Unified Structural Model Research Articles

Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis

The linear distribution of genes across chromosomes and the spatial localization of genes within the nucleus are related to their transcriptional regulation. The mechanistic consequences of linear gene order, and how it may relate to the functional output of genome organization, remain to be fully resolved, however. Here we tested the relationship between linear and 3D organization of gene regulation during myogenesis. Our analysis has identified a subset of topologically associated domains (TADs) that are significantly enriched for muscle-specific genes. These lineage-enriched TADs demonstrate an expression-dependent pattern of nuclear organization that influences the positioning of adjacent nonenriched TADs. Therefore, lineage-enriched TADs inform cell-specific genome organization during myogenesis. The reduction of allelic spatial distance of one of these domains, which contains Myogenin, correlates with reduced transcriptional variability, identifying a potential role for lineage-specific nuclear topology. Using a fusion-based strategy to decouple mitosis and myotube formation, we demonstrate that the cell-specific topology of syncytial nuclei is dependent on cell division. We propose that the effects of linear and spatial organization of gene loci on gene regulation are linked through TAD architecture, and that mitosis is critical for establishing nuclear topologies during cellular differentiation.

Comparison of Super Structure-Sub Structure Separation Analysis and Unification Analysis about Building Structures

일반적으로 건축물의 구조해석과 설계에 있어 작업효율을 확보하기 위하여 상부구조물과 하부구조물을 별도로 모델링하여 해석 및 설계를 진행하는 분리해석 방법을 사용한다. 하지만, 상기 분리해석을 사용할 경우, 상부구조물의 고정지점과 변형된 기초구조물과는 실제 연결된 지점에서 변위차가 발생하여 구조해석의 기본요건인 변형적합성 조건을 만족하지 못하게 되고 상부구조-하부구조의 상호작용을 고려하지 못하기 때문에 실제와는 다른 구조해석 및 설계결과를 초래할 수 있다. 본 연구에서는 초고층 철골구조물을 대상으로 구조물의 부등침하 등에 큰 영향을 미치는 상재(常載)하중에 대한 분리해석과 일체해석의 해석결과 차이를 비교 분석하였다. 분석결과에 따르면 분리해석방법을 사용할 경우, 상부구조물의 구조해석에 있어 기초의 변형을 고려하지 못하기 때문에 부재력을 과소평가할 수 있고 이로인해 비안전측 설계결과를 가지고 올 수 있다. 하부 기초구조물을 분리해석으로 해석하였을 경우, 상부구조물의 강성을 고려하지 못하기 때문에 기초의 부등침하 과대평가, 부재력의 과대/과소 평가를 초래할 수 있어 비경제적이고 불안전한 설계결과를 가져올 수 있다. 특히, 기초의 변형이 상부구조물에 큰 영향을 미칠 수 있는 건축구조물, 지반의 강성이 작아서 기초에 큰 변형이 예상되는 건축물, 지반조건이 불균질하여 부등침하가 예상되는 건축구조물 등에는 분리해석을 지양해야 할 것이다. In the case of structural analysis for building structures, the super-structure and the sub-structure are analyzed by using separate structural models in the field because of time saving, facile result interpretation and easy analysis of dynamic behavior. However this separate structural model violated the compatibility condition of structural analysis and it can not consider the interaction of super- and sub- structures. In the present study, the analysis results of this separate model were compared to those of the unified model of super- and sub- structures which can consider the interaction of super- and sub- structures and reflect the realistic boundary conditions. According to the comparison results, the the analysis model using separate models can underestimate the member force and deflection of structural members in the super-structures and overestimate the deflection and member force of sub-structures. Therefore, in the case of high-rise buildings, irregular shaped buildings, buildings which are expected to be affected by large differential settlement and remodeling buildings, the unified structural model for super- and sub- structures was recommended for structural analysis instead of the separate structural model.

Structural modeling and convergence analysis of consensus-based time synchronization algorithms over networks: Non-topological conditions

This paper raises a quite general problem: how to characterize necessary conditions of bounded convergence, namely the divergence conditions, of a consensus-based time synchronization (CBTS) algorithm over a network with random communication delays. We firstly present a unified structural model of CBTS algorithms. Then, we fit different CBTS algorithms, such as DCTS, ATS, WMTS and LSTS, into the same structural model with just different algorithm parameters. To characterize divergence conditions, we focus on the algorithm structure and algorithm parameters rather than the topology graph of the network. By studying the asymptotic property of the relative drift estimation error of CBTS algorithms, we discover (almost sure) divergence conditions and mean-square divergence conditions of CBTS algorithms. Using these conditions we clearly point out that the DCTS algorithm is divergent, the ATS algorithm is divergent almost surely, the WMTS algorithm is mean-square divergent, but the LSTS overcomes all of these divergence conditions. The results of this paper provide a fundamental guideline for designing future time synchronization algorithms.

