Nanostructure and mechanics of mummified type I collagen from the 5300-year-old Tyrolean Iceman

Skin protects the body from pathogens and degradation. Mummified skin in particular is extremely resistant to decomposition. External influences or the action of micro-organisms, however, can degrade the connective tissue and lay the subjacent tissue open. To determine the degree of tissue preservation in mummified human skin and, in particular, the reason for its durability, we investigated the structural integrity of its main protein, type I collagen. We extracted samples from the Neolithic glacier mummy known as ‘the Iceman’. Atomic force microscopy (AFM) revealed collagen fibrils that had characteristic banding patterns of 69 ± 5 nm periodicity. Both the microstructure and the ultrastructure of dermal collagen bundles and fibrils were largely unaltered and extremely well preserved by the natural conservation process. Raman spectra of the ancient collagen indicated that there were no significant modifications in the molecular structure. However, AFM nanoindentation measurements showed slight changes in the mechanical behaviour of the fibrils. Young's modulus of single mummified fibrils was 4.1 ± 1.1 GPa, whereas the elasticity of recent collagen averages 3.2 ± 1.0 GPa. The excellent preservation of the collagen indicates that dehydration owing to freeze-drying of the collagen is the main process in mummification and that the influence of the degradation processes can be addressed, even after 5300 years

LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)

Background: Leucine-rich repeats (LRRs) are present in more than 6000 proteins. They are found in organisms ranging from viruses to eukaryotes and play an important role in protein-ligand interactions. To date, more than one hundred crystal structures of LRR containing proteins have been determined. This knowledge has increased our ability to use the crystal structures as templates to model LRR proteins with unknown structures. Since the individual three-dimensional LRR structures are not directly available from the established databases and since there are only a few detailed annotations for them, a conformational LRR database useful for homology modeling of LRR proteins is desirable. Description: We developed LRRML, a conformational database and an extensible markup language (XML) description of LRRs. The release 0.2 contains 1261 individual LRR structures, which were identified from 112 PDB structures and annotated manually. An XML structure was defined to exchange and store the LRRs. LRRML provides a source for homology modeling and structural analysis of LRR proteins. In order to demonstrate the capabilities of the database we modeled the mouse Toll-like receptor 3 (TLR3) by multiple templates homology modeling and compared the result with the crystal structure. Conclusion: LRRML is an information source for investigators involved in both theoretical and applied research on LRR proteins. It is available at http://zeus.krist.geo.uni-muenchen.de/similar to lrrml

Initial coupling and reaction progression of directly deposited biradical graphene nanoribbon monomers on iodine-passivated versus pristine Ag(111)

The development of widely applicable methods for the synthesis of C-C-bonded nanostructures on inert and insulating surfaces is a challenging yet rewarding milestone in the field of on-surface synthesis. This would enable studies of nearly unperturbed covalent nanostructures with unique electronic properties as graphene nanoribbons (GNR) and π-conjugated 2D polymers. The prevalent Ullmann-type couplings are almost exclusively carried out on metal surfaces to lower the temperature required for initial dehalogenation well below the desorption threshold. To overcome the necessity for the activation of monomers on the target surface, we employ a recently developed Radical Deposition Source (RaDeS) for the direct deposition of radicals onto inert surfaces for subsequent coupling by addition reactions. The radicals are generated en route by indirect deposition of halogenated precursors through a heated reactive tube, where the dehalogenation reaction proceeds. Here, we use the ditopic 6,11-diiodo-1,2,3,4-tetraphenyltriphenylene (DITTP) precursor that afforded chevron-like GNR on Au(111) via the usual two-staged reaction comprised of monomer-coupling into covalent polymers and subsequent formation of an extended GNR by intramolecular cyclodehydrogenation (CDH). As a model system for inert surfaces, we use Ag(111) passivated with a closed monolayer of chemisorbed iodine that behaves in an inert manner with respect to dehalogenation reactions and facilitates the progressive coupling of radicals into extended covalent structures. We deposit the DITTP-derived biradicals onto both iodine-passivated and pristine Ag(111) surfaces. While on the passivated surface, we directly observe the formation of covalent polymers, on pristine Ag(111) organometallic intermediates emerge instead. This has decisive consequences for the further progression of the reaction: heating the organometallic chain directly on Ag(111) results in complete desorption, whereas the covalent polymer on iodine-passivated Ag(111) can be transformed into the GNR. Yet, the respective CDH proceeds directly on Ag(111) after thermal desorption of the iodine passivation. Accordingly, future work is aimed at the further development of approaches for the complete synthesis of GNR on inert surfaces

Competitive metal‐coordination of hexaaminotriphenylene on Cu(111) by intrinsic copper versus extrinsic nickel adatoms

The interplay between self‐assembly and surface chemistry of 2,3,6,7,10,11‐hexaminotriphenylene (HATP) on Cu(111) was complementarily studied by high‐resolution Scanning‐Tunneling‐Microscopy (STM) and X‐ray Photoelectron Spectroscopy (XPS) under ultra‐high vacuum conditions. To shed light on competitive metal‐coordination, comparative experiments were carried out on pristine and nickel‐covered Cu(111). Directly after room temperature deposition of HATP onto pristine Cu(111) self‐assembled aggregates were observed by STM, while XPS indicated non‐deprotonated amino groups. Annealing up to 200 °C activated the progressive single deprotonation of all amino groups as indicated by chemical shifts of both N 1s and C 1s core levels in the XP spectra. This enabled the formation of topologically versatile π‐d conjugated coordination networks with intrinsic copper adatoms. The basic motif of these networks was a metal‐organic trimer, where three HATP molecules were coordinated by Cu3 clusters, as corroborated by accompanying Density Functional Theory (DFT) simulations. Additional deposition of more reactive nickel atoms resulted in both chemical and structural changes with deprotonation and formation of bis(diimino)‐Ni bonded networks already at room temperature. Even though fused hexagonal pores were observed, extended honeycomb networks remained elusive, as tentatively explained by a restricted reversibility of these metal‐organic bonds

