Selected Publications
Recent Publications
- Ethan N. H. Phan and Chi H. Mak, (2016) “Free energy landscapes of RNA two- and three-way junctions,” RNA (submitted).
- 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
- Chi H. Mak, (2016) “Unraveling base stacking driving forces in DNA," J. Phys. Chem. B 120, 6010-6020. DOI:10.1021/acs.jpcb.6b01934
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Chi H. Mak, (2012) “The Loops MC program suite: An all-purpose RNA simulation package”, available to academic researchers under the GPL license.
- 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
- 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.
- 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
- 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
- C.H. Mak, (2008) “RNA conformational sampling: I. Single nucleotide loop closure,” J. Comput. Chem., 29, 926. DOI:10.1002/jcc.20851
- 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
- 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
- Mak, C. H. (2006) "A large-scale simulation of two-dimensional melting of hard discs," Phys. Rev. E 73 , 065104-065104.
- Mak, C. H., (2005) "Stochastic potential switching algorithm for Monte Carlo simulations of complex systems," J. Chem. Phys. 122 , 214110-214110.
- Mak, C. H., Zakharov, S. and Spry, D. B. (2005) "Superfluidity in CH4-doped H2 nanoclusters," J. Chem. Phys. 122 , 104301-104301.