@article{18031, abstract = {Molecular-scale components are expected to be central to the realization of nanoscale electronic devices1,2,3. Although molecular-scale switching has been reported in atomic quantum point contacts4,5,6, single-molecule junctions provide the additional flexibility of tuning the on/off conductance states through molecular design. To date, switching in single-molecule junctions has been attributed to changes in the conformation or charge state of the molecule7,8,9,10,11,12. Here, we demonstrate reversible binary switching in a single-molecule junction by mechanical control of the metal–molecule contact geometry. We show that 4,4'-bipyridine–gold single-molecule junctions can be reversibly switched between two conductance states through repeated junction elongation and compression. Using first-principles calculations, we attribute the different measured conductance states to distinct contact geometries at the flexible but stable nitrogen–gold bond: conductance is low when the N–Au bond is perpendicular to the conducting π-system, and high otherwise. This switching mechanism, inherent to the pyridine–gold link, could form the basis of a new class of mechanically activated single-molecule switches.}, author = {Quek, Su Ying and Kamenetska, Maria and Steigerwald, Michael L. and Choi, Hyoung Joon and Louie, Steven G. and Hybertsen, Mark S. and Neaton, J. B. and Venkataraman, Latha}, issn = {1748-3395}, journal = {Nature Nanotechnology}, number = {4}, pages = {230--234}, publisher = {Springer Nature}, title = {{Mechanically controlled binary conductance switching of a single-molecule junction}}, doi = {10.1038/nnano.2009.10}, volume = {4}, year = {2009}, } @article{1825, abstract = {Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response—precise or input-dependent, exponential or power-law—as special cases of the same model. }, author = {Tamar Friedlander and Brenner, Naama}, journal = {PNAS}, number = {52}, pages = {22558 -- 22563}, publisher = {National Academy of Sciences}, title = {{Adaptive response by state-dependent inactivation}}, doi = {10.1073/pnas.0902146106 }, volume = {106}, year = {2009}, } @article{18356, abstract = {Similarity is one of the most important abstract concepts in human perception of the world. In computer vision, numerous applications deal with comparing objects observed in a scene with some a priori known patterns. Often, it happens that while two objects are not similar, they have large similar parts, that is, they are partially similar. Here, we present a novel approach to quantify partial similarity using the notion of Pareto optimality. We exemplify our approach on the problems of recognizing non-rigid geometric objects, images, and analyzing text sequences.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Bruckstein, Alfred M. and Kimmel, Ron}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, number = {2}, pages = {163--183}, publisher = {Springer Nature}, title = {{Partial similarity of objects, or how to compare a centaur to a horse}}, doi = {10.1007/s11263-008-0147-3}, volume = {84}, year = {2009}, } @article{18357, abstract = {This paper explores the problem of similarity criteria between nonrigid shapes. Broadly speaking, such criteria are divided into intrinsic and extrinsic, the first referring to the metric structure of the object and the latter to how it is laid out in the Euclidean space. Both criteria have their advantages and disadvantages: extrinsic similarity is sensitive to nonrigid deformations, while intrinsic similarity is sensitive to topological noise. In this paper, we approach the problem from the perspective of metric geometry. We show that by unifying the extrinsic and intrinsic similarity criteria, it is possible to obtain a stronger topology-invariant similarity, suitable for comparing deformed shapes with different topology. We construct this new joint criterion as a tradeoff between the extrinsic and intrinsic similarity and use it as a set-valued distance. Numerical results demonstrate the efficiency of our approach in cases where using either extrinsic or intrinsic criteria alone would fail.