Transmission-dominated mid-infrared supermirrors with finesse exceeding 200 000

We fabricate and characterize substrate-transferred single-crystal mirror coatings with 9.33 $\pm$ 0.17 ppm of transmittance and 4.27 $\pm$ 0.52 ppm of excess optical loss, corresponding to a transmission-loss dominated reflectance of 99.9986% at 4.45 $\mu$m. For the first time, a cavity finesse > 200 000 is achieved in the mid-infrared.Comment: Sept 21: Minor revisions to conform to 2-page length requirement including abbr. refs.; Figure font sizes increase

Simultaneously-Measured Mid-Infrared Refractive Indices of GaAs/AlGaAs

We present our results for a simultaneous measurement of the refractive indices of Gallium Arsenide (GaAs) and Aluminum Gallium Arsenide (Al$_\mathrm{x}$Ga$_\mathrm{1-x}$As) in the spectral region from $2.0$ to $7.1\,\mathrm{\mu}\mathrm{m}$ ($5000$ to $1400\,\mathrm{cm^{-1}}$). These values are obtained from a monocrystalline thin-film multilayer Bragg mirror of excellent purity (background doping $\leq 1 \times 10^{-14}\,\mathrm{cm^{-3}}$), grown via molecular beam epitaxy. To recover the refractive indices over such a broad wavelength range, we fit a dispersion model for each material. For that, we measure both a photometrically accurate transmittance spectrum of the Bragg mirror via Fourier-transform infrared spectrometry and the individual physical layer thicknesses of the structure via scanning electron microscopy. To infer the uncertainty of the refractive index values, we estimate relevant measurement uncertainties and propagate them via a Monte-Carlo-type method. This method conclusively yields propagated relative uncertainties on the order of $10^{-4}$ over the measured spectral range for both GaAs and Al$_{0.929}$Ga$_{0.071}$As. The fitted model can also approximate the refractive index for MBE-grown Al$_\mathrm{x}$Ga$_\mathrm{1-x}$As for $0 \leq x \leq 1$. These updated values will be essential in the design and fabrication of next-generation active and passive optical devices in a spectral region which is of high interest in many fields, e.g., laser design and cavity-enhanced spectroscopy.Comment: 20 pages, 5 figures, submitted to PR

Rigid Chiral Membranes

Statistical ensembles of flexible two-dimensional fluid membranes arise naturally in the description of many physical systems. Typically one encounters such systems in a regime of low tension but high stiffness against bending, which is just the opposite of the regime described by the Polyakov string. We study a class of couplings between membrane shape and in-plane order which break 3-space parity invariance. Remarkably there is only {\it one} such allowed coupling (up to boundary terms); this term will be present for any lipid bilayer composed of tilted chiral molecules. We calculate the renormalization-group behavior of this relevant coupling in a simplified model and show how thermal fluctuations effectively reduce it in the infrared.Comment: 11 pages, UPR-518T (This replaced version has fonts not used removed.

Mechanistic insights into on-surface reactions from isothermal temperature-programmed X-ray photoelectron spectroscopy

On-surface synthesis often proceeds under kinetic control due to the irreversibility of key reaction steps, rendering kinetic studies pivotal. The accurate quantification of reaction rates also bears potential for unveiling reaction mechanisms. Temperature-Programmed X-ray Photoelectron Spectroscopy (TP-XPS) has emerged as an analytical tool for kinetic studies with splendid chemical and sufficient temporal resolution. Here, we demonstrate that the common linear temperature ramps lead to fitting ambiguities. Moreover, pinpointing the reaction order remains intricate, although this key parameter entails information on atomistic mechanisms. Yet, TP-XPS experiments with a stepped temperature profile comprised of isothermal segments facilitate the direct quantification of rate constants from fitting time courses. Thereby, rate constants are obtained for a series of temperatures, which allows independent extraction of both activation energies and pre-exponentials from Arrhenius plots. By using two analogous doubly versus triply brominated aromatic model compounds, we found that their debromination on Ag(111) is best modeled by second-order kinetics and thus proceeds via the involvement of a second, non-obvious reactant. Accordingly, we propose that debromination is activated by surface supplied Ag adatoms. This hypothesis is supported by Density Functional Theory (DFT) calculations. We foresee auspicious prospects for this TP-XPS variant for further exploring the kinetics and mechanisms of on-surface reactions

Instabilities and disorder of the domain patterns in the systems with competing interactions

The dynamics of the domains is studied in a two-dimensional model of the microphase separation of diblock copolymers in the vicinity of the transition. A criterion for the validity of the mean field theory is derived. It is shown that at certain temperatures the ordered hexagonal pattern becomes unstable with respect to the two types of instabilities: the radially-nonsymmetric distortions of the domains and the repumping of the order parameter between the neighbors. Both these instabilities may lead to the transformation of the regular hexagonal pattern into a disordered pattern.Comment: ReVTeX, 4 pages, 3 figures (postscript); submitted to Phys. Rev. Let

A Phase-Field Model of Spiral Dendritic Growth

Domains of condensed-phase monolayers of chiral molecules exhibit a variety of interesting nonequilibrium structures when formed via pressurization. To model these domain patterns, we add a complex field describing the tilt degree of freedom to an (anisotropic) complex-phase-field solidification model. The resulting formalism allows for the inclusion of (in general, non-reflection symmetric) interactions between the tilt, the solid-liquid interface, and the bond orientation. Simulations demonstrate the ability of the model to exhibit spiral dendritic growth.Comment: text plus Four postscript figure file