Zhong-Can Ou-Yang

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Using polymer elastic theory and known RNA free energies, we construct a Monte Carlo algorithm to simulate the single RNA folding and unfolding by mechanical force on the secondary structure level. For the constant force ensemble, we simulate the force-extension curves of the P5ab, P5abc deltaA, and P5abc molecules in equilibrium. For the constant extension(More)
We establish a sequence-dependent kinetic model for the later stage of transcription initiation by RNA polymerase. We suggest that there are three reaction pathways, the abortive pathway, the scrunching pathway and the escape pathway, competitive with each other at each site during the transcription initiation. Using this three-pathway model, we mainly(More)
The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiments showed that the waiting time distribution and other properties of single enzyme molecules were not consistent with the prediction based on the ensemble viewpoint. They have contributed to the slow(More)
– The maximum matching problem on random graphs is studied analytically by the cavity method of statistical physics. When the average vertex degree c is larger than 2.7183, groups of max-matching patterns which differ greatly from each other gradually emerge. An analytical expression for the max-matching size is also obtained, which agrees well with(More)
Peptide-based self-assembling systems are increasingly attractive because of their wide range of applications in different fields. Peptide nanostructures are flexible with changes in the ambient conditions. Herein, a reversible shape transition between self-assembled dipeptide nanotubes (DPNTs) and vesicle-like structures is observed upon a change in the(More)
Recently experiments showed that some biological noncovalent bonds increase their lifetimes when they are stretched by an external force, and their lifetimes will decrease when the force increases further. Several specific quantitative models have been proposed to explain the intriguing transitions from the "catch bond" to the "slip bond." In this work we(More)
We study the general energy and shape of the two-dimensional solid monolayer domains with the dipole-dipole interactions. Compared with the domain energy without tilted dipole moments [M. Iwamoto and Z. C. Ou-Yang, Phys. Rev. Lett. 93, 206101 (2004)], the general dipolar energy is not only shape and size but also boundary orientation dependent. The general(More)
Recent experiments found that some adhesive receptor-ligand complexes have counterintuitive catch-slip transition behaviors: the mean lifetimes of these complexes first increase (catch) with initial application of a small external force, and then decrease (slip) when the force is beyond some threshold. In this work we suggest that the forced dissociation of(More)
Using simple polymer elastic theory and known RNA free energies, we study the single RNA folding and unfolding on the secondary structure level under mechanical constant force by stochastic kinetic simulation. As a primary application, this method is used to simulate the experiment performed by Science 292, 733 (2001)]. The extension-force curves in(More)
We develop a continue time Monte Carlo algorithm to simulate single RNAs unfolded by a time-dependent external force on the secondary structure level. Two recent unfolding RNA experiments carried out by Bustamante group are mainly investigated. We find that, in contrast to popular two-state assumption about the RNAs free energy landscape along the molecular(More)