Small Substructures Research Articles

Cu5In3‐Cu3In2 Revisited

The η‐phase field of the Cu–In system is unusually rich and shows wealth of phases that are all related to the B8 (NiAs/Ni2In) type. Previous electron diffraction work has revealed extensive super structure ordering; in this study, we report single crystal diffraction experiments on high‐quality samples of two of the phases in the system, ht1‐Cu5In3 and ht2‐Cu5In3. Both these phases constitute super structures, caused by the ordering of interstitials. The structure ht2‐Cu5In3 is a relatively simple structure with a bidimensional modulation but where only first order satellites are visible, indicating incomplete order whereas ht1‐Cu5In3 displays many high order satellites and the refined structure exhibit nearly perfect order with step‐function‐like occupancy domains. The refinement of the structure of ht1‐Cu5In3 is challenging for several reasons. It is difficult to integrate the data because of the unusual combination of very closely spaced satellites caused by q‐vectors close to (1/3 1/3 0) and a paucity of reflections in total, caused by the small substructure. A second challenge is the refinement of what amounts to a two‐dimensional step function. In effect, the shape of a two‐dimensional occupation domain is defined by a Fourier series and the problem of defining that shape is non‐trivial.

Balanced diagonals in frequency squares

We say that a diagonal in an array is λ-balanced if each entry occurs λ times. Let L be a frequency square of type F(n;λ); that is, an n×n array in which each entry from {1,2,…,m=n∕λ} occurs λ times per row and λ times per column. We show that if m⩽3, L contains a λ-balanced diagonal, with only one exception up to equivalence when m=2. We give partial results for m⩾4 and suggest a generalization of Ryser’s conjecture, that every Latin square of odd order has a transversal. Our method relies on first identifying a small substructure with the frequency square that facilitates the task of locating a balanced diagonal in the entire array.

Modal Substructuring of Geometrically Nonlinear Plates

AbstractThis work considers model reduction of geometrically nonlinear finite element (FE) model of a plate structure developed in a commercial FE package. The structure is first divided into smaller substructures. Since there is normally no access to the nonlinear stiffness tensors in FE packages, a non‐intrusive method is used in this paper to reduce the order of each substructure separately. In order to generate the nonlinear reduced order model (NLROM), the reduced substructures are assembled using the coupling procedure of the Component Mode Synthesis (CMS) method. As a linear basis, truncated free and fixed interface modes are used here to check the efficiency of the developed NLROM based on them. A plate structure subjected to large deflections is considered in this study to implement the substructuring method. For the sake of validation, Nonlinear Normal Modes (NNMs) are employed to check the convergence of NLROMs in a broadband frequency range. (© 2017 Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Dark matter annihilation feedback in cosmological simulations – I: Code convergence and idealized haloes

We describe and test a novel Dark Matter Annihilation Feedback (DMAF) scheme that has been implemented into the well known cosmological simulation code \textsf{GADGET-2}. In the models considered here, dark matter can undergo self-annihilation/decay into radiation and baryons. These products deposit energy into the surrounding gas particles and then the dark matter/baryon fluid is self-consistently evolved under gravity and hydrodynamics. We present tests of this new feedback implementation in the case of idealised dark matter halos with gas components for a range of halo masses, concentrations and annihilation rates. For some dark matter models, DMAF's ability to evacuate gas is enhanced in lower mass, concentrated halos where the injected energy is comparable to its gravitational binding energy. Therefore, we expect the strongest signs of dark matter annihilation to imprint themselves onto the baryonic structure of concentrated dwarf galaxies through their baryonic fraction and star formation history. Finally we present preliminary results of the first self-consistent DMAF cosmological box simulations showing that the small scale substructure is washed out for large annihilation rates.

