Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the PSII yield, which only emerges on the 100 nm scale of the grana membrane and determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 nm x 200 nm patch of the grana membrane. We demonstrate that single molecule measurements of qE are consistent with a weak-quenching regime. Consequently, excitation transport can be rigorously coarse-grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. A diffusion-corrected lake model substantially improves the PSII yield determined from variable chlorophyll fluorescence measurements and offers an improved model of PSII for photosynthetic metabolism.Comment: 19 pages, 4 figures, 3 supplementary figure

Mechanistic Regimes of Vibronic Transport in a Heterodimer and the Design Principle of Incoherent Vibronic Transport in Phycobiliproteins

Following the observation of coherent oscillations in non-linear spectra of photosynthetic pigment protein complexes, particularly phycobilliprotein such as PC645, coherent vibronic transport has been suggested as a design principle for novel light harvesting materials operating at room temperature. Vibronic transport between energetically remote pigments is coherent when the presence of a resonant vibration supports transient delocalization between the pair of electronic excited states. Here, we establish the mechanism of vibronic transport for a model heterodimer across a wide range of molecular parameter values. The resulting mechanistic map demonstrates that the molecular parameters of phycobiliproteins in fact support incoherent vibronic transport. This result points to an important design principle: incoherent vibronic transport is more efficient than a coherent mechanism when energetic disorder exceeds the coupling between the donor and vibrationally excited acceptor states. Finally, our results suggest that the role of coherent vibronic transport in pigment protein complexes should be reevaluated

Generalized Kasha's Scheme for Classifying Two-Dimensional Excitonic Molecular Aggregates: Temperature Dependent Absorption Peak Frequency Shift

We propose a generalized theoretical framework for classifying two-dimensional (2D) excitonic molecular aggregates based on an analysis of temperature dependent spectra. In addition to the monomer-aggregate absorption peak shift, which defines the conventional J- and H-aggregates, we incorporate the peak shift associated with increasing temperature as a measure to characterize the exciton band structure. First we show that there is a one-to-one correspondence between the monomer-aggregate and the T-dependent peak shifts for Kasha's well-established model of 1D aggregates, where J-aggregates exhibit further redshift upon increasing temperature and H-aggregates exhibit further blueshift. On the contrary, 2D aggregate structures are capable of supporting the two other combinations: blueshifting J-aggregates and redshifting H-aggregates, owing to their more complex exciton band structures. Secondly, using spectral lineshape theory, the T-dependent shift is associated with the relative abundance of states on each side of the bright state. We further establish that the density of states can be connected to the microscopic packing condition leading to these four classes of aggregates by separately considering the short and long-range contribution to the excitonic couplings. In particular the T-dependent shift is shown to be an unambiguous signature for the sign of net short-range couplings: Aggregates with net negative (positive) short-range couplings redshift (blueshift) with increasing temperature. Lastly, comparison with experiments shows that our theory can be utilized to quantitatively account for the observed but previously unexplained T-dependent absorption lineshapes. Thus, our work provides a firm ground for elucidating the structure-function relationships for molecular aggregates and is fully compatible with existing experimental and theoretical structure characterization tools.Comment: 29 pages, 4 figure

Long-range energy transport in photosystem II.

We simulate the long-range inter-complex electronic energy transfer in photosystem II-from the antenna complex, via a core complex, to the reaction center-using a non-Markovian (ZOFE) quantum master equation description that allows the electronic coherence involved in the energy transfer to be explicitly included at all length scales. This allows us to identify all locations where coherence is manifested and to further identify the pathways of the energy transfer in the full network of coupled chromophores using a description based on excitation probability currents. We investigate how the energy transfer depends on the initial excitation-localized, coherent initial excitation versus delocalized, incoherent initial excitation-and find that the overall energy transfer is remarkably robust with respect to such strong variations of the initial condition. To explore the importance of vibrationally enhanced transfer and to address the question of optimization in the system parameters, we systematically vary the strength of the coupling between the electronic and the vibrational degrees of freedom. We find that the natural parameters lie in a (broad) region that enables optimal transfer efficiency and that the overall long-range energy transfer on a ns time scale appears to be very robust with respect to variations in the vibronic coupling of up to an order of magnitude. Nevertheless, vibrationally enhanced transfer appears to be crucial to obtain a high transfer efficiency, with the latter falling sharply for couplings outside the optimal range. Comparison of our full quantum simulations to results obtained with a "classical" rate equation based on a modified-Redfield/generalized-Förster description previously used to simulate energy transfer dynamics in the entire photosystem II complex shows good agreement for the overall time scales of excitation energy transport

