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- C H Mak
- Physical review. E, Statistical, nonlinear, and…
- 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)

- Chi H Mak
- The journal of physical chemistry. B
- 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)

- Chi H Mak, Phuong Pham, Samir A Afif, Myron F Goodman
- The Journal of biological chemistry
- 2013

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)

- Gayan Senavirathne, Jeffrey G Bertram, +5 authors David Rueda
- Nature communications
- 2015

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)

- C H Mak
- The Journal of chemical physics
- 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)

- C H Mak, Paul S Henke
- Journal of chemical theory and computation
- 2013

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)

- C H Mak, Wen-Yeuan Chung, Nikolay D Markovskiy
- Journal of chemical theory and computation
- 2011

In this paper, we describe how the inverse kinematic solution to the loop closure problem may be generalized to reclose a RNA segment of arbitrary length containing any number of nucleotides without disturbing the atomic positions of the rest of the molecule. This generalization is made possible by representing the boundary conditions of the closure in… (More)

- Chi H Mak, Phuong Pham, Samir A Afif, Myron F Goodman
- Physical review. E, Statistical, nonlinear, and…
- 2015

Enzymes that rely on random walk to search for substrate targets in a heterogeneously dispersed medium can leave behind complex spatial profiles of their catalyzed conversions. The catalytic signatures of these random-walk enzymes are the result of two coupled stochastic processes: scanning and catalysis. Here we develop analytical models to understand the… (More)

- C H Mak
- The Journal of chemical physics
- 2009

A practical method to tackle the sign problem in real-time path integral simulations is proposed based on the multilevel blocking idea. The formulation is made possible by using a cumulant expansion of the action, which in addition to addressing the sign problem, provides an unbiased estimator for the action from a statistically noisy sample of real-time… (More)

- Chi H Mak
- The journal of physical chemistry. B
- 2015

While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate… (More)