}, author = {Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, issn = {1573-1405}, journal = {International Journal of Computer Vision}, number = {3}, pages = {281--301}, publisher = {Springer Nature}, title = {{Topology-invariant similarity of nonrigid shapes}}, doi = {10.1007/s11263-008-0172-2}, volume = {81}, year = {2009}, } @inproceedings{18391, abstract = {We introduce a design of a coded light-based 3D color video camera optimized for build up cost as well as accuracy in depth reconstruction and acquisition speed. The components of the system include a monochromatic camera and an off-the-shelf LED projector synchronized by a miniature circuit. The projected patterns are captured and processed at a rate of 200 fps and allow for real-time reconstruction of both depth and color at video rates. The reconstruction and display are performed at around 30 depth profiles and color texture per second using a graphics processing unit (GPU).}, author = {Rubinstein, O. and Honen, Y. and Bronstein, Alexander and Bronstein, M. M. and Kimmel, R.}, booktitle = {12th International Conference on Computer Vision Workshops}, location = {Kyoto, Japan}, publisher = {IEEE}, title = {{3D-color video camera}}, doi = {10.1109/iccvw.2009.5457433}, year = {2009}, } @inproceedings{18392, abstract = {Feature-based methods have recently gained popularity in computer vision and pattern recognition communities, in applications such as object recognition and image retrieval. In this paper, we explore analogous approaches in the 3D world applied to the problem of non-rigid shape search and retrieval in large databases.}, author = {Ovsjanikov, Maks and Bronstein, Alexander and Bronstein, Michael M. and Guibas, Leonidas J.}, booktitle = {12th International Conference on Computer Vision Workshops}, isbn = {9781424444427}, location = {Kyoto, Japan}, publisher = {IEEE}, title = {{Shape Google: A computer vision approach to isometry invariant shape retrieval}}, doi = {10.1109/iccvw.2009.5457682}, year = {2009}, } @inproceedings{18393, abstract = {Shape-from-X is a generic type of inverse problems in computer vision, in which a shape is reconstructed from some measurements. A specially challenging setting of this problem is the case in which the reconstructed shapes are non-rigid. In this paper, we propose a framework for intrinsic regularization of such problems. The assumption is that we have the geometric structure of a shape which is intrinsically (up to bending) similar to the one we would like to reconstruct. For that goal, we formulate a variation with respect to vertex coordinates of a triangulated mesh approximating the continuous shape. The numerical core of the proposed method is based on differentiating the fast marching update step for geodesic distance computation.}, author = {Devir, Yohai S. and Rosman, Guy and Bronstein, Alexander and Bronstein, Michael M. and Kimmel, Ron}, booktitle = {12th International Conference on Computer Vision Workshops}, isbn = {9781424444427}, location = {Kyoto, Japan}, publisher = {IEEE}, title = {{On reconstruction of non-rigid shapes with intrinsic regularization}}, doi = {10.1109/iccvw.2009.5457688}, year = {2009}, } @article{18438, abstract = {Partial matching of geometric structures is important in computer vision, pattern recognition and shape analysis applications. The problem consists of matching similar parts of shapes that may be dissimilar as a whole. Recently, it was proposed to consider partial similarity as a multi-criterion optimization problem trying to simultaneously maximize the similarity and the significance of the matching parts. A major challenge in that framework is providing a quantitative measure of the significance of a part of an object. Here, we define the significance of a part of a shape by its discriminative power with respect do a given shape database — that is, the uniqueness of the part. We define a point-wise significance density using a statistical weighting approach similar to the term frequency-inverse document frequency (tf-idf) weighting employed in search engines. The significance measure of a given part is obtained by integrating over this density. Numerical experiments show that the proposed approach produces intuitive significant parts, and demonstrate an improvement in the performance of partial matching between shapes. }, author = {Bronstein, Alexander and Bronstein, Michael M. and Carmon, Yair and Kimmel, Ron}, issn = {1882-6695}, journal = {IPSJ Transactions on Computer Vision and Applications}, pages = {105--114}, publisher = {Information Processing Society of Japan}, title = {{Partial similarity of shapes using a statistical significance measure}}, doi = {10.2197/ipsjtcva.1.105}, volume = {1}, year = {2009}, } @article{7751, abstract = {This work demonstrates that environmental conditions experienced by individuals can shape their development and affect the stability of genetic associations. The implication of this observation is that the environmental response may