Structural Architecture Research Articles

Conformation of factor Xa in solution revealed by single-molecule spectroscopy

BackgroundAll current X-ray structures of factor (F)Xa are devoid of the γ-carboxyglutamate (Gla) domain and fail to reveal the overall conformation of the free protein. The recent cryogenic electron microscopy (cryo-EM) structure of FXa in the prothrombinase complex is the only structure of full-length FXa and shows that the Gla domain is positioned at an angle relative to the epidermal growth factor 1 domain. ObjectivesEstablish if the curved conformation of FXa revealed by cryo-EM is also present in solution. MethodsThe conformation of FXa in solution was studied by single-molecule Förster resonance energy transfer. ResultsThe conformation of full-length FXa in solution is resolved for the first time. The conformation is curved and extremely sensitive to Ca2+. It does not differ significantly from its zymogen form or from that present in the prothrombinase complex free or bound to the physiologic substrates prothrombin and meizothrombin. ConclusionMeasurements by single-molecule Förster resonance energy transfer reveal that FXa has a curved conformation in solution, free or bound to physiologic ligands, and validate the recent cryo-EM structures of prothrombinase. The drastic conformational changes observed in the absence of Ca2+ suggest that the structural architecture of FXa changes upon administration of vitamin K antagonists that perturb the interaction of the Gla domain with divalent cations.

Dynamic Expansions and Retinal Expression of Spectrally Distinct Short-Wavelength Opsin Genes in Sea Snakes.

The photopigment-encoding visual opsin genes that mediate color perception show great variation in copy number and adaptive function across vertebrates. An open question is how this variation has been shaped by the interaction of lineage-specific structural genomic architecture and ecological selection pressures. We contribute to this issue by investigating the expansion dynamics and expression of the duplicated Short-Wavelength-Sensitive-1 opsin (SWS1) in sea snakes (Elapidae). We generated one new genome, 45 resequencing datasets, 10 retinal transcriptomes, and 81 SWS1 exon sequences for sea snakes, and analyzed these alongside 16 existing genomes for sea snakes and their terrestrial relatives. Our analyses revealed multiple independent transitions in SWS1 copy number in the marine Hydrophis clade, with at least three lineages having multiple intact SWS1 genes: the previously studied Hydrophis cyanocinctus and at least two close relatives of this species; Hydrophis atriceps and Hydrophis fasciatus; and an individual Hydrophis curtus. In each lineage, gene copy divergence at a key spectral tuning site resulted in distinct UV and Violet/Blue-sensitive SWS1 subtypes. Both spectral variants were simultaneously expressed in the retinae of H. cyanocinctus and H. atriceps, providing the first evidence that these SWS1 expansions confer novel phenotypes. Finally, chromosome annotation for nine species revealed shared structural features in proximity to SWS1 regardless of copy number. If these features are associated with SWS1 duplication, expanded opsin complements could be more common in snakes than is currently recognized. Alternatively, selection pressures specific to aquatic environments could favor improved chromatic distinction in just some lineages.

Advancing electrochemical CO2 reduction with group 11 metal nanoclusters for renewable energy solutions

AbstractUnderstanding the intricate relationship between structure and properties is paramount in distinguishing nanocluster (NC) materials from their counterparts. Despite the progress in synthesizing new NCs, the sluggish exploration of their potential applications persists due to the difficulty in stabilizing these materials. However, recent investigations have unveiled their remarkable efficacy as catalysts in electrochemical CO2 reduction reactions, surpassing traditional materials. This discovery, addressing urgent global concerns, has quickly drawn significant attention to this field, leading to its rapid expansion. Hence, there is an urgent need to outline this research landscape and pinpoint effective strategies, marking a significant advancement. In this context, our endeavor is dedicated to offering researchers a thorough understanding of recently synthesized NC materials. We aim to elucidate their distinct structural architectures and associated properties essential for catalyst design. We envision that this systematic review will serve as a guiding beacon for future research endeavors in this burgeoning field.

