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

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

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

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

The Wide Field Imaging Interferometry Testbed

We are developing a Wide-Field Imaging Interferometry Testbed (WIIT) in support of design studies for NASA's future space interferometry missions, in particular the SPIRIT and SPECS far-infrared/submillimeter interferometers. WIIT operates at optical wavelengths and uses Michelson beam combination to achieve both wide-field imaging and high-resolution spectroscopy. It will be used chiefly to test the feasibility of using a large-format detector array at the image plane of the sky to obtain wide-field interferometry images through mosaicing techniques. In this setup each detector pixel records interferograms corresponding to averaging a particular pointing range on the sky as the optical path length is scanned and as the baseline separation and orientation is varied. The final image is constructed through spatial and spectral Fourier transforms of the recorded interferograms for each pixel, followed by a mosaic/joint-deconvolution procedure of all the pixels. In this manner the image within the pointing range of each detector pixel is further resolved to an angular resolution corresponding to the maximum baseline separation for fringe measurements. We present the motivation for building the testbed, show the optical, mechanical, control, and data system design, and describe the image processing requirements and algorithms. WIIT is presently under construction at NASA's Goddard Space Flight Center.Comment: 7 pages, 3 figures, IEEE Aerospace Conference 200

Multi-market minority game: breaking the symmetry of choice

Generalization of the minority game to more than one market is considered. At each time step every agent chooses one of its strategies and acts on the market related to this strategy. If the payoff function allows for strong fluctuation of utility then market occupancies become inhomogeneous with preference given to this market where the fluctuation occured first. There exists a critical size of agent population above which agents on bigger market behave collectively. In this regime there always exists a history of decisions for which all agents on a bigger market react identically.Comment: 15 pages, 12 figures, Accepted to 'Advances in Complex Systems

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

Microtremor response of a mass movement in Federal District of Brazil

The present study provides a brief description of the ambient noise recorded at a slow moving mass movement in Ribeirão Contagem Basin. The area is an interesting natural laboratory as river detachment processes in a number of different stages can be identified and are easily accessible. We investigate the site dynamic characteristics of the study area by recording ambient noise time-series at nine points, using portable nine three-component short period seismometers. The time-series are processed to give both horizontal to vertical spectral ratio (HVSR) curves as well as time-frequency plots of noise power spectral density (SPD). The HVSR curves illustrate and quantify aspects of site resonance effects due to underlying geology. Probability density function (PDF) shows that noise level lies well between new high noise model (NHNM) and new lower noise model (NLNM) and their probabilities are higher above 2 Hz. HVSR curves present a uniform lithologically controlled peak at 2 Hz. Directional properties of the wavefield are determined by beamforming method. The f-k analysis results in the E-W component show that at 5 Hz phase velocities are close to 1700 m/s while at 10 Hz dropped to 250 m/s. We observed that between 5 and 16 Hz the incoming wavefield arrive from 260 degrees. Further studies will apply a detailed noise analysis for the understanding of dynamics of the mass movement, which is triggered by the river erosion