An optimization model for metabolic pathways

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Different mathematical methods have emerged in the post-genomic era to determine metabolic pathways. These methods can be divided into stoichiometric methods and path finding methods. In this paper we detail a novel optimization model, based upon integer linear programming, to determine metabolic pathways. Our model links reaction stoichiometry with path finding in a single approach. We test the ability of our model to determine 40 annotated Escherichia coli metabolic pathways. We show that our model is able to determine 36 of these 40 pathways in a computationally effective manner. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp441/DC1)

Temperature contour maps at the strain-induced martensitic transition of a Cu–Zn–Al shape-memory single crystal

We study temperature changes at the reverse strain-induced martensitic transformation in a Cu–Zn–Al single crystal. Infrared thermal imaging reveals a markedly inhomogeneous temperature distribution. The evolution of the contour temperature maps enables information to be extracted on the kinetics of the interface motion

Driving rate effects in avalanche-mediated, first-order phase transitions

We have studied the driving rate and temperature dependence of the power-law exponents that characterize the avalanche distribution in first-order phase transitions. Measurements of acoustic emission in structural transitions in Cu-Zn-Al and Cu-Al-Ni are presented. We show how the observed behaviour emerges within a general framework of competing time scales of avalanche relaxation, driving rate, and thermal fluctuations. We have confirmed our findings by numerical simulations of a prototype model.Comment: 4 pages, 3 figure

Statistical similarity between the compression of a porous material and earthquakes

It has been long stated that there are profound analogies between fracture experiments and earthquakes; however, few works attempt a complete characterization of the parallelisms between these so separate phenomena. We study the Acoustic Emission events produced during the compression of Vycor (SiO2). The Gutenberg-Richter law, the modified Omori's law, and the law of aftershock productivity are found to hold for a minimum of 5 decades, are independent of the compression rate, and keep stationary for all the duration of the experiments. The waiting-time distribution fulfills a unified scaling law with a power-law exponent close to 2.45 for long times, which is explained in terms of the temporal variations of the activity rate.Comment: 4 pages and a bit more, 4 figure

Estudio de la abducción del hombro mediante videofotogrametría (VFG) y radiología seriada (RX) simultánea

El complejo articular del hombro posee la mayor movilidad de todas las articulaciones del cuerpo. Está formado por un conjunto de estructuras: articulación escapulohumeral, acromioclavicular, esternoclavicular, escapulotorácica (seudoarticulación de la escápula con la pared torácica) que actuan coordinadamente unas con otras para situar la extremidad superior y, en definitiva la mano, en cualquier sitio del espacio. El estudio del movimiento de este complejo articular del hombro ha sido motivo de muchas investigaciones que han generado temas de controversia durante los últimos cien años. Desde su origen, las articulaciones han ido evolucionando hasta especializarse para efectuar unos determinados movimientos más específicos y precisos, al mismo tiempo que han ido abandonando otros. La articulaciones multiaxiales, las más proximales de las extremidades como el muslo, son las que han persistido con un mayor grado de movilidad y las que, por tanto, requieren un control muscular más preciso. La evolución hacia la bipedestación, implica una serie de cambios: aparición de lordosis en la columna, aumento del diámetro transversal del tórax juntamente con un desplazamiento hacia atrás de la clavícula y la escápula permitiendo así mayor amplitud de movimientos, sobretodo en la rotación y en la función prensil de la extremidad superior. En el muslo, se sacrificó la estabilidad para adquirir más movilidad4

Path finding methods accounting for stoichiometry in metabolic networks

Graph-based methods have been widely used for the analysis of biological networks. Their application to metabolic networks has been much discussed, in particular noting that an important weakness in such methods is that reaction stoichiometry is neglected. In this study, we show that reaction stoichiometry can be incorporated into path-finding approaches via mixed-integer linear programming. This major advance at the modeling level results in improved prediction of topological and functional properties in metabolic networks

