A numerical method based on nonlinear incremental dynamic analysis is proposed in this paper to develop seismic fragility curves for rectangular subway station buried in layered soil and subjected to ...transverse seismic excitations. The proposed method primarily consists of four parts, namely, model verification, damage quantification, ground motion processing, and seismic performance assessment. The main section of the Daikai subway station collapsed during the Kobe Earthquake is used as an example to demonstrate the detailed procedure of the proposed method in construction of seismic fragility curves for underground structures. Results from the nonlinear soil-structure interaction model in this paper is firstly verified against the results from existing literature. The threshold values of different damage states of the underground structure are quantified by interstory drift ratio obtained from the nonlinear static pushover analysis of the soil-structure interaction system. Based on the results of the incremental dynamic analysis, it is found that the peak acceleration at the ground surface is an efficient and appropriate intensity measure of the ground motions for shallowly buried underground structure. The proposed method is validated by comparing with the existing empirical and numerical seismic fragility curves of buried rectangular underground structures and can be used as an effective approach in the development of seismic fragility database for underground structures.
This paper presents an efficient approach for the modal analysis of coupled soil-structure systems, for which the dynamic response is strongly influenced by the embedment in the soil. The methodology ...is based on a finite element-perfectly matched layer model that allows for the derivation of frequency-independent system matrices and the computation of the modal properties of the coupled system. This is achieved by solving a nonlinear eigenproblem using a Compact Rational Krylov (CoRK) eigensolver. A procedure is developed to sort the computed eigenpairs, filter out the spurious modes of the system which are related to the near-field and truncated far-field soil subdomains and select the physical structural modes of system. The proposed method can be used in the dynamic assessment and structural identification of strongly coupled soil-structure systems such as fully or partially buried structures and allows for the interpretation of experimentally identified modal properties of these systems, especially in the presence of highly damped or closely spaced coupled modes. The applicability and the scalability of the proposed approach for 2D and 3D problems is demonstrated in two case studies.
•A FE-PML model together with a CoRK eigensolver are employed for modal analysis of coupled soil-structure systems.•The concept of the stabilization diagram is used to filter out the spurious modes of system.•A criteria is developed to select the physical structural modes of system.•The measured modal properties of a full-scale bridge-soil system is used to demonstrate the methodology.
The interstory drift ratios (IDRs) associated with the performance objectives for the underground structure are not well defined. In this paper, four levels of performance objectives are defined for ...shallow‐buried subway station structure: operational, immediate occupancy, life safety, and collapse prevention. In order to develop IDRs corresponding to these performance objectives, 18 subway station structures were selected for this study. Pushover analyses were conducted using three‐dimensional finite‐element models considering two conditions of seismic loading: vertical and horizontal ground motions; and horizontal ground motion only. Shear‐displacement capacity curves of the 18 subway station structures were obtained, and IDR limits were defined for each structure based on the relationship between the capacity curves and performance objective. Statistical analysis of the results demonstrated that the IDR limits considering the vertical ground motion (characterized by the same frequency with horizontal component) are smaller than that without consideration of the vertical ground motion. Based on these results, the IDR limit of 0.05%, 0.21%, 0.46%, and 0.72% is assigned for the four performance levels, respectively, for rectangular frame underground structures. The performance evaluation applied to Daikai station based on the proposed limits is found to be consistent with the actual postearthquake damage observations. The proposed limits of IDR could provide some guidance to the seismic design of underground structures, and could form the basis for developing appropriate performance limits for seismic provisions in design codes relevant to underground structures.
The number of membrane protein structures in the Protein Data Bank is becoming significant and growing. Here, the transmembrane domain structures of the helical membrane proteins are evaluated to ...assess the influences of the membrane mimetic environments. Toward this goal, many of the biophysical properties of membranes are discussed and contrasted with those of the membrane mimetics commonly used for structure determination. Although the mimetic environments can perturb the protein structures to an extent that potentially gives rise to misinterpretation of functional mechanisms, there are also many structures that have a native-like appearance. From this assessment, an initial set of guidelines is proposed for distinguishing native-like from nonnative-like membrane protein structures. With experimental techniques for validation and computational methods for refinement and quality assessment and enhancement, there are good prospects for achieving native-like structures for these very important proteins.
