The solution space of metabolic networks: producibility, robustness and fluctuations

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of its main areas of application is the study of cellular metabolic networks. We briefly and selectively review the main approaches to this problem and then, building on recent work, we provide a characterization of the productive capabilities of the metabolic network of the bacterium E.coli in a specified growth medium in terms of the producible biochemical species. While a robust and physiologically meaningful production profile clearly emerges (including biomass components, biomass products, waste etc.), the underlying constraints still allow for significant fluctuations even in key metabolites like ATP and, as a consequence, apparently lay the ground for very different growth scenarios.Comment: 10 pages, prepared for the Proceedings of the International Workshop on Statistical-Mechanical Informatics, March 7-10, 2010, Kyoto, Japa

Dynamics of a particle confined in a two-dimensional dilating and deforming domain

Some recent results concerning a particle confined in a one-dimensional box with moving walls are briefly reviewed. By exploiting the same techniques used for the 1D problem, we investigate the behavior of a quantum particle confined in a two-dimensional box (a 2D billiard) whose walls are moving, by recasting the relevant mathematical problem with moving boundaries in the form of a problem with fixed boundaries and time-dependent Hamiltonian. Changes of the shape of the box are shown to be important, as it clearly emerges from the comparison between the "pantographic", case (same shape of the box through all the process) and the case with deformation.Comment: 13 pages, 2 figure

MAGDA: A Mobile Agent based Grid Architecture

Mobile agents mean both a technology and a programming paradigm. They allow for a flexible approach which can alleviate a number of issues present in distributed and Grid-based systems, by means of features such as migration, cloning, messaging and other provided mechanisms. In this paper we describe an architecture (MAGDA – Mobile Agent based Grid Architecture) we have designed and we are currently developing to support programming and execution of mobile agent based application upon Grid systems

Transient fluctuation relations for time-dependent particle transport

We consider particle transport under the influence of time-varying driving forces, where fluctuation relations connect the statistics of pairs of time reversed evolutions of physical observables. In many "mesoscopic" transport processes, the effective many-particle dynamics is dominantly classical, while the microscopic rates governing particle motion are of quantum-mechanical origin. We here employ the stochastic path integral approach as an optimal tool to probe the fluctuation statistics in such applications. Describing the classical limit of the Keldysh quantum nonequilibrium field theory, the stochastic path integral encapsulates the quantum origin of microscopic particle exchange rates. Dynamically, it is equivalent to a transport master equation which is a formalism general enough to describe many applications of practical interest. We apply the stochastic path integral to derive general functional fluctuation relations for current flow induced by time-varying forces. We show that the successive measurement processes implied by this setup do not put the derivation of quantum fluctuation relations in jeopardy. While in many cases the fluctuation relation for a full time-dependent current profile may contain excessive information, we formulate a number of reduced relations, and demonstrate their application to mesoscopic transport. Examples include the distribution of transmitted charge, where we show that the derivation of a fluctuation relation requires the combined monitoring of the statistics of charge and work

Theory of controlled quantum dynamics

We introduce a general formalism, based on the stochastic formulation of quantum mechanics, to obtain localized quasi-classical wave packets as dynamically controlled systems, for arbitrary anharmonic potentials. The control is in general linear, and it amounts to introduce additional quadratic and linear time-dependent terms to the given potential. In this way one can construct for general systems either coherent packets moving with constant dispersion, or dynamically squeezed packets whose spreading remains bounded for all times. In the standard operatorial framework our scheme corresponds to a suitable generalization of the displacement and scaling operators that generate the coherent and squeezed states of the harmonic oscillator.Comment: LaTeX, A4wide, 28 pages, no figures. To appear in J. Phys. A: Math. Gen., April 199

The tris formulation of Fluorouracil is more cardiotoxic than the sodium-salt formulations

The cardiotoxicity of 5-fluorouracil (FU) was attributed to degradation compounds present in the injected vials, fluoroacetaldehyde (Facet) and fluoromalonaldehydic acid (FMald). FU-NaOH vials were much less cardiotoxic than FU-Tris vials on the isolated perfused rabbit heart model since Facet and FMald are stored in stable depot forms in FU-Tris vials whereas, in FU-NaOH vials, they are extensively transformed. Cardiotoxic fluoroacetate (FAG), coming from Facet metabolization, was found in urine of patients, with a ratio FAC /FU catabolites 10-30 fold lower in patients treated with FU-NaOH than in those treated with FU-Tris

Two new intermediate polars with a soft X-ray component

Aims. We analyze the first X-ray observations with XMM-Newton of 1RXS J070407.9+262501 and 1RXS 180340.0+401214, in order to characterize their broad-band temporal and spectral properties, also in the UV/optical domain, and to confirm them as intermediate polars. Methods. For both objects, we performed a timing analysis of the X-ray and UV/optical light curves to detect the white dwarf spin pulsations and study their energy dependence. For 1RXS 180340.0+401214 we also analyzed optical spectroscopic data to determine the orbital period. X-ray spectra were analyzed in the 0.2–10.0 keV range to characterize the emission properties of both sources. Results. We find that the X-ray light curves of both systems are energy dependent and are dominated, below 3–5 keV, by strong pulsations at the white dwarf rotational periods (480 s for 1RXS J070407.9+262501 and 1520.5 s for 1RXS 180340.0+401214). In 1RXS 180340.0+401214 we also detect an X-ray beat variability at 1697 s which, together with our new optical spectroscopy, favours an orbital period of 4.4 h that is longer than previously estimated. Both systems show complex spectra with a hard (temperature up to 40 keV) optically thin and a soft (kT ∼ 85–100 eV) optically thick components heavily absorbed by material partially covering the X-ray sources. Conclusions. Our observations confirm the two systems as intermediate polars and also add them as new members of the growing group of “soft” systems which show the presence of a soft X-ray blackbody component. Differences in the temperatures of the blackbodies are qualitatively explained in terms of reprocessing over different sizes of the white dwarf spot. We suggest that systems showing cooler soft X-ray blackbody components also possess white dwarfs irradiated by cyclotron radiation

Generalized minority games with adaptive trend-followers and contrarians

We introduce a simple extension of the minority game in which the market rewards contrarian (resp. trend-following) strategies when it is far from (resp. close to) efficiency. The model displays a smooth crossover from a regime where contrarians dominate to one where trend-followers dominate. In the intermediate phase, the stationary state is characterized by non-Gaussian features as well as by the formation of sustained trends and bubbles.Comment: 4 pages, 6 figure