Anisotropic friction model of DNA electrophoresis in polymer solutions: Comparison with direct observations

The electrophoresis of DNA chains in uncrosslinked polymer solutions with a Brownian dynamics simulation with an anisotropic friction tensor was analyzed. According to the degree of anisotropy, three types of migration behavior are obtained: fluctuation without or with periodicity between U‐shaped and compact conformations, or migration with linear conformation. We found good agreement between our simulation results and the direct observations of DNA by fluorescence microscopy. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 1316–1322, 2003     

Constructing a new optical sensor for monitoring ammonia in water samples using bis(acetylacetoneethylendiamine)-tributylphosphin cobalt(III) tetraphenylborate complex-coated triacetylcellulose.

A new ammonia optical sensor was designed using bis(acetylacetoneethylendiamine)tributylphosphin cobalt(III) tetraphenylborate complex, coated on transparent triacetylcellulose film as membrane. The change in the absorbance of the optode at the maximum wavelength of 408 nm was related to ammonia concentration in aqueous samples. A buffer solution with a pH of 9 (sodium borate-HCl) was used. The optode was fully regenerated in pH 2. The linear dynamic range for determination of ammonia was 3.3 x 10(-4) to 6.9 x 10(-3) mol l(-1) with a detection limit of 5.0 x 10(-5) mol l(-1) and a response time range of 4 - 6 min. This membrane was successfully applied for determination of ammonia in drinking water.     

Sympathetic cooling rate of gas-phase ions in a radio-frequency-quadrupole ion trap

We theoretically investigated the mass dependence of the sympathetic cooling rate of gas-phase ions trapped in a linear radio-frequency-quadrupole ion trap. Using an a priori molecular dynamical calculation, tracing numerically with Newtonian equations of motion, we found that ions with a mass greater than 0.54±0.04 times that of the laser-cooled ions are sympathetically cooled; otherwise, they are heated. To understand the mass dependence obtained using the molecular-dynamical calculation, we made a heat-exchange model of sympathetic cooling, which shows that the factor of 0.54±0.04 is a consequence of absence of micro-motion along the axis of the linear ion trap. Received: 10 December 2001 / Revised version: 28 January 2002 / Published online: 14 March 2002     

A rate-dependent algebraic stress model for turbulence

Based on the stress transport model, a rate-dependent algebraic expression for the Reynolds stress tensor is developed. It is shown that the new model includes the normal stress effects and exhibits viscoelastic behavior. Furthermore, it is compatible with recently developed improved models of turbulence. The model is also consistent with the limiting behavior of turbulence in the inertial sublayer and is capable of predicting secondary flows in noncircular ducts. The TEACH code is modified according to the requirements of the rate-dependent model and is used to predict turbulent flow fields in a channel and behind a backward-facing step. The predicted results are compared with the available experimental data and those obtained from the standard k-ε and algebraic stress models. It is shown that the predictions of the new model are in better agreements with the experimental data.     

Synthesis and simple separation of β-pyrrole sulfonated porphycenes

New water-soluble porphycenes having sulfonic acid groups at the β-pyrrolic positions were synthesized and characterized by UV-vis, NMR, IR, and mass spectroscopy as well as elemental analyses. The series of mono- to tri-sulfonato derivatives were simply separated by the extraction method.     

Mechanism of gold adsorption by persimmon tannin gel.

Gold adsorption by persimmon tannin (PT) gel from a solution containing hydrogen tetrachloroaurate(III) was examined. A flow-rate examination in a column system indicated the reduction of Au(III) ion to Au(0). XRD patterns clarified the existence of Au(0) on the gel which adsorbed gold. The gel could also adsorb colloidal Au(0) prepared independently. A model consisting of ligand exchange, Au(III) reduction to Au(0), and resulting Au(0) adsorption by PT gel was presented for the gold adsorption mechanism.     

Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues

Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays.

We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.     

Fluorination of 2-alkyl-substituted oxanes. The synthesis and purification of perfluoro(2-alkyl-substituted oxane)s

Five kinds of 2-alkyl-substituted oxanes like 2-ethyloxane, 2-n-propyloxane, 2-iso-propyloxane, 2-n-butyloxane and 2-n-amyloxane were fluorinated electrochemically to give the corresponding perfluoro(2-alkyloxane)s. The perfluoro(2-alkyloxane)s were obtained in good yields from these starting materials together with isomeric perfluoro(2-alkyloxolane)s, perfluoro(2-alkyl-5-methyloxolane)s and perfluoro(dialkyl ether)s. The purification of the perfluoro(2-alkyloxane)s which contained small amounts of isomeric perfluoro(2-alkyloxolane)s was successfully achieved by recovering the former unreacted after treating these mixture with anhydrous aluminum chloride at 150 /sR 160 °C during /sR 48 hrs in order to convert the latter into the easy-separable perfluoro(2,5,5- trichloro-2-alkyloxolane)s. Small quantities of new perfluoro(5,5-dichloroalkanoyl chloride)s were also among the chlorination products. The spectroscopic data as well as the physical properties of these new fluorination products, and perfluoro(2,5,5-trichloro-2-alkyloxolane)s and perfluoro(5,5-dichloroalkanoyl chloride)s are presented.