Biomedical subjects

Zhong-Can Ou-Yang

Publications and source records attributed to Zhong-Can Ou-Yang.

8 recordsLinked to original sources

PubMed2006

Collapse transition of two-dimensional flexible and semiflexible polymers.

The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive bending stiffness (Delta>0), the collapse transition is first order; it becomes second order only in the limiting case of zero bending stiffness (Delta triple bond 0). These analytical results are confirmed by Monte Carlo simulations. We also suggest some possible future experiments.

DNA↗

PubMed2006

Single molecule Michaelis-Menten equation beyond quasistatic disorder.

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 conformational changes of a single enzyme in the catalytic processes. In this work, we study the general dynamics of single enzymes in the presence of dynamic disorder. We find that, within the time separation regimes, i.e., the slow reaction and nondiffusion limits, the Michaelis-Menten equation holds exactly. In particular, by employing the decoupling approximation we demonstrate analytically that the classic Michaelis-Menten equation is still an excellent approximation in the presence of general dynamic disorder.

Catalysis↗

PubMed2006

Surface freezing in normal alkanes: a statistical physics approach.

The present paper aims to understand the surface freezing occurring on the interface between liquid normal alkane and air. After proposing a simple microscopic model, it reveals that the model can describe the surface freezing of normal alkanes. Subsequently, surface freezing is immediately proved to be a first order phase transition, which has been illustrated by numerous experiments. Moreover, our calculation predicts a new first order phase transition on the interface. These two transitions correspond to the liquid to monolayer and monolayer to perfect solid transitions, respectively. A phase diagram is obtained directly from the calculations as well. The model indicates that both van der Waals interaction and the entropy influenced by the surface are essential for explaining the surface phase transition.

Journal Article↗

PubMed2005

Force unfolding single RNAs.

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 extension, the molecules used in the experiments do not present apparent energy barriers. The strong cooperative folding and unfolding transitions of the RNAs observed in the experiments and in our simulations arise from the interaction of the molecules and the light trap. In addition, we also investigate the properties of Jarzynski's remarkable equality, whose experimental test has received considerable attention.

Computer Simulation↗

PubMed2004

Shape deformation and circle instability in two-dimensional lipid domains by dipolar force: a shape- and size-dependent line tension model.

The dipolar energy of a solid monolayer domain surrounded by a fluid phase at an air-water interface is derived approximately as a sum of an additionally negative line tension and a curvature-elastic energy at the boundary. Variation of the domain energy yields an equilibrium domain shape equation. The obvious solutions of the domain shape equation clearly predict a circle, torus, D-form, S-form, and serpentine manner shape found experimentally, depending on the difference in the Gibbs free energy between the solid and fluid phases and the total line tension. Analysis of linear instability for a circle with a fixed area shows that, above a threshold size, the circle can be deformed into an m-sided quasipolygon. The good agreement with the observation and numerical calculation reported by Lee and McConnell [J. Phys. Chem. 91, 9532 (1993)]] shows the quantitative validity of the present theory.

Lipids↗

PubMed2004

Monte Carlo simulation for single RNA unfolding by force.

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 ensemble, we focus on the mechanical behaviors of the RNA P5ab molecule, which include the unfolding force dependence on the pulling speed, the force-hysteresis phenomenon, and the coincidence of stretching-relaxing force-curves in thermal equilibrium. We particularly simulate the time traces of the end-to-end distance of the P5ab under the constant force in equilibrium, which also have been recorded in the recent experiment. The reaction rate constants for the folding and unfolding are calculated. Our results show that the agreement between the simulation and the experimental measurements is satisfactory.

Algorithms↗

PubMed2004

Group structure of the membrane shape equation.

The purpose of this paper is to study the geometry in the plane of the membrane equation or a section equation of a general membrane shape, where the invariance under the group of contact transformations is required. The discussion is mainly based on Cartan's theory of the Lie group. One may find that the relative invariance does not vanish, it is also possible to define a generalized geometry in the plane with the elements of contact of the second order x, y, y', y'' as the elements of the space and with a certain five-parameter group as its fundamental group. In the example of axisymmetric membrane shape equation, one may find that the membrane shape is a five-parameter group and characterized by twelve group structure parameters which are functions of pressure difference, tensile stress and asymmetry effect of the membrane or its environment. When these varieties of membrane or environment change, the structure constants vary; then one can obtain directly the change of symmetric group and the information on the membrane shape variation.

Algorithms↗

PubMed2002

Classification of amino acids based on statistical results of known structures and cooperativity of protein folding.

It has been found that the 20 kinds of amino acids have different frequencies of occurrence in alpha,beta, and coil structures [P. Y. Chou and G. D. Fasman, Biochemistry 13, 211 (1974)]. Based on more known structures of proteins, frequencies for each amino acid in alpha and beta secondary structures are recalculated. Next step, under the approximation ignoring the chain connectivity of proteins, energy parameters to form alpha and beta secondary structures for each amino acid are obtained. According to the hydrophobicity and energies in alpha and beta secondary structures, 20 kinds of amino acids are classified. The results suggest that dividing amino acids to five or nine groups is desirable. At last, a protein model considering both two-body hydrophobic interaction and one-body energy to form secondary structures, hydrophobic-polar alphabeta model, is introduced. It is shown that the consistency among various energy terms makes the cooperativity of protein folding closer to the experiments.

Amino Acid Sequence↗