The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks

<p>Abstract</p> <p>Background</p> <p>Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emphasize the global characterization of regulatory systems, the practical approaches focus on the role of distinct molecules and genes in regulation. To bridge the gap between these opposite approaches, one needs to combine 'general' with 'particular' properties and translate abstract topological features of large systems into testable functional characteristics of individual components. Here, we propose a new topological parameter – the pairwise disconnectivity index of a network's element – that is capable of such bridging.</p> <p>Results</p> <p>The pairwise disconnectivity index quantifies how crucial an individual element is for sustaining the communication ability between connected pairs of vertices in a network that is displayed as a directed graph. Such an element might be a vertex (i.e., molecules, genes), an edge (i.e., reactions, interactions), as well as a group of vertices and/or edges. The index can be viewed as a measure of topological redundancy of regulatory paths which connect different parts of a given network and as a measure of sensitivity (robustness) of this network to the presence (absence) of each individual element. Accordingly, we introduce the notion of a path-degree of a vertex in terms of its corresponding incoming, outgoing and mediated paths, respectively. The pairwise disconnectivity index has been applied to the analysis of several regulatory networks from various organisms. The importance of an individual vertex or edge for the coherence of the network is determined by the particular position of the given element in the whole network.</p> <p>Conclusion</p> <p>Our approach enables to evaluate the effect of removing each element (i.e., vertex, edge, or their combinations) from a network. The greatest potential value of this approach is its ability to systematically analyze the role of every element, as well as groups of elements, in a regulatory network.</p

Ultrafast ionization and fragmentation dynamics of polycyclic atomatic hydro-carbons by XUV radiation

In the interstellar medium polycyclic aromatic hydrocarbon molecules (PAH) are exposed to strong ionizing radation leading to complex organic photochemistry. We investigated these ultrafast fragmentation reactions after ionization of the PAHs phenanthrene, fluorene and pyrene at a wavelength of 30.3 nm using pump probe spectroscopy at a free electron laser. We observe double ionization and afterwards hydrogen abstraction and acetylene loss with characteristic time scales for the reaction processes below one hundred femtoseconds

Time-resolved relaxation and fragmentation of polycyclic aromatic hydrocarbons investigated in the ultrafast XUV-IR regime

Polycyclic aromatic hydrocarbons (PAHs) play an important role in interstellar chemistry and are subject to high energy photons that can induce excitation, ionization, and fragmentation. Previous studies have demonstrated electronic relaxation of parent PAH monocations over 10–100 femtoseconds as a result of beyond-Born-Oppenheimer coupling between the electronic and nuclear dynamics. Here, we investigate three PAH molecules: fluorene, phenanthrene, and pyrene, using ultrafast XUV and IR laser pulses. Simultaneous measurements of the ion yields, ion momenta, and electron momenta as a function of laser pulse delay allow a detailed insight into the various molecular processes. We report relaxation times for the electronically excited PAH*, PAH+* and PAH2+* states, and show the time-dependent conversion between fragmentation pathways. Additionally, using recoil-frame covariance analysis between ion images, we demonstrate that the dissociation of the PAH2+ ions favors reaction pathways involving two-body breakup and/or loss of neutral fragments totaling an even number of carbon atoms

Fragmentation dynamics of fluorene explored using ultrafast XUV-Vis pump-probe spectroscopy

We report on the use of extreme ultraviolet (XUV, 30.3&#xA0;nm) radiation from the Free-electron LASer in Hamburg (FLASH) and visible (Vis, 405&#xA0;nm) photons from an optical laser to investigate the relaxation and fragmentation dynamics of fluorene ions. The ultrashort laser pulses allow to resolve the molecular processes occurring on the femtosecond timescales. Fluorene is a prototypical small polycyclic aromatic hydrocarbon (PAH). Through their infrared emission signature, PAHs have been shown to be ubiquitous in the universe, and they are assumed to play an important role in the chemistry of the interstellar medium. Our experiments track the ionization and dissociative ionization products of fluorene through time-of-flight mass spectrometry and velocity-map imaging. Multiple processes involved in the formation of each of the fragment ions are disentangled through analysis of the ion images. The relaxation lifetimes of the excited fluorene monocation and dication obtained through the fragment formation channels are reported to be in the range of a few tens of femtoseconds to a few picoseconds