Self-assembled alkanethiol monolayers on gold surfaces: resolving the complex structure at the interface by STM.

The surface properties of metals and metal oxides can be modified by adding a single layer of organic molecules. A most popular route for depositing such a molecular layer is via the formation of self-assembled monolayers (SAMs). The molecules that form SAMs have a functionality which binds to the surface and the adsorption is self-regulated to terminate at exactly one single molecular layer. The very first example, which has become the most widely studied system, of SAMs on metal surfaces consists of chemisorbed alkylthiolate on gold. Despite the simplicity in the preparation of alkanethiol SAMs and the seemingly straightforward structure of such SAMs, the detailed bonding between the sulfur head group and gold is still subject to debate. Experimental and theoretical effort in the last six years has led to a much improved understanding of this classical system of SAMs. In this review, we will highlight the most recent progress in the study of the interfacial structure of alkanethiol SAMs on gold. We focus on the important phenomenon of phase transition that occurs from n-propanethiol to n-butanethiol, and propose a unified structural model to explain how the (3 × 4) phase for short chain alkanethiol monolayers (methyl-, ethyl- and propylthiolate monolayers) changes into the (3 × 2√3)-rect./c(4 × 2) phase for long chain molecular monolayers.

A level-set-based topology and shape optimization method for continuum structure under geometric constraints

Recent advances in level-set-based shape and topology optimization rely on free-form implicit representations to support boundary deformations and topological changes. In practice, a continuum structure is usually designed to meet parametric shape optimization, which is formulated directly in terms of meaningful geometric design variables, but usually does not support free-form boundary and topological changes. In order to solve the disadvantage of traditional step-type structural optimization, a unified optimization method which can fulfill the structural topology, shape, and sizing optimization at the same time is presented. The unified structural optimization model is described by a parameterized level set function that applies compactly supported radial basis functions (CS-RBFs) with favorable smoothness and accuracy for interpolation. The expansion coefficients of the interpolation function are treated as the design variables, which reflect the structural performance impacts of the topology, shape, and geometric constraints. Accordingly, the original topological shape optimization problem under geometric constraint is fully transformed into a simple parameter optimization problem; in other words, the optimization contains the expansion coefficients of the interpolation function in terms of limited design variables. This parameterization transforms the difficult shape and topology optimization problems with geometric constraints into a relatively straightforward parameterized problem to which many gradient-based optimization techniques can be applied. More specifically, the extended finite element method (XFEM) is adopted to improve the accuracy of boundary resolution. At last, combined with the optimality criteria method, several numerical examples are presented to demonstrate the applicability and potential of the presented method.

Hierarchical Structural Model of AC/DC Power Systems

The hierarchical decomposition and modeling method of large-scale power systems proposed previously is expanded to be suitable for AC/DC power systems in this paper. In the new model of AC/DC systems, DC systems will have the same position as AC systems. The components in AC/DC power systems are classified into three categories, namely conversion components, DC components and AC components. By analyzing the difference between DC interface and AC interface, the unified structural model suitable for any kind of component in AC/DC systems is built. Then, the hierarchical structural model is derived based on the hierarchical decomposition method. The main characteristics of the proposed AC/DC model are the same as that of previous AC model.

Ga<sub>2</sub>O<sub>3</sub>-ZnO系ホモロガス相の構造と高次元空間モデル

Long-period structures of homologous phases Ga2O3（ZnO）m are closely related to the wurtzite structure of ZnO, and structural evolution is discussed based on the results from structure analyses. A unified structure model for Ga2O3（ZnO）m is established in（3+1）dimensional superspace. Zig-zag functions with large amplitudes are used as modulation functions in the model, which is a common feature in structures constructed by the so-called unit-cell twining. Advantages of the superspace description for homologous phases are explained in relation to the process of identification of materials.

