An extinction rule for a class of 1D quasicrystals

We study decorated one-dimensional quasicrystal obtained by a non-standard projection of a part of two-dimensional lattice. We focus on the impact of varying relative positions of decorated sites. First, we give general expression for the structure factor. Subsequently we analyze an example of extinction rule.Comment: 5 pages, 2 figures, LaTex2e, to appear in ICQ9 Proceeding (Philosophical Magazine

Stable single α-Helices are constant force springs in proteins

Single α-helix (SAH) domains are rich in charged residues (Arg, Lys, and Glu) and stable in solution over a wide range of pH and salt concentrations. They are found in many different proteins where they bridge two functional domains. To test the idea that their high stability might enable these proteins to resist unfolding along their length, the properties and unfolding behavior of the predicted SAH domain from myosin-10 were characterized. The expressed and purified SAH domain was highly helical, melted non-cooperatively, and was monomeric as shown by circular dichroism and mass spectrometry as expected for a SAH domain. Single molecule force spectroscopy experiments showed that the SAH domain unfolded at very low forces (<30 pN) without a characteristic unfolding peak. Molecular dynamics simulations showed that the SAH domain unfolds progressively as the length is increased and refolds progressively as the length is reduced. This enables the SAH domain to act as a constant force spring in the mechanically dynamic environment of the cell

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability

Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability. Substituting Lys with Arg (or vice versa) in the naturally-occurring myosin-6 SAH similarly increased (or decreased) its stability. However, Arg-rich de novo sequences (ER3 (AEEERRR) and EK1R2 (AEEEKRR)) aggregated. Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu-Lys. This promiscuous nature of Arg helps explain the increased propensity of de novo Arg-rich SAHs to aggregate. Importantly, the specific K:R ratio is likely to be important in determining helical stability in de novo and naturally-occurring polypeptides, giving new insight into how single α-helices are stabilized

A robust, scanning quantum system for nanoscale sensing and imaging

Controllable atomic-scale quantum systems hold great potential as sensitive tools for nanoscale imaging and metrology. Possible applications range from nanoscale electric and magnetic field sensing to single photon microscopy, quantum information processing, and bioimaging. At the heart of such schemes is the ability to scan and accurately position a robust sensor within a few nanometers of a sample of interest, while preserving the sensor's quantum coherence and readout fidelity. These combined requirements remain a challenge for all existing approaches that rely on direct grafting of individual solid state quantum systems or single molecules onto scanning-probe tips. Here, we demonstrate the fabrication and room temperature operation of a robust and isolated atomic-scale quantum sensor for scanning probe microscopy. Specifically, we employ a high-purity, single-crystalline diamond nanopillar probe containing a single Nitrogen-Vacancy (NV) color center. We illustrate the versatility and performance of our scanning NV sensor by conducting quantitative nanoscale magnetic field imaging and near-field single-photon fluorescence quenching microscopy. In both cases, we obtain imaging resolution in the range of 20 nm and sensitivity unprecedented in scanning quantum probe microscopy

M\"ossbauer, nuclear inelastic scattering and density functional studies on the second metastable state of Na2[Fe(CN)5NO]⋅\cdot2H2O

The structure of the light-induced metastable state SII of Na2[Fe(CN)5NO]$\cdot$2H2O 14 was investigated by transmission M\"ossbauer spectroscopy (TMS) in the temperature range 15 between 85 and 135 K, nuclear inelastic scattering (NIS) at 98 K using synchrotron 16 radiation and density functional theory (DFT) calculations. The DFT and TMS results 17 strongly support the view that the NO group in SII takes a side-on molecular orientation 18 and, further, is dynamically displaced from one eclipsed, via a staggered, to a second 19 eclipsed orientation. The population conditions for generating SII are optimal for 20 measurements by TMS, yet they are modest for accumulating NIS spectra. Optimization 21 of population conditions for NIS measurements is discussed and new NIS experiments on 22 SII are proposed

Dynamics of Metal Centers Monitored by Nuclear Inelastic Scattering

Nuclear inelastic scattering of synchrotron radiation has been used now since 10 years as a tool for vibrational spectroscopy. This method has turned out especially useful in case of large molecules that contain a M\"ossbauer active metal center. Recent applications to iron-sulfur proteins, to iron(II) spin crossover complexes and to tin-DNA complexes are discussed. Special emphasis is given to the combination of nuclear inelastic scattering and density functional calculations

Spectral sensitive phonon wipeout due to a fluctuating spin state in a Fe2+ coordination polymer

Raman scattering in the spin-crossover system [Fe(pmd)(H2O){Au(CN)2}2]*H2O reveals a complex three-phase spin-state transition in contrast to earlier observations in magnetization measurements. We observe different spin state phases as function of temperature and electromagnetic radiation in the visible spectral range. There exists a fluctuating spin state phase with an unexpected wipeout of the low frequency phonon scattering intensity. Furthermore we observe one phase with reduced symmetry that is attributed to a cooperative Jahn-Teller effect. Pronounced electron-phonon interaction manifests itself as a strong Fano-resonance of phonons related to {FeN6} and {FeN4O2} coordination octahedra. Density functional theory supports this interpretation.Comment: 9 pages, 9 figures, 3 table

Crystal structure of bis(triphenylphosphonium) hexabromadigallate(II) in the correct space group: conformational complexity in a heteroethan

Sherpa Romeo green journal. Open access article. Creative Commons Attribution 4.0 License (CC-BY) appliesThe crystal structure of [Ph3PH]2[Ga2Br6], previously described as having a disordered anion in the space group R̄ 3, has been re-determined in the correct space group P̄ 3, where it is fully ordered. Interestingly, two-thirds of the [Ga2Br6]2− dianions have an intermediate conformation with a Br–Ga–Ga–Br torsion angle of 36.91 (1)°, while the remaining is staggered as required from adopting a site with inversion symmetry. In the lattice, [Ph3PH]+ ions lie along the same threefold axes as the dianions and are oriented such that the P–H bond is directed towards a gallium atom. The phosphonium ions lie back-to-back and interact with relatively strong T-interactions between phenyl rings on adjacent cations. DFT calculations at the B3LYP/6–311+G(fd,) level have been used to determine the barriers to rotation in [Ga2X6]2− ions. For X = Cl and X = Br, the barriers are found to be very small, with values of 4.3 and 5.1 kJ mol−1 for the two halogens.Ye

Characterization of long and stable de novo single alpha-helix domains provides novel insight into their stability

Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability. Substituting Lys with Arg (or vice versa) in the naturally-occurring myosin-6 SAH similarly increased (or decreased) its stability. However, Arg-rich de novo sequences (ER3 (AEEERRR) and EK1R2 (AEEEKRR)) aggregated. Combining a PDB analysis with molecular modelling provides a rational explanation, demonstrating that Glu and Arg form salt bridges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu–Lys. This promiscuous nature of Arg helps explain the increased propensity of de novo Arg-rich SAHs to aggregate. Importantly, the specific K:R ratio is likely to be important in determining helical stability in de-novo and naturally-occurring polypeptides, giving new insight into how single α-helices are stabilized