Preserving energy resp. dissipation in numerical PDEs using the “Average Vector Field” method

We give a systematic method for discretizing Hamiltonian partial differential equations (PDEs) with constant symplectic structure, while preserving their energy exactly. The same method, applied to PDEs with constant dissipative structure, also preserves the correct monotonic decrease of energy. The method is illustrated by many examples. In the Hamiltonian case these include: the sine–Gordon, Korteweg–de Vries, nonlinear Schrödinger, (linear) time-dependent Schrödinger, and Maxwell equations. In the dissipative case the examples are: the Allen–Cahn, Cahn–Hilliard, Ginzburg–Landau, and heat equations.     

High‐Throughput Bioassays using “Dip‐and‐Go” Multiplexed Electrospray Mass Spectrometry

A multiplexed system based on inductive nanoelectrospray mass spectrometry (nESI‐MS) has been developed for high‐throughput screening (HTS) bioassays. This system combines inductive nESI and field amplification micro‐electrophoresis to achieve a “dip‐and‐go” sample loading and purification strategy that enables nESI‐MS based HTS assays in 96‐well microtiter plates. The combination of inductive nESI and micro‐electrophoresis makes it possible to perform efficient in situ separations and clean‐up of biological samples. The sensitivity of the system is such that quantitative analysis of peptides from 1–10 000 nm can be performed in a biological matrix. A prototype of the automation system has been developed to handle 12 samples (one row of a microtiter plate) at a time. The sample loading and electrophoretic clean‐up of biosamples can be done in parallel within 20 s followed by MS analysis at a rate of 1.3 to 3.5 s per sample. The system was used successfully for the quantitative analysis of BACE1‐catalyzed peptide hydrolysis, a prototypical HTS assay of relevance to drug discovery. IC₅₀ values for this system were in agreement with LC‐MS but recorded in times more than an order of magnitude shorter.     

Photochemistry of formic acid monomer at 222 nm

The yields of CO₂ and CO formed from the gas-phase photolysis at 222 nm of very low pressures of formic acid where the monomer predominates have been determined using FTIR spectroscopy. The observed ratio of CO₂/CO approaches unity as the formic acid pressure approaches zero. Previous studies have shown that the quantum yield for HCOOH + hv → OH + HCO (or H + CO) is 0.70 at 298 K. The present experimental results indicate that the ratio of the quantum yields of the possible molecular photolysis channels forming H₂ + CO₂ (?_1b) and H₂O + CO (?_1c) is ca. 1. Including this result in an analysis of previously reported quantum yields of CO and CO₂ determined at higher pressures of formic acid, where both monomer and dimer contribute significantly to the products, indicates that ?_1b = ?_1c = 0. © 1994 John Wiley & Sons, Inc.     

MECHANISM OF ENZYME INACTIVATION BY ULTRAVIOLET LIGHT AND THE PHOTOCHEMISTRY OF AMINO ACIDS (AT 2537 Å)*

Abstract— >The inactivation of the enzymes chymotrypsin, lysozyme, ribonuclease, and trypsin by ultraviolet light can be accounted for quantitatively by summing the products of (1) the probability that light is absorbed by a given amino acid residue, the molecular extinc tion coefficient, and (2) the probability that absorbed light induces a chemical change in the residue, the quantum yield for the residue. The principal residues involved are cystyl and tryptophanyl. Peptide bond rupture is not important. Energy transfer among chromophores within molecules of enzymes need not be invoked in order to account for photochemical inactivation.
Quantum yields for the destruction of a number of amino acids at 2537 A have been measured.     

Photochemistry of tobacco mosaic virus RNA. Effect of HCN

Abstract— In attempting to sort out possible mechanisms of photoreactivation of tobacco mosaic virus RNA (TMV-RNA) inactivated by ultraviolet radiation (u.v.) in buffer of ionic strength 0.25, we have investigated the effect of HCN on the quantum yield for u.v. inactivation of TMV-RNA and on the percent photoreactivation of inactivated TMV-RNA. Some photo-products produced by irradiation of model substances, polyuridylic acid (poly U) and polycytidylic acid (poly C), in the presence of HCN have also been studied. The ratio of the quantum yield for inactivation of TMV-RNA in the presence of HCN to that in the absence of HCN is 1.5, under non-photoreactivating conditions. By comparison, the ratio of the initial rates of loss of uracil residues in poly U under comparable conditions is 1.6; by contrast, the rate of loss of cytosine residues in poly C is unaffected by HCN. This similarity of ratios between poly U and TMV-RNA suggests that two of the mechanisms of u.v. inactivation of TMV-RNA at high ionic strength are akin to known reactions of uracil residues in poly U, i.e. hydrate and dimer formation. The photohydration reaction in poly U, as measured by the heat reversal of hydrated residues to uracil residues, is almost abolished by HCN, and the rate of dimerization, as measured by the appearance of dimer containing oligonucleotides following enzymatic hydrolysis of irradiated poly U, is reduced to half by HCN. HCN does not affect the rate of hydration of cytosine residues in poly C. Since photoreactivation of RNA inactivated in presence of HCN is only 60 per cent of that in absence of HCN it is suggested that uracil dimers are somehow involved in photoreactivation of TMV-RNA inactivated at high ionic strength.     

Kinetics of base hydrolysis of [Co(tetren)dmf]3+ and [Co(tetren)-dmso]3+ (tetren=1,11-diamino-3,6,9-triazaundecane)

The complexes [Co(tetren)dmf](ClO4)3 and [Co(tetren)-dmso](ClO4)3 have been prepared from alpha alpha-[Co(tetren)-Cl](ClO4)Cl (tetren=1,11-diamino-3,6,9-triazaundecane). 1H-n.m.r. and i.r. measurements confirm that the complexes contain O-bonded dmf and dmso. A biphasic reaction is observed in the base hydrolysis of the dmf derivative, monitored by the pH-stat method, with the fast reaction having kOH=1.2*104dm3mol-1s-1 and the slower reaction kOH=1.9*102dm3mol-1s-1 at 25degC and I=0.1moldm3. The fast reaction is assigned to the hydrolysis of the alpha beta(R)-[Co(tetren)dmf]3+ and the slower reaction to that of the alpha The reaction appears to proceed predominantly by a DCB pathway without parallel hydrolysis of coordinated dmf, which has been observed in the hydrolysis of [Co-(NH3)5dmf]3+. Base hydrolysis of [Co(tetren)dmso]3+ was monitored spectrophotometrically over the pH range 4.2 to 5.0. A single reaction was observed with kOH=1.9*106dm3mol-1 s-1 at 25°C and I=0.1 moldm-3. The rapid base hydrolysis is attributed to hydrolysis of the alpha beta(R)- or the alpha beta(S)-[Co(tetren)-dmso]3+ isomer rather than the alpha alpha-isomer. This revised version was published online in June 2006 with corrections to the Cover Date.     

Devices and architectures for photonic chip-scale integration

Silicon nanophotonics holds the promise of dramatically advancing the state of the art in computing by enabling parallel architectures that combine unprecedented performance and ease of use with affordable power consumption. This paper presents a design study for a many-core architecture called Corona which utilizes dense wavelength division multiplexing (DWDM) for on- and off-chip communication together with the devices which will be needed to implement such a communication infrastructure.