Erick Fredj

Evidence for Submesoscale Barriers to Horizontal Mixing in the Ocean from Current Measurements and Aerial Photographs

Abstract Ocean submesoscale (∼2–20 km) mixing processes play a major role in ocean dynamics, in physical–biological interactions (e.g., in the dispersion of larvae), and in the dispersion of pollutants. In this paper, horizontal mixing on a scale of a few kilometers is investigated, from observations of surface currents, using highly resolved (300 m) high-frequency radar. These results show the complexity of ocean mixing on scales of a few kilometers and the existence of temporary barriers to mixing that can affect the dispersion of biological materials and pollutants. These barriers are narrow [O(100 m)] and can survive for a few days. The existence of these barriers is supported in simultaneous aerial photographs. The barriers observed here may require a new approach to the way horizontal mixing is parameterized in ocean and climate models.

Simulation of vibrational dephasing of I2 in solid Kr using the semiclassical Liouville method

In this paper, we present simulations of the decay of quantum coherence between vibrational states of I(2) in its ground (X) electronic state embedded in a cryogenic Kr matrix. We employ a numerical method based on the semiclassical limit of the quantum Liouville equation, which allows the simulation of the evolution and decay of quantum vibrational coherence using classical trajectories and ensemble averaging. The vibrational level-dependent interaction of the I(2)(X) oscillator with the rare-gas environment is modeled using a recently developed method for constructing state-dependent many-body potentials for quantum vibrations in a many-body classical environment [J. M. Riga, E. Fredj, and C. C. Martens, J. Chem. Phys. 122, 174107 (2005)]. The vibrational dephasing rates gamma(0n) for coherences prepared between the ground vibrational state mid R:0 and excited vibrational state mid R:n are calculated as a function of n and lattice temperature T. Excellent agreement with recent experiments performed by Karavitis et al. [Phys. Chem. Chem. Phys. 7, 791 (2005)] is obtained.

A new hybrid algorithm for finding the lowest minima of potential surfaces: approach and application to peptides.

A new algorithm is presented for finding the global minimum, and other low‐lying minima, of a potential energy surface (PES) of biological molecules. The algorithm synergetically combines three well‐known global optimization methods: the diffusion equation method (DEM), which involves smoothing the PES; a simulated annealing (SA) algorithm; and evolutionary programming (EP), whose population‐oriented approach allows for a parallel search over different regions of the PES. Tests on five peptides having between 6 and 9 residues show that the code implementing the new combined algorithm is efficient and is found to outperform the constituent methods, DEM and SA. Results of the algorithm, in the gas phase and with the GBSA implicit solvent model, are compared with crystallographic data for the test peptides; good accord is found in all cases. Also, for all but one of the examples, our hybrid algorithm finds a minimum deeper than those obtained by a very extensive scan. TINKERs implementation of the OPLS‐AA force field is employed for the structure prediction. The results show that the new algorithm is a powerful structure predictor, when a reliable potential function is available. Our implementation of the algorithm is time‐efficient, and requires only modest computational resources. Work is underway on applications of the new algorithm to structural prediction of proteins and other biological macro‐molecules.

Anharmonic vibrational frequency calculations of 5,6-dihydrouracil and its complex with water : testing improved semiempirical potentials for biological molecules

The anharmonic vibrational spectra of the mutant nucleobase 5,6 dihydrouracil (DHU) and its complex with water are computed and the results are analysed with focus on the properties of the anharmonic coupling between different modes. A recently proposed potential surface is used, based on improving the potential from semiempirical PM3 electronic structure theory. This improved potential energy surface is obtained by a coordinate scaling that yields agreement for harmonic frequencies obtained through ab initio (MP2) or DFT methods. The improved PM3 potentials implemented herein give anharmonic frequencies that are in good agreement with experiment for isolated DHU. Similarly anharmonic frequencies for the DHU-water complex give good agreement when compared to experiments carried out on a remarkably similar model system; uracil-water. This supports the use of the improved PM3 potentials for the spectrochemical description of nucleobases and related molecules. The anharmonic frequencies for the scaled PM3 potential are computed by the vibrational self-consistent field (VSCF) method. The anharmonic coupling interaction between different vibrational modes are analyzed and characterized. For example, the CO out of plane bending mode in isolated DHU was observed to couple most strongly with the NH stretch mode at 3478 cm−1. In the case of the DHU-H2O complex, strong coupling was observed between the O–3H water stretch and the CO out of plane bending modes of DHU at 759 cm−1. The results suggest insights into patterns of intramolecular vibrational energy transfer in DHU and DHU–H2O.