The Finne fault zone (central Germany): structural analysis of a partially inverted extensional fault zone by balanced cross-sections

The Finne fault zone, located in central Germany to the southwest of the Harz mountains, was studied by means of detailed map analysis, investigations of fault displacement and balanced cross-sections for the most strongly deformed area in the center of the fault zone (ca. 50 % of total fault zone length). The system of the Finne fault zone shows a nearly 100-km-long straight flexure that symbolizes the morphological and geological northeastern border of the Thuringian basin. In the central part, which should be surveyed here, the fault zone corresponds to a distinctive narrow band of highly deformed Triassic sedimentary rocks. The northwestern and especially the southeastern parts of the research area are developed as several parallel branch faults. In the southeastern elongation of the fault zone, which is not part of our survey, the sedimentary cover is missing. Here, it is possible to gain insight to the fact that the basement is also involved to the kinematics of the fault zone. Based on our results, we propose a subdivision of the fault zone into four sectors. From the northwest to the southeast, we interpret the structure of these sectors to reflect (1) a compressional flexure, (2) an overthrust graben, and (3) a partially inverted and folded half graben. In the extreme southeast (4), the fault zone is characterized by an anticline with some strike-slip movement parallel to the fold axis. This segmentation is caused by a thrust fault system whose strike direction deviates slightly from that of the earlier formed graben system. The structural configuration can be explained by a two-phase deformation, in which the contractional strain exceeded the preceding extensional deformation. In the investigated area, the horizontal shortening attains a maximum of ca. 1 km. The present study confirms many earlier hypotheses, presents new results on the deformation history of the fault zone, and attempts to evaluate the deformation in a regional geological context. The results of earlier studies were refined and revised using modern methods, and a unified structural and kinematic model of the Finne fault zone was created.

The Significance of G Protein-Coupled Receptor Crystallography for Drug Discovery

Crucial as molecular sensors for many vital physiological processes, seven-transmembrane domain G protein-coupled receptors (GPCRs) comprise the largest family of proteins targeted by drug discovery. Together with structures of the prototypical GPCR rhodopsin, solved structures of other liganded GPCRs promise to provide insights into the structural basis of the superfamily's biochemical functions and assist in the development of new therapeutic modalities and drugs. One of the greatest technical and theoretical challenges to elucidating and exploiting structure-function relationships in these systems is the emerging concept of GPCR conformational flexibility and its cause-effect relationship for receptor-receptor and receptor-effector interactions. Such conformational changes can be subtle and triggered by relatively small binding energy effects, leading to full or partial efficacy in the activation or inactivation of the receptor system at large. Pharmacological dogma generally dictates that these changes manifest themselves through kinetic modulation of the receptor's G protein partners. Atomic resolution information derived from increasingly available receptor structures provides an entrée to the understanding of these events and practically applying it to drug design. Supported by structure-activity relationship information arising from empirical screening, a unified structural model of GPCR activation/inactivation promises to both accelerate drug discovery in this field and improve our fundamental understanding of structure-based drug design in general. This review discusses fundamental problems that persist in drug design and GPCR structural determination.

Quasicrystalline Phase Transformation in the Quaternary and Ternary Systems AlCuMnFe and AlPdMn

An unified structural model has been devised [1] that describes both icosahedral phasesi-AlPdMn and i-AlCuFe. The model suggests that possible icosahedral structures could be found inalloys with general composition Al61:8(PdjCu)21:35(MnjFe)8:29(AljFejMn)4:28(AljCu)4:28. Applied to the systems AlCuMnFe [2] and AlPdFe [3], thisformula leads to the compositions Al66:08Cu21:35Mn8:29Fe4:28 and Al70:36Pd21:35Fe8:29 that have bothbeen synthetized by rapid quenching and annealing.The as-quenched quaternary alloy Al66:08Cu21:35Mn8:29Fe4:28 exhibits a F-icosahedral phase that trans-forms into a decagonal phase after annealing. Its 10-fold axis aligns along one of the 5-fold axes ofthe icosahedral phase. This implies a group-subgroup transformation, with the kernel group ̅5m, anal-ogous to the one observed during CFC to HCP transformations, with kernel ̅3m.The as-quenched and annealed ternary alloy Al70:36Pd21:35Fe8:29 is similar to i-AlPdMn with an iso-morphic substitution of Mn with Fe. A study of the phase diagram of the system AlPdFe [3] showsthat the results are compatible with the structural model proposed here in strong relations with thosepresented in [1] for i-AlPdMn.

