SMO: An Integrated Approach to Intra-array and Inter-array Storage Optimization

The polyhedral model provides an expressive intermediate representation that is convenient for the analysis and subsequent transformation of affine loop nests. Several heuristics exist for achieving complex program transformations in this model. However, there is also considerable scope to utilize this model to tackle the problem of automatic memory footprint optimization. In this paper, we present a new automatic storage optimization technique which can be used to achieve both intra-array as well as inter-array storage reuse with a pre-determined schedule for the computation. Our approach works by finding statement-wise storage partitioning hyper planes that partition a unified global array space so that values with overlapping live ranges are not mapped to the same partition. Our heuristic is driven by a fourfold objective function which not only minimizes the dimensionality and storage requirements of arrays required for each high-level statement, but also maximizes inter statement storage reuse. The storage mappings obtained using our heuristic can be asymptotically better than those obtained by any existing technique. We implement our technique and demonstrate its practical impact by evaluating its effectiveness on several benchmarks chosen from the domains of image processing, stencil computations, and high-performance computing.

Molecular Dynamics Simulation of Peeling a DNA Molecule on Substrate

Molecular dynamics (MD) simulations are performed to study adhesion and peeling of a short fragment of single strand DNA (ssDNA) molecule from a graphite surface. The critical peel-off force is found to depend on both the peeling angle and the elasticity of ssDNA. For the short ssDNA strand under investigation, we show that the simulation results can be explained by a continuum model of an adhesive elastic band on substrate. The analysis suggests that it is often the peak value, rather than the mean value, of adhesion energy which determines the peeling of a nanoscale material.

Characterization of a liquid crystal microlens array using multiwalled carbon nanotube electrodes.

Reconfigurable liquid crystal microlenses employing arrays of multiwalled carbon nanotubes (MWNTs) have been designed and fabricated. The cells consist of arrays of 2 microm high MWNTs grown by plasma-enhanced chemical vapor deposition on silicon with a top electrode of indium tin oxide coated glass positioned 20 microm above the silicon and the gap filled with the nematic liquid crystal BLO48. Simulations have found that, while its nematic liquid crystal aligns with MWNTs within a distance of 10nm, this distance is greatly enhanced by the application of an external electric field. Polarized light experiments show that light is focused with focal lengths ranging from approximately 7 microm to 12 microm.

Capacitive nanoelectromechanical switch based on suspended carbon nanotube array

We present the fabrication and high frequency characterization of a capacitive nanoelectromechanical system (NEMS) switch using a dense array of horizontally aligned single-wall carbon nanotubes (CNTs). The nanotubes are directly grown onto metal layers with prepatterned catalysts with horizontal alignment in the gas flow direction. Subsequent wetting-induced compaction by isopropanol increases the nanotube density by one order of magnitude. The actuation voltage of 6 V is low for a NEMS device, and corresponds to CNT arrays with an equivalent Young's modulus of 4.5-8.5 GPa, and resistivity of under 0.0077 Ω·cm. The high frequency characterization shows an isolation of -10 dB at 5 GHz. © 2010 American Institute of Physics.

Microfabrication and application of reservoir pins for liquid transfer in biotechnology

Microarraying involves laying down genetic elements onto a solid substrate for DNA analysis on a massively parallel scale. Microarrays are prepared using a pin-based robotic platform to transfer liquid samples from microtitre plates to an array pattern of dots of different liquids on the surface of glass slides where they dry to form spots diameter < 200 μm. This paper presents the design, materials selection, micromachining technology and performance of reservoir pins for microarraying. A conical pin is produced by (i) conventional machining of stainless steel or wet etching of tungsten wire, followed by (ii) micromachining with a focused laser to produce a microreservoir and a capillary channel structure leading from the tip. The pin has a flat end diameter < 100 μm from which a 500 μm long capillary channel < 15 μm wide leads up the pin to a reservoir. Scanning electron micrographs of the metal surface show roughness on the scale of 10 μm, but the pins nevertheless give consistent and reproducible spotting performance. The pin capacity is 80 nanolitres of fluid containing DNA, and at least 50 spots can be printed before replenishing the reservoir. A typical robot holds can hold up to 64 pins. This paper discusses the fabrication technology, the performance and spotting uniformity for reservoir pins, the possible limits to miniaturization of pins using this approach, and the future prospects for contact and non-contact arraying technology.

A Label-Free Protein Microfluidic Array for Parallel Immunoassays

A label-free protein microfluidic array for immunoassays based on the combination of imaging ellipsometry and an integrated microfluidic system is presented. Proteins can be patterned homogeneously on substrate in array format by the microfluidic system simultaneously. After preparation, the protein array can be packed in the microfluidic system which is full of buffer so that proteins are not exposed to denaturing conditions. With simple microfluidic channel junction, the protein microfluidic array can be used in serial or parallel format to analyze single or multiple samples simultaneously. Imaging ellipsometry is used for the protein array reading with a label-free format. The biological and medical applications of the label-free protein microfluidic array are demonstrated by screening for antibody–antigen interactions, measuring the concentration of the protein solution and detecting five markers of hepatitis B.

Quasi-Dammann Grating With Proportional Intensity Array Spots

A quasi-Dammann grating is proposed to generate array spots with proportional-intensity orders in the far field. To describe the performance of the grating, the uniformities of the array spots are redefined. A two-dimensional even-sampling encode scheme is adopted to design the quasi-Dammann grating. Numerical solutions of the binary-phase quasi-Dammann grating with proportional-intensity orders are given. The experimental results with a third-order quasi-Dammann grating, which has an intensity proportion of 3:2:1 from zero order to second order, are presented. (C) 2008 Optical Society of America

Metric representation of DNA sequences

A metric representation of DNA sequences is borrowed from symbolic dynamics. In view of this method, the pattern seen in the chaos game representation of DNA sequences is explained as the suppression of certain nucleotide strings in the DNA sequences. Frequencies of short nucleotide strings and suppression of the shortest ones in the DNA sequences can be determined by using the metric representation.