Mesh Simplification Based on Edge Collapsing Could Improve Computational Efficiency in Near Infrared Optical Tomographic Imaging

The diffusion equation-based modeling of near infrared light propagation in tissue is achieved by using finite-element mesh for imaging real-tissue types, such as breast and brain. The finite-element mesh size (number of nodes) dictates the parameter space in the optical tomographic imaging. Most commonly used finite-element meshing algorithms do not provide the flexibility of distinct nodal spacing in different regions of imaging domain to take the sensitivity of the problem into consideration. This study aims to present a computationally efficient mesh simplification method that can be used as a preprocessing step to iterative image reconstruction, where the finite-element mesh is simplified by using an edge collapsing algorithm to reduce the parameter space at regions where the sensitivity of the problem is relatively low. It is shown, using simulations and experimental phantom data for simple meshes/domains, that a significant reduction in parameter space could be achieved without compromising on the reconstructed image quality. The maximum errors observed by using the simplified meshes were less than 0.27% in the forward problem and 5% for inverse problem.

Lexicon-free, novel segmentation of online handwritten indic words

Research in the field of recognizing unlimited vocabulary, online handwritten Indic words is still in its infancy. Most of the focus so far has been in the area of isolated character recognition. In the context of lexicon-free recognition of words, one of the primary issues to be addressed is that of segmentation. As a preliminary attempt, this paper proposes a novel script-independent, lexicon-free method for segmenting online handwritten words to their constituent symbols. Feedback strategies, inspired from neuroscience studies, are proposed for improving the segmentation. The segmentation strategy has been tested on an exhaustive set of 10000 Tamil words collected from a large number of writers. The results show that better segmentation improves the overall recognition performance of the handwriting system.

Template-free electrochemical nanofabrication of polyaniline nanobrush and hybrid polyaniline with carbon nanohorns for supercapacitors.

Polyaniline (PANI) nanobrushes were synthesized by template-free electrochemical galvanostatic methods. When the same method was applied to the carbon nanohorn (CNH) solution containing aniline monomers, a hybrid nanostructure containing PANI and CNHs was enabled after electropolymerization. This is the first report on the template-free method to make PANI nanobrushes and homogeneous hybrid soft matter (PANI) with carbon nanoparticles. Raman spectroscopy was used to analyze the interaction between CNH and PANI. Electrochemical nanofabrication offers simplicity and good control when used to make electronic devices. Both of these materials were applied in supercapacitors and an improvement capacitive current by using the hybrid material was observed.

Interplay of martensitic phase transformation and plastic slip in polycrystals

Inspired by key experimental and analytical results regarding Shape Memory Alloys (SMAs), we propose a modelling framework to explore the interplay between martensitic phase transformations and plastic slip in polycrystalline materials, with an eye towards computational efficiency. The resulting framework uses a convexified potential for the internal energy density to capture the stored energy associated with transformation at the meso-scale, and introduces kinetic potentials to govern the evolution of transformation and plastic slip. The framework is novel in the way it treats plasticity on par with transformation.

We implement the framework in the setting of anti-plane shear, using a staggered implicit/explict update: we first use a Fast-Fourier Transform (FFT) solver based on an Augmented Lagrangian formulation to implicitly solve for the full-field displacements of a simulated polycrystal, then explicitly update the volume fraction of martensite and plastic slip using their respective stick-slip type kinetic laws. We observe that, even in this simple setting with an idealized material comprising four martensitic variants and four slip systems, the model recovers a rich variety of SMA type behaviors. We use this model to gain insight into the isothermal behavior of stress-stabilized martensite, looking at the effects of the relative plastic yield strength, the memory of deformation history under non-proportional loading, and several others.

We extend the framework to the generalized 3-D setting, for which the convexified potential is a lower bound on the actual internal energy, and show that the fully implicit discrete time formulation of the framework is governed by a variational principle for mechanical equilibrium. We further propose an extension of the method to finite deformations via an exponential mapping. We implement the generalized framework using an existing Optimal Transport Mesh-free (OTM) solver. We then model the $\alpha$--$\gamma$ and $\alpha$--$\varepsilon$ transformations in pure iron, with an initial attempt in the latter to account for twinning in the parent phase. We demonstrate the scalability of the framework to large scale computing by simulating Taylor impact experiments, observing nearly linear (ideal) speed-up through 256 MPI tasks. Finally, we present preliminary results of a simulated Split-Hopkinson Pressure Bar (SHPB) experiment using the $\alpha$--$\varepsilon$ model.