influence the evolution of traits in the wild. Here, we examined how the genetic architecture of a suite of sexually dimorphic traits changed as a function of environmental conditions in an unmanaged population of Soay sheep (Ovis aries) on the island of Hirta, St. Kilda, northwest Scotland. We examined the stability of phenotypic, genetic, and environmental (residual) covariance in males during the first year of life between horn length, body weight, and parasite load in environments of different quality. We then examined the same covariance structures across environments within and between the adult sexes. We found significant genotype-by-environment interactions for lamb male body weight and parasite load, leading to a change in the genetic correlation among environments. Horn length was genetically correlated with body weight in males but not females and the genetic correlation among traits within and between the sexes was dependent upon the environmental conditions experienced during adulthood. Genetic correlations were smaller in more favorable environmental conditions, suggesting that in good environments, loci are expressed that have sex-specific effects. The reduction in genetic correlation between the sexes may allow independent evolutionary trajectories for each sex. This study demonstrates that the genetic architecture of traits is not stable under temporally varying environments and highlights the fact that evolutionary processes may depend largely upon ecological conditions. ENVIRONMENTAL heterogeneity has long been recognized as an important factor influencing the evolution of fitness-related traits in the wild (Roff 2002). The evolution of a trait depends upon the selection upon it, underlying genetic variation, and to a large degree the genetic relationships with other traits (Lynch and Walsh 1998). There is evidence that selection can vary considerably from year to year (Price et al. 1984; Robinson et al. 2008) and genetic variability in quantitative traits can change in response to environmental conditions (Hoffmann and Merilä 1999; Charmantier and Garant 2005). However, we know surprisingly little about the influence of environmental conditions on genetic correlations between traits in wild populations. Laboratory evidence suggests that the environment may influence genetic relationships between traits (Sgrò and Hoffmann 2004), but estimates obtained in a controlled or in an arbitrary range of conditions show a lack of concordance with those obtained in wild habitats (Conner et al. 2003). As a result, laboratory and environment-specific estimates of genetic correlations can make predictions for a trait's evolution, but these are valid only for the environment in which they were measured. Therefore, at present, it is difficult to generalize about the evolution of a trait that is expressed in populations that experience variable environmental conditions (Steppan et al. 2002). The influence of changing environmental conditions on the G matrix (the matrix of additive genetic variance and covariances corresponding to a set of traits) has been the focus of theoretical quantitative genetic studies (e.g., Jones et al. 2003). There is evidence of genotype-by-environment interaction for many traits expressed in wild populations (Charmantier and Garant 2005) and thus we may also expect that associations between traits may depend upon the environmental conditions encountered by an individual. Genetic correlations among traits may arise from pleiotropy, where a given locus affects more than one trait (Cheverud 1988; Lynch and Walsh 1998), which may limit the potential for those traits to evolve independently. There has recently been much interest in assessing genetic correlations between the sexes (Rice and Chippindale 2001; Foerster et al. 2007; Poissant et al. 2008), but all of these predictions have also been made in average environmental conditions. For sexually dimorphic traits, expectations of between-sex genetic correlations are unclear (Lande 1980; Badyaev 2002). We might expect that the genetic determination of a trait and the patterns of genetic covariance between traits may differ both within and between the sexes, producing the differences in trait growth that are commonly observed (Lande 1980; Badyaev 2002; Roff 2002), but so far evidence suggests that genetic expression in both sexes is influenced by the same developmental pathway (Roff 2002; Jensen et al. 2003; Parker and Garant 2005). However, to our knowledge, no study has yet determined whether genetic correlations, both within and