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  • C H Mak
  • 2006
Large-scale computer simulations with more than four million particles have been performed to study the melting transition in a two-dimensional hard disk fluid. The van der Waals loop previously observed in the pressure-density relationship of smaller simulations is shown to disappear systematically with increase in sample size, but even with these large(More)
We formulated a master equation-based mathematical model to analyze random scanning and catalysis for enzymes that act on single-stranded DNA (ssDNA) substrates. Catalytic efficiencies and intrinsic scanning distances are deduced from the distribution of positions and gap lengths between a series of catalytic events occurring over time, which are detected(More)
Activation-induced deoxycytidine deaminase (AID) generates antibody diversity in B cells by initiating somatic hypermutation (SHM) and class-switch recombination (CSR) during transcription of immunoglobulin variable (IgV) and switch region (IgS) DNA. Using single-molecule FRET, we show that AID binds to transcribed dsDNA and translocates unidirectionally in(More)
  • Chi H Mak
  • 2016
Base stacking is a key determinant of nucleic acid structures, but the precise origin of the thermodynamic driving force behind the stacking of nucleobases remains open. The rather mild stacking free energy measured experimentally, roughly a kcal/mol depending on the identity of the bases, is physiologically significant because while base stacking confers(More)
  • C H Mak
  • 2005
This paper describes a new Monte Carlo method based on a novel stochastic potential switching algorithm. This algorithm enables the equilibrium properties of a system with potential V to be computed using a Monte Carlo simulation for a system with a possibly less complex stochastically altered potential V. By proper choices of the stochastic switching and(More)
Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above.(More)
  • C. H. Mak
  • 2008
We consider the loop-closure problem for nucleic acids and describe an efficient numerical algorithm for closing single-nucleotide loops in nucleic acids. Using six new internal coordinates to represent the nucleotide conformation, which we call the R-representation, the original closure problem with six free torsion angles in each nucleotide can be reduced(More)
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA(More)
A nucleic acid folds according to its free energy, but persistent residual conformational fluctuations remain along its sugar-phosphate backbone even after secondary and tertiary structures have been assembled, and these residual conformational entropies provide a rigorous lower bound for the folding free energy. We extend a recently reported algorithm to(More)
We present an implicit ion model fo the calculation of the electrostatic free energies of RNA conformations in the presence of divalent counterions such as Mg(2+). The model was applied to the native and several non-native structures of the hammerhead ribozyme and the group I intron in Tetrahymena to study the stability of candidate unfolding intermediates.(More)