Natural and laser-induced cavitation in corn stems: On the mechanisms of acoustic emissions

Water in plant xylem is often superheated, and therefore in a meta-stable state. Under certain conditions, it may suddenly turn from the liquid to the vapor state. This cavitation process produces acoustic emissions. We report the measurement of ultrasonic acoustic emissions (UAE) produced by natural and induced cavitation in corn stems. We induced cavitation and UAE in vivo, in well controlled and reproducible experiments, by irradiating the bare stem of the plants with a continuous-wave laser beam. By tracing the source of UAE, we were able to detect absorption and frequency filtering of the UAE propagating through the stem. This technique allows the unique possibility of studying localized embolism of plant conduits, and thus to test hypotheses on the hydraulic architecture of plants. Based on our results, we postulate that the source of UAE is a transient "cavity oscillation" triggered by the disruptive effect of cavitation inception.Comment: 8 pages, 5 figure

Notes on Graph Cuts with Submodular Edge Weights

Generalizing the cost in the standard min-cut problem to a submodular cost function immediately makes the problem harder. Not only do we prove NP hardness even for nonnegative submodular costs, but also show a lower bound of (|V |1/3) on the approximation factor for the (s, t) cut version of the problem. On the positive side, we propose and compare three approximation algorithms with an overall approximation factor of O(min|V |,p|E| log |V |) that appear to do well in practice

Natural and laser-induced cavitation in corn stems: On the mechanisms of acoustic emissions

Water in plant xylem is often superheated, and therefore in a meta-stable state. Under certain conditions, it may suddenly turn from the liquid to the vapor state. This cavitation process produces acoustic emissions. We report the measurement of ultrasonic acoustic emissions (UAE) produced by natural and induced cavitation in corn stems. We induced cavitation and UAE in vivo, in well controlled and reproducible experiments, by irradiating the bare stem of the plants with a continuous-wave laser beam. By tracing the source of UAE, we were able to detect absorption and frequency filtering of the UAE propagating through the stem. This technique allows the unique possibility of studying localized embolism of plant conduits, and thus to test hypotheses on the hydraulic architecture of plants. Based on our results, we postulate that the source of UAE is a transient “cavity oscillation” triggered by the disruptive effect of cavitation inception.Facultad de Ingenierí

Enhancement of photoacoustic detection of inhomogeneities in polymers

We report a series of experiments on laser pulsed photoacoustic excitationin turbid polymer samples addressed to evaluate the sound speed in the samples and the presence of inhomogeneities in the bulk. We describe a system which allows the direct measurement of the speed of the detected waves by engraving the surface of the piece under study with a fiduciary pattern of black lines. We also describe how this pattern helps to enhance the sensitivity for the detection of an inhomogeneity in the bulk. These two facts are useful for studies in soft matter systems including, perhaps, biological samples. We have performed an experimental analysis on Grilon(R) samples in different situations and we show the limitations of the method.Comment: 8 pages, 7 figure

In-situ bandaged Josephson junctions for superconducting quantum processors

Shadow evaporation is commonly used to micro-fabricate the key element of superconducting qubits—the Josephson junction. However, in conventional two-angle deposition circuit topology, unwanted stray Josephson junctions are created which contribute to dielectric loss. So far, this could be avoided by shorting the stray junctions with a so-called bandage layer deposited in an additional lithography step, which may further contaminate the chip surface. Here, we present an improved shadow evaporation technique allowing one to fabricate sub-micrometer-sized Josephson junctions together with bandage layers in a single lithography step. We also show that junction aging is significantly reduced when junction electrodes are passivated in an oxygen atmosphere directly after deposition

Natural and laser-induced cavitation in corn stems: On the mechanisms of acoustic emissions

Water in plant xylem is often superheated, and therefore in a meta-stable state. Under certain conditions, it may suddenly turn from the liquid to the vapor state. This cavitation process produces acoustic emissions. We report the measurement of ultrasonic acoustic emissions (UAE) produced by natural and induced cavitation in corn stems. We induced cavitation and UAE in vivo, in well controlled and reproducible experiments, by irradiating the bare stem of the plants with a continuous-wave laser beam. By tracing the source of UAE, we were able to detect absorption and frequency filtering of the UAE propagating through the stem. This technique allows the unique possibility of studying localized embolism of plant conduits, and thus to test hypotheses on the hydraulic architecture of plants. Based on our results, we postulate that the source of UAE is a transient “cavity oscillation” triggered by the disruptive effect of cavitation inception.Facultad de Ingenierí

