The dynamics of neural networks is often characterized by collective behavior and quasi synchrono... more The dynamics of neural networks is often characterized by collective behavior and quasi synchronous events, where a large fraction of neurons fire in short time intervals, separated by uncorrelated firing activity. These global temporal signals are crucial for brain functioning and they strongly depend on the topology of the network and on the fluctuations of the connectivity. We propose a heterogeneous mean-field approach to neural dynamics on random networks, that explicitly preserves the disorder in the topology at growing network sizes, and leads to a set of self-consistent equations. Within this approach, we provide an effective description of microscopic and large scale temporal signals in a leaky integrate-and-fire model with short term plasticity, where quasi-synchronous events arise. Our equations provide a clear analytical picture of the dynamics, evidencing the contributions of both periodic (locked) and aperiodic (unlocked) neurons to the measurable average signal. In pa...
A vast literature is nowadays devoted to the search of correlations between transcription related... more A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes. In particular, we have analyzed base composition, periodicity and information content in sets of aligned promoters clustered according to functional information in order to obtain an insight on the main structural differences between promoters regulating genes with different functions. Our results show that when we select promoters according to some biological information, in a single species, at least in vertebrates, we observe structurally different classes of sequences. The highly variable and differentiated gene expression patterns may explain the great extent of structural differentiation observed in complex organisms. In fact, despite our analysis is focused on Homo sapiens, we provide also a comparison with other species, selected at different positions in the phylogenetic tree.
Steady non-equilibrium states are investigated in a one-dimensional setup in the presence of two ... more Steady non-equilibrium states are investigated in a one-dimensional setup in the presence of two thermodynamic currents. Two paradigmatic nonlinear oscillators models are investigated: an XY chain and the discrete nonlinear Schr\"odinger equation. Their distinctive feature is that the relevant variable is an angle in both cases. We point out the importance of clearly distinguishing between energy and heat flux. In fact, even in the presence of a vanishing Seebeck coefficient, a coupling between (angular) momentum and energy arises, mediated by the unavoidable presence of a "coherent" energy flux. Such a contribution is the result of the "advection" induced by the position-dependent angular velocity. As a result, in the XY model, the knowledge of the two diagonal elements of the Onsager matrix suffices to reconstruct its transport properties. The analysis of the nonequilibrium steady states finally allows to strengthen the connection between the two models.
Localization and Energy Transfer in Nonlinear Systems - Proceedings of the Third Conference, 2003
ABSTRACT We study the energy relaxation process produced by damping 2D lattices of classical anha... more ABSTRACT We study the energy relaxation process produced by damping 2D lattices of classical anharmonic oscillators at the edges. Spontaneous emergence of localised vibrations dramatically slows down dissipation and gives rise to quasi-stationary residual states where energy is trapped in the form of a gas of weakly interacting discrete breathers. We show that the existence of a gap in the breather spectrum in 2D causes the localisation process to become activated. We investigate such a mechanism by studying the localisation time and the average density of localised objects.
The dynamics of plasmas (as well as of gravitational systems), due to the long-range nature of th... more The dynamics of plasmas (as well as of gravitational systems), due to the long-range nature of the 1/r 2 force, is principally dominated by mean field effects rather than by inter-particle collisions. Due to the ex-tremely large number of particles it is often natural to adopt a description in the continuum collisionless limit in terms of the Collisionless Boltzmann Equation (CBE) coupled with the Maxwell Equations (i.e. the Vlasov Equation). In fact, much numerical modeling of both neutral and non-neutral collisionless plasmas is done with schemes based on the CBE [7,13], such as the widely used Particle in Cell (PIC). However, there are regimes in which a description (at least statistical) of the particle collision is needed. For example, in tokamaks when-ever a hot plasma region is connected to the (colder) wall, a strong temperature gradient appears [6,11]. In this case, the properties of the plasma and therefore its collisionality vary strongly along the temperature gradient af...