Quantum vibrational state-dependent potentials for classical many-body simulations

In this paper, we present a method for constructing simple state-dependent many-body potentials for quantum vibrations in a classical bath. The approach is based on an adiabatic separation between high-frequency quantum vibrational modes of the solute and the lower frequency classical motion of the solvent, and on a first-order perturbation theory description of the dependence of the quantum energies on bath configuration. In the simplest realization of the method, the delocalized quantum probability density of the vibrational mode is approximated by a sum of two delta functions, with positions and weights chosen to represent the lowest three moments of the exact distribution. Thus, in the many-body description of the system, each atom describing the quantum vibration is represented by a pair of particles. These quantum particles are held in rigid relative position and interact with the bath via potentials the magnitudes of which are modified by the delta-function weights. The resulting approach allows the classical molecular dynamics of molecules in arbitrary quantum vibrational states to be simulated with a little more effort than a purely classical description. The applicability of the method is illustrated in many-body simulations of the dephasing of vibrational superposition states of I(2) in a cryogenic krypton matrix, yielding results in good agreement with experiment.

New Lagrangian diagnostics for characterizing fluid flow mixing

A new kind of Lagrangian diagnostic family is proposed and a specific form of it is suggested for characterizing mixing: the extreme (maximal/minimal) extent of a trajectory and some of its variants. It enables the detection of coherent structures and their dynamics in two- (and potentially three-) dimensional unsteady flows in both bounded and open domains. Its computation is simple and provides new insights regarding the mixing properties on both short and long time scales and on both spatial plots and distribution diagrams. We demonstrate its applicability to two dimensional flows using two toy models and a data set of surface currents from the South Atlantic.

Gap Filling of the Coastal Ocean Surface Currents from HFR Data: Application to the Mid-Atlantic Bight HFR Network

AbstractHigh-frequency radar (HFR) surface current data are an increasingly utilized tool for capturing complex dynamics of coastal ocean systems worldwide. The radar is uniquely capable of sampling relevant temporal and spatial scales of nearshore processes that impact event response activities and basic coastal ocean research. HFR is a shore-based remote sensing system and is therefore subject to data gaps, which are predominately due to environmental effects, like increased external noise or low signal due to ocean surface conditions. Many applications of these surface current data require that these gaps be filled, such as Lagrangian numerical models, to estimate material transport and dispersion. This study introduces a new penalized least squares regression method based on a three-dimensional discrete cosine transform method to reconstruct hourly HFR surface current data with a horizontal resolution of 6 km. The method explicitly uses both time and space variability to predict the missing value. Fur...

AUTOMATIC MACHINE LEARNING OF KEYPHRASE EXTRACTION FROM SHORT HTML DOCUMENTS WRITTEN IN HEBREW

Keyphrases extracted from documents may save precious time for tasks such as filtering, summarization, and categorization. A few such systems are available for documents written in English. In this paper, we propose a model called LEH_KEY (Learning to Extract Hebrew KEYphrases) that for the first time learns to extract keyphrases for documents written in Hebrew. Firstly, we introduce a relatively high number (15) of baseline extraction methods as opposed to other related systems that use combinations of a low number (two/three) of baseline extraction methods. In contrast, we have investigated various combinations of larger number of baseline methods and various machine learning methods have been tested. The best results have been achieved by a combination of six baseline methods using J48 (an improved variant of C4.5). Our results have been found to be at least of equal quality to those achieved by extraction systems for documents written in English, which are regarded as state-of-the art.

