arXiv subjects

Zhong-can Ou-Yang

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

At least 19 recordsLinked to original sources

arXiv2019

Defect removal by solvent vapor annealing in thin films of lamellar diblock copolymers

Solvent vapor annealing (SVA) is known to be a simple, low-cost and highly efficient technique to produce defect-free diblock copolymer (BCP) thin films. Not only can the solvent weaken the BCP segmental interactions, but it can vary the characteristic spacing of the BCP microstructures. We carry out systematic theoretical studies on the effect of adding solvent into lamellar BCP thin films on the defect removal close to the BCP order-disorder transition. We find that the increase of the lamellar spacing, as is induced by addition of solvent, facilitates more efficient removal of defects. The stability of a particular defect in a lamellar BCP thin film is given in terms of two key controllable parameters: the amount of BCP swelling and solvent evaporation rate. Our results highlight the SVA mechanism for obtaining defect-free BCP thin films, as is highly desired in nanolithography and other industrial applications.

cond-mat.soft↗

arXiv2014

Nonequilibrium work equalities in isolated quantum systems

We briefly introduce the quantum Jarzynski and Bochkov-Kuzovlev equalities in isolated quantum Hamiltonian systems, which includes the origin of the equalities, their derivations using a quantum Feynman-Kac formula, the quantum Crooks equality, the evolution equations governing the characteristic functions of the probability density functions for the quantum work, the recent experimental verifications. Some results are given here first time. We particularly emphasize the formally structural consistence between these quantum equalities and their classical counterparts, which shall be useful in understanding the existing equalities and pursuing new fluctuation relations in other complex quantum systems.

cond-mat.stat-mech↗

arXiv2013

Radius-Voltage Relation of Graphene Bubbles Controlled by Gate Voltage

Graphene on the substrate can form bubbles rising above the sheet. In some cases, the bubble is a perfect spherical surface crown, and its radius can be adjusted by external electric field. In this manuscript, we theoretically investigate the voltage dependence of the spherical bubble's radius. The calculated results are in good agreement with recent experiments on the graphene bubble controlled by applied gate voltage [Appl. Phys. Lett. 99, 093103 (2011)].

cond-mat.mes-hall↗

arXiv2013

Shape transition of unstrained flattest single-walled carbon nanotubes under pressure

Single walled carbon nanotube's cross section can be flattened under hydrostatic pressure. One example is the cross section of a single walled carbon nanotube successively deforms from the original round shape to oval shape, then to peanut-like shape. At the transition point of reversible deformation between convex shape and concave shape, the side wall of nanotube is flattest. This flattest tube has many attractive properties. In the present work, an approximate approach is developed to determine the equilibrium shape of this unstrained flattest tube and the curvature distribution of this tube. Our results are in good agreement with recent numerical results, and can be applied to the study of pressure controlled electric properties of single walled carbon nanotubes. The present method can also be used to study other deformed inorganic and organic tube-like structures.

cond-mat.mes-hall↗

arXiv2009

Linear response theory and transient fluctuation theorems for diffusion processes: a backward point of view

On the basis of perturbed Kolmogorov backward equations and path integral representation, we unify the derivations of the linear response theory and transient fluctuation theorems for continuous diffusion processes from a backward point of view. We find that a variety of transient fluctuation theorems could be interpreted as a consequence of a generalized Chapman-Kolmogorov equation, which intrinsically arises from the Markovian characteristic of diffusion processes.

cond-mat.stat-mech↗

arXiv2009

A generalized integral fluctuation theorem for general jump processes

Using the Feynman-Kac and Cameron-Martin-Girsanov formulas, we obtain a generalized integral fluctuation theorem (GIFT) for discrete jump processes by constructing a time-invariable inner product. The existing discrete IFTs can be derived as its specific cases. A connection between our approach and the conventional time-reversal method is also established. Different from the latter approach that was extensively employed in existing literature, our approach can naturally bring out the definition of a time-reversal of a Markovian stochastic system. Additionally, we find the robust GIFT usually does not result into a detailed fluctuation theorem.

