Biomedical subjects

Chin-Kun Hu

Publications and source records attributed to Chin-Kun Hu.

6 recordsLinked to original sources

PubMed2003

Parallel tempering simulations of HP-36.

We report results from all-atom Monte Carlo simulations of the 36-residue villin headpiece subdomain HP-36. Protein-solvent interactions are approximated by an implicit solvent model. The parallel tempering is used to overcome the problem of slow convergence in low-temperature protein simulations. Our results show that this technique allows one to sample native-like structures of small proteins and points out the need for improved energy functions.

Algorithms↗

PubMed2002

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 the RG approach to the Bak-Tang-Wiesenfeld sandpile model [Phys. Rev. Lett. 59, 381 (1987)] and consider both the reduced-high RG equations proposed by Pietronero, Vespignani, and Zapperi (PVZ) [Phys. Rev. Lett. 72, 1690 (1994)], and the real-height RG equations proposed by Ivashkevich [Phys. Rev. Lett. 76, 3368 (1996)]. Using this algorithm, we are able to carry out RG transformations more quickly with large cell size, e.g., 3x3 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 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 tau 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.

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PubMed2002

Critical behavior of semi-infinite random systems at the special surface transition.

We use a three-dimensional massive field theory up to the two-loop approximation to study the critical behavior of semi-infinite quenched random Ising-like systems at the special surface transition. Besides, we extend up to the next-to leading order, the previous first-order results of the sqrt[epsilon] expansion obtained by Ohno and Okabe [Phys. Rev. B 46, 5917 (1992)]. The numerical estimates for surface critical exponents in both cases are computed by means of the Padé analysis. Moreover, in the case of the massive field theory we perform Padé-Borel resummation of the resulting two-loop series expansions for surface critical exponents. The most reliable estimates for critical exponents of semi-infinite systems with quenched bulk randomness at the special surface transition, which we can obtain in the frames of the present approximation scheme, are eta(//)=-0.238, Delta(1)=1.098, eta( perpendicular )=-0.104, beta(1)=0.258, gamma(11)=0.839, gamma(1)=1.426, delta(1)=6.521, and delta(11)=4.249. These values are different from critical exponents for pure semi-infinite Ising-like systems and show that in a system with quenched bulk randomness the plane boundary is characterized by a new set of critical exponents at the special surface transition.

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PubMed2002

Exact finite-size corrections for the square-lattice Ising model with Brascamp-Kunz boundary conditions.

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 F and the specific heat C of the critical ferromagnetic Ising model on the Mu x 2 Nu square lattice with Brascamp-Kunz (BK) boundary conditions [J. Math. Phys. 15, 66 (1974)] and compare such results with those under toroidal boundary conditions. When the ratio xi/2=(Mu+1)/2 Nu is smaller than 1 the behaviors of finite-size corrections for C are quite different for BK and toroidal boundary conditions; when ln(xi/2) is larger than 3, finite-size corrections for C in two boundary conditions approach the same values. In the limit Nu-->infinity we obtain the expansion of the free energy for infinitely long strip with BK boundary conditions. Our results are consistent with the conformal field theory prediction for the mixed boundary conditions by Cardy [Nucl. Phys. B 275, 200 (1986)] although the definitions of boundary conditions in two cases are different in one side of the long strip.

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PubMed2002

Random-cluster multihistogram sampling for the q-state Potts model.

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 states per spin q. Proper combination of histograms allows for the evaluation of thermal averages in a broad range of K and q values, including noninteger values of q. Due to restrictions in the sampling process correct normalization of the combined histogram data is nontrivial. We discuss the different possibilities and analyze their respective ranges of applicability.

Journal Article↗

PubMed2002

Exact amplitude ratio and finite-size corrections for the MxN square lattice Ising model.

Let f, U, and C represent, respectively, the free energy, the internal energy, and the specific heat of the critical Ising model on the MxN square lattice with periodic boundary conditions, and f(infinity) represents f for fixed M/N and N-->infinity. We find that f, U, and C can be written as N(f-f(infinity))= summation operator(infinity)(i=1)f(2i-1)/N(2i-1), U=-square root of [2]+ summation operator(infinity)(i=1)u(2i-1)/N(2i-1), and C=8 ln N/pi+ summation operator(infinity)(i=0)c(i)/N(i), i.e., Nf and U are odd functions of N(-1). We also find that u(2i-1)/c(2i-1)=1/square root of [2] and u(2i)/c(2i)=0 for 1 < or = i <infinity and obtain closed form expressions for f, U, and C up to orders 1/N(5), 1/N(5), and 1/N(3), respectively, which implies an analytic equation for c(5).

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