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

Correlation between microstructure and superconducting properties of MgB2 bulk samples with Mg addition and Mg/hBN co-additions

The microstructure of polycrystalline MgB2 has a strong influence on the current carrying ability, with grain boundaries and non-superconducting nanoparticles acting as good flux pinning centres which improve the local (intrinsic) critical current density (Jc) of the material, whereas porosity and poor connectivity between grains or particles adversely affect macroscopic current transport. Previous studies have found that hexagonal boron nitride (hBN) doping improves intrinsic Jc by introducing nanoscale flux pinning centres, and Mg doping improves extrinsic Jc by liquid-assisted sintering. Here we investigate the effect of co-doping with 5 wt.% Mg and 1 wt.% hBN with the aim of combining the improved intrinsic and extrinsic properties in bulk MgB2 samples fabricated using field assisted sintering. Additionally, the influence of ball milling and processing temperatures on MgB2 samples with only Mg additions is reported. By correlating microstructure with superconducting properties, we show that the presence of Mg liquid during processing of Mg-doped samples accelerates the reaction between BN and MgB2, forming an impurity phase, MgNB9, the presence of which is detrimental to superconducting performance. Nevertheless, we have achieved a considerable improvement in performance of samples doped only with Mg by increasing the sintering temperature

Strain in epitaxial MnSi films on Si(111) in the thick film limit studied by polarization-dependent extended x-ray absorption fine structure

We report a study of the strain state of epitaxial MnSi films on Si(111) substrates in the thick film limit (100-500~\AA) as a function of film thickness using polarization-dependent extended x-ray absorption fine structure (EXAFS). All films investigated are phase-pure and of high quality with a sharp interface between MnSi and Si. The investigated MnSi films are in a thickness regime where the magnetic transition temperature $T_\mathrm{c}$ assumes a thickness-independent enhanced value of $\geq$43~K as compared with that of bulk MnSi, where $T_\mathrm{c} \approx 29~{\rm K}$. A detailed refinement of the EXAFS data reveals that the Mn positions are unchanged, whereas the Si positions vary along the out-of-plane [111]-direction, alternating in orientation from unit cell to unit cell. Thus, for thick MnSi films, the unit cell volume is essentially that of bulk MnSi --- except in the vicinity of the interface with the Si substrate (thin film limit). In view of the enhanced magnetic transition temperature we conclude that the mere presence of the interface, and its specific characteristics, strongly affects the magnetic properties of the entire MnSi film, even far from the interface. Our analysis provides invaluable information about the local strain at the MnSi/Si(111) interface. The presented methodology of polarization dependent EXAFS can also be employed to investigate the local structure of other interesting interfaces.Comment: 11 pages, 10 figure

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

RadICAL stack: A localisation method for dynamic gamma/neutron fields

A variation of the RadICAL (Radiation Imaging Cylinder Activity Locator) system capable of operating in a dynamic environment, such as that created by active interrogation techniques, has been developed. RadICAL is a novel method for locating a radiological source using a rotating detector element. The detector geometry is that of a thin sheet and is rotated to present a constantly changing surface area to the source; it therefore generates a characteristic temporal response which can be used to determine the source direction. The time required to determine the direction of a source make it unsuitable for dynamic environments and so an alternative method is presented that uses a stack of identical scintillator slabs positioned at fixed horizontal angles around a central axis. By comparing count rates from each slab to a standard response curve, using a specially developed algorithm, the direction of a source can be determined without the need to rotate the detector. EJ-299-33 plastic scintillator was used to allow detection of separate neutron and gamma events in a mixed field through pulse shape discrimination. A four element detector was built and shown to achieve a positional accuracy of approximately 4.4 degrees when exposed to a 1.44MBq 137 Cs source at distances of up to 2m. The same detector was used to discriminate separate neutron and gamma events in a mixed field, which allows for the possibility of locating a neutron source within a gamma rich environment

Neutron/gamma pulse shape discrimination in EJ-299-34 at high flux

The effect of scintillator geometry on the quality of neutron/γ pulse shape discrimination (PSD) in EJ-299 plastic scintillator, using a digital charge integration PSD algorithm has been studied. It is shown that the PSD Figure of Merit (FOM) reduces as the geometry of the scintillator moves from a cube-like shape towards a flat panel shape. The PSD performance in this material at high flux irradiation is investigated with performance deteriorating at rates of ∼107 photons/s. The use of EJ-299 for security applications, with a focus on active interrogation environments is explored in conjunction with a system capable of neutron/γ separation and localisation

Fluctuations, line tensions, and correlation times of nanoscale islands on surfaces

We analyze in detail the fluctuations and correlations of the (spatial) Fourier modes of nano-scale single-layer islands on (111) fcc crystal surfaces. We analytically show that the Fourier modes of the fluctuations couple due to the anisotropy of the crystal, changing the power spectrum of the fluctuations, and that the actual eigenmodes of the fluctuations are the appropriate linear combinations of the Fourier modes. Using kinetic Monte Carlo simulations with bond-counting parameters that best match realistic energy barriers for hopping rates, we deduce absolute line tensions as a function of azimuthal orientation from the analyses of the fluctuation of each individual mode. The autocorrelation functions of these modes give the scaling of the correlation times with wavelength, providing us with the rate-limiting kinetics driving the fluctuations, here step-edge diffusion. The results for the energetic parameters are in reasonable agreement with available experimental data for Pb(111) surfaces, and we compare the correlation times of island-edge fluctuations to relaxation times of quenched Pb crystallites.Comment: 11 pages, 8 figures; to appear in PRB 70, xxx (15 Dec 2004), changes in MC and its implication

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

Individual grain boundary properties and overall performance of metal-organic deposition coated conductors

have investigated single grain boundaries (GBs) isolated in coated conductors produced by metal-organic deposition. When a magnetic field is swept in the film plane, an angle-dependent crossover from boundary to grain limited critical current density J(c) is found. In the force-free orientation, even at fields as high as 8 T, the GBs still limit Jc. We deduce that this effect is a direct consequence of GB meandering. We have employed these single GB results to explain the dependence of Jc of polycrystalline tracks on their width: in-plane measurements become flatter as the tracks are narrowed down. This result is consistent with the stronger GB limitation at field configurations close to force-free found from the isolated boundaries. Our study shows that for certain geometries even at high fields the effect of GBs cannot be neglected.This work was supported by the Engineering and Physical Sciences Research Council [grant numbers EP/C011546/1 and EP/C011554/1