@article {2012,
	title = {Modeling and control of quantum systems: An introduction},
	journal = {IEEE Transactions on Automatic Control. Volume 57, Issue 8, 2012, Article number6189035, Pages 1898-1917},
	year = {2012},
	publisher = {Institute of Electrical and Electronics Engineers},
	abstract = {The scope of this work is to provide a self-contained introduction to a selection of basic theoretical aspects in the modeling and control of quantum mechanical systems, as well as a brief survey on the main approaches to control synthesis. While part of the existing theory, especially in the open-loop setting, stems directly from classical control theory (most notably geometric control and optimal control), a number of tools specifically tailored for quantum systems have been developed since the 1980s, in order to take into account their distinctive features: the probabilistic nature of atomic-scale physical systems, the effect of dissipation and the irreversible character of the measurements have all proved to be critical in feedback-design problems. The relevant dynamical models for both closed and open quantum systems are presented, along with the main results on their controllability and stability. A brief review of several currently available control design methods is meant to provide the interested reader with a roadmap for further studies},
	doi = {10.1109/TAC.2012.2195830},
	url = {http://hdl.handle.net/1963/6505},
	author = {Claudio Altafini and Francesco Ticozzi}
}
@article {2010,
	title = {Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks},
	journal = {BMC Systems Biology 2010, 4:83},
	year = {2010},
	publisher = {BioMed Central},
	abstract = {Background. \\nFor large-scale biological networks represented as signed graphs, the index of frustration measures how far a network is from a monotone system, i.e., how incoherently the system responds to perturbations.\\nResults. \\nIn this paper we find that the frustration is systematically lower in transcriptional networks (modeled at functional level) than in signaling and metabolic networks (modeled at stoichiometric level). A possible interpretation of this result is in terms of energetic cost of an interaction: an erroneous or contradictory transcriptional action costs much more than a signaling/metabolic error, and therefore must be avoided as much as possible. Averaging over all possible perturbations, however, we also find that unlike for transcriptional networks, in the signaling/metabolic networks the probability of finding the system in its least frustrated configuration tends to be high also in correspondence of a moderate energetic regime, meaning that, in spite of the higher frustration, these networks can achieve a globally ordered response to perturbations even for moderate values of the strength of the interactions. Furthermore, an analysis of the energy landscape shows that signaling and metabolic networks lack energetic barriers around their global optima, a property also favouring global order.\\nConclusion. \\nIn conclusion, transcriptional and signaling/metabolic networks appear to have systematic differences in both the index of frustration and the transition to global order. These differences are interpretable in terms of the different functions of the various classes of networks.},
	doi = {10.1186/1752-0509-4-83},
	url = {http://hdl.handle.net/1963/4055},
	author = {Giovanni Iacono and Claudio Altafini}
}
@article {2009,
	title = {mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle},
	journal = {BMC Systems Biology (2009) 3:18},
	year = {2009},
	publisher = {BioMed Central},
	abstract = {Background: In yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods.\\nResults: The dynamical regulation due to mRNA stability is found to be an important aspect of the genome-wide coordination of the long-period yeast metabolic cycle. It is shown that for periodic genes, arranged in classes according either to expression profile or to function, the pulses of mRNA abundance have phase and width which are directly proportional to the corresponding turnover rates.\\nConclusion: The cascade of events occurring during the yeast metabolic cycle (and their correlation with mRNA turnover) reflects to a large extent the gene expression program observable in other dynamical contexts such as the response to stresses/stimuli.},
	doi = {10.1186/1752-0509-3-18},
	url = {http://hdl.handle.net/1963/3630},
	author = {Nicola Soranzo and Mattia Zampieri and Lorenzo Farina and Claudio Altafini}
}
@article {2003,
	title = {Motion on submanifolds of noninvariant holonomic constraints for a kinematic control system evolving on a matrix Lie group},
	journal = {Syst. Control Lett. 50 (2003) 241-250},
	year = {2003},
	publisher = {Elsevier},
	abstract = {For a control system on a matrix Lie group with one or more configuration constraints that are not left/right invariant, finding the combinations of (kinematic) control inputs satisfying the motion constraints is not a trivial problem. Two methods, one coordinate-dependent and the other coordinate-free are suggested. The first is based on the Wei-Norman formula; the second on the calculation of the annihilator of the coadjoint action of the constraint one-form at each point of the group manifold. The results are applied to a control system on SE(3) with a holonomic inertial constraint involving the noncommutative part in a nontrivial way. The difference in terms of compactness of the result between the two methods is considerable.},
	doi = {10.1016/S0167-6911(03)00168-3},
	url = {http://hdl.handle.net/1963/3018},
	author = {Claudio Altafini and Ruggero Frezza}
}
