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

The Magnetization of Cu_2(C_5H_{12}N_2)_2Cl_4 : A Heisenberg Spin Ladder System

We study the magnetization of a Heisenberg spin ladder using exact diagonalization techniques, finding three distinct magnetic phases. We consider the results in relation to the experimental behaviour of the new copper compound Cu_2(C_5H_{12}N_2)_2Cl_4 and deduce that the compound is well described by such a model with a ratio of `chain' to `rung' bond strengths (J/J^\prime) of the order of 0.2, consistent with results from the magnetic susceptibility. The effects of temperature, spin impurities and additional diagonal bonds are presented and we give evidence that these diagonal bonds are indeed of a ferromagnetic nature.Comment: Latex file (4 pages), related figures (encapsulated postscript) appende

Localized spin ordering in Kondo lattice models

Using a non-Abelian density matrix renormalization group method we determine the phase diagram of the Kondo lattice model in one dimension, by directly measuring the magnetization of the ground-state. This allowed us to discover a second ferromagnetic phase missed in previous approaches. The phase transitions are found to be continuous. The spin-spin correlation function is studied in detail, and we determine in which regions the large and small Fermi surfaces dominate. The importance of double-exchange ordering and its competition with Kondo singlet formation is emphasized in understanding the complexity of the model.Comment: Revtex, 4 pages, 4 eps figures embedde

Enabling the Collaborative Definition of DSMLs

International audienceSoftware development processes are collaborative in nature. Neglecting the key role of end-users leads to software that does not satisfy their needs. This collaboration becomes specially important when creating Domain-Specific Modeling Languages (DSMLs), which are (modeling) languages specifically designed to carry out the tasks of a particular domain. While end-users are actually the experts of the domain for which a DSML is developed, their participation in the DSML specification process is still rather limited nowadays. In this paper we propose a more community-aware language development process by enabling the active participation of all community members (both developers and end-users of the DSML) from the very beginning. Our proposal is based on a DSML itself, called Collaboro, which allows representing change proposals on the DSML design and discussing (and tracing back) possible solutions, comments and decisions arisen during the collaboration

The Heisenberg model on the 1/5-depleted square lattice and the CaV4O9 compound

We investigate the ground state structure of the Heisenberg model on the 1/5-depleted square lattice for arbitrary values of the first- and second-neighbor exchange couplings. By using a mean-field Schwinger-boson approach we present a unified description of the rich ground-state diagram, which include the plaquette and dimer resonant-valence-bond phases, an incommensurate phase and other magnetic orders with complex magnetic unit cells. We also discuss some implications of ours results for the experimental realization of this model in the CaV4O9 compound.Comment: 4 pages, Latex, 7 figures included as eps file

Intermediate temperature dynamics of one-dimensional Heisenberg antiferromagnets

We present a general theory for the intermediate temperature (T) properties of Heisenberg antiferromagnets of spin-S ions on p-leg ladders, valid for 2Sp even or odd. Following an earlier proposal for 2Sp even (Damle and Sachdev, cond-mat/9711014), we argue that an integrable, classical, continuum model of a fixed-length, 3-vector applies over an intermediate temperature range; this range becomes very wide for moderate and large values of 2Sp. The coupling constants of the effective model are known exactly in terms of the energy gap above the ground state (for 2Sp even) or a crossover scale (for 2Sp odd). Analytic and numeric results for dynamic and transport properties are obtained, including some exact results for the spin-wave damping. Numerous quantitative predictions for neutron scattering and NMR experiments are made. A general discussion on the nature of T>0 transport in integrable systems is also presented: an exact solution of a toy model proves that diffusion can exist in integrable systems, provided proper care is taken in approaching the thermodynamic limit.Comment: 38 pages, including 12 figure

Diagonalization in Reduced Hilbert Spaces using a Systematically Improved Basis: Application to Spin Dynamics in Lightly Doped Ladders

