Network theory approach for data evaluation in the dynamic force spectroscopy of biomolecular interactions

Investigations of molecular bonds between single molecules and molecular complexes by the dynamic force spectroscopy are subject to large fluctuations at nanoscale and possible other aspecific binding, which mask the experimental output. Big efforts are devoted to develop methods for effective selection of the relevant experimental data, before taking the quantitative analysis of bond parameters. Here we present a methodology which is based on the application of graph theory. The force-distance curves corresponding to repeated pulling events are mapped onto their correlation network (mathematical graph). On these graphs the groups of similar curves appear as topological modules, which are identified using the spectral analysis of graphs. We demonstrate the approach by analyzing a large ensemble of the force-distance curves measured on: ssDNA-ssDNA, peptide-RNA (system from HIV1), and peptide-Au surface. Within our data sets the methodology systematically separates subgroups of curves which are related to different intermolecular interactions and to spatial arrangements in which the molecules are brought together and/or pulling speeds. This demonstrates the sensitivity of the method to the spatial degrees of freedom, suggesting potential applications in the case of large molecular complexes and situations with multiple binding sites

Correlative Microscopy of Morphology and Luminescence of Cu porphyrin aggregates

Transfer of energy and information through molecule aggregates requires as one important building block anisotropic, cable-like structures. Knowledge on the spatial correlation of luminescence and morphology represents a prerequisite in the understanding of internal processes and will be important for architecting suitable landscapes. In this context we study the morphology, fluorescence and phosphorescence of molecule aggregate structures on surfaces in a spatially correlative way. We consider as two morphologies, lengthy strands and isotropic islands. It turns out that phosphorescence is quite strong compared to fluorescence and the spatial variation of the observed intensities is largely in line with the amount of dye. However in proportion, the strands exhibit more fluorescence than the isotropic islands suggesting weaker non-radiative channels. The ratio fluorescence to phosphorescence appears to be correlated with the degree of aggregation or internal order. The heights at which luminescence saturates is explained in the context of attenuation and emission multireflection, inside the dye. This is supported by correlative photoemission electron microscopy which is more sensitive to the surface region. The lengthy structures exhibit a pronounced polarization dependence of the luminescence with a relative dichroism up to about 60%, revealing substantial perpendicular orientation preference of the molecules with respect to the substrate and parallel with respect to the strands

High resolution characterisation of microstructural evolution in Rbx_{x}Fe2−y_{2-y}Se2_{2} crystals on annealing

The superconducting and magnetic properties of phase-separated A$_x$Fe$_{2-y}$Se$_2$ compounds are known to depend on post-growth heat treatments and cooling profiles. This paper focusses on the evolution of microstructure on annealing, and how this influences the superconducting properties of Rb$_x$Fe$_2-y$Se$_2$ crystals. We find that the minority phase in the as-grown crystal has increased unit cell anisotropy (c/a ratio), reduced Rb content and increased Fe content compared to the matrix. The microstructure is rather complex, with two-phase mesoscopic plate-shaped features aligned along {113} habit planes. The minority phase are strongly facetted on the {113} planes, which we have shown to be driven by minimising the volume strain energy introduced as a result of the phase transformation. Annealing at 488K results in coarsening of the mesoscopic plate-shaped features and the formation of a third distinct phase. The subtle differences in structure and chemistry of the minority phase(s) in the crystals are thought to be responsible for changes in the superconducting transition temperature. In addition, scanning photoemission microscopy has clearly shown that the electronic structure of the minority phase has a higher occupied density of states of the low binding energy Fe3d orbitals, characteristic of crystals that exhibit superconductivity. This demonstrates a clear correlation between the Fe-vacancy-free phase with high c/a ratio and the electronic structure characteristics of the superconducting phase.Comment: 6 figures v2 is exactly the same as v1. The typesetting errors in the abstract have been correcte

Quantum interference structures in the conductance plateaus of gold nanojunctions

The conductance of breaking metallic nanojunctions shows plateaus alternated with sudden jumps, corresponding to the stretching of stable atomic configurations and atomic rearrangements, respectively. We investigate the structure of the conductance plateaus both by measuring the voltage dependence of the plateaus' slope on individual junctions and by a detailed statistical analysis on a large amount of contacts. Though the atomic discreteness of the junction plays a fundamental role in the evolution of the conductance, we find that the fine structure of the conductance plateaus is determined by quantum interference phenomenon to a great extent.Comment: 4 pages, 4 figure

Correlations in nano-scale step fluctuations: comparison of simulation and experiments

We analyze correlations in step-edge fluctuations using the Bortz-Kalos-Lebowitz kinetic Monte Carlo algorithm, with a 2-parameter expression for energy barriers, and compare with our VT-STM line-scan experiments on spiral steps on Pb(111). The scaling of the correlation times gives a dynamic exponent confirming the expected step-edge-diffusion rate-limiting kinetics both in the MC and in the experiments. We both calculate and measure the temperature dependence of (mass) transport properties via the characteristic hopping times and deduce therefrom the notoriously-elusive effective energy barrier for the edge fluctuations. With a careful analysis we point out the necessity of a more complex model to mimic the kinetics of a Pb(111) surface for certain parameter ranges.Comment: 10 pages, 9 figures, submitted to Physical Review

Microstructural analysis of phase separation in iron chalcogenide superconductors

The interplay between superconductivity, magnetism and crystal structure in iron-based superconductors is a topic of great interest amongst the condensed matter physics community as it is thought to be the key to understanding the mechanisms responsible for high temperature superconductivity. Alkali metal doped iron chalcogenide superconductors exhibit several unique characteristics which are not found in other iron-based superconducting materials such as antiferromagnetic ordering at room temperature, the presence of ordered iron vacancies and high resistivity normal state properties. Detailed microstructural analysis is essential in order to understand the origin of these unusual properties. Here we have used a range of complementary scanning electron microscope based techniques, including high-resolution electron backscatter di raction mapping, to assess local variations in composition and lattice parameter with high precision and sub-micron spatial resolution. Phase separation is observed in the Csx Fe2-ySe2 crystals, with the minor phase distributed in a plate-like morphology throughout the crystal. Our results are consistent with superconductivity occurring only in the minority phase.Comment: Accepted for publication in a special edition of Supercond. Sci. Techno

Transition from tunneling to direct contact in tungsten nanojunctions

We apply the mechanically controllable break junctions technique to investigate the transition from tunneling to direct contact in tungsten. This transition is quite different from that of other metals and is determined by the local electronic properties of the tungsten surface and the relief of the electrodes at the point of their closest proximity. The conductance traces show a rich variety of patterns from the avalanche-like jump to a mesoscopic contact to the completely smooth transition between direct contact and tunneling. Due to the occasional absence of an adhesive jump the conductance of the contact can be continuously monitored at ultra-small electrode separations. The conductance histograms of tungsten are either featureless or show two distinct peaks related to the sequential opening of spatially separated groups of conductance channels. The role of surface states of tungsten and their contribution to the junction conductance at sub-Angstrom electrode separations are discussed.Comment: 6 pages, 6 figure