Recognizing RNA structural motifs in HT-SELEX data for ribosomal protein S15

BackgroundProteins recognize many different aspects of RNA ranging from single stranded regions to discrete secondary or tertiary structures. High-throughput sequencing (HTS) of in vitro selected populations offers a large scale method to study RNA-proteins interactions. However, most existing analysis methods require that the binding motifs are enriched in the population relative to earlier rounds, and that motifs are found in a loop or single stranded region of the potential RNA secondary structure. Such methods do not generalize to all RNA-protein interaction as some RNA binding proteins specifically recognize more complex structures such as double stranded RNA.ResultsIn this study, we use HT-SELEX derived populations to study the landscape of RNAs that interact with Geobacillus kaustophilus ribosomal protein S15. Our data show high sequence and structure diversity and proved intractable to existing methods. Conventional programs identified some sequence motifs, but these are found in less than 5-10% of the total sequence pool. Therefore, we developed a novel framework to analyze HT-SELEX data. Our process accounts for both sequence and structure components by abstracting the overall secondary structure into smaller substructures composed of a single base-pair stack, which allows us to leverage existing approaches already used in k-mer analysis to identify enriched motifs. By focusing on secondary structure motifs composed of specific two base-pair stacks, we identified significantly enriched or depleted structure motifs relative to earlier rounds.ConclusionsDiscrete substructures are likely to be important to RNA-protein interactions, but they are difficult to elucidate. Substructures can help make highly diverse sequence data more tractable. The structure motifs provide limited accuracy in predicting enrichment suggesting that G. kaustophilus S15 can either recognize many different secondary structure motifs or some aspects of the interaction are not captured by the analysis. This highlights the importance of considering secondary and tertiary structure elements and their role in RNA-protein interactions.

Novel morphologies of intermetallic phases in Sn-Ni peritectic alloys

The novel morphologies of intermetallic phases with narrow composition ranges are observed in Sn-Ni peritectic alloys after experiencing deep acid etching. Both the primary Ni3Sn2 and peritectic Ni3Sn4 phases are intermetallic compounds with narrow composition ranges, and the former one has a larger range. Although dendritic growth of primary Ni3Sn2 phases can be observed, they are shown to be composed of small faceted sub-structures. In addition, a faceted to non-faceted morphology transition of peritectic Ni3Sn4 phase which is observed at a constant growth velocity is also confirmed. These finds are helpful for growth control of intermetallic phases.

Modal Substructuring of Geometrically Nonlinear Finite Element Models with Interface Reduction

Substructuring methods have been widely used in structural dynamics to divide large, complicated finite element models into smaller substructures. For linear systems, many methods have been developed to reduce the subcomponents down to a low-order set of equations using a special set of component modes, and these are then assembled to approximate the dynamics of a large-scale model. In this paper, a substructuring approach is developed for coupling geometrically nonlinear structures, where each subcomponent is drastically reduced to a low-order set of nonlinear equations using a truncated set of fixed-interface and characteristic constraint modes. The method used to extract the coefficients of the nonlinear reduced-order model is nonintrusive, in that it does not require any modification to the commercial finite element code but computes the reduced-order model from the results of several nonlinear static analyses. The nonlinear reduced-order models are then assembled to approximate the nonlinear differential equations of the global assembly. The method is demonstrated on the coupling of two geometrically nonlinear plates with simple supports at all edges. The plates are joined at a continuous interface through the rotational degrees of freedom, and the nonlinear normal modes of the assembled equations are computed to validate the models. The proposed substructuring approach reduces a 12,861-degree-of-freedom model down to only 23 degrees of freedom while still accurately reproducing the nonlinear normal modes.

Numerical studies on the effect of measurement noises on the online parametric identification of a cable-stayed bridge

System identification of structures is one of the important aspects of structural health monitoring. The accuracy and efficiency of identification results is affected severely by measurement noises, especially when the structure system is large, such as bridge structures, and when online system identification is required. In this paper, the least square estimation (LSE) method is used combined with the substructure approach for identifying structural parameters of a cable-stay bridge with large degree of freedoms online. Numerical analysis is carried out by first dividing the bridge structure into smaller substructures and then estimates the parameters of each substructure online using LSE method. Simulation results demonstrate that the proposed approach is capable of identifying structural parameters, however, the accuracy and efficiency of identification results depend highly on the noise sensitivities of loading region, loading pattern as well as element size.

Bayesian comparison of protein structures using partial Procrustes distance.

