Hybrid Petri net based modeling for biological pathway simulation

Hybrid Petri net (HPN) is an extension of the Petri net formalism, which enables us to handle continuous information in addition to discrete information. Firstly, this paper demonstrates how biological pathways can be modeled by the integration of discrete and continuous elements, with an example of the λ phage genetic switch system including induction and retroregulation mechanisms. Although HPN allows intuitive modeling of biological pathways, some fundamental biological processes such as complex formation cannot be represented with HPN. Thus, this paper next provides the formal definition of hybrid functional Petri net with extension (HFPNe), which has high potential for modeling various kinds of biological processes. Cell Illustrator is a software tool developed on the basis of the definition of HFPNe. Hypothesis creation by Cell Illustrator is demonstrated with the example of the cyanobacterial circadian gene clock system. Finally, our ongoing tasks, which include the development of a computational platform for systems biology, are presented.     

Tabu search for attribute reduction in rough set theory

In this paper, we consider a memory-based heuristic of tabu search to solve the attribute reduction problem in rough set theory. The proposed method, called tabu search attribute reduction (TSAR), is a high-level TS with long-term memory. Therefore, TSAR invokes diversification and intensification search schemes besides the TS neighborhood search methodology. TSAR shows promising and competitive performance compared with some other CI tools in terms of solution qualities. Moreover, TSAR shows a superior performance in saving the computational costs.     

Voltammetric study of electrocatalysis for dioxygen reduction by trinuclear rutheniumammine complex confined in a polymer membrane

Electrocatalytic O₂ reduction was studied using a modified electrode coated with a Nafion membrane (Nf) dispersing a trinuclear ruthenium ammine complex ([(NH₃)₅Ru^IIIORu^IV(NH₃)₄ORu^III(NH₃)₅]Cl₆, Ru-red). When measuring cyclic voltammogram under O₂ atmosphere (at 0.5 mV s⁻¹), catalytic currents due to O₂ reduction were found to develop below −0.2 V (vs. Ag/AgCl). Since Ru-red undergoes irreversible decomposition into the mononuclear complexes via the reduced state (Ru^III-Ru^III-Ru^III) (∼−0.1 V), it is suggested that the electrocatalysis originates from the decomposed species (initial active species: Ru^II(NH₃)₅(OH₂) and Ru^II(NH₃)₄(OH₂)₂) rather than from the Ru-red. Although the present electrocatalyst was also applied to H₂O₂ reduction system, the catalytic activity was found to be poor from the voltammetric behavior. It appeared that the kinetics of the electrocatalysis is much faster in the O₂ reduction than in the H₂O₂ one. A selective and direct catalysis for O₂ reduction into H₂O was suggested from a ring-disk voltammogram to take place by an aggregate of the mononuclear ruthenium complexes in the polymer matrix. In addition, it was found that electrocatalytic O₂ reduction involves a slow kinetic process, so that factors affecting the overall kinetics were discussed in terms of the catalysis mechanism.     

Bubble wake visualization by using photochromic dye

Wake structure of a single “clean bubble”, rising in rectilinear, zigzagging or spiraling path, is experimentally investigated. A single nitrogen gas bubble was produced in a silicone oil pool and the wake structure development in the rear of the rising bubble was visualized by using photochromic dye. The flexibility of this visualization method enabled us to distinguish wake from drift easily. Both bubble motion and wake structure were recorded by using stereo high-speed video camera simultaneously. We present the first experimental support for the existence of the standing eddy at the rear of the clean bubble, as predicted by a previous numerical study by Ryskin and Leal [1984. Journal of Fluid Mechanics 148, 19-35], Dandy and Leal [1986. Physics of Fluids 29(5), 1360-1366] and Blanco and Magnaudet [1995. Physics of Fluids 7(6), 1265-1274]. We study motion of a pair of vortex filaments, which is called double-threaded type wake, in the case of bubble rising in an axi-asymmetric path. Visualization results of multiple formations of horse-shoe type vortices in one period of zigzag motion of rising bubble with shape oscillations, which has not been observed in previous studies are also presented.     

High-intensity multi-bunch beam generation by a photo-cathode RF gun

A multi-bunch photo-cathode RF gun system has been developed as an electron source for the production of intense quasi-monochromatic X-rays based on inverse Compton scattering. The desired multi-bunch beam is 100 bunches/pulse with a total charge of 500 nC and a bunch spacing of 2.8 ns. We modified the gun cavity of a ‘BNL-type IV’ RF gun to allow a CsTe cathode plug in the end plate. The system uses a four-dipole chicane beam line to allow the injection of laser light normal to the cathode surface. We compensate the gun cavity beam loading caused by the high-intensity multi-bunch electron beam by injecting the laser pulse before RF power has filled the cavity. We have achieved a total intensity of 220 nC in 100 bunches with a bunch-to-bunch energy spread under 1.3% (peak-to-peak). This paper concentrates on experiments to generate the high-intensity multi-bunch beam with compensation of the bunch-to-bunch energy spread due to heavy beam loading.     

A novel chromatographic separation technique using tertiary pyridine resin for the partitioning of trivalent actinides and lanthanides

A novel chromatographic separation technique using a tertiary pyridine type resin has been applied to the partitioning of the trivalent actinides (An) and lanthanides (Ln) and several successful results have been shown. In an alcoholic hydrochloric acid system, the trivalent An were clearly separated from the Ln, while no such group separation was achieved in an alcoholic nitric acid system. On the other hand, the nitric acid system was more effective for the intragroup (i.e. individual) separation of the trivalent An and the Ln than the hydrochloric acid system. On the basis of these results, a novel concept for the partitioning of the trivalent An and Ln using the present separation technique and its flowchart have been proposed with its advantages and disadvantages.     

A fast and compact elimination method of empty elements from a double‐array structure

A double‐array is a well‐known data structure to implement the trie. However, the space efficiency of the double‐array degrades with the number of key deletions because the double‐array keeps empty elements produced by the key deletion. This paper presents a fast and compact elimination method of empty elements using properties of the trie nodes that have no siblings. The present elimination method is implemented by C language. From simulation results for large sets of keys, the present elimination method is about 30–330 times faster than the conventional elimination method and maintains high space efficiency. Copyright © 2003 John Wiley & Sons, Ltd.