Kyung Hyuk Kim
Kids game "Spaceship Control" I made this C++ program for my son by using the Allegro library.
My research specialty is in computational and mathematical analysis
of stochastic and deterministic biological models, specializing in the
field of systems and synthetic biology. In recent years, gene regulatory networks have
been synthetically designed and implemented for both basic research and
specific application. Unlike other engineered systems such as electrical circuits or
mechanical devices, cellular networks are inherently noisy due to the molecular
nature of biochemical reaction events. This inherent stochasticity makes it difficult
to characterize the functions of engineered cellular networks. In addition, context
dependency and undesirable cross-talk between synthetic and natural systems
make the characterization even more difficult. The noise can however be useful
and exploited in systems ranging from cellular differentiation and viral fate
decision, to system input-output responses.
During my doctoral studies, I conducted mathematical and computational
(Monte-Carlo simulations) analyses on non-equilibrium stochastic processes
under the direction of both Prof. den Nijs (Physics, University of Washington) and Prof. Qian (Applied Mathematics, University of Washington). In my post-doctoral research, my main effort has been investigating
stochastic biological networks with regard to modularity and stochasticity,
by using my inter-disciplinary background knowledge and skills developed in
physics and applied mathematics. I have been taking a leading role in
supporting computational and mathematical research conducted by the group of Prof.
Herbert Sauro (Bioengineering, University of Washington), in particular,
focusing on synthetic network design and analysis. All my post-doctoral
work was supported by an NSF grant in Theoretical Biology (awarded $660K), for
which I wrote the main research plan.
Gene regulatory networks: - Modularity
- Applied the engineering concept of fan-out to gene regulatory networks for quantifying the degree of modularity (J. Biol. Eng).
- Proposed an experimental method for measuring fan-out and retroactivity based on gene expression noise (Biophys. J).
- Gene circuit analysis by mapping between gene regulatory networks and analog electrical circuits (future work, J. Biol. Eng).
- Stochasticity
- "Stochastic Control Analysis" (SCA): Developed a sensitivity analysis method for adjusting phenotypes by noise control (PLoS Computational Biology, Mathematical Biosciences).
- Analyzed noise propagation and its effect on system sensitivities in reaction networks (submitted work).
- Application of SCA to real biological systems such as stochastic switching in the HIV-1 long terminal repeat (LTR) promoter activity (future work).
- Inter-cellular interactions and cellular communities
- Provided a mathematical modeling and analysis of co-operative synthetic yeast strains in collaboration with Prof. Shou at the Fred Hutchinson Cancer Research Center (work in progress; reference).
- Evolution stability in synthetic genetic circuits
- Designing fitness landscapes for gene regulatory networks (future work).
- Characterizing and engineering cellular networks using stochastic measurements
- Experimental verification of fan-out and retroactivity; Noise control for desired system functions such as circuit response and signal-to-noise ratios (future work).
Metabolic networks: - Extended the metabolic control analysis (MCA) to the stochastic regime (PLoS Computational Biology, Mathematical Biosciences).
- Visualization of signal propagation in biological networks (work in progress).
- Metabolic flux optimization under the constraint of the total enzyme mass (work in progress).
Non-equilibrium statistical physics (graduate study): - Extended the Jarzynski equality and the fluctuation theorems for feed-back control systems (Physical Review E, Physical Review Letters)
- One-dimension stochastic flow (two-species asymmetric exclusion process) and its universal scaling behaviors (critical phenomena) and phase transition (Phys. Rev. E)
Publications K. H. Kim, H. Qian, and H. M. Sauro. Increasing the Sensitivity of Reaction Systems by Exploiting Stochastic Fluctuations. (Submitted) W. B. Copeland, D. Chandran, B. A. Bartley, M. Galdzicki, K. H. Kim, C. Maranas, S. C. Sleight, and H. M. Sauro. Computational Tools for Metabolic Engineering. (Submitted to Metabolic Engineering).
K. H. Kim and H. Qian. Fluctuation Theorems of a Molecular Refrigerator. Phys. Rev. E 75, 022102 (2007)
Book Chapters
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