arXiv subjects

Chin-Kun Hu

Publications and source records attributed to Chin-Kun Hu.

At least 55 records · Page 3Linked to original sources

arXiv2006

Quasispecies Theory for Multiple-Peak Fitness Landscapes

We use a path integral representation to solve the Eigen and Crow-Kimura molecular evolution models for the case of multiple fitness peaks with arbitrary fitness and degradation functions. In the general case, we find that the solution to these molecular evolution models can be written as the optimum of a fitness function, with constraints enforced by Lagrange multipliers and with a term accounting for the entropy of the spreading population in sequence space. The results for the Eigen model are applied to consider virus or cancer proliferation under the control of drugs or the immune system.

q-bio.PE↗

arXiv2006

Logarithmic Conformal Field Theory and Boundary Effects in the Dimer Model

We study the finite-size corrections of the dimer model on $\infty \times N$ square lattice with two different boundary conditions: free and periodic. We find that the finite-size corrections in a crucial way depend on the parity of $N$; we also show that such unusual finite-size behavior can be fully explained in the framework of the $c=-2$ logarithmic conformal field theory.

cond-mat.stat-mech↗

arXiv2005

Watanabe and Hu Reply

The article is an reply to comments on the paper [H. Watanabe, S. Yukawa, N. Ito, and C.-K. Hu, Phys. Rev. Lett. vol. 93, 19601 (2004)] by G. Pruessner and N. R. Moloney published in [Phys. Rev. Lett. vo. 95, 258901 (2005)]. In this reply, we also point out that the exponents $a$ and $b$ in the 2004 paper just mentioned can be calculated from mapping functions.

cond-mat.stat-mech↗

arXiv2005

Adhesion Induced DNA Naturation

DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface, the entropy gain is smaller than in the bulk, leading to a stronger binding and, upon neglecting self-avoidance, absence of a denatured phase. Now consider conditions where the binding potentials are too weak for naturation, and the surface potential too weak to adsorb single strands. In a variational approach it is shown that their combined action may lead to a naturated adsorbed phase. Conditions for the absence of naturation and adsorption are derived too. The phase diagram is constructed qualitatively.

cond-mat.soft↗

arXiv2004

Unzipping of DNA with correlated base-sequence

We consider force-induced unzipping transition for a heterogeneous DNA model with a correlated base-sequence. Both finite-range and long-range correlated situations are considered. It is shown that finite-range correlations increase stability of DNA with respect to the external unzipping force. Due to long-range correlations the number of unzipped base-pairs displays two widely different scenarios depending on the details of the base-sequence: either there is no unzipping phase-transition at all, or the transition is realized via a sequence of jumps with magnitude comparable to the size of the system. Both scenarios are different from the behavior of the average number of unzipped base-pairs (non-self-averaging). The results can be relevant for explaining the biological purpose of correlated structures in DNA.

cond-mat.soft↗

arXiv2004

Global Optimization of Minority Game by Smart Agents

We propose a new model of minority game with so-called smart agents such that the standard deviation and the total loss in this model reach the theoretical minimum values in the limit of long time. The smart agents use trail and error method to make a choice but bring global optimization to the system, which suggests that the economic systems may have the ability to self-organize into a highly optimized state by agents who are forced to make decisions based on inductive thinking for their limited knowledge and capabilities. When other kinds of agents are also present, the experimental results and analyses show that the smart agent can gain profits from producers and are much more competent than the noise traders and conventional agents in original minority game.

cond-mat.stat-mech↗

arXiv2004

Eigen model as a quantum spin chain: exact dynamics

We map Eigen model of biological evolution [Naturwissenschaften {\bf 58}, 465 (1971)] into a one-dimensional quantum spin model with non-Hermitean Hamiltonian. Based on such a connection, we derive exact relaxation periods for the Eigen model to approach static energy landscape from various initial conditions. We also study a simple case of dynamic fitness function.

