F.J. Doyle III, A.P. Packard, and M. Morari, “Robust Controller Design for a Nonlinear CSTR”, Chem. Eng. Sci., 44, 1929-1947, 1989.
   
  N. Collings, F.J. Doyle III, A.N. Hayhurst, and D.B. Kittelson, “Charged Species in the Exhaust of a Spark Ignition Engine as Studied with Langmuir Probes and a Mass Spectrometer”, Combustion Science and Technology, 62, 31-59, 1989.
   
  F.J. Doyle III, R. Jackson, and P. Ginestra, “The Phenomenon of Mechanical Pinning in an Annular Moving Bed Reactor with Crossflow of Gas”, Chem. Eng. Sci., 41, 1485-1495, 1986.
   
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