Four-Dimensional Digital Monitoring and Registering of Historical Architecture for the Preservation of Cultural Heritage

Preserving cultural heritage through monitoring, registering, and analyzing damage in historical architectural structures presents significant financial and logistical burdens. Developed approaches for monitoring and registering 4D (4-dimensional)-scanned range and raster images of damaged objects were investigated in a case study of historical Baron Palace in Egypt. In the methodology, we first prepared and observed the damaged historical models. The damaged historical models were scanned using a laser scanner at a predetermined date and time. Simultaneously, digital images of the models were captured (by a calibrated digital camera) and stored on a researcher’s tablet device. By observing and comparing the scanned models with the digital images, geometric defects and their extent are identified. Then, the observed data components were detected on the map. Then, damaged statue materials were investigated using system of energy dispersive (SEM; scanning electron microscope, Gemini Zeiss-Ultra 55) and XRF (X-ray fluorescence) spectroscopic analysis to identify the statue’s marble elements, and the results indicate that SEM-EDX and XRF analyses accurately identify major and minor compositions of the damaged statue. Then, the damaged models were registered in two stages. In the registration stages, the corresponding points were determined automatically by detecting the closest points in the clouds and ICP (iterative closest point) algorithm in RiSCAN. The point clouds (of the Palace and damaged statues) gave very detailed resolutions and more realistic images in RiSCAN, but it is a costly program. Finally, the accuracies of the registration tasks were assessed; the standard deviations are within acceptable limits and tend to increase irregularly as the number of polydata observations used in the registration calculations increase.

Natural Fiber-Reinforced Mycelium Composite for Innovative and Sustainable Construction Materials

Fiber-reinforced mycelium (FRM) composites offer an innovative and sustainable approach to construction materials for architectural structures. Mycelium, the root structure of fungi, can be combined with various natural fibers (NF) to create a strong and lightweight material with environmental benefits. Incorporating NF like hemp, jute, or bamboo into the mycelium matrix enhances mechanical properties. This combination results in a composite that boasts enhanced strength, flexibility, and durability. Natural FRM composites offer sustainability through the utilization of agricultural waste, reducing the carbon footprint compared to conventional construction materials. Additionally, the lightweight yet strong nature of the resulting material makes it versatile for various construction applications, while its inherent insulation properties contribute to improved energy efficiency in buildings. Developing and adopting natural FRM composites showcases a promising step towards sustainable and eco-friendly construction materials. Ongoing research and collaboration between scientists, engineers, and the construction industry will likely lead to further improvements and expanded applications. This article provides a comprehensive analysis of the current research and applications of natural FRM composites for innovative and sustainable construction materials. Additionally, the paper reviews the mechanical properties and potential impacts of these natural FRM composites in the context of sustainable architectural construction practices. Recently, the applicability of mycelium-based materials has extended beyond their original domains of biology and mycology to architecture.

Cumulative phylogenetic, sequence and structural analysis of Insulin superfamily proteins provide unique structure-function insights.

The insulin superfamily proteins (ISPs), in particular, insulin, IGFs and relaxin proteins are key modulators of animal physiology. They are known to have evolved from the same ancestral gene and have diverged into proteins with varied sequences and distinct functions, but maintain a similar structural architecture stabilized by highly conserved disulphide bridges. The recent surge of sequence data and the structures of these proteins prompted a need for a comprehensive analysis, which connects the evolution of these sequences (427 sequences) in the light of available functional and structural information including representative complex structures of ISPs with their cognate receptors. This study reveals (a) unusually high sequence conservation of IGFs (>90 % conservation in 184 sequences) and provides a possible structure-based rationale for such high sequence conservation; (b) provides an updated definition of the receptor-binding signature motif of the functionally diverse relaxin family members (c) provides a probable non-canonical C-peptide cleavage site in a few insulin sequences. The high conservation of IGFs appears to represent a classic case of resistance to sequence diversity exerted by physiologically important interactions with multiple partners. We also propose a probable mechanism for C-peptide cleavage in a few distinct insulin sequences and redefine the receptor-binding signature motif of the relaxin family. Lastly, we provide a basis for minimally modified insulin mutants with potential therapeutic application, inspired by concomitant changes observed in other insulin superfamily protein members supported by molecular dynamics simulation.