... Gian-Luca Oppo Department of Physics and Applied Physics, University of Strathclyde, Glasgow,... more ... Gian-Luca Oppo Department of Physics and Applied Physics, University of Strathclyde, Glasgow, G)ONG, United Kingdom ... 1063-651X/94/49(3)/2009(14)/$06. 00 49 2009 1994 The American Physical Society Page 2. 2010 KAPRAL, LIVI, OPPO, AND POLITI ties. ...
Journal of Physics B: Atomic, Molecular and Optical Physics, 2007
... Roberto Franzosi1 , Roberto Livi2 and Gian-Luca Oppo3,4 ... Recent theoretical studies of the... more ... Roberto Franzosi1 , Roberto Livi2 and Gian-Luca Oppo3,4 ... Recent theoretical studies of the dynamics of BECs in optical lattices have suggested experiments where phenomena like the nonlinear LandauZener effect, Bloch oscillations, Josephson-junction behaviour and ...
In this paper, we propose a computational strategy for performing genome-wide analyses of interge... more In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features.
We study a simple stochastic model of neuronal excitatory and inhibitory interactions. The model ... more We study a simple stochastic model of neuronal excitatory and inhibitory interactions. The model is defined on a directed lattice and internodes couplings are modulated by a nonlinear function that mimics the process of synaptic activation. We prove that such a system behaves as a fully tunable amplifier: the endogenous component of noise, stemming from finite size effects, seeds a coherent (exponential) amplification across the chain generating giant oscillations with tunable frequencies, a process that the brain could exploit to enhance, and eventually encode, different signals. On a wider perspective, the characterized amplification process could provide a reliable pacemaking mechanism for biological systems. The device extracts energy from the finite size bath and operates as an out of equilibrium thermal machine, under stationary conditions.
The dynamics of neural networks is often characterized by collective behavior and quasi synchrono... more The dynamics of neural networks is often characterized by collective behavior and quasi synchronous events, where a large fraction of neurons fire in short time intervals, separated by uncorrelated firing activity. These global temporal signals are crucial for brain functioning and they strongly depend on the topology of the network and on the fluctuations of the connectivity. We propose a heterogeneous mean-field approach to neural dynamics on random networks, that explicitly preserves the disorder in the topology at growing network sizes, and leads to a set of self-consistent equations. Within this approach, we provide an effective description of microscopic and large scale temporal signals in a leaky integrate-and-fire model with short term plasticity, where quasi-synchronous events arise. Our equations provide a clear analytical picture of the dynamics, evidencing the contributions of both periodic (locked) and aperiodic (unlocked) neurons to the measurable average signal. In pa...
A vast literature is nowadays devoted to the search of correlations between transcription related... more A vast literature is nowadays devoted to the search of correlations between transcription related functions and the composition of sequences upstream the Transcription Start Site. Little is known about the possible functional effects of nucleotide distributions on the conformational landscape of DNA in such regions. We have used suitable statistical indicators for identifying sequences that may play an important role in regulating transcription processes. In particular, we have analyzed base composition, periodicity and information content in sets of aligned promoters clustered according to functional information in order to obtain an insight on the main structural differences between promoters regulating genes with different functions. Our results show that when we select promoters according to some biological information, in a single species, at least in vertebrates, we observe structurally different classes of sequences. The highly variable and differentiated gene expression patterns may explain the great extent of structural differentiation observed in complex organisms. In fact, despite our analysis is focused on Homo sapiens, we provide also a comparison with other species, selected at different positions in the phylogenetic tree.
Steady non-equilibrium states are investigated in a one-dimensional setup in the presence of two ... more Steady non-equilibrium states are investigated in a one-dimensional setup in the presence of two thermodynamic currents. Two paradigmatic nonlinear oscillators models are investigated: an XY chain and the discrete nonlinear Schr\"odinger equation. Their distinctive feature is that the relevant variable is an angle in both cases. We point out the importance of clearly distinguishing between energy and heat flux. In fact, even in the presence of a vanishing Seebeck coefficient, a coupling between (angular) momentum and energy arises, mediated by the unavoidable presence of a "coherent" energy flux. Such a contribution is the result of the "advection" induced by the position-dependent angular velocity. As a result, in the XY model, the knowledge of the two diagonal elements of the Onsager matrix suffices to reconstruct its transport properties. The analysis of the nonequilibrium steady states finally allows to strengthen the connection between the two models.