Desenvolvimento de um simulador numérico empregando o método Smoothed Particle Hydrodynamics para a resolução de escoamentos incompressíveis. Implementação computacional em paralelo (CUDA)

Neste trabalho, foi desenvolvido um simulador numérico baseado no método livre de malhas Smoothed Particle Hydrodynamics (SPH) para a resolução de escoamentos de fluidos newtonianos incompressíveis. Diferentemente da maioria das versões existentes deste método, o código numérico faz uso de uma técnica iterativa na determinação do campo de pressões. Este procedimento emprega a forma diferencial de uma equação de estado para um fluido compressível e a equação da continuidade a fim de que a correção da pressão seja determinada. Uma versão paralelizada do simulador numérico foi implementada usando a linguagem de programação C/C++ e a Compute Unified Device Architecture (CUDA) da NVIDIA Corporation. Foram simulados três problemas, o problema unidimensional do escoamento de Couette e os problemas bidimensionais do escoamento no interior de uma Cavidade (Shear Driven Cavity Problem) e da Quebra de Barragem (Dambreak).

Metal-free growth of Si/SiO2 nanowires by annealing SiOx (x < 2) films deposited by PECVD

A new metal catalysis-free method of fabricating Si or SiO2 nanowires (NWs) compatible with Si CMOS technology was proposed by annealing SiOx (x < 2) films deposited by plasma -enhanced chemical vapor deposition (PECVD). The effects of the Si content (x value) and thickness of SiOx films, the annealing process and flowing gas ambient on the NW growth were studied in detail. The results indicated that the SiOx film of a thickness below 300 rim with x value close to 1 was most favorable for NW growth upon annealing at 1000-1150 degrees C in the flowing gas mixture of N-2 and H-2. NWs of 50-100nm in diameter and tens of micrometers in length were synthesized by this method. The formation mechanism was likely to be related to a new type of oxide assisted growth (OAG) mechanism, with Si nanoclusters in SiOx films after phase separation serving as the nuclei for the growth of NWs in SiOx films > 200nm, and SiO molecules from thin SiO, film decomposition inducing the NW growth in films < 100nm. An effective preliminary method to control NW growth direction was also demonstrated by etching trenches in SiOx films followed by annealing.

Sensitive, Label-Free Protein Assay Using 1-ethyl-3-methylimidazolium Tetrafluoroborate Supported Microchip Electrophoresis with Laser-Induced Fluorescence Detection

Based on the dimer-monomer equilibrium movement of the fluorescent dye Pyronin Y (PY), a rapid, simple, highly sensitive, label-free method for protein detection was developed by microchip electrophoresis with LIF detection. PY formed a nonfluorescent dimer induced by the premicellar aggregation of an anionic surfactant, SDS, however, the fluorescence intensity of the system increased dramatically when proteins such as BSA, bovine hemoglobin, cytochrome c, and trypsin were added to the solution due to the transition of dimer to fluorescent monomer. Furthermore, 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF(4)) instead of PBS was applied as running buffers in microchip electrophoresis.

Enhanced catalytic DNAzyme for label-free colorimetric detection of DNA

A DNAzyme-based label-free method for the colorimetric detection of DNA is introduced, with a supramolecular hemin G-quartet complex as the sensing element and a 36-mer single-strand DNA as the analyte that is detected at 10 nM.

Adaptive recognition of small molecules by nucleic acid aptamers through a label-free approach

We report a novel label-free method for the investigation of the adaptive recognition of small molecules by nucleic acid aptamers using capillary electrophoresis analysis. Cocaine and argininamide were chosen as model molecules, and the two corresponding DNA aptamers were used. These single-strand DNAs folded into their specific secondary structures, which were mainly responsible for the binding of the target molecules with high affinity and specificity. For molecular recognition, the nucleic acid structures then underwent additional conformational changes, while keeping the target molecules stabilized by intermolecular hydrogen bonds. The intrinsic chemical and physical properties of the target molecules enabled them to act as indicators for adaptive binding. Thus any labeling or modification of the aptamers or target molecules were made obsolete. This label-free method for aptamer-based molecular recognition was also successfully applied to biological fluids and therefore indicates that this approach is a promising tool for bioanalysis.

One-step synthesis of 3D dendritic gold/polypyrrole nanocomposites via a self-assembly method

Novel spherical three-dimensional (3D) dendritic gold-polypyrrole nanocomposites were successfully prepared in the presence of an amphiphilic p-toluene sulfonic acid (TSA) as dopant and surfactant via a self-assembly process which is based on the oxidation of pyrrole (Py) and the reduction of the chloroaurate ions, yielding PPy and Au(0) simultaneously. It was found that the probability of obtaining dendritic Au@PPy/TSA nanostructures depended on the concentration of TSA and the rate of addition of the oxidant (HAuCl4), It was also proposed that the supramolecular micelles formed by Py and TSA play the role of a 'soft template' to produce the dendritic Au@PPy/TSA nanocomposites.

