Low-frequency interaction between horizontal and overturning gyres in the ocean

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 35 (2008): L18614, doi:10.1029/2008GL035206.Low-frequency variability of the horizontal circulation in an idealized, eddy-permitting, numerical model drives the dominant mode of low-frequency variability in the meridional overturning circulation. This coupling takes place through the influence of lateral advection in the cyclonic high-latitude boundary current on the mixed layer depth along the boundary. The mean and low-frequency variability of the meridional overturning circulation are well predicted by a diagnostic estimate that assumes the downwelling is controlled by the thermal wind shear within the mixed layer along the boundary, which is in turn determined by a simple balance between lateral advection and surface cooling. The more general result is the demonstration that the mean and low frequency variability of the meridional overturning streamfunction are controlled by the baroclinic pressure gradient within the mixed layer along the boundary, which may be influenced by numerous factors such as low-frequency variability in lateral advection, wind stress, surface buoyancy fluxes, or ice melt and freshwater runoff.This work was supported by NSF grants OCE-0423975 and OCE-0726339

Permutation-invariant distance between atomic configurations

We present a permutation-invariant distance between atomic configurations, defined through a functional representation of atomic positions. This distance enables to directly compare different atomic environments with an arbitrary number of particles, without going through a space of reduced dimensionality (i.e. fingerprints) as an intermediate step. Moreover, this distance is naturally invariant through permutations of atoms, avoiding the time consuming associated minimization required by other common criteria (like the Root Mean Square Distance). Finally, the invariance through global rotations is accounted for by a minimization procedure in the space of rotations solved by Monte Carlo simulated annealing. A formal framework is also introduced, showing that the distance we propose verifies the property of a metric on the space of atomic configurations. Two examples of applications are proposed. The first one consists in evaluating faithfulness of some fingerprints (or descriptors), i.e. their capacity to represent the structural information of a configuration. The second application concerns structural analysis, where our distance proves to be efficient in discriminating different local structures and even classifying their degree of similarity

Analysis of Different Types of Regret in Continuous Noisy Optimization

The performance measure of an algorithm is a crucial part of its analysis. The performance can be determined by the study on the convergence rate of the algorithm in question. It is necessary to study some (hopefully convergent) sequence that will measure how "good" is the approximated optimum compared to the real optimum. The concept of Regret is widely used in the bandit literature for assessing the performance of an algorithm. The same concept is also used in the framework of optimization algorithms, sometimes under other names or without a specific name. And the numerical evaluation of convergence rate of noisy algorithms often involves approximations of regrets. We discuss here two types of approximations of Simple Regret used in practice for the evaluation of algorithms for noisy optimization. We use specific algorithms of different nature and the noisy sphere function to show the following results. The approximation of Simple Regret, termed here Approximate Simple Regret, used in some optimization testbeds, fails to estimate the Simple Regret convergence rate. We also discuss a recent new approximation of Simple Regret, that we term Robust Simple Regret, and show its advantages and disadvantages.Comment: Genetic and Evolutionary Computation Conference 2016, Jul 2016, Denver, United States. 201

The Coherent Structures of Shallowwater Turbulence: Deformationradius Effects, Cyclone/Anticyclone Asymmetry and Gravitywave Generation

Over a large range of Rossby and Froude numbers, we investigate the dynamics of initially balanced decaying turbulence in a shallow rotating fluid layer. As in the case of incompressible two‐dimensional decaying turbulence, coherent vortex structures spontaneously emerge from the initially random flow. However, owing to the presence of a free surface, a wealth of new phenomena appear in the shallow‐water system. The upscale energy cascade, common to strongly rotating flows, is arrested by the presence of a finite Rossby deformation radius. Moreover, in contrast to near‐geostrophic dynamics, a strong asymmetry is observed to develop as the Froude number is increased, leading to a clear dominance of anticyclonic vortices over cyclonic ones, even though no β effect is present in the system. Finally, we observe gravity waves to be generated around the vortex structures, and, in the strongest cases, they appear in the form of shocks. We briefly discuss the relevance of this study to the vortices observed in Jupiter’s atmosphere