MOA-2009-BLG-387Lb: A massive planet orbiting an M dwarf

We report the discovery of a planet with a high planet-to-star mass ratio in the microlensing event MOA-2009-BLG-387, which exhibited pronounced deviations over a 12-day interval, one of the longest for any planetary event. The host is an M dwarf, with a mass in the range 0.07 M_sun < M_host < 0.49M_sun at 90% confidence. The planet-star mass ratio q = 0.0132 +- 0.003 has been measured extremely well, so at the best-estimated host mass, the planet mass is m_p = 2.6 Jupiter masses for the median host mass, M = 0.19 M_sun. The host mass is determined from two "higher order" microlensing parameters. One of these, the angular Einstein radius \theta_E = 0.31 +- 0.03 mas, is very well measured, but the other (the microlens parallax \pi_E, which is due to the Earth's orbital motion) is highly degenate with the orbital motion of the planet. We statistically resolve the degeneracy between Earth and planet orbital effects by imposing priors from a Galactic model that specifies the positions and velocities of lenses and sources and a Kepler model of orbits. The 90% confidence intervals for the distance, semi-major axis, and period of the planet are 3.5 kpc < D_L < 7.9 kpc, 1.1 AU < a < 2.7AU, and 3.8 yr < P < 7.6 yr, respectively.Comment: 20 pages including 8 figures. A&A 529 102 (2011

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development

Planck 2015 results. XIII. Cosmological parameters

We present results based on full-mission Planck observations of temperature and polarization anisotropies of the CMB. These data are consistent with the six-parameter inflationary LCDM cosmology. From the Planck temperature and lensing data, for this cosmology we find a Hubble constant, H0= (67.8 +/- 0.9) km/s/Mpc, a matter density parameter Omega_m = 0.308 +/- 0.012 and a scalar spectral index with n_s = 0.968 +/- 0.006. (We quote 68% errors on measured parameters and 95% limits on other parameters.) Combined with Planck temperature and lensing data, Planck LFI polarization measurements lead to a reionization optical depth of tau = 0.066 +/- 0.016. Combining Planck with other astrophysical data we find N_ eff = 3.15 +/- 0.23 for the effective number of relativistic degrees of freedom and the sum of neutrino masses is constrained to < 0.23 eV. Spatial curvature is found to be |Omega_K| < 0.005. For LCDM we find a limit on the tensor-to-scalar ratio of r <0.11 consistent with the B-mode constraints from an analysis of BICEP2, Keck Array, and Planck (BKP) data. Adding the BKP data leads to a tighter constraint of r < 0.09. We find no evidence for isocurvature perturbations or cosmic defects. The equation of state of dark energy is constrained to w = -1.006 +/- 0.045. Standard big bang nucleosynthesis predictions for the Planck LCDM cosmology are in excellent agreement with observations. We investigate annihilating dark matter and deviations from standard recombination, finding no evidence for new physics. The Planck results for base LCDM are in agreement with BAO data and with the JLA SNe sample. However the amplitude of the fluctuations is found to be higher than inferred from rich cluster counts and weak gravitational lensing. Apart from these tensions, the base LCDM cosmology provides an excellent description of the Planck CMB observations and many other astrophysical data sets

Planck 2015 results. XIV. Dark energy and modified gravity

We study the implications of Planck data for models of dark energy (DE) and modified gravity (MG), beyond the cosmological constant scenario. We start with cases where the DE only directly affects the background evolution, considering Taylor expansions of the equation of state, principal component analysis and parameterizations related to the potential of a minimally coupled DE scalar field. When estimating the density of DE at early times, we significantly improve present constraints. We then move to general parameterizations of the DE or MG perturbations that encompass both effective field theories and the phenomenology of gravitational potentials in MG models. Lastly, we test a range of specific models, such as k-essence, f(R) theories and coupled DE. In addition to the latest Planck data, for our main analyses we use baryonic acoustic oscillations, type-Ia supernovae and local measurements of the Hubble constant. We further show the impact of measurements of the cosmological perturbations, such as redshift-space distortions and weak gravitational lensing. These additional probes are important tools for testing MG models and for breaking degeneracies that are still present in the combination of Planck and background data sets. All results that include only background parameterizations are in agreement with LCDM. When testing models that also change perturbations (even when the background is fixed to LCDM), some tensions appear in a few scenarios: the maximum one found is \sim 2 sigma for Planck TT+lowP when parameterizing observables related to the gravitational potentials with a chosen time dependence; the tension increases to at most 3 sigma when external data sets are included. It however disappears when including CMB lensing