Analysis and parametric optimization of 1H off-resonance relaxation NMR experiments designed to map polypeptide self-recognition and other noncovalent interactions

The measurement of 1H off-resonance nonselective relaxation rates (R(theta,ns)) has been recently proposed as an effective method to probe peptide self-recognition, opening new perspectives in the understanding of the prefibrillization oligomerization processes in amylodogenesis. However, a full analysis and parametric optimization of the NMR experiments designed to measure R(theta,ns) relaxation rates is still missing. Here we analyze the dependence of the R(theta,ns) rates upon three critical parameters: the tilt angle of the effective field during the spin lock, the static magnetic field, and finally the repetition delay. Our analysis reveals that the tilt angle theta = 35.5 degrees not only minimizes spin-diffusion, but also avoids experimental artifacts such as J-transfer and poor adiabaticity. In addition, we found that when the dominant relaxation mechanism is caused by uncorrelated pairwise 1H dipole-1H dipole interactions the R(35.5 degrees,ns) rate is not significantly affected by static field variations, suggesting a wide applicability of the 1H off-resonance nonselective relaxation experiment. Finally, we show that the self-recognition maps based on the comparative analysis of the R(35.5 degrees,ns) rates can tolerate decreases in the interscan delays without significantly compromising the identification of critical self-association loci. These considerations not only provide a better understanding of the 1H off-resonance nonselective relaxation, but they also serve as guidelines for the optimal setup of this experiment.     

Determination of carbon nanotube density by gradient sedimentation

Density gradient centrifugation is a high-resolution technique for the separation and characterization of large molecules and stable complexes. We have analyzed various nanotube structures by preparative centrifugation in sodium metatungstate-water solutions. Bundled, isolated and acid-treated single-walled nanotubes (SWNTs) and multiwall nanotubes (MWNTs) formed sharp bands at well-defined densities. The structure of the material in each band was confirmed by transmission electron microscopy and Raman spectroscopy. Our data suggest respective densities of 1.87, 2.13, 1.74, and 2.1 g/cm(3) for bundled, isolated, and acid-treated SWNTs and MWNTs. These measured results compare well with their calculated densities.     

Ytterbium-doped Y2O3 nanoparticle silica optical fibers for high power fiber lasers with suppressed photodarkening

We report efficient laser demonstration and spectroscopic characteristics of a Yb-doped Y₂O₃ (or Y₃Al₅O₁₂) nanoparticle silica fiber developed by conventional fiber fabrication technique. The spectroscopy study evidences modification in the environment of Yb ions by the Y₂O₃ nanoparticles. As a result, photodarkening induced loss is reduced by 20 times relative to Yb-doped aluminosilicate fibers. The fiber is suitable for power scaling with good laser slope efficiency of 79%.     

Topological Majorana and Dirac zero modes in superconducting vortex cores

We provide an argument based on flux insertion to show that certain superconductors with a nontrivial topological invariant have protected zero modes in their vortex cores. This argument has the flavor of a two-dimensional index theorem and applies to disordered systems as well. It also provides a new way of understanding the zero modes in the vortex cores of a spinless px+ipy superconductor. Applying this approach to superconductors with and without time-reversal and spin-rotational symmetry, we predict the necessary and sufficient conditions for protected zero modes to exist in their vortices.     

Multimodal nonlinear optical polarizing microscopy of long-range molecular order in liquid crystals

We demonstrate orientation-sensitive multimodal nonlinear optical polarizing microscopy capable of probing orientational, polar, and biaxial features of mesomorphic ordering in soft matter. This technique achieves simultaneous imaging in broadband coherent anti-Stokes Raman scattering, multiphoton excitation fluorescence, and multiharmonic generation polarizing microscopy modes and is based on the use of a single femtosecond laser and a photonic crystal fiber as sources of the probing light. We show the viability of this technique for mapping of three-dimensional patterns of molecular orientations and show that images obtained in different microscopy modes are consistent with each other.     