An important topic in bioinformatics is the protein structure alignment. Some statistical methods have been proposed for this problem, but most of them align two protein structures based on the global geometric information without considering the effect of neighbourhood in the structures. In this paper, we provide a Bayesian model to align protein structures, by considering the effect of both local and global geometric information of protein structures. Local geometric information is incorporated to the model through the partial Procrustes distance of small substructures. These substructures are composed of β-carbon atoms from the side chains. Parameters are estimated using a Markov chain Monte Carlo (MCMC) approach. We evaluate the performance of our model through some simulation studies. Furthermore, we apply our model to a real dataset and assess the accuracy and convergence rate. Results show that our model is much more efficient than previous approaches.

Crystal Structure of the Maturation Protein from Bacteriophage Qβ

Virions of the single-stranded RNA bacteriophages contain a single copy of the maturation protein, which is bound to the phage genome and is required for the infectivity of the particles. The maturation protein mediates the adsorption of the virion to bacterial pili and the subsequent release and penetration of the genome into the host cell. Here, we report a crystal structure of the maturation protein from bacteriophage Qβ. The protein has a bent, highly asymmetric shape and spans 110Å in length. Apart from small local substructures, the overall fold of the maturation protein does not resemble that of other known proteins. The protein is organized in two distinct regions, an α-helical part with a four-helix core, and a β stranded part that contains a seven-stranded sheet in the central part and a five-stranded sheet at the tip of the protein. The Qβ maturation protein has two distinct, positively charged areas at opposite sides of the α-helical part, which are involved in genomic RNA binding. The maturation protein binds to each of the surrounding coat protein dimers in the capsid differently, and the interaction is considerably weaker compared to coat protein interdimer contacts. The coat protein- or RNA-binding residues are not preserved among different ssRNA phage maturation proteins; instead, the distal end of the α-helical part is the most evolutionarily conserved, suggesting the importance of this region for maintaining the functionality of the protein.

Value of graph topology in vascular biometrics

Biometrics such as retina, palm vein, wrist vein and hand vein are becoming increasingly popular because of ease of use, in-built liveness detection and a contact free capture process. Here the authors show the benefits of graph representation for all such vascular biometrics and the advantages of graph topology in matching vascular biometric graphs. The authors find that different types of small substructures dominate in the four classes of vascular graphs due to the way the vasculature is built in the human body. The authors show that simple graph structures can be used to bring down the registration time by over 50% compared with registration using edges alone, and that cost functions that include matching the local graph neighbourhood around compared node pairs improve matching performance. Distance measures based on the number of vertices or edges in the maximum common subgraph are shown to discriminate significantly better than using a simple count of matched vertices, as in the iterative closest point based point pattern matching. For graphs whose topology is close to that of proximity graphs, edge-based distance measures were found to perform best. These results are demonstrated for all four vascular modalities.

Molecular interactions of small molecule inhibitors targeting cytoplasmic TIR domains.

Abstract Regulation of Toll-like receptor (TLR) signaling using small molecule agonists and antagonists have been widely sought after for controlling inflmation and disease. Most studies have focused on therapeutic targeting of TLR extracellular ligand binding domains. Recently, Computer-aided drug design (CADD) screens specifically targeting intracellular Toll-Interleukin-1 receptor resistance domains have identified and functionally characterized several small molecule and peptide inhibitors which protect against lethality in animal models of infection, inflammation and disease. We have sought to structurally characterize the molecular interactions of CADD derived small molecule inhibitors with respective TLR-TIR domains by determining the X-ray co-crystal structures of TLR2 –TIR domain in the presence of C29 and its substructure O-vanillin. Positive electron density is observed near the BB loop and residue Ile 685 of native TLR2-TIR in the presence of the small molecule inhibitor (C29) exhibit compared with the native apo form of this structure. However, the presence of (S-(DIMETHYLARSENIC) CYSTEINE) in this crystallization condition complicate analysis. To rule out the effects of DMSO and (S-(DIMETHYLARSENIC) CYSTEINE) we sought to examine small molecule inhibitor C29L substructure (o-Vanillin) in a second crystal form of TLR2 and which contains a more simplified crystallization condition grown in the presence of 1mM of C29L. This co-crystal exhibits positive electron density located in an around the BB loop compared with apo forms of this structure. Additionally, in this recent structure form we observe additional DD loop density previously not defined in the originally reported crystal form.

