Monte Carlo Algorithm, Sh. Hayryan, R. Ghulghazaryan, N. Poklar Ulrih, Jan Meinke, ...
published in
Simulation of RNA Folding on the Simple Cubic Lattice (2009)
S. Hayryan, K. G. Sargsyan, Jan H. Meinke, Ipan Mohanty, ...
published in
The intermediate evolution phase in case of truncated selection (2009)
Saakian, David B., Biebricher, Christof K., Hu, Chin-Kun
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...
Replicators in Fine-grained Environment: Adaptation and Polymorphism (2009)
Allahverdyan, Armen E., Hu, Chin-Kun
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...
How adsorption influences DNA denaturation (2009)
Allahverdyan, A. E., Gevorkian, Zh. S., Hu, Chin-Kun, Nieuwenhuizen, Th. M.
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...
Long DNA molecule as a pseudoscalar liquid crystal (2009)
Petrosyan, K. G., Hu, Chin-Kun
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...
DNA Bubble Life Time in Denaturation (2008)
Gevorkian, Zh. S., Hu, Chin-Kun
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...
Mapping functions and critical behavior of percolation on rectangular domains (2008)
Watanabe, Hiroshi, Hu, Chin-Kun
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...
Kouza, Maksim, Hu, Chin-Kun, Li, Mai Suan
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...
Effect of finite size on cooperativity and rates of protein folding (2006)
Kouza, Maksim, Li, Mai Suan, O'Brien Jr., Edward P., Hu, Chin-Kun, Thirumalai, D.
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...
Folding of the Protein Domain hbSBD (2006)
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
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...
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin (2006)
Li, Mai Suan, Kouza, Maksim, Hu, Chin-Kun
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...
Gevorkyan, Ashot S., Hu, Chin-Kun
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...
Quasispecies Theory for Multiple-Peak Fitness Landscapes (2006)
Saakian, D. B., Munoz, E., Hu, Chin-Kun, Deem, M. W.
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...
Logarithmic Conformal Field Theory and Boundary Effects in the Dimer Model (2005)
Izmailian, N. Sh., Priezzhev, V. B., Ruelle, Philippe, Hu, Chin-Kun
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...
Watanabe, Hiroshi, Hu, Chin-Kun
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....
Adhesion Induced DNA Naturation (2005)
Allahverdyan, A. E., Gevorkian, Zh. S., Hu, Chin-Kun, Nieuwenhuizen, Th. M.
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...
We present a systematic procedure for the direct calculation of the free energy and its first and second derivatives for the Ising model in one to three dimensions with a wide class of symmetry...
Unzipping of DNA with correlated base-sequence (2004)
Allahverdyan, A. E., Gevorkian, Zh. S., Hu, Chin-Kun, Wu, Ming-Chya
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...
Global Optimization of Minority Game by Smart Agents (2004)
Xie, Yan-Bo, Wang, Bing-Hong, Hu, Chin-Kun, Zhou, Tao
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....
Eigen model as a quantum spin chain: exact dynamics (2004)
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...
Helix-coil Transition in Closed Circular DNA (2004)
Morozov, V. F., Hayryan, Shura, Mamasakhlisov, E. Sh., Grigoryan, A. V., Badasyan, A. V., Hu, Chin-Kun
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...
Hayryan, Shura, Hu, Chin-Kun, Skřivánek, Jaroslav, Hayryan, Edik, Pokorny, Imrich
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...
Synchronized clusters in coupled map networks: Stability analysis (2003)
Jalan, Sarika, Amritkar, R. E., Hu, Chin-Kun
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...
Crossover between special and ordinary transitions in random semi-infinite Ising-like systems (2003)
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...
Povolotsky, A. M., Priezzhev, V. B., Hu, Chin-Kun
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...
Universal Finite-size Scaling Functions with Exact Non-universal Metric Factors (2003)
Wu, Ming-Chya, Hu, Chin-Kun, Izmailian, N. Sh.
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...
The Asymmetric Avalanche Process (2002)
Povolotsky, A. M., Priezzhev, V. B., Hu, Chin-Kun
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...
Renormalization group approach to an Abelian sandpile model on planar lattices (2002)
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...
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...
Izmailian, N. Sh., Oganesyan, K. B., Hu, Chin-Kun
Finite-size scaling, finite-size corrections, and boundary effects for critical systems have attracted much attention in recent years. Here we derive exact finite-size corrections for the free energy...
