Structural Relaxation of Materials with Spin-Orbit Coupling: Analytical Forces in Spin-Current DFT

Analytical gradients of the total energy are provided for local density and generalized-gradient hybrid approximations to generalized Kohn-Sham spin-current density functional theory (SCDFT). It is shown that gradients may be determined analytically, in a two-component framework, including spin-orbit coupling (SOC), with high accuracy. We demonstrate that renormalization of the electron-electron potential by SOC-induced spin-currents can account for considerable modification of crystal structures. In the case of Iodine-based molecular crystals, the effect may amount to more than half of the total modification of the structure by SOC. Such effects necessitate an SCDFT, rather than DFT, formulation, in which exchange-correlation functionals are endowed with an explicit dependence on spin-current densities. An implementation is presented in the \textsc{Crystal} program

The Nascent Kuroshio of Lamon Bay

A northward flowing current, emanating from the North Equatorial Current (NEC) bifurcation at the Philippine margin, enters Lamon Bay along Luzon's eastern coast. There the NEC tropical water masses merge with subtropical water of the western North Pacific to form the Kuroshio. A northward flowing western boundary current is first observed near 16.5°N, marking the initiation of the Kuroshio. The current feeding into the nascent Kuroshio of Lamon Bay is bracketed by an anticyclonic dipole to its northeast and a cyclonic dipole to its southwest. Ship based observational programs in the spring seasons of 2011 and 2012, detect a shift of the Lamon Bay thermohaline stratification with marked enrichment of NEC tropical thermocline water in 2012 relative to a dominant western North Pacific subtropical stratification of 2011. Temperature - salinity time series from moorings spanning the two ship based observations, identify the timing of the transition as December 2011. The NEC bifurcation was further south in May 2012 than in May 2011. We suggest that the more southern bifurcation in May 2012 induced increased NEC thermocline water injection into Lamon Bay and nascent Kuroshio, increasing the linkage of the western North Pacific subtropical and tropical thermoclines. This connection was reduced in May 2011 as the NEC bifurcation shifted into a more northerly position and western North Pacific subtropical thermocline dominated Lamon Bay stratification

Improving surface current resolution using direction finding algorithms for multiantenna high-frequency radars

Author Posting. © American Meteorological Society, 2019. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of the Atmospheric and Oceanic Technology 36(10), (2019): 1997-2014, doi: 10.1175/JTECH-D-19-0029.1.While land-based high-frequency (HF) radars are the only instruments capable of resolving both the temporal and spatial variability of surface currents in the coastal ocean, recent high-resolution views suggest that the coastal ocean is more complex than presently deployed radar systems are able to reveal. This work uses a hybrid system, having elements of both phased arrays and direction finding radars, to improve the azimuthal resolution of HF radars. Data from two radars deployed along the U.S. East Coast and configured as 8-antenna grid arrays were used to evaluate potential direction finding and signal, or emitter, detection methods. Direction finding methods such as maximum likelihood estimation generally performed better than the well-known multiple signal classification (MUSIC) method given identical emitter detection methods. However, accurately estimating the number of emitters present in HF radar observations is a challenge. As MUSIC’s direction-of-arrival (DOA) function permits simple empirical tests that dramatically aid the detection process, MUSIC was found to be the superior method in this study. The 8-antenna arrays were able to provide more accurate estimates of MUSIC’s noise subspace than typical 3-antenna systems, eliminating the need for a series of empirical parameters to control MUSIC’s performance. Code developed for this research has been made available in an online repository.This analysis was supported by NSF Grants OCE-1657896 and OCE-1736930 to Kirincich, OCE-1658475 to Emery and Washburn and OCE-1736709 to Flament. Flament is also supported by NOAA’s Integrated Ocean Observing System through Award NA11NOS0120039. The authors thank Lindsey Benjamin, Alma Castillo, Ken Constantine, Benedicte Dousset, Ian Fernandez, Mael Flament, Dave Harris, Garrett Hebert, Ben Hodges, Victoria Futch, Matt Guanci, and Philip Moravcik for assistance in building, deploying, and operating the radars.2020-04-1

Observations of vortices and vortex Rossby waves in the lee of an island

A 9-month deployment of high-frequency radio (HFR) current meters and moored ADCPs in the lee of Oahu, Hawaii, gives some dynamical insights in the generation and evolution of vortices in the lee of islands. For mountainous islands lying in relatively strong and steady winds, such as the Hawaiian archipelago in the trade winds, vortices can be generated by Ekman pumping associated with orographic wind stress curls. An anticyclone generated in the lee of Oahu in October 2002 reaches a negative absolute vorticity for 4 days, before quickly decaying and broadening, possibly as a result of inertial instability. A large cyclone, generated in December 2002 in the lee of Hawaii, drifted northwestward and stalled southwest of Oahu in March-April 2003. Vortex Rossby waves developing on its periphery were observed by the HFRs with a northeastward phase propagation, 110 km wavelength and 16 days period