Physics-based discrete models for magneto-mechanical metamaterials

Magneto-mechanical metamaterials are emerging smart materials whose mechanical responses can be tailored through structure architecture and magnetic interactions. The latter provides additional freedom in the material design space and leads to novel behaviors due to its nonlocal nature. The enriched functionalities open new possibilities in various applications, such as actuators, energy absorbers, and soft robots. However, the nonlinear and nonlocal coupling between elastic and magnetic forces poses a great challenge in the modeling and simulation of these systems, further hindering theory-based rational design strategies. Here, we focus on a class of magneto-mechanical metamaterials comprising elastic solids embedded with rigid permanent magnets. The clear separation between elastic and magnetic forces simplifies the design and fabrication process, yet their nonlocal interplay still allows for complex behaviors. We present a simulation framework for such magneto-mechanical metamaterials by combining a lattice spring model for the elastic solid with the dipole model for the magnetic interactions and implementing it in the LAMMPS molecular dynamics software. We demonstrate the capabilities of our framework by simulating a few representative structures, including shape-locking lattice metamaterials, a soft cellular solid with controllable buckling, and a metamaterial chain with phase-transforming behavior. For the shape-locking lattice metamaterials, we successfully capture the magnetic-actuation-driven reconfiguration and the nonlinear mechanical response of the curved lattices. For the soft cellular solid, we identify its buckling patterns under external non-uniform magnetic fields and simulate a buckling evolution process consistent with experiments. For the metamaterial chain, we include the strong long-range interactions among the embedded magnets and reproduce the controllable phase transitions in the experiments. Our work provides a simple yet versatile simulation methodology to investigate the nonlinear mechanical behaviors in the presence of strong external and internal magnetic forces, which will facilitate the design and analysis of magneto-mechanical materials. It can also be applied to other magnetically-driven smart structures, such as soft robots.

Bacterial protein acetylation: mechanisms, functions, and methods for study.

Lysine acetylation is an evolutionarily conserved protein modification that changes protein functions and plays an essential role in many cellular processes, such as central metabolism, transcriptional regulation, chemotaxis, and pathogen virulence. It can alter DNA binding, enzymatic activity, protein-protein interactions, protein stability, or protein localization. In prokaryotes, lysine acetylation occurs non-enzymatically and by the action of lysine acetyltransferases (KAT). In enzymatic acetylation, KAT transfers the acetyl group from acetyl-CoA (AcCoA) to the lysine side chain. In contrast, acetyl phosphate (AcP) is the acetyl donor of chemical acetylation. Regardless of the acetylation type, the removal of acetyl groups from acetyl lysines occurs only enzymatically by lysine deacetylases (KDAC). KATs are grouped into three main superfamilies based on their catalytic domain sequences and biochemical characteristics of catalysis. Specifically, members of the GNAT are found in eukaryotes and prokaryotes and have a core structural domain architecture. These enzymes can acetylate small molecules, metabolites, peptides, and proteins. This review presents current knowledge of acetylation mechanisms and functional implications in bacterial metabolism, pathogenicity, stress response, translation, and the emerging topic of protein acetylation in the gut microbiome. Additionally, the methods used to elucidate the biological significance of acetylation in bacteria, such as relative quantification and stoichiometry quantification, and the genetic code expansion tool (CGE), are reviewed.

