Selected Publications

Recent Publications

  1. Ethan N. H. Phan and Chi H. Mak, (2016) “Free energy landscapes of RNA two- and three-way junctions,” RNA (submitted).
  2. 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, (2016) “Solvent Thermodynamic Driving Force Controls Stacking Interactions between Polyaromatics," J. Phys. Chem. C 120, 23858–23869. DOI: 10.1021/acs.jpcc.6b08292
  3. Chi H. Mak, (2016) “Unraveling base stacking driving forces in DNA," J. Phys. Chem. B 120, 6010-6020. DOI:10.1021/acs.jpcb.6b01934
  4. Gayan Senavirathne, Jeff Bertram, Malgorzata Jaszcuzur, Phuong Pham, Chi H. Mak, Myron F. Goodman and David Rueda, (2015) “Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution,” Nature Comm.6, 10209. DOI:10.1038/ncomms10209
  5. Paul S. Henke and Chi H. Mak, (2016) “An implicit counterion force field for RNA molecular dynamics simulations,” J. Chem. Phys. 144, 105104.  DOI:10.1063/1.4943387
  6. Chi H. Mak, Phuong Pham, Samir A. Afif and Myron F. Goodman, (2015) “Random-walk enzymes,” Phys. Rev. E 92, 032717. DOI:10.1103/PhysRevE.92.032717
  7. Chi H. Mak, (2015) “An 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. DOI:10.1021/acs.jpcb.5b08077
  8. Chi H. Mak, Levanna L. Sani and Amber N. Villa, (2015) “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. DOI:10.1021/acs.jpcb.5b04839
  9. Paul S. Henke and Chi H. Mak, (2014) “Free energy of RNA-counterion interactions in a tight-binding model computed by a discrete space mapping,” J. Chem. Phys. 141, 064116. DOI:10.1063/1.4892059
  10. Chi H. Mak, Tyler Matossian and Wen-Yeuan Chung, (2014) “Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy,” Biophysical J. 106, 1497. DOI:10.1016/j.bpj.2014.02.015
  11. Chi H. Mak, Phuong Pham, Samir A. Afif and Myron F. Goodman, (2013) “Mathematical model for scanning and catalysis on single-stranded DNA, Illustrated with activation-induced deoxycytidine deaminase,” J. Biol. Chem. 288, 29786. [J. Biol. Chem. Paper of the Week] DOI:10.1074/jbc.M113.506550
  12. C. H. Mak and Paul Henke, (2013) “Ions and RNAs: Free energies of counterion-mediated RNA fold stabilities,” J. Chem. Theory Comput., 9, 621. DOI:10.1021/ct300760y
  13. Chi H. Mak, (2012) “The Loops MC program suite: An all-purpose RNA simulation package”, available to academic researchers under the GPL license.
  14. C.H. Mak, Wen-Yeuan Chung and Nikolay D. Markovskiy, (2011) “RNA conformational sampling: II. Arbitrary length multinucleotide loop closure,” J. Chem. Theory Comput., 7, 1198. DOI:10.1021/ct100681j
  15. C.H. Mak, (2011) “Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure,” Molec. Simulat. 37, 537.
  16. C.H. Mak, (2009) “The sign problem in real-time path integral simulations: Using the cumulant action to implement multi-level blocking,” J. Chem. Phys., 131, 044125. DOI:10.1063/1.3193706
  17. Nikolay D. Markovsky and C.H. Mak, (2009) “Path integral studies of the rotations of methane and its heavier isotopomers in 4He nanoclusters,” J. Phys. Chem. A, 113, 9165. DOI:10.1021/jp900718d
  18. C.H. Mak, (2008) “RNA conformational sampling: I. Single nucleotide loop closure,” J. Comput. Chem., 29, 926. DOI:10.1002/jcc.20851
  19. C.H. Mak, (2007) “A large-scale simulation of two-dimensional melting of hard discs,” Phys. Rev. E, 73, 065104. DOI:10.1103/PhysRevE.73.065104
  20. C.H. Mak and Arun K. Sharma, (2007) “Reverse Monte Carlo method and its implications for generalized cluster algorithms,” Phys. Rev. Lett., 98, 180602. DOI:10.1103/PhysRevLett.98.180602
  21. Mak, C. H. (2006) "A large-scale simulation of two-dimensional melting of hard discs," Phys. Rev. E 73 , 065104-065104.
  22. Mak, C. H., (2005) "Stochastic potential switching algorithm for Monte Carlo simulations of complex systems," J. Chem. Phys. 122 , 214110-214110.
  23. Mak, C. H., Zakharov, S. and Spry, D. B. (2005) "Superfluidity in CH4-doped H2 nanoclusters," J. Chem. Phys. 122 , 104301-104301.
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