Interplay between excitation kinetics and reaction-center dynamics in purple bacteria

Photosynthesis is arguably the fundamental process of Life, since it enables energy from the Sun to enter the food-chain on Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations which traverse a complex biomolecular membrane, getting captured and fueling chemical reactions within a reaction-center in order to produce nutrients. The precise nature of these dynamical processes -- which lie at the interface between quantum and classical behaviour, and involve both noise and coordination -- are still being explored. Here we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of {\it Rsp. Photometricum} purple bacteria. Using stochastic realisations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the reaction center dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.Comment: 21 pages, 13 figures, accepted for publication in New Journal of Physic

Nonlinear Outcome of Gravitational Instability in Disks with Realistic Cooling

We consider the nonlinear outcome of gravitational instability in optically thick disks with a realistic cooling function. We use a numerical model that is local, razor-thin, and unmagnetized. External illumination is ignored. Cooling is calculated from a one-zone model using analytic fits to low temperature Rosseland mean opacities. The model has two parameters: the initial surface density Sigma_0 and the rotation frequency Omega. We survey the parameter space and find: (1) The disk fragments when t_c,eff Omega = 1, where t_c,eff is an effective cooling time defined as the average internal energy of the model divided by the average cooling rate. This is consistent with earlier results that used a simplified cooling function. (2) The initial cooling time t_c0 or a uniform disk with Q = 1 can differ by orders of magnitude from t_c,eff in the nonlinear outcome. The difference is caused by sharp variations in the opacity with temperature. The condition t_c0 Omega = 1 therefore does not necessarily indicate where fragmentation will occur. (3) The largest difference between t_c,eff and t_c0 is near the opacity gap, where dust is absent and hydrogen is largely molecular. (4) In the limit of strong illumination the disk is isothermal; we find that an isothermal version of our model fragments for Q < 1.4. Finally, we discuss some physical processes not included in our model, and find that most are likely to make disks more susceptible to fragmentation. We conclude that disks with t_c,eff Omega < 1 do not exist.Comment: 30 pages, 12 figure

Dynamical systems analysis of fluid transport in time-periodic vortex ring flows

It is known that the stable and unstable manifolds of dynamical systems theory provide a powerful tool for understanding Lagrangian aspects of time-periodic flows. In this work we consider two time-periodic vortex ring flows. The first is a vortex ring with an elliptical core. The manifolds provide information about entrainment and detrainment of irrotational fluid into and out of the volume transported with the ring. The likeness of the manifolds with features observed in flow visualization experiments of turbulent vortex rings suggests that a similar process might be at play. However, what precise modes of unsteadiness are responsible for stirring in a turbulent vortex ring is left as an open question. The second situation is that of two leapfrogging rings. The unstable manifold shows striking agreement with even the fine features of smoke visualization photographs, suggesting that fluid elements in the vicinity of the manifold are drawn out along it and begin to reveal its structure. We suggest that interpretations of these photographs that argue for complex vorticity dynamics ought to be reconsidered. Recently, theoretical and computational tools have been developed to locate structures analogous to stable and unstable manifolds in aperiodic, or finite-time systems. The usefulness of these analogs is demonstrated, using vortex ring flows as an example, in the paper by Shadden, Dabiri, and Marsden [Phys. Fluids 18, 047105 (2006)]

Metal Insulator transition at B=0 in p-SiGe

Observations are reported of a metal-insulator transition in a 2D hole gas in asymmetrically doped strained SiGe quantum wells. The metallic phase, which appears at low temperatures in these high mobility samples, is characterised by a resistivity that decreases exponentially with decreasing temperature. This behaviour, and the duality between resistivity and conductivity on the two sides of the transition, are very similar to that recently reported for high mobility Si-MOSFETs.Comment: 4 pages, REVTEX with 3 ps figure

Temporal structure in neuronal activity during working memory in Macaque parietal cortex

A number of cortical structures are reported to have elevated single unit firing rates sustained throughout the memory period of a working memory task. How the nervous system forms and maintains these memories is unknown but reverberating neuronal network activity is thought to be important. We studied the temporal structure of single unit (SU) activity and simultaneously recorded local field potential (LFP) activity from area LIP in the inferior parietal lobe of two awake macaques during a memory-saccade task. Using multitaper techniques for spectral analysis, which play an important role in obtaining the present results, we find elevations in spectral power in a 50--90 Hz (gamma) frequency band during the memory period in both SU and LFP activity. The activity is tuned to the direction of the saccade providing evidence for temporal structure that codes for movement plans during working memory. We also find SU and LFP activity are coherent during the memory period in the 50--90 Hz gamma band and no consistent relation is present during simple fixation. Finally, we find organized LFP activity in a 15--25 Hz frequency band that may be related to movement execution and preparatory aspects of the task. Neuronal activity could be used to control a neural prosthesis but SU activity can be hard to isolate with cortical implants. As the LFP is easier to acquire than SU activity, our finding of rich temporal structure in LFP activity related to movement planning and execution may accelerate the development of this medical application.Comment: Originally submitted to the neuro-sys archive which was never publicly announced (was 0005002

Absorption lines from magnetically-driven winds in X-ray binaries

High resolution X-ray spectra of black hole X-ray binaries (BHBs) show blueshifted absorption lines from disk winds which seem to be equatorial. Winds occur in the Softer (disk-dominated) states of the outburst and are less prominent or absent in the Harder (power-law dominated) states. We use self-similar magneto-hydrodynamic (MHD) accretion-ejection models to explain the disk winds in BHBs. In our models, the density at the base of the outflow from the accretion disk is not a free parameter, but is determined by solving the full set of dynamical MHD equations. Thus the physical properties of the outflow are controlled by the global structure of the disk. We studied different MHD solutions characterized by different values of (a) the disk aspect ratio ($\varepsilon$) and (b) the ejection efficiency ($p$). We use two kinds of MHD solutions depending on the absence (cold solution) or presence (warm solution) of heating at the disk surface. Such heating could be from e.g. dissipation of energy due to MHD turbulence in the disk or from illumination. We use each of these MHD solutions to predict the physical parameters of an outflow; put limits on the ionization parameter ($\xi$), column density and timescales, motivated by observational results; and thus select regions within the outflow which are consistent with the observed winds. The cold MHD solutions cannot account for winds due to their low ejection efficiency. But warm solutions can explain the observed physical quantities in the wind because they can have sufficiently high values of $p$ ($\gtrsim 0.1$, implying larger mass loading at the base of the outflow). Further from our thermodynamic equilibrium curve analysis for the outflowing gas, we found that in the Hard state a range of $\xi$ is thermodynamically unstable, and had to be excluded. This constrain made it impossible to have any wind at all, in the Hard state.Comment: 16 Pages, 10 figures in the main body and 4 figures in the appendix. Accepted for publication in A&

Electronic and Structural Properties of C36_{36} Molecule

The extended SSH model and Bogoliubov-de Gennes(BdeG) formalism are applied to investigate the electronic properties and stable lattice configurations of C$_{36}$. We focus the problem on the molecule's unusual $D_{6h}$ symmetry. The electronic part of the Hamiltonian without Coulomb interaction is solved analytically. We find that the gap between HOMO and LUMO is small due to the long distance hopping between the 2nd and 5th layers. The charge densities of HOMO and LUMO are mainly distributed in the two layers, that causes a large splitting between the spin triplet and singlet excitons. The differences of bond lengths, angles and charge densities among the molecule and polarons are discussed.Comment: 15 pages, 4 figures, 4 Table