cond-mat.stat-mech↗

arXiv2004

Helix-coil Transition in Closed Circular DNA

A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The basic assumption is that the reduced energy of the hydrogen bond is not constant through the transition process but depends effectively on the fraction of already broken bonds. A transformation formula is obtained which relates the temperature of ccDNA at a given degree of helicity during the transition to the temperature of the corresponding linear chain at the same degree of helicity. The formula provides a simple method to calculate the melting curve for the ccDNA from the experimental melting curve of the linear DNA with the same nucleotide sequence.

q-bio.BM↗

arXiv2003

A New Analytical Method for Computing Solvent Accessible Surface Area and its Gradients for Macromolecules

In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a new analytical method for this purpose. In the proposed algorithm, we consider the transformation which maps the spherical circles of intersection of atomic surfaces in three-dimensional space onto the circles on a two-dimensional plane and the problem of computing solvent accessible surface area is transformed into the problem of computing corresponding curve integrals on the plane. This allows to consider only integrals over the circular trajectories on the plane. The algorithm is suitable for parallelization. Testings on several small proteins have shown a high accuracy of the algorithm and a good performance.

cond-mat↗

arXiv2003

Synchronized clusters in coupled map networks: Stability analysis

We study self-organized (s-) and driven (d-) synchronization in coupled map networks for some simple networks, namely two and three node networks and their natural generalization to globally coupled and complete bipartite networks. We use both linear stability analysis and Lyapunov function approach for this study and determine stability conditions for synchronization. We see that most of the features of coupled dynamics of small networks with two or three nodes, are carried over to the larger networks of the same type. The phase diagrams for the networks studied here have features very similar to the different kinds of networks studied in Ref. \cite{sarika-REA2}. The analysis of the dynamics of the difference variable corresponding to any two nodes shows that when the two nodes are in driven synchronization, all the coupling terms cancel out whereas when they are in self-organized synchronization, the direct coupling term between the two nodes adds an extra decay term while the other couplings cancel out.

nlin.CD↗

arXiv2003

Crossover between special and ordinary transitions in random semi-infinite Ising-like systems

We investigate the crossover behavior between special and ordinary surface transitions in three-dimensional semi-infinite Ising-like systems with random quenched bulk disorder. We calculate the surface crossover critical exponent $Φ$, the critical exponents of the layer, $α_{1}$, and local specific heats, $α_{11}$, by applying the field theoretic approach directly in three spatial dimensions ($d=3$) up to the two-loop approximation. The numerical estimates of the resulting two-loop series expansions for the surface critical exponents are computed by means of Padé and Padé-Borel resummation techniques. We find that $Φ$, $α_{1}$, $α_{11}$ obtained in the present paper are different from their counterparts of pure Ising systems. The obtained results confirm that in a system with random quenched bulk disorder the plane boundary is characterized by a new set of critical exponents.

cond-mat.dis-nn↗

arXiv2003

Transition from KPZ to Tilted Interface Critical Behavior in a Solvable Asymmetric Avalanche Model

We use a discrete-time formulation to study the asymmetric avalanche process [Phys. Rev. Lett. vol. 87, 084301 (2001)] on a finite ring and obtain an exact expression for the average avalanche size of particles as a function of toppling probabilities depending on parameters $μ$ and $α$. By mapping the model below and above the critical line onto driven interface problems, we show how different regimes of avalanches may lead to different types of critical interface behavior characterized by either annealed or quenched disorders and obtain exactly the related critical exponents which violate a well-known scaling relation when $α\ne 2$.

cond-mat.stat-mech↗

arXiv2003

The Asymmetric Avalanche Process

An asymmetric stochastic process describing the avalanche dynamics on a ring is proposed. A general kinetic equation which incorporates the exclusion and avalanche processes is considered. The Bethe ansatz method is used to calculate the generating function for the total distance covered by all particles. It gives the average velocity of particles which exhibits a phase transition from an intermittent to continuous flow. We calculated also higher cumulants and the large deviation function for the particle flow. The latter has the universal form obtained earlier for the asymmetric exclusion process and conjectured to be common for all models of the Kardar-Parisi-Zhang universality class .

