Stress Engineering using Si3N4 for stiction free release of SOI beams

We report on the effect of thin silicon nitride (Si3N4) induced tensile stress on the structural release of 200nm thick SOI beam, in the surface micro-machining process. A thin (20nm / 100nm) LPCVD grown Si3N4 is shown to significantly enhance the yield of released beam in wet release technique. This is especially prominent with increase in beam length, where the beams have higher tendency for stiction. We attribute this yield enhancement to the nitride induced tensile stress, as verified by buckling tendency and resonance frequency data obtained from optical profilometry and laser doppler vibrometry.

Poly(alkylene itaconate)s - an interesting class of polyesters with periodically located exo-chain double bonds susceptible to Michael addition

Itaconic acid is a bio-sourced dicarboxylic acid that carries a double bond; although several reports have dealt with the radical-initiated chain polymerization of dialkyl itaconates, only a few studies have utilized it as a di-acid monomer to prepare polyesters. In this study, we demonstrate that dibutyl itaconate can be melt-condensed with aliphatic diols to generate unsaturated polyesters; importantly, we show that the double bonds remain unaffected during the melt polymerization. A particularly useful attribute of these polyesters is that the exo-chain double bonds are conjugated to the ester carbonyl and, therefore, can serve as excellent Michael acceptors. A variety of organic thiols, such as alkane thiols, MPEG thiol, thioglycerol, derivatized cysteine etc., were shown to quantitatively Michael-add to the exo-chain double bonds and generate interesting functionalized polyesters. Similarly, organic amines, such as N-methyl-benzylamine, diallyl amine and proline, also add across the double bond; thus, these poly(alkylene itaconate)s could serve as potentially bio-benign polyesters that could be quantitatively transformed into a variety of interesting and potentially useful functionalized polymers.

CH-RES-TOCSY: Enantiomers spectral resolution and measurement of heteronuclear residual dipolar couplings

A new 2D NMR technique cited as CH-RES-TOCSY, for complete unraveling the spectra of enantiomers and for the measurement of structurally important C-HRDC sis reported. The spectral overlap and complexity of peaks were reduced by the blend of selective excitation and homo-decoupling. Differential values of C-H RDCs of enantiomers (R and S) are exploited to separate the enantiomeric peaks. The complete unraveling of the spectra of both the enantiomers is achieved by incorporating a TOCSY mixing blockprior to signal acquisition. The additional application of the method is demonstrated for the assignment of symmetric isomers. (C) 2015 Elsevier B.V. All rights reserved.

Identification of local variations within secondary structures of proteins

Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely -helices, 3(10)-helices, -helices, extended -strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from -helices and extended -strands, 3(10)-helices and -helices were also found to occur in substantial numbers. ASSP was able to discriminate non--helical segments from flanking -helices, which were often identified as part of -helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at .

Soft Real Time Implementation of a Cognitive Radio Testbed for Frequency Hopping Primary Satisfying QoS Requirements

The Cognitive Radio (CR) is a promising technology which provides a novel way to subjugate the issue of spectrum underutilization caused due to the fixed spectrum assignment policies. In this paper we report the design and implementation of a soft-real time CR MAC, consisting of multiple secondary users, in a frequency hopping (Fit) primary scenario. This MAC is capable of sensing the spectrum and dynamically allocating the available frequency bands to multiple CR users based on their QoS requirements. As the primary is continuously hopping, a method has also been implemented to detect the hop instant of the primary network. Synchronization usually requires real time support, however we have been able to achieve this with a soft-real time technique which enables a fully software implementation of CR MAC layer. We demonstrate the wireless transmission and reception of video over this CR testbed through opportunistic spectrum access. The experiments carried out use an open source software defined radio package called GNU Radio and a basic radio hardware component USRP.

Al based ultra-fine eutectic with high room temperature plasticity and elevated temperature strength

Developments of aluminum alloys that can retain strength at and above 250 degrees C present a significant challenge. In this paper we report an ultrafine scale Al-Fe-Ni eutectic alloy with less than 3.5 aa transition metals that exhibits room temperature ultimate tensile strength of similar to 400 MPa with a tensile ductility of 6-8%. The yield stress under compression at 300 degrees C was found to be 150 MPa. We attribute it to the refinement of the microstructure that is achieved by suction casting in copper mold. The characterization using scanning and transmission electron microscopy (SEM and TEM) reveals an unique composite structure that contains the Al-Al3Ni rod eutectic with spacing of similar to 90 nm enveloped by a lamellar eutectic of Al-Al9FeNi (similar to 140 nm). Observation of subsurface deformation under Vickers indentation using bonded interface technique reveals the presence of extensive shear banding during deformation that is responsible for the origin of ductility. The dislocation configuration in Al-Al3Ni eutectic colony indicates accommodation of plasticity in alpha-Al with dislocation accumulation at the alpha-Al/Al3Ni interface boundaries. In contrast the dislocation activities in the intermetallic lamellae are limited and contain set of planner dislocations across the plates. We present a detailed analysis of the fracture surface to rationalize the origin of the high strength and ductility in this class of potentially promising cast alloy. (C) 2015 Elsevier B.V. All rights reserved.