Enhancement of photoacoustic detection of inhomogeneities in polymers

We report a series of experiments on laser pulsed photoacoustic excitation in turbid polymer samples addressed to evaluate the sound speed in the samples and the presence of inhomogeneities in the bulk. We describe a system which allows the direct measurement of the speed of the detected waves by engraving the surface of the piece under study with a fiduciary pattern of black lines. We also describe how this pattern helps to enhance the sensitivity for the detection of an inhomogeneity in the bulk. These two facts are useful for studies in soft matter systems including, perhaps, biological samples. We have performed an experimental analysis on Grilon®samples in different situations and we show the limitations of the method.Facultad de Ingenierí

Wettability, photoactivity, and antimicrobial activity of glazed ceramic tiles coated with titania films containing tungsten

Self-cleaning coatings are advanced materials for the removal of pollutants and microorganisms by combining wettability, photocatalytic degradation, and antimicrobial activity. In this work, we propose a rational design of self-cleaning films based on TiO2 synthesized by sol-gel on commercial glazed ceramic tiles for building's indoor applications. The synthesis strategy is based on hydrolysis and condensation of Ti-isopropoxide in the presence of W(VI) precursors to tune defects and crystallinity of the resulting W-TiO2 thin film. From the microstructure and surface composition analysis for different tungsten contents and annealing temperatures, we conclude that the film is composed by sintered TiO2 particles with adsorbed polytungstates (WOx) that inhibit anatase/rutile transformation. Polytungstates on TiO2 also induce surface defects that enhance water contact angle and inactivation of Escherichia coli under visible light. The presence of W(VI) has a negligible effect toward crystal violet degradation either under visible or under UV light. These results provide evidence on the existence of at least two different types of defects: (i) intrinsic defect from a sol-gel route and (ii) induced defect by tungsten species on the surface. Understanding the correlation between composition, structure, and self-cleaning properties provides a base for an efficient design of low-cost self-cleaning ceramic tiles that can be fully manufactured in an industrial plant.3121762917636Agências de fomento estrangeiras apoiaram essa pesquisa, mais informações acesse artig

Duration learning for analysis of nanopore ionic current blockades

<p>Abstract</p> <p>Background</p> <p>Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin transmembrane channel interacts with a translocating molecule in a nontrivial way, frequently evidenced by a complex ionic flow blockade pattern. Typically, recorded current blockade signals have several levels of blockade, with various durations, all obeying a fixed statistical profile for a given molecule. Hidden Markov Model (HMM) based duration learning experiments on artificial two-level Gaussian blockade signals helped us to identify proper modeling framework. We then apply our framework to the real multi-level DNA hairpin blockade signal.</p> <p>Results</p> <p>The identified upper level blockade state is observed with durations that are geometrically distributed (consistent with an a physical decay process for remaining in any given state). We show that mixture of convolution chains of geometrically distributed states is better for presenting multimodal long-tailed duration phenomena. Based on learned HMM profiles we are able to classify 9 base-pair DNA hairpins with accuracy up to 99.5% on signals from same-day experiments.</p> <p>Conclusion</p> <p>We have demonstrated several implementations for <it>de novo </it>estimation of duration distribution probability density function with HMM framework and applied our model topology to the real data. The proposed design could be handy in molecular analysis based on nanopore current blockade signal.</p

Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory

<p>Abstract</p> <p>Background</p> <p>The Baum-Welch learning procedure for Hidden Markov Models (HMMs) provides a powerful tool for tailoring HMM topologies to data for use in knowledge discovery and clustering. A linear memory procedure recently proposed by <it>Miklós, I. and Meyer, I.M. </it>describes a memory sparse version of the Baum-Welch algorithm with modifications to the original probabilistic table topologies to make memory use independent of sequence length (and linearly dependent on state number). The original description of the technique has some errors that we amend. We then compare the corrected implementation on a variety of data sets with conventional and checkpointing implementations.</p> <p>Results</p> <p>We provide a correct recurrence relation for the emission parameter estimate and extend it to parameter estimates of the Normal distribution. To accelerate estimation of the prior state probabilities, and decrease memory use, we reverse the originally proposed forward sweep. We describe different scaling strategies necessary in all real implementations of the algorithm to prevent underflow. In this paper we also describe our approach to a linear memory implementation of the Viterbi decoding algorithm (with linearity in the sequence length, while memory use is approximately independent of state number). We demonstrate the use of the linear memory implementation on an extended Duration Hidden Markov Model (DHMM) and on an HMM with a spike detection topology. Comparing the various implementations of the Baum-Welch procedure we find that the checkpointing algorithm produces the best overall tradeoff between memory use and speed. In cases where sequence length is very large (for Baum-Welch), or state number is very large (for Viterbi), the linear memory methods outlined may offer some utility.</p> <p>Conclusion</p> <p>Our performance-optimized Java implementations of Baum-Welch algorithm are available at <url>http://logos.cs.uno.edu/~achurban</url>. The described method and implementations will aid sequence alignment, gene structure prediction, HMM profile training, nanopore ionic flow blockades analysis and many other domains that require efficient HMM training with EM.</p