USC.edu

Chiho Mak

Professor of Chemistry and Quantitative and Computational Biology
Email mak@tyrosine.usc.edu Office SSC 704 Office Phone (213) 740-4101

Center, Institute & Lab Affiliations

  • Center for Applied Mathematical Sciences,

Education

  • Ph.D. Stanford University, 1988
  • B.S. University of California, Berkeley, 1984
    • Postdoctoral Research Fellow, University of California, Berkeley, 1988 – 1990

  • Summary Statement of Research Interests

    Professor Mak studies and develops theoretical methods to understand the role of quantum mechanics in chemical processes occurring in clusters, liquids and proteins. He carries out computer simulations to study these processes, providing accurate solutions to the quantum dynamics of these systems. In the last few years, his research has continually pushed the capabilities of path integral simulations to new frontiers. He is currently studying computerized alternatives to determine the tertiary structures of RNAs and proteins. His “RNA folding” research is aimed at developing novel computer algorithms that are capable of predicting the tertiary structures of RNAs from their primary sequences alone.

    Research Keywords

    quantum dynamics and tunneling in condensed phases, electron transfer reactions in solution, biological and solid state systems, interfacial properties of polymer blends and solutions, RNA and protein folding and tertiary structures

  • Journal Article

    • Mak, C. H. (2011). Loops MC: An All-Atom Monte Carlo Simulation Program for RNAs Based on Inverse Kinematic Loop Closure. Molecular Simulation. Vol. 37 (7), pp. 537-556.
    • Mak, C. H., Chung, W., Markivskiy, N. D. (2011). RNA Conformational Sampling: II. Arbitrary-Length Multi-Nucleotide Loop Closure. Journal of Chemical Theory and Computation. Vol. 7 (4), pp. 1198-1207.
    • Mak, C. H. (2009). The sign problem in real-time path integral simulations: Using the cumulant action to implement multilevel blocking. Journal of Chemical Physics. Vol. 131 (4), pp. 044125.
    • Markovskiy, N. D., Mak, C. H. (2009). Path Integral Studies of the Rotations of Methane and Its Heavier Isotopomers in He-4 Nanoclusters. Journal of Physical Chemistry A. Vol. 113 (32), pp. 9165-9173.
    • Mak, C. H. (2008). RNA conformational sampling. I. Single-nucleotide loop closure. Journal of Computational Chemistry. Vol. 29 (6), pp. 926-933.
    • Mak, C. H., Sharma, A. K. (2007). Reverse monte carlo method and its implications for generalized cluster algorithms. Phys. Rev. Lett.. Vol. 98
    • Mak, C. H. (2006). Large-scale simulations of the two-dimensional melting of hard disks. Phys. Rev. E. Vol. 73
    • Mak, C. H., Zakharov, S., Spry, D. B. (2005). Superfluidity in CH4-doped H-2 nanoclusters. J. Chem. Phys.. Vol. 122
    • Mak, C. H. (2005). Stochastic potential switching algorithm for Monte Carlo simulations of complex systems. J. Chem. Phys.. Vol. 122
    • Mak, C. H. (2004). A multigrid algorithm for sampling imaginary-time paths in quantum Monte Carlo simulations. J. Phys. Chem. B. Vol. 108, pp. 6760-6766.
    • USC Associates Award For Excellence In Teaching, 2008-2009
    • USC Provost’s Teaching with Technology Prize, 2007-2008
    • NIH/NSF Career Development Award, 1992 – 1997
    • Dreyfus Award, 1994
    • Sloan Research Fellowship Recipient, 1991 – 1993
    • USC Zumberge Research and Innovation Fund Award, 1990-1991
    • Dreyfus Award, 1990
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