Algorithms for computing a primary ideal decomposition without producing intermediate redundant components

In Noro (2010) we proposed an algorithm for computing a primary ideal decomposition by using the notion of a separating ideal and showed that it can efficiently decompose several examples which are hard to decompose using existing algorithms. In particular, the number of redundant components produced in the algorithm is zero or very small in many examples, but no theoretical explanation for the efficiency was given.In this paper we define a more sophisticated class of separating ideals: saturated separating ideals. By using this notion we modify the algorithm of Noro (2010) such that it directly outputs a minimal primary decomposition without producing any intermediate redundant component.By modifying the process of extraction of a primary component via the pseudo-primary decomposition proposed in Shimoyama and Yokoyama (1996), we find a method for intermediate decomposition of an ideal and propose a variant of the new primary decomposition algorithm based on this intermediate decomposition. Our experiment shows that this variant efficiently decomposes many examples which are still hard to decompose even if we apply the original version of the new algorithm. Furthermore, in this algorithm we can bypass the computation of primary components and obtain directly the set of all associated primes of an ideal.     

Rapid conversion of toluene by an acinetobacter sp. Tol 5 mutant showing monolayer adsorption to water-oil interface

Two-liquid-phase partitioning bioreactors (TPPBs) consist of an aqueous phase containing microorganism cells and a water-immiscible, non-bioavailable organic phase, and have been investigated for use in bioconversion of toxic, hydrophobic chemicals. We achieved a toluene conversion rate 10-fold faster than any experimental data previously demonstrated, using a novel bacterium in a TPPB employing silicone oil. The bacterium was a bald mutant of toluene-degrading Acinetobacter sp. Tol 5, which has numerous filamentous cell appendages, hydrophobic cell surfaces, adheres to solid surfaces, and self-agglutinates. The bald mutant cells lack the appendages, have decreased adhesiveness to solid surfaces, retain the hydrophobic cell surface, and reversibly adsorb to the surface of oil droplets dispersed in an aqueous phase. The effects of toluene concentration, aqueous and oil phase volume ratios, and cell concentration on the initial conversion rate of toluene were investigated. Volume ratios did not significantly affect conversion rate, and the rate greater than 1 g/(l.h) was attained even in W/O emulsion containing 80% oil. As cell concentration increased, the volumetric conversion rate increased, but the specific conversion rate decreased. The highest volumetric conversion rate, 3.1 g/(l.h), was achieved using 8.20 g/l cells in a TPPB containing 20% oil.     

Changes in cell proliferative activity in granulation tissue invading the root canal

Root canal models were implanted in rats in order to investigate histologically the movement of granulation tissue invading apical canals and dead spaces and changes in cell proliferative activity as indicated by 3H-thymidine. The models were prepared to have 1, 2, and 3 mm apical canals, with and without dead spaces, to simulate preparations short of the apex and obturation to several levels. After 12 wks implantation of the models without dead spaces, granulation tissue invading 1 mm apical canals did not degenerate and cell proliferative activity remained high. However, tissue invading the 2 and 3 mm apical canals tended to be necrotic and cell proliferative activity was decreased. In the models with dead spaces, the tissue in the 1 and 2 mm apical canals developed and invaded the dead spaces, and still possessed proliferative activity 12 wks after implantation. In contrast, the tissue in the 3 mm apical canals did not invade the dead spaces, even after 12 wks, and no proliferative activity was observed.     

A separation method for DNA computing based on concentration control

A separation method for DNA computing based on concentration control is presented. The concentration control method was earlier developed and has enabled us to use DNA concentrations as input data and as filters to extract target DNA. We have also applied the method to the shortest path problems, and have shown the potential of concentration control to solve large-scale combinatorial optimization problems. However, it is still quite difficult to separate different DNA with the same length and to quantify individual DNA concentrations. To overcome these difficulties, we use DGGE and CDGE in this paper. We demonstrate that the proposed method enables us to separate different DNA with the same length efficiently, and we actually solve an instance of the shortest path problems. Masahito Yamamoto, Ph.D.: He is associate professor of information engineering at Hokkaido University. He received Ph.D. from the Graduate School of Engineering, Hokkaido University in 1996. His current research interests include DNA computing based the laboratory experiments. He is a member of Operations Research Society of Japan, Japanese Society for Artificial Intelligence, Information Processing Society of Japan etc. Atsushi Kameda, Ph.D.: He is the research staff of Japan Science and Technology Corporation, and has participated in research of DNA computing in Hokkaido University. He received his Ph.D. from Hokkaido University in 2001. For each degree he majored in molecular biology. His research theme is about the role of polyphosphate in the living body. As one of the researches relevant to it, he constructed the ATP regeneration system using two enzyme which makes polyphosphate the phosphagen. Nobuo Matsuura: He is a master course student of Division of Systems and Information Engineering of Hokkaido University. His research interests relate to DNA computing with concentration control for shortest path problems, as a means of solution of optimization problems with bimolecular. Toshikazu Shiba, Ph.D.: He is associate, professor of biochemical engineering at Hokkaido University. He received his Ph.D. from Osaka University in 1991. He majored in molecular genetics and biochemistry. His research has progressed from bacterial molecular biology (regulation of gene expression of bacterial cells) to tissue engineering (bone regeneration). Recently, he is very interested in molecular computation and trying to apply his biochemical idea to information technology. Yumi Kawazoe: She is a master course student of Division of Molecular Chemistry of Hokkaido University. Although her major is molecular biology, she is very interested in molecular computation and bioinformatics. Azuma Ohuchi, Ph.D.: He is professor of Information Engineering at the University of Hokkaido, Sapporo, Japan. He has been developing a new field of complex systems engineering, i.e., Harmonious Systems Engineering since 1995. He has published numerous papers on systems engineering, operations research, and computer science. In addition, he is currently supervising projects on DNA computing, multi-agents based artificial market systems, medical informatics, and autonomous flying objects. He was awarded “The 30th Anniversary Award for Excellent Papers” by the Information Processing Society of Japan. He is a member of Operations Research Society of Japan, Japanese Society for Artificial Intelligence, Information Processing Society of Japan, Japan Association for Medical Informatics, IEEE Computer Society, IEEE System, Man and Cybernetics Society etc. He received PhD from Hokkaido University in 1976.     