Correlation function of random heteropolymer solutions (2002)
Gevorkian, Zh. S., Hu, Chin-Kun
We study the density-density correlation function of the dense random heteropolymer solutions. We show that a phase transition is possible due to the heterogeneity of polymers. We also show that the...
New Phase Transition in Polymer Solutions with Multicomponent Solvent (2002)
Gevorkian, Zh. S., Hu, Chin-Kun
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....
Proteinlike behavior of a spin system near the transition between ferromagnet and spin glass (2001)
Lin, Chai-Yu, Hu, Chin-Kun, Hansmann, Ulrich H. E.
A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state...
Random-cluster multi-histogram sampling for the q-state Potts model (2001)
Weigel, Martin, Janke, Wolfhard, Hu, Chin-Kun
Using the random-cluster representation of the $q$-state Potts models we consider the pooling of data from cluster-update Monte Carlo simulations for different thermal couplings $K$ and number of...
Surface critical behavior of random systems at the special transition (2001)
We study the surface critical behavior of semi-infinite quenched random Ising-like systems at the special transition using three dimensional massive field theory up to the two-loop approximation....
Ivashkevich, E. V., Izmailian, N. Sh., Hu, Chin-Kun
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...
Hsu, Hsiao-Ping, Lin, Simon C., Hu, Chin-Kun
Percolation models with multiple percolating clusters have attracted much attention in recent years. Here we use Monte Carlo simulations to study bond percolation on $L_{1}\times L_{2}$ planar random...
Pattern Competition in the Photorefractive Semiconductors (2001)
Shiau, Yuo-Hsien, Hu, Chin-Kun
We analytically study the photorefractive Gunn effect in n-GaAs subjected to two external laser beams which form a moving interference pattern (MIP) in the semiconductor. When the intensity of the...
Exact Phase Diagram for an Asymmetric Avalanche Process (2001)
Hu, Chin-Kun, Ivashkevich, E. V., Povolotsky, A. M., Priezzhev, V. B.
Multifractal characterization of stochastic resonance (2000)
Silchenko, Alexander, Hu, Chin-Kun
We use a multifractal formalism to study the effect of stochastic resonance in a noisy bistable system driven by various input signals. To characterize the response of a stochastic bistable system we...
Surface critical behavior of random systems at the ordinary transition (2000)
Shpot, M., Usatenko, Z., Hu, Chin-Kun
We calculate the surface critical exponents of the ordinary transition occuring in semi-infinite, quenched dilute Ising-like systems. This is done by applying the field theoretic approach directly in...
Exact Universal Amplitude Ratios for Two-Dimensional Ising Models and a Quantum Spin Chain (2000)
Izmailian, N. Sh., Hu, Chin-Kun
We have derived analytic expressions for the amplitudes of correction terms in the critical free energy and inverse correlation length expansions for square, honeycomb, and plane-triangular lattices...
Izmailian, N. Sh., Hu, Chin-Kun
Let f, U and C represent, respectively, the free energy, the internal energy and the specific heat of the critical Ising model on the square M x N lattice with periodic boundary conditions. We find...
Cluster Analysis of the Ising Model and Universal Finite-Size Scaling (2000)
Okabe, Yutaka, Kaneda, Kazuhisa, Tomita, Yusuke, Kikuchi, Macoto, Hu, Chin-Kun
The recent progress in the study of finite-size scaling (FSS) properties of the Ising model is briefly reviewed. We calculate the universal FSS functions for the Binder parameter $g$ and the...
Partition function zeros of the Q-state Potts model for non-integer Q (1999)
Kim, Seung-Yeon, Creswick, Richard J., Chen, Chi-Ning, Hu, Chin-Kun
The distribution of the zeros of the partition function in the complex temperature plane (Fisher zeros) of the two-dimensional Q-state Potts model is studied for non-integer Q. On $L\times L$...
Gevorkian, Zh. S., Chen, C. P., Hu, Chin-Kun
We have considered X-ray radiation of a relativistic charged particle moving in a system consisting of microspheres distributed randomly in a dielectric material. A new mechanism based on the...
The 6-vertex model of hydrogen-bonded crystals with bond defects (1999)
Izmailian, N. Sh., Hu, Chin-Kun, Wu, F. Y.
It is shown that the percolation model of hydrogen-bonded crystals, which is a 6-vertex model with bond defects, is completely equivalent with an 8-vertex model in an external electric field. Using...
Inversion Symmetry and Critical Exponents of Dissipating Waves in the Sandpile Model (1999)
Hu, Chin-Kun, Ivashkevich, E. V., Lin, Chai-Yu, Priezzhev, V. B.