between the sexes, vary across gradients of the environmental conditions encountered by individuals in the wild (Garant et al. 2008). This study aims to assess the stability of phenotypic, genetic, and environmental (residual) associations between traits, within and between the sexes, across a range of environmental conditions experienced by a wild population. We focus on the traits of horn length, body weight, and parasite load in a feral population of Soay sheep (Ovis aries) from the island of Hirta, St. Kilda, United Kingdom. Weather conditions, population density, and consequently resource availability fluctuate from year to year, providing substantial differences between individuals in the environments they experience and thus their survival rates (Clutton-Brock and Pemberton 2004). These varying conditions, combined with a large pedigree and extensive repeated morphological measures, provide an excellent opportunity to assess the potential effects of environmental heterogeneity on genetic architecture of traits. Previous studies on this population have shown additive genetic variance for many morphological traits (Milner et al. 2000; Coltman et al. 2001; Wilson et al. 2005), genetic correlations between traits (Coltman et al. 2001), and genotype-by-environment interactions for birth weight (Wilson et al. 2006). Here we apply a random regression animal model approach to assess the extent to which quantitative genetic parameters of a range of morphological traits measured during life vary as a function of environmental conditions. We then extend this methodology to the multivariate case, testing whether the phenotypic covariance structure, and the underlying G matrix, depends on the environmental conditions experienced. Since the traits considered here are known to be sexually dimorphic and there are differences in trait growth and survival across ages, we look at sex-specific traits in lambs and then across all ages.}, author = {Robinson, Matthew Richard and Wilson, Alastair J. and Pilkington, Jill G. and Clutton-Brock, Tim H. and Pemberton, Josephine M. and Kruuk, Loeske E. B.}, issn = {0016-6731}, journal = {Genetics}, number = {4}, pages = {1639--1648}, publisher = {Genetics Society of America}, title = {{The impact of environmental heterogeneity on genetic architecture in a wild population of soay sheep}}, doi = {10.1534/genetics.108.086801}, volume = {181}, year = {2009}, } @article{8026, abstract = {Recent theoretical work has provided a basic understanding of signal propagation in networks of spiking neurons, but mechanisms for gating and controlling these signals have not been investigated previously. Here we introduce an idea for the gating of multiple signals in cortical networks that combines principles of signal propagation with aspects of balanced networks. Specifically, we studied networks in which incoming excitatory signals are normally cancelled by locally evoked inhibition, leaving the targeted layer unresponsive. Transmission can be gated 'on' by modulating excitatory and inhibitory gains to upset this detailed balance. We illustrate gating through detailed balance in large networks of integrate-and-fire neurons. We show successful gating of multiple signals and study failure modes that produce effects reminiscent of clinically observed pathologies. Provided that the individual signals are detectable, detailed balance has a large capacity for gating multiple signals.}, author = {Vogels, Tim P and Abbott, L F}, issn = {1097-6256}, journal = {Nature Neuroscience}, number = {4}, pages = {483--491}, publisher = {Springer Nature}, title = {{Gating multiple signals through detailed balance of excitation and inhibition in spiking networks}}, doi = {10.1038/nn.2276}, volume = {12}, year = {2009}, } @article{8474, abstract = {Hydrogen bonds are ubiquitous interactions in proteins, and are important for their folding and functionality. Scalar coupling constants across hydrogen bonds in the protein backbone, some as small as 0.5 Hz, can be directly measured in the solid state by NMR spectroscopy (see figure). The nuclei on both sides of the hydrogen bond can be identified and the size of the coupling constant can be measured accurately.}, author = {Schanda, Paul and Huber, Matthias and Verel, René and Ernst, Matthias and Meier, Beat H.