Moon Ki Kim
Assistant Professor, Dept. of Mechanical and Industrial Engineering
207B Engineering Laboratory, University of Massachusetts
Amherst, MA 01003-9292
(413) 545-2357
mkkim@ecs.umass.edu
http://biomechanics.ecs.umass.edu/
Computational Theoretical Biology
My current research interests include computational structural biology, computer-aided medical robot, and bioMEMS. I have been working on computational structural biology with various mechanical engineering tools to tackle biological problems. Using the fundamentals of mechanical engineering, we cannot only develop computationally efficient methods for molecular dynamics simulations, but also establish theoretical principles which may elucidate the biological function of a macromolecule from its structure, as well as protein folding theory. For example, I have successfully done harmonic and/or anharmonic analysis to generate feasible reaction pathways between two different conformations of a macromolecule.
| Research Interest | Potential Application |
|---|---|
| Computational Theoretical Biology (Protein Dynamics, Gene Regulation) | Understanding of the relationship between structure and function in macromolecules. Computer simulation of the effect of new drug |
| Protein Folding Theory Based on Robot Kinematics | Conjecture of tertiary structure from primary sequence of a protein. Drug design |
| BioMEMS | Development of mechanochemical micro (or nano) systems for disease diagnosis and drug delivery |
| Robot Kinematics and Haptics | Fast searching algorithm for protein folding. Haptic-based medical instrument design |
| Computational Analysis of Nanoscale Structure | Simulation of static and dynamic properties of nanostructures |
Honors and Awards
- Graduate Research Fellowship, Johns Hopkins University, 2001
- Research Fellowship, Korea Science and Engineering Foundation, 1999
- Outstanding Thesis Award, Korean Society of Mechanical Engineers, 1998
- Graduate Research Fellowship, Seoul National University, 1997
- Fellowship from Ilju Scholarship and Culture Foundation, Korea, 1993
Publications
- Kim, M.K., Jernigan, R.L., Chirikjian, G.S., "Efficient Generation of Feasible Pathways for Protein Conformational Transitions", Biophysical Journal, Vol. 83, pp. 1620-1630, 2002.
- Kim, M.K., Chirikjian, G.S., Jernigan, R.L., “Elastic Models of Conformational Transitions in Macromolecules”, Journal of Molecular Graphics and Modelling, Vol. 21, pp. 151-160, 2002.
- Kim, M.K., Jernigan, R.L., Chirikjian, G.S., “An Elastic Network Model of HK97 Capsid Maturation”, Journal of Structural Biology, Vol. 143, pp. 107-117, 2003.
- Kim, M.K., Li, W., Shapiro, B.A., Chirikjian, G.S., “A Comparison between Elastic Network Interpolation and MD Simulation of 16S Ribosomal RNA”, Journal of Biomolecular Structure and Dynamics, Vol. 21, pp. 395-405, 2003.
- Kim, C.S., Hong, K.S., Kim, M.K., "Nonlinear Robust Control of a Hydraulic Elevator: Experiment-Based Modeling and Two-Stage Lyapunov Redesign", Control Engineering Practice, Vol 13, pp. 789-803, 2005.
- Kim, M.K., Jernigan, R.L., Chirikjian, G.S., "Rigid-Cluster Models of Conformational Transitions in Macromolecular Machines and Assemblies," Biophysical Journal, Vol. 89, pp. 1-13, 2005.