A method is proposed to improve the accuracy of approximate techniques for strongly correlated electrons that use reduced Hilbert spaces. As a first step, the method involves a change of basis that incorporates exactly part of the short distance interactions. The Hamiltonian is rewritten in new variables that better represent the physics of the problem under study. A Hilbert space expansion performed in the new basis follows. The method is successfully tested using both the Heisenberg model and the $t-J$ model with holes on 2-leg ladders and chains, including estimations for ground state energies, static correlations, and spectra of excited states. An important feature of this technique is its ability to calculate dynamical responses on clusters larger than those that can be studied using Exact Diagonalization. The method is applied to the analysis of the dynamical spin structure factor $S(q,\omega)$ on clusters with $2 \times 16$ sites and 0 and 2 holes. Our results confirm previous studies (M. Troyer, H. Tsunetsugu, and T. M. Rice, Phys. Rev. $B 53$, 251 (1996)) which suggested that the state of the lowest energy in the spin-1 2-holes subspace corresponds to the bound state of a hole pair and a spin-triplet. Implications of this result for neutron scattering experiments both on ladders and planes are discussed.Comment: 9 pages, 8 figures, Revtex + psfig; changed conten

Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness

<p>Abstract</p> <p>Background</p> <p>Two HIV-1 positive patients, L and P, participating in the Amsterdam Cohort studies acquired an HIV-1 superinfection within half a year from their primary HIV-1 infection (Jurriaans <it>et al</it>., <it>JAIDS </it>2008, <b>47:</b>69-73). The aim of this study was to compare the replicative fitness of the primary and superinfecting HIV-1 strains of both patients. The use of isolate-specific primer sets indicated that the primary and secondary strains co-exist in plasma at all time points after the moment of superinfection.</p> <p>Results</p> <p>Biological HIV-1 clones were derived from peripheral blood CD4 + T cells at different time point, and identified as the primary or secondary virus through sequence analysis. Replication competition assays were performed with selected virus pairs in PHA/IL-2 activated peripheral blood mononuclear cells (PBMC's) and analyzed with the Heteroduplex Tracking Assay (HTA) and isolate-specific PCR amplification. In both cases, we found a replicative advantage of the secondary HIV-1 strain over the primary virus. Full-length HIV-1 genomes were sequenced to find possible explanations for the difference in replication capacity. Mutations that could negatively affect viral replication were identified in the primary infecting strains. In patient L, the primary strain has two insertions in the LTR promoter, combined with a mutation in the <it>tat </it>gene that has been associated with decreased replication capacity. The primary HIV-1 strain isolated from patient P has two mutations in the LTR that have been associated with a reduced replication rate. In a luciferase assay, only the LTR from the primary virus of patient P had lower transcriptional activity compared with the superinfecting virus.</p> <p>Conclusions</p> <p>These preliminary findings suggest the interesting scenario that superinfection occurs preferentially in patients infected with a relatively attenuated HIV-1 isolate.</p

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis

Characterization of the Molecular Determinants of Primary HIV-1 Vpr Proteins: Impact of the Q65R and R77Q Substitutions on Vpr Functions

Although HIV-1 Vpr displays several functions in vitro, limited information exists concerning their relevance during infection. Here, we characterized Vpr variants isolated from a rapid and a long-term non-progressor (LTNP). Interestingly, vpr alleles isolated from longitudinal samples of the LTNP revealed a dominant sequence that subsequently led to diversity similar to that observed in the progressor patient. Most of primary Vpr proteins accumulated at the nuclear envelope and interacted with host-cell partners of Vpr. They displayed cytostatic and proapoptotic activities, although a LTNP allele, harboring the Q65R substitution, failed to bind the DCAF1 subunit of the Cul4a/DDB1 E3 ligase and was inactive. This Q65R substitution correlated with impairment of Vpr docking at the nuclear envelope, raising the possibility of a functional link between this property and the Vpr cytostatic activity. In contradiction with published results, the R77Q substitution, found in LTNP alleles, did not influence Vpr proapoptotic activity