Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

Cylindrically symmetric models of gravitational collapse to black holes: a short review

We survey results about exact cylindrically symmetric models of gravitational collapse in General Relativity. We focus on models which result from the matching of two spacetimes having collapsing interiors which develop trapped surfaces and vacuum exteriors containing gravitational waves. We collect some theorems from the literature which help to decide a priori about eventual spacetime matchings. We revise, in more detail, some toy models which include some of the main mathematical and physical issues that arise in this context, and compute the gravitational energy flux through the matching boundary of a particular collapsing region. Along the way, we point out several interesting open problems.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Search for New Phenomena in Dijet Angular Distributions in Proton-Proton Collisions at s√=8 TeV Measured with the ATLAS Detector

A search for new phenomena in LHC proton-proton collisions at a center-of-mass energy of s√=8 TeV was performed with the ATLAS detector using an integrated luminosity of 17.3 fb−1. The angular distributions are studied in events with at least two jets; the highest dijet mass observed is 5.5 TeV. All angular distributions are consistent with the predictions of the Standard Model. In a benchmark model of quark contact interactions, a compositeness scale below 8.1 TeV in a destructive interference scenario and 12.0 TeV in a constructive interference scenario is excluded at 95% CL; median expected limits are 8.9 TeV for the destructive interference scenario and 14.1 TeV for the constructive interference scenario.

Angular distributions in tt¯H(H→bb¯) reconstructed events at the LHC

The associated production of a Higgs boson and a top-quark pair, tt¯H, in proton-proton collisions is addressed in this paper for a center of mass energy of 13TeV at the LHC. Dileptonic final states of tt¯H events with two oppositely charged leptons and four jets from the decays t→bW+→bℓ+νℓ, t¯→b¯W−→b¯ℓ−ν¯ℓ and h→bb¯, are used. Signal events, generated with MadGraph5_aMC@NLO, are fully reconstructed by applying a kinematic fit. New angular distributions of the decay products as well as angular asymmetries are explored in order to improve discrimination of tt¯H signal events over the dominant irreducible background contribution, tt¯bb¯. Even after the full kinematic fit reconstruction of the events, the proposed angular distributions and asymmetries are still quite different in the tt¯H signal and the dominant background (tt¯bb¯).

Reprogramming energy metabolism and inducing angiogenesis : co-expression of monocarboxylate transporters with VEGF family members in cervical adenocarcinomas

Reprogramming energy metabolism and inducing angiogenesis: co-expression of monocarboxylate transporters with VEGF family members in cervical adenocarcinomas.