@article {2013,
	title = {Common dynamical features of sensory adaptation in photoreceptors and olfactory sensory neurons.},
	journal = {Nature. Scientific Reports 3, Article number: 1251, Published  : 13 February 2013},
	year = {2013},
	publisher = {SISSA},
	abstract = {<p>Sensory systems adapt, i.e., they adjust their sensitivity to external stimuli according to the ambient level. In this paper we show that single cell electrophysiological responses of vertebrate olfactory receptors and of photoreceptors to different input protocols exhibit several common features related to adaptation, and that these features can be used to investigate the dynamical structure of the feedback regulation responsible for the adaptation. In particular, we point out that two different forms of adaptation can be observed, in response to steps and to pairs of pulses. These two forms of adaptation appear to be in a dynamical trade-off: the more adaptation to a step is close to perfect, the slower is the recovery in adaptation to pulse pairs and viceversa. Neither of the two forms is explained by the dynamical models currently used to describe adaptation, such as the integral feedback model.</p>},
	doi = {10.1038/srep01251},
	author = {Giovanna De Palo and Giuseppe Facchetti and Monica Mazzolini and Anna Menini and Vincent Torre and Claudio Altafini}
}
@article {2011,
	title = {Computing global structural balance in large-scale signed social networks.},
	journal = {Proceedings of the National Academy of Sciences of the United States of America. Volume 108, Issue 52, 27 December 2011, Pages 20953-20958},
	number = {PMID:22167802;},
	year = {2011},
	note = {Free fulltext article in Pubmed Central},
	publisher = {National Academy of Sciences},
	abstract = {Structural balance theory affirms that signed social networks (i.e., graphs whose signed edges represent friendly/hostile interactions among individuals) tend to be organized so as to avoid conflictual situations, corresponding to cycles of negative parity. Using an algorithm for ground-state calculation in large-scale Ising spin glasses, in this paper we compute the global level of balance of very large online social networks and verify that currently available networks are indeed extremely balanced. This property is explainable in terms of the high degree of skewness of the sign distributions on the nodes of the graph. In particular, individuals linked by a large majority of negative edges create mostly \\\"apparent disorder,\\\" rather than true \\\"frustration.\\\"},
	keywords = {Combinatorial optimization},
	doi = {10.1073/pnas.1109521108},
	url = {http://hdl.handle.net/1963/6426},
	author = {Giuseppe Facchetti and Giovanni Iacono and Claudio Altafini}
}
@article {2009,
	title = {Characterization of the time course of changes of the evoked electrical activity in a model of a chemically-induced neuronal plasticity},
	journal = {BMC Research Notes (2009) 2:13},
	year = {2009},
	publisher = {BioMed Central},
	abstract = {BACKGROUND: Neuronal plasticity is initiated by transient elevations of neuronal networks activity leading to changes of synaptic properties and providing the basis for memory and learning 1. An increase of electrical activity can be caused by electrical stimulation 2 or by pharmacological manipulations: elevation of extracellular K+ 3, blockage of inhibitory pathways 4 or by an increase of second messengers intracellular concentrations 5. Neuronal plasticity is mediated by several biochemical pathways leading to the modulation of synaptic strength, density of ionic channels and morphological changes of neuronal arborisation 6. On a time scale of a few minutes, neuronal plasticity is mediated by local protein trafficking 7 while, in order to sustain modifications beyond 2-3 h, changes of gene expression are required 8. FINDINGS: In the present manuscript we analysed the time course of changes of the evoked electrical activity during neuronal plasticity and we correlated it with a transcriptional analysis of the underlying changes of gene expression. Our investigation shows that treatment for 30 min. with the GABAA receptor antagonist gabazine (GabT) causes a potentiation of the evoked electrical activity occurring 2-4 hours after GabT and the concomitant up-regulation of 342 genes. Inhibition of the ERK1/2 pathway reduced but did not abolish the potentiation of the evoked response caused by GabT. In fact not all the genes analysed were blocked by ERK1/2 inhibitors. CONCLUSION: These results are in agreement with the notion that neuronal plasticity is mediated by several distinct pathways working in unison.},
	doi = {10.1186/1756-0500-2-13},
	url = {http://hdl.handle.net/1963/3706},
	author = {Frederic D. Broccard and Silvia Pegoraro and Maria Elisabetta Ruaro and Claudio Altafini and Vincent Torre}
}
@article {2009,
	title = {Controllability and simultaneous controllability of isospectral bilinear control systems on complex flag manifolds},
	journal = {Systems Control Lett. 58 (2009) 213-216},
	year = {2009},
	publisher = {Elsevier},