Boosting the annihilation boost: Tidal effects on dark matter subhalos and consistent luminosity modeling

In the cold dark matter paradigm, structures form hierarchically, implying that large structures contain smaller substructures. These subhalos will enhance signatures of dark matter annihilation such as gamma rays. In the literature, typical estimates of this boost factor assume a concentration-mass relation for field halos, to calculate the luminosity of subhalos. However, since subhalos accreted in the gravitational potential of their host loose mass through tidal stripping and dynamical friction, they have a quite characteristic density profile, different from that of the field halos of the same mass. In this work, we quantify the effect of tidal stripping on the boost factor, by developing a semi-analytic model that combines mass-accretion history of both the host and subhalos as well as subhalo accretion rates. We find that when subhalo luminosities are treated consistently, the boost factor increases by a factor 2-5, compared to the typical calculation assuming a field-halo concentration. This holds for host halos ranging from sub-galaxy to cluster masses and is independent of the subhalo mass function or specific concentration-mass relation. The results are particularly relevant for indirect dark matter searches in the extragalactic gamma-ray sky.

Novel antennal lobe substructures revealed in the small hive beetle Aethina tumida.

The small hive beetle, Aethina tumida, is an emerging pest of social bee colonies. A. tumida shows a specialized life style for which olfaction seems to play a crucial role. To better understand the olfactory system of the beetle, we used immunohistochemistry and 3-D reconstruction to analyze brain structures, especially the paired antennal lobes (AL), which represent the first integration centers for odor information in the insect brain. The basic neuroarchitecture of the A. tumida brain compares well to the typical beetle and insect brain. In comparison to other insects, the AL are relatively large in relationship to other brain areas, suggesting that olfaction is of major importance for the beetle. The AL of both sexes contain about 70 olfactory glomeruli with no obvious size differences of the glomeruli between sexes. Similar to all other insects including beetles, immunostaining with an antiserum against serotonin revealed a large cell that projects from one AL to the contralateral AL to densely innervate all glomeruli. Immunostaining with an antiserum against tachykinin-related peptides (TKRP) revealed hitherto unknown structures in the AL. Small TKRP-immunoreactive spherical substructures are in both sexes evenly distributed within all glomeruli. The source for these immunoreactive islets is very likely a group of about 80 local AL interneurons. We offer two hypotheses on the function of such structures.

Structure and dynamics of the supercluster of galaxies SC0028-0005

According to the standard cosmological scenario, superclusters are objects that have just passed the turn-around point and are collapsing. The dynamics of very few superclusters have been analysed up to now. In this paper, we study the supercluster SC0028-0005, at redshift 0.22, identify the most prominent groups and/or clusters that make up the supercluster, and investigate the dynamic state of this structure. For the membership identification, we have used photometric and spectroscopic data from Sloan Digital Sky Survey Data Release 10, finding six main structures in a flat spatial distribution. We have also used a deep multiband observation with MegaCam/Canada–France–Hawaii Telescope to estimate de mass distribution through the weak-lensing effect. For the dynamical analysis, we have determined the relative distances along the line of sight within the supercluster using the Fundamental Plane of early-type galaxies. Finally, we have computed the peculiar velocities of each of the main structures. The 3D distribution suggests that SC0028-005 is indeed a collapsing supercluster, supporting the formation scenario of these structures. Using the spherical collapse model, we estimate that the mass within r = 10 Mpc should lie between 4 and 16 × 1015 M⊙. The farthest detected members of the supercluster suggest that within ∼60 Mpc the density contrast is δ ∼ 3 with respect to the critical density at z = 0.22, implying a total mass of ∼4.6–16 × 1017 M⊙, most of which in the form of low-mass galaxy groups or smaller substructures.

Motif analysis in directed ordered networks and applications to food webs.

