Selected Publications

Publications

  1. Zhen, K. J., Khan, M. M., Mak, C. H., Lewis, K. B. & Somorjai, G. A. Partial Oxidation of Methane with Nitrous-Oxide over V2o5-Sio2 Catalyst. J Catal 94, 501-507 (1985).
  2. Deckert, A. A., Brand, J. L., Mak, C. H. & George, S. M. The Decomposition Kinetics of Methanol on Ru(001) Studied Using Laser-Induced Thermal-Desorption. Abstr Pap Am Chem S 192, 124-Coll (1986).
  3. Deckert, A. A., Brand, J. L., Mak, C. H. & George, S. M. Decomposition of Methanol on Ru(001) Studied Using Laser-Induced Thermal-Desorption. J Opt Soc Am B 3, P68-P69 (1986).
  4. Mak, C. H., Brand, J. L., Deckert, A. A. & George, S. M. Surface-Diffusion of Hydrogen on Ru(001) Studied Using Laser-Induced Thermal-Desorption. J Chem Phys 85, 1676-1680 (1986).
  5. Mak, C. H., Brand, J. L., Deckert, A. A. & George, S. M. Surface-Diffusion of Hydrogen on Ru(001) Studies Using Laser-Induced Thermal-Desorption. J Opt Soc Am B 3, P150-P151 (1986).
  6. Mak, C. H. & George, S. M. A Simplified Method to Determine the Coverage Dependence of Surface-Diffusion Coefficients. Surf Sci 172, 509-523 (1986).
  7. Deckert, A. A., Brand, J. L., Mak, C. H., Koehler, B. G. & George, S. M. The Decomposition of Methanol on Ru(001) Studied Using Laser-Induced Thermal-Desorption. J Chem Phys 87, 1936-1947 (1987).
  8. Deckert, A. A., Brand, J. L., Mak, C. H., Koehler, B. G. & George, S. M. The Decomposition Kinetics of Methanol on Ru(001) Studied Using Laser-Induced Thermal-Desorption. J Vac Sci Technol A 5, 518-519 (1987).
  9. Mak, C. H., Brand, J. L., Deckert, A. A., Koehler, B. G. & George, S. M. Surface-Diffusion Measured Using Laser-Induced Thermal-Desorption. Abstr Pap Am Chem S 194, 171-Phys (1987).
  10. Mak, C. H., Brand, J. L., Koehler, B. G. & George, S. M. Coverage Dependence of the Surface-Diffusion Coefficient for Hydrogen on Ru(001). Surf Sci 191, 108-120 (1987).
  11. Mak, C. H., Brand, J. L., Koehler, B. G. & George, S. M. Isotope Effect in the Surface-Diffusion of Hydrogen and Deuterium on Ru(001). Surf Sci 188, 312-320 (1987).
  12. Mak, C. H. & George, S. M. Surface-Diffusion of Hydrogen on Ru(001) - Transition-State Theory Calculations. Chem Phys Lett 135, 381-386 (1987).
  13. Mak, C. H., Koehler, B. G., Brand, J. L. & George, S. M. Surface-Diffusion of Hydrogen on Carbon-Covered Ru(001) Surfaces Studied Using Lasear-Induced Thermal-Desorption. J Chem Phys 87, 2340-2345 (1987).
  14. Brand, J. L., Mak, C. H., Deckert, A. A., Koehler, B. G. & George, S. M. Surface-Diffusion of Hydrogen on Carbon-Covered and Sulfur-Covered Ru(001) Studied Using Laser-Induced Thermal-Desorption. J Vac Sci Technol A 6, 842-843 (1988).
  15. George, S. M. et al. Kinetics of Diffusion and Desorption on Chemically-Modified Ru(001) Surfaces. Abstr Pap Am Chem S 195, 163-Coll (1988).
  16. Gupta, P., Mak, C. H., Coon, P. A. & George, S. M. Oxidation-Kinetics of Silicon Surfaces in the Submonolayer Regime. Abstr Pap Am Chem S 196, 162-Coll (1988).
  17. Koehler, B. G., Mak, C. H., Arthur, D. A., Coon, P. A. & George, S. M. Desorption-Kinetics of Hydrogen and Deuterium from Si(111) 7x7 Studied Using Laser-Induced Thermal-Desorption. J Chem Phys 89, 1709-1718 (1988).
  18. Mak, C. H., Andersen, H. C. & George, S. M. Monte-Carlo Studies of Diffusion on Inhomogeneous Surfaces. J Chem Phys 88, 4052-4061 (1988).
  19. Mak, C. H., Deckert, A. A. & George, S. M. Effects of Coadsorbed Carbon-Monoxide on the Surface-Diffusion of Hydrogen on Ru(001). J Chem Phys 89, 5242-5250 (1988).
