A statistical mechanics description of environmental variability in metabolic networks

Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks display considerable asymmetry. In this paper, we explore possible evolutionary factors pertaining to the reduced symmetry observed in these networks, and demonstrate the important role environmental variability plays in shaping their structural organization. Interpreting the returnability index as an equilibrium constant for a reaction network in equilibrium with a hypothetical reference system, enables us to quantify the extent to which a metabolic network is in disequilibrium. Further, by introducing a new directed centrality measure via an extension of the subgraph centrality metric to directed networks, we are able to characterise individual metabolites by their participation within metabolic pathways. To demonstrate these ideas, we study 116 metabolic networks of bacteria. In particular, we find that the equilibrium constant for the metabolic networks decreases significantly in-line with variability in bacterial habitats, supporting the view that environmental variability promotes disequilibrium within these biochemical reaction system

Dissection of GTPase activating proteins reveals functional asymmetry in the COPI coat of budding yeast.

The Arf GTPase controls formation of the COPI vesicle coat. Recent structural models of COPI revealed the positioning of two Arf1 molecules in contrasting molecular environments. Each of these pockets for Arf1 is expected to also accommodate an Arf GTPase-activating protein (ArfGAP). Structural evidence and protein interactions observed between isolated domains indirectly suggests that each niche may preferentially recruit one of the two ArfGAPs known to affect COPI, Gcs1/ArfGAP1 and Glo3/ArfGAP2/3, although only partial structures are available. The functional role of the unique non-catalytic domain of either ArfGAP has not been integrated into the current COPI structural model. Here, we delineate key differences in the consequences of triggering GTP hydrolysis via the activity of one versus the other ArfGAP. We demonstrate that Glo3/ArfGAP2/3 specifically triggers Arf1 GTP hydrolysis impinging on the stability of the COPI coat. We show that the yeast homologue of AMP kinase, Snf1, phosphorylates the region of Glo3 that is critical for this effect and thereby regulates its function in the COPI-vesicle cycle. Our results revise the model of ArfGAP function in the molecular context of COPI

Experimental test for interpreting the increase in sensibility of doped CR-39

In recent years the sensibility of CR-39 to nuclear tracks has been increased by doping the corresponding monomer with dioctyl phtalate. At this regard, two theoretical approaches are current managed to explain this phenomenon: either the doping react with the active radicals in the chain blocking them, stopping crosslinking between chains, or alternatively that the doping gets between them giving wider space between the crosslinkined chains

Heavy Quark Fluorescence

Heavy hadrons containing heavy quarks (for example, Upsilon-mesons) feature a scale separation between the heavy quark mass (about 4.5 GeV for the b-quark) and the QCD scale (about 0.3 GeV}) that controls effective masses of lighter constituents. Therefore, as in ordinary molecules, the de-excitation of the lighter, faster degrees of freedom leaves the velocity distribution of the heavy quarks unchanged, populating the available decay channels in qualitatively predictable ways. Automatically an application of the Franck-Condon principle of molecular physics explains several puzzling results of Upsilon(5S) decays as measured by the Belle collaboration, such as the high rate of Bs*-anti Bs* versus Bs*-anti Bs production, the strength of three-body B-anti B + pion decays, or the dip in B momentum shown in these decays. We argue that the data is showing the first Sturm-Liouville zero of the Upsilon(5S) quantum mechanical squared wavefunction, and providing evidence for a largely b-anti b composition of this meson.Comment: 4 pages, 4 figures, Figure 2 updated and some typos corrected. To be published in Physical Review Letter

Causality detection and turbulence in fusion plasmas

This work explores the potential of an information-theoretical causality detection method for unraveling the relation between fluctuating variables in complex nonlinear systems. The method is tested on some simple though nonlinear models, and guidelines for the choice of analysis parameters are established. Then, measurements from magnetically confined fusion plasmas are analyzed. The selected data bear relevance to the all-important spontaneous confinement transitions often observed in fusion plasmas, fundamental for the design of an economically attractive fusion reactor. It is shown how the present method is capable of clarifying the interaction between fluctuating quantities such as the turbulence amplitude, turbulent flux, and Zonal Flow amplitude, and uncovers several interactions that were missed by traditional methods.Comment: 26 pages, 14 figure

