Dinoflagellate cyst-based reconstructions of mid to late Holocene winter sea-surface temperature and productivity from an anoxic fjord in the NE Pacific Ocean

Published contemporary dinoflagellate distributional data from the NE Pacific margin and estuarine environments (n = 136) were re-analyzed using Canonical Correspondence Analysis (CCA) and partial Canonical Correspondence Analysis (pCCA). These analyses illustrated the dominant controls of winter temperature and productivity on the distribution of dinoflagellate cysts in this region. Dinoflagellate cyst-based predictive models for winter temperature and productivity were developed from the contemporary distributional data using the modern analogue technique and applied to subfossil data from two mid to late Holocene (~5500 calendar years before present–present) cores; TUL99B03 and TUL99B11, collected from Effingham Inlet, a 15 km long anoxic fjord located on the southwest coast of Vancouver Island that directly opens to the Pacific Ocean through Barkley Sound. Sedimentation within these basins largely comprises annually deposited laminated couplets, each made up of a winter deposited terrigenous layer and spring to fall deposited diatomaceous layer. The Effingham Inlet dinoflagellate cyst record provides evidence of a mid-Holocene gradual decline in winter SST, ending with the initiation of neoglacial advances in the region by ~3500 cal BP. A reconstructed Late Holocene increase in winter SST was initiated by a weakening of the California Current, which would have resulted in a warmer central gyre and more El Niño-like conditions.

Metastable anions of dinitrobenzene: Resonances for electron attachment and kinetic energy release

Attachment of free, low-energy electrons to dinitrobenzene (DNB) in the gas phase leads to DNB as well as several fragment anions. DNB, (DNB-H), (DNB-NO), (DNB-2NO), and (DNB-NO2) are found to undergo metastable (unimolecular) dissociation. A rich pattern of resonances in the yield of these metastable reactions versus electron energy is observed; some resonances are highly isomer-specific. Most metastable reactions are accompanied by large average kinetic energy releases (KER) that range from 0.5 to 1.32 eV, typical of complex rearrangement reactions, but (1,3-DNB-H)(-) features a resonance with a KER of only 0.06 eV for loss of NO. (1,3-DNB-NO)(-) offers a rare example of a sequential metastable reaction, namely, loss of NO followed by loss of CO to yield C5H4O- with a large KER of 1.32 eV. The G4(MP2) method is applied to compute adiabatic electron affinities and reaction energies for several of the observed metastable channels. (C) 2010 American Institute of Physics. [doi:10.1063/1.3514931]

Approximating the Set of Local Minima in Partial RNA Folding Landscapes

Motivation: We study a stochastic method for approximating the set of local minima in partial RNA folding landscapes associated with a bounded-distance neighbourhood of folding conformations. The conformations are limited to RNA secondary structures without pseudoknots. The method aims at exploring partial energy landscapes pL induced by folding simulations and their underlying neighbourhood relations. It combines an approximation of the number of local optima devised by Garnier and Kallel (2002) with a run-time estimation for identifying sets of local optima established by Reeves and Eremeev (2004).

Results: The method is tested on nine sequences of length between 50 nt and 400 nt, which allows us to compare the results with data generated by RNAsubopt and subsequent barrier tree calculations. On the nine sequences, the method captures on average 92% of local minima with settings designed for a target of 95%. The run-time of the heuristic can be estimated by O(n2D?ln?), where n is the sequence length, ? is the number of local minima in the partial landscape pL under consideration and D is the maximum number of steepest descent steps in attraction basins associated with pL.

CoMFA and homology-based models of the glycine binding site of N-methyl-D-aspartate receptor

Homology modeling was used to build 3D models of the N-methyl-D-aspartate (NMDA) receptor glycine binding site on the basis of an X-ray structure of the water-soluble AMPA-sensitive receptor. The docking of agonists and antagonists to these models was used to reveal binding modes of ligands and to explain known structure-activity relationships. Two types of quantitative models, 3D-QSAR/CoMFA and a regression model based on docking energies, were built for antagonists (derivatives of 4-hydroxy-2-quinolone, quinoxaline-2,3-dione, and related compounds). The CoMFA steric and electrostatic maps were superimposed on the homology-based model, and a close correspondence was marked. The derived computational models have permitted the evaluation of the structural features crucial for high glycine binding site affinity and are important for the design of new ligands.

Exciton-mediated photothermal cooling in GaAs membranes

Cooling of the mechanical motion of a GaAs nano-membrane using the photothermal effect mediated by excitons was recently demonstrated by some of the authors (Usami et al 2012 Nature Phys. 8 168) and provides a clear example of the use of thermal forces to cool down mechanical motion. Here, we report on a single-free-parameter theoretical model to explain the results of this experiment which matches the experimental data remarkably well.

Nonlinear Field Line Random Walk and Generalized Compound Diffusion of Charged Particles

A new nonlinear theory for the perpendicular transport of charged particles is presented. This approach is based on an improved nonlinear treatment of field line random walk in combination with a generalized compound diffusion model. The generalized compound diffusion model is much more systematic and reliable, in comparison to previous theories. Furthermore, the new theory shows remarkably good agreement with test-particle simulations and heliospheric observations.