Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer.

The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.

Towards the continuum limit in transport coefficient computations

The analytic continuation needed for the extraction of transport coefficients necessitates in principle a continuous function of the Euclidean time variable. We report on progress towards achieving the continuum limit for 2-point correlator measurements in thermal SU(3) gauge theory, with specific attention paid to scale setting. In particular, we improve upon the determination of the critical lattice coupling and the critical temperature of pure SU(3) gauge theory, estimating r0Tc ≃ 0.7470(7) after a continuum extrapolation. As an application the determination of the heavy quark momentum diffusion coefficient from a correlator of colour-electric fields attached to a Polyakov loop is discussed.

Nonperturbative estimate of the heavy quark momentum diffusion coefficient

We estimate the momentum diffusion coefficient of a heavy quark within a pure SU(3) plasma at a temperature of about 1.5Tc. Large-scale Monte Carlo simulations on a series of lattices extending up to 1923×48 permit us to carry out a continuum extrapolation of the so-called color-electric imaginary-time correlator. The extrapolated correlator is analyzed with the help of theoretically motivated models for the corresponding spectral function. Evidence for a nonzero transport coefficient is found and, incorporating systematic uncertainties reflecting model assumptions, we obtain κ=(1.8–3.4)T3. This implies that the “drag coefficient,” characterizing the time scale at which heavy quarks adjust to hydrodynamic flow, is η−1D=(1.8–3.4)(Tc/T)2(M/1.5  GeV)  fm/c, where M is the heavy quark kinetic mass. The results apply to bottom and, with somewhat larger systematic uncertainties, to charm quarks.

A Bayesian approach to estimating the intraclass correlation coefficient

A Bayesian approach to estimating the intraclass correlation coefficient was used for this research project. The background of the intraclass correlation coefficient, a summary of its standard estimators, and a review of basic Bayesian terminology and methodology were presented. The conditional posterior density of the intraclass correlation coefficient was then derived and estimation procedures related to this derivation were shown in detail. Three examples of applications of the conditional posterior density to specific data sets were also included. Two sets of simulation experiments were performed to compare the mean and mode of the conditional posterior density of the intraclass correlation coefficient to more traditional estimators. Non-Bayesian methods of estimation used were: the methods of analysis of variance and maximum likelihood for balanced data; and the methods of MIVQUE (Minimum Variance Quadratic Unbiased Estimation) and maximum likelihood for unbalanced data. The overall conclusion of this research project was that Bayesian estimates of the intraclass correlation coefficient can be appropriate, useful and practical alternatives to traditional methods of estimation. ^

(Table 1) Attenuation coefficient of lateral propagating light in sea ice, southern Beaufort Sea

The attenuation property of a lateral propagating light (LPL) in sea ice was measured using an artificial lamp in the Canadian Arctic during the 2007/2008 winter. A measurement method is proposed and applied whereby a recording instrument is buried in the sea ice and an artificial lamp is moved across the instrument. The apparent attenuation coefficient µ(lamda) for the lateral propagating light is obtained from the measured logarithmic relative variation rate. With the exception of blue and red lights, the attenuation coefficient changed little with wavelength, but changed considerably with depth. The vertical decrease of the attenuation coefficient was found to be correlated with salinity: the greater the salinity, the greater the attenuation coefficient. A clear linear relation of salinity and the lateral attenuation coefficient with R2 = 0.939 exists to address the close correlation of the attenuation of LPL with the scattering from the brine. The observed attenuation coefficient of LPL is much larger than that of the vertical propagation light, which we speculate to be caused by scattering. Part of this scattered component is transmitted out of the sea ice from the upper and lower surfaces.