Molecular Determinants and Thermodynamics of the Amyloid Precursor Protein Transmembrane Domain Implicated in Alzheimer's Disease

The deposition of toxic amyloid-β (Aβ) peptide aggregates in the brain is a hallmark of Alzheimer's disease. The intramembrane proteolysis by γ-secretase of the amyloid precursor protein β-carboxy-terminal fragment (APP-βCTF) constitutes the final step in the production of Aβ peptides. Mounting evidence suggests that APP-βCTF is a transmembrane domain (TMD) dimer, and that dimerization might modulate the production of Aβ species that are prone to aggregation and are therefore most toxic. We combined experimental and computational approaches to study the molecular determinants and thermodynamics of APP-βCTF dimerization, and we produced a unifying structural model that reconciles much of the published data. Using a cell assay that exploits a dimerization-dependent activator of transcription, we identified specific dimerization-affecting mutations located mostly at the N-terminus of the TMD of APP-βCTF. The ability of selected mutants to affect the dimerization of full-length APP-βCTF was confirmed by fluorescence resonance energy transfer experiments. Free-energy estimates of the wild type and mutants of the TMD of APP-βCTF derived from enhanced molecular dynamics simulations showed that the dimeric state is composed of different arrangements, in which either 709GXXXA 713 or 700GXXXG 704GXXXG 708 interaction motifs can engage in symmetric or asymmetric associations. Mutations along the TMD of APP-βCTF were found to modulate the relative free energy of the dimeric configurations and to differently affect the distribution of interfaces within the dimeric state. This observation might have important biological implications, since dimers with a different arrangement of the transmembrane helices are likely to be recognized differently by γ-secretase and to lead to a variation in Aβ levels.

Assessing the Impact of Eliminating Affirmative Action in Higher Education

This research examines the determinants of the match between high school seniors and postsecondary institutions in the United States. I model college application decisions as a nonsequential search problem and specify a unified structural model of college application, admission, and matriculation decisions that are all functions of unobservable individual heterogeneity. The results indicate that black and Hispanic representation at all 4‐year colleges is predicted to decline modestly—by 2%—if race‐neutral college admissions policies are mandated nationwide. However, race‐neutral admissions are predicted to decrease minority representation at the most selective 4‐year institutions by 10%.

Turning exploration risk into a carbon storage opportunity in the UK Southern North Sea

ABSTRACT Interpretation of a large, well-calibrated 3D seismic data volume in the UK Southern North Sea (SNS) suggests that the occurrence of two little known and hitherto poorly documented carbon dioxide (CO 2 )-rich gas discoveries is strongly controlled by the style and timing of deformation and the presence of a regional Upper Permian (Zechstein Supergroup) evaporite super-seal. It can now be shown that the CO 2 -rich accumulations are limited to Rotliegend Group, Leman Sandstone Formation (LSF) reservoirs located on the western edge of a major, extensional fault block, the Fizzy Horst, that lies on the eastern flank of a through-going NNW-striking, partially-inverted depocentre, termed the Brown Graben. Significantly, unlike other structures, which experienced Cenozoic compressional reactivation, the traps containing the CO 2 are located adjacent to deep-seated faults upon which contractional reactivation occurred only during the Late Cretaceous suggesting a spatial and temporal control on its occurrence. The structural results provide a robust, unifying and testable structural model through which to assess the inherent exploration risk of drilling unwanted, CO 2 -prone traps in this part of the prospective basin. Conversely, the fact that CO 2 was evidently sealed over geological time-scales shows the significance and long-lived ( c . 50 Ma) effectiveness of the Zechstein Supergroup evaporite canopy in retaining CO 2 , as well as larger and less mobile methane (CH 4 ) molecules. The results thus highlight the potential that traps containing LSF reservoirs have as future sites for CO 2 storage (carbon sequestration) in the SNS.

The COPII cage: unifying principles of vesicle coat assembly

Communication between compartments of the exocytic and endocytic pathways in eukaryotic cells involves transport carriers - vesicles and tubules - that mediate the vectorial movement of cargo. Recent studies of transport-carrier formation in the early secretory pathway have provided new insights into the mechanisms of cargo selection by coat protein complex-II (COPII) adaptor proteins, the construction of cage-protein scaffolds and fission. These studies are beginning to produce a unifying molecular and structural model of coat function in the formation and fission of vesicles and tubules in endomembrane traffic.

Phenomenological band structure model of magnetic coupling in semiconductors

A unified band structure model is proposed to explain the magnetic ordering in Mn-doped semiconductors. This model is based on the p–d and d–d level repulsions between the Mn ions and host elements and can successfully explain magnetic ordering observed in all Mn doped II–VI and III–V semiconductors such as CdTe, GaAs, ZnO, and GaN. The model can also be used to explain the interesting behavior of GaMnN, which changes from ferromagnetic ordering to antiferromagnetic ordering as the Mn concentration increases. This model, therefore, is useful to provide a simple guideline for future band structure engineering of magnetic semiconductors.

