Building Proteins in a Day: Efficient 3D Molecular Reconstruction

Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D structures from 2D images. This paper addresses the challenging problem of 3D reconstruction from 2D Cryo-EM images. A new framework for estimation is introduced which relies on modern stochastic optimization techniques to scale to large datasets. We also introduce a novel technique which reduces the cost of evaluating the objective function during optimization by over five orders or magnitude. The net result is an approach capable of estimating 3D molecular structure from large scale datasets in about a day on a single workstation.Comment: To be presented at IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 201

Crystal constructions in Number Theory

Weyl group multiple Dirichlet series and metaplectic Whittaker functions can be described in terms of crystal graphs. We present crystals as parameterized by Littelmann patterns and we give a survey of purely combinatorial constructions of prime power coefficients of Weyl group multiple Dirichlet series and metaplectic Whittaker functions using the language of crystal graphs. We explore how the branching structure of crystals manifests in these constructions, and how it allows access to some intricate objects in number theory and related open questions using tools of algebraic combinatorics

Observations on the distribution of meroplankton during an upwelling event

The distribution of the larvae of benthic invertebrates was investigated relative to hydrographic structures as a test of the hypothesi\u27s that larvae behave as if they are passive particles. Observations of larval and oceanographic distributions were made off Duck, North Carolina, USA in August 1994. Conditions were characterized by wind-driven coastal upwelling;flow was generally offshore near the surface and onshore below the pycnocline. Within 5 km of the shore the pycnocline was bent upward by the upwelling and it intersected the surface along most of the transects. In zooplankton samples, 20 taxa of larvae were counted (10 bivalve veligers, nine gastropod veligers and one polychaete larvae). Using cluster analysis, larvae were separated into groups with similar Patterns of distribution and similar affinities to water properties. The larvae in Cluster 3 did not display a consistent distribution pattern beyond that they tended to be found in warmer surface waters. An earlier paper described the distribution of larvae in the same location during a downwelling event [A. Shanks et al. (2002) J. Plankton Res., 24, 391-416]. Two of the clusters identified during this previous study were quite similar in composition to Clusters 1 and 2 in this study. In both studies, Cluster 1 larvae were found below the pycnocline, but during the upwelling event they were transported shoreward with the advection of the subpycnocline waters by the upwelling circulation. Within 5 km of the shore, Cluster 1 larvae were found at depths shallower than the base of the pycnocline and were often found in patches of high larval concentration. The patches were located where the waters were upwelling. Cluster 2 larvae were found within 5 km of the shore in both studies and tended to be highly concentrated in convergences or divergences. Larvae in Cluster 1 generally appeared to be dispersing as passive particles, except within the zone of upwelling where they may have been swimming against the upwelling flow leading to higher larval concentrations. Cluster 2 larvae appeared to be consistently concentrated in areas of vertical currents, suggesting that they may be attempting to maintain a Preferred depth in the face of the vertical flow which would lead to high larval concentration and nearshore larval distributions despite extensive cross-she ( movement of water. Despite their slow swimming speeds, the larvae in Clusters 1 and 2 were not swept offshore by the upwelling event

Providential Tides: the Double Low Water of Narragansett Bay

We investigate a mechanism for producing double-lows and double-highs in the semi-diurnal tide by selective amplification of higher harmonics in a resonant gulf. A double low water is observed at Providence, RI, near the head of Narragansett Bay on days when there is a flattening of the low water tidal curve at Newport, at the mouth of the bay. The flattening is caused by an unusually large quarter-diurnal component to the tide at Newport. The quarter diurnal component has the right phase (a maximum close to the time of the minimum in the semi-diurnal tide) to produce a prolonged flattening of the tidal curve around low water. The natural period of Narragansett Bay (for quarter-wavelength resonance) is close to 4 h and the quarter diurnal tide is amplified, relative to the semi-diurnal tide, within the bay. The selective amplification of the higher harmonic further prolongs the flattening effect at Providence and, occasionally, is sufficient to create a double low water at the head of the bay from quarter and semi-diurnal tides alone. More often, though, a sixth-diurnal harmonic produced within the bay, added to the flattened low water at Providence, creates the double low water. This mechanism of selective amplification of tidal harmonics could be relevant to double tides elsewhere

Climate change and health effects in Northwest Alaska

This article provides examples of adverse health effects, including weather-related injury, food insecurity, mental health issues, and water infrastructure damage, and the responses to these effects that are currently being applied in two Northwest Alaska communities