Why the all-electron full-potential approach is suitable for calculations on fullerenes and nanotubes?

Already 30 years have passed since the first prediction of C60 by Professor Osawa. A family of cage-type fullerenes and carbon nanotubes were experimentally found as the third form of carbon molecules in the 1980s. After this discovery, much research has been conducted experimentally and theoretically on these new materials. The all-electron full-potential approach is important for fully understanding the quantum mechanical behavior of the fullerenes and related molecules. We show some results of band calculations and ab initio molecular dynamics.     

Effect of solute mixing in the liquid propellant of a pulsed plasma thruster

Sodium chloride or ammonia was dissolved in the water propellant of pulsed plasma thrusters to improve the performance. Pulsed plasma thrusters using liquid propellant utilize water as attractive alternative instead of Teflon. Water propellant enables in controlling propellant mass flow and leads to high specific impulse. However, liquid propellant pulsed plasma thrusters have larger plasma resistance and lower thrust power ratio than the common Teflon propellant thruster. Here, sodium chloride and ammonia solution of water were examined to decrease that plasma resistance. As a result, emission lines attributed from the solute were observed using sodium chloride aqueous solution propellant, and a 5% reduction of the plasma resistance was shown, and the thrust to power was increased. However, ammonia aqueous solution decreased the thruster performance.     

Ultra-stable nanoparticles of CdSe revealed from mass spectrometry

Nanoparticles under a few nanometres in size have structures and material functions that differ from the bulk because of their distinct geometrical shapes and strong quantum confinement. These qualities could lead to unique device applications. Our mass spectral analysis of CdSe nanoparticles reveals that (CdSe)(33) and (CdSe)(34) are extremely stable: with a simple solution method, they grow in preference to any other chemical compositions to produce macroscopic quantities. First-principles calculations predict that these are puckered (CdSe)(28)-cages, with four- and six-membered rings based on the highly symmetric octahedral analogues of fullerenes, accommodating either (CdSe)(5) or (CdSe)(6) inside to form a three-dimensional network with essentially heteropolar sp(3)-bonding. This is in accordance with our X-ray and optical analyses. We have found similar mass spectra and atomic structures in CdS, CdTe, ZnS and ZnSe, demonstrating that mass-specified and macroscopically produced nanoparticles, which have been practically limited so far to elemental carbon, can now be extended to a vast variety of compound systems.     

Silicon subiodide clusters

Silicon subiodide clusters (Si(n)I(m), n = 1-20) produced by laser ablation of bulk powder silicone tetraiodide have been investigated by time-of-flight mass spectroscopy and ab initio calculations. Both experimental results and theoretical calculations revealed a tendency to form different structures of the clusters depending on n: chain, ring, and cage structures for n < or = 6, 6 < n < 16, and n > or = 16, respectively. The results showed that iodine, like hydrogen, can be used for stable silicon cluster termination.     

An Artificial Intelligence Approach for Modeling and Prediction of Water Diffusion Inside a Carbon Nanotube

Modeling of water flow in carbon nanotubes is still a challenge for the classic models of fluid dynamics. In this investigation, an adaptive-network-based fuzzy inference system (ANFIS) is presented to solve this problem. The proposed ANFIS approach can construct an input–output mapping based on both human knowledge in the form of fuzzy if-then rules and stipulated input–output data pairs. Good performance of the designed ANFIS ensures its capability as a promising tool for modeling and prediction of fluid flow at nanoscale where the continuum models of fluid dynamics tend to break down.