Cross over of recurrence networks to random graphs and random geometric graphs

Recurrence networks are complex networks constructed from the time series of chaotic dynamical systems where the connection between two nodes is limited by the recurrence threshold. This condition makes the topology of every recurrence network unique with the degree distribution determined by the probability density variations of the representative attractor from which it is constructed. Here we numerically investigate the properties of recurrence networks from standard low-dimensional chaotic attractors using some basic network measures and show how the recurrence networks are different from random and scale-free networks. In particular, we show that all recurrence networks can cross over to random geometric graphs by adding sufficient amount of noise to the time series and into the classical random graphs by increasing the range of interaction to the system size. We also highlight the effectiveness of a combined plot of characteristic path length and clustering coefficient in capturing the small changes in the network characteristics.     

On the Possible Roles of the Zn Cation in the Carbon Dioxide Hydration Reaction: An Ab Initio RHF-SCF MO Study of Transition Structures on the [OH2 + CO2] [ZnOH2CO2]2+ and [Zn(NH3)3OH2CO2]2+ Reactive Hypersurfaces

Transition structures and related minima on the reactive energy hypersurfaces for the hydration of carbon dioxide in the presence of a bare zinc ion and with the cation liganded with three ammonia molecules are determined in the RHF MO SCF framework at a relatively high level of basis-set representation. For the sake of comparison, the standard intramolecular proton transfer model in absence of zinc is revisited and the corresponding transition structure (TS) located. In the coordination sphere of zinc, the standard mechanism of hydration in vacuo is modified: a nucleophilic attack of water onto zinc-activated carbon dioxide. The reactive path goes via TS signaling synchronous movements in the coordination sphere of zinc: Water goes away from and carbon dioxide toward the metal. For the model systems [ZnOH₂CO₂]²⁺, this TS connects with a valley having a geminal carbonic acid (gCA) as product; the carbon–oxygen interaction of the in vacuo complex H₂O···CO₂ is transformed into a covalent bond by its binding to zinc: H₂O—CO₂-Zn is a minimum on this energy hypersurface. The standard path for intramolecular proton transfer, namely, H₂O—CO₂—Zn changing into (HO)₂—CO—Zn, is not catalyzed by the metal. For the ammonia-ligand model system, the carbon dioxide hydration follows the same pathway as in the bare-zinc case. A possible irreversible mechanism of carbon dioxide hydration catalyzed by carbonic anhydrases at pH lower than 6 can be suggested based on the present study; here, a central role is played by an intermolecular deprotonation of gCA by water found at the active-site cleft around the metal center. This zinc–water mechanism is extrapolated to include a general acid catalysis of bicarbonate/carbon dioxide interconversion in water. Results obtained with a hydronium ion replacing zinc and an ancillary water acting as a proton acceptor for the gCA strongly suggest that, in water at pHs lower than 7, direct deprotonation of gCA offers a low-activation channel to produce carbonic acid; in the reverse direction, protonation of the hydroxyl oxygen in bicarbonate leading to gCA offers a reasonable answer to the instability of this anion in solution at low pH. This picture agrees with the one reported by Paneth and O'Leary. [J. Am. Chem. Soc. 107, 7381 (1985)] based on experimental kinetic information.     

A CC2 dielectric continuum model and a CC2 molecular mechanics model

In this paper we present theory and applications for the second-order approximate singles and doubles coupled cluster (CC2) electronic structure method coupled to either a dielectric continuum (the CC2/DC model) or a molecular mechanical intermolecular force field (the CC2/MM model). Calculations of the interaction energy, solvation energy, electric dipole moment and electric quadrupole moment of liquid water are presented using the correlated CC2 approach. The results are compared to the corresponding results using the uncorrelated Hartree-Fock (HF) and the correlated coupled cluster singles and doubles (CCSD) methods. Also, a hierarchy in the coupling between the quantum mechanical (QM) and the molecular mechanical (MM) part of the system is investigated in the QM/MM model for the three different electronic structure methods.     

