Bulk and single-molecule characterization of an improved molecular beacon utilizing H-dimer excitonic behavior

Pairs of fluorophores in close proximity often show self-quenching of fluorescence by the well-known H-dimer mechanism. We use a pair of fluorophores in the new dicyanomethylenedihydrofuran (DCDHF) dye family in the design and characterization of a new fluorescent probe for nucleic acid detection, which we refer to as a self-quenched intramolecular dimer (SQuID) molecular beacon (MB). We obtain a quenching efficiency of 97.2%, higher than the only other reported value for a MB employing fluorophore self-quenching by H-dimer formation. Furthermore, the excellent single-molecule (SM) emitter characteristics of the DCDHF dyes allow observation of individual SQuID MB-target complexes immobilized on a surface, where the doubled SM emission intensity of our target-bound beacon ensures a higher signal-to-background ratio than conventional fluorophore-quencher MBs. Additional advantages of the SQuID MB are single-pot labeling, visible colorimetric detection of the target, and intrinsic single-molecule two-step photobleaching behavior, which offers a specific means of discriminating between functional MBs and spurious fluorescence.     

Silicon radicals in silicon oxynitride: a theoretical ESR study

Quantum mechanical calculations are performed on a series of silicon radical defects. These are the upward arrow Si[triple bond]O(3-x)Nx, upward arrow Si[triple bond]N(3-x)Si(x), and upward arrow Si[triple bond]Si(3-x)Ox defects, where x takes on values between 0 and 3. The defects under study constitute a central silicon radical, upward arrow Si, with differing first-nearest-neighbor substitution, as may be found at a Si/SiOxNy interface. These first-nearest neighbor atoms are connected to the silicon radical via three single covalent bonds, denoted as " [triple bond] ". A hybrid defect, upward arrow Si[triple bond]ONSi, is also included. Calculations are performed on gas-phase-like cluster models, as well as more-constrained hybrid quantum and molecular mechanical (QM/MM) models. The isotropic hyperfine coupling constants of these defects are calculated via density functional theory (DFT). Trends in these calculated hyperfines are consistent between the different models utilized. Analysis of the electronic structure and geometries of defects correlate well with trends in the electronegativity of the first-nearest-neighbor atoms. Changes in radical hybridization, induced by changes in the first-nearest-neighbor composition, are the primary factor that affects the calculated hyperfines. Furthermore, comparisons to experimental results are encouraging. Agreement is found between experiments on amorphous to crystalline materials.     

Structural characterization of epitaxial Cr(x)Mo(1-x) alloy thin films

To develop a model system containing regularly spaced misfit dislocations for studies of the radiation resistance of nanoscale defects, epitaxial thin films of Cr, Mo, and Cr(x)Mo(1-x) alloys were deposited on MgO(001) by molecular beam epitaxy. Film compositions were chosen to vary the lattice mismatch with MgO. The film structure was investigated by x-ray diffraction (XRD), Rutherford backscattering spectrometry (RBS) and scanning transmission electron microscopy (STEM). Epitaxial films with reasonably high crystalline quality and abrupt interfaces were achieved at a relatively low deposition temperature, as confirmed by STEM. However, it was found by XRD and RBS in the channeling geometry that increasing the Mo content of the CrMo alloy films degraded the crystalline quality, despite the improved lattice match with MgO. XRD rocking curve data indicated that regions of different crystalline order may be present within the films with higher Mo content. This is tentatively ascribed to spinodal decomposition into Cr-rich and Mo-rich regions, as predicted by the Cr(x)Mo(1-x) phase diagram.     

Sparse direct factorizations through unassembled hyper-matrices

We set out to efficiently compute the solution of a sequence of linear systems A_ix_i = b_i, where the matrix A_i is tightly related to matrix A_{i –1}. In the setting of an hp -adaptive Finite Element Method, the sequence of matrices A_i results from successive local refinements of the problem domain. At any step i > 1, a factorization already exists and it is the updated linear system relative to the refined mesh for which a factorization must be computed in the least amount of time. This observation holds the promise of a tremendous reduction in the cost of an individual refinement step. We argue that traditional matrix storage schemes, whether dense or sparse, are a bottleneck, limiting the potential efficiency of the solvers. We propose a new hierarchical data structure, the Unassembled Hyper-Matrix (UHM), which allows the matrix to be stored as a tree of unassembled element matrices, hierarchically ordered to mirror the refinement history of the physical domain. The factorization of such an UHM proceeds in terms of element matrices, only assembling nodes when they need to be eliminated. Efficiency comes in terms of both performance and space requirements. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Surfactin-like structures of five cyclic depsipeptides from the marine isolate ofBacillus pumilus

Five cyclic depsipeptides with molecular masses of 1007, 1021, 1021, 1035, and 1035 were obtained fromBacillus pumilus KMM 150 associated with Australian marine spongeIrcinia sp. Their structures were assigned by mass spectrometric techniques (high-resolution fast atom bombardment and electron impact mass spectrometry), chemical modification, and extensive spectroscopic analysis, including several types of two-dimensional NMR.Deceased.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 979–983, May, 1995.The authors are grateful to Dr. V. V. Mikhailov, the Head of the Laboratory of marine microbiology of PIBC of the Far-Eastern Branch of the RAS, and to Dr. E. P. Ivanova for isolation, systematic determination, and cultivation of the strain KMM 150. The authors are also thankful to T. I. Zykova for carrying out the fermentative hydrolysis of peptide4c.