UCSB Chem Engineering

Institute for Collaborative Biotechnologies

Biomolecular Science and Engineering Program (BMSE)

Center for Control, Dynamical Systems, & Computation

Journal Articles    |    Archival Book Chapters    |    Books

Journal Articles

For a complete list of articles, click HERE

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 .

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