31 research outputs found

    A nonlinear method of removing harmonic noise in geophysical data

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    A nonlinear, adaptive method to remove the harmonic noise that commonly resides in geophysical data is proposed in this study. This filtering method is based on the ensemble empirical mode decomposition algorithm in conjunction with the logarithmic transform. We present a synthetic model study to investigate the capability of signal reconstruction from the decomposed data, and compare the results with those derived from other 2-D adaptive filters. Applications to the real seismic data acquired by using an ocean bottom seismograph and to a shot gather of the ground penetrating radar demonstrate the robustness of this method. Our work proposes a concept that instead of Fourier-based approaches, the harmonic noise removal in geophysical data can be achieved effectively by using an alternative nonlinear adaptive data analysis method, which has been applied extensively in other scientific studies

    Gauge copies in the Landau-DeWitt gauge: a background invariant restriction

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    The Landau background gauge, also known as the Landau-DeWitt gauge, has found renewed interest during the past decade given its usefulness in accessing the confinement-deconfinement transition via the vacuum expectation value of the Polyakov loop, describable via an appropriate background. In this Letter, we revisit this gauge from the viewpoint of it displaying gauge (Gribov) copies. We generalize the Gribov-Zwanziger effective action in a BRST and background invariant way; this action leads to a restriction on the allowed gauge fluctuations, thereby eliminating the infinitesimal background gauge copies. The explicit background invariance of our action is in contrast with earlier attempts to write down and use an effective Gribov-Zwanziger action. It allows to address certain subtleties arising in these earlier works, such as a spontaneous and thus spurious Lorentz symmetry breaking, something which is now averted.Comment: 14 pages. v2: version to appear in Phys.Lett.B, with minor modifications and extra reference

    Structural Modifications of Residual Lignins from Sisal and Flax Pulps during Soda-AQ Pulping and TCF/ECF Bleaching

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    We have studied the structural modifications of lignins from sisal and flax during their soda-anthraquinone (AQ) pulping and subsequent totally chlorine-free (TCF) and elementary chlorine-free (ECF) bleaching. For this purpose, residual lignins were isolated from pulps, analyzed by Py-GC/MS, 2D-NMR, and GPC, and their characteristics were compared to the ā€œmilled-woodā€ lignin of the raw materials. Soda-AQ pulping caused a preferential removal of S-lignin and cleavage of Ī²ā€“<i>O</i>ā€“4ā€² linkages, but the structure of the residual lignin remained relatively similar to native lignin. TCF bleaching barely affected the lignin structure, and noticeable amounts of Ī²ā€“<i>O</i>ā€“4ā€² linkages still occur in these pulps. In contrast, ECF bleaching caused strong modifications in the lignin structure with the complete removal of lignin markers in ECF-bleached sisal pulp. However, residual lignin was still present in ECF-bleached flax pulp, with a predominance of G- and H-lignin units and the presence of Ī²ā€“<i>O</i>ā€“4ā€² linkages

    Well-Defined Oligo- and Polysaccharides as Ideal Probes for Structural Studies

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    Polysaccharides are the most abundant organic materials in nature, yet correlations between their three-dimensional structure and macroscopic properties have not been established. Automated glycan assembly enables the preparation of well-defined oligo- and polysaccharides resembling natural as well as unnatural structures. These synthetic glycans are ideal probes for the fundamental study of polysaccharides. According to molecular modeling simulations and NMR analysis, different classes of polysaccharides adopt fundamentally different conformations that are drastically altered by single-site substitutions. Larger synthetic polysaccharides are obtained via a ā€œLEGOā€-like approach as a first step toward the production of tailor-made carbohydrate-based materials

    Well-Defined Oligo- and Polysaccharides as Ideal Probes for Structural Studies

    No full text
    Polysaccharides are the most abundant organic materials in nature, yet correlations between their three-dimensional structure and macroscopic properties have not been established. Automated glycan assembly enables the preparation of well-defined oligo- and polysaccharides resembling natural as well as unnatural structures. These synthetic glycans are ideal probes for the fundamental study of polysaccharides. According to molecular modeling simulations and NMR analysis, different classes of polysaccharides adopt fundamentally different conformations that are drastically altered by single-site substitutions. Larger synthetic polysaccharides are obtained via a ā€œLEGOā€-like approach as a first step toward the production of tailor-made carbohydrate-based materials

