Two complementary operations inspired by the DNA hairpin formation: Completion and reduction

We consider two complementary operations: Hairpin completion introduced in [D. Cheptea, C. Martin-Vide, V. Mitrana, A new operation on words suggested by DNA biochemistry: Hairpin completion, in: Proc. Transgressive Computing, 2006, pp. 216–228] with motivations coming from DNA biochemistry and hairpin reduction as the inverse operation of the hairpin completion. Both operations are viewed here as formal operations on words and languages. We settle the closure properties of the classes of regular and linear context-free languages under hairpin completion in comparison with hairpin reduction. While the class of linear context-free languages is exactly the weak-code image of the class of the hairpin completion of regular languages, rather surprisingly, the weak-code image of the class of the hairpin completion of linear context-free languages is a class of mildly context-sensitive languages. The closure properties with respect to the hairpin reduction of some time and space complexity classes are also studied. We show that the factors found in the general cases are not necessary for regular and context-free languages. This part of the paper completes the results given in the earlier paper, where a similar investigation was made for hairpin completion. Finally, we briefly discuss the iterated variants of these operations.     

Solving the irregular strip packing problem via guided local search for overlap minimization

The irregular strip-packing problem (ISP) requires a given set of non-convex polygons to be placed without overlap within a rectangular container having a fixed width and a variable length, which is to be minimized. As a core sub-problem to solve ISP, we consider an overlap minimization problem (OMP) whose objective is to place all polygons into a container with given width and length so that the total amount of overlap between polygons is made as small as possible. We propose to use directional penetration depths to measure the amount of overlap between a pair of polygons, and present an efficient algorithm to find a position with the minimum overlap for each polygon when it is translated in a specified direction. Based on this, we develop a local search algorithm for OMP that translates a polygon in horizontal and vertical directions alternately. Then we incorporate it in our algorithm for OMP, which is a variant of the guided local search algorithm. Computational results show that our algorithm improves the best-known values of some well-known benchmark instances.     

A Bayesian solution to the multiple composite hypothesis testing for fault diagnosis in dynamic systems

This paper is concerned with model-based isolation and estimation of additive faults in discrete-time linear Gaussian systems. The isolation problem is stated as a multiple composite hypothesis testing on the innovation sequence of the Kalman filter (KF) that considers the system operating under fault-free conditions. Fault estimation is carried out, after isolating a fault mode, by using the Maximum a Posteriori (MAP) criterion. An explicit solution is presented for both fault isolation and estimation when the parameters of the fault modes are assumed to be realizations of specific random variables (RV).     

On the possible patterns of inputs for block sorting in the Burrows-Wheeler transformation

Block sorting in the Burrows-Wheeler transformation is to sort all of the n circular shifts of a string of length n lexicographically. We introduce a notion called the width of a sequence of n strings of length n and show that the values of widths are very different between the two types of sequences of strings; (1) a sequence of n randomly generated strings of length n, and (2) the sequence of n circular shifts of a randomly generated string of length n.     

Performance of SOR methods on modern vector and scalar processors

The building-cube method (BCM) is a new generation algorithm for CFD simulations. The basic idea of BCM is to simplify the algorithm in all stages of flow computation to achieve large-scale simulations. Calculation of a pressure field using the Successive Over Relaxation (SOR) method consumes most of the total execution time required for BCM. In this paper, effective implementations on modern vector and scalar processors are investigated. NEC SX-9 and Intel Nehalem-EX are the latest vector and scalar processors. Those processors have much higher peak performances than their previous-generation processors. However, their memory bandwidth improvement cannot catch up with the performance improvement of processors. This is the so-called memory wall problem. In our paper, we discuss optimization techniques for implementation of the SOR method based on architectural characteristics of these modern processors, and evaluate their effects on the sustained performances of these processors for BCM.     

Fabrication of sub-micron structures for MEMS using deep X-ray lithography

Fabrication techniques of microstructures with high resolution and high aspect ratio are necessary for practical microelectromechanical systems (MEMS) that have high performance and integration. In order to fabricate microstructures with sub-micron resolution and high aspect ratio, deep X-ray lithography has been investigated using the compact synchrotron radiation (SR) light source called “AURORA”. An X-ray mask for sub-micron deep X-ray lithography, which is composed of 1 μm thick Au as absorbers, 2 μm thick SiC as a membrane and 625 μm thick Si as a frame, was designed. In preliminary experiments, the following results were achieved: EB resist microstructures with an aspect ratio of 22 corresponding with 0.07 μm width and 1.3 μm height were formed; a 10 μm thick PMMA resist containing no warp was formed by direct polymerization, enabling more precise gap control.     

Technique for anisotropic extension of organic crystals: application to temperature dependence of electrical resistance

We have developed a technique for the anisotropic extension of fragile molecular crystals. The pressure medium and the instrument, which extends the pressure medium, are both made from epoxy resin. Since the thermal contraction of our instrument is identical to that of the pressure medium, the strain applied to the pressure medium has no temperature dependence down to 2 K. Therefore, the degree of extension applied to the single crystal at low temperatures is uniquely determined from the degree of extension in the pressure medium and thermal contractions of the epoxy resin and the single crystal at ambient pressure. Using this novel instrument, we have measured the temperature dependence of the electrical resistance of metallic, superconducting, and insulating materials. The experimental results are discussed from the viewpoint of the extension (compression) of the lattice constants along the parallel (perpendicular) direction.     

Accumulation of triosephosphate isomerase, with sequence homology to Beta amyloid peptides, in vessel walls of the newborn piglet hippocampus

We investigated whether beta-amyloid (Abeta)-like immunoreactivity was seen in the brains of newborn piglets. The immunoreactivity for Abeta(1-42) and Abeta(1-40) proteins, but not Abeta precursor protein, was present in CD68-positive perivascular cells of the hippocampus and in parts of the meninges. It was colocalized with immunoreactivity for receptor for advanced glycation end product and tumor necrosis factor-alpha. The protein with a molecular mass of 27 kDa, which was recognized by the Abeta antibodies, was identified as triosephosphate isomerase (TPI) with sequence homology to Abeta peptides by N-terminal amino acid sequencing, mass fingerprint analysis using matrix-associated laser desorption/ionization mass spectrometry, and Western blotting. Western blotting assay also revealed that detectable expression of Abeta proteins were not seen in the piglet brains. These findings indicate that TPI with sequence homology to Abeta peptides accumulates in perivascular cells of the microglia/macrophage lineage located around arterial vessels of the newborn piglet hippocampus.