}, issn = {1433-7851}, journal = {Angewandte Chemie International Edition}, keywords = {General Chemistry, Catalysis}, number = {49}, pages = {9322--9325}, publisher = {Wiley}, title = {{Direct detection of 3hJN' hydrogen-bond scalar couplings in proteins by solid-state NMR spectroscopy}}, doi = {10.1002/anie.200904411}, volume = {48}, year = {2009}, } @article{8475, author = {Schanda, Paul}, issn = {0079-6565}, journal = {Progress in Nuclear Magnetic Resonance Spectroscopy}, number = {3}, pages = {238--265}, publisher = {Elsevier}, title = {{Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox of fast biomolecular NMR spectroscopy}}, doi = {10.1016/j.pnmrs.2009.05.002}, volume = {55}, year = {2009}, } @article{8476, abstract = {Atomic-resolution information on the structure and dynamics of nucleic acids is essential for a better understanding of the mechanistic basis of many cellular processes. NMR spectroscopy is a powerful method for studying the structure and dynamics of nucleic acids; however, solution NMR studies are currently limited to relatively small nucleic acids at high concentrations. Thus, technological and methodological improvements that increase the experimental sensitivity and spectral resolution of NMR spectroscopy are required for studies of larger nucleic acids or protein−nucleic acid complexes. Here we introduce a series of imino-proton-detected NMR experiments that yield an over 2-fold increase in sensitivity compared to conventional pulse schemes. These methods can be applied to the detection of base pair interactions, RNA−ligand titration experiments, measurement of residual dipolar 15N−1H couplings, and direct measurements of conformational transitions. These NMR experiments employ longitudinal spin relaxation enhancement techniques that have proven useful in protein NMR spectroscopy. The performance of these new experiments is demonstrated for a 10 kDa TAR-TAR*GA RNA kissing complex and a 26 kDa tRNA.}, author = {Farjon, Jonathan and Boisbouvier, Jérôme and Schanda, Paul and Pardi, Arthur and Simorre, Jean-Pierre and Brutscher, Bernhard}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {24}, pages = {8571--8577}, publisher = {American Chemical Society}, title = {{Longitudinal-relaxation-enhanced NMR experiments for the study of nucleic acids in solution}}, doi = {10.1021/ja901633y}, volume = {131}, year = {2009}, } @article{8477, abstract = {An optimized NMR experiment that combines the advantages of methyl-TROSY and SOFAST-HMQC has been developed. It allows the recording of high quality methyl 1H−13C correlation spectra of protein assemblies of several hundreds of kDa in a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nanomachines while they perform their biological function in vitro.}, author = {Amero, Carlos and Schanda, Paul and Durá, M. Asunción and Ayala, Isabel and Marion, Dominique and Franzetti, Bruno and Brutscher, Bernhard and Boisbouvier, Jérôme}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {10}, pages = {3448--3449}, publisher = {American Chemical Society}, title = {{Fast two-dimensional NMR spectroscopy of high molecular weight protein assemblies}}, doi = {10.1021/ja809880p}, volume = {131}, year = {2009}, } @article{8478, abstract = {Allosteric regulation is an effective mechanism of control in biological processes. In allosteric proteins a signal originating at one site in the molecule is communicated through the protein structure to trigger a specific response at a remote site. Using NMR relaxation dispersion techniques we directly observe the dynamic process through which the KIX domain of CREB binding protein communicates allosteric information between binding sites. KIX mediates cooperativity between pairs of transcription factors through binding to two distinct interaction surfaces in an allosteric manner. We show that binding the activation domain of the mixed lineage leukemia (MLL) transcription factor to KIX induces a redistribution of the relative populations of KIX conformations toward a high-energy state in which the allosterically activated second binding site is already preformed, consistent with the Monod−Wyman−Changeux (WMC) model of allostery. The structural rearrangement process that links the two conformers and by which allosteric information is communicated occurs with a time constant of 3 ms at 27 °C. Our dynamic NMR data reveal that an evolutionarily conserved network of hydrophobic amino acids constitutes the pathway through which information is transmitted.}, author = {Brüschweiler, Sven and Schanda, Paul and Kloiber, Karin and Brutscher, Bernhard and Kontaxis, Georg and Konrat, Robert and Tollinger, Martin}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, number = {8}, pages = {3063--3068}, publisher = {American Chemical Society}, title = {{Direct observation of the dynamic process underlying allosteric signal transmission}}, doi = {10.1021/ja809947w}, volume = {131}, year = {2009}, } @article{8479, abstract = {Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1H–15N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds.