Adaptively Biased Molecular Dynamics for Free Energy Calculations

We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential, and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters, and an $O(t)$ numerical cost with molecular dynamics time $t$. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.Comment: Revised version to appear in Journal of Chemical Physic

I materiali oftalmici per le montature. Percorso nella storia dell'occhialeria dai primi modelli ai giorni nostri

Questo testo parla di materiali per le montature. Non lo fa in maniera semplice, ovvero non consiste di un elenco dei materiali utilizzati per costruire gli occhiali con pregi e difetti. O meglio, tratta anche di questo ovviamente, ma partendo da lontano, dal XIII secolo, da quando il primo paio di occhiali è stato inventato. Dunque è un percorso nella storia, una lente d'ingrandimento per osservare come nei secoli si sono evolute le montature, come sono mutate le loro forme e il materiale di cui sono costruite fino ad arrivare ai giorni nostri. A partire dall’intuizione di Roger Bacon del 1267, e dalla successiva concretizzazione di essa nei successivi decenni, sono state sperimentate una vastità immensa di montature: dagli occhiali in corno a snodo e a perno, ai famosi modelli di Norimberga, ai fassamani e stringinaso, alla comparsa delle prime stanghette. Le problematiche, indifferentemente dal momento storico, sono sempre state legate a leggerezza e stabilità dell’occhiale sul volto; per questo motivo si è cercato un materiale che rappresentasse il giusto compromesso e si rivelasse l’ideale per questi parametri. Infatti i primi modelli costruiti in materiale naturale hanno presto lasciato il posto agli occhiali in metallo che permettevano di essere realizzati con strutture più snelle e meno ingombranti; questi materiali sono stati a loro volta modificati chimicamente o sostituiti dalle materie plastiche nel tardo ‘800 per far fronte alle problematiche di allergie. Nell’età contemporanea le attenzioni si sono spostate anche sul fornire alla montatura le più interessanti soluzioni “hi-tech” e di design. Una cospicua sezione dell’ elaborato è infatti dedicata alla descrizione dei materiali utilizzati negli anni Duemila nell’industria dell’occhialeria: dall’acciaio al magnesio, dall’acetato al legno sono sviscerate peculiarità strutturali e complicanze di lavorazione. E’ inoltre offerto un approccio filosofico-sociale legato al significato che l’occhiale ha avuto nelle varie società dal medioevo ad oggi: esso è stato semplice mezzo retroattivo per correggere la vista, ha avuto per molti anni un’ accezione negativa, è stato poi strumento di identificazione e vero e proprio status symbol.ope

Comment on ``Theory of Spinodal Decomposition''

I comment on a paper by S. B. Goryachev [PRL vol 72, p.1850 (1994)] that presents a theory of non-equilibrium dynamics for scalar systems quenched into an ordered phase. Goryachev incorrectly applies only a global conservation constraint to systems with local conservation laws.Comment: 2 pages LATeX (REVTeX macros), no figures. REVISIONS --- more to the point. microscopic example added, presentation streamlined, long-range interactions mentioned, to be published in Phys. Rev. Let

Development of a hypersensitive periodate-cleavable amino acid that is methionine- and disulfide-compatible and its application in MHC exchange reagents for T cell Characterisation

Incorporation of cleavable linkers into peptides and proteins is of particular value in the study of biological processes. Here we describe the synthesis of a cleavable linker that is hypersensitive to oxidative cleavage as the result of the periodate reactivity of a vicinal amino alcohol moiety. Two strategies directed towards the synthesis of a building block suitable for solid-phase peptide synthesis were developed: a chemoenzymatic route, involving l-threonine aldolase, and an enantioselective chemical route; these led to α,γ-diamino-β-hydroxybutanoic acids in diastereoisomerically mixed and enantiopure forms, respectively. Incorporation of the 1,2-amino alcohol linker into the backbone of a peptide generated a conditional peptide that was rapidly cleaved at very low concentrations of sodium periodate. This cleavable peptide ligand was applied in the generation of MHC exchange reagents for the detection of antigen-specific T cells in peripheral blood cells. The extremely low concentration of periodate required to trigger MHC peptide exchange allowed the co-oxidation of methionine and disulfide residues to be avoided. Conditional MHC reagents hypersensitive to periodate can now be applied without limitations when UV irradiation is undesired or less practical

