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Recent Publications - Frank Doyle


[1] Rodriguez Fernandez, M., Palerm, C. C., Bevier, W. C., Zisser, H., Jovanovic, L., Doyle, F. J.. Robust parameter estimation in a model for glucose kinetics in type 1 diabetes patients. Diabetes, 55:A561-A561, 2006.
[2] Doyle, F. J., Gunawan, R., Bagheri, N., Mirsky, H., To, T. L.. Circadian rhythm: A natural, robust, multi-scale control system. Computers & Chemical Engineering, 30:1700-1711, 2006.
[3] Gadkar, K. G., Mahadevan, R., Doyle, F. J.. Optimal genetic manipulations in batch bioreactor control. Automatica, 42:1723-1733, 2006.
[4] Gunawan, R., Doyle, F. J.. Isochron-based phase response analysis of circadian rhythms. Biophysical Journal, 91:2131-2141, 2006.
[5] Dua, P., Doyle, F. J., Pistikopoulos, E. N.. Model-based blood glucose control for Type 1 diabetes via parametric programming. IEEE Transactions on Biomedical Engineering, 53:1478-1491, 2006.
[6] Mercangoz, M., Doyle, F. J.. Model-based control in the pulp and paper industry. IEEE Control Systems Magazine, 26:30-39, 2006.
[7] Owens, C., Zisser, H., Jovanovic, L., Srinivasan, B., Bonvin, D., Doyle, F. J.. Run-to-run control of blood glucose concentrations for people with type 1 diabetes mellitus. IEEE Transactions on Biomedical Engineering, 53:996-1005, 2006.
[8] Gadkar, K. G., Varner, J., Doyle, F. J.. 'Model identification of signal transduction networks from data using a state regulator problem' (vol 2, pg 17, 2006). IEE Proceedings Systems Biology, 153:91-91, 2006.
[9] Doyle, F. J.. Selected systems biology papers from the International Conference on Foundations of Systems Biology in Engineering (FOSBE 2005). IEE Proceedings Systems Biology, 152:173-173, 2005.
[10] Raden, D., Hildebrandt, S., Xu, P., Bell, E., Doyle, F. J., Robinson, A. S.. Analysis of cellular response to protein overexpression. IEE Proceedings Systems Biology, 152:285-289, 2005.
[11] Gadkar, K. G., Varner, J., Doyle, F. J.. Model identification of signal transduction networks from data using a state regulator problem. Systems Biology, 2:17-30, 2005.
[12] Park, M. J., Dokucu, M. T., Doyle, F. J.. Modeling and sensitivity analysis of particle size distribution and chain length distribution in a semibatch emulsion copolymerization reactor. Macromolecular Theory and Simulations, 14:474-490, 2005.
[13] Xu, P., Raden, D., Doyle, F. J., Robinson, A. S.. Analysis of unfolded protein response during single-chain antibody expression in Saccaromyces cerevisiae reveals different roles for BiP and PDI in folding. Metabolic Engineering, 7:269-279, 2005.
[14] Gadkar, K. G., Gunawan, R., Doyle, F. J.. Iterative approach to model identification of biological networks. Bmc Bioinformatics, 6, 2005.
[15] Zak, D. E., Vadigepalli, R., Gonye, G. E., Doyle, F. J., Schwaber, J. S., Ogunnaike, B. A.. Unconventional systems analysis problems in molecular biology: a case study in gene regulatory network modeling. Computers & Chemical Engineering, 29:547-563, 2005.
[16] Zak, D. E., Stelling, J., Doyle, F. J.. Sensitivity analysis of oscillatory (bio)chemical systems. Computers & Chemical Engineering, 29:663-673, 2005.
[17] Saffer, D. R., Doyle, F. J.. Efficient linear programming formulations of model predictive control for cross-directional control of a paper machine. Industrial & Engineering Chemistry Research, 44:2134-2144, 2005.
[18] Gunawan, R., Cao, Y., Petzold, L., Doyle, F. J.. Sensitivity analysis of discrete stochastic systems. Biophysical Journal, 88:2530-2540, 2005.
[19] Junker, S. T., Birkmire, R. W., Doyle, F. J.. Mass and heat transfer modeling of a physical vapor deposition effusion source. Aiche Journal, 51:878-894, 2005.
[20] Hernjak, N., Doyle, F. J.. Glucose control design using nonlinearity assessment techniques. Aiche Journal, 51:544-554, 2005.
[21] Xu, P., Doyle, F. J., Robinson, A. S.. Investigation of cell stress during heterologous protein expression using a green fluorescent protein stress sensor.. Abstracts of Papers of the American Chemical Society, 227:U227-U227, 2004.