Martensitic transition and magnetoresistance in a Cu-Al-Mn shape memory alloy. Influence of aging

We have studied the effect of ageing within the miscibility gap on the electric, magnetic and thermodynamic properties of a non-stoichiometric Heusler Cu-Al-Mn shape-memory alloy, which undergoes a martensitic transition from a $bcc$-based ($\beta$-phase) towards a close-packed structure ($M$-phase). Negative magnetoresistance which shows an almost linear dependence on the square of magnetization with different slopes in the $M$- and $\beta$-phases, was observed. This magnetoresistive effect has been associated with the existence of Mn-rich clusters with the Cu$_2$AlMn-structure. The effect of an applied magnetic field on the martensitic transition has also been studied. The entropy change between the $\beta$- and $M$-phases shows negligible dependence on the magnetic field but it decreases significantly with annealing time within the miscibility gap. Such a decrease is due to the increasing amount of Cu$_2$MnAl-rich domains that do not transform martensitically.Comment: 9 pages, 9 figures, accepted for publication in PR

On the athermal character of structural phase transitions

The significance of thermal fluctuations on nucleation in structural first-order phase transitions has been examined. The prototype case of martensitic transitions has been experimentally investigated by means of acoustic emission techniques. We propose a model based on the mean first-passage time to account for the experimental observations. Our study provides a unified framework to establish the conditions for isothermal and athermal transitions to be observed.Comment: 5 pages, 4 figures, accepted in Phys. Rev. Let

Disorder induced critical phenomena in magnetically glassy Cu-Al-Mn alloys

Measurements of magnetic hysteresis loops in Cu-Al-Mn alloys of different Mn content at low temperatures are presented. The loops are smooth and continuous above a certain temperature, but exhibit a magnetization discontinuity below that temperature. Scaling analysis suggest that this system displays a disorder induced phase transition line. Measurements allow to determine the critical exponents $\beta=0.03\pm 0.01$ and $\beta \delta = 0.4 \pm 0.1$ in agreement with those reported recently [Berger et al., Phys. Rev. Lett. {\bf 85}, 4176 (2000)]Comment: 4 pages, 5 figure

Metabolic pathway analysis via integer linear programming

The understanding of cellular metabolism has been an intriguing challenge in classical cellular biology for decades. Essentially, cellular metabolism can be viewed as a complex system of enzyme-catalysed biochemical reactions that produces the energy and material necessary for the maintenance of life. In modern biochemistry, it is well-known that these reactions group into metabolic pathways so as to accomplish a particular function in the cell. The identification of these metabolic pathways is a key step to fully understanding the metabolic capabilities of a given organism. Typically, metabolic pathways have been elucidated via experimentation on different organisms. However, experimental findings are generally limited and fail to provide a complete description of all pathways. For this reason it is important to have mathematical models that allow us to identify and analyze metabolic pathways in a computational fashion. This is precisely the main theme of this thesis. We firstly describe, review and discuss existent mathematical/computational approaches to metabolic pathways, namely stoichiometric and path finding approaches. Then, we present our initial mathematical model named the Beasley-Planes (BP) model, which significantly improves on previous stoichiometric approaches. We also illustrate a successful application of the BP model to optimally disrupt metabolic pathways. The main drawback of the BP model is that it needs as input extra pathway knowledge. This is especially inappropriate if we wish to detect unknown metabolic pathways. As opposed to the BP model and stoichoimetric approaches, this issue is not found in path finding approaches. For this reason a novel path finding approach is built and examined in detail. This analysis serves us as inspiration to build the Improved Beasley-Planes (IBP) model. The IBP model incorporates elements of both stoichometric and path finding approaches. Though somewhat less accurate than the BP model, the IBP model solves the issue of extra pathway knowledge. Our research clearly demonstrates that there is a significant chance of developing a mathematical optimisation model that underlies many/all metabolic pathways.EThOS - Electronic Theses Online ServiceUniversity of NavarraGBUnited Kingdo