Sea breeze, coastal upwelling modeling to support offshore wind energy planning and operations

In July 2014, BOEM issued the NJ Proposed Sale Notice of nearly 344,000 acres designated for offshore wind (OSW) energy development. The BOEM lease auction is expected to take place during the current year. The OSW developer(s) who win the lease(s) will submit their development application to the NJ Board of Public Utilities (NJ BPU). These applications must include a wind resource assessment and economic analysis. One major focus in the NJ BPU OSW rules is that applications “shall account for the coincidence between time of generation for the project and peak electricity demand.” Preliminary data analysis shows two mesoscale processes-coastal upwelling and sea breeze-may have a significant impact on wind generation during peak electricity demand. Tasked by NJ BPU, the Rutgers University Center for Ocean Observing Leadership (RUCOOL) is using the Weather Research and Forecasting (WRF) model to resolve these processes and quantify their impact on the wind resource. The WRF model set-up used is designed specifically for coastal/offshore regions, with three pertinent features for these regions. First, innovative satellite sea surface temperature (SST) composites at 2km resolution are used to resolve coastal upwelling. These composites integrate a) our own declouding algorithm set for the Mid Atlantic Bight to remove cloudy pixels from Advanced Very High Resolution Radiometer (AVHRR) SST scans, and b) coldest pixel composites of the resulting declouded AVHRR SST scans, rather than warmest pixel composites that would effectively remove coastal upwelling. Second, microscale grid spacing (<;1km) is used in WRF to resolve the sea breeze circulation, which can vary at meso- to microscales. Finally, validation of the WRF simulations is performed against coastal/offshore wind monitoring sites with atmospheric heights up to 200m, in order to ensure adequate model performance in coastal/offshore conditions. Three main results will be presented in this paper: (i) Coastal upwelling can produce high wind shear (~8 ms-1 across rotor blade dimensions). These significant shear values could potentially pose engineering challenges and should be considered in wind resource assessments. (ii) Lagrangian Coherent Structure (LCS) methodology can be used to identify key boundaries and fronts within the sea breeze circulation. While the onshore component of the sea breeze is well observed, very little is known about its unobserved offshore component, where OSW turbines will be installed. (iii) Power generation from a hypothetical 3000 MW OSW scenario off NJ was analyzed during three different sea breeze cases (one with strong upwelling, one with weak upwelling, and one without upwelling). Significant variability in power production occurred within each case and across the three sea breeze cases (net capacity factor ranged from 1 to 95%). WRF OSW potential power production data are being ingested by an electricity grid model to evaluate the impact of OSW energy penetration into the electrical power grid along with evaluating the economic portion of the applications. NJ is leading development of such an advanced joint atmospheric-economic modeling capability for determining the viability of OSW projects. Ongoing work includes development of a coupled atmosphere-ocean model (WRF-ROMS, Regional Ocean Modeling System), which will provide improved capabilities to diagnose coastal airsea processes (sea breeze and coastal upwelling) for OSW resource assessment (i.e. lowering uncertainty by including relevant mesoscale processes in simulations), and to more accurately predict these processes for operational forecasting during OSW construction and O&M phases.

Variability in summer surface residence time within a West Antarctic Peninsula biological hotspot

Palmer Deep canyon along the central West Antarctic Peninsula is known to have higher phytoplankton biomass than the surrounding non-canyon regions, but the circulation mechanisms that transport and locally concentrate phytoplankton and Antarctic krill, potentially increasing prey availability to upper-trophic-level predators such as penguins and cetaceans, are currently unknown. We deployed a three-site high-frequency radar network that provided hourly surface circulation maps over the Palmer Deep hotspot. A series of particle release experiments were used to estimate surface residence time and connectivity across the canyon. The majority of residence times fell between 1.0 and 3.5 days, with a mean of 2 days and a maximum of 5 days. We found a highly significant negative relationship between wind speed and residence time. Our residence time analysis indicates that the elevated phytoplankton biomass over the central canyon is transported into and out of the hotspot on time scales much shorter than the observed phytoplankton growth rate, suggesting that the canyon may not act as an incubator of phytoplankton productivity as previously suggested. It may instead serve more as a conveyor belt of phytoplankton biomass produced elsewhere, continually replenishing the phytoplankton biomass for the local Antarctic krill community, which in turn supports numerous top predators. This article is part of the theme issue ‘The marine system of the West Antarctic Peninsula: status and strategy for progress in a region of rapid change’.