Polynomiality of primal-dual affine scaling algorithms for nonlinear complementarity problems

This paper provides an analysis of the polynomiality of primal-dual interior point algorithms for nonlinear complementarity problems using a wide neighborhood. A condition for the smoothness of the mapping is used, which is related to Zhu’s scaled Lipschitz condition, but is also applicable to mappings that are not monotone. We show that a family of primal-dual affine scaling algorithms generates an approximate solution (given a precision ε) of the nonlinear complementarity problem in a finite number of iterations whose order is a polynomial ofn, ln(1/ε) and a condition number. If the mapping is linear then the results in this paper coincide with the ones in Jansen et al., SIAM Journal on Optimization 7 (1997) 126–140. Research supported in part by Grant-in-Aids for Encouragement of Young Scientists (06750066) from the Ministry of Education, Science and Culture, Japan. Research supported by Dutch Organization for Scientific Research (NWO), grant 611-304-028     

Parallel Implementation of Successive Convex Relaxation Methods for Quadratic Optimization Problems

As computing resources continue to improve, global solutions for larger size quadrically constrained optimization problems become more achievable. In this paper, we focus on larger size problems and get accurate bounds for optimal values of such problems with the successive use of SDP relaxations on a parallel computing system called Ninf (Network-based Information Library for high performance computing).     

Versatile synthesis of epicatechin series procyanidin oligomers, and their antioxidant and DNA polymerase inhibitory activity

Proanthocyanidins, known as condensed tannins or oligomeric flavonoids, exist in many edible plants and show various interesting biological activities. We have developed a simple and versatile method of synthesizing procyanidin oligomers consisting of (−)-epicatechin and (+)-catechin. This method is applicable to the synthesis of various 3-O-substituted oligomers. We report here the stereoselective and length controlled synthesis of [4-8]-condensed (−)-epicatechin series procyanidin oligomers. We described the details of the synthesis of an two tetramers, (−)-epicatechin-(−)-epicatechin-(−)-epicatechin-(−)-epicatechin and (−)-epicatechin-(−)-epicatechin-(−)-epicatechin-(+)-catechin (arecatannin A1), (−)-epicatechin pentamer and two 3,3″,3?-tri-O-galloyl trimers, (−)-epicatechin-(−)-epicatechin-(−)-epicatechin-3,3″,3?-tri-O-gallate and (−)-epicatechin-(−)-epicatechin-(+)-catechin-3,3″,3?-tri-O-gallate with the condensation method using TMSOTf as a catalyst. The ability of DPPH radical scavenging activity and DNA polymerase inhibitory activity of these oligomeric compounds were investigated.     

HPLC for Separation and Quantification of Deoxyribonucleic Acid Fragments and Measurement of Deoxyribonucleic Acid Degradation

DNA quantification has made its mark in pharmaceutical analysis and the life sciences. In particular, in the quality control of nucleic acid drugs and the detection and quantification of genetically modified organisms, evaluation of the DNA degradation rate has become imperative. In this study, by using high-performance liquid chromatography with an anion-exchange column, we established a method for the separation and quantification of DNA fragments in mixed DNA samples. By using a NaCl concentration gradient, DNA fragments in mixed DNA sample were separated well. A calibration curve from 0.05 to 12.4 ng μL^?1 was obtained with high linearity and the correlation coefficient was 0.9999. The limit of detection was 0.02 ng μL^?1 and the limit of quantification was 0.06 ng μL^?1 for S/N = 3 or S/N = 10, respectively. The relative standard deviation was less than 2 % in the measurement of peak area repeatability. The recovery of approximately 1 ng μL^?1 of a specific DNA spiked in a mixed DNA sample was 99.9 ± 3.6 %. The method was able to measure the degradation rate of 600 bp DNA with a variation of approximately 1 %.     

Facile synthesis of platinum nanoparticle-containing porous carbons,and their application to amperometric glucose biosensing

This study describes the facile synthesis of platinum nanoparticle-containing porous carbons (Pt/C) by carbonization of freeze-dried agarose gels containing potassium tetrachloroplatinate under a nitrogen atmosphere at 800 °C. By adjusting the ratio between agarose and platinate in the freeze-dried gels, the Pt content in the final Pt/C products could be systematically varied from 0–10 wt.%. Transmission electron microscopy, inductively coupled plasma atomic emission spectrometry, X-ray photoelectron spectroscopy, Raman spectroscopy, and nitrogen physisorption measurements revealed that the Pt/C materials obtained by this method possess high surface areas (350–500 m² g⁻¹), narrow Pt nanoparticle size distributions (6 ± 3 nm) and nanocrystalline graphite –like carbon character. By immobilization of glucose oxidase on the surface of a 4 wt.% Pt/C electrocatalyst prepared by this route, a very sensitive amperometric glucose biosensor was obtained (response time <2 min, sensitivity 1.9 mA M⁻¹; and a linear response with glucose concentration up to 10 mM). The simplicity and versatility of the described synthetic method suggests its application to the preparation of carbon supported noble metal catalysts including palladium/C and gold/C.

