arXiv subjects

Chin-Kun Hu

Publications and source records attributed to Chin-Kun Hu.

At least 37 records · Page 2Linked to original sources

arXiv2010

On trajectories of vortices in the compressible fluid on a two-dimensional manifold

For the model of a compressible barotropic fluid on a two dimensional rotating Riemmanian manifold we discuss a special class of smooth solutions having a form of a steady non-singular vortex moving with a bearing field. The model can be obtained from the system of primitive equations governing the motion of air over the Earth surface after averaging over the height and therefore the solution obtained can be interpreted as a tropical cyclone which is known as a long time existing stable vortex. We consider approximations of $l$- plane and $β$ - plane used in geophysics for modeling of middle scale processes and equations on the whole sphere as well. We show that the solutions of the mentioned form satisfy the equations of the model either exactly or with a discrepancy which is small in a neighborhood of the trajectory of the center of vortex. We perform a numeric study of the change of the shape of the vortex affected by the neglecting the discrepancy term.

math-ph↗

arXiv2010

Glassy state of native collagen fibril

Our micromechanical experiments show that at physiological temperatures type I collagen fibril has several basic features of the glassy state. The transition out of this state [softening transition] essentially depends on the speed of heating v, e.g., for v=1 C/min it occurs around 70 C and is displayed by a peak of the internal friction and decreasing Young's modulus. The softening transition decreases by 45 C upon decreasing the heating speed to v=0.1 C/min. For temperatures 20-30 C the native collagen fibril demonstrates features of mechanical glassines at oscillation frequencies 0.1-3 kHz; in particular, the internal friction has a sharp maximum as a function of the frequency. This is the first example of biopolymer glassines at physiological temperatures, because well-known glassy features of DNA and globular proteins are seen only for much lower temperatures (around 200 K).

cond-mat.soft↗

arXiv2010

DNA Bubble Life Time in Denaturation

We have investigated the denaturation bubble life time for a homogeneous as well as for a heterogeneous DNA within a Poland-Scheraga model. It is shown that at criticality the bubble life time for a homogeneous DNA is finite provided that the loop entropic exponent c>2 and has a scaling dependence on DNA length for c<2. Heterogeneity in the thermodynamical limit makes the bubble life time infinite for any entropic exponent.

cond-mat.soft↗

arXiv2010

Effect of time delay on the onset of synchronization of the stochastic Kuramoto model

We consider the Kuramoto model of globally coupled phase oscillators with time-delayed interactions, that is subject to the Ornstein-Uhlenbeck (Gaussian) colored or the non-Gaussian colored noise. We investigate numerically the interplay between the influences of the finite correlation time of noise $τ$ and the time delay $τ_{d}$ on the onset of the synchronization process. Both cases for identical and nonidentical oscillators had been considered. Among the obtained results for identical oscillators is a large increase of the synchronization threshold as a function of time delay for the colored non-Gaussian noise compared to the case of the colored Gaussian noise at low noise correlation time $τ$. However, the difference reduces remarkably for large noise correlation times. For the case of nonidentical oscillators, the incoherent state may become unstable around the maximum value of the threshold (as a function of time delay) even at lower coupling strength values in the presence of colored noise as compared to the noiseless case. We had studied the dependence of the critical value of the coupling strength (the threshold of synchronization) on given parameters of the stochastic Kuramoto model in great details and presented results for possible cases of colored Gaussian and non-Gaussian noises.

cond-mat.stat-mech↗

arXiv2010

Boundary conditions and amplitude ratios for finite-size corrections of a one-dimensional quantum spin model

We study the influence of boundary conditions on the finite-size corrections of a one-dimensional (1D) quantum spin model by exact and perturbative theoretic calculations. We obtain two new infinite sets of universal amplitude ratios for the finite-size correction terms of the 1D quantum spin model of $N$ sites with free and antiperiodic boundary conditions. The results for the lowest two orders are in perfect agreement with a perturbative conformal field theory scenario proposed by Cardy [Nucl. Phys. B {\bf 270}, 186 (1986)].

cond-mat.stat-mech↗

arXiv2010

Typhoon eye trajectory based on a mathematical model: comparing with observational data

