A dedicated algorithm for calculating ground states for the triangular random bond Ising model

In the presented article we present an algorithm for the computation of ground state spin configurations for the 2d random bond Ising model on planar triangular lattice graphs. Therefore, it is explained how the respective ground state problem can be mapped to an auxiliary minimum-weight perfect matching problem, solvable in polynomial time. Consequently, the ground state properties as well as minimum-energy domain wall (MEDW) excitations for very large 2d systems, e.g. lattice graphs with up to N=384x384 spins, can be analyzed very fast. Here, we investigate the critical behavior of the corresponding T=0 ferromagnet to spin-glass transition, signaled by a breakdown of the magnetization, using finite-size scaling analyses of the magnetization and MEDW excitation energy and we contrast our numerical results with previous simulations and presumably exact results.Comment: 5 pages, 5 figure

Using network-flow techniques to solve an optimization problem from surface-physics

The solid-on-solid model provides a commonly used framework for the description of surfaces. In the last years it has been extended in order to investigate the effect of defects in the bulk on the roughness of the surface. The determination of the ground state of this model leads to a combinatorial problem, which is reduced to an uncapacitated, convex minimum-circulation problem. We will show that the successive shortest path algorithm solves the problem in polynomial time.Comment: 8 Pages LaTeX, using Elsevier preprint style (macros included

Tubulin glycylation controls primary cilia length

International audienc

Lower Critical Dimension of Ising Spin Glasses

Exact ground states of two-dimensional Ising spin glasses with Gaussian and bimodal (+- J) distributions of the disorder are calculated using a ``matching'' algorithm, which allows large system sizes of up to N=480^2 spins to be investigated. We study domain walls induced by two rather different types of boundary-condition changes, and, in each case, analyze the system-size dependence of an appropriately defined ``defect energy'', which we denote by DE. For Gaussian disorder, we find a power-law behavior DE ~ L^\theta, with \theta=-0.266(2) and \theta=-0.282(2) for the two types of boundary condition changes. These results are in reasonable agreement with each other, allowing for small systematic effects. They also agree well with earlier work on smaller sizes. The negative value indicates that two dimensions is below the lower critical dimension d_c. For the +-J model, we obtain a different result, namely the domain-wall energy saturates at a nonzero value for L\to \infty, so \theta = 0, indicating that the lower critical dimension for the +-J model exactly d_c=2.Comment: 4 pages, 4 figures, 1 table, revte

Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine†

This is the peer reviewed version of the following article: DeVore, N. M., Meneely, K. M., Bart, A. G., Stephens, E. S., Battaile, K. P. and Scott, E. E. (2012), Structural comparison of cytochromes P450 2A6, 2A13, and 2E1 with pilocarpine. FEBS Journal, 279: 1621–1631. doi:10.1111/j.1742-4658.2011.08412.x, which has been published in final form at http://doi.org/10.1111/j.1742-4658.2011.08412.x. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.Human xenobiotic-metabolizing cytochrome P450 (P450) enzymes can each bind and monooxygenate a diverse set of substrates, including drugs, often producing a variety of metabolites. Additionally a single ligand can interact with multiple cytochrome P450 enzymes, but often the protein structural similarities and differences that mediate such overlapping selectivity are not well understood. Even though the P450 superfamily has a highly canonical global protein fold, there are large variations in the active site size, topology, and conformational flexibility. We have determined how a related set of three human cytochrome P450 enzymes bind and interact with a common inhibitor, the muscarinic receptor agonist drug pilocarpine. Pilocarpine binds and inhibits the hepatic CYP2A6 and respiratory CYP2A13 enzymes much more efficiently than the hepatic CYP2E1 enzyme. To elucidate key amino acids involved in pilocarpine binding, crystal structures of CYP2A6 (2.4 Å), CYP2A13 (3.0 Å), CYP2E1 (2.35 Å), and a CYP2A6 mutant enzyme, CYP2A6 I208S/I300F/G301A/S369G (2.1 Å), have been determined with pilocarpine in the active site. In all four structures, pilocarpine coordinates to the heme iron, but comparisons reveal how individual amino acids lining the active sites of these three distinct human enzymes interact differently with the inhibitor pilocarpine. HYPERLINKING TO DATABASES: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/) with the following codes: CYP2A6 with pilocarpine (3T3R), CYP2A6 I208S/I300F/G301A/S369G with pilocarpine (3T3Q), CYP2A13 with pilocarpine (3T3S), and CYP2E1 with pilocarpine (3T3Z)