cond-mat.stat-mech↗

arXiv2003

Universal Finite-size Scaling Functions with Exact Non-universal Metric Factors

Using exact partition functions and finite-size corrections for the Ising model on finite square, plane triangular, and honeycomb lattices, we obtain universal finite-size scaling functions for the specific heat, the internal energy, and the free energy of the Ising model on these lattices with exact non-universal metric factors.

cond-mat.stat-mech↗

arXiv2002

Renormalization group approach to an Abelian sandpile model on planar lattices

One important step in the renormalization group (RG) approach to a lattice sandpile model is the exact enumeration of all possible toppling processes of sandpile dynamics inside a cell for RG transformations. Here we propose a computer algorithm to carry out such exact enumeration for cells of planar lattices in RG approach to Bak-Tang-Wiesenfeld sandpile model [Phys. Rev. Lett. {\bf 59}, 381 (1987)] and consider both the reduced-high RG equations proposed by Pietronero, Vespignani, and Zapperi (PVZ) [Phys. Rev. Lett. {\bf 72}, 1690 (1994)] and the real-height RG equations proposed by Ivashkevich [Phys. Rev. Lett. {\bf 76}, 3368 (1996)]. Using this algorithm we are able to carry out RG transformations more quickly with large cell size, e.g. $3 \times 3$ cell for the square (sq) lattice in PVZ RG equations, which is the largest cell size at the present, and find some mistakes in a previous paper [Phys. Rev. E {\bf 51}, 1711 (1995)]. For sq and plane triangular (pt) lattices, we obtain the only attractive fixed point for each lattice and calculate the avalanche exponent $τ$ and the dynamical exponent $z$. Our results suggest that the increase of the cell size in the PVZ RG transformation does not lead to more accurate results. The implication of such result is discussed.

cond-mat.stat-mech↗

arXiv2002

Exact partition functions of the Ising model on MxN planar lattices with periodic-aperiodic boundary conditions

The Grassmann path integral approach is used to calculate exact partition functions of the Ising model on MxN square (sq), plane triangular (pt) and honeycomb (hc) lattices with periodic-periodic (pp), periodic-antiperiodic (pa), antiperiodic-periodic (ap) and antiperiodic-antiperiodic (aa) boundary conditions. The partition functions are used to calculate and plot the specific heat, $C/k_B$, as a function of the temperature, $θ=k_BT/J$. We find that for the NxN sq lattice, $C/k_B$ for pa and ap boundary conditions are different from those for aa boundary conditions, but for the NxN pt and hc lattices, $C/k_B$ for ap, pa, and aa boundary conditions have the same values. Our exact partition functions might also be useful for understanding the effects of lattice structures and boundary conditions on critical finite-size corrections of the Ising model.

cond-mat.stat-mech↗

arXiv2002

New Phase Transition in Polymer Solutions with Multicomponent Solvent

Considering the density-density correlation function of a concentrated polymer solution with multicomponent solvent we find a phase transition due to the heterogeneity of excluded volume constant. This new phase transition implies a strong enhancement of the scattered light intensity in the critical region, which can explain a recent experiment showing strong light scattering from a ternary polymer system consisting of polyethylene oxide (PEO) dissolved in nitroethane and 3methyl-pentane.

cond-mat.soft↗

arXiv2002

Kronecker's Double Series and Exact Asymptotic Expansion for Free Models of Statistical Mechanics on Torus

For the free models of statistical mechanics on torus, exact asymptotic expansions of the free energy, the internal energy and the specific heat in the vicinity of the critical point are found. It is shown that there is direct relation between the terms of the expansion and the Kronecker's double series. The latter can be expressed in terms of the elliptic theta-functions in all orders of the asymptotic expansion.

cond-mat.stat-mech↗