  20. Mak, C. H., Koehler, B. G. & George, S. M. Surface-Diffusion of Cycloalkanes on Ru(001). J Vac Sci Technol A 6, 856-857 (1988).
  21. Gupta, P., Mak, C. H., Coon, P. A. & George, S. M. Oxidation-Kinetics of Si(111) 7x7 in the Submonolayer Regime. Phys Rev B 40, 7739-7749 (1989).
  22. Koehler, B. G., Mak, C. H. & George, S. M. Decomposition of H2o on Si(111)7 X 7 Studied Using Laser-Induced Thermal-Desorption. Surf Sci 221, 565-589 (1989).
  23. Mak, C. H., Koehler, B. G. & George, S. M. Laser-Induced Thermal-Desorption of Silicon-Containing Surface-Reaction Intermediates from Si(111)7x7. Surf Sci 208, L42-L52 (1989).
  24. Mak, C. H. & Andersen, H. C. Low-Temperature Approximations for Feynman Path-Integrals and Their Applications in Quantum Equilibrium and Dynamic Problems. J Chem Phys 92, 2953-2965 (1990).
  25. Mak, C. H. & Chandler, D. Solving the Sign Problem in Quantum Monte-Carlo Dynamics. Phys Rev A 41, 5709-5712 (1990).
  26. Mak, C. H. & Chandler, D. Coherent-Incoherent Transition and Relaxation in Condensed-Phase Tunneling Systems. Phys Rev A 44, 2352-2369 (1991).
  27. Mak, C. H. Stochastic Method for Real-Time Path Integrations. Phys Rev Lett 68, 899-902 (1992).
  28. Egger, R. & Mak, C. H. Quantum Monte-Carlo Simulations of Tunneling in Electron-Transfer Systems. Abstr Pap Am Chem S 206, 237-Phys (1993).
  29. Egger, R. & Mak, C. H. Dynamical Effects in the Calculation of Quantum Rates for Electron-Transfer Reactions. J Chem Phys 99, 2541-2549 (1993).
  30. Mak, C. H. & Gehlen, J. N. A Dynamic Test of the Centroid Formulation of Quantum Transition-State Theory for Electron-Transfer Reactions. Chem Phys Lett 206, 130-136 (1993).
  31. Egger, R. & Mak, C. H. Low-Temperature Dynamical Simulation of Spin-Boson Systems. Phys Rev B 50, 15210-15220 (1994).
  32. Egger, R. & Mak, C. H. Dissipative 3-State System and the Primary Electron-Transfer in the Bacterial Photosynthetic Reaction-Center. J Phys Chem-Us 98, 9903-9918 (1994).
  33. Egger, R., Mak, C. H. & Weiss, U. Rate Concept and Retarded Master-Equations for Dissipative Tight-Binding Models. Phys Rev E 50, R655-R658 (1994).
  34. Egger, R., Mak, C. H. & Weiss, U. Quantum Rates for Nonadiabatic Electron-Transfer. J Chem Phys 100, 2651-2660 (1994).
  35. Mak, C. H. & Egger, R. Macroscopic Manifestation of Quantum Coherence in Condensed-Phase Reactions. Abstr Pap Am Chem S 208, 43-Phys (1994).
  36. Mak, C. H. & Egger, R. Quantum Monte-Carlo Study of Tunneling Diffusion in a Dissipative Multistate System. Phys Rev E 49, 1997-2008 (1994).
  37. Yang, W. & Mak, C. H. Transferable Tight-Binding Potential for Reactive Systems in Condensed-Phase. Abstr Pap Am Chem S 208, 371-Phys (1994).
  38. Leung, K., Egger, R. & Mak, C. H. Dynamical Simulation of Transport in One-Dimensional Quantum Wires. Phys Rev Lett 75, 3344-3347 (1995).
  39. Liu, A. J., Drovetsky, B. & Mak, C. H. Nematic-Isotropic Interfaces in Semiflexible Blends. Abstr Pap Am Chem S 209, 166-Phys (1995).
  40. Mak, C. H. & Egger, R. On the Mechanism of the Primary Charge Separation in Bacterial Photosynthesis. Chem Phys Lett 238, 149-155 (1995).
  41. Wang, Y. & Mak, C. H. Transferable Tight-Binding Potential for Hydrocarbons. Chem Phys Lett 235, 37-46 (1995).
  42. Mak, C. H. & Egger, R. Monte Carlo methods for real-time path integration. Adv Chem Phys 93, 39-76 (1996).
  43. Mak, C. H. & Stockburger, J. T. Slow modes and electron transfer: The real(-time) story. Abstr Pap Am Chem S 212, 321-Phys (1996).