	abstract = {For isospectral bilinear control systems evolving on the so-called complex flag manifolds (i.e., on the orbits of the Hermitian matrices under unitary conjugation action) it is shown that controllability is almost always verified. Easy and generic sufficient conditions are provided. The result applies to the problem of density operator controllability of finite dimensional quantum mechanical systems. In addition, we show that systems having different drifts (corresponding for example to different Larmor frequencies) are simultaneously controllable by the same control field.},
	doi = {10.1016/j.sysconle.2008.10.008},
	url = {http://hdl.handle.net/1963/3523},
	author = {Claudio Altafini}
}
@article {2007,
	title = {Comparing association network algorithms for reverse engineering of large scale gene regulatory networks: synthetic vs real data},
	journal = {Bioinformatics 23 (2007) 1640-1647},
	year = {2007},
	abstract = {Motivation: Inferring a gene regulatory network exclusively from microarray expression profiles is a difficult but important task. The aim of this work is to compare the predictive power of some of the most popular algorithms in different conditions (like data taken at equilibrium or time courses) and on both synthetic and real microarray data. We are in particular interested in comparing similarity measures both of linear type (like correlations and partial correlations) and of nonlinear type (mutual information and conditional mutual information), and in investigating the underdetermined case (less samples than genes). Results: In our simulations we see that all network inference algorithms obtain better performances from data produced with \\\"structural\\\" perturbations, like gene knockouts at steady state, than with any dynamical perturbation. The predictive power of all algorithms is confirmed on a reverse engineering problem from E. coli gene profiling data: the edges of the \\\"physical\\\" network of transcription factor-binding sites are significantly overrepresented among the highest weighting edges of the graph that we infer directly from the data without any structure supervision. Comparing synthetic and in vivo data on the same network graph allows us to give an indication of how much more complex a real transcriptional regulation program is with respect to an artificial model. Availability: Software and supplementary material are freely available at the URL http://people.sissa.it/~altafini/papers/SoBiAl07/},
	doi = {10.1093/bioinformatics/btm163},
	url = {http://hdl.handle.net/1963/2028},
	author = {Nicola Soranzo and Ginestra Bianconi and Claudio Altafini}
}
@article {2005,
	title = {Commuting multiparty quantum observables and local compatibility},
	journal = {Phys. Rev. A 72 (2005) 012112},
	number = {SISSA;93/2004/M},
	year = {2005},
	abstract = {A formula for the commutator of tensor product matrices is used to shows that, for qubits, compatibility of quantum multiparty observables almost never implies local compatibility at each site and to predict when this happens/does not happen in a concise manner. In particular, it is shown that two {\textquoteleft}{\textquoteleft}fully nontrivial\\\'\\\' $n$-qubit observables are compatible locally and globally if and only if they are equal up to sign. In addition, the formula gives insight into the construction of new paradoxes of the type of the Kochen-Specker Theorem, which can then be easily rephrased into proposals for new no hidden variable experiments of the type of the {\textquoteleft}{\textquoteleft}Bell Theorem without inequalities\\\'\\\'.},
	doi = {10.1103/PhysRevA.72.012112},
	url = {http://hdl.handle.net/1963/2228},
	author = {Claudio Altafini}
}
@article {2004,
	title = {Coherent control of open quantum dynamical systems},
	journal = {Phys. Rev. A 70 (2004) 062321},
	number = {SISSA;90/2004/M},
	year = {2004},
	abstract = {A systematic analysis of the behavior of the quantum Markovian master equation driven by coherent control fields is proposed. Its irreversible character is formalized using control-theoretic notions and the sets of states that can be reached via cohere nt controls are described. The analysis suggests to which extent (and how) it is possible to counteract the effect of dissipation.},
	doi = {10.1103/PhysRevA.70.062321},
	url = {http://hdl.handle.net/1963/2227},
	author = {Claudio Altafini}
}
@article {2003,
	title = {Controllability properties for finite dimensional quantum Markovian master equations},
	journal = {J. Math. Phys. 44 (2003) 2357-2372},
	number = {SISSA;7/2003/M},
	year = {2003},
	publisher = {American Institute of Physics},
	abstract = {Various notions from geometric control theory are used to characterize the behavior of the Markovian master equation for N-level quantum mechanical systems driven by unitary control and to describe the structure of the sets of reachable states. It is shown that the system can be accessible but neither small-time controllable nor controllable in finite time. In particular, if the generators of quantum dynamical semigroups are unital, then the reachable sets admit easy characterizations as they monotonically grow in time. The two level case is treated in detail.},
	doi = {10.1063/1.1571221},
	url = {http://hdl.handle.net/1963/2909},
	author = {Claudio Altafini}
}
@article {2002,
	title = {Controllability of quantum mechanical systems by root space decomposition of su(N)},
	journal = {J.Math.Phys. 43(2002), no.5, 2051},
	number = {SISSA;42/2002/M},
	year = {2002},
	publisher = {SISSA Library},
	doi = {10.1063/1.1467611},
	url = {http://hdl.handle.net/1963/1613},
	author = {Claudio Altafini}
}