Systems approaches and algorithms for discovery of combinatorial therapies

Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification of control parameters presents an extreme challenge due to the combinatorial explosion of control possibilities in combination therapy and to the incomplete knowledge of the systems biology of cells. In this review paper we describe the main current and proposed approaches to the design of combinatorial therapies, including the empirical methods used now by clinicians and alternative approaches suggested recently by several authors. New approaches for designing combinations arising from systems biology are described. We discuss in special detail the design of algorithms that identify optimal control parameters in cellular networks based on a quantitative characterization of control landscapes, maximizing utilization of incomplete knowledge of the state and structure of intracellular networks. The use of new technology for high-throughput measurements is key to these new approaches to combination therapy and essential for the characterization of control landscapes and implementation of the algorithms. Combinatorial optimization in medical therapy is also compared with the combinatorial optimization of engineering and materials science and similarities and differences are delineated.Comment: 25 page

The Cleavable Carboxyl-Terminus of the Small Coat Protein of Cowpea Mosaic Virus Is Involved in RNA Encapsidation

AbstractThe site of cleavage of the small coat protein of cowpea mosaic virus has been precisely mapped and the proteolysis has been shown to result in the loss of 24 amino acids from the carboxyl-terminus of the protein. A series of premature termination and deletion mutants was constructed to investigate the role or roles of these carboxyl-terminal amino acids in the viral replication cycle. Mutants containing premature termination codons at or downstream of the cleavage site were viable but reverted to wild-type after a single passage through cowpea plants, indicating that the carboxyl-terminal amino acids are important. Mutants with the equivalent deletions were genetically stable and shown to be debilitated with respect to virus accumulation. The specific infectivity of preparations of a deletion mutant (DM4) lacking all 24 amino acids was 6-fold less than that of a wild-type preparation. This was shown to be a result of DM4 preparations containing a much increased percentage (73%) of empty (RNA-free) particles, a finding that implicates the cleavable carboxyl-terminal residues in the packaging of the virion RNAs

A comparison of vegetable leaves and replicated biomimetic surfaces on the binding of Escherichia coli and Listeria monocytogenes

Biofouling in the food industry is a huge issue, and one possible way to reduce surface fouling is to understand how naturally cleaning surfaces based on biomimetic designs influence bacterial binding. Four self-cleaning leaves (Tenderheart cabbage, Cauliflower, White cabbage and Leek) were analysed for their surface properties and artificial re-plicates were produced. The leaves and surfaces were subjected to attachment, adhesion and retention assays using Escherichia coli and Listeria monocytogenes. For the attachment assays, the lowest cell numbers occurred on the least hydrophobic and smooth surfaces but were higher than the flat control surface, regardless of the strain. Following the ad-hesion assays, using L. monocytogenes, the Tenderheart and Cauliflower biomimetic re-plicated leaves resulted in significantly lowered cell adhesion. Following the retention assays, White cabbage demonstrated lower cell retention for both types of bacteria on the biomimetic replicated surface compared to the flat control surface. The biomimetic sur-faces were also more efficient at avoiding bacterial retention than natural leaves, with reductions of about 1 and 2 Log in L. monocytogenes and E. coli retention, respectively, on most of the produced surfaces. Although the surfaces were promising in reducing bac-terial binding, the results suggested that different experimental assays exerted different influences on the conclusions. This work demonstrated that consideration needs to be given to the environmental factors where the surface is to be used and that bacterial species influence the propensity of biofouling on a surface. (c) 2022 The Author(s). Published by Elsevier Ltd on behalf of Institution of Chemical Engineers. This is an open access article under the CC BY license (http://creative-commons.org/licenses/by/4.0/)

