Ostracoda of the Family Cytheruridae from the Gulf of Panama

The present paper represents the first in a series on ostracoda from Gulf of Panama, and deals with Cytheruridae which comprise 31 species distributed among nine genera. Three genera : Serrocytherura, Nearocytherura, and Lobosocytheropteron; and twelve species : Eucytherura sanjoensis, E. pinasensis, Gytherura nodosa, C. purii, Semicytherura reticuliforma, Serrocytherura panamaensis, Kangarina complicata, K. delicata, K. pervadera, Lobosocytheropteron perlasensis, L. bartolomensis and L. pinasensis, are described as new. Several microstructures peculiar to certain genera were recognized with the aid of the scanning electron microscope. Noteworthy are : 1) the weak reticulation in the lateral surface in forms referred to Kangarina; 2) in Eucytherura, each solum has sieve-plate-like coarse perforations, which correspond to internal openings; 3) in Paracytheridea, the presence of papillae, rings, sieve plates and simple pores armored by papillae; and 4) relatively large, simple internal openings in forms of Kangarina that serve to distinguish "Kangarina." Under the scanning electron microscope the wide extension of calcified posterior inner lamella which has been a basis for Semicytherura is not necessarily distinct from non-calcified one. Under the circumstances, in this report, the species referred to Semicytherura are based on the wide extension of posterior inner lamella observed without concern as to whether well calcified or not. Using frequency of occurrence rather than presence-absence data, four main distributional patterns are recognized among the cytherurid species. The major patterns and their subdivisions are : I. Widespread pattern : These forms prevail widely on the entire shelf area. I-A. Bahia San Miguel subdivision : Semicytherura sandbergi and Nearocytherura bananaformis are found abundantly in the Bahia San Miguel as well as in the outer area. This distribution suggests that those forms do not have any preference for particular environmental condition in this Gulf. I-B. Punta Garachine subdivision : Kangarina pervadera, Eucytherura guaymasensis, and Cytheropteron assimiloides are distributed widely, but are absent from Bahia San Miguel, and seem to show preferences for the outer shelf area. II. Eastern pattern : The forms in this pattern are distributed in the eastern half of the Gulf, with rare occurrence from the other realms. II-A. Archipelago subdivision : Among the eastern pattern, Paracytheridea tschoppi, P. clara, and Cytherura nodosa occurred dominantly in the areas around Archipielago de las Perlas and Bahia San Miguel, showing a preference for shallow water. II-B. Bahia Pinas subdivision : Lobosocytheropteron pinasensis and L. bartolomensis frequently occurred off Bahia Pinas, showing a preference for outer shelf area. II-C. Off Bahia Pinas subdivision : The forms prevail in the restricted to the southeastern part of the Gulf and are not found on inner shelf. This subdivision may show a narrow tolerance to the environmental condition and represented by Kangarina complicata. III. West-Central pattern : The forms representing this pattern prevail frequently in the southwestern to central parts of the Gulf and are very rarely found from the other realm. The pattern is represented by Kangarina delicata and Eucytherura sanjoensis which are dominant at depths of about 100 m. IV. Outer Shelf pattern : Four species are found in low numbers at three stations with depths more than 1000 m. Three of these species are not found on inner shelf. These are Lobosocytheropteron? sp. A, L.? sp. B, and L.? sp. C

Quantum entanglement in photosynthetic light harvesting complexes

Light harvesting components of photosynthetic organisms are complex, coupled, many-body quantum systems, in which electronic coherence has recently been shown to survive for relatively long time scales despite the decohering effects of their environments. Within this context, we analyze entanglement in multi-chromophoric light harvesting complexes, and establish methods for quantification of entanglement by presenting necessary and sufficient conditions for entanglement and by deriving a measure of global entanglement. These methods are then applied to the Fenna-Matthews-Olson (FMO) protein to extract the initial state and temperature dependencies of entanglement. We show that while FMO in natural conditions largely contains bipartite entanglement between dimerized chromophores, a small amount of long-range and multipartite entanglement exists even at physiological temperatures. This constitutes the first rigorous quantification of entanglement in a biological system. Finally, we discuss the practical utilization of entanglement in densely packed molecular aggregates such as light harvesting complexes.Comment: 14 pages, 7 figures. Improved presentation, published versio