Minimum of η/s\eta/s and the phase transition of the Linear Sigma Model in the large-N limit

We reexamine the possibility of employing the viscosity over entropy density ratio as a diagnostic tool to identify a phase transition in hadron physics to the strongly coupled quark-gluon plasma and other circumstances where direct measurement of the order parameter or the free energy may be difficult. It has been conjectured that the minimum of eta/s does indeed occur at the phase transition. We now make a careful assessment in a controled theoretical framework, the Linear Sigma Model at large-N, and indeed find that the minimum of eta/s occurs near the second order phase transition of the model due to the rapid variation of the order parameter (here the sigma vacuum expectation value) at a temperature slightly smaller than the critical one.Comment: 22 pages, 19 figures, v2, some references and several figures added, typos corrected and certain arguments clarified, revised for PR

Sacramento River Predator Diet Analysis: A Comparative Study

This study examined diets of two predatory fish species, the native Sacramento Pikeminnow (Ptychocheilus grandis) and the introduced Striped Bass (Morone saxatilis), in the Sacramento River, California, USA. Both species have been implicated in native species declines through predation, eliciting our investigation of their diets in the Sacramento River. Sampling occurred between March and November 2017, and was conducted via hook and line on a 35-km reach near Chico, California. Habitat types sampled include engineered structures (water diversions and beam bridges), rip-rapped channel edges, and natural riverbank. Stomach contents were collected via gastric lavage and later processed using visual, gravimetric, and genetic techniques. Diets of Sacramento Pikeminnow and Striped Bass were highly similar as determined through index of relative importance and PERMANOVA modeling. Water temperature was the only variable that significantly affected diet composition. Results reflect similar dietary niches for both species in the Sacramento River

"Clumpiness" Mixing in Complex Networks

Three measures of clumpiness of complex networks are introduced. The measures quantify how most central nodes of a network are clumped together. The assortativity coefficient defined in a previous study measures a similar characteristic, but accounts only for the clumpiness of the central nodes that are directly connected to each other. The clumpiness coefficient defined in the present paper also takes into account the cases where central nodes are separated by a few links. The definition is based on the node degrees and the distances between pairs of nodes. The clumpiness coefficient together with the assortativity coefficient can define four classes of network. Numerical calculations demonstrate that the classification scheme successfully categorizes 30 real-world networks into the four classes: clumped assortative, clumped disassortative, loose assortative and loose disassortative networks. The clumpiness coefficient also differentiates the Erdos-Renyi model from the Barabasi-Albert model, which the assortativity coefficient could not differentiate. In addition, the bounds of the clumpiness coefficient as well as the relationships between the three measures of clumpiness are discussed.Comment: 47 pages, 11 figure

Local Two-Photon Couplings and the J=0 Fixed Pole in Real and Virtual Compton Scattering

The local coupling of two photons to the fundamental quark currents of a hadron gives an energy-independent contribution to the Compton amplitude proportional to the charge squared of the struck quark, a contribution which has no analog in hadron scattering reactions. We show that this local contribution has a real phase and is universal, giving the same contribution for real or virtual Compton scattering for any photon virtuality and skewness at fixed momentum transfer squared t. The t-dependence of this J=0 fixed Regge pole is parameterized by a yet unmeasured even charge-conjugation form factor of the target nucleon. The t=0 limit gives an important constraint on the dependence of the nucleon mass on the quark mass through the Weisberger relation. We discuss how this 1/x form factor can be extracted from high energy deeply virtual Compton scattering and examine predictions given by models of the H generalized parton distribution.Comment: 20 pages, 15 figure