De-DUFing the DUFs: Deciphering distant evolutionary relationships of Domains of Unknown Function using sensitive homology detection methods

Background: In the post-genomic era where sequences are being determined at a rapid rate, we are highly reliant on computational methods for their tentative biochemical characterization. The Pfam database currently contains 3,786 families corresponding to ``Domains of Unknown Function'' (DUF) or ``Uncharacterized Protein Family'' (UPF), of which 3,087 families have no reported three-dimensional structure, constituting almost one-fourth of the known protein families in search for both structure and function. Results: We applied a `computational structural genomics' approach using five state-of-the-art remote similarity detection methods to detect the relationship between uncharacterized DUFs and domain families of known structures. The association with a structural domain family could serve as a start point in elucidating the function of a DUF. Amongst these five methods, searches in SCOP-NrichD database have been applied for the first time. Predictions were classified into high, medium and low-confidence based on the consensus of results from various approaches and also annotated with enzyme and Gene ontology terms. 614 uncharacterized DUFs could be associated with a known structural domain, of which high confidence predictions, involving at least four methods, were made for 54 families. These structure-function relationships for the 614 DUF families can be accessed on-line at http://proline.biochem.iisc.ernet.in/RHD_DUFS/. For potential enzymes in this set, we assessed their compatibility with the associated fold and performed detailed structural and functional annotation by examining alignments and extent of conservation of functional residues. Detailed discussion is provided for interesting assignments for DUF3050, DUF1636, DUF1572, DUF2092 and DUF659. Conclusions: This study provides insights into the structure and potential function for nearly 20 % of the DUFs. Use of different computational approaches enables us to reliably recognize distant relationships, especially when they converge to a common assignment because the methods are often complementary. We observe that while pointers to the structural domain can offer the right clues to the function of a protein, recognition of its precise functional role is still `non-trivial' with many DUF domains conserving only some of the critical residues. It is not clear whether these are functional vestiges or instances involving alternate substrates and interacting partners. Reviewers: This article was reviewed by Drs Eugene Koonin, Frank Eisenhaber and Srikrishna Subramanian.

Suspensions of polymer-grafted nanoparticles with added polymers-Structure and effective pair-interactions

We present the results of combined experimental and theoretical (molecular dynamics simulations and integral equation theory) studies of the structure and effective interactions of suspensions of polymer grafted nanoparticles (PGNPs) in the presence of linear polymers. Due to the absence of systematic experimental and theoretical studies of PGNPs, it is widely believed that the structure and effective interactions in such binary mixtures would be very similar to those of an analogous soft colloidal material-star polymers. In our study, polystyrene-grafted gold nanoparticles with functionality f = 70 were mixed with linear polystyrene (PS) of two different molecular weights for obtaining two PGNP: PS size ratios, xi = 0.14 and 2.76 (where, xi = M-g/M-m, M-g and M-m being the molecular weights of grafting and matrix polymers, respectively). The experimental structure factor of PGNPs could be modeled with an effective potential (Model-X), which has been found to be widely applicable for star polymers. Similarly, the structure factor of the blends with xi = 0.14 could be modeled reasonably well, while the structure of blends with xi = 2.76 could not be captured, especially for high density of added polymers. A model (Model-Y) for effective interactions between PGNPs in a melt of matrix polymers also failed to provide good agreement with the experimental data for samples with xi = 2.76 and high density of added polymers. We tentatively attribute this anomaly in modeling the structure factor of blends with xi = 2.76 to the questionable assumption of Model-X in describing the added polymers as star polymers with functionality 2, which gets manifested in both polymer-polymer and polymer-PGNP interactions especially at higher fractions of added polymers. The failure of Model-Y may be due to the neglect of possible many-body interactions among PGNPs mediated by matrix polymers when the fraction of added polymers is high. These observations point to the need for a new framework to understand not only the structural behavior of PGNPs but also possibly their dynamics and thermo-mechanical properties as well. (C) 2015 AIP Publishing LLC.

