Lattice dynamics effects on small polaron properties

This study details the conditions under which strong-coupling perturbation theory can be applied to the molecular crystal model, a fundamental theoretical tool for analysis of the polaron properties. I show that lattice dimensionality and intermolecular forces play a key role in imposing constraints on the applicability of the perturbative approach. The polaron effective mass has been computed in different regimes ranging from the fully antiadiabatic to the fully adiabatic. The polaron masses become essentially dimension independent for sufficiently strong intermolecular coupling strengths and converge to much lower values than those tradition-ally obtained in small-polaron theory. I find evidence for a self-trapping transition in a moderately adiabatic regime at an electron-phonon coupling value of .3. Our results point to a substantial independence of the self-trapping event on dimensionality.Comment: 8 pages, 5 figure

Different classes of genomic inserts contribute to human antibody diversity

Recombination of antibody genes in B cells can involve distant genomic loci and contribute a foreign antigen-binding element to form hybrid antibodies with broad reactivity for Plasmodium falciparum. So far, antibodies containing the extracellular domain of the LAIR1 and LILRB1 receptors represent unique examples of cross-chromosomal antibody diversification. Here, we devise a technique to profile non-VDJ elements from distant genes in antibody transcripts. Independent of the preexposure of donors to malaria parasites, non-VDJ inserts were detected in 80% of individuals at frequencies of 1 in 10(4) to 10(5) B cells. We detected insertions in heavy, but not in light chain or T cell receptor transcripts. We classify the insertions into four types depending on the insert origin and destination: 1) mitochondrial and 2) nuclear DNA inserts integrated at VDJ junctions; 3) inserts originating from telomere proximal genes; and 4) fragile sites incorporated between J-to-constant junctions. The latter class of inserts was exclusively found in memory and in in vitro activated B cells, while all other classes were already detected in naïve B cells. More than 10% of inserts preserved the reading frame, including transcripts with signs of antigen-driven affinity maturation. Collectively, our study unravels a mechanism of antibody diversification that is layered on the classical V(D)J and switch recombination

Phase diagram of the Holstein polaron in one dimension

The behavior of the 1D Holstein polaron is described, with emphasis on lattice coarsening effects, by distinguishing between adiabatic and nonadiabatic contributions to the local correlations and dispersion properties. The original and unifying systematization of the crossovers between the different polaron behaviors, usually considered in the literature, is obtained in terms of quantum to classical, weak coupling to strong coupling, adiabatic to nonadiabatic, itinerant to self-trapped polarons and large to small polarons. It is argued that the relationship between various aspects of polaron states can be specified by five regimes: the weak-coupling regime, the regime of large adiabatic polarons, the regime of small adiabatic polarons, the regime of small nonadiabatic (Lang-Firsov) polarons, and the transitory regime of small pinned polarons for which the adiabatic and nonadiabatic contributions are inextricably mixed in the polaron dispersion properties. The crossovers between these five regimes are positioned in the parameter space of the Holstein Hamiltonian.Comment: 19 pages, 9 figure

Spinodally decomposed patterns in rapidly quenched Co-Cu melts

The Co-Cu system is analyzed in the region of metastable miscibility gap with separation of the undercooled melt into Co-rich and Cu-rich liquids [1]. Phase separation of undercooled and quenched samples of Co50Cu50 melt are investigated experimentally using electromagnetic levitation (EML) technique, quenching the undercooled melt onto a Pb-solder coated copper chill substrate and by splat quenching methods. It is found that quenching of the liquid samples with cooling rates of 106-107 K/s leads to a frozen in microstructure of spinodally decomposed liquids. The composition of the Co-rich phase measured by TEM-EDS is Co71.7Cu28.3 and that of the Cu-rich phase is Co26.8Cu73.2. These compositions are inside the spinodal region and close to the calculated spinodal boundary in the phase diagram of the Co-Cu system. The spinodally separated samples have periodicity of mean distance between patterns of about 0.12-0.4 μm. Using the model of fast spinodal decomposition (see Ref. [2] and references therein), computational modelling is carried out using semi-implicit numeric scheme as described in Ref. [3]. The results of modelling confirm the ability to quantitatively reproduce experimentally frozen spinodal patterns by their periodicity. The calculated time for the complete phase separation into the Co-rich and Cu-rich phases (in evolution spinodally decomposing patterns) is greater than the time for samples solidifying at cooling rates of 106-107 K/s. References [1] M. Kolbe, C.D. Cao, X.Y. Lu, P.K. Galenko, B. Wei, D.M. Herlach, Materials Science and Engineering A 375-377, 520 (2004). [2] P. Galenko, D. Jou, Physica A 388, 3113 (2009). [3] N. Lecoq, H. Zapolsky, P. Galenko, The European Physical Journal ST 177 165 (2009)