The Subaru high-z quasar survey: discovery of faint z~6 quasars

We present the discovery of one or two extremely faint z~6 quasars in 6.5 deg^2 utilizing a unique capability of the wide-field imaging of the Subaru/Suprime-Cam. The quasar selection was made in (i'-z_B) and (z_B-z_R) colors, where z_B and z_R are bandpasses with central wavelengths of 8842A and 9841A, respectively. The color selection can effectively isolate quasars at z~6 from M/L/T dwarfs without the J-band photometry down to z_R<24.0, which is 3.5 mag. deeper than SDSS. We have selected 17 promising quasar candidates. The follow-up spectroscopy for seven targets identified one apparent quasar at z=6.156 with M_1450=-23.10. We also identified one possible quasar at z=6.041 with a faint continuum of M_1450=-22.58 and a narrow Lyman-alpha emission with HWHM=427 km/s, which cannot be distinguished from Lyman-alpha emitters. We derive the quasar luminosity function at z~6 by combining our faint quasar sample with the bright quasar samples by SDSS and CFHQS. Including our data points invokes a higher number density in the faintest bin of the quasar luminosity function than the previous estimate employed. This suggests a steeper faint-end slope than lower-z, though it is yet uncertain based on a small number of spectroscopically identified faint quasars and several quasar candidates are still remain to be diagnosed. The steepening of the quasar luminosity function at the faint-end does increase the expected emission rate of the ionizing photon, however, it only changes by a factor of ~2-6. This was found to be still insufficient for the required photon budget of reionization at z~6.Comment: 10 pages, 8 figures. Accepted for publication in Ap

Pattern scaling using ClimGen: monthly-resolution future climate scenarios including changes in the variability of precipitation

Development, testing and example applications of the pattern-scaling approach for generating future climate change projections are reported here, with a focus on a particular software application called “ClimGen”. A number of innovations have been implemented, including using exponential and logistic functions of global-mean temperature to represent changes in local precipitation and cloud cover, and interpolation from climate model grids to a finer grid while taking into account land-sea contrasts in the climate change patterns. Of particular significance is a new approach for incorporating changes in the inter-annual variability of monthly precipitation simulated by climate models. This is achieved by diagnosing simulated changes in the shape of the gamma distribution of monthly precipitation totals, applying the pattern-scaling approach to estimate changes in the shape parameter under a future scenario, and then perturbing sequences of observed precipitation anomalies so that their distribution changes according to the projected change in the shape parameter. The approach cannot represent changes to the structure of climate timeseries (e.g. changed autocorrelation or teleconnection patterns) were they to occur, but is shown here to be more successful at representing changes in low precipitation extremes than previous pattern-scaling methods

Hierarchical Equations of Motion Approach to Quantum Thermodynamics

We present a theoretical framework to investigate quantum thermodynamic processes under non-Markovian system-bath interactions on the basis of the hierarchical equations of motion (HEOM) approach, which is convenient to carry out numerically "exact" calculations. This formalism is valuable because it can be used to treat not only strong system-bath coupling but also system-bath correlation or entanglement, which will be essential to characterize the heat transport between the system and quantum heat baths. Using this formalism, we demonstrated an importance of the thermodynamic effect from the tri-partite correlations (TPC) for a two-level heat transfer model and a three-level autonomous heat engine model under the conditions that the conventional quantum master equation approaches are failed. Our numerical calculations show that TPC contributions, which distinguish the heat current from the energy current, have to be take into account to satisfy the thermodynamic laws.Comment: 9 pages, 4 figures. As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and G. Adesso (eds.), "Thermodynamics in the quantum regime - Recent Progress and Outlook", (Springer International Publishing