  44. Stockburger, J. T. & Mak, C. H. A dynamical theory of electron transfer: Crossover from weak to strong electronic coupling. J Chem Phys 105, 8126-8135 (1996).
  45. Belyaev, V. V. & Mak, C. H. Quantum conduction mechanisms in polyene molecular wires. Abstr Pap Am Chem S 213, 334-Phys (1997).
  46. Chu, J. C. & Mak, C. H. Large-scale molecular dynamics studies of the adsorption of polyelectrolytes onto charged surfaces. Abstr Pap Am Chem S 213, 345-Phys (1997).
  47. Lucke, A. et al. The direct observation of electronic coherence in electron transfer reactions possible? J Chem Phys 107, 8397-8408 (1997).
  48. Drovetsky, B. Y., Chu, J. C. & Mak, C. H. Computer simulations of self-avoiding polymerized membranes. J Chem Phys 108, 6554-6557 (1998).
  49. Luck, A., Winterstetter, M., Weiss, U. & Mak, C. H. Quantum Monte Carlo simulations of driven spin-boson systems. Phys Rev E 58, 5565-5573 (1998).
  50. Mak, C. H., Egger, R. & Weber-Gottschick, H. Multilevel blocking approach to the fermion sign problem in path-integral Monte Carlo simulations. Phys Rev Lett 81, 4533-4536 (1998).
  51. Stockburger, J. T. & Mak, C. H. Dynamical simulation of current fluctuations in a dissipative two-state system. Phys Rev Lett 80, 2657-2660 (1998).
  52. Chu, J. C. & Mak, C. H. Inter- and intrachain attractions in solutions of flexible polyelectrolytes at nonzero concentration. J Chem Phys 110, 2669-2679 (1999).
  53. Drovetsky, B. Y., Liu, A. J. & Mak, C. H. Nematic-isotropic interfaces in semiflexible polymer blends. J Chem Phys 111, 4334-4342 (1999).
  54. Egger, R., Hausler, W., Mak, C. H. & Grabert, H. Crossover from fermi liquid to wigner molecule behavior in quantum dots (vol 82, pg 3320, 1999). Phys Rev Lett 83, 462-462 (1999).
  55. Egger, R., Hausler, W., Mak, C. H. & Grabert, H. Crossover from fermi liquid to Wigner molecule behavior in quantum dots. Phys Rev Lett 82, 3320-3323 (1999).
  56. Lucke, A., Mak, C. H. & Stockburger, J. T. Semiclassical dynamics of nonadiabatic transitions in discrete-state systems using spin coherent-state path integrals. J Chem Phys 111, 10843-10851 (1999).
  57. Mak, C. H. & Egger, R. A multilevel blocking approach to the sign problem in real-time quantum Monte Carlo simulations. J Chem Phys 110, 12-14 (1999).
  58. Stockburger, J. T. & Mak, C. H. Stochastic Liouvillian algorithm to simulate dissipative quantum dynamics with arbitrary precision. J Chem Phys 110, 4983-4985 (1999).
  59. Egger, R., Muhlbacher, L. & Mak, C. H. Path-integral Monte Carlo simulations without the sign problem: Multilevel blocking approach for effective actions. Phys Rev E 61, 5961-5966 (2000).
  60. Mak, C. H., Chung, Y. Y. Y. & Ko, R. C. Single-stranded endonuclease activity in the excretory-secretory products of Trichinella spiralis and Trichinella pseudospiralis. Parasitology 120, 527-533 (2000).
  61. Mak, C. H. & Dikovsky, M. Proton tunneling dynamics simulation with ten explicit degrees of freedom. Abstr Pap Am Chem S 220, U191-U191 (2000).
  62. Mak, C. H. & Zini, L. R. New algorithm for the ab initio folding of small globular proteins. Abstr Pap Am Chem S 220, U173-U173 (2000).
  63. Dikovsky, M. V. & Mak, C. H. Analysis of the multilevel blocking approach to the fermion sign problem: Accuracy, errors, and practice. Phys Rev B 63 (2001).
  64. Egger, R. & Mak, C. H. Multilevel blocking Monte Carlo simulations for quantum dots. Int J Mod Phys B 15, 1416-1425 (2001).
  65. Mak, C. H. Superfluidity in CH4-doped H2 nanoclusters. Abstr Pap Am Chem S 228, U273-U273 (2004).
  66. Mak, C. H. A multigrid algorithm for sampling imaginary-time paths in quantum Monte Carlo simulations. J Phys Chem B 108, 6760-6766 (2004).
