Geometry and symmetry presculpt the free-energy landscape of proteins

We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and energetic constraints placed by the hydrogen bonds and sterics, and hydrophobicity are sufficient to yield a free energy landscape with broad minima even for a homopolymer. These minima correspond to marginally compact structures comprising the menu of folds that proteins choose from to house their native-states in. Our results provide a general framework for understanding the common characteristics of globular proteins.Comment: 23 pages, 5 figure

A framework for automatically checking anonymity with μ CRL

We present a powerful and flexible method for automatically checking anonymity in a possibilistic general-purpose process algebraic verification toolset. We propose new definitions of a choice anonymity degree and a player anonymity degree, to quantify the precision with which an intruder is able to single out the true originator of a given event or to associate the right event to a given protocol participant. We show how these measures of anonymity can be automatically calculated from a protocol specification in µCRL, by using a combination of dedicated tools and existing state-of-the-art µCRL tools. To illustrate the flexibility of our method we test the Dining Cryptographers problem and the FOO 92 voting protocol. Our definitions of anonymity provide an accurate picture of the different ways that anonymity can break down, due for instance to coallitions of inside intruders. Our calculations can be performed on a cluster of machines, allowing us to check protocols for large numbers of participants

Batalin-Vilkovisky Integrals in Finite Dimensions

The Batalin-Vilkovisky method (BV) is the most powerful method to analyze functional integrals with (infinite-dimensional) gauge symmetries presently known. It has been invented to fix gauges associated with symmetries that do not close off-shell. Homological Perturbation Theory is introduced and used to develop the integration theory behind BV and to describe the BV quantization of a Lagrangian system with symmetries. Localization (illustrated in terms of Duistermaat-Heckman localization) as well as anomalous symmetries are discussed in the framework of BV.Comment: 35 page

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Analysing Unlinkability and Anonymity Using the Applied Pi Calculus

Abstract—An attacker that can identify messages as coming from the same source, can use this information to build up a picture of targets ’ behaviour, and so, threaten their privacy. In response to this danger, unlinkable protocols aim to make it impossible for a third party to identify two runs of a protocol as coming from the same device. We present a framework for analysing unlinkability and anonymity in the applied pi calculus. We show that unlinkability and anonymity are complementary properties; one does not imply the other. Using our framework we show that the French RFID e-passport preserves anonymity but it is linkable therefore anyone carrying a French e-passport can be physically traced. I

LeakWatch: Estimating Information Leakage from Java Programs

Abstract. Programs that process secret data may inadvertently reveal information about those secrets in their publicly-observable output. This paper presents LeakWatch, a quantitative information leakage analysis tool for the Java programming language; it is based on a flexible “point-to-point ” information leakage model, where secret and publiclyobservable data may occur at any time during a program’s execution. LeakWatch repeatedly executes a Java program containing both secret and publicly-observable data and uses robust statistical techniques to provide estimates, with confidence intervals, for min-entropy leakage (using a new theoretical result presented in this paper) and mutual information. We demonstrate how LeakWatch can be used to estimate the size of information leaks in a range of real-world Java programs

From coordination to stochastic models of QoS

Reo is a channel-based coordination model whose operational semantics is given by Constraint Automata (CA). Quantitative Constraint Automat

Compositionality Results for Quantitative Information Flow

International audienceIn the min-entropy approach to quantitative information flow, the leakage is defined in terms of a minimization problem, which, in case of large systems, can be computationally rather heavy. The same happens for the recently proposed generalization called g-vulnerability. In this paper we study the case in which the channel associated to the system can be decomposed into simpler channels, which typically happens when the observables consist of several components. Our main contribution is the derivation of bounds on the g-leakage of the whole system in terms of the g-leakage of its components

Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the performance of different aligners and help detect systematic errors in alignments, a number of benchmarking strategies have been pursued. Here we present an overview of the main strategies--based on simulation, consistency, protein structure, and phylogeny--and discuss their different advantages and associated risks. We outline a set of desirable characteristics for effective benchmarking, and evaluate each strategy in light of them. We conclude that there is currently no universally applicable means of benchmarking MSA, and that developers and users of alignment tools should base their choice of benchmark depending on the context of application--with a keen awareness of the assumptions underlying each benchmarking strategy.Comment: Revie