No spin-glass transition in the "mobile-bond" model

The recently introduced ``mobile-bond'' model for two-dimensional spin glasses is studied. The model is characterized by an annealing temperature T_q. On the basis of Monte Carlo simulations of small systems it has been claimed that this model exhibits a non-trivial spin-glass transition at finite temperature for small values of T_q. Here the model is studied by means of exact ground-state calculations of large systems up to N=256^2. The scaling of domain-wall energies is investigated as a function of the system size. For small values T_q<0.95 the system behaves like a (gauge-transformed) ferromagnet having a small fraction of frustrated plaquettes. For T_q>=0.95 the system behaves like the standard two-dimensional +-J spin-glass, i.e. it does NOT exhibit a phase transition at T>0.Comment: 4 pages, 5 figures, RevTe

Dynamics of the Wang-Landau algorithm and complexity of rare events for the three-dimensional bimodal Ising spin glass

We investigate the performance of flat-histogram methods based on a multicanonical ensemble and the Wang-Landau algorithm for the three-dimensional +/- J spin glass by measuring round-trip times in the energy range between the zero-temperature ground state and the state of highest energy. Strong sample-to-sample variations are found for fixed system size and the distribution of round-trip times follows a fat-tailed Frechet extremal value distribution. Rare events in the fat tails of these distributions corresponding to extremely slowly equilibrating spin glass realizations dominate the calculations of statistical averages. While the typical round-trip time scales exponential as expected for this NP-hard problem, we find that the average round-trip time is no longer well-defined for systems with N >= 8^3 spins. We relate the round-trip times for multicanonical sampling to intrinsic properties of the energy landscape and compare with the numerical effort needed by the genetic Cluster-Exact Approximation to calculate the exact ground state energies. For systems with N >= 8^3 spins the simulation of these rare events becomes increasingly hard. For N >= 14^3 there are samples where the Wang-Landau algorithm fails to find the true ground state within reasonable simulation times. We expect similar behavior for other algorithms based on multicanonical sampling.Comment: 9 pages, 12 figure

IFI35, mir-99a and HCV Genotype to Predict Sustained Virological Response to Pegylated-Interferon Plus Ribavirin in Chronic Hepatitis C

International audienceAlthough, the treatment of chronic hepatitis C (CHC) greatly improved with the use of direct antiviral agents, pegylated-interferon (PEG-IFN) plus ribavirin remains an option for many patients, worldwide. The intra-hepatic level of expression of interferon stimulated genes (ISGs) and the rs12979860 CC genotype located within IFNL3 have been associated with sustained virological response (SVR), in patients with CHC. The aim of the study was to identify micro-RNAs associated with SVR and to build an accurate signature to predict SVR. Pre-treatment liver biopsies from 111 patients, treated with PEG-IFN plus ribavirin, were studied. Fifty-seven patients had SVR, 36 non-response (NR) and 18 relapse (RR). The expression of 851 human miRNAs and 30 selected mRNAs, including ISGs, was assessed by RT-qPCR. In the first group of patients (screen), 20 miRNAs out of the 851 studied were deregulated between NRs and SVRs. From the 4 miRNAs validated (mir-23a, mir-181a*, mir-217 and mir-99a), in the second group of patients (validation), 3 (mir-23a, mir-181a* and mir-99a) were down-regulated in NRs as compared to SVRs. The ISGs, studied, were accumulated in SVRs and IFNL3 rs12979860 CT/TT carriers compared respectively to NRs and CC carriers. Combining, clinical data together with the expression of selected genes and micro-RNAs, we identified a signature (IFI35, mir-99a and HCV genotype) to predict SVR (AUC:0.876) with a positive predictive value of 86.54% with high sensibility (80%) and specificity (80.4%). This signature may help to characterize patients with low chance to respond to PEG-IFN/ribavirin and to elucidate mechanisms of NR

Generating droplets in two-dimensional Ising spin glasses by using matching algorithms

We study the behavior of droplets for two dimensional Ising spin glasses with Gaussian interactions. We use an exact matching algorithm which enables study of systems with linear dimension L up to 240, which is larger than is possible with other approaches. But the method only allows certain classes of droplets to be generated. We study single-bond, cross and a category of fixed volume droplets as well as first excitations. By comparison with similar or equivalent droplets generated in previous works, the advantages but also the limitations of this approach are revealed. In particular we have studied the scaling behavior of the droplet energies and droplet sizes. In most cases, a crossover of the data can be observed such that for large sizes the behavior is compatible with the one-exponent scenario of the droplet theory. Only for the case of first excitations, no clear conclusion can be reached, probably because even with the matching approach the accessible system sizes are still too small.Comment: 11 pages, 16 figures, revte