2,042 research outputs found

    Sperimentazione di una metodologia di gerarchizzazione del territorio, basata sulla teoria dei grafi, ed analisi di sensibilità dei risultati

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    relazione tenuta da S. Fabbro alla IX Conferenza Italiana di Scienze Regionali, 7-9 Novembre, Torino e pubblicata nel preprint della Conferenz

    Isola dei Granai, Danzica

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    Presentazione del progetto per la trasformazione dell'Isola dei granai in centro città, redatto da G. Polesello con i suoi allievi (R. Fein, M. El Daccache, A. Dal Fabbro, M. Iori, S. Maffioletti, M. Montuori, P. Valle) in occasione del Seminario internazionale organizzato dall'Ordine degli Architetti della Polonia, Danzica 1989

    Valori divisi o condivisi? Uno scenario territoriale e di rilancio per la Capitale europea della cultura 2025

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    Il testo prende le mosse dal lavoro svolto da un gruppo di ricerca del Dipartimento di Ingegneria e Architettura-Università degli Studi di Trieste, che si è occupato di definire per il territorio transfrontaliero del GECT isontino (Gorizia-Nova Gorica-Šempeter Vrtojba) possibili modelli di pianificazione e progettazione urbanistica sostenibile. Nella fattispecie, chi scrive ha delineato il Documento strategico preliminare alla definizione delle Direttive per il nuovo Prg, che l’Amministrazione comunale di Gorizia, a vent’anni dall’approvazione del piano redatto da Gregotti e Associati, ha necessità di varare, per ripensare il futuro di una città da anni in crisi di idee per il proprio rilancio e finanche di identità. Per ripartire dal patrimonio urbano e territoriale di Gorizia, e della città transfrontaliera che il GECT rappresenta, e rimettere in discussione i suoi valori e il modo di metterli in gioco in uno scenario futuro per le tre città, si è delineato uno scenario, costruito per un orizzonte temporale che va al 2040, che ha come primo step di validazione un evento di grande importanza per un territorio tanto a lungo in crisi: la designazione di Nova Gorica, in stretta relazione con Gorizia e in collaborazione l’intero territorio transfrontaliero isontino, come Capitale Europea della Cultura (CEC) 2025. Un appuntamento al quale la città deve fin d’ora prepararsi, ripartendo da un importante patrimonio culturale spesso negletto, che comprende palazzi e ville storiche, giardini, musei, gli spazi urbani della “Nizza austriaca” asburgica, così come numerose architetture e parti urbane del Novecento

    Dynamics of allosteric action in multisite protein modification

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    Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e., the attachment of a phosphoryl ðPO3 Þ group, is the most studied form of protein modification, and is known to regulate the functions of many proteins, protein behavior can also be modified by nitrosylation, acetylation, methylation, etc. A protein can have multiple modification sites, and displays some form of transition only when enough sites are modified. In a previous paper we have modeled the generic equilibrium properties of multisite protein modification [R. Chignola, C. Dalla Pellegrina, A. Del Fabbro, E. Milotti, Physica A 371 (2006) 463] and we have shown that it can account both for sharp, robust thresholds and for information transfer between processes with widely separated timescales. Here we use the same concepts to expand that analysis starting from a dynamical description of multisite modification: we give analytical results for the basic dynamics and numerical results in an example where the modification chain is cascaded with a Michaelis–Menten step. We modify the dynamics and analyze an example with realistic phosphorylation/dephosphorylation steps, and give numerical evidence of the independence of the allosteric effect from the details of the attachment–detachment processes. We conclude that multisite protein modification is dynamically equivalent to the classic allosteric effect

    Numerical integration methods for large-scale biophysical simulations

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    Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species, and in the regulation of transport of molecules into and out of the cell or cellular compartments. Enzyme action is almost invariably modeled with the quasi-steady-state Michaelis–Menten formula or its close relative, the Hill formula: this description leads to systems of equations that may be stiff and hard to integrate, and poses unusual computational challenges in simulations where a smooth evolution is interrupted by the discrete events that mark the cells' lives, like initiation and termination of DNA synthesis or mitosis. These discrete events lead to abrupt parameter changes and to variable system size. This is the case of a numerical model (Virtual Biophysics Lab – VBL) that we are developing to simulate the growth of three-dimensional tumor cell aggregates (spheroids). The underlying cellular events have characteristic timescales that span approximately 12 orders of magnitude, and thus the program must be robust and stable. Moreover the program must be able to manage a very large number of equations (of the order of 107–108), and finally it must be able to accept frequent modifications of the underlying theoretical model. Here we study the applicability of known integration methods to this context – quite unusual from the point of view of the standard theory of differential equations, but extremely relevant to biophysics – and we describe the results of numerical tests in situations similar to those found in actual simulations

    Dynamics of intracellular Ca^{2+} oscillations in the presence of multisite Ca^{2+}-binding proteins

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    We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. These multisite calcium-binding proteins set a sharp threshold for calcium oscillations, and calcium oscillations stop at high concentrations of calcium-binding proteins. However even in these adverse conditions, internal noise, which shows up spontaneously in cells in the process of calcium wave formation, can lead to self-oscillations. This produces oscillatory behaviors strikingly similar to those observed in real cells. In addition, for given intracellular concentrations of both calcium and calcium-binding proteins the regularity of these oscillations changes and reaches a maximum as a function of the noise variance, and we find that the overall system dynamics displays coherence resonance. Thus it turns out that the calcium-binding proteins can have an important and non-trivial regularizing role
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