PREDICTION OF AEROFOIL WAKE SUBJECTED TO THE EFFECTS OF CURVATURE AND PRESSURE GRADIENT

Experimental data on the development of wakes in a straight duct, a curved duct, a curved diffuser and a straight diffuser are compared with computations based on a finite volume scheme incorporating the k– ε model of turbulence. The results show that the computations based on the standard k–ε model are able to satisfactorily capture only the mean velocity profiles. To improve the predictions, several modifications to the model are tried out. Close agreement between experiment and computation as regards the velocity profiles, wake parameters and profiles of the turbulent kinetic energy k and Reynolds shear stress ⌅{uv} is obtained when modification to the model constant C_μ, based on the curvature parameter and the ratio of the production of turbulent kinetic energy to its rate of dissipation, is incorporated. The modified model is also able to capture the asymmetry in the profiles of k and ⌅{uv} caused by the curvature and its enhancement due to the additional presence of an adverse pressure gradient.     

SENSIBILISIERTE PHOTOOXIDATION DURCH METHYLENBLAU, THIOPYRONIN UND PYRONIN — II. PHYSIKOCHEMISCHE GRUNDLAGEN DER PHOTODYNAMISCHEN WIRKUNG VON THIOPYRONIN

Abstract— The physical-chemical properties of thiopyronine which result in its outstanding photodynamic effectiveness (in comparison to methylene blue and pyronine) are: (1) High velocity of free radical generation (kinetics followed by spectroscopy after flash photolysis). (2) High velocity of reoxidation of free radical (rate constant determined by kinetic spectroscopy under aerobic conditions). (3) Fairly positive reduction potential of oxidized free radical (from polarographic analysis of redox behavior). (4) Irreversible oxidation behavior of leuco-thiopyronin in contrast to leuco-methylene blue (the structure of leuco-thiopyronin was elucidated by NMR-analysis). (5) Fairly high equilibrium constant for complex formation with DN A (determination by high sensitive pulse-polarography).
From the sedimentation behavior and T-jump relaxation of in vitro photodynamically treated DNA it is shown that not only does guanine photooxidation take place but also single- and double-strand breaks can occur. The mechanism of this phenomenon is not yet elucidated.     

Efficacy,Beliefs, and Investment in Step-Level Public Goods

A central concept for understanding social dilemma behavior is the efficacy of an actor's cooperative behavior in terms of increasing group well-being. We report a decision and game theoretical analysis of efficacy in step-level public goods (SPGs). Previous research shows a positive relation between efficacy and contributions to SPGs and explains this relation by a purely motivational account. We show, however, that from a decision and game theory perspective an increasing relationship is not general, but only follows from very specific assumptions about players’ information and beliefs. We offer 3 examples of how the predicted efficacy–contribution relation depends on players’ information and beliefs. We discuss the implications of our results for the social psychology of efficacy in social dilemmas.     

The QM/MM approach for wavefunctions,energies and response functions within self-consistent field and coupled cluster theories

This paper presents the coupled cluster/molecular mechanics (CC/MM) and self-consistent field/molecular mechanics (SCF/MM) approaches for wavefunctions, energies and response properties. Two physically different theories are derived, the mean-field and the direct-field interaction approaches, together with expressions for the optimization condition of both variational and non-variational wavefunctions and energies. Also derived are the linear response functions at the CC/MM and SCF/MM levels of theory, and the expressions are compared with the vacuum response functions.     

Nonlocal reaction--diffusion equations and nucleation

A nonlocal reaction-diffusion equation is presented and analysedusing matched asymptotic expansions and multiple timescales.The problem models a binary mixture undergoing phase separation.The particular form of the equation is motivated by argumentsfrom the calculus of variations, with the nonlocality arisingfrom an enforcement of conservation of mass. It is shown thatthe evolution of the solution can be characterized by trackingthe motion of fronts separating phases. The propagation of theinterfaces is found to be a coarsening process which dependsin a nonlocal fashion on mean curvature. Several special featuresof the equations of motion for the fronts are studied, and therelation of this evolution to Cahn-Hilliard theory and nucleationis discussed