First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen

The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.Comment: 12 pages, 3 figures; 3(PPG)_6 xyz file attached; v2: minor modification

Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states

Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N′-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.Peer reviewe

Two Approaches to Dislocation Nucleation in the Supported Heteroepitaxial Equilibrium Islanding Phenomenon

We study the dislocation formation in 2D nanoscopic islands with two methods, the Molecular Static method and the Phase Field Crystal method. It is found that both methods indicate the same qualitative stages of the nucleation process. The dislocations nucleate at the film-substrate contact point and the energy decreases monotonously when the dislocations are farther away from the island-wetting film contact points than the distance of the highest energy barrier.Comment: 4 page

Direct observation of mono-vacancy and self-interstitial recovery in tungsten

Reliable and accurate knowledge of the physical properties of elementary point defects is crucial for predictive modeling of the evolution of radiation damage in materials employed in harsh conditions. We have applied positron annihilation spectroscopy to directly detect mono-vacancy defects created in tungsten through particle irradiation at cryogenic temperatures, as well as their recovery kinetics. We find that efficient self-healing of the primary damage takes place through Frenkel pair recombination already at 35 K, in line with an upper bound of 0.1 eV for the migration barrier of self-interstitials. Further self-interstitial migration is observed above 50 K with activation energies in the range of 0.12-0.42 eV through the release of the self-interstitial atoms from impurities and structural defects and following recombination with mono-vacancies. Mono-vacancy migration is activated at around 550 K with a migration barrier of E-m(V) = 1.85 +/- 0.05 eV. (C) 2019 Author(s).Peer reviewe

Enhanced Antibody Production in Clever-1/Stabilin-1-Deficient Mice

Clever-1, encoded by the Stab1 gene, is a scavenger and leukocyte trafficking receptor expressed by subsets of vascular and lymphatic endothelial cells and immunosuppressive macrophages. Monocyte Clever-1 also modulates T cell activation. However, nothing is known about the possible links between B cell function and Clever-1. Here, we found that Stab1 knockout mice (Stab1(-/-)) lacking the Clever-1 protein from all cells present with abnormally high antibody levels under resting conditions and show enhanced humoral immune responses after immunization with protein and carbohydrate antigens. Removal of the spleen does not abolish the augmented basal and post-immunization antibody levels in Clever-1-deficient mice. The increased IgG production is also present in mice in which Clever-1 is selectively ablated from macrophages. When compared to wildtype macrophages, Clever-1-deficient macrophages show increased TNF-alpha synthesis. In co-culture experiments, monocytes/macrophages deficient of Clever-1 support higher IgM production by B cells, which is blocked by TNF-alpha depletion. Collectively, our data show that the excessive inflammatory activity of monocytes/macrophages in the absence of Clever-1 results in augmented humoral immune responses in vivo

Pim-1 Kinase Expression Predicts Radiation Response in Squamocellular Carcinoma of Head and Neck and Is under the Control of Epidermal Growth Factor Receptor

Pim-1 is an oncogenic serine/threonine kinase with poorly defined function in epithelial cancers. In this study, we determined 1) associations of Pim-1 expression with clinicopathological parameters including responsiveness to irradiation in squamocellular cancers of head and neck and 2) how Pim-1 expression is controlled subsequent to irradiation. Moderate to high expression of Pim-1 correlated to poor response to radiation therapy (P = .003). It is also associated to the expression of epidermal growth factor receptor (EGFR, P < .0001), which has been shown to be activated by irradiation. In radioresistant tumors, irradiation promoted nuclear translocation of Pim-1 (P < .005). When directly testing EGFR dependence of Pim-1 expression, up-regulation and nuclear translocation of Pim-1 could be induced through stimulation of EGFR with its ligands EGF or transforming growth factor a. Both ligand- and irradiation-induced changes in Pim-1 expression and localization could be inhibited by the monoclonal anti-EGFR antibody cetuximab and by the tyrosine kinase inhibitor gefitinib also targeting EGFR. These results suggest that irradiation-induced activation of EGFR upregulates Pim-1, and Pim-1 may be used as a novel predictive marker of radiation response in patients with squamocellular cancers of head and neck.</p

Ion beam shaping and downsizing of nanostructures

We report a new approach for progressive and well-controlled downsizing of nanostructures below the 10 nm scale. Low energetic ion beam (Ar+) is used for gentle surface erosion, progressively shrinking the dimensions with ~ 1 nm accuracy. The method enables shaping of nanostructure geometry and polishing the surface. The process is clean room / high vacuum compatible being suitable for various applications. Apart from technological advantages, the method enables study of various size phenomena on the same sample between sessions of ion beam treatment.Comment: 14 pages, 6 figure

Surface Enhanced Second Harmonic Generation from Macrocycle, Catenane, and Rotaxane Thin Films: Experiments and Theory

Surface enhanced second harmonic generation (SE SHG) experiments on molecular structures, macrocycles, catenanes, and rotaxanes, deposited as monolayers and multilayers by vacuum sublimation on silver, are reported. The measurements show that the molecules form ordered thin films, where the highest degree of order is observed in the case of macrocycle monolayers and the lowest in the case of rotaxane multilayers. The second harmonic generation activity is interpreted in terms of electric field induced second harmonic (EFISH) generation where the electric field is created by the substrate silver atoms. The measured second order nonlinear optical susceptibility for a rotaxane thin film is compared with that obtained by considering only EFISH contribution to SHG intensity. The electric field on the surface of a silver layer is calculated by using the Delphi4 program for structures obtained with TINKER molecular mechanics/dynamics simulations. An excellent agreement is observed between the calculated and the measured SHG susceptibilities.