  67. Cheney, B. G. & Mak, C. H. A new method for large-scale Monte Carlo simulations of water and aqueous solutions. Abstr Pap Am Chem S 229, U749-U750 (2005).
  68. Mak, C. H. Stochastic potential switching algorithm for Monte Carlo simulations of complex systems. J Chem Phys 122 (2005).
  69. Mak, C. H., Zakharov, S. & Spry, D. B. Superfluidity in CH4-doped H-2 nanoclusters. J Chem Phys 122 (2005).
  70. Mak, C. H. Large-scale simulations of the two-dimensional melting of hard disks. Phys Rev E 73 (2006).
  71. Mak, C. H., Poon, M. W., Lun, H. M., Kwok, P. Y. & Ko, R. C. Heat-inducible translationally controlled tumor protein of Trichinella pseudospiralis: cloning and regulation of gene expression. Parasitol Res 100, 1105-1111 (2007).
  72. Mak, C. H. & Sharma, A. K. Reverse monte carlo method and its implications for generalized cluster algorithms. Phys Rev Lett 98 (2007).
  73. Mak, C. H. RNA conformational sampling. I. Single-nucleotide loop closure. J Comput Chem 29, 926-933 (2008).
  74. Mak, C. H. The sign problem in real-time path integral simulations: Using the cumulant action to implement multilevel blocking. J Chem Phys 131 (2009).
  75. Markovskiy, N. D. & Mak, C. H. Path Integral Studies of the Rotations of Methane and Its Heavier Isotopomers in He-4 Nanoclusters. J Phys Chem A 113, 9165-9173 (2009).
  76. Mak, C. H. Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure. Mol Simulat 37, 537-556 (2011).
  77. Mak, C. H., Chung, W. Y. & Markovskiy, N. D. RNA Conformational Sampling: II. Arbitrary Length Multinucleotide Loop Closure. J Chem Theory Comput 7, 1198-1207 (2011).
  78. Farhi, A. et al. Temperature Integration: An efficient procedure for calculation of free energy differences. Physica A 392, 5836-5844 (2013).
  79. Mak, C. H. & Henke, P. S. Ions and RNAs: Free Energies of Counterion-Mediated RNA Fold Stabilities. J Chem Theory Comput 9, 621-639 (2013).
  80. Mak, C. H., Pham, P., Afif, S. A. & Goodman, M. F. A Mathematical Model for Scanning and Catalysis on Single-stranded DNA, Illustrated with Activation-induced Deoxycytidine Deaminase. J Biol Chem 288, 29786-29795 (2013).
  81. Henke, P. S. & Mak, C. H. Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping. J Chem Phys 141 (2014).
  82. Henke, P. S. & Mak, C. H. Exploring the Energy Landscape of RNA: A Direct Evaluation of the Counterion Mediated Free Energy. Biophys J 106, 280a-280a (2014).
  83. Mak, C. H., Matossian, T. & Chung, W. Y. Conformational Entropy of the RNA Phosphate Backbone and Its Contribution to the Folding Free Energy. Biophys J 106, 1497-1507 (2014).
  84. Mak, C. H. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures. J Phys Chem B 119, 14840-14856 (2015).
  85. Mak, C. H., Pham, P., Afif, S. A. & Goodman, M. F. Random-walk enzymes. Phys Rev E 92, 032717 (2015).
  86. Mak, C. H., Sani, L. L. & Villa, A. N. Residual Conformational Entropies on the Sugar-Phosphate Backbone of Nucleic Acids: An Analysis of the Nucleosome Core DNA and the Ribosome. J Phys Chem B 119, 10434-10447 (2015).
  87. Senavirathne, G. et al. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun 6, 10209 (2015).
  88. Paul S. Henke and Chi H. Mak, An implicit counterion force field for RNA molecular dynamics simulations, J. Chem. Phys. 144, 105104 (2016).
  89. Chi H. Mak, “Unraveling base stacking driving forces in DNA," J. Phys. Chem. B 120, 6010-6020 (2016).
  90. Aaron S. Rury, Christine Ferry, Jonathan Ryan Hunt, Myungjin Lee, Dibyendu Mondal, Sean M. O. O’Connell, Ethan N. H. Phan, Zaili Peng, Pavel Pokhilko, Daniel Sylvinson, Yingsheng Zhou, and Chi H. Mak, Solvent Thermodynamic Driving Force Controls Stacking Interactions between Polyaromatics, J. Phys. Chem. C 120, 23858–23869. DOI: 10.1021/acs.jpcc.6b08292
  91. Ethan N. H. Phan and Chi H. Mak, Free energy landscapes of RNA two- and three-way junctions, RNA, submitted (2016).