An Investigation into the Variables Influencing the Structural Bamboo Architecture Using Filled Concrete and Cement Mortar

Bamboo, as a green building material, plays a vital role in construction. Bamboo has good properties and appearance, making it highly attractive for building structures and designs. Since the compressive capacity of bamboo is considerably lower than its tensile capacity, with the ratio typically ranging between 300% to 900%, this limits its application dimensions in construction. Therefore, filling the original bamboo structural members with specific materials or applying different connection methods can not only maintain the appearance of the bamboo structure but also improve its compressive capacity and overall durability, thus expanding the application range of bamboo structural members and enhancing the performance of the architectural design process. Two hollow bamboo specimens were among the eight BFC specimens tested for this paper. Key components such as transverse stiffeners, steel bars, filler materials, and bamboo nodes were examined for their influence on the specimens’ ductility, peak strain, ultimate bearing capacity, and failure mechanisms. The test results showed that the ratio of the ultimate bearing capacity of BFC specimens to hollow bamboo samples could reach up to 538%, while the peak strain differences were minimal. A non-linear finite element model was developed and its accuracy confirmed based on the test results. This work proposes a new approach to determine the final axial compressive capacity of BFC columns by creating an elastic model of transversely isotropic cylinders. As a result, the primary goal of this study is to establish a foundation for more scientific building design techniques and procedures by examining the axial compression mechanics of structural bamboo filled with cement and concrete (BFC) and how it influences building design.

Biometric variability of inflorescence and flower traits among ex situ accessions of the neotropical oilseed palm Acrocomia Mart.

The oilseed palm genus Acrocomia is suitable for sustainable oil production in South America. The high phenotypic diversity of wild populations poses a challenge for the delimitation of the genus. Comparing the inflorescence architecture, a first-order panicle, and staminate and pistillate flower traits could be a valuable tool in resolving the taxonomic disarray. Thus, this study aims to characterize the differences in the inflorescence architecture and floral structures of three common and economically significant Acrocomia species: A. aculeata, A. totai, and A. intumescens. Biometric traits of the inflorescence architecture and floral structures of various Acrocomia accessions in an ex situ germplasm collection in Brazil were assessed. The unweighted pair group method with arithmetic mean (UPGMA) cluster analysis based on the Gower distance was used to measure dissimilarities between the individual plants of the accessions. To our best knowledge, this study provides the first evidence of the presence of second-order rachillae in the genus Acrocomia. Evaluated traits showed a high level of variation within and between accessions, emphasizing the phenotypic diversity of the genus. The accessions of A. totai were distinguishable from those of the other two species by their inflorescence architecture and flower traits. The dissimilarities between A. aculeata and A. intumescens were not sufficient to differentiate both. In conclusion, the quantitative assessment of inflorescence and floral traits is a valuable tool for taxonomic resolution of the genus.

Sustainable Living: Young Adults Prolonging the Material Life Cycle of Objects Through the Appreciation of Used Furniture, Interiors, and Building Design

AbstractYoung adults acquire furniture from retail stores, second-hand shops, flea markets, and online marketplaces; they also inherit items from family members. While scholars have focused on consumers who acquire second-hand objects and appreciate inherited furniture, limited attention has been paid to the meanings of second-hand and inherited objects as elements of sustainable home interior decoration. Based on qualitative data, we analyze how young adults living in three northern European cities value used interior-decoration objects and how this enhances sustainable ways of using goods. Our study shows that young people appreciate architectural structures and interior-design aesthetics as well as inherited and recycled items in their homemaking. The building and home-decor style of the era shape the way consumers acquire used interior-design materials and objects. Moreover, young adults engage with inherited and purchased second-hand furniture by incorporating narratives about social ties during their acquisition. The durability of materials is valued in both inherited and second-hand furniture. Thus, young adults prolong the life spans of home-decor items, and they contribute to a sustainable, low-speed circular economy linked to homemaking.

