15,142 research outputs found
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.
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
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
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
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)
Model transformation of metabolic networks using a Petri net based framework
The different modeling approaches in Systems Biology create models with different levels of detail. The transformation techniques in Petri net theory can provide a solid framework for zooming between these different levels of abstraction and refinement. This work presents a Petri net based approach to Metabolic Engineering that implements model reduction methods to reduce the complexity of large-scale metabolic networks.
These methods can be complemented with kinetics inference to build dynamic models with a smaller number of parameters. The central carbon metabolism model of E. coli is used as a test-case to illustrate the application of these concepts. Model transformation is a promising mechanism to facilitate pathway analysis and dynamic modeling at the genome-scale level.(undefined
Bromeliaceae species from coastal restinga habitats, Brazilian states of Rio de Janeiro, EspÃrito Santo, and Bahia.
Bromeliaceae is one of the most representative plant families in restinga habitats. We analyzed the speciesrichness and composition of Bromeliaceae in 13 restinga habitats along the Brazilian coast. We found a total of 41species distributed along the restinga habitats studied. The restinga of Praia do Sul, in the state of Rio de Janeiro, hadthe highest number of species (15), whereas the restinga of Abaeté, in the state of Bahia, had the lowest (4). Our dataare suggestive that the Doce River may represent the limit of distribution for some bromeliad species, with some speciesoccurring only south of that river and others occurring only to the north of it. The differences in Bromeliaceae speciescomposition among restinga habitats probably are not only due to differences in local environmental conditions, butalso due to the geographic distribution pattern of each species and to the present degree of disturbance at each restinga
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
Novel modeling formalisms and simulation tools in computational biosystems
Living organisms are complex systems that emerge
from the fundamental building blocks of life. Systems
Biology is a recent field of science that studies these
complex phenomena at the cellular level (Kitano 2002).
Understanding the mechanisms of the cell is essential
for research and development in several areas such as
drug discovery and biotechnological production. In the
latter, metabolic engineering is used for building mutant
microbial strains with increased productivity of
compounds with industrial interest, such as biofuels
(Stephanopoulos 1998). Using computational models of
cellular metabolism, it is possible to systematically test
and predict the optimal manipulations, such as gene
knockouts, that produce the ideal phenotype for a
specific application. These models are typically built in
an iterative cycle of experiment and refinement, by
multidisciplinary research teams that include biologists,
engineers and computer scientists.
The interconnection between different cellular
processes, such as metabolism and genetic regulation,
reflects the importance of the holistic approach claimed
by the Systems Biology paradigm in replacement of
traditional reductionist methods. Although most cellular
components have been studied individually, the
behavior of the cell emerges from the network-level
interaction and requires an integrative analysis. Recent
high–throughput methods have generated the so- called
omics data (e.g.: genomics, transcriptomics, proteomics,
metabolomics, fluxomics) that have allowed the
reconstruction of biological networks (Palsson 2006).
However, despite the great advances in the area, we are
still far from a whole-cell computational model that is
able to simulate all the components of a living cell. Due
to the enormous size and complexity of intracellular
biological networks, computational cell models tend to
be partial and focused on the application of interest.
Also, due to the multidisciplinarity of the field, these
models are based on several different kinds of
formalisms. Therefore, it is important to develop a
framework with common modeling formalisms, analysis
and simulation methods, that is able to accommodate
different kinds biological networks, with different types
of entities and their interactions, into genome-scale
integrated models. Cells are composed by thousands of
components that interact in myriad ways. Despite this
intricate interconnection it is usual to divide and classify
these networks according to biological function. The
main types of networks are signaling, gene regulatory
and metabolic. Signal transduction is a process for
cellular communication where the cell receives and
responds to external stimuli through signaling cascades
(Gomperts et al. 2009; Albert and Wang 2009). These
cascades affect gene regulation, which is the method for
controlling gene expression, and consequently several
cellular functions (Schlittand and Brazma 2007;
Karlebach and Sgamir 2008). Many genes encode
enzymes which are responsible for catalyzing
biochemical reactions. The complex network of these
reactions forms the cellular metabolism that sustains the
cell’s growth and energy requirements (Steuer and
Junker 2009; Palsson 2006).
The objectives of this work, in the context of a PhD
thesis, consist in re-search and selection of an
appropriate modeling formalism to develop a
framework for integration of different biological
networks, with focus on regulatory and metabolic
networks, and the implementation of suitable analysis,
simulation and optimization methods. To achieve these
goals, it is necessary to resolve many modeling issues,
such as the integration of discrete and continuous
events, representation of network topology, support for
different levels of abstraction, lack of parameters and
model complexity. This framework will be used for the
implementation of an integrated model of E. coli, a
widely used organism for industrial application
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
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