[22] Gadkar, K. G., Doyle, F. J., Edwards, J. S., Mahadevan, R.. Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnology and Bioengineering, 89:243-251, 2005.
[23] Saffer, D. R., Doyle, F. J.. Analysis of linear programming in model predictive control. Computers & Chemical Engineering, 28:2749-2763, 2004.
[24] Saffer, D. R., Castro, J. J., Doyle, F. J.. A variable time delay compensator for multivariable linear processes. Journal of Process Control, 15:215-222, 2005.
[25] Dufour, P., Bhartiya, S., Dhurjati, P. S., Doyle, F. J.. Neural network-based software sensor: Training set design and application to a continuous pulp digester. Control Engineering Practice, 13:135-143, 2005.
[26] Wang, Y., Doyle, F. J.. Reachability of particle size distribution in semibatch emulsion polymerization. Aiche Journal, 50:3049-3059, 2004.
[27] Park, M. J., Dokucu, M. T., Doyle, F. J.. Regulation of the emulsion particle size distribution to an optimal trajectory using partial least squares model-based predictive control. Industrial & Engineering Chemistry Research, 43:7227-7237, 2004.
[28] Zisser, H., Jovanovic, L., Doyle, F., Owens, C., Ospina, P., Mesipam, J., O'Leary, J., Salmi, D.. The "euglycemic diet" facilitates euglycemia with less insulin in persons with type 1 diabetes (T1DM). Diabetes, 53:A591-A592, 2004.
[29] Feather, D., Harrell, D., Lieberman, R., Doyle, F. J.. Hybrid approach to polymer grade transition control. Aiche Journal, 50:2502-2513, 2004.
[30] Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J., Doyle, J.. Robustness of cellular functions. Cell, 118:675-685, 2004.
[31] Stelling, J., Gilles, E. D., Doyle, F. J.. Robustness properties of circadian clock architectures. Proceedings of the National Academy of Sciences of the United States, 101:13210-13215, 2004.
[32] Kremling, A., Fischer, S., Gadkar, K., Doyle, F. J., Sauter, T., Bullinger, E., Allgower, F., Gilles, E. D.. A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions. Genome Research, 14:1773-1785, 2004.
[33] Bhartiya, S., Doyle, F. J.. Mathematical model predictions of a plugging phenomenon in an industrial single-vessel pulp digester. Industrial & Engineering Chemistry Research, 43:5225-5232, 2004.
[34] Doyle, F. J.. Editorial - Control at the molecular level. IEEE Transactions on Control Systems Technology, 12:1-1, 2004.
[35] Park, N. J., Doyle, F. J.. Nonlinear model order reduction and control of particle size distribution in a semibatch vinyl acetate/butyl acrylate emulsion copolymerization reactor. Korean Journal of Chemical Engineering, 21:168-176, 2004.
[36] Castro, J. J., Doyle, F. J.. A pulp mill benchmark problem for control: application of plantwide control design. Journal of Process Control, 14:329-347, 2004.
[37] Immanuel, C. D., Doyle, F. J.. A sensitivity approach to reachability analysis for particle size distribution in semibatch emulsion polymerization. Industrial & Engineering Chemistry Research, 43:327-339, 2004.
[38] Junker, S. T., Birkmire, R. W., Doyle, F. J.. Manufacture of thin-film solar cells: Modeling and control of Cu(InGa)Se-2 physical vapor deposition onto a moving substrate. Industrial & Engineering Chemistry Research, 43:566-576, 2004.
[39] BenAmor, S., Doyle, F. J., McFarlane, R.. Polymer grade transition control using advanced real-time optimization software. Journal of Process Control, 14:349-364, 2004.
[40] Zak, D. E., Gonye, G. E., Schwaber, J. S., Doyle, F. J.. 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.
[41] Castro, J. J., Doyle, F. J.. A pulp mill benchmark problem for control: problem description. Journal of Process Control, 14:17-29, 2004.
[42] Gadkar, K. G., Doyle, F. J., Crowley, T. J., Varner, J. D.. Cybernetic model predictive control of a continuous bioreactor with cell recycle. Biotechnology Progress, 19:1487-1497, 2003.
[43] Hernjak, N., Doyle, F. J.. Correlation of process nonlinearity with closed-loop disturbance rejection. Industrial & Engineering Chemistry Research, 42:4611-4619, 2003.
[44] Immanuel, C. D., Doyle, F. J.. Hierarchical multiobjective strategy for particle-size distribution control. Aiche Journal, 49:2383-2399, 2003.