FORTIFICATION LINE OF THE GRAND DUCHY OF LITHUANIA: A NEW STAGE OF DEFENSE ARCHITECTURE OF THE EASTERN EUROPE SPACE

The theme of the history of medieval defensive architecture in the Northern Black Sea region becomes extremely relevant in the realities of the modern history of Ukraine, when the Russian invaders try to capture the southern lands of Ukraine and defend the idea of belonging of these territories to Russia with pseudo-historical concepts of «Russian peace». The results of the historical and archaeological study of the South of Ukraine, especially in recent decades, demonstrate other circumstances of the development of the South. They make it possible to highlight the main trends of the evolution of the region in direct continuity with the previous history of Russia in new historical circumstances. This is the time when the Kyiv principality became part of the Grand Duchy of Lithuania, Russia and Zhemaitia, the borders of which reach the Black Sea coast in the late 14th — early 15th century. Here the turbulent activity of the Grand Duke of Lithuania Vytautas unfolds in the construction of fortresses, customs houses, the arrangement of crossings and port facilities. The defensive architecture of the Southern region of the Grand Duchy of Lithuania, Russia and Zhemaitia takes place during the formation of a new map of Eastern Europe, with the presence of Lithuania, the formation of early Ukraine on the heritage of Russia, the formation of the Crimean Tatar people and its statehood, the active activity of the Principality of Moldavia in connection with the presence and influences of Genoa, contacts with Poland, influence of Ottoman Empire and other states of that time. It was the time of construction of the castle fortification, which belonged to the first stage of adaptation of military affairs to the artillery of the contemporary world, which covers the time of the 14th— 16th centuries. The comparative castellology gave the possibilities to study some regularity in the typological model of fortresses. This method was used in the course of study of fortresses of Vitovt’s fortification line, such as Tiagin fortress. It allows establishing the common features of the planning structure of the fortification architecture of the Northern Black Sea region — a new stage of evolution, which was characterized by stone castle architecture. In turn, they met the needs of the stage of development of artillery at the end of the 14th and the beginning of the 16th centuries. Medieval Europe, in which the influences of various cultures of the East and the West intersect, new defense opportunities and prospects are developing.

On the fusion between interferometric satellite data and in situ measurements for the monitoring of built heritage

Over the past decades, earthquakes, and other catastrophic events has highlighted the increasingly growing vulnerability of infrastructures, buildings, and architectural heritage structures. In addition to catastrophic events, often related to climate change, another fundamental aspect is represented by the lack of maintenance and monitoring of the asset. In the field of preservation of buildings and infrastructures, Structural Health Monitoring techniques can effectively contribute to the assessment of the health state of structures. In the case of structural monitoring using data-driven approaches, since the information depends on the type of data used, a great resource for knowing as much as possible about the structure is represented by the combination of multiple data. Thanks to the integration of different types of data, it is possible to know the conditions of the structure in more detail as different aspects can be combined. In this context, together with the data obtained from in situ monitoring systems, data obtained remotely, i.e. satellite data, can be used. There are different types of satellite data that can be used to study different aspects, e.g., multispectral data, hyperspectral data, and interferometric data, and they can make different contribution to civil engineering. In this paper, the exploitability of open-source interferometric data is investigated and they are studied for the purpose of their integration with data obtained from a monitoring system installed on a monumental building, in order to monitor and observe structural health.

Impact of Block Ratio, Polymer Architecture, and Soft Segment Structure on Modified Asphalt Rheological Performance

Impact of Block Ratio, Polymer Architecture, and Soft Segment Structure on Modified Asphalt Rheological Performance

A Functional Switch Between Asperfumene and Fusicoccadiene Synthase and Entrance to Asperfumene Biosynthesis through a Vicinal Deprotonation-Reprotonation Process.

The diterpene synthase AfAS was identified from Aspergillus fumigatiaffinis. Its amino acid sequence and-according to a structural model-active site architecture are highly similar to those of the fusicocca-2,10(14)-diene synthase PaFS, but AfAS produces a structurally much more complex diterpene with a novel 6-5-5-5 tetracyclic skeleton called asperfumene. The cyclisation mechanism of AfAS was elucidated through isotopic labelling experiments and DFT calculations. The reaction cascade proceeds in its initial steps through similar intermediates as for the PaFS cascade, but then diverges through an unusual vicinal deprotonation-reprotonation process that triggers a skeletal rearrangement at the entrance to the steps leading to the unique asperfumene skeleton. The structural model revealed only one major difference between the active sites: The PaFS residue F65 is substituted by I65 in AfAS. Intriguingly, site-directed mutagenesis experiments with both diterpene synthases revealed that position 65 serves as a bidirectional functional switch for the biosynthesis of tetracyclic asperfumene versus structurally less complex diterpenes.