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

Digital image analysis around isotropic points for photoelastic pattern recognition

Fringe tracking and fringe order assignment have become the central topics of current research in digital photoelasticity. Isotropic points (IPs) appearing in low fringe order zones are often either overlooked or entirely missed in conventional as well as digital photoelasticity. We aim to highlight image processing for characterizing IPs in an isochromatic fringe field. By resorting to a global analytical solution of a circular disk, sensitivity of IPs to small changes in far-field loading on the disk is highlighted. A local theory supplements the global closed-form solutions of three-, four-, and six-point loading configurations of circular disk. The local theoretical concepts developed in this paper are demonstrated through digital image analysis of isochromatics in circular disks subjected to three-and four-point loads. (C) 2015 Society of Photo-Optical Instrumentation Engineers (SPIE)

Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum

Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) C-13-H-1] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a ``uniqueness score'' and a ``coverage score''. Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of deduttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMIR-based metabolomics data by reducing existing impediments.

BIOCARDS AND LEVEL OF ABSTRACTION

Biocards are formal descriptions of biological phenomena and their underlying functional principles. They are used in bioinspired design to document search results and to communicate the findings for use in the further design process. The present study explored the effect of abstraction level used in biocards. This was done in two workshops conducted with design students in Denmark and India. Students were given a design assignment and instructions for how to perform the BID ideation work. Half of the students were given biocards with abstract descriptions while the other half got biocards with concrete descriptions. The novelty of found solutions was evaluated by the students by rating novelty of each solution on a scale from 1 to 5. Mean values for abstract descriptions were 0,3 higher than for concrete descriptions indicating that more innovative solutions were found when students used biocards with abstract descriptions compared to concrete descriptions. The difference in mean value is significant with a confidence level better than 1%. It seems likely that more abstract descriptions in biocards helps avoiding design fixation in biomimetic design work.

Weak-coupling superconductivity in a strongly correlated iron pnictide

Iron-based superconductors have been found to exhibit an intimate interplay of orbital, spin, and lattice degrees of freedom, dramatically affecting their low-energy electronic properties, including superconductivity. Albeit the precise pairing mechanism remains unidentified, several candidate interactions have been suggested to mediate the superconducting pairing, both in the orbital and in the spin channel. Here, we employ optical spectroscopy (OS), angle-resolved photoemission spectroscopy (ARPES), ab initio band-structure, and Eliashberg calculations to show that nearly optimally doped NaFe0.978Co0.022As exhibits some of the strongest orbitally selective electronic correlations in the family of iron pnictides. Unexpectedly, we find that the mass enhancement of itinerant charge carriers in the strongly correlated band is dramatically reduced near the Gamma point and attribute this effect to orbital mixing induced by pronounced spin-orbit coupling. Embracing the true band structure allows us to describe all low-energy electronic properties obtained in our experiments with remarkable consistency and demonstrate that superconductivity in this material is rather weak and mediated by spin fluctuations.

DNA methylation analysis of phenotype specific stratified Indian population

Background: DNA methylation and its perturbations are an established attribute to a wide spectrum of phenotypic variations and disease conditions. Indian traditional system practices personalized medicine through indigenous concept of distinctly descriptive physiological, psychological and anatomical features known as prakriti. Here we attempted to establish DNA methylation differences in these three prakriti phenotypes. Methods: Following structured and objective measurement of 3416 subjects, whole blood DNA of 147 healthy male individuals belonging to defined prakriti (Vata, Pitta and Kapha) between the age group of 20-30years were subjected to methylated DNA immunoprecipitation (MeDIP) and microarray analysis. After data analysis, prakriti specific signatures were validated through bisulfite DNA sequencing. Results: Differentially methylated regions in CpG islands and shores were significantly enriched in promoters/UTRs and gene body regions. Phenotypes characterized by higher metabolism (Pitta prakriti) in individuals showed distinct promoter (34) and gene body methylation (204), followed by Vata prakriti which correlates to motion showed DNA methylation in 52 promoters and 139 CpG islands and finally individuals with structural attributes (Kapha prakriti) with 23 and 19 promoters and CpG islands respectively. Bisulfite DNA sequencing of prakriti specific multiple CpG sites in promoters and 5'-UTR such as; LHX1 (Vata prakriti), SOX11 (Pitta prakriti) and CDH22 (Kapha prakriti) were validated. Kapha prakriti specific CDH22 5'-UTR CpG methylation was also found to be associated with higher body mass index (BMI). Conclusion: Differential DNA methylation signatures in three distinct prakriti phenotypes demonstrate the epigenetic basis of Indian traditional human classification which may have relevance to personalized medicine.