Topological characterization of crystalline ice structures from coordination sequences

Topological properties of crystalline ice structures are studied by considering ring statistics, coordination sequences, and topological density of different ice phases. The coordination sequences (number of sites at topological distance k from a reference site) have been obtained by direct enumeration until at least 40 coordination spheres for different ice polymorphs. This allows us to study the asymptotic behavior of the mean number of sites in the k-th shell, M_k, for high values of k: M_k ~ a k^2, a being a structure-dependent parameter. Small departures from a strict parabolic dependence have been studied by considering first and second differences of the series {M_k} for each structure. The parameter a ranges from 2.00 for ice VI to 4.27 for ice XII, and is used to define a topological density for these solid phases of water. Correlations between such topological density and the actual volume of ice phases are discussed. Ices Ih and Ic are found to depart from the general trend in this correlation due to the large void space in their structures.Comment: 10 pages, 7 figures, 3 table

Molecular Tilt on Monolayer-Protected Nanoparticles

The structure of the tilted phase of monolayer-protected nanoparticles is investigated by means of a simple Ginzburg-Landau model. The theory contains two dimensionless parameters representing the preferential tilt angle and the ratio (epsilon) between the energy cost due to spatial variations in the tilt of the coating molecules and that of the van der Waals interactions which favors uniform tilt. We analyze the model for both spherical and octahedral particles. On spherical particles, we find a transition from a tilted phase, at small (epsilon), to a phase where the molecules spontaneously align along the surface normal and tilt disappears. Octahedral particles have an additional phase at small characterized by the presence of six topological defects. These defective configurations provide preferred sites for the chemical functionalization of monolayer-protected nanoparticles via place-exchange reactions and their consequent linking to form molecules and\ud bulk materials

Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

Helical Chirality: a Link between Local Interactions and Global Topology in DNA

DNA supercoiling plays a major role in many cellular functions. The global DNA conformation is however intimately linked to local DNA-DNA interactions influencing both the physical properties and the biological functions of the supercoiled molecule. Juxtaposition of DNA double helices in ubiquitous crossover arrangements participates in multiple functions such as recombination, gene regulation and DNA packaging. However, little is currently known about how the structure and stability of direct DNA-DNA interactions influence the topological state of DNA. Here, a crystallographic analysis shows that due to the intrinsic helical chirality of DNA, crossovers of opposite handedness exhibit markedly different geometries. While right-handed crossovers are self-fitted by sequence-specific groove-backbone interaction and bridging Mg2+ sites, left-handed crossovers are juxtaposed by groove-groove interaction. Our previous calculations have shown that the different geometries result in differential stabilisation in solution, in the presence of divalent cations. The present study reveals that the various topological states of the cell are associated with different inter-segmental interactions. While the unstable left-handed crossovers are exclusively formed in negatively supercoiled DNA, stable right-handed crossovers constitute the local signature of an unusual topological state in the cell, such as the positively supercoiled or relaxed DNA. These findings not only provide a simple mechanism for locally sensing the DNA topology but also lead to the prediction that, due to their different tertiary intra-molecular interactions, supercoiled molecules of opposite signs must display markedly different physical properties. Sticky inter-segmental interactions in positively supercoiled or relaxed DNA are expected to greatly slow down the slithering dynamics of DNA. We therefore suggest that the intrinsic helical chirality of DNA may have oriented the early evolutionary choices for DNA topology

Design of crystal-like aperiodic solids with selective disorder--phonon coupling

Functional materials design normally focuses on structurally-ordered systems because disorder is considered detrimental to many important physical properties. Here we challenge this paradigm by showing that particular types of strongly-correlated disorder can give rise to useful characteristics that are inaccessible to ordered states. A judicious combination of low-symmetry building unit and high-symmetry topological template leads to aperiodic "procrystalline" solids that harbour this type of topological disorder. We identify key classes of procrystalline states together with their characteristic diffraction behaviour, and establish a variety of mappings onto known and target materials. Crucially, the strongly-correlated disorder we consider is associated with specific sets of modulation periodicities distributed throughout the Brillouin zone. Lattice dynamical calculations reveal selective disorder-phonon coupling to lattice vibrations characterised by these same periodicities. The principal effect on the phonon spectrum is to bring about dispersion in energy rather than wave-vector, as in the poorly-understood "waterfall" effect observed in relaxor ferroelectrics. This property of procrystalline solids suggests a mechanism by which strongly-correlated topological disorder might allow new and useful functionalities, including independently-optimised thermal and electronic transport behaviour as required for high-performance thermoelectrics.Comment: 4 figure

Unprecedented chemical transformation: crystallographic evidence for 1,1,2,2-tetrahydroxyethane captured within an Fe6Dy3 single molecule magnet

A nonanuclear {Fe6Dy3} coordination cluster displaying SMM behaviour in which an unprecedented chemical transformation provides structural information for the existence of 1,1,2,2-tetrahydroxyethane is reported

Long range coherent magnetic bound states in superconductors

The quantum coherent coupling of completely different degrees of freedom is a challenging path towards creating new functionalities for quantum electronics. Usually the antagonistic coupling between spins of magnetic impurities and superconductivity leads to the destruction of the superconducting order. Here we show that a localized classical spin of an iron atom immersed in a superconducting condensate can give rise to new kind of long range coherent magnetic quantum state. In addition to the well-known Shiba bound state present on top of an impurity we reveal the existence of a star shaped pattern which extends as far as 12 nm from the impurity location. This large spatial dispersion turns out to be related, in a non-trivial way, to the superconducting coherence length. Inside star branches we observed short scale interference fringes with a particle-hole asymmetry. Our theoretical approach captures these features and relates them to the electronic band structure and the Fermi wave length of the superconductor. The discovery of a directional long range effect implies that distant magnetic atoms could coherently interact leading to new topological superconducting phases with fascinating properties