cond-mat.stat-mech↗

arXiv2009

Response delay as a strategy for survival in fluctuating environment

Response time-delay is an ubiquitous phenomenon in biological systems. Here we use a simple stochastic population model with time-delayed switching-rate conversion to quantitatively study the biological influence of the response time-delay on the survival fitness of cells living in periodically fluctuating and stochastic environment, respectively. Our calculation and simulation show that for the cells having a slow rate transition into fit phenotype and a fast rate transition into unfit phenotype, the response time-delay can always enhance their fitness during the environment change. Particularly, in the periodic or stochastic environment with small variance, the optimal fitness achieved by these cells is superior to that of cells with reverse switching rates even if the latter exhibits rapid response. These results suggest that the response time delay may be utilized by cells to enhance their adaptation to the fluctuating environment.

q-bio.PE↗

arXiv2009

A generalized integral fluctuation theorem for diffusion processes

We present a generalized integral fluctuation theorem (GIFT) for general diffusion processes using the Feynman-Kac and Cameron-Martin-Girsanov formulas. Existing IFTs can be thought of to be its specific cases. We interpret the origin of this theorem in terms of time-reversal of stochastic systems.

cond-mat.stat-mech↗

arXiv2008

Elasticity of Spider dragline Silks Viewed as Nematics: Yielding Induced by Isotropic-Nematic Phase Transition

Spider dragline silk shows well-known outstanding mechanical properties. However, its sigmoidal shape of the measured stress-strain curves (i.e. the yield) can not be described by classical polymer theories and recent hierarchical chain model. To solve the long lasting problem, we generalized the Maier-Saupe theory of nematics to construct an elastic model for the polypeptide chain network of the dragline silk. The comprehensive agreement between theory and experiments on the stress-strain curve strongly indicates the dragline silks to belong to liquid crystal elastomers. Especially, the remarkable yielding elasticity of the silk is understood for the first time as the force-induced isotropic-nematic phase transition of the chain network. Our theory also predicts a drop of the stress in supercontracted dragline silk, an early found effect of humidity on the mechanical property in many silks.

physics.bio-ph↗

arXiv2007

Bayesian analysis of time series of single RNA under fluctuating force

Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's intrinsic kinetic parameters from the time series obtained by forced folding/unfolding experiment done in the light tweezer, where the molecule is flanked by long double-stranded DNA/RNA handles and tethered between two big beads. We first construct a coarse-grain physical model of the experimental system. The model has captured the major physical factors: the Brownian motion of the bead, the molecular structural transition, and the elasticity of the handles and RNA. Then based on an analytic solution of the model, a Bayesian method using Monte Carlo Markov Chain is proposed to infer the intrinsic kinetic parameters of the RNA from the noisy time series of the distance or force. Because the force fluctuation induced by the Brownian motion of the bead and the structural transition can significantly modulate the transition rates of the RNA, we prove that, this statistic method is more accurate and efficient than the conventional histogram fitting method in inferring the molecule's intrinsic parameters.

cond-mat.soft↗

arXiv2006

Phonon Dispersion in Chiral Single Wall Carbon Nanotubes

The phonon dispersion of chiral single wall carbon nanotubes has been obtained from $6\times 6$ dyanimic matrix. The present manuscript is the extension of G. D. Mahan and Gun Sang Jeon's work on armchair and zigzag nanotubes. [see P. R. B., {\bf 70}, 075405 (2004)]. We use spring and mass model with the proper phonon potential suggested by \cite{M2}. We can calculate the dispersion of single wall carbon nanotubes near $Γ$ point with arbitrary chirality. The results are compatible with Mahan et. al's results for armchair and zigzag SWNTs.

cond-mat.mes-hall↗

arXiv2006

Stochastic dynamics of adhesion catch-slip bond cluster

We present a general stochastic dynamic model of a cluster of biological complexes with fluctuating dissociation and association rates. The master equation has analytical solutions in two limiting cases: the vanishing force with reflecting boundary condition and slow reaction limit. In particular, the latter can describe the dynamics of a catch-slip bond cluster under a constant force. We find that if the rebinding rate vanishes, the size of the cluster matters little to the cluster lifetime within the whole catch force regime. The large cluster rapidly decays and single catch bond governs the final dynamic behaviors of the cluster. The catch behavior would be further amplified in the presence of large nonvanishing rebinding rates.

cond-mat.soft↗

arXiv2006

Bell Rate Model with Dynamic Disorder: Model and Its Application in the Receptor-ligand Forced Dissociation Experiments