Climate and biotic evolution during the Permian-Triassic transition in the temperate Northern Hemisphere, Kuznetsk Basin, Siberia, Russia

The Siberian Traps volcanism is widely considered the main cause of the end-Permian mass extinction, the greatest biological crisis in the Earth history. While the extinction is interpreted as catastrophic and sudden with estimates of duration of approximately 35–40 thousand years from marine strata in South China, various lines of evidence have emerged for a more complex, prolonged, and diachronous extinction pattern. We present here the results of a multidisciplinary study of the Permian-Triassic continental transition in the Kuznetsk Basin, Russia. The region is proximal to the Siberian Traps LIP and the detrimental effects of the flood basalt volcanism in the Kuznetsk Basin may have been of similar scale as in the main area of the Siberian Traps distribution (Tunguska and Taymyr regions). Whereas earlier work has placed the Permian-Triassic boundary position between the coal-bearing Tailugan Formation and the volcanoclastic Maltsev Formation, here we revised the traditional model using three independent methods: radioisotopic CA-IDTIMS U-Pb zircon ages, δ13Corg isotope values and paleomagnetic proxies. The regional extinction of the humid-dominated forest flora (cordaites) and the aridity-induced biotic turnover in the Kuznetsk Basin occurred 820 kyr earlier than the end-Permian extinction event recorded in South China at 251.94 Ma. The biota in Kuznetsk Basin at the turnover subsequently diversified (with some exceptions) across the Permian-Triassic transition. By compiling a large taxonomic database, we find that marine and terrestrial biotic diversity in Siberia progressively increased from the beginning of the Permian up to the middle Roadian (early Guadalupian global glacial event). After that time, the diversity at the species and generic level progressively and slowly declined towards the aforementioned latest Changhsingian (252.76 Ma) biotic turnover. Starting from this time, the biota rapidly diversified in the latest Changhsingian and Early-Middle Triassic. We suggest that the Permian-Triassic mass extinction mostly occurred in the tropics and subtropics due to the strong climatic warming, which was relatively low in late Changhsingian and gradually but quickly extends in the latest Changhsingian to an abnormally high temperature and extremely low oxygenated water in the oceans that was deadly for most marine animals. The warm climate shift poleward during Permian-Triassic transition in the middle-high latitudes caused the replacement (turnover) of the humid-related biotas by the dry climate-related and more diverse communities, which continued to expand throughout the Triassic in both marine and terrestrial habitats. The pattern of the Permian-Triassic event in both marine and terrestrial habitats was more intricate in terms of extinction, turnover, and diversity of biota within the different climatic zones and environmental habitats than has been generally considered

Global time scale and regional stratigraphic reference scales of Central and West Europe, East Europe, Tethys, South China, and North America as used in the Devonian-Carboniferous-Permian Correlation Chart 2003 (DCP 2003)