Structural Modeling and Aeroelastic Analysis of High-Aspect-Ratio Composite Wings

A unified structural model for high-aspect-ratio composite wing with arbitrary cross-section is developed. Two types of lay-ups of the composite wing, namely, circumferentially uniform stiffness (CUS) configuration and circumferentially asymmetric stiffness (CAS) configuration, are investigated. The present structural modeling method is validated through ANSYS FEM software for the case of a composite box beam. Then, the case of a single-cell composite wing with NACA0012 airfoil shape is considered. To investigate the aeroelastic problem of high-aspect-ratio composite wings, the linear ONERA aerodynamic model is used to model the unsteady aerodynamic loads under the case of small angle of attack. Finally, flutter speeds of the high-aspect-ratio wing with various composite ply angles are determined by using U-g method.

Scanning tunneling microscopy study of GaAs(001) surfaces

While GaAs(001) is the most commonly used substrate in fabrication of wireless and opto-electronic devices based on III–V compound semiconductors by molecular beam epitaxy (MBE), metallorganic chemical vapor deposition (MOCVD) and related techniques, its surface structure have been disputed since the beginning of development of the techniques. Invention of scanning tunneling microscopy (STM) has revolutionized the approach of surface/interface investigation, contributing greatly in the atomistic understanding of the GaAs surface phases. This paper reviews the STM studies of principal reconstructions, from As-rich c(4×4), 2×4, 2×6 to Ga-rich 4×2 and 4×6, found on the GaAs (001) surface. These studies, together with advanced theoretical efforts, have helped us to establish a unified structural model for various reconstructions, with which we can now explain most of the observations and long-standing controversies in atomic structures and surface stoichiometries.

A new unifying structural model of heteropolymolybdate salts: Microstructure and thermal stability of a series of molecular oxides

AbstractPowder X‐ray diffraction and cryo electron diffraction techniques supported by computer simulations were used to determine the secondary structures of the series of heteropoly acid (HPA) compounds CsxH4‐x PVMo11O40·nH2O (0≤x≤4). The structures of the caesium salts (2≤x≤4) are simple cubic with space group Pn3m. The free acid exhibits a triclinic lattice (P−1) for the majority of all crystals. A small fraction of thin crystals was detected with simple cubic structure (Pn3m). Computer simulations of the X‐ray diffraction patterns suggested that the structure of Cs2H2PVMo11O40·5H2O contains defects in the cation lattice. The caesium ion occupancy is 2/3. [H5O2]+‐groups occupy 1/3 of the cation positions. The diffraction pattern of Cs4PVMo11O40·5H2O could be simulated when only 3/4 of the anion positions are occupied. Cs3HPVMo11O40·7H2O crystallises in a simple cubic lattice without any defects.The secondary structures of the investigated heteropoly salts can, therefore, be described by a single structure with variable site occupations, with the exception of Cs3HPVMo11O40·7H2O (caesium ion occupancy of 1 and poly anion occupancy of 1). All salts belong to one phase with large stoichiometric variations. A mixture of acid and caesium salt, with the acid epitactly grown on the salts, an intergrowth‐structure witii varying caesium ion content, mixed crystals as well as the coexistence of a nanocrystalline X‐ray‐invisible form of free acid besides caesium salt could be excluded for the partly neutralised materials. Selected physico‐chemical properties of the HPA compounds, which depend on the caesium ion content, will be rationalised widi the knowledge of the secondary structures.

Atomic structures of gallium-rich GaAs(001)-4×2 and GaAs(001)-4×6 surfaces

Scanning tunneling microscopy is applied for the first time to an atomic-resolution investigation of the 4×2 and 4×6 phases on a gallium-rich GaAs(001) surface obtained by molecular-beam epitaxy and migration-enhanced epitaxy. A unified structural model is proposed with consideration of the results of experiments and first-principles calculations of the total energy. In this model the 4×2 phase consists of two Ga dimers in the top layer and a Ga dimer in the third layer, and the 4×6 phase is matched to periodically arranged Ga clusters at the corners of a 4×6 unit cell on top of the 4×2 phase.

A novel family of ubiquitous heavy metal ion transport proteins.

We describe a novel diverse family of metal ion transporter (CDF) proteins (the cation diffusion facilitator (CDF) family) with members occurring in both prokaryotes and eukaryotes. Thirteen sequenced protein members of the CDF family have been identified, several of which have been shown to transport cobalt, cadmium and/or zinc. All members of the CDF family possess six putative transmembrane spanners with strongest conservation in the four N-terminal spanners, and on the basis of the analyses, we present a unified structural model. Members of the family are shown to exhibit an unusual degree of size variation, sequence divergence, and differences in cell localization and polarity. The phylogenetic tree for the CDF family reveals that prokaryotic and eukaryotic proteins cluster separately. It allows functional predictions for some uncharacterized members of this family. A signature sequence specific for the CDF family is derived.