We propose a model based on the primitive system of the Navier-Stokes equations in a bidimensional framework as the $l$ - plane approximation, which allows us to explain the variety of tracks of tropical cyclones (typhoons). Our idea is to construct special analytical solutions with a linear velocity profile for the Navier-Stokes systems. The evidence of the structure of linear velocity near the center of vortex can be proven by the observational data. We study solutions with the linear-velocity property for both barotropic and baroclinic cases and show that they follow the same equations in describing the trajectories of the typhoon eye at the equilibrium state (that relates to the conservative phase of the typhoon dynamics). Moreover, at the equilibrium state, the trajectories can be viewed as a superposition of two circular motions: one has period $2π/l,$ the other one has period $2π/b_0,$ where $l$ is the Coriolis parameter and $b_0$ is the height-averaged vorticity at the center of cyclone. Also, we compare our theoretical trajectories based on initial conditions from the flow with tracks obtained from the observational database. It is worth to mention that under certain conditions our results are still compatible with observational data although we did not truly consider the influence of steering effect. %Note that the %motion of the typhoon eye can not be totally determinated by initial %conditions due to the effect of ambient pressure field ("steering" %effect). Finally, we propose the parameter-adopting method so that one could correct the weather prediction in real time. Examples of our analysis and the use of parameter-adopting method for the historic trajectories are provided.

math-ph↗

arXiv2009

Protein-mediated Loops and Phase Transition in Nonthermal Denaturation of DNA

We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a first-order phase transition. We estimate the denaturation transition time near the phase transition, which can be compared with experimental data. The model describes the formation of multiple loops via dynamical (fluctuational) linking between looping proteins, that is essential in many cellular biological processes.

cond-mat.soft↗

arXiv2009

Protein mechanical unfolding: importance of non-native interactions

Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied by all-atom molecular dynamics simulations, using the GROMOS96 force field 43a1 and the simple point charge explicit water solvent. Our study reveals an important role of non-native interactions in the unfolding process. Namely, the existence of a peak centered at the end-to-end extension 22 nm in the force-extension curve, is associated with breaking of non-native hydrogen bonds. Such a peak has been observed in experiments but not in Go models, where non-native interactions are neglected. We predict that an additional peak occurs at 2 nm using not only GROMOS96 force field 43a1 but also Amber 94 and OPLS force fields. This result would stimulate further experimental studies on elastic properties of DDFLN4.

q-bio.BM↗

arXiv2009

The intermediate evolution phase in case of truncated selection

Using methods of statistical physics, we present rigorous theoretical calculations of Eigen's quasispecies theory with the truncated fitness landscape which dramatically limits the available sequence space of a reproducing quasispecies. Depending on the mutation rates, we observe three phases, a selective one, an intermediate one with some residual order and a completely randomized phase. Our results are applicable for the general case of fitness landscape.

q-bio.PE↗

arXiv2009

How adsorption influences DNA denaturation

The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the surface, the denaturation phase-transition disappears. Instead, there is a smooth crossover to a weakly naturated state. Our second conclusion is that even when the inter-strand attraction alone is too weak for creating a naturated state at the given temperature, and also the surface-strand attraction alone is too weak for creating an adsorbed state, the combined effect of the two attractions can lead to a naturated and adsorbed state.

cond-mat.soft↗

arXiv2009

Replicators in Fine-grained Environment: Adaptation and Polymorphism

Selection in a time-periodic environment is modeled via the two-player replicator dynamics. For sufficiently fast environmental changes, this is reduced to a multi-player replicator dynamics in a constant environment. The two-player terms correspond to the time-averaged payoffs, while the three and four-player terms arise from the adaptation of the morphs to their varying environment. Such multi-player (adaptive) terms can induce a stable polymorphism. The establishment of the polymorphism in partnership games [genetic selection] is accompanied by decreasing mean fitness of the population.

q-bio.PE↗

arXiv2009

Long DNA molecule as a pseudoscalar liquid crystal

We show that a long DNA molecule can form a novel condensed phase of matter, the pseudoscalar liquid crystal, that consists of aperiodically ordered DNA fragments in right-handed B and left-handed Z forms. We discuss the possibility of transformation of B-DNA into Z-DNA and vice versa via first-order phase transitions as well as transformations from the phase with zero total chirality into pure B- or Z-DNA samples through second-order phase transitions. The presented minimalistic phenomenological model describes the pseudoscalar liquid crystal phase of DNA and the phase transition phenomena. We point out to a possibility that a pseudoscalar liquid nano-crystal can be assembled via DNA-programming.

cond-mat.soft↗

arXiv2008

Mapping functions and critical behavior of percolation on rectangular domains

The existence probability $E_p$ and the percolation probability $P$ of the bond percolation on rectangular domains with different aspect ratios $R$ are studied via the mapping functions between systems with different aspect ratios. The superscaling behavior of $E_p$ and $P$ for such systems with exponents $a$ and $b$, respectively, found by Watanabe, Yukawa, Ito, and Hu in [Phys. Rev. Lett. \textbf{93}, 190601 (2004)] can be understood from the lower order approximation of the mapping functions $f_R$ and $g_R$ for $E_p$ and $P$, respectively; the exponents $a$ and $b$ can be obtained from numerically determined mapping functions $f_R$ and $g_R$, respectively.

cond-mat.stat-mech↗

arXiv2007

New force replica exchange method and protein folding pathways probed by force-clamp technique

