Spectral properties of molecular oligomers. A non-Markovian quantum state diffusion approach

Absorption spectra of small molecular aggregates (oligomers) are considered. The dipole-dipole interaction between the monomers leads to shifts of the oligomer spectra with respect to the monomer absorption. The line-shapes of monomer as well as oligomer absorption depend strongly on the coupling to vibrational modes. Using a recently developed approach [Roden et. al, PRL 103, 058301] we investigate the length dependence of spectra of one-dimensional aggregates for various values of the interaction strength between the monomers. It is demonstrated, that the present approach is well suited to describe the occurrence of the J- and H-bands

Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.

HIV/SIV Nef mediates many cellular processes through interactions with various cytoplasmic and membrane-associated host proteins, including the signalling zeta subunit of the T-cell receptor (TCRzeta). Here, the crystallization strategy, methods and refinement procedures used to solve the structures of the core domain of the SIVmac239 isolate of Nef (Nef(core)) in complex with two different TCRzeta fragments are described. The structure of SIVmac239 Nef(core) bound to the longer TCRzeta polypeptide (Leu51-Asp93) was determined to 3.7 A resolution (R(work) = 28.7%) in the tetragonal space group P4(3)2(1)2. The structure of SIVmac239 Nef(core) in complex with the shorter TCRzeta polypeptide (Ala63-Arg80) was determined to 2.05 A resolution (R(work) = 17.0%), but only after the detection of nearly perfect pseudo-merohedral crystal twinning and proper assignment of the orthorhombic space group P2(1)2(1)2(1). The reduction in crystal space-group symmetry induced by the truncated TCRzeta polypeptide appears to be caused by the rearrangement of crystal-contact hydrogen-bonding networks and the substitution of crystallographic symmetry operations by similar noncrystallographic symmetry (NCS) operations. The combination of NCS rotations that were nearly parallel to the twin operation (k, h, -l) and a and b unit-cell parameters that were nearly identical predisposed the P2(1)2(1)2(1) crystal form to pseudo-merohedral twinning

Automatic structures, rational growth and geometrically finite hyperbolic groups

We show that the set $SA(G)$ of equivalence classes of synchronously automatic structures on a geometrically finite hyperbolic group $G$ is dense in the product of the sets $SA(P)$ over all maximal parabolic subgroups $P$. The set $BSA(G)$ of equivalence classes of biautomatic structures on $G$ is isomorphic to the product of the sets $BSA(P)$ over the cusps (conjugacy classes of maximal parabolic subgroups) of $G$. Each maximal parabolic $P$ is a virtually abelian group, so $SA(P)$ and $BSA(P)$ were computed in ``Equivalent automatic structures and their boundaries'' by M.Shapiro and W.Neumann, Intern. J. of Alg. Comp. 2 (1992) We show that any geometrically finite hyperbolic group has a generating set for which the full language of geodesics for $G$ is regular. Moreover, the growth function of $G$ with respect to this generating set is rational. We also determine which automatic structures on such a group are equivalent to geodesic ones. Not all are, though all biautomatic structures are.Comment: Plain Tex, 26 pages, no figure

Graphical augmentations to the funnel plot assess the impact of additional evidence on a meta-analysis

AbstractObjectiveWe aim to illustrate the potential impact of a new study on a meta-analysis, which gives an indication of the robustness of the meta-analysis.Study Design and SettingA number of augmentations are proposed to one of the most widely used of graphical displays, the funnel plot. Namely, 1) statistical significance contours, which define regions of the funnel plot in which a new study would have to be located to change the statistical significance of the meta-analysis; and 2) heterogeneity contours, which show how a new study would affect the extent of heterogeneity in a given meta-analysis. Several other features are also described, and the use of multiple features simultaneously is considered.ResultsThe statistical significance contours suggest that one additional study, no matter how large, may have a very limited impact on the statistical significance of a meta-analysis. The heterogeneity contours illustrate that one outlying study can increase the level of heterogeneity dramatically.ConclusionThe additional features of the funnel plot have applications including 1) informing sample size calculations for the design of future studies eligible for inclusion in the meta-analysis; and 2) informing the updating prioritization of a portfolio of meta-analyses such as those prepared by the Cochrane Collaboration

Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology

Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer‐scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self‐assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site‐specific (spatially addressable) DNA ‘staples’. This revolutionary approach has led to the creation of a multitude of two‐dimensional and three‐dimensional scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. WIREs Nanomed Nanobiotechnol 2012, 4:139–152. doi: 10.1002/wnan.170 For further resources related to this article, please visit the WIREs website .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/90282/1/170_ftp.pd

Ru–Ag and Ru–Au dicarbene complexes from an abnormal carbene ruthenium system

The first complexes containing an anionic dicarbene connected to two different d-block elements are reported. The synthetic pathway entails metalation and transmetalation reactions, starting from a cationic abnormal Ru-NHC complex

Phytometric intelligence sensors

Methods and apparatus for determining when plants require watering, and methods of attending to the watering of plants including signaling the grower that the plants are in need of hydration are provided. The novel methods include real-time measurement of plant metabolics and phytometric physiology changes of intrinsic physical or behavioral traits within the plant such as determining physiological flux measurement of enzyme flux due to environmental changes such as the wind and drought stress, soil and plant mineral deficiencies, or the interaction with a bio-control for organic disease control including, cell movement, signal transduction, internal chemical processes and external environmental processes including when plants require watering, and methods of attending to the watering of plants including signaling the grower that the plants are in need of hydration

Two center multipole expansion method: application to macromolecular systems

We propose a new theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well known fast multipole method. Its efficiency, accuracy and applicability to macromolecular systems is analyzed and discussed in detail.Comment: 23 pages, 7 figures, 1 tabl

Prediction of leaf:stem ratio in grasses using near infrared reflectance spectroscopy

Leaf:stem ratio of grass stands is an important factor affecting diet selection, quality, and forage intake. Estimates of leaf:stem ratios commonly are based on a labor intensive process of hand separating leaf and stem fractions. Near infrared reflectance spectroscopy (NIRS) has been used successfully to predict forage quality and botanical composition of vegetation samples. The objective of this study was to evaluate the use of NIRS to predict leaf:stem ratios in big bluestem (Andropogon gerardii Vitman), switchgrass (Punicum virgatum L.), and smooth bromegrass (Bromus inermis Leyss.). A total of 72 hand-clipped samples of each species was taken from seeded monocultures in eastern Nebraska throughout the 1992,1993, and 1994 growing seasons. Leaf:stem ratio was determined first for each sample and then the entire sample was ground. Samples were scanned by a Perstorp model 6500 near infrared scanning monochromator. Three calibration equations were developed based on using 18, 36, and 54 (l/4, l/2, and 3/4 of total samples, respectively) samples. These 3 calibration equations were used to determine the number of samples necessary to achieve an r2 of 0.70 or higher for each data set. Big bluestem and switchgrass had coefficients of determination (r2) of ≤ 0.69 for all calibration equations except for the equation using only 18 samples of big bluestem r2 = 0.60). Smooth bromegrass had a r2 ranging from only 0.06 to 0.14 for the calibration equations regardless of the number of samples used. Near infrared reflectance spectroscopy was a rapid means of estimating leaf:stem ratios in monocultures of big bluestem and switchgrass but it was not suitable for smooth bromegrass