Photoresist functionalisation method for high-density protein microarrays using photolithography

Since the last decade, there is a growing need for patterned biomolecules for various applications ranging from diagnostic devices to enabling fundamental biological studies with high throughput. Protein arrays facilitate the study of protein-protein, protein-drug or protein-DNA interactions as well as highly multiplexed immunosensors based on antibody-antigen recognition. Protein microarrays are typically fabricated using piezoelectric inkjet printing with resolution limit of similar to 70-100 mu m limiting the array density. A considerable amount of research has been done on patterning biomolecules using customised biocompatible photoresists. Here, a simple photolithographic process for fabricating protein microarrays on a commercially available diazo-naphthoquinone-novolac-positive tone photoresist functionalised with 3-aminopropyltriethoxysilane is presented. The authors demonstrate that proteins immobilised using this procedure retain their activity and therefore form functional microarrays with the array density limited only by the resolution of lithography, which is more than an order of magnitude compared with inkjet printing. The process described here may be useful in the integration of conventional semiconductor manufacturing processes with biomaterials relevant for the creation of next-generation bio-chips.

Ultrahigh-temperature metamorphism from an unusual corundum plus orthopyroxene intergrowth bearing Al-Mg granulite from the Southern Marginal Zone, Limpopo Complex, South Africa

The Southern Marginal Zone of the Limpopo Complex is composed of granite-greenstone cratonic rocks reworked by a Neoarchean high-grade tectono-metamorphic event. Petrographic and mineral chemical characterization of an Al-Mg granulite from this zone is presented here. The granulite has a gneissic fabric with distinct Al-rich and Si-rich layers, with the former preserving the unusual lamellar (random and regular subparallel) intergrowths of corundum and symplectic intergrowth of spinel with orthopyroxene. The Al-rich layer preserves mineral assemblages such as rutile with orthopyroxene + sillimanite +/- A quartz, Al-rich orthopyroxene (similar to 11 wt%), spinel + quartz, and corundum in possible equilibrium with quartz, while the Si-rich layer preserves antiperthites and orthopyroxene + sillimanite +/- A quartz, all considered diagnostic of ultrahigh-temperature metamorphism. Application of Al-in-opx thermometry, ternary feldspar thermometry and construction of suitable pressure-temperature phase diagrams, compositional and model proportion isopleth results indicate P-T conditions as high as similar to 1,050-1,100 A degrees C, and similar to 10-12 kbars for the Al-Mg granulite. Our report of ultrahigh-temperature conditions is significant considering that the very high temperature was reached during decompression of an otherwise high-pressure granulite complex (clockwise P-T path), whereas most other ultrahigh-temperature granulites are linked to magma underplating at the base of the crust (counterclockwise P-T path).

Comments on ``Effects of current density on the formation and microstructure of Sn-9Zn, Sn-8Zn-3Bi and Sn-3Ag-0.5Cu solder joints''

Othman et al. (Intermetallics 2012;22:1-6) recently published a manuscript on ``Effects of current density on the formation and microstructure of Sn-9Zn, Sn-8Zn-3Bi and Sn-3Ag-0.5Cu solder joints''. We found problems in calculation of diffusion parameters. Even the comment on the formation of Cu5Zn8 instead of Cu6Sn5 is not correct. In this comment, we have explained the correct procedure to calculate the diffusion coefficients. Further, we have also explained the reason for the formation of Cu5Zn8 instead of Cu6Sn5 in the Cu/Sn-9Zn system. (C) 2012 Elsevier Ltd. All rights reserved.

Non-covalent functionalization using lithographically patterned polyelectrolyte multilayers for high-density microarrays

We describe a method to fabricate high-density biological microarrays using lithographic patterning of polyelectrolyte multi layers formed by spin assisted electrostatic layer-by-layer assembly. Proteins or DNA can be immobilized on the polyelectrolyte patterns via electrostatic attachment leading to functional microarrays. As the immobilization is done using electrostatically assembled polyelectrolyte anchor, this process is substrate independent and is fully compatible with a standard semiconductor fabrication process flow. Moreover, the electrostatic assembly of the anchor layer is a fast process with reaction saturation times of the order of a few minutes unlike covalent schemes that typically require hours to reach saturation. The substrate independent nature of this technique is demonstrated by functionalizing glass slides as well as regular transparency sheets using the same procedure. Using a model protein assay, we demonstrate that the non-covalent immobilization scheme described here has competitive performance compared to conventional covalent immobilization schemes described in literature. (C) 2012 Elsevier B.V. All rights reserved.

