On the dimensional dependence of duality groups for massive p-forms

We study the soldering formalism in the context of abelian p-form theories. We develop further the fusion process of massless antisymmetric tensors of different ranks into a massive p-form and establish its duality properties. To illustrate the formalism we consider two situations. First the soldering mass generation mechanism is compared with the Higgs and Julia-Toulouse mechanisms for mass generation due to condensation of electric and magnetic topological defects. We show that the soldering mechanism interpolates between them for even dimensional spacetimes, in this way confirming the Higgs/Julia-Toulouse duality proposed by Quevedo and Trugenberger \cite{QT} a few years ago. Next, soldering is applied to the study of duality group classification of the massive forms. We show a dichotomy controlled by the parity of the operator defining the symplectic structure of the theory and find their explicit actions.Comment: Reference [8] has been properly place

Bounds on topological Abelian string-vortex and string-cigar from information-entropic measure

In this work we obtain bounds on the topological Abelian string-vortex and on the string-cigar, by using a new measure of configurational complexity, known as configurational entropy. In this way, the information-theoretical measure of six-dimensional braneworlds scenarios are capable to probe situations where the parameters responsible for the brane thickness are arbitrary. The so-called configurational entropy (CE) selects the best value of the parameter in the model. This is accomplished by minimizing the CE, namely, by selecting the most appropriate parameters in the model that correspond to the most organized system, based upon the Shannon information theory. This information-theoretical measure of complexity provides a complementary perspective to situations where strictly energy-based arguments are inconclusive. We show that the higher the energy the higher the CE, what shows an important correlation between the energy of the a localized field configuration and its associated entropic measure.Comment: 6 pages, 7 figures, final version to appear in Phys. Lett.

Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands

The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined with self-interaction corrected density functional theory, we calculate the fully self-consistent coherent I-V curve of various double-strand polymeric DNA fragments. We show that electronic wave-function localization, induced either by the native electrical dipole and/or by the electrostatic disorder originating from the first few water solvation layers, drastically suppresses the magnitude of the elastic conductance of A-DNA oligonucleotides. We then argue that electron transport through DNA is the result of sequence-specific short-range tunneling across a few bases combined with general diffusive/inelastic processes.Comment: 15 pages, 13 figures, 1 tabl

Secure and trustworthy remote JavaScript execution

Javascript is used more and more as a programming language to develop web applications in order to increase the user experience and application interactivity. Although Javascript is a powerful technology that offers these characteristics, it is also a potential web application attack vector that can be exploited to impact the end-user, since it can be maliciously intercepted and modified. Today, web browsers act as worldwide open windows, executing, on a given user machine (computer, smartphone, tablet or any other), remote code. Therefore, it is important to ensure the trust on the execution of this remote code. This trust should be ensured at the JavaScript remote code producer, during transport and also locally before being executed on the end-user web-browser. In this paper, the authors propose and present a mechanism that allows the secure production and verification of web-applications JavaScript code. The paper also presents a set of tools that were developed to offer JavaScript code protection and ensure its trust at the production stage, but also a proxy-based mechanism that ensures end-users the un-modified nature and source validation of the remote JavaScript code prior to its execution by the end-user browser.info:eu-repo/semantics/acceptedVersio

Modelling allosteric regulation for prediction of flux control in the central carbon metabolism of E. coli

Rational strain design is a fundamental step in the development of microbial cell factories. Multiple genetic manipulations are often required in order to redirect the metabolic flux towards a product of industrial interest. Most manipulation targets are focused on central carbon metabolism, which provides the molecular precursors and the energy required for other biochemical pathways. However, the complex regulation of those pathways is still not completely unraveled. Recent studies have shown that central carbon metabolism is mostly regulated at post-transcriptional levels. In this work, we explore the role of allosteric regulation in the control of metabolic fluxes. We begin by expanding a metabolic network reconstruction of the central carbon metabolism of E. coli with allosteric interaction information from relevant databases. This model is used to integrate a multi-omic dataset for this organism. We analyze the coordinated changes in enzyme, metabolite and flux levels between multiple experimental conditions, and observe cases where allosteric regulators have a major contribution in the metabolic flux changes. We then develop a method for systematic prediction of potential cases of allosteric control for given metabolic perturbations. This is a valuable approach for predicting coordinated flux changes that would not be predicted with a purely stoichiometric model representation.BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes, REF. NORTE-07-0124-FEDER-00002

Modeling formalisms in systems biology

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.Research supported by grants SFRH/BD/35215/2007 and SFRH/BD/25506/2005 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal Program through the project "Bridging Systems and Synthetic Biology for the development of improved microbial cell factories" (MIT-Pt/BS-BB/0082/2008)

Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli

Redesign of microbial metabolism is a critical step in biotechnology for the production of industrially relevant compounds. Central carbon metabolism provides the energy and building blocks required for cellular growth and synthesis of the desired byproducts and, consequently, it is the main target for intervention in most rational strain design approaches. However, the complexity of central carbon metabolism is still not completely understood. Recent studies in different organisms show that flux control in central carbon metabolism is predominantly regulated by non-transcriptional mechanisms, leaving post-translational modifications, allosteric regulation, and thermodynamics as main candidates. In this work, we extend a model of central carbon metabolism of E.coli with allosteric interactions in order to reveal a hidden topology in metabolic networks. We use this model to integrate a multi-omic dataset containing transcript, protein, flux and metabolite levels to further dissect and analyze the contribution of allosteric regulation for metabolic flux control

Transcriptional vs post-transcriptional regulation of the central carbon metabolism of E. coli

Transcriptomics data are currently one of the most available types of large-scale biological data. A large number of methods have been developed to improve constraint-based simulations using these data. We recently performed a systematic comparison of these methods and observed that, at least for central carbon metabolism, there is no significant improvement in the prediction of flux distributions when gene expression data is used. These results are consistent with recent studies, in different organisms, showing that central carbon metabolism is predominantly regulated at post-transcriptional levels. Central carbon metabolism provides the precursors for the production of multiple compounds used in industrial biotechnology. Hence, it is the main target for intervention in most rational strain design strategies. However, its complexity is still not completely understood. In this work, we analyze the role of allosteric regulation, one of the main mechanisms of post-transcriptional regulation, for the control of central carbon metabolism. We extend a model of central carbon metabolism of E. coli with allosteric interactions, revealing a hidden topology in metabolic networks. We use this model to integrate a multi-omic dataset containing transcript, protein, flux and metabolite levels to further dissect the contribution of different types of regulation for metabolic flux control in these central pathways. Situations of predominant allosteric control could be identified, highlighting the importance of this kind of regulation in central carbon metabolism