We have developed a new extended replica exchange method to study thermodynamics of a system in the presence of external force. Our idea is based on the exchange between different force replicas to accelerate the equilibrium process. We have shown that the refolding pathways of single ubiquitin depend on which terminus is fixed. If the N-end is fixed then the folding pathways are different compared to the case when both termini are free, but fixing the C-terminal does not change them. Surprisingly, we have found that the anchoring terminal does not affect the pathways of individual secondary structures of three-domain ubiquitin, indicating the important role of the multi-domain construction. Therefore, force-clamp experiments, in which one end of a protein is kept fixed, can probe the refolding pathways of a single free-end ubiquitin if one uses either the poly-ubiquitin or a single domain with the C-terminus anchored. However, it is shown that anchoring one end does not affect refolding pathways of the titin domain I27, and the force-clamp spectroscopy is always capable to predict folding sequencing of this protein. We have obtained the reasonable estimate for unfolding barrier of ubiqutin. The linkage between residue Lys48 and the C-terminal of ubiquitin is found to have the dramatic effect on the location of the transition state along the end-to-end distance reaction coordinate, but the multi-domain construction leaves the transition state almost unchanged. We have found that the maximum force in the force-extension profile from constant velocity force pulling simulations depends on temperature nonlinearly. However, for some narrow temperature interval this dependence becomes linear, as have been observed in recent experiments.

q-bio.BM↗

arXiv2006

Effect of finite size on cooperativity and rates of protein folding

We analyze the dependence of cooperativity of the thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, $N$, using lattice models with side chains,off-lattice Go models and the available experimental data. A dimensionless measure of cooperativity, $Ω_c$ ($0 < Ω_c < \infty$), scales as $Ω_c \sim N^ζ$. The results of simulations and the analysis of experimental data further confirm the earlier prediction that $ζ$ is universal with $ζ= 1 +γ$, where exponent $γ$ characterizes the susceptibility of a self-avoiding walk. This finding suggests that the structural characteristics in the denaturated state are manifested in the folding cooperativity at the transition temperature. The folding rates $k_F$ for the Go models and a dataset of 69 proteins can be fit using $k_F = k_F^0 \exp(-cN^β)$. Both $β= 1/2$ and 2/3 provide a good fit of the data. We find that $k_F = k_F^0 \exp(-cN^{1/2})$, with the average (over the dataset of proteins) $k_F^0 \approx (0.2μs)^{-1}$ and $c \approx 1.1$, can be used to estimate folding rates to within an order of magnitude in most cases. The minimal models give identical $N$ dependence with $c \approx 1$. The prefactor for off-lattice Go models is nearly four orders of magnitude larger than the experimental value.

q-bio.BM↗

arXiv2006

Folding of the Protein Domain hbSBD

The folding of the alpha-helice domain hbSBD of the mammalian mitochondrial branched-chain alpha-ketoacid dehydrogenase (BCKD) complex is studied by the circular dichroism technique in absence of urea. Thermal denaturation is used to evaluate various thermodynamic parameters defining the equilibrium unfolding, which is well described by the two-state model with the folding temperature T_f = 317.8 K and the enthalpy change Delta H_g = 19.67 kcal/mol. The folding is also studied numerically using the off-lattice coarse-grained Go model and the Langevin dynamics. The obtained results, including the population of the native basin, the free energy landscape as a function of the number of native contacts and the folding kinetics, also suggest that the hbSBD domain is a two-state folder. These results are consistent with the biological function of hbSBD in BCKD.

q-bio.BM↗

arXiv2006

Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin

The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force quench refolding times scale as tau_F ~ exp(f_q*x_F/k_B*T), where f_q is the quench force and x_F = 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to x_F = 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state x_UF=0.24 nm which is in reasonable agreement with the experimental data.

q-bio.BM↗

arXiv2006

Random 3D Spin System Under the External Field and Dielectric Permittivity Superlattice Formation

A dielectric medium consisting of roughly polarized molecules is treated as a 3D disordered spin system (spin glass). A microscopic approach for the study of statistical properties of this system on micrometer space scale and nanosecond time scale of standing electromagnetic wave is developed. Using ergodic hypothesis the initial 3D spin problem is reduced to two separate 1D problems along external field propagation. The first problem describes the disordered spin chain system while the second one describes a disordered N-particle quantum system with relaxation in the framework of Langevin-Schroedinger (L-Sch) type equation. Statistical properties of both systems are investigated in detail. Basing on these constructions, the coefficient of polarizability, related to collective orientational effects, is calculated. Clausius-Mossotti formula for dielectric constant is generalized. For dielectric permittivity function generalized equation is found taking into account Clausius-Mossotti generalized formula.

cond-mat.soft↗