Ostracoda of the Family Loxoconchidae from the Gulf of Panama

Of 234 stations sampled in Gulf of Panama, ostracode specimens were found at 121 stations. The present paper represents the second in a series on Ostracoda from Gulf of Panama, and deals with Loxoconchidae which comprises 11 species distributed among six genera. One genus : Touroconcha; and three species : Loxoconcha dorsobulba, Palmoconcha minima, and Nipponocythere nagaseae; are described as new. In addition to the conventional description of new species, the micro-ornamentations of valve surface are shown through scanning electronic microscopy, and their characteristics and differences are demonstrated for the respective species. In the Gulf, Palmoconcha laevimarginata Swain and Gilby, 1974, Loxocorniculum sculptoides Swain, 1967 and Nipponocythere nagaseae n. sp. prevail widely, and are especially common on the outer shelf area. Palmoconcha minima n. sp. and Loxocorniculum fischeri (Brady, 1869) have a restricted distribution in the Gulf, but are sometimes common on the outer shelf area. All these forms have been recorded from the Eastern Tropical Pacific and Caribbean-Gulf Coast regions, and would probably be useful in constructing respective characteristic faunas. On the other hand, Loxoconcha dorsobulba n. sp. and Loxocorniculum schusterae (Hartmann, 1959) are common only on the inner shelf area, and seem to be more or less endemic

Multiscale photosynthetic exciton transfer

Photosynthetic light harvesting provides a natural blueprint for bioengineered and biomimetic solar energy and light detection technologies. Recent evidence suggests some individual light harvesting protein complexes (LHCs) and LHC subunits efficiently transfer excitons towards chemical reaction centers (RCs) via an interplay between excitonic quantum coherence, resonant protein vibrations, and thermal decoherence. The role of coherence in vivo is unclear however, where excitons are transferred through multi-LHC/RC aggregates over distances typically large compared with intra-LHC scales. Here we assess the possibility of long-range coherent transfer in a simple chromophore network with disordered site and transfer coupling energies. Through renormalization we find that, surprisingly, decoherence is diminished at larger scales, and long-range coherence is facilitated by chromophoric clustering. Conversely, static disorder in the site energies grows with length scale, forcing localization. Our results suggest sustained coherent exciton transfer may be possible over distances large compared with nearest-neighbour (n-n) chromophore separations, at physiological temperatures, in a clustered network with small static disorder. This may support findings suggesting long-range coherence in algal chloroplasts, and provides a framework for engineering large chromophore or quantum dot high-temperature exciton transfer networks.Comment: 9 pages, 6 figures. A significantly updated version is now published online by Nature Physics (2012

Suppression of quantum oscillations and the dependence on site energies in electronic excitation transfer in the Fenna-Matthews-Olson trimer

Energy transfer in the photosynthetic complex of the Green Sulfur Bacteria known as the Fenna-Matthews-Olson (FMO) complex is studied theoretically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll (BChl) molecule into account. We find that in all considered cases there is very little transfer between the monomers. Since it is believed that the eighth BChl is located near the main light harvesting antenna we look at the differences in transfer between the situation when BChl 8 is initially excited and the usually considered case when BChl 1 or 6 is initially excited. We find strong differences in the transfer dynamics, both qualitatively and quantitatively. When the excited state dynamics is initialized at site eight of the FMO complex, we see a slow exponential-like decay of the excitation. This is in contrast to the oscillations and a relatively fast transfer that occurs when only seven sites or initialization at sites 1 and 6 is considered. Additionally we show that differences in the values of the electronic transition energies found in the literature lead to a large difference in the transfer dynamics

The Physical Basis for Long-lived Electronic Coherence in Photosynthetic Light Harvesting Systems

The physical basis for observed long-lived electronic coherence in photosynthetic light-harvesting systems is identified using an analytically soluble model. Three physical features are found to be responsible for their long coherence lifetimes: i) the small energy gap between excitonic states, ii) the small ratio of the energy gap to the coupling between excitonic states, and iii) the fact that the molecular characteristics place the system in an effective low temperature regime, even at ambient conditions. Using this approach, we obtain decoherence times for a dimer model with FMO parameters of $\approx$ 160 fs at 77 K and $\approx$ 80 fs at 277 K. As such, significant oscillations are found to persist for 600 fs and 300 fs, respectively, in accord with the experiment and with previous computations. Similar good agreement is found for PC645 at room temperature, with oscillations persisting for 400 fs. The analytic expressions obtained provide direct insight into the parameter dependence of the decoherence time scales.Comment: 5 figures; J. Phys. Chem. Lett. (2011