Localization and Energy Transfer in Nonlinear Systems - Proceedings of the Third Conference, 2003
ABSTRACT We study the energy relaxation process produced by damping 2D lattices of classical anha... more ABSTRACT We study the energy relaxation process produced by damping 2D lattices of classical anharmonic oscillators at the edges. Spontaneous emergence of localised vibrations dramatically slows down dissipation and gives rise to quasi-stationary residual states where energy is trapped in the form of a gas of weakly interacting discrete breathers. We show that the existence of a gap in the breather spectrum in 2D causes the localisation process to become activated. We investigate such a mechanism by studying the localisation time and the average density of localised objects.
The dynamics of plasmas (as well as of gravitational systems), due to the long-range nature of th... more The dynamics of plasmas (as well as of gravitational systems), due to the long-range nature of the 1/r 2 force, is principally dominated by mean field effects rather than by inter-particle collisions. Due to the ex-tremely large number of particles it is often natural to adopt a description in the continuum collisionless limit in terms of the Collisionless Boltzmann Equation (CBE) coupled with the Maxwell Equations (i.e. the Vlasov Equation). In fact, much numerical modeling of both neutral and non-neutral collisionless plasmas is done with schemes based on the CBE [7,13], such as the widely used Particle in Cell (PIC). However, there are regimes in which a description (at least statistical) of the particle collision is needed. For example, in tokamaks when-ever a hot plasma region is connected to the (colder) wall, a strong temperature gradient appears [6,11]. In this case, the properties of the plasma and therefore its collisionality vary strongly along the temperature gradient af...
... Gian-Luca Oppo Department of Physics and Applied Physics, University of Strathclyde, Glasgow,... more ... Gian-Luca Oppo Department of Physics and Applied Physics, University of Strathclyde, Glasgow, G)ONG, United Kingdom ... 1063-651X/94/49(3)/2009(14)/$06. 00 49 2009 1994 The American Physical Society Page 2. 2010 KAPRAL, LIVI, OPPO, AND POLITI ties. ...
Journal of Physics B: Atomic, Molecular and Optical Physics, 2007
... Roberto Franzosi1 , Roberto Livi2 and Gian-Luca Oppo3,4 ... Recent theoretical studies of the... more ... Roberto Franzosi1 , Roberto Livi2 and Gian-Luca Oppo3,4 ... Recent theoretical studies of the dynamics of BECs in optical lattices have suggested experiments where phenomena like the nonlinear LandauZener effect, Bloch oscillations, Josephson-junction behaviour and ...
In this paper, we propose a computational strategy for performing genome-wide analyses of interge... more In this paper, we propose a computational strategy for performing genome-wide analyses of intergenic sequences in bacterial genomes. Following similar directions of a previous paper, where a method for genome-wide analysis of eucaryotic Intergenic sequences was proposed, here we developed a tool for implementing similar concepts in bacteria genomes. This allows us to (i) classify intergenic sequences into clusters, characterized by specific global structural features and (ii) draw possible relations with their functional features.
We study a simple stochastic model of neuronal excitatory and inhibitory interactions. The model ... more We study a simple stochastic model of neuronal excitatory and inhibitory interactions. The model is defined on a directed lattice and internodes couplings are modulated by a nonlinear function that mimics the process of synaptic activation. We prove that such a system behaves as a fully tunable amplifier: the endogenous component of noise, stemming from finite size effects, seeds a coherent (exponential) amplification across the chain generating giant oscillations with tunable frequencies, a process that the brain could exploit to enhance, and eventually encode, different signals. On a wider perspective, the characterized amplification process could provide a reliable pacemaking mechanism for biological systems. The device extracts energy from the finite size bath and operates as an out of equilibrium thermal machine, under stationary conditions.
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Papers by Roberto Livi