}, author = {Gal, Maayan and Kern, Thomas and Schanda, Paul and Frydman, Lucio and Brutscher, Bernhard}, issn = {0925-2738}, journal = {Journal of Biomolecular NMR}, keywords = {Spectroscopy, Biochemistry}, pages = {1--10}, publisher = {Springer Nature}, title = {{An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates}}, doi = {10.1007/s10858-008-9284-9}, volume = {43}, year = {2009}, } @article{8508, abstract = {We study generic unfoldings of homoclinic tangencies of two-dimensional area-preserving diffeomorphisms (conservative New house phenomena) and show that they give rise to invariant hyperbolic sets of arbitrarily large Hausdorff dimension. As applications, we discuss the size of the stochastic layer of a standard map and the Hausdorff dimension of invariant hyperbolic sets for certain restricted three-body problems. We avoid involved technical details and only concentrate on the ideas of the proof of the presented results.}, author = {Gorodetski, Anton and Kaloshin, Vadim}, issn = {0081-5438}, journal = {Proceedings of the Steklov Institute of Mathematics}, keywords = {Mathematics (miscellaneous)}, number = {1}, pages = {76--90}, publisher = {Springer Nature}, title = {{Conservative homoclinic bifurcations and some applications}}, doi = {10.1134/s0081543809040063}, volume = {267}, year = {2009}, } @article{88, abstract = {We have developed a tunable source of Mie scale microdroplet aerosols that can be used for the generation of energetic ions. To demonstrate this potential, a terawatt Ti: Al2 O3 laser focused to 2×10 19 W/cm2 was used to irradiate heavy water (D2 O) aerosols composed of micron-scale droplets. Energetic deuterium ions, which were generated in the laser-droplet interaction, produced deuterium-deuterium fusion with approximately 2×10^3 fusion neutrons measured per joule of incident laser energy. }, author = {Higginbotham, Andrew P and Semonin, Octavi and Bruce, S and Chan, C and Maindi, M and Donnelly, Tom and Maurer, M and Bang, Woosuk and Churina, I.V and Osterholz, Jens and Kim, I and Bernstein, Aaron and Ditmire, Todd}, journal = {Review of Scientific Instruments}, number = {6}, publisher = {American Institute of Physics}, title = {{Generation of Mie size microdroplet aerosols with applications in laser-driven fusion experiments}}, doi = {10.1063/1.3155302}, volume = {80}, year = {2009}, } @article{908, abstract = {Although some data link archaeal and eukaryotic translation, the overall mechanism of protein synthesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demonstrated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recognizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed.}, author = {Alkalaeva, Elena Z and Eliseev, Boris D and Ambrogelly, Alexandre and Vlasov, Peter K and Fyodor Kondrashov and Gundllapalli, Sarath B and Frolova, Ludmila Y and Söll, Dieter G and Kisselev, Lev L}, journal = {FEBS Letters}, number = {21}, pages = {3455 -- 3460}, publisher = {Elsevier}, title = {{Translation termination in pyrrolysine-utilizing archaea}}, doi = {10.1016/j.febslet.2009.09.044}, volume = {583}, year = {2009}, } @article{9147, abstract = {As part of an ongoing effort to develop a parameterization of wave-induced abyssal mixing, the authors derive an heuristic model for nonlinear wave breaking and energy dissipation associated with internal tides. Then the saturation and dissipation of internal tides for idealized and observed topography samples are investigated. One of the main results is that the wave-induced mixing could be more intense and more confined to the bottom than previously assumed in numerical models. Furthermore, in this model wave breaking and mixing clearly depend on the small scales of the topography below 10 km or so, which is below the current resolution of global bathymetry. This motivates the use of a statistical approach to represent the unresolved topography when addressing the role of internal tides in mixing the deep ocean.}, author = {Muller, Caroline J and Bühler, Oliver}, issn = {1520-0485}, journal = {Journal of Physical Oceanography}, keywords = {Oceanography}, number = {9}, pages = {2077--2096}, publisher = {American Meteorological Society}, title = {{Saturation of the internal tides and induced mixing in the abyssal ocean}}, doi = {10.1175/2009jpo4141.1}, volume = {39}, year = {2009}, }