The boundaries of the Devonian, Carboniferous, and Permian stages of the Global Stratigraphic Reference Scale (abbreviated to Global Stratigraphic Scale-GSS) are described in relation to the biostratigraphic and/or lithostratigraphic units of the Regional Stratigraphic Reference Scales (abbreviated to Regional Stratigraphic Scales-RSS) of Central and West Europe, East Europe, Tethys, South China (eastern Tethys), and North America. In their type regions the boundaries of GSS units rarely coincide with those of homonymous RSS units. Moreover, the definitions of some RSS units have changed several times over the last decades, and subsequent misunderstanding of the stratigraphical significance of these changes has often introduced errors into proposed global correlation charts. The stratigraphic framework proposed in our global Devonian-Carboniferous-Permian Correlation Chart 2003 [DCP 2003 (Devonian-Carboniferous-Permian Correlation Chart 2003, Menning, M., Schneider, J. W., Alekseev, A. S., Amon, E. O., Becker, G., von Bitter, P. H., Boardman, D. R., Bogoslovskaya, M., Braun, A., Brocke, R., Chernykh, V., Chuvashov, B. I., Clayton, G., Dusar, M., Davydov, V. I., Dybova-Jachowicz, S., Forke, H. C., Gibling, M., Gilmour, E. H., Goretzki, J., Grunt, T. A., Hance, L., Heckel, P. H., Izokh, N. G., Jansen, U., Jin Y.-G., Jones, P., Käding, K.-Ch., Kerp, H., Kiersnowski, H., Klets, A., Klug, Ch., Korn, D., Kossovaya, O., Kotlyar, G. V., Kozur, H. W., Laveine, J.-P., Martens, Th., Nemyrovska, T. I., Nigmadganov, A. I., Paech, H.-J., Peryt, T. M., Rohn, R., Roscher, M., Rubidge, B., Schiappa, T. A., Schindler, E., Skompski, S., Ueno, K., Utting, J., Vdovenko, M. V., Villa, E., Voigt, S., Wahlman, G. P., Wardlaw, B. R., Warrington, G., Weddige, K., Werneburg, R., Weyer, D., Wilde, V., Winkler Prins, C. F., Work, D. M., 2004). Abschlußkolloquium DFG-Schwerpunktprogramm 1054: Evolution des Systems Erde während des jüngeren Paläozoikums im Spiegel der Sedimentgeochemie. Abstracts Univ. Erlangen, Germany, 2004, p. 43.] (herein abbreviated to DCP 2003, and cited as DCP, 2003 in references) is an attempt to reduce these errors. The DCP 2003 is the stratigraphic base for Project 1054 of the Deutsche Forschungsgemeinschaft (DFG) "The evolution of the Late Palaeozoic in the light of sedimentary geochemistry". This composite time scale has been carefully balanced, as far as data allows, to remove unnecessary, artificial compression and expansion of time intervals, biozonations and depositional events. The ages selected in DCP 2003 are markedly different to those in the Geologic Time Scale 1989 [GTS 1989 (Harland, W.B., Armstrong, R.L., Cox, A.V., Craig, L.E., Smith, A.G., Smith, D.G., 1990). A geologic time scale 1989. Cambridge Univ. Press, Cambridge.; Harland, W.B., Armstrong, R.L., Cox, A.V., Craig, L.E., Smith, A.G., Smith, D.G., 1990. A geologic time scale 1989. Cambridge Univ. Press, Cambridge, pp. 1-263.] and in Gradstein and Ogg [Gradstein, F.M., Ogg, J., 1996. A Phanerozoic time scale. Episodes 19 (1/2), 3-4, insert.), whereas they are closer to those of the Geologic Time Scale 2004 [GTS 2004; Gradstein, F.M., Ogg, J.G., Smith, A.G., 2004. A Geologic Time Scale 2004. Cambridge Univ. Press, Cambridge, pp. 1-589.]. Mostly, the ages are rounded to the nearest 0.5 Ma in order to avoid estimates of questionable accuracy, whereas ages of 0.1 Ma in the GTS 2004 and their error bars of ± 0.4 Ma to ± 2.8 Ma for the Devonian to Permian stage boundaries suggest an improved accuracy. In contrast, in the DCP 2003 questionable ages and positions of stratigraphic boundaries are marked by arrows