Networks for systems biology: conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

Shape corrections to exchange-correlation potentials by gradient-regulated seamless connection of model potentials for inner and outer region

Shape corrections to the standard approximate Kohn-Sham exchange-correlation (xc) potentials are considered with the aim to improve the excitation energies (especially for higher excitations) calculated with time-dependent density functional perturbation theory. A scheme of gradient-regulated connection (GRAC) of inner to outer parts of a model potential is developed. Asymptotic corrections based either on the potential of Fermi and Amaldi or van Leeuwen and Baerends (LB) are seamlessly connected to the (shifted) xc potential of Becke and Perdew (BP) with the GRAC procedure, and are employed to calculate the vertical excitation energies of the prototype molecules N-2, CO, CH2O, C2H4, C5NH5, C6H6, Li-2, Na-2, K-2. The results are compared with those of the alternative interpolation scheme of Tozer and Handy as well as with the results of the potential obtained with the statistical averaging of (model) orbital potentials. Various asymptotically corrected potentials produce high quality excitation energies, which in quite a few cases approach the benchmark accuracy of 0.1 eV for the electronic spectra. Based on these results, the potential BP-GRAC-LB is proposed for molecular response calculations, which is a smooth potential and a genuine "local" density functional with an analytical representation. (C) 2001 American Institute of Physics.

Comparative performances of birnessite and cryptomelane MnO as electrode material in neutral aqueous lithium salt for supercapacitor application

Na-doped Birnessite-type manganese oxide (d-MnO) has been synthesized using the chemical method and characterized through X-ray diffraction and SEM, showing the lamellar structure and high crystal structure. A comparative study of the electrochemical performances of this material with those of the commercial Cryptomelane-type MnO has then been undertaken in ten neutral aqueous electrolytes for supercapacitor applications. Aqueous electrolytes, containing a lithium salt, LiX (where X = SO , NO, CHCO , CHSO, ClO , CHCO, TFSI, Beti, BOB, or Lact), have been first prepared under neutral pH conditions to reach the salt concentration, providing the maximum in conductivity. Their transport properties are then investigated through conductivities, viscosities, and self-diffusion coefficient measurements. Second, the thermal behaviors of these electrolytic aqueous solutions are then evaluated by using a differential scanning calorimeter from (213.15 to 473.15) K in order to access their liquid range temperatures. Cyclic voltammograms (CV) in three electrode configurations are thereafter investigated using Na Birnessite and Cryptomelane as working electrode material from (-0.05 to 1.5) V versus Ag/AgCl at various sweep rates from (2 to 100) mV·s. According to anion nature/structure and manganese oxide material type, different CV responses are observed, presenting a pure capacitive profile for Beti or CH CO and an additional pseudocapacitive signal for the smallest anions, such as ClO and NO . The capacitances, energies, and efficiencies are finally calculated. These results indicate clearly that electrolytes based on a mineral lithium salt under neutral pH condition and high salt concentration (up to 5 mol·L) have better electrochemical performances than organic ones, up to 1.4 V with good material stability and capacity retention. The relationship between transport properties, electrostatic and steric hindrance considerations of hydrated ions, and their electrochemical performances is discussed in order to understand further the lithium intercalation-deintercalation processes in the lamellar or tunnel structure of investigated MnO. © 2013 American Chemical Society.

Implementing efficient graphs in connection networks

We consider the problem of sharing the cost of a network that meets the connection demands of a set of agents. The agents simultaneously choose paths in the network connecting their demand nodes. A mechanism splits the total cost of the network formed among the participants. We introduce two new properties of implementation. The first property, Pareto Nash implementation (PNI), requires that the efficient outcome always be implemented in a Nash equilibrium and that the efficient outcome Pareto dominates any other Nash equilibrium. The average cost mechanism and other asymmetric variations are the only mechanisms that meet PNI. These mechanisms are also characterized under strong Nash implementation. The second property, weakly Pareto Nash implementation (WPNI), requires that the least inefficient equilibrium Pareto dominates any other equilibrium. The egalitarian mechanism (EG) and other asymmetric variations are the only mechanisms that meet WPNI and individual
rationality. EG minimizes the price of stability across all individually rational mechanisms. © Springer-Verlag Berlin Heidelberg 2012