Gunawan:Publications

Journal Articles

 * G. Jia and R. Gunawan. Parameter estimation of kinetic models from metabolic profiles:two-phase dynamic decoupling method. Bioinformatics., 27 (14) 1964-1970
 * Z. Y. Tam, Y. H. Cai and R. Gunawan. Elucidating cytochrome C release from mitochondria: insights from an in silico three-dimensional model. Biophys. J., 99:3155-3163, 2010. (cover article)
 * S. K. Poovathingal and R. Gunawan. Global parameter estimation of stochastic biochemical systems. BMC Bioinformatics, 11:414, 2010.
 * J. Gruber, S. K. Poovathingal, N. L. Fang, R. Gunawan and B. Halliwell. Caenorhabditis elegans lifespan studies: the challenge of maintaining synchronous cohorts, Rejuvenation Research, 13:347-349, 2010.
 * S. Srinath and R. Gunawan. Parameter identifiability of power-law biochemical system models. J. Biotechnol, 2010. 149:132-140, 2010.
 * S. K. Poovathingal, J. Gruber, B. Halliwell, and R. Gunawan. Stochastic drift in mitochondrial DNA point mutations: a novel perspective ex silico. PLoS Comput Biol, 5:e1000572, 2009. (featured research Nov 2009, listed in Faculty 1000 Biology)
 * T. M. Perumal, Y. Wu, and R. Gunawan. Dynamical analysis of cellular networks based on the Green’s function matrix. J. theor Biol, 261:248-259, 2009.
 * R. Gunawan, I. Fusman, and R. D. Braatz. Parallel high-resolution finite volume simulation of particulate processes. AIChE J., 54:1449-1458, 2008.
 * S. Taylor, R. Gunawan, L. R. Petzold, and F. J. Doyle III. Sensitivity measures for oscillating systems: application to mammalian circadian gene network. IEEE Trans. Automatic Control, 153:177-188, 2008.
 * R. Gunawan and F. J. Doyle III. Phase sensitivity analysis of circadian rhythm entrainment. J. Biol. Rhythms., 22:180-194, 2007.
 * 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. Circadian rhythm: A natural, robust, multi-scale control system.   Comp. & Chem. Eng., 30:1700-1711, 2006.
 * R. D. Braatz, R. C. Alkire, E. G. Seebauer, T. O. Drews, E. Rusli, M. Karulkar, F. Xue, Y. Qin, M. Y. L. Jung and R. Gunawan. A multiscale systems approach to microelectronics processes.   Comp. & Chem. Eng., 30:1643-1656, 2006.
 * R. D. Braatz, R. C. Alkire, E. G. Seebauer, E. Rusli, R. Gunawan, T. O. Drews, X. Li, and Y. He. Perspectives on the dynamics and control of multiscale systems. J. Process Control, 16:193-204, 2006.
 * K. Gadkar, R. Gunawan, and F. J. Doyle III. Iterative approach to model identification of biological networks. BMC Bioinformatics, 6:155-174, 2005.
 * R. Gunawan, Y. Cao, L. Petzold, and F. J. Doyle III. Sensitivity analysis of discrete stochastic system. Biophys. J., 88:2530-2540, 2005.
 * M. Y. L. Jung, R. Gunawan, R. D. Braatz, and E. G. Seebauer. Pair diffusion and kick-out: Contributions to diffusion of boron in silicon. AIChE J., 50:3248-3256, 2004.
 * R. Gunawan, I. Fusman, and R. D. Braatz. High resolution algorithms for multidimensional population balance equations. AIChE J., 50:2738-2749, 2004.
 * M. Y. L. Jung, R. Gunawan, R. D. Braatz, and E. G. Seebauer. Effect of near-surface band bending on dopant profiles in ion-implanted silicon. J. Appl. Phys., 95:1134-1140, 2004.
 * M. Y. L. Jung, R. Gunawan, R. D. Braatz, and E. G. Seebauer. A simplified picture for transient enhanced diffusion of boron in silicon. J. Electrochem. Soc., 151:G1-G7, 2004.
 * R. Gunawan, M. Y. L. Jung, E. G. Seebauer, and R. D. Braatz. Optimal control of rapid thermal annealing in a semiconductor process. J. Process Control, 14:423-430, 2004.
 * K. Dev, M. Y. L. Jung, R. Gunawan, R. D. Braatz, and E. G. Seebauer. Mechanism for coupling between properties of interfaces and bulk semiconductors. Phys. Rev. B., 68:195311-195316, 2003.
 * M. Y. L. Jung, R. Gunawan, R. D. Braatz, and E. G. Seebauer. Ramp-rate effects on transient enhanced diffusion and dopant activation. J. Electrochem. Soc., 150:G838-G842, 2003.
 * R. Gunawan, M. Y. L. Jung, R. D. Braatz, and E. G. Seebauer. Parameter sensitivity analysis applied to modeling transient enhanced diffusion and activation of boron in silicon. J. Electrochem. Soc., 150:G758-G765, 2003.
 * R. Gunawan, M. Y. L. Jung, E. G. Seebauer, and R. D. Braatz. Maximum a posteriori estimation of transient enhanced diffusion kinetics. AIChE J., 49:2114-2123, 2003.
 * R. Gunawan, D. L. Ma, M. Fujiwara, and R. D. Braatz. Identification of kinetic parameters in a multidimensional crystallization process. Int. J. Modern Phys. B, 16:367-374, 2002.
 * M. Fujiwara, J. C. Pirkle Jr., T. Togkalidou, D. L. Ma, R. Gunawan, and R. D. Braatz. A holistic approach to materials process design. J. Materials Edu., 24:65-70, 2002.
 * R. Gunawan, E. L. Russell, and R. D. Braatz. Comparison of theoretical and computational characteristics of dimensionality reduction methods for large scale uncertain systems. J. Process Control, 11:543-552, 2001.