An argument-based approach to cope with trust and pluralism in web news reports

Due to the huge amount of multi-source news that are available on the Web at any time, it is crucial to provide intelligent mechanisms to select and rank news reports. Over the last few years, a number of approaches based on criteria such as freshness, relevance and viewer profile have been proposed. However, most existing news processing services do not deal with credibility from a qualitative perspective, and do not provide mechanisms to cope with controversial news reports. To fill this gap, this paper proposes a news service framework that brings the notions of trust and pluralism into play. The proposed framework is based on a set of basic postulates characterizing the nature of trust. In our proposal, trust is modeled using Defeasible Logic Programming, a general-purpose defeasible argumentation formalism based on logic programming. Our approach helps identify antagonism among sources of news and facilitates the analysis of opposing positions. This allows us to integrate dialectical reasoning into a news recommender system, which has the capability of providing a reasoned basis for the news presented to the viewer.Red de Universidades con Carreras en Informática (RedUNCI

Modeling news trust: A defeasible logic programming approach

Deciding whether to trust an information sources on the Web has been recognized as one of the main problems in today’s Information Society. In particular, assessing the credibility of news is a major research challenge. Typically, criteria such as freshness, relevance and viewer profile have been used by news services to rank news. However, these services do not deal with credibility from a qualitative perspective, and do not provide mechanisms to cope with controversial news reports. To fill this gap, this paper proposes a novel framework that brings the notions of trust and pluralism into play. In our proposal, we integrate dialectical reasoning into a news recommender system. The system is based on a set of basic principles characterizing the nature of trust. We use Defeasible Logic Programming (DeLP), a general–purpose defeasible argumentation formalism based on logic programming, to model the notion of trust. Our approach helps identify antagonism among sources of news and facilitates the analysis of opposing positionsFil: Sagui, Fernando Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; ArgentinaFil: Maguitman, Ana Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; ArgentinaFil: Chesñevar, Carlos Iván. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; ArgentinaFil: Simari, Guillermo Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; Argentin

Late stage, non-equilibrium dynamics in the dipolar Ising model

Magnetic domain structures are a fascinating area of study with interest deriving both from technological applications and fundamental scientific questions. The nature of the striped magnetic phases observed in ultra-thin films is one such intriguing system. The non-equilibrium dynamics of such systems as they evolve toward equilibrium has only recently become an area of interest and previous work on model systems showed evidence of complex, slow dynamics with glass-like properties as the stripes order mesoscopically. To aid in the characterization of the observed phases and the nature of the transitions observed in model systems we have developed an efficient method for identifying clusters or domains in the spin system, where the clusters are based on the stripe orientation. Thus we are able to track the growth and decay of such clusters of stripes in a Monte Carlo simulation and observe directly the nature of the slow dynamics. We have applied this method to consider the growth and decay of ordered domains after a quench from a saturated magnetic state to temperatures near and well below the critical temperature in the two dimensional dipolar Ising model. We discuss our method of identifying stripe domains or clusters of stripes within this model and present the results of our investigations.Comment: 17 pages, 12 figures, submitted to JMM

A defeasible reasoning web service

In this article we outline a research line whose main goal is to give access to the software agents inhabiting the Web to a powerful inference service built around Defeasible Logic Programming (DeLP), a formalism that combines features of Logic Programming with Defeasible Argumentation. To do so, the web service prototype we proposed is the next logical step to take in order to allow agents to draw conclusions through DeLP within the Semantic Web.Eje: Agentes y Sistemas InteligentesRed de Universidades con Carreras en Informática (RedUNCI