Lithography-free micro- and nanostructuring based on conventional plasma etching

In now-a-days semiconductor and MEMS technologies the photolithography is the working horse for fabrication of functional devices. The conventional way (so called Top-Down approach) of microstructuring starts with photolithography, followed by patterning the structures using etching, especially dry etching. The requirements for smaller and hence faster devices lead to decrease of the feature size to the range of several nanometers. However, the production of devices in this scale range needs photolithography equipment, which must overcome the diffraction limit. Therefore, new photolithography techniques have been recently developed, but they are rather expensive and restricted to plane surfaces. Recently a new route has been presented - so-called Bottom-Up approach - where from a single atom or a molecule it is possible to obtain functional devices. This creates new field - Nanotechnology - where one speaks about structures with dimensions 1 - 100 nm, and which has the possibility to replace the conventional photolithography concerning its integral part - the self-assembly. However, this technique requires additional and special equipment and therefore is not yet widely applicable. This work presents a general scheme for the fabrication of silicon and silicon dioxide structures with lateral dimensions of less than 100 nm that avoids high-resolution photolithography processes. For the self-aligned formation of extremely small openings in silicon dioxide layers at in depth sharpened surface structures, the angle dependent etching rate distribution of silicon dioxide against plasma etching with a fluorocarbon gas (CHF3) was exploited. Subsequent anisotropic plasma etching of the silicon substrate material through the perforated silicon dioxide masking layer results in high aspect ratio trenches of approximately the same lateral dimensions. The latter can be reduced and precisely adjusted between 0 and 200 nm by thermal oxidation of the silicon structures owing to the volume expansion of silicon during the oxidation. On the basis of this a technology for the fabrication of SNOM calibration standards is presented. Additionally so-formed trenches were used as a template for CVD deposition of diamond resulting in high aspect ratio diamond knife. A lithography-free method for production of periodic and nonperiodic surface structures using the angular dependence of the etching rate is also presented. It combines the self-assembly of masking particles with the conventional plasma etching techniques known from microelectromechanical system technology. The method is generally applicable to bulk as well as layered materials. In this work, layers of glass spheres of different diameters were assembled on the sample surface forming a mask against plasma etching. Silicon surface structures with periodicity of 500 nm and feature dimensions of 20 nm were produced in this way. Thermal oxidation of the so structured silicon substrate offers the capability to vary the fill factor of the periodic structure owing to the volume expansion during oxidation but also to define silicon dioxide surface structures by selective plasma etching. Similar structures can be simply obtained by structuring silicon dioxide layers on silicon. The method offers a simple route for bridging the Nano- and Microtechnology and moreover, an uncomplicated way for photonic crystal fabrication.

Fast three dimensional r-adaptive mesh redistribution

This paper describes a fast and reliable method for redistributing a computational mesh in three dimensions which can generate a complex three dimensional mesh without any problems due to mesh tangling. The method relies on a three dimensional implementation of the parabolic Monge–Ampère (PMA) technique, for finding an optimally transported mesh. The method for implementing PMA is described in detail and applied to both static and dynamic mesh redistribution problems, studying both the convergence and the computational cost of the algorithm. The algorithm is applied to a series of problems of increasing complexity. In particular very regular meshes are generated to resolve real meteorological features (derived from a weather forecasting model covering the UK area) in grids with over 2×107 degrees of freedom. The PMA method computes these grids in times commensurate with those required for operational weather forecasting.

Vocal folds vibrations with a three-dimensional deformable model

In this work a computational method is presented to simulate the movements of vocal folds in three dimensions. The proposed model consists of a mesh free structure where each vertex is connected its neighbor through a group spring-damper. Forced oscillations were studied by time varying surface forces. The preliminary results using this model are similar with the literature and with the experimental stroboscopic observations of larynx. © 2006 IEEE.

A 2-D delaunay refinement algorithm using an initial prerefinement from the boundary mesh

An improvement to the quality bidimensional Delaunay mesh generation algorithm, which combines the mesh refinement algorithms strategy of Ruppert and Shewchuk is proposed in this research. The developed technique uses diametral lenses criterion, introduced by L. P. Chew, with the purpose of eliminating the extremely obtuse triangles in the boundary mesh. This method splits the boundary segment and obtains an initial prerefinement, and thus reducing the number of necessary iterations to generate a high quality sequential triangulation. Moreover, it decreases the intensity of the communication and synchronization between subdomains in parallel mesh refinement. © 2008 IEEE.

Graded meshes in bio-thermal problems with transmission-line modeling method

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)