[45] Immanuel, C. D., Doyle, F. J.. Computationally efficient solution of population balance models incorporating nucleation, growth and coagulation: application to emulsion polymerization. Chemical Engineering Science, 58:3681-3698, 2003.
[46] Doyle, F. J., Harrison, C. A., Crowley, T. J.. Hybrid model-based approach to batch-to-batch control of particle size distribution in emulsion polymerization. Computers & Chemical Engineering, 27:1153-1163, 2003.
[47] Immanuel, C. D., Crowley, T. J., Meadows, E. S., Cordeiro, C. F., Doyle, F. J.. Evolution of multimodal particle size distribution in vinyl acetate/butyl acrylate emulsion copolymerizations. Journal of Polymer Science Part A-Polymer Chemistry, 41:2232-2249, 2003.
[48] Vadigepalli, R., Doyle, F. J.. Structural analysis of large-scale systems for distributed state estimation and control applications. Control Engineering Practice, 11:895-905, 2003.
[49] Immanuel, C. D., Doyle, F. J., Cordeiro, C. F., Sundaram, S. S.. Population balance PSD model for emulsion polymerization with steric stabilizers. Aiche Journal, 49:1392-1404, 2003.
[50] Mahadevan, R., Doyle, F. J.. Efficient optimization approaches to nonlinear model predictive control. International Journal of Robust and Nonlinear Control, 13:309-329, 2003.
[51] Mahadevan, R., Doyle, F. J.. On-line optimization of recombinant product in a fed-batch bioreactor. Biotechnology Progress, 19:639-646, 2003.
[52] Bhartiya, S., Dufour, P., Doyle, F. J.. Fundamental thermal-hydraulic pulp digester model with grade transition. Aiche Journal, 49:411-425, 2003.
[53] Meadows, E. S., Crowley, T. J., Immanuel, C. D., Doyle, F. J.. Nonisothermal modeling and sensitivity studies for batch and semibatch emulsion polymerization of styrene. Industrial & Engineering Chemistry Research, 42:555-567, 2003.
[54] Vadigepalli, R., Doyle, F. J.. A distributed state estimation and control algorithm for plantwide processes. IEEE Transactions on Control Systems Technology, 11:119-127, 2003.
[55] Immanuel, C. D., Doyle, F. J.. Open-loop control of particle size distribution in semi-batch emulsion copolymerization using a genetic algorithm. Chemical Engineering Science, 57:4415-4427, 2002.
[56] Saffer, D. R., Doyle, F. J.. Closed-loop identification with MPC for an industrial scale CD-control problem. IEE Proceedings-Control Theory and Applications, 149:448-456, 2002.
[57] Kauffman, K. J., Pridgen, E. M., Doyle, F. J., Dhurjati, P. S., Robinson, A. S.. Decreased protein expression and intermittent recoveries in BiP levels result from cellular stress during heterologous protein expression in Saccharomyces cerevisiae. Biotechnology Progress, 18:942-950, 2002.
[58] Mahadevan, R., Edwards, J. S., Doyle, F. J.. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophysical Journal, 83:1331-1340, 2002.
[59] Immanuel, C. D., Cordeiro, C. F., Sundaram, S. S., Meadows, E. S., Crowley, T. J., Doyle, F. J.. Modeling of particle size distribution in emulsion co-polymerization: comparison with experimental data and parametric sensitivity studies. Computers & Chemical Engineering, 26:1133-1152, 2002.
[60] Mahadevan, R., Doyle, F. J., Allcock, A. C.. Control-relevant scheduling of polymer grade transitions. Aiche Journal, 48:1754-1764, 2002.
[61] Mahoney, A. W., Doyle, F. J., Ramkrishna, D.. Inverse problems in population balances: Growth and nucleation from dynamic data. Aiche Journal, 48:981-990, 2002.
[62] Castro, J. J., Doyle, F. J.. Plantwide control of the fiber line in a pulp mill. Industrial & Engineering Chemistry Research, 41:1310-1320, 2002.
[63] Gatzke, E. P., Doyle, F. J.. Use of multiple models and qualitative knowledge for on-line moving horizon disturbance estimation and fault diagnosis. Journal of Process Control, 12:339-352, 2002.
[64] Saffer, D. R., Doyle, F. J., Rigopoulos, A., Wisnewski, P.. MPC study for a dual headbox CD control problem. Pulp & Paper-Canada, 102:97-101, 2001.
