NONPHOTOCHEMICAL HOLE BURNING OF THE B800-B850 ANTENNA COMPLEX OF Rhodopseudomonas acidophila

Detailed burn wavelength-dependent hole-burning studies of the title complex have been performed. The zero-phonon hole (ZPH) widths for B800 at 4.2 K are 6.0 ± 0.3 cm and are discussed in terms of B80O-B850 and B800-B800 energy transfer. The B800* lifetime is 1.8 ± 0.2 ps. The site inhomogeneous broadening (r,) of B800 is 240 cm^?1. The B850 (located at 864 nm at 4.2 K) hole spectra reveal that B850 suffers from significant homogeneous broadening, which is attributed to unit cell exciton level structure and ultrafast interexciton level relaxation. Novel ZPH action spectra lead to the resolution of a minor component at 885 nm, which is the analogue of B870 of Rhodobacter sphaeroides previously assigned as the lowest exciton level of the B850 exciton band. The B870 ZPH width of 2.0 ± 0.2 cm^?1for Rhodopseudomonas acidophila leads to a total dephasing time of 5.3 ps, which is attributed to exciton scattering that stems from the energetic inequivalence of neighboring B850 unit cells.     

Parameter inference in small world network disease models with approximate Bayesian Computational methods

Small world network models have been effective in capturing the variable behaviour of reported case data of the SARS coronavirus outbreak in Hong Kong during 2003. Simulations of these models have previously been realized using informed “guesses” of the proposed model parameters and tested for consistency with the reported data by surrogate analysis. In this paper we attempt to provide statistically rigorous parameter distributions using Approximate Bayesian Computation sampling methods. We find that such sampling schemes are a useful framework for fitting parameters of stochastic small world network models where simulation of the system is straightforward but expressing a likelihood is cumbersome.     

Adjusting learning motivation to promote cooperation

An evolutionary prisoner’s dilemma game with players adjusting their learning motivation is studied. At each time step, each player can adjust his/her learning motivation according to the difference between the current payoff and payoff aspiration. Greater payoff aspiration means stronger learning motivation, and vice versa. We find that the density of cooperation in a spatial prisoner’s dilemma game is enhanced when the learning motivation mechanism is considered. Meanwhile, we show that proper noise can not only induce the highest cooperation level but also can maintain the cooperation phenomenon even though there is more temptation to defect.     

Complex network from pseudoperiodic time series: topology versus dynamics

We construct complex networks from pseudoperiodic time series, with each cycle represented by a single node in the network. We investigate the statistical properties of these networks for various time series and find that time series with different dynamics exhibit distinct topological structures. Specifically, noisy periodic signals correspond to random networks, and chaotic time series generate networks that exhibit small world and scale free features. We show that this distinction in topological structure results from the hierarchy of unstable periodic orbits embedded in the chaotic attractor. Standard measures of structure in complex networks can therefore be applied to distinguish different dynamic regimes in time series. Application to human electrocardiograms shows that such statistical properties are able to differentiate between the sinus rhythm cardiograms of healthy volunteers and those of coronary care patients.     

Intermolecular pi-to-pi bonding between stacked aromatic dyads. Experimental and theoretical binding energies and near-IR optical transitions for phenalenyl radical/radical versus radical/cation dimerizations

The high symmetry and stability of phenalenyl systems, both as the planar pi-radical (P*) and as the pi-cation (P+), are desirable characteristics of prototypical aromatic donor/acceptor pairs that encourage their use as (binary) models for the study of intermolecular interactions extant in stacked molecular arrays. Thus, quantitative ESR spectroscopy of the paramagnetic P* identifies its spontaneous self-association to the diamagnetic P2, previously characterized as the stacked pi-dimer by X-ray crystallography. Likewise, the rapid cross-association of P* with the closed-shell P+ leads to the stacked pi-dimer cation P2*+ with the "doubled" ESR spectrum diagnostic of complete (odd) electron delocalization. These pi-associations are confirmed by UV-vis studies that reveal diagnostic near-IR bands of both P2 and P2*+-strongly reminiscent of intermolecular charge-transfer absorptions in related aromatic (donor/acceptor) pi-associations. Ab initio molecular-orbital calculations for the pi-dimer P2 predict a binding energy of DeltaED = -11 kcal mol(-1), which is in accord with the experimental enthalpy change of DeltaHD = -9.5 kcal mol(-1) in dichloromethane solution. Most importantly, the calculations reproduce the intermonomer spacings and reveal the delicate interplay of attractive covalent and dispersion forces, balanced against the repulsions between filled orbitals. For comparison, the binding energy in the structurally related cationic pi-pimer P2*+ is calculated to be significantly larger with DeltaEP approximately -20 kcal mol(-1) (gas phase), owing to favorable electrostatic interactions not present in the neutral pi-dimer (which outweigh the partial loss of covalent interactions). As a result, our theoretical formulation can correctly account for the experimental enthalpy change in solution of DeltaHP = -6.5 kcal mol(-1) by the inclusion of differential ionic solvation in the formation of the pi-pimer.     

REPAIR OF PYRIMIDINE DIMERS IN ULTRAVIOLET-IRRADIATED CHLAM YDOMONAS

Abstract— A UV-specific endonuclease was used to monitor the presence of UV-induced pyrimidine dimers in the DNA of Chlamydomonas reinhardi . All of the dimers induced by 50 J/m² of 254 nm light are removed by a 2 h exposure to photoreactivating light. Nearly all of the dimers are removed by the wild-type strain of Chlamydomonas upon incubation for 24h in the dark. Two UV-sensitive mutants, UVS 1 and UVS 6, are deficient in removal of dimers in the dark. These results are interpreted to mean that Chlamydomonas has an excision-repair pathway for coping with UV-induced damage.