We extend the Bell forced dissociation rate model to take account into dynamic disorder. The motivation of the present work is from the recent forced dissociation experiments of the adhesive receptor-ligand complexes, in which some complexes were found to increase their mean lifetimes (catch bonds) when they are stretched by mechanical force, while the force increases beyond some thresholds their lifetimes decrease (slip bonds). Different from our previous model of force modulating dynamic disorder, in present work we allow that the projection of force onto the direction from the bound to the transition state of complex could be negative. Our quantitative description is based on a one-dimension diffusion-assisted reaction model. We find that, although the model can well describe the catch-slip transitions observed in the single bond P-selctin glycoprotein ligand 1(PSGL-1)-P- and L-selectin forced dissociation experiments, it might be physically unacceptable because the model predicts a slip-catch bond transitions when the conformational diffusion coefficient tends to zero.

cond-mat.soft↗

arXiv2006

Single Molecule Michaelis-Menten Equation beyond Quasi-Static Disorder

The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiment showed that the waiting time distribution and other properties of single enzyme molecule are not consistent with the prediction based on the viewpoint of ensemble. It has been contributed to the slow inner conformational changes of single enzyme in the catalytic processes. In this work we study the general dynamics of single enzyme in the presence of dynamic disorder. We find that at two limiting cases, the slow reaction and nondiffusion limits, Michaelis-Menten equation exactly holds although the waiting time distribution has a multiexponential decay behaviors in the nondiffusion limit.Particularly, the classic Michaelis-Menten equation still is an excellent approximation other than the two limits.

cond-mat.soft↗

arXiv2006

Dynamic disorder in receptor-ligand forced dissociation experiments

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". Different from the previous efforts, in this work we propose that the dynamic disorder of the force-dependent dissociation rate can account for the counterintuitive behaviors of the bonds. A Gaussian stochastic rate model is used to quantitatively describe the transitions observed recently in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin force rupture experiment [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193]. Our model agrees well to the experimental data. We conclude that the catch bonds could arise from the stronger positive correlation between the height of the intrinsic energy barrier and the distance from the bound state to the barrier; classical pathway scenario or {\it a priori} catch bond assumption is not essential.

cond-mat.stat-mech↗

arXiv2006

Force Modulating Dynamic Disorder: Physical Theory of Catch-slip bond Transitions in Receptor-Ligand Forced Dissociation Experiments

Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific chemical kinetic models have been developed to explain the intriguing transitions from the "catch-bonds" to the "slip-bonds". In this work we suggest that the counterintuitive forced dissociation of the complexes is a typical rate process with dynamic disorder. An uniform one-dimension force modulating Agmon-Hopfield model is used to quantitatively describe the transitions observed in the single bond P-selctin glycoprotein ligand 1(PSGL-1)$-$P-selectin forced dissociation experiments, which were respectively carried out on the constant force [Marshall, {\it et al.}, (2003) Nature {\bf 423}, 190-193] and the force steady- or jump-ramp [Evans {\it et al.}, (2004) Proc. Natl. Acad. Sci. USA {\bf 98}, 11281-11286] modes. Our calculation shows that the novel catch-slip bond transition arises from a competition of the two components of external applied force along the dissociation reaction coordinate and the complex conformational coordinate: the former accelerates the dissociation by lowering the height of the energy barrier between the bound and free states (slip), while the later stabilizes the complex by dragging the system to the higher barrier height (catch).

q-bio.CB↗

arXiv2005

Force Unfolding Single RNAs: from Equilibrium to Far-from Equilibrium

We summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to protein cases, using the single polymer elastic theory and the well known RNA secondary structure free energy knowledge, we can successively simulate various behaviors of force unfolding RNAs under different experimental setups from equilibrium to far-from equilibrium. Particularly, our simulation would be helpful in understanding Jarzynski's remarkable equality, which its experimental test has received considerable attention.

cond-mat.soft↗

arXiv2004

Stretching single RNAs: exact numerical and stochastic simulation methods

Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the constant extension ensembles, we find the two independent methods agree with each other quite well. To show the precision of our methods in predicting unfolding experiments, the unfolding forces of different RNA molecules under different experimental conditions are calculated. We find that the ionic corrections on the RNA free energies alone might not account for the apparent differences between the theoretical calculations and the experimental data; an ionic correction to the persistent length of single-stranded RNA should be necessary.

q-bio.BM↗