Direct probing of sorbent-solvent interactions for amylose tris(3,5-dimethylphenylcarbamate) using infrared spectroscopy, X-ray diffraction, solid-state NMR, and DFT modeling

The sorbent-solvent interactions for amylose tris(3, 5-dimethylphenylcarbamate) (ADMPC) with five commonly used solvents, hexane, methanol, ethanol, 2-propanol (IPA), and acetonitrile (ACN), are studied using attenuated total reflection infrared spectroscopy (ATR-IR) of thin sorbent films, X-ray diffraction (XRD) of thin films, (13)C cross polarization/magic angle spinning (CP/MAS) and MAS solid state NMR of polymer-coated silica beads (commercially termed "Chiralpak AD"), and DFT modeling. The ADMPC-polymer-coated silica beads are used commercially for analytical and preparative scale separations of chiral enantiomers. The polymer forms helical rods with intra- and inter-rod hydrogen bonds (H-bonds). There are various nm-sized cavities formed between the polymer side-chains and rods. The changes in the H-bonding states of the C=O and NH groups of the polymer upon absorption of each of the five solvents at 25 degrees C are determined with ATR-IR. The IR wavenumbers, the H-bonding interaction energies, and the H-bonding distances of the polymer side-chains with each of the solvent molecules are predicted using the DFT/B3LYP/6-311+g(d,p) level of theory. The changes in the polymer crystallinity upon absorption of each solvent are characterized with XRD. The changes in the polymer crystallinity and the H-bonding states of C=O groups are also probed with (13)C CP/MAS solid-state NMR. The changes in the polymer side-chain mobility are detected using (13)C MAS solid-state NMR. The H-bonding states of the polymer change upon absorption of each polar solvent and usually result in an increase in the polymer crystallinity and the side-chain mobility. The polymer rods are reorganized upon solvent absorption, and the distance between the rods increases with the increase in the solvent molecular size. These results have implications for understanding the role of the solvent in modifying the structure and behavior of the polymer sorbents.     

On the structural properties of small-world networks with range-limited shortcut links

We explore a new variant of Small-World Networks (SWNs), in which an additional parameter (r$r$) sets the length scale over which shortcuts are uniformly distributed. When r=0$r=0$ we have an ordered network, whereas r=1$r=1$ corresponds to the original Watts–Strogatz SWN model. These limited range SWNs have a similar degree distribution and scaling properties as the original SWN model. We observe the small-world phenomenon for r?1$r?1$, indicating that global shortcuts are not necessary for the small-world effect. For limited range SWNs, the average path length changes nonmonotonically with system size, whereas for the original SWN model it increases monotonically. We propose an expression for the average path length for limited range SWNs based on numerical simulations and analytical approximations.     

Size-dependent chemical transformation,structural phase change,and optical properties of nanowires

Nanowires offer a unique approach for the bottom-up assembly of electronic and photonic devices with the potential of integrating photonics with existing technologies. The anisotropic geometry and mesoscopic length scales of nanowires also make them very interesting systems to study a variety of size-dependent phenomenon where finite-size effects become important. We will discuss the intriguing size-dependent properties of nanowire systems with diameters in the 5–300?nm range, where finite-size and interfacial phenomena become more important than quantum mechanical effects. The ability to synthesize and manipulate nanostructures by chemical methods allows tremendous versatility in creating new systems with well-controlled geometries, dimensions, and functionality, which can then be used for understanding novel processes in finite-sized systems and devices.     

Layer thinning transition in an achiral four-ring hockey stick shaped liquid crystal

Depolarized reflected light microscopy and high resolution optical reflectivity measurements have been conducted on free-standing films of an achiral four-ring hockey stick shaped liquid crystal exhibiting SmA-B2–SmX* transition sequence. A layer thinning transition above the bulk isotropic-SmA phase transition has been observed. This behaviour was highly irreproducible, indicating an irregular layer thinning transition. From optical reflectivity data, both thickness of the free-standing films and the smectic interlayer spacing were determined. This is the first report of the layer thinning transition in a hockey stick shaped liquid crystal.     

The complex role of the triphenylmethyl motif in anticancer compounds

Compounds incorporating the triphenylmethyl motif constitute an emerging family of potent anticancer agents. Although several small molecules containing this pharmacophore have now been identified, the mechanism of cell death induction for some of these compounds is unknown. In an effort to define their mechanism of action, and to distinguish subtypes within the group of compounds containing the triphenylmethyl moiety, we have created novel triphenylmethyl-containing small molecules and have evaluated them in a battery of biological assays. Here we show that several phosphonate and phosphonochloridates possessing the triphenylmethyl motif potently induce death of multiple cancer cell lines in culture. Further assays evaluating the ability to cause cell cycle arrest, inhibit tubulin polymerization, dissociate mitochondrial-bound hexokinase in cancer cells, and inhibit calcium-dependent potassium ion channels indicate that triphenylmethyl-containing compounds can be placed into at least four distinct categories, each with a different mechanism of action.