Mean-value identities as an opportunity for Monte Carlo error reduction

In the Monte Carlo simulation of both Lattice field-theories and of models of Statistical Mechanics, identities verified by exact mean-values such as Schwinger-Dyson equations, Guerra relations, Callen identities, etc., provide well known and sensitive tests of thermalization bias as well as checks of pseudo random number generators. We point out that they can be further exploited as "control variates" to reduce statistical errors. The strategy is general, very simple, and almost costless in CPU time. The method is demonstrated in the two dimensional Ising model at criticality, where the CPU gain factor lies between 2 and 4.Comment: 10 pages, 2 tables. References updated and typos correcte

Lattice-Spin Mechanism in Colossal Magnetoresistant Manganites

We present a single-orbital double-exchange model, coupled with cooperative phonons (the so called breathing-modes of the oxygen octahedra in manganites). The model is studied with Monte Carlo simulations. For a finite range of doping and coupling constants, a first-order Metal-Insulator phase transition is found, that coincides with the Paramagnetic-Ferromagnetic phase transition. The insulating state is due to the self-trapping of every carrier within an oxygen octahedron distortion.Comment: 4 pages, 5 figures, ReVTeX macro, accepted for publication in PR

Optimized Monte Carlo Method for glasses

A new Monte Carlo algorithm is introduced for the simulation of supercooled liquids and glass formers, and tested in two model glasses. The algorithm is shown to thermalize well below the Mode Coupling temperature and to outperform other optimized Monte Carlo methods. Using the algorithm, we obtain finite size effects in the specific heat. This effect points to the existence of a large correlation length measurable in equal time correlation functions.Comment: Proceedings of "X International workshop on Disordered Systems" held in Molveno (Italy), March 200

Finite size effects in the specific heat of glass-formers

We report clear finite size effects in the specific heat and in the relaxation times of a model glass former at temperatures considerably smaller than the Mode Coupling transition. A crucial ingredient to reach this result is a new Monte Carlo algorithm which allows us to reduce the relaxation time by two order of magnitudes. These effects signal the existence of a large correlation length in static quantities.Comment: Proceeding of "3rd International Workshop on Complex Systems". Sendai (Japan). To appear on AIP Conference serie

On the critical behavior of the specific heat in glass-formers

We show numeric evidence that, at low enough temperatures, the potential energy density of a glass-forming liquid fluctuates over length scales much larger than the interaction range. We focus on the behavior of translationally invariant quantities. The growing correlation length is unveiled by studying the Finite Size effects. In the thermodynamic limit, the specific heat and the relaxation time diverge as a power law. Both features point towards the existence of a critical point in the metastable supercooled liquid phase.Comment: Version to be published in Phys. Rev.

Temperature chaos in 3D Ising Spin Glasses is driven by rare events

Temperature chaos has often been reported in literature as a rare-event driven phenomenon. However, this fact has always been ignored in the data analysis, thus erasing the signal of the chaotic behavior (still rare in the sizes achieved) and leading to an overall picture of a weak and gradual phenomenon. On the contrary, our analysis relies on a large-deviations functional that allows to discuss the size dependencies. In addition, we had at our disposal unprecedentedly large configurations equilibrated at low temperatures, thanks to the Janus computer. According to our results, when temperature chaos occurs its effects are strong and can be felt even at short distances.Comment: 5 pages, 5 figure

Temperature chaos is a non-local effect

Temperature chaos plays a role in important effects, like for example memory and rejuvenation, in spin glasses, colloids, polymers. We numerically investigate temperature chaos in spin glasses, exploiting its recent characterization as a rare-event driven phenomenon. The peculiarities of the transformation from periodic to anti-periodic boundary conditions in spin glasses allow us to conclude that temperature chaos is non-local: no bounded region of the system causes it. We precise the statistical relationship between temperature chaos and the free-energy changes upon varying boundary conditions.Comment: 15 pages, 8 figures. Version accepted for publication in JSTA

Ontological realism, concepts and classification in molecular biology: Development and application of the gene ontology

Purpose – The purpose of this article is to evaluate the development and use of the gene ontology (GO), a scientific vocabulary widely used in molecular biology databases, with particular reference to the relation between the theoretical basis of the GO, and the pragmatics of its application. Design/methodology/approach – The study uses a combination of bibliometric analysis, content analysis and discourse analysis. These analyses focus on details of the ways in which the terms of the ontology are amended and deleted, and in which they are applied by users. Findings – Although the GO is explicitly based on an objective realist epistemology, a considerable extent of subjectivity and social factors are evident in its development and use. It is concluded that bio-ontologies could beneficially be extended to be pluralist, while remaining objective, taking a view of concepts closer to that of more traditional controlled vocabularies. Originality/value – This is one of very few studies which evaluate the development of a formal ontology in relation to its conceptual foundations, and the first to consider the GO in this way

Comprehensive study of the critical behavior in the diluted antiferromagnet in a field

We study the critical behavior of the Diluted Antiferromagnet in a Field with the Tethered Monte Carlo formalism. We compute the critical exponents (including the elusive hyperscaling violations exponent $\theta$). Our results provide a comprehensive description of the phase transition and clarify the inconsistencies between previous experimental and theoretical work. To do so, our method addresses the usual problems of numerical work (large tunneling barriers and self-averaging violations).Comment: 4 pages, 2 figure