The analysis of small recurrent substructures, so called network motifs, has become a standard tool of complex network science to unveil the design principles underlying the structure of empirical networks. In many natural systems network nodes are associated with an intrinsic property according to which they can be ordered and compared against each other. Here, we expand standard motif analysis to be able to capture the hierarchical structure in such ordered networks. Our new approach is based on the identification of all ordered 3-node substructures and the visualization of their significance profile. We present a technique to calculate the fine grained motif spectrum by resolving the individual members of isomorphism classes (sets of substructures formed by permuting node-order). We apply this technique to computer generated ensembles of ordered networks and to empirical food web data, demonstrating the importance of considering node order for food-web analysis. Our approach may not only be helpful to identify hierarchical patterns in empirical food webs and other natural networks, it may also provide the base for extending motif analysis to other types of multi-layered networks.

Macromolecular ab initio phasing enforcing secondary and tertiary structure.

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

Light scattering microscopy with angular resolution and its possible application to apoptosis.

An inverted microscope has been modified for light scattering experiments with high angular resolution in combination with transmission, wide-field fluorescence or laser scanning microscopy. Supported by simulations of Mie scattering, this method permits detection of morphological changes of 3T3 fibroblasts on apoptosis and formation of spherically shaped cells of about 20 μm diameter, in agreement with visual observation. Smaller sub-structures (e.g. cell nuclei) as well as cell clusters may possibly contribute to the scattering behaviour. Results of 2-dimensional cell cultures are confirmed by 3-dimensional multicellular spheroids of 3T3 fibroblasts and HeLa 2E8 cervix carcinoma cells, where in most cases no morphological changes are discernable. This offers some advantage of light scattering microscopy for label-free detection of apoptosis and may represent a first step towards label-free in vivo diagnostics.

Substructure isolation and damage identification using free responses

Structural health monitoring (SHM) has become a hot and intensively researched field in civil engineering. Thereinto, damage identification play an important role in maintaining structural integrity and safety. Many effective methods have been proposed for damage identification. However, accurate global identification of large real-world structures is not easy due to their complex and often unknown boundary conditions, nonlinear components, insensitivity of global response to localized damages, etc. Furthermore, global identification often requires lots of sensors and involves large number of unknowns. This is costly, rarely feasible in practice, and usually yields severely ill-conditioned identification problems. Substructuring approach is a possible solution: substructuring methods can focus on local small substructures; they need only a few sensors placed on the substructure and yield smaller and numerically much more feasible identification problems. This paper proposed an improved substructure method using local free response for substructure damage identification. The virtual supports are constructed by Substructure Isolation Method (SIM) using the linear combination of the substructural responses. The influence of the global errors is isolated by adding the virtual supports on the main degree of freedoms (DOFs) of the substructure. Through the correlation analysis, the substructural modes are selected and used for damage identification of the substructure. A plain model of cable stayed bridge is used for the verification of the proposed method.

Post-mortem magnetic resonance microscopy (MRM) of the murine brain at 7 Tesla results in a gain of resolution as compared to in vivo MRM.

Small-animal MRI with high field strength allows imaging of the living animal. However, spatial resolution in in vivo brain imaging is limited by the scanning time. Measurements of fixated mouse brains allow longer measurement time, but fixation procedures are time consuming, since the process of fixation may take several weeks. We here present a quick and simple post-mortem approach without fixation that allows high-resolution MRI even at 7 Tesla (T2-weighted MRI). This method was compared to in vivo scans with optimized spatial resolution for the investigation of anesthetized mice (T1-weighted MRI) as well as to ex situ scans of fixed brains (T1- and T2-weighted scans) by using standard MRI-sequences, along with anatomic descriptions of areas observable in the MRI, analysis of tissue shrinkage and post-processing procedures (intensity inhomogeneity correction, PCNN3D brain extract, SPMMouse segmentation, and volumetric measurement). Post-mortem imaging quality was sufficient to determine small brain substructures on the morphological level, provided fast possibilities for volumetric acquisition and for automatized processing without manual correction. Moreover, since no fixation was used, tissue shrinkage due to fixation does not occur as it is, e.g., the case by using ex vivo brains that have been kept in fixatives for several days. Thus, the introduced method is well suited for comparative investigations, since it allows determining small structural alterations in the murine brain at a reasonable high resolution even by MRI performed at 7 Tesla.