Topological electron density analysis and electrostatic properties of aspirin: an experimental and theoretical study

The topological and the electrostatic properties of the aspirin drug molecule were determined from high-resolution X-ray diffraction data at 90 K, and the corresponding results are compared with the theoretical calculations. The electron density at the bond critical point of all chemical bonds induding the intermolecular interactions of aspirin has been quantitatively described using Bader's quantum theory of ``Atoms in Molecules''. The electrostatic potential of the molecule emphasizes the preferable binding sites of the drug and the interaction features of the molecule, which are crucial for drug-receptor recognition. The topological analysis of hydrogen bonds reveals the strength of intermolecular interactions.

Size-dependent density of nanoparticles and nanostructured materials

We discuss the size-dependent density of nanoparticles and nanostructured materials keeping the recent experimental results in mind. The density is predicted to increase with decreasing size for nanoparticles but it can decrease with size for nanostructured materials that corroborates the experimental results reported in the literature. (C) 2012 Elsevier B.V. All rights reserved.

Charge Density Analysis of Ferulic Acid: Robustness of a Trifurcated C-H center dot center dot center dot O Hydrogen Bond

The toplogical features of a sporadic trifurcated C-H center dot center dot center dot O interaction region, where an oxygen atom acts as an acceptor of three weak hydrogen bonds, has been investigated by experimental and theoretical charge density analysis of ferulic acid. The interaction energy of the asymmetric molecular dimer formed by the trifurcated C-H center dot center dot center dot O motif, based on the multipolar model, is shown to be greater than the corresponding asymmetric O-H center dot center dot center dot O dimer in this crystal structure. Further, the hydrogen bond energies associated with these interaction motifs have been estimated from the local kinetic and potential energy densities at the bond critical points. The trends suggest that the interaction energy of the trifurcated C-H center dot center dot center dot O region is comparable to that of a single O-H center dot center dot center dot O hydrogen bond.

Role of carrier density and disorder on anisotropic charge transport in polypyrrole

Polypyrrole (PPy) has been synthesized electrochemically on platinum substrate by varying synthesis temperature and dopant concentration. The charge transport in PPy has been investigated as a function of temperature for both in-plane and out-of-plane geometry in a wide temperature range of 5K-300 K. The charge transport showed strong anisotropy and various mechanisms were used to explain the transport. The conductivity ratio, sigma(r) = sigma(300 K)/sigma(5 K) is calculated for each sample to quantify the relative disorder. At all the temperatures, the conductivity values for in-plane transport are found to be more for PPy synthesized at lower temperature, while the behavior is found to be different for out-of-plane transport. The carrier density is found to play a crucial role in case of in-plane transport. An effort has been made to correlate charge transport to morphology by analyzing temperature and frequency dependence of conductivity. Charge transport in lateral direction is found to be dominated by hopping whereas tunneling mechanisms are dominated in vertical direction. Parameters such as density of states at the Fermi level N(E-F)], average hopping distance (R), and average hopping energy (W) have been estimated for each samples in both geometry. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4775405]

Flux density calibration in diffuse optical tomographic systems

The solution of the forward equation that models the transport of light through a highly scattering tissue material in diffuse optical tomography (DOT) using the finite element method gives flux density (Phi) at the nodal points of the mesh. The experimentally measured flux (U-measured) on the boundary over a finite surface area in a DOT system has to be corrected to account for the system transfer functions (R) of various building blocks of the measurement system. We present two methods to compensate for the perturbations caused by R and estimate true flux density (Phi) from U-measured(cal). In the first approach, the measurement data with a homogeneous phantom (U-measured(homo)) is used to calibrate the measurement system. The second scheme estimates the homogeneous phantom measurement using only the measurement from a heterogeneous phantom, thereby eliminating the necessity of a homogeneous phantom. This is done by statistically averaging the data (U-measured(hetero)) and redistributing it to the corresponding detector positions. The experiments carried out on tissue mimicking phantom with single and multiple inhomogeneities, human hand, and a pork tissue phantom demonstrate the robustness of the approach. (C) 2013 Society of Photo-Optical Instrumentation Engineers (SPIE) DOI: 10.1117/1.JBO.18.2.026023]

Vibrational spectroscopy and density functional theory analysis of 3-O-caffeoylquinic acid

Density functional theory (DFT) calculations are being performed to investigate the geometric, vibrational, and electronic properties of the chlorogenic acid isomer 3-CQA (1R,3R,4S,5R)-3-{(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-1,4, 5-trihydroxycyclohexanecarboxylic acid), a major phenolic compound in coffee. DFT calculations with the 6-311G(d,p) basis set produce very good results. The electrostatic potential mapped onto an isodensity surface has been obtained. A natural bond orbital analysis (NBO) has been performed in order to study intramolecular bonding, interactions among bonds, and delocalization of unpaired electrons. HOMO-LUMO studies give insights into the interaction of the molecule with other species. The calculated HOMO and LUMO energies indicate that a charge transfer occurs within the molecule. (C) 2012 Elsevier B.V. All rights reserved.

