Critical exponents for the 3D Ising model

The authors present a status report on the ongoing analysis of the 3D Ising model with nearest-neighbor interactions using the Monte Carlo Renormalization Group (MCRG) and finite size scaling (FSS) methods on 64{sup 3}, 128{sup 3}, and 256{sup 3} simple cubic lattices. Their MCRG estimates are K{sup c}{sub nn} = 0.221655(1)(1) and {nu} = 0.625(1). The FSS results for K{sup c} are consistent with those from MCRG but the value of {nu} is not. Their best estimate {eta} = 0.025(6) covers the spread in the MCRG and FSS values. A surprise of their calculation is the estimate {omega} {approx} 0.7 for the correction-to-scaling exponent. The authors also present results for the renormalized coupling g{sub R} along the MCRG flow and argue that the data supports the validity of hyperscaling for the 3D Ising model

W196 and the ß -Hairpin Motif Modulate the Redox Switch of Conformation and the Biomolecular Interaction Network of the Apoptosis-Inducing Factor

The human apoptosis-inducing factor (hAIF) is a moonlight flavoprotein involved in mitochondrial respiratory complex assembly and caspase-independent programmed cell death. These functions might be modulated by its redox-linked structural transition that enables hAIF to act as a NAD(H/+) redox sensor. Upon reduction with NADH, hAIF undergoes a conformational reorganization in two specific insertions - the flexible regulatory C-loop and the 190-202 ß-harpin - promoting protein dimerization and the stabilization of a long-life charge transfer complex (CTC) that modulates its monomer-dimer equilibrium and its protein interaction network in healthy mitochondria. In this regard, here, we investigated the precise function of the ß-hairpin in the AIF conformation landscape related to its redox mechanism, by analyzing the role played by W196, a key residue in the interaction of this motif with the regulatory C-loop. Mutations at W196 decrease the compactness and stability of the oxidized hAIF, indicating that the ß-hairpin and C-loop coupling contribute to protein stability. Kinetic studies complemented with computational simulations reveal that W196 and the ß-hairpin conformation modulate the low efficiency of hAIF as NADH oxidoreductase, contributing to configure its active site in a noncompetent geometry for hydride transfer and to stabilize the CTC state by enhancing the affinity for NAD+. Finally, the ß-hairpin motif contributes to define the conformation of AIF's interaction surfaces with its physiological partners. These findings improve our understanding on the molecular basis of hAIF''s cellular activities, a crucial aspect for clarifying its associated pathological mechanisms and developing new molecular therapies

Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets

Whole genome expression profiles are widely used to discover molecular subtypes of diseases. A remaining challenge is to identify the correspondence or commonality of subtypes found in multiple, independent data sets generated on various platforms. While model-based supervised learning is often used to make these connections, the models can be biased to the training data set and thus miss inherent, relevant substructure in the test data. Here we describe an unsupervised subclass mapping method (SubMap), which reveals common subtypes between independent data sets. The subtypes within a data set can be determined by unsupervised clustering or given by predetermined phenotypes before applying SubMap. We define a measure of correspondence for subtypes and evaluate its significance building on our previous work on gene set enrichment analysis. The strength of the SubMap method is that it does not impose the structure of one data set upon another, but rather uses a bi-directional approach to highlight the common substructures in both. We show how this method can reveal the correspondence between several cancer-related data sets. Notably, it identifies common subtypes of breast cancer associated with estrogen receptor status, and a subgroup of lymphoma patients who share similar survival patterns, thus improving the accuracy of a clinical outcome predictor

Mean Field Behavior of Cluster Dynamics

The dynamic behavior of cluster algorithms is analyzed in the classical mean field limit. Rigorous analytical results below $T_c$ establish that the dynamic exponent has the value $z_{sw}=1$ for the Swendsen-Wang algorithm and $z_{uw}=0$ for the Wolff algorithm. An efficient Monte Carlo implementation is introduced, adapted for using these algorithms for fully connected graphs. Extensive simulations both above and below $T_c$ demonstrate scaling and evaluate the finite-size scaling function by means of a rather impressive collapse of the data.Comment: Revtex, 9 pages with 7 figure

Critical exponents of a three dimensional O(4) spin model

By Monte Carlo simulation we study the critical exponents governing the transition of the three-dimensional classical O(4) Heisenberg model, which is considered to be in the same universality class as the finite-temperature QCD with massless two flavors. We use the single cluster algorithm and the histogram reweighting technique to obtain observables at the critical temperature. After estimating an accurate value of the inverse critical temperature \Kc=0.9360(1), we make non-perturbative estimates for various critical exponents by finite-size scaling analysis. They are in excellent agreement with those obtained with the $4-\epsilon$ expansion method with errors reduced to about halves of them.Comment: 25 pages with 8 PS figures, LaTeX, UTHEP-28

Cumulants of the three state Potts model and of nonequilibrium models with C3v symmetry

The critical behavior of two-dimensional stochastic lattice gas models with C3v symmetry is analyzed. We study the cumulants of the order parameter for the three state (equilibrium) Potts model and for two irreversible models whose dynamic rules are invariant under the symmetry operations of the point group C3v. By means of extensive numerical analysis of the phase transition we show that irreversibility does not affect the critical behavior of the systems. In particular we find that the Binder reduced fourth order cumulant takes a universal value U* which is the same for the three state Potts model and for the irreversible models. The same universal behavior is observed for the reduced third-order cumulant.Comment: gzipped tar file containing: 1 latex file + 6 eps figure

A Study of Two-Temperature Non-Equilibrium Ising Models: Critical Behavior and Universality

We study a class of 2D non-equilibrium Ising models based on competing dynamics induced by contact with heat-baths at two different temperatures. We make a comparative study of the non-equilibrium versions of Metropolis, heat bath/Glauber and Swendsen-Wang dynamics and focus on their critical behavior in order to understand their universality classes. We present strong evidence that some of these dynamics have the same critical exponents and belong to the same universality class as the equilibrium 2D Ising model. We show that the bond version of the Swendsen-Wang update algorithm can be mapped into an equilibrium model at an effective temperature.Comment: 12 pages of LaTeX plus 18 pages of postscript figures in a uuencoded file (608k