Integration of Large Multielement Geochemical, Aeromagnetic, and Gravity Data to Geologically Map a Largely Covered Area: A Case Study from the Central African Copperbelt in Northern Zambia

Abstract This study provides a method to map lithology, stratigraphy, and structures in areas with limited outcrop using mineral exploration data from multielement soil geochemical surveys, airborne and ground geophysical surveys, and drill hole data sourced from multiple exploration companies and campaigns. The 45- by 50-km study area is located in the southern portion of the Congolese Copperbelt, where the regional geology, structure, and overall basin architecture were not well understood, partly due to thick saprolite cover. The results demonstrate that the integration of such data sets allows the creation of a geologically coherent map, which can then be used to investigate basin architecture and identify basin-forming structures.

Examining the Ex(Im)plicit Qualities in Japanese Spatial Atmosphere through Haiku 俳句 and Haiga 俳画 Examples: The Layer of Narration

Abstract: In any focus on an aesthetic experience one may find both sensational and cognitive qualities, referred to as the scene and scenario, respectively. Hence, an experiencer tries to decipher the scenario— a narration—by sensing the scene— space—through the spatial atmosphere. Thus, space starts to transform into a poetic experience. Japanese architecture, on account of a number of inherent qualities, has the capability to convey such narrations in spaces. In Japanese examples, an experiencer tries to derive the narration that emanates from explicit qualities—sensational, such as textual, visual, audial, or tactile phenomena—with his/her implicit qualities—cognitive/intellectual abilities. The article examines the layer of narration of Japanese architectural structure through haiku 俳句 and haiga 俳画 examples, and in doing so, utilizes the layers proposed on behalf of the explicit and implicit qualities: nature-based and feeling-based .

Structural architecture of Gebel Hamza, Northwestern sector of Cairo-Suez District, Egypt

Structural architecture of Gebel Hamza, Northwestern sector of Cairo-Suez District, Egypt

Integration of electromagnetic and mechanical models for effective lightning protection in buildings

The study focused on the design of an advanced algorithm for the optimal sizing of protection systems against atmospheric discharges in architectural structures, applying the rolling sphere method. This technique facilitated the incorporation of user-specified parameters through an advanced graphical interface. The methodology began with the exhaustive accumulation of data relevant to the project. Risk indices were estimated through sophisticated risk analysis software applications. If adjustments were required, the process continued; If not, the building was considered to be adequately secured. The ground resistivity was evaluated according to IEEE Std. 81, and the rolling sphere method was implemented according to IEC 662305-3. The grounding systems were configured in accordance with IEEE Std. 142 and IEEE Std. 80. To analyze the interaction of electrical discharges with the protected building, the electrical equivalents of elements such as meshes, fused copper rods were computed. , and conductors positioned horizontally and vertically. Using these data, a model was built in ATPDraw, interconnected with Python for the generation of graphical representations of the current waves in the different protection subsystems. To conclude and corroborate the effectiveness of the process, the risk indices were reevaluated. The validation of the algorithm was achieved by minimizing the margin of error to insignificant levels by incorporating standardized data proposed by organizations such as IEC and IEEE, thus confirming the precision of the designed algorithm

Abstracting the Architecture Design System to Create New Applications

In software engineering, application design and architecture play an important function of their improvement, maintenance and scalability. This paper explores the idea of ​​abstracting architectural design approaches to facilitate the advent of latest packages. By decoupling structure from unique application contexts, builders have the ability to test new technologies, adapt to evolving wishes, and scale their programs. Finally, this paper recommends to adopt abstract architecture design systems as a method for software improvement. By offering a based framework for constructing new packages, the abstraction of architectural design structures empowers developers to innovate, iterate and optimize in a dynamic business surroundings, and truly fosters a tradition of continuous improvement and excellence in the application development exercise.