This study describes the facile synthesis of platinum nanoparticle-containing porous carbons (Pt/C) by carbonization of freeze-dried agarose gels containing potassium tetrachloroplatinate. The Pt/C materials exhibited excellent electrocatalytic activities, as demonstrated by their successful integration into amperometric glucose biosensor

     

Cobalt oxide supported gold nanoparticles as a stable and readily-prepared precursor for the in situ generation of cobalt carbonyl like species

A treatment of cobalt oxide supported gold nanoparticles (Au/Co₃O₄) under syngas atmosphere effectively generated a cobalt carbonyl-like active species in the reaction vessel. The preparation of Au/Co₃O₄ was quite simple and the in situ generated cobalt species could be used as a stable and easy handling alternative for dicobalt octacarbonyl without bothersome purification prior to use. The reactions, which are sensitive to the purity of the dicobalt octacarbonyl, such as the alkoxycarbonylation of epoxides and the Pauson-Khand reaction, smoothly progressed with Au/Co₃O₄.     

Prolongation of the active lifetime of a biomolecular motor for in vitro motility assay by using an inert atmosphere

Over the last few decades, the in vitro motility assay has been performed to probe the biophysical and chemo-mechanical properties as well as the self-organization process of biomolecular motor systems such as actin-myosin and microtubule-kinesin. However, aggression of the reactive oxygen species (ROS) and concomitant termination of the activity of biomolecular motors during investigation remains a drawback of this assay. Despite enzymatic protection that makes use of a combination of glucose, glucose oxidase, and catalase, the active lifetime of biomolecular motors is found to be only a few hours and this short lifetime restricts further study on those systems. We have solved this problem by using a newly developed system of the in vitro motility assay that is conducted in an inert nitrogen gas atmosphere free of ROS. Using microtubule-kinesin as a model system we have shown that our system has prolonged the active lifetime of the biomolecular motor until several days and even a week by protecting it from oxidative damage.     

Phosphoproteome Profiling Using a Fluorescent Phosphosensor Dye in Two-Dimensional Polyacrylamide Gel Electrophoresis

We validated the novel PhosphoQUANTI SolidBlue Complex (PQSC) dye for the sensitive fluorescent detection of phosphorylated proteins in polyacrylamide- and two-dimensional gel electrophoresis (PAGE and 2DE, respectively). PQSC can detect as little as 15.6 ng of ß-casein, a pentaphosphorylated protein, and 61.3 ng of ovalbumin, a diphosphorylated protein. Fluorescence intensity correlates with the number of phosphorylated residues on the protein. To demonstrate the specificity of PQSC for phosphoproteins, enzymatically dephosphorylated lysates of Swiss 3T3 cells were separated in 2DE gels and stained by PQSC. The fluorescence signals in these gels were markedly reduced following dephosphorylation. When the phosphorylated proteins in Swiss 3T3 cell lysates were concentrated using a phosphoprotein enrichment column, the majority of phosphoproteins showed fluorescence signals in the pI 4–5 range. Finally, we performed phosphoproteome analysis to study differences in the protein phosphorylation profiles of proliferating and quiescent Swiss 3T3 cells. Over 135 discernible protein spots were detected, from which a selection of 15 spots were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). The PQSC staining procedure for phosphoprotein detection is simple, reversible, and fully compatible with MALDI TOF-MS.     

Anomalous dielectric behavior and thermal motion of water molecules confined in channels of porous coordination polymer crystals

Guest water molecules confined in channels of porous coordination polymer crystals [Ln(2)Cu(3)(IDA)(6)]·nH(2)O (Ln = La, Nd, Sm, Gd, Ho, Er; IDA = [NH(CH(2)COO)(2)](2-); n ≈ 9) exhibited large dielectric constants (ε) and antiferroelectric behaviors at high temperatures (e.g., ε(Sm) ≈ 1300 at 400 K). In addition, plots of the temperature dependence of ε showed broad peaks at ～170 K, below which ε became very small. These puzzling temperature dependences of ε are consistent with the results of molecular dynamics simulations, suggesting the "freezing of thermal motion" of water molecules at ～170 K.