    Well-Defined Oligo- and Polysaccharides as Ideal Probes for Structural Studies

    No full text
    Polysaccharides are the most abundant organic materials in nature, yet correlations between their three-dimensional structure and macroscopic properties have not been established. Automated glycan assembly enables the preparation of well-defined oligo- and polysaccharides resembling natural as well as unnatural structures. These synthetic glycans are ideal probes for the fundamental study of polysaccharides. According to molecular modeling simulations and NMR analysis, different classes of polysaccharides adopt fundamentally different conformations that are drastically altered by single-site substitutions. Larger synthetic polysaccharides are obtained via a ā€œLEGOā€-like approach as a first step toward the production of tailor-made carbohydrate-based materials

    NMR and Molecular Recognition of Nā€‘Glycans: Remote Modifications of the Saccharide Chain Modulate Binding Features

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    Glycans play a key role as recognition elements in the communication of cells and other organisms. Thus, the analysis of carbohydrateā€“protein interactions has gained significant importance. In particular, nuclear magnetic resonance (NMR) techniques are considered powerful tools to detect relevant features in the interaction between sugars and their natural receptors. Here, we present the results obtained in the study on the molecular recognition of different mannose-containing glycans by <i>Pisum sativum</i> agglutinin. NMR experiments supported by Corcema-ST analysis, isothermal titration calorimetry (ITC) experiments, and molecular dynamics (MD) protocols have been successfully applied to unmask important binding features and especially to determine how a remote branching substituent significantly alters the binding mode of the sugar entity. These results highlight the key influence of common structural modifications in natural glycans on molecular recognition processes and underscore their importance for the development of biomedical applications

    Well-Defined Oligo- and Polysaccharides as Ideal Probes for Structural Studies

    No full text
    Polysaccharides are the most abundant organic materials in nature, yet correlations between their three-dimensional structure and macroscopic properties have not been established. Automated glycan assembly enables the preparation of well-defined oligo- and polysaccharides resembling natural as well as unnatural structures. These synthetic glycans are ideal probes for the fundamental study of polysaccharides. According to molecular modeling simulations and NMR analysis, different classes of polysaccharides adopt fundamentally different conformations that are drastically altered by single-site substitutions. Larger synthetic polysaccharides are obtained via a ā€œLEGOā€-like approach as a first step toward the production of tailor-made carbohydrate-based materials

    Well-Defined Oligo- and Polysaccharides as Ideal Probes for Structural Studies

    No full text
    Polysaccharides are the most abundant organic materials in nature, yet correlations between their three-dimensional structure and macroscopic properties have not been established. Automated glycan assembly enables the preparation of well-defined oligo- and polysaccharides resembling natural as well as unnatural structures. These synthetic glycans are ideal probes for the fundamental study of polysaccharides. According to molecular modeling simulations and NMR analysis, different classes of polysaccharides adopt fundamentally different conformations that are drastically altered by single-site substitutions. Larger synthetic polysaccharides are obtained via a ā€œLEGOā€-like approach as a first step toward the production of tailor-made carbohydrate-based materials

    Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations

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    Protein dynamics related to function can nowadays be structurally well characterized (i.e., instances obtained by high resolution structures), but they are still ill-defined energetically, and the energy landscapes are only accessible computationally. This is the case for glucoseā€“galactose binding protein (GGBP), where the crystal structures of the apo and holo states provide structural information for the domain rearrangement upon ligand binding, while the time scale and the energetic determinants for such concerted dynamics have been so far elusive. Here, we use GGBP as a paradigm to define a functional conformational landscape, both structurally and energetically, by using an innovative combination of paramagnetic NMR experiments and MD simulations. Anisotropic NMR parameters induced by self-alignment of paramagnetic metal ions was used to characterize the ensemble of conformations adopted by the protein in solution while the rate of interconversion between conformations was elucidated by long molecular dynamics simulation on two states of GGBP, the closed-liganded (<i>holo_cl</i>) and open-unloaded (<i>apo_op</i>) states. Our results demonstrate that, in its apo state, the protein coexists between open-like (68%) and closed-like (32%) conformations, with an exchange rate around 25 ns. Despite such conformational heterogeneity, the presence of the ligand is the ultimate driving force to unbalance the equilibrium toward the <i>holo_cl</i> form, in a mechanism largely governed by a conformational selection mechanism
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