Mid- and Far-Infrared Marker Bands of the Metal Coordination Sites of the Histidine Side Chains in the Protein Cu,Zn-Superoxide Dismutase

International audienceVibrational spectroscopy gives important information on the properties of ligand and metal–ligand bonds in metalloenzymes. Infrared spectroscopy is appealing for the study of metal active sites that are not amenable to Raman spectroscopy. We present a combined experimental and theoretical approach to analyze the mid- and far-IR spectra of Cu,Zn-superoxide dismutase (Cu,Zn-SOD) as a probe of the histidine ligands. This metalloenzyme provides a unique model to identify specific IR signatures of metal–histidine coordination and to study their alterations as a function of the metal (copper/zinc), the copper valence state (+I/+II), the histidine coordination mode (Nτ and Nπ) and the histidine protonation state. DFT calculations combined with normal mode descriptions from potential energy distribution calculations were performed on two slightly different cluster models. Differences in the constraints at the side chain of one histidine Cu ligand sensibly modify the geometric parameters and vibrational properties. Electrochemically induced FTIR difference spectroscopy provided mid- and far-IR fingerprint spectra of the Cu protein in aqueous media that are sensitive to the redox state of the Cu centre at the active site. Comparisons of the DFT predictions with the experimental IR modes of the histidine ligands at the Cu,Zn-SOD active site showed that useful mid-IR markers of histidine Nτ and Nπ coordination were predicted with good accuracy. The DFT analysis further demonstrated a link between the ν(C4–C5) mode frequency of His46 and the specific properties of the His46–Cu bond in Cu,Zn-SOD. A combined theoretical and experimental approach on samples in H2O and 2H2O or 15N-labelled samples identified the contributions from the histidine side chain modes in the 669–629 cm–1 region

Altimeter processing tools for analyzing mesoscale ocean features

Satellite altimeters provide many opportunities for oceanographers to supplement their research with a valuable new data set. The recent GEOSAT exact repeat mission is the first of several altimeter missions proposed during the next decade. To utilize this new data, a software package was developed at the Woods Hole Oceanographic Institution and the University of Hawaii to facilitate the extraction of useful information from the NODC distributed GEOSAT data tapes. This software package was written with portability and modularity in mind. It should be possible to use this package with little or no modifications on data from future altimeters. The code was written in C and tested on Sun workstations and is oriented toward UNIX operating systems. However, since standard code was used, the programs should port easily to other computer systems. The modularity of the code should enable users to create additional programs. Additional programs designed to handle collocated water vapor corrections are also included for comparison.Funding was provided by the Office of Naval Research through Grant No. N00014-86-K-0751

MARINE-EXPRESS: taking advantage of high throughput cloning and expression strategies for the post-genomic analysis of marine organisms

Background: The production of stable and soluble proteins is one of the most important steps prior to structural and functional studies of biological importance. We investigated the parallel production in a medium throughput strategy of genes coding for proteins from various marine organisms, using protocols that involved recombinatorial cloning, protein expression screening and batch purification. This strategy was applied in order to respond to the need for post-genomic validation of the recent success of a large number of marine genomic projects. Indeed, the upcoming challenge is to go beyond the bioinformatic data, since the bias introduced through the genomes of the so called model organisms leads to numerous proteins of unknown function in the still unexplored world of the oceanic organisms. Results: We present here the results of expression tests for 192 targets using a 96-well plate format. Genes were PCR amplified and cloned in parallel into expression vectors pFO4 and pGEX-4T-1, in order to express proteins N-terminally fused to a six-histidine-tag and to a GST-tag, respectively. Small-scale expression and purification permitted isolation of 84 soluble proteins and 34 insoluble proteins, which could also be used in refolding assays. Selected examples of proteins expressed and purified to a larger scale are presented. Conclusions: The objective of this program was to get around the bottlenecks of soluble, active protein expression and crystallization for post-genomic validation of a number of proteins that come from various marine organisms. Multiplying the constructions, vectors and targets treated in parallel is important for the success of a medium throughput strategy and considerably increases the chances to get rapid access to pure and soluble protein samples, needed for the subsequent biochemical characterizations. Our set up of a medium throughput strategy applied to genes from marine organisms had a mean success rate of 44% soluble protein expression from marine bacteria, archaea as well as eukaryotic organisms. This success rate compares favorably with other protein screening projects, particularly for eukaryotic proteins. Several purified targets have already formed the base for experiments aimed at post-genomic validation

Northern Adriatic response to a wintertime bora wind event

The unprecedented suite of research activities that focused on the Adriatic in winter 2003 provided a multi-faceted view of bora events and the resulting oceanic response