Patent

 * “Methods for controlling dopant concentration and activation in semiconductor structures” with E. G. Seebauer, R. D. Braatz and M. Y. L. Jung, US Patent 7,846,822.

Book Chapter

 * H. Mirsky, J. Stelling, R. Gunawan, N. Bagheri, S. R. Taylor, E. Kwei, J. E. Shoemaker, and F. J. Doyle III. Automatic Control in Systems Biology. In S. Y. Nof (Ed.), Handbook of Automation, Springer-Verlag, 2009.
 * S. Hildebrandt, N. Bagheri, R. Gunawan, H. Mirsky, J. Shoemaker, S. Taylor, L. R. Petzold and F. J. Doyle III. Systems Analysis in Biological Networks. In E. T. Liu, G. P. Noland, and D. A. Lauffenburger (Eds.), Systems Biomedicine: Concepts and Prespectives, Academic Press, 2009.
 * R. Gunawan, K. Gadkar, and F. J. Doyle III. Methods to identify cellular architecture and dynamics from experimental data. In Z. Szallasi, V. Periwal, and J. Stelling (Eds.), System Modeling in Cellular Biology, MIT Press, 2006.
 * J. Shoemaker, R. Gunawan, and F. J. Doyle III. Model-based Optimal Experimental Design in Biological Systems. In J. Varner (Eds.), Methods in Molecular Biology: Caspases, to be published by Humana Press, 2006. in preparation
 * S. Hildebrandt, N. Bagheri, R. Gunawan, H. Mirsky, J. Shoemaker, S. Taylor, and F. J. Doyle III. Systems Analysis of Biological Networks in Systems Biology, to be published by Academic Press, 2006.

Peer reviewed Conference Proceedings

 * Suresh P, Gruber J, Halliwell B, and Gunawan R. (2010) Random Drift of Mitochondrial DNA Deletions in Sarcopenia, In 11th International Conference on Systems Biology'', Edinburgh, UK, Oct 11-15 (poster).


 * Suresh P, Gruber J, Halliwell B, and Gunawan R. (2010) Sarcopenia in silico, In AiChe annual general meeting, Salt Lake City, USA, Nov 7-12.


