Duccio Fanelli

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The issue of protein dynamics and its implications in the biological function of proteins are arousing greater and greater interest in different fields of molecular biology. In cryo-electron tomography experiments one may take several snapshots of a given biological macromolecule. In principle, a large enough collection of snapshots of the molecule may then(More)
A generic feature of systems with long-range interactions is the presence of quasistationary states with non-Gaussian single particle velocity distributions. For the case of the Hamiltonian mean-field model, we demonstrate that a maximum entropy principle applied to the associated Vlasov equation explains known features of such states for a wide range of(More)
The dynamics of a one-dimensional self-gravitating medium, with initial density almost uniform is studied. Numerical experiments are performed with ordered and with Gaussian random initial conditions. The phase space portraits are shown to be qualitatively similar to shock waves, in particular with initial conditions of Brownian type. The PDF of the mass(More)
A stochastic version of the Brusselator model is proposed and studied via the system size expansion. The mean-field equations are derived and shown to yield to organized Turing patterns within a specific parameters region. When determining the Turing condition for instability, we pay particular attention to the role of cross-diffusive terms, often neglected(More)
We study a simplified scheme of k coupled autocatalytic reactions, previously introduced by Togashi and Kaneko. The role of stochastic fluctuations is elucidated through the use of the van Kampen system-size expansion and the results compared with direct stochastic simulations. Regular temporal oscillations are predicted to occur for the concentration of(More)
The ultimate performance of a storage-ring free-electron laser in terms of light stability and extracted power depends on the possibility of simultaneously controlling the electron-beam and laser dynamics. As a preliminary requirement, the level of longitudinal and transverse electron-beam stability must be high enough to guarantee the laser start-up and(More)
In structural studies of proteins, the first task is to identify the different parts of the protein. We present a robust method using a fuzzy framework for delineating a protein and to identify its parts. The method is used in a study of the immunoglobulin G antibody, individually imaged using cryo electron tomography, with satisfactory results.
We analyze a pair of diffusion equations which are derived in the infinite system-size limit from a microscopic, individual based, stochastic model. Deviations from the conventional Fickian picture are found which ultimately relate to the depletion of resources on which the particles rely. The macroscopic equations are studied both analytically and(More)
Dynamical processes on networks have generated widespread interest in recent years. The theory of pattern formation in reaction-diffusion systems defined on symmetric networks has often been investigated, due to its applications in a wide range of disciplines. Here we extend the theory to the case of directed networks, which are found in a number of(More)
A general formalism is developed to construct a Markov chain model that converges to a one-dimensional map in the infinite population limit. Stochastic fluctuations are therefore internal to the system and not externally specified. For finite populations an approximate Gaussian scheme is devised to describe the stochastic fluctuations in the nonchaotic(More)