Inter-annual and inter-seasonal variability of the Orkney wave power resource

The waters surrounding the Orkney archipelago in the north of Scotland are one of the key regions in the world suitable for exploitation of both wave and tidal energy resources. Accordingly, Orkney waters are currently host to 1.08 GW of UK Crown Estate leased wave and tidal energy projects, with a further 0.5 GW leased in the southern part of the adjacent Pentland Firth. Although several wave resource models exist of the region, most of these models are commercial, and hence the results not publicly available, or have insufficient spatial/temporal resolution to accurately quantify the wave power resource of the region. In particular, no study has satisfactorily resolved the inter-annual and inter-seasonal variability of the wave resource around Orkney. Here, the SWAN wave model was run at high resolution on a high performance computing system, quantifying the Orkney wave power resource over a ten year period (2003–2012), a decade which witnessed considerable inter-annual variability in the wave climate. The results of the validated wave model demonstrate that there is considerable variability of the wave resource surrounding Orkney, with an extended winter (December–January–February–March, DJFM) mean wave power ranging from 10 to 25 kW/m over the decade of our study. Further, the results demonstrate that there is considerably less uncertainty (30%) in the high energy region to the west of Orkney during winter months, in contrast to much greater uncertainty (60%) in the lower energy region to the east of Orkney. The DJFM wave resource to the west of Orkney correlated well with the DJFM North Atlantic Oscillation (NAO). Although a longer simulated time period would be required to fully resolve inter-decadal variability, these preliminary results demonstrate that due to considerable inter-annual variability in the NAO, it is important to carefully consider the time period used to quantify the wave power resource of Orkney, or regions with similar exposure to the North Atlantic. Finally, our study reveals that there is significantly less variability in the practical wave power resource, since much of the variability in the theoretical resource is contained within relatively few extreme events, when a wave device enters survival mode

Physical controls on the macrofaunal benthic biomass in Barrow Canyon, Chukchi Sea

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 126(5), (2021): e2020JC017091, https://doi.org/10.1029/2020JC017091.A region of exceptionally high macrofaunal benthic biomass exists in Barrow Canyon, implying a carbon export process that is locally concentrated. Here we offer an explanation for this benthic “hotspot” using shipboard data together with a set of dynamical equations. Repeat occupations of the Distributed Biological Observatory transect in Barrow Canyon reveal that when the northward flow is strong and the density front in the canyon is sharp, plumes of fluorescence and oxygen extend from the pycnocline to the seafloor in the vicinity of the hotspot. By solving the quasi-geostrophic omega equation with an analytical flow field fashioned after the observations, we diagnose the vertical velocity in the canyon. This reveals that, as the along stream flow converges into the canyon, it drives a secondary circulation cell with strong downwelling on the cyclonic side of the northward flow. The downwelling quickly advects material from the pycnocline to the seafloor in a vertical plume analogous to those seen in the observations. The plume occurs only when the phytoplankton reside in the pycnocline, since the near-surface vertical velocity is weak, also consistent with the observations. Using a wind-based proxy to represent the strength of the northward flow and hence the pumping, in conjunction with a satellite-derived phytoplankton source function, we construct a time series of carbon supply to the bottom of Barrow Canyon.This work was funded by National Science Foundation grants PLR-1504333 and OPP-1733564 (Robert S. Pickart, Frank Bahr), OPP-1822334 (Michael A. Spall), PLR-1304563 (Kevin R. Arrigo), OPP-1204082 and OPP-1702456 (Jacqueline M. Grebmeier); National Oceanic and Atmospheric Administration grants NA14OAR4320158 and NA19OAR4320074 (Robert S. Pickart, Peigen Lin, Leah T. McRaven), CINAR-22309.02 (Jacqueline M. Grebmeier)

Simulation-based optimal Bayesian experimental design for nonlinear systems

The optimal selection of experimental conditions is essential to maximizing the value of data for inference and prediction, particularly in situations where experiments are time-consuming and expensive to conduct. We propose a general mathematical framework and an algorithmic approach for optimal experimental design with nonlinear simulation-based models; in particular, we focus on finding sets of experiments that provide the most information about targeted sets of parameters. Our framework employs a Bayesian statistical setting, which provides a foundation for inference from noisy, indirect, and incomplete data, and a natural mechanism for incorporating heterogeneous sources of information. An objective function is constructed from information theoretic measures, reflecting expected information gain from proposed combinations of experiments. Polynomial chaos approximations and a two-stage Monte Carlo sampling method are used to evaluate the expected information gain. Stochastic approximation algorithms are then used to make optimization feasible in computationally intensive and high-dimensional settings. These algorithms are demonstrated on model problems and on nonlinear parameter estimation problems arising in detailed combustion kinetics.Comment: Preprint 53 pages, 17 figures (54 small figures). v1 submitted to the Journal of Computational Physics on August 4, 2011; v2 submitted on August 12, 2012. v2 changes: (a) addition of Appendix B and Figure 17 to address the bias in the expected utility estimator; (b) minor language edits; v3 submitted on November 30, 2012. v3 changes: minor edit