 * Suresh P, Gruber J, Halliwell B, Gunawan R. (2010) Elucidating Mechanisms of Age-dependent Accumulation of Mitochondrial DNA Deletions – An in silico Approach, In Gordon Research Conference on Biology of Aging, Switzerland, Aug 22-27. (poster).


 * Srinath S, Gunawan R. (2010) Parameter Identifiability of Metabolic Network Models, In Satellite Conference of the International Congress of Mathematics, Hyderabad, India, Aug 16-18


 * Perumal TM, Gunawan R. (2010) In analyzing the complex dynamics of biochemical pathways, In Satellite Conference of the International Congress of Mathematics, Hyderabad, India, Aug 16-18


 * Srinath S, Yuan Z, Gunawan R. (2010) Identifiability Analysis of Decoupled Power-Law Models, In 5th International Symposium on Design, Operation and Control of Chemical Processes (PSE Asia), Singapore, July 25-28


 * Gengjie J, Gunawan R. (2010) Parameter Estimation of Kinetic Models from Incomplete Metabolic Profiles, In 5th International Symposium on Design, Operation and Control of Chemical Processes (PSE Asia), Singapore, July 25-28


 * Srinath S, Gunawan R. (2010) Parameter Identifiability in Kinetic Modeling of Metabolic Pathways, In Metabolic Engineering Conference VIII, Jeju Island, South Korea, Jun 13 - 17 (poster)


 * Perumal TM, Gunawan R. (2009) Information transfer in Biological Network Motifs, In 10th International Conference on Systems Biology (ICSB), Stanford, California, USA, Aug 30 - Sep 4 (poster)


 * Suresh P, Gruber J, Halliwell B, Gunawan R. (2009) Stochasticity in mitochondrial DNA point mutation and its relevance in Caenorhabditis elegans Aging, In 10th International Conference on Systems Biology (ICSB), Stanford, California, USA, Aug 30 - Sep 4 (poster)


 * Perumal TM, Gunawan R. (2009) Information-theoretic global robustness analysis of cellular systems: A molecular perturbation approach, In Third International Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, USA, August 9 - 12, PP: 52 - 55 (poster)


 * Suresh P, Gruber J, Halliwell B, Gunawan R. (2009) A global approach for estimating the kinetic parameters of stochastic biological systems, In Third International Conference on Foundations of Systems Biology in Engineering (FOSBE), Denver, Colorado, USA, August 9 - 12, PP: 56 - 59 (poster)


 * Srinath S, Gunawan R . (2009) Identifiability Analysis of Metabolic Networks, In 11th International Conference on Molecular Systems Biology (ICMSB), Shanghai, China, June 21-25


 * Suresh P, Gruber J, Halliwell B, Gunawan R . (2008) Aging Studies: A Stochastic Approach in point mutation dynamics in mouse model In AiChe annual general meeting, Philadelphia, USA, Nov 16-21


 * Perumal TM, Yan W, Gunawan R . (2008) Robustness Analysis of Cellular Systems for In Silico Drug Discovery, In 17th World Congress - The International Federation of Automatic Control (IFAC), Seoul, Korea, July 6-11, PP: 12607-12612


 * Perumal TM, Yan W, Gunawan R. (2008) In Silico Dynamical Analysis of Cellular Systems: A Molecular Perturbation Approach, In 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Singapore, March 30 - April 2 (poster)


 * Suresh P, Gruber J, Halliwell B, Gunawan R. (2008) Aging Studies: A Stochastic Approach, In 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Singapore, March 30 - April 2 (poster)


 * Perumal TM, Yan W, Gunawan R . (2008) In Silico Molecular Analysis: Application to Fas-Induced Apoptotic Pathway, In 10th International Conference on Molecular Systems Biology (ICMSB)'', Manila, Philippines, February 25-28 (poster)


 * Perumal TM, Yan W, Gunawan R . (2007) In Silico Molecular Analysis: Application to the Fas-induced Apoptotic Pathway, In 8th International Conference on Systems Biology (ICSB), California, USA, October 1-6 (poster)