[65] Gatzke, E. P., Doyle, F. J.. Model predictive control of a granulation system using soft output constraints and prioritized control objectives. Powder Technology, 121:149-158, 2001.
[66] Vadigepalli, R. A., Doyle, F. J., Schwaber, J. S.. Analysis and neuronal modeling of the nonlinear characteristics of a local cardiac reflex in the rat. Neural Computation, 13:2239-2271, 2001.
[67] Mahadevan, R., Agrawal, S. K., Doyle, F. J.. Differential flatness based nonlinear predictive control of fed-batch bioreactors. Control Engineering Practice, 9:889-899, 2001.
[68] Castro, J. J., Doyle, F. J., Kendi, T.. Mathematical model for the simulation and control of rotary lime kilns - Open-loop simulations agree with the literature. Pulp & Paper-Canada, 102:48-51, 2001.
[69] Doyle, F. J., Puig, L. J., Kayihan, F.. Grade transition modelling in continuous pulp digesters for reaction profile control - It has been used in a simulation to measure the effectiveness of MPC. Pulp & Paper-Canada, 102:56-59, 2001.
[70] Parker, R. S., Doyle, F. J.. Control-relevant modeling in drug delivery. Advanced Drug Delivery Reviews, 48:211-228, 2001.
[71] Wisnewski, P. A., Doyle, F. J.. Model-based predictive control studies for a continuous pulp digester. IEEE Transactions on Control Systems Technology, 9:435-444, 2001.
[72] Vadigepalli, R., Gatzke, E. P., Doyle, F. J.. Robust control of a multivariable experimental four-tank system. Industrial & Engineering Chemistry Research, 40:1916-1927, 2001.
[73] Parker, R. S., Doyle, F. J.. Optimal control of a continuous bioreactor using an empirical nonlinear model. Industrial & Engineering Chemistry Research, 40:1939-1951, 2001.
[74] Doyle, F., Ray, H., Rivera, D., Lee, J., Ogunnaike, T., Allgower, F.. In honor of Dave Smith. Journal of Process Control, 11:109-110, 2001.
[75] Parker, R. S., Heemstra, D., Doyle, F. J., Pearson, R. K., Ogunnaike, B. A.. The identification of nonlinear models for process control using tailored "plant-friendly" input sequences. Journal of Process Control, 11:237-250, 2001.
[76] Bequette, B. W., Doyle, F. J.. Automated control in biomedicine. IEEE Engineering in Medicine and Biology Magazine, 20:22-23, 2001.
[77] Parker, R. S., Doyle, F. J., Peppas, N. A.. The intravenous route to blood glucose control. IEEE Engineering in Medicine and Biology Magazine, 20:65-73, 2001.
[78] Parker, R. S., Doyle, F. J., Ward, J. H., Peppas, N. A.. Robust H-infinity glucose control in diabetes using a physiological model. Aiche Journal, 46:2537-2549, 2000.
[79] Doyle, F. J., Ohshima, M.. Preface. Journal of Process Control, 10:387-387, 2000.
[80] Crowley, T. J., Meadows, E. S., Kostoulas, E., Doyle, F. J.. Control of particle size distribution described by a population balance model of semibatch emulsion polymerization. Journal of Process Control, 10:419-432, 2000.
[81] Gatzke, E. P., Meadows, E. S., Wang, C., Doyle, F. J.. Model based control of a four-tank system. Computers & Chemical Engineering, 24:1503-1509, 2000.
[82] Doyle, F. J., Ohshima, M.. Preface to the Special Section on process control. Control Engineering Practice, 8:781-781, 2000.
[83] Kayihan, A., Doyle, F. J.. Friction compensation for a process control valve. Control Engineering Practice, 8:799-812, 2000.
[84] Podual, K., Doyle, F. J., Peppas, N. A.. 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.
[85] Podual, K., Doyle, F. J., Peppas, N. A.. Glucose-sensitivity of glucose oxidase-containing cationic copolymer hydrogels having poly(ethylene glycol) grafts. Journal of Controlled Release, 67:9-17, 2000.
[86] Vadigepalli, R., Doyle, F. J., Schwaber, J. S.. Modeling and analysis of local cardiac control in the rat. Faseb Journal, 14:A376-A376, 2000.
[87] Balasubramhanya, L. S., Doyle, F. J.. Nonlinear model-based control of a batch reactive distillation column. Journal of Process Control, 10:209-218, 2000.
[88] Podual, K., Doyle, F. J., Peppas, N. A.. Preparation and dynamic response of cationic copolymer hydrogels containing glucose oxidase. Polymer, 41:3975-3983, 2000.

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