Smart Geodesic Tracing in GRworkbench

We have developed a new tool for numerical work in General Relativity: GRworkbench. We discuss how GRworkbench's implementation of a numerically-amenable analogue to Differential Geometry facilitates the development of robust and chart-independent numerical algorithms. We consider, as an example, geodesic tracing on two charts covering the exterior Schwarzschild space-time.     

Bengazoles C-G from the Sponge Jaspis sp. Synthesis of the Side Chain and Determination of Absolute Configuration

Five new antifungal bengazoles (C-G) were isolated and fully characterized from a marine sponge of the genus Jaspis sp. Bengazoles C-G, together with the known bengazoles A and B, comprise a homologous series of n, iso, and anteiso fatty acid esters (C(13)-C(16)) of the same heterocyclic bis(oxazolyl)methanol parent. The complete relative and absolute configurations of the bengazoles were determined by application of the modified Mosher method and interpretation of exciton coupling in the CD spectra of the tetra-p-bromobenzoate derivatives of bengazole A and that of a model tetrol synthesized in seven steps from L-fucose.     

PICOSECOND LASER SPECTROSCOPY AND OPTICALLY DETECTED MAGNETIC RESONANCE ON A MODEL PHOTOSYNTHETIC SYSTEM

Fluorescence-detected magnetic resonance of triplets in zero magnetic field (FDMR), fluorescence fading (FF) due to triplet-formation, both at 4.2 K, and prompt fluorescence decay kinetics (FDK) at room temperature have been measured for free pheophorbide- a (f-Pheo) and bound (b-Pheo) to a synthetic polypeptide (L-L ys -L-A la -L-A la )_n, dissolved in dimethylformamide (DMF). Fluorescence decay kinetics measurements of f-Pheo in DMF yielded 1-5 ns lifetimes, for b-Pheo in DMF a ~ 50 ps decay-component was found emitting at 730–750 nm. Zero-field splitting parameters |D| and |E| of the lowest triplet state T₁ were determined from FDMR spectra as (337 and 24) 10^-4 cm^-1 for f-Pheo and (359 and 25) 10^-4 cm^-1 for b-Pheo, both in DMF. Decay rate constants of the three spin levels of T¹ of b-Pheo ( K _x= 1200 50 s^-1, k _y= 440 25 s^-1, k _z= 80 5 s^-1) and relative steady-state populations (N_x= 28 2%, N_y= 47 2%, N_z= 26 2%) determined from FF curves predict a fluorescence decrease at the D–E and D + E FDMR transitions, whereas experimentally a fluorescence increase is observed. The FDMR sign-inversion results from singlet-singlet energy transfer from b-Pheo monomers to their aggregates, followed by fast intersystem crossing to T₁. These results indicate that aggregates are formed by two or more b-Pheo molecules at different positions on the folded polypeptide chain. This situation resembles that in chlorophyll-proteins, containing low-lying traps, resulting from interaction of chromophores with other chromophores and with the protein environment.     

An efficient solution for resolving iTRAQ and TMT channel cross‐talk

Isobaric tagging reagents such as isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tag (TMT) typically have isotopic impurities that cause significant cross‐talk between channels. Here, we present an efficient solution to compensate for channel cross‐talk using linear algebra and find that it is between 20× and 120× faster than previous methods. We also find that the effects of channel cross‐talk are as important to manage as the effects of ratio compression because of precursor impurities, and we have released an open‐source tool to perform both types of calculations.     

The Hopf conjecture for manifolds with low cohomogeneity or high symmetry rank

We prove that the Euler characteristic of an even-dimensional compact manifold with positive (nonnegative) sectional curvature is positive (nonnegative) provided that the manifold admits an isometric action of a compact Lie group with principal isotropy group and cohomogeneity such that . Moreover, we prove that the Euler characteristic of a compact Riemannian manifold or with positive sectional curvature is positive if admits an effective isometric action of a torus , i.e., if the symmetry rank of is .

     

Cooperativity in drug-DNA recognition: a molecular dynamics study.

NMR studies have shown that the minor groove-binding ligand Hoechst 33258 binds to the two T4/A4 tracts within the duplex d(CTTTTCGAAAAG)2 in a highly cooperative manner, such that in titration experiments no intermediate 1:1 complex can be detected. The NMR-derived structures of the free DNA and the 2:1 complex have been obtained, but can shed little light on what the origins of this cooperativity may be. Here we present the results of a series of molecular dynamics simulations on the free DNA, the 1:1 complex, and the 2:1 complex, which have been designed to enable us to calculate thermodynamic parameters associated with the molecular recognition events. The results of the molecular dynamics studies confirm that structural factors alone cannot explain the cooperativity observed, indeed when enthalpic and hydration factors are looked at in isolation, the recognition process is predicted to be slightly anticooperative. However, when changes in configurational entropy are taken into account as well, the overall free energy differences are such that the calculated cooperativity is in good agreement with that observed experimentally. The results indicate the power of molecular dynamics methods to provide reasonable explanations for phenomena that are difficult to explain on the basis of static models alone, and provide a nice example of the concept of "allostery without conformational change".