Statistics of waves of topplings in the Sandpile model is analysed both analytically and numerically. It is shown that the probability distribution of dissipating waves of topplings that touch the...
Cluster Analysis and Finite-Size Scaling for Ising Spin Systems (1999)
Tomita, Yusuke, Okabe, Yutaka, Hu, Chin-Kun
Based on the connection between the Ising model and a correlated percolation model, we calculate the distribution function for the fraction ($c$) of lattice sites in percolating clusters in subgraphs...
Geometry, thermodynamics, and finite-size corrections in the critical Potts model (1999)
Hu, Chin-Kun, Chen, Jau-Ann, Izmailian, N. Sh., Kleban, P.
We establish an intriguing connection between geometry and thermodynamics in the critical q-state Potts model on two-dimensional lattices, using the q-state bond-correlated percolation model (QBCPM)...
Exact phase diagrams for an Ising model on a two-layer Bethe lattice (1999)
Hu, Chin-Kun, Izmailian, N. Sh., Oganesyan, K. B.
Using an iteration technique, we obtain exact expressions for the free energy and the magnetization of an Ising model on a two - layer Bethe lattice with intralayer coupling constants J1 and J2 for...
Exact correlation functions of Bethe lattice spin models in external fields (1999)
Hu, Chin-Kun, Izmailian, N. Sh.
We develop a transfer matrix method to compute exactly the spin-spin correlation functions of Bethe lattice spin models in the external magnetic field h and for any temperature T. We first compute...
Phase Diagram of Ising Models with Random Sublattice Vacancies. (1998)
We use a modified Kadanoff's variational method to calculate the phase diagram of an Ising model with random vacancies on one of two interpenetrating sublattices of the isotropic square (SQ) and...
Criterion for First-Order Phase Transitions. (1998)
We show, via scaling arguments, that a first order transition occurs when the appropriate susceptibility (second derivative of the free energy) diverges proportional to the volume of the system. This...
Cooper, N. R., Halperin, B. I., Hu, Chin-Kun, Ruzin, I. M.
A recent theory has provided a possible explanation for the ``non-universal scaling'' of the low-temperature conductance (and conductivity) peak-heights of two-dimensional electron systems in the...
Li, Mai Suan, Hu, Chin-Kun, Klimov, Dmitri K., Thirumalai, D.
Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004)...
Exact solution of the Eigen model with general fitness functions and degradation rates
Saakian, David B., Hu, Chin-Kun
We present an exact solution of Eigen’s quasispecies model with a general degradation rate and fitness functions, including a square root decrease of fitness with increasing Hamming distance from...
Folding of the Protein Domain hbSBD
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
The folding of the α-helix domain hbSBD of the mammalian mitochondrial branched-chain α-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal...
Li, Mai Suan, Hu, Chin-Kun, Klimov, Dmitri K., Thirumalai, D.
Mechanical folding trajectories for polyproteins starting from initially stretched conformations generated by single-molecule atomic force microscopy experiments [Fernandez, J. M. & Li, H. (2004)...
Folding of the Protein Domain hbSBD
Kouza, Maksim, Chang, Chi-Fon, Hayryan, Shura, Yu, Tsan-hung, Li, Mai Suan, Huang, Tai-huang, ...
The folding of the α-helix domain hbSBD of the mammalian mitochondrial branched-chain α-ketoacid dehydrogenase complex is studied by the circular dichroism technique in absence of urea. Thermal...
Exact solution of the Eigen model with general fitness functions and degradation rates
Saakian, David B., Hu, Chin-Kun
We present an exact solution of Eigen’s quasispecies model with a general degradation rate and fitness functions, including a square root decrease of fitness with increasing Hamming distance from...
Refolding upon Force Quench and Pathways of Mechanical and Thermal Unfolding of Ubiquitin
Li, Mai Suan, Kouza, Maksim, Hu, Chin-Kun
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Cα-Gō model and the Langevin dynamics. It is shown that the refolding...
Chang, Chung-Ke, Hsu, Yen-Lan, Chang, Yuan-Hsiang, Chao, Fa-An, Wu, Ming-Chya, Huang, Yu-Shan, ...
The nucleocapsid protein (N) of the severe acute respiratory syndrome coronavirus (SARS-CoV) packages the viral genomic RNA and is crucial for viability. However, the RNA-binding mechanism is poorly...
Global Optimization of Minority Game by Smart Agents
Yan-Bo Xie, Bing-Hong Wang, Chin-Kun Hu, Tao Zhou
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....