Distortion of the L→M transition in the photocycle of the bacteriorhodopsin mutant D96N: a time-resolved step-scan FTIR investigation

AbstractThe D96N mutant of bacteriorhodopsin has often been taken as a model system to study the M intermediate of the wild type photocycle due to the long life time of the corresponding intermediate of the mutant. Using time-resolved step-scan FTIR spectroscopy in combination with a sample changing wheel we investigated the photocycle of the mutant with microsecond time resolution. Already after several microseconds an intermediate similar to the MN state is observed, which contrasts with the M state of the wild type protein. At reduced hydration M and N intermediates similar to those of wild type BR can be detected. These results have a bearing on the interpretation of the photocycle of this mutant. A mechanism is suggested for the fast rise of MN which provides some insight into the molecular events involved in triggering the opening of the cytosolic channel also of the wild type protein

General relativistic radiation hydrodynamics of accretion flows: II. Treating stiff source terms and exploring physical limitations

We present the implementation of an implicit-explicit (IMEX) Runge-Kutta numerical scheme for general relativistic hydrodynamics coupled to an optically thick radiation field in two existing GR-hydrodynamics codes. We argue that the necessity of such an improvement arises naturally in astrophysically relevant regimes where the optical thickness is high as the equations become stiff. By performing several 1D tests we verify the codes' new ability to deal with this stiffness and show consistency. Then, still in 1D, we compute a luminosity versus accretion rate diagram for the setup of spherical accretion onto a Schwarzschild black hole and find good agreement with previous work. Lastly, we revisit the supersonic Bondi Hoyle Lyttleton (BHL) accretion in 2D where we can now present simulations of realistic temperatures, down to T~10^6 K. Here we find that radiation pressure plays an important role, but also that these highly dynamical set-ups push our approximate treatment towards the limit of physical applicability. The main features of radiation hydrodynamics BHL flows manifest as (i) an effective adiabatic index approaching gamma_effective ~ 4/3; (ii) accretion rates two orders of magnitude lower than without radiation pressure; (iii) luminosity estimates around the Eddington limit, hence with an overall radiative efficiency as small as eta ~ 10^{-2}; (iv) strong departures from thermal equilibrium in shocked regions; (v) no appearance of the flip-flop instability. We conclude that the current optically thick approximation to the radiation transfer does give physically substantial improvements over the pure hydro also in set-ups departing from equilibrium, and, once accompanied by an optically thin treatment, is likely to provide a fundamental tool for investigating accretion flows in a large variety of astrophysical systems