Gap-Dependent Quasiparticle Dynamics and Coherent Acoustic Phonons in CaFe2As2 across Spin Density Wave Phase Transition

We report ultrafast quasiparticle (QP) dynamics and coherent acoustic phonons in undoped CaFe2As2 iron pnictide single crystals exhibiting spin-density wave (SDW) and concurrent structural phase transition at temperature T-SDW similar to 165K using femtosecond time-resolved pump-probe spectroscopy. The contributions in transient differential reflectivity arising from exponentially decaying QP relaxation and oscillatory coherent acoustic phonon mode show large variations in the vicinity of T-SDW. From the temperature-dependence of the QP recombination dynamics in the SDW phase, we evaluate a BCS-like temperature dependent charge gap with its zero-temperature value of similar to(1.6 perpendicular to 0.2)k(B)T(SDW), whereas, much above T-SDW, an electron-phonon coupling constant of similar to 0.13 has been estimated from the linear temperature-dependence of the QP relaxation time. The long-wavelength coherent acoustic phonons with typical time-period of similar to 100 ps have been analyzed in the light of propagating strain pulse model providing important results for the optical constants, sounds velocity and the elastic modulus of the crystal in the whole temperature range of 3 to 300 K.

Performance improvement of short-length regular low-density parity-check codes with low-complexity post-processing

It is well known that extremely long low-density parity-check (LDPC) codes perform exceptionally well for error correction applications, short-length codes are preferable in practical applications. However, short-length LDPC codes suffer from performance degradation owing to graph-based impairments such as short cycles, trapping sets and stopping sets and so on in the bipartite graph of the LDPC matrix. In particular, performance degradation at moderate to high E-b/N-0 is caused by the oscillations in bit node a posteriori probabilities induced by short cycles and trapping sets in bipartite graphs. In this study, a computationally efficient algorithm is proposed to improve the performance of short-length LDPC codes at moderate to high E-b/N-0. This algorithm makes use of the information generated by the belief propagation (BP) algorithm in previous iterations before a decoding failure occurs. Using this information, a reliability-based estimation is performed on each bit node to supplement the BP algorithm. The proposed algorithm gives an appreciable coding gain as compared with BP decoding for LDPC codes of a code rate equal to or less than 1/2 rate coding. The coding gains are modest to significant in the case of optimised (for bipartite graph conditioning) regular LDPC codes, whereas the coding gains are huge in the case of unoptimised codes. Hence, this algorithm is useful for relaxing some stringent constraints on the graphical structure of the LDPC code and for developing hardware-friendly designs.

Evaluation of census techniques to estimate the density of slender Loris (Loris lydekkerianus) in Southern India

Reliable estimates of species density are fundamental to planning conservation strategies for any species; further, it is equally crucial to identify the most appropriate technique to estimate animal density. Nocturnal, small-sized animal species are notoriously difficult to census accurately and this issue critically affects their conservation status, We carried out a field study in southern India to estimate the density of slender loris, a small-sized nocturnal primate using line and strip transects. Actual counts of study individuals yielded a density estimate of 1.61 ha(-1); density estimate from line transects was 1.08 ha(-1); and density estimates varied from 1.06 ha(-1) to 0.59 ha(-1) in different fixed-width strip transects. We conclude that line and strip transects may typically underestimate densities of cryptic, nocturnal primates.

Performance and reliability of Gd2O3 and stacked Gd2O3-Eu2O3 metal-insulator-metal capacitors

Gd2O3-based metal-insulator-metal capacitors have been characterized with single layer (Gd2O3) and bilayer (Gd2O3/Eu2O3 and Eu2O3/Gd2O3) stacks for analog and DRAM applications. Although single layer Gd2O3 capacitors provide highest capacitance density (15 fF/mu m(2)), they suffer from high leakage current density, poor capacitance density-voltage linearity, and reliability. The stacked dielectrics help to reduce leakage current density (1.2x10(-5) A/cm(2) and 2.7 x 10(-5) A/cm(2) for Gd2O3/Eu2O3 and Eu2O3/Gd2O3, respectively, at -1 V), improve quadratic voltage coefficient of capacitance (331 ppm/V-2 and 374 ppm/V-2 for Gd2O3/Eu2O3 and Eu2O3/Gd2O3, respectively, at 1 MHz), and improve reliability, with a marginal reduction in capacitance density. This is attributed to lower trap heights as determined from Poole-Frenkel conduction mechanism, and lower defect density as determined from electrode polarization model.