994 research outputs found

    Force and energy dissipation variations in non-contact atomic force spectroscopy on composite carbon nanotube systems

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    UHV dynamic force and energy dissipation spectroscopy in non-contact atomic force microscopy were used to probe specific interactions with composite systems formed by encapsulating inorganic compounds inside single-walled carbon nanotubes. It is found that forces due to nano-scale van der Waals interaction can be made to decrease by combining an Ag core and a carbon nanotube shell in the Ag@SWNT system. This specific behaviour was attributed to a significantly different effective dielectric function compared to the individual constituents, evaluated using a simple core-shell optical model. Energy dissipation measurements showed that by filling dissipation increases, explained here by softening of C-C bonds resulting in a more deformable nanotube cage. Thus, filled and unfilled nanotubes can be discriminated based on force and dissipation measurements. These findings have two different implications for potential applications: tuning the effective optical properties and tuning the interaction force for molecular absorption by appropriately choosing the filling with respect to the nanotube.Comment: 22 pages, 6 figure

    Seeds for effective oligonucleotide design

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    Background: DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms.\ud Results: We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F-score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.\ud Conclusions: Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide desig

    Testing the magnetotail configuration based on observations of low‐altitude isotropic boundaries during quiet times

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    We investigate the configuration of the geomagnetic field on the nightside magnetosphere during a quiet time interval based on National Oceanic and Atmospheric Administration Polar Orbiting Environment Satellites Medium Energy Proton and Electron Detector (NOAA/POES MEPED) measurements in combination with numerical simulations of the global terrestrial magnetosphere using the Space Weather Modeling Framework. Measurements from the NOAA/POES MEPED low‐altitude data sets provide the locations of isotropic boundaries; those are used to extract information regarding the field structure in the source regions in the magnetosphere. In order to evaluate adiabaticity and mapping accuracy, which is mainly controlled by the ratio between the radius of curvature and the particle’s Larmor radius, we tested the threshold condition for strong pitch angle scattering based on the MHD magnetic field solution. The magnetic field configuration is represented by the model with high accuracy, as suggested by the high correlation coefficients and very low normalized root‐mean‐square errors between the observed and the modeled magnetic field. The scattering criterion, based on the values of k=Rcρ ratio at the crossings of magnetic field lines, associated with isotropic boundaries, with the minimum B surface, predicts a critical value of kCR∌33. This means that, in the absence of other scattering mechanisms, the strong pitch angle scattering takes place whenever the Larmor radius is ∌33 times smaller than the radius of curvature of the magnetic field, as predicted by the Space Weather Modeling Framework.Key PointsWe tested the threshold condition for strong pitch angle scattering based on the MHD magnetic fieldSWMF model suggests a threshold condition for strong pitch angle scattering of k = 33For quiet time, the k parameter varies within 2 orders of magnitudePeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/135070/1/jgra52310.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/135070/2/jgra52310_am.pd

    On Maximal Unbordered Factors

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    Given a string SS of length nn, its maximal unbordered factor is the longest factor which does not have a border. In this work we investigate the relationship between nn and the length of the maximal unbordered factor of SS. We prove that for the alphabet of size σ≄5\sigma \ge 5 the expected length of the maximal unbordered factor of a string of length~nn is at least 0.99n0.99 n (for sufficiently large values of nn). As an application of this result, we propose a new algorithm for computing the maximal unbordered factor of a string.Comment: Accepted to the 26th Annual Symposium on Combinatorial Pattern Matching (CPM 2015

    Finding All Solutions of Equations in Free Groups and Monoids with Involution

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    The aim of this paper is to present a PSPACE algorithm which yields a finite graph of exponential size and which describes the set of all solutions of equations in free groups as well as the set of all solutions of equations in free monoids with involution in the presence of rational constraints. This became possible due to the recently invented emph{recompression} technique of the second author. He successfully applied the recompression technique for pure word equations without involution or rational constraints. In particular, his method could not be used as a black box for free groups (even without rational constraints). Actually, the presence of an involution (inverse elements) and rational constraints complicates the situation and some additional analysis is necessary. Still, the recompression technique is general enough to accommodate both extensions. In the end, it simplifies proofs that solving word equations is in PSPACE (Plandowski 1999) and the corresponding result for equations in free groups with rational constraints (Diekert, Hagenah and Gutierrez 2001). As a byproduct we obtain a direct proof that it is decidable in PSPACE whether or not the solution set is finite.Comment: A preliminary version of this paper was presented as an invited talk at CSR 2014 in Moscow, June 7 - 11, 201

    Assessing the role of oxygen on ring current formation and evolution through numerical experiments

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    We address the effect of ionospheric outflow and magnetospheric ion composition on the physical processes that control the development of the 5 August 2011 magnetic storm. Simulations with the Space Weather Modeling Framework are used to investigate the global dynamics and energization of ions throughout the magnetosphere during storm time, with a focus on the formation and evolution of the ring current. Simulations involving multifluid (with variable H+/O+ ratio in the inner magnetosphere) and single‐fluid (with constant H+/O+ ratio in the inner magnetosphere) MHD for the global magnetosphere with inner boundary conditions set either by specifying a constant ion density or by physics‐based calculations of the ion fluxes reveal that dynamical changes of the ion composition in the inner magnetosphere alter the total energy density of the magnetosphere, leading to variations in the magnetic field as well as particle drifts throughout the simulated domain. A low oxygen to hydrogen ratio and outflow resulting from a constant ion density boundary produced the most disturbed magnetosphere, leading to a stronger ring current but misses the timing of the storm development. Conversely, including a physics‐based solution for the ionospheric outflow to the magnetosphere system leads to a reduction in the cross‐polar cap potential (CPCP). The increased presence of oxygen in the inner magnetosphere affects the global magnetospheric structure and dynamics and brings the nightside reconnection point closer to the Earth. The combination of reduced CPCP together with the formation of the reconnection line closer to the Earth yields less adiabatic heating in the magnetotail and reduces the amount of energetic plasma that has access to the inner magnetosphere.Key PointsLow O+/H+ ratio produced stronger ring currentInclusion of physics‐based ionospheric outflow leads to a reduction in the CPCPOxygen presence is linked to a nightside reconnection point closer to the EarthPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/112251/1/jgra51856.pd
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