Principal Bundles and the Dixmier Douady Class

A systematic consideration of the problem of the reduction and “lifting” of the structure group of a principal bundle is made and a variety of techniques in each case are explored and related to one another. We apply these to the study of the Dixmier-Douady class in various contexts including string structures, bundles and other examples motivated by considerations from quantum field theory. Received: 26 February 1997 / Accepted: 5 August 1997     

New faster CHARMM molecular dynamics engine

We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores. © 2013 Wiley Periodicals, Inc.     

The implementation of a fast and accurate QM/MM potential method in Amber

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.     

Sulfate migration in oligosaccharides induced by negative ion mode ion trap collision‐induced dissociation

Migration of sulfate groups between hydroxyl groups was identified after collision‐induced dissociation (CID) of sulfated oligosaccharides in an ion trap mass spectrometer in negative ion mode. Analysis of various sulfated oligosaccharides showed that this was a common phenomenon and was particularly prominent in sulfated oligosaccharides also containing sialic acid. It was also shown that the level of migration was increased when the sulfate was positioned on the flexible areas of the oligosaccharides not involved in the pyranose ring, such as the extra‐cyclic C‐6 carbon of hexoses or N‐acetylhexosamines, or on reduced oligosaccharide. This suggested that migration is dependent on the spatial availability of the sulfate in the ion trap during collision. It is proposed that the migration is initiated when the negatively charged ‐SO₃^– residue attached to the oligosaccharide precursor becomes protonated by a CID‐induced proton transfer. This is supported by the CID fragmentation of precursor ions depleted of acidic protons such as doubly charged [M – 2H]^2– ions or the sodiated [M + Na – 2H]^– ions of oligosaccharides containing one sulfate and one sialic acid in the same molecule. Compared to the CID fragmentation of their monocharged [M – H]^– ions, no migration was observed in CID of proton depleted precursors. Alternative fragmentation parameters to suppress migration of sulfated oligosaccharides also showed that it was not present when sulfated oligosaccharides were fragmented by HCD (High‐Energy C‐trap Dissociation) in an Orbitrap mass spectrometer. Copyright © 2011 John Wiley & Sons, Ltd.     

The reaction of IO with CH3SCH3: products and temperature dependent rate coefficients by laser induced fluorescence

The technique of pulsed laser photolysis was coupled to laser induced fluorescence detection of iodine oxide (IO) to measure rate coefficients, k(1)(T), for the title reaction IO + CH3SCH3 --> products (R1). A value of k1(298 K) = (1.44 +/- 0.15) x 10(-14) cm3 molecule(-1) s(-1) was obtained, independent of bath gas pressure (50 < P((N2 or air))/Torr < 300). The expression k1(T) = (3.2 +/- 1.4)x 10(-13)exp[(-925 +/- 136)/T)] adequately described the data over the range of temperatures (256 < T/K < 341) covered. Uncertainties (2sigma) in the 298 K rate coefficient and the pre-exponential factor include an estimate of systematic error. The conventional Arrhenius behaviour of k1(T) and the lack of pressure dependence are suggestive of an abstraction mechanism, characterised by an energy barrier of E approximately 8 kJ mol(-1). The product yield for production of I-atoms was determined indirectly to be close to unity, indicating that the reaction proceeds via transfer of the O-atom from IO to CH3SCH3 to form CH3S(O)CH3. In general, the values of k1(T) measured in this work indicate that has little impact on the chemistry of the atmosphere.     

Determination of the adsorption isotherm of methanol on the surface of ice. An experimental and grand canonical Monte Carlo simulation study

The adsorption isotherm of methanol on ice at 200 K has been determined both experimentally and by using the Grand Canonical Monte Carlo computer simulation method. The experimental and simulated isotherms agree well with each other; their deviations can be explained by a small (about 5 K) temperature shift in the simulation data and, possibly, by the non-ideality of the ice surface in the experimental situation. The analysis of the results has revealed that the saturated adsorption layer is monomolecular. At low surface coverage, the adsorption is driven by the methanol-ice interaction; however, at full coverage, methanol-methanol interactions become equally important. Under these conditions, about half of the adsorbed methanol molecules have one hydrogen-bonded water neighbor, and the other half have two hydrogen-bonded water neighbors. The vast majority of the methanols have a hydrogen-bonded methanol neighbor, as well.     

Absorption cross section and photolysis of OIO

Pulsed laser photolysis combined with transient absorption spectroscopy and resonance fluorescence was used to examine the photolysis of OIO at a number of wavelengths corresponding to absorption bands in its visible spectrum between approximately 530 and 570 nm. Photolysis at 532 nm was found to result in substantial depopulation of the absorbing ground state, enabling an estimate for the absorption cross section of OIO at 610.2 nm of (6 +/- 2) x 10(-18) cm2 molecule(-1) to be obtained. No evidence was found for I atom formation following photolysis of OIO at 532, 562.3, 567.9 and 573.8 nm, enabling an upper limit to the I atom quantum yield of < 0.05 (560-580 nm) and < 0.24 (532 nm) to be established.     

Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose Iβ

The Family 7 cellobiohydrolase (Cel7A) from Trichoderma reesei consists of a carbohydrate-binding module (CBM) joined by a linker to a catalytic domain. Cellulose hydrolysis is limited by the accessibility of Cel7A to crystalline substrates, which is perceived to be primarily mediated by the CBM. Here, the binding of CBM to the cellulose Iβ fiber is characterized by combined Brownian dynamics (BD) and molecular dynamics (MD) simulations. The results confirm that CBM prefers to dock to the hydrophobic than to the hydrophilic fiber faces. Both electrostatic (ES) and van der Waals (VDW) interactions are required for achieving the observed binding preference. The VDW interactions play a more important role in stabilizing the CBM-fiber binding, whereas the ES interactions contribute through the formation of a number of hydrogen bonds between the CBM and the fiber. At long distances, an ES steering effect is also observed that tends to align the CBM in an antiparallel manner relative to the fiber axis. Furthermore, the MD results reveal hindered diffusion of the CBM on all fiber surfaces. The binding of the CBM to the hydrophobic surfaces is found to involve partial dewetting at the CBM-fiber interface coupled with local structural arrangements of the protein. The present simulation results complement and rationalize a large body of previous work and provide detailed insights into the mechanism of the CBM-cellulose fiber interactions.