In recent years, three‐dimensional density maps reconstructed from single particle images obtained by electron cryo‐microscopy (cryo‐EM) have reached unprecedented resolution. However, map ...interpretation can be challenging, in particular if the constituting structures require de‐novo model building or are very mobile. Herein, we demonstrate the potential of convolutional neural networks for the annotation of cryo‐EM maps: our network Haruspex has been trained on a carefully curated set of 293 experimentally derived reconstruction maps to automatically annotate RNA/DNA as well as protein secondary structure elements. It can be straightforwardly applied to newly reconstructed maps in order to support domain placement or as a starting point for main‐chain placement. Due to its high recall and precision rates of 95.1 % and 80.3 %, respectively, on an independent test set of 122 maps, it can also be used for validation during model building. The trained network will be available as part of the CCP‐EM suite.
Haruspex is a new tool to identify secondary structure and RNA/DNA in cryo‐EM reconstruction maps. It uses a neural network which has been trained on a carefully curated set of 293 experimentally derived reconstructions and can be straightforwardly applied to newly reconstructed maps to support model building and validation.
We have designed and synthesized five azulene derivatives containing gold-binding groups at different points of connectivity within the azulene core to probe the effects of quantum interference ...through single-molecule conductance measurements. We compare conducting paths through the 5-membered ring, 7-membered ring, and across the long axis of azulene. We find that changing the points of connectivity in the azulene impacts the optical properties (as determined from UV-vis absorption spectra) and the conductivity. Importantly, we show here that simple models cannot be used to predict quantum interference characteristics of nonalternant hydrocarbons. As an exemplary case, we show that azulene derivatives that are predicted to exhibit destructive interference based on widely accepted atom-counting models show a significant conductance at low biases. Although simple models to predict the low-bias conductance do not hold with all azulene derivatives, we demonstrate that the measured conductance trend for all molecules studied actually agrees with predictions based on the more complete GW calculations for model systems.
Summary
Soil salinity acts as a critical environmental filter on microbial communities, but the consequences for microbial diversity and biogeochemical processes are poorly understood. Here, we ...characterized soil bacterial communities and microbial functional genes in a coastal estuarine wetland ecosystem across a gradient (~5 km) ranging from oligohaline to hypersaline habitats by applying the PCR‐amplified 16S rRNA (rRNA) genes sequencing and microarray‐based GeoChip 5.0 respectively. Results showed that saline soils in marine intertidal and supratidal zone exhibited higher bacterial richness and Faith's phylogenetic diversity than that in the freshwater‐affected habitats. The relative abundance of taxa assigned to Gammaproteobacteria, Bacteroidetes and Firmicutes was higher with increasing salinity, while those affiliated with Acidobacteria, Chloroflexi and Cyanobacteria were more prevalent in wetland soils with low salinity. The phylogenetic inferences demonstrated the deterministic role of salinity filtering on the bacterial community assembly processes. The abundance of most functional genes involved in carbon degradation and nitrogen cycling correlated negatively with salinity, except for the hzo gene, suggesting a critical role of the anammox process in tidal affected zones. Overall, the salinity filtering effect shapes the soil bacterial community composition, and soil salinity act as a critical inhibitor in the soil biogeochemical processes in estuary ecosystems.
Cobalt oxide (Co3O4) nanocrystals have been synthesized successfully via a facile combustion method. The Li ions incorporated into the Co3O4 lattice should serve as a self-promoter for the ...crystallization, resulting in the drastic increase of particle size. The Li addition can complex the structure of the energy band gap. The optical absorption spectra indicate that the direct band gap of Co3O4 varied from 3.11 and 1.62 to 3.29-3.98eV after introducing Li ions. This approach provides economically viable route for large-scale synthesis of this kind of nanomaterials.
With the development of urbanization, underground structures unavoidably come within the vicinity of ground surface structures, and interaction between ground structure, soil, and underground ...structure interaction can significantly affect the seismic response of underground structures. Three-dimensional high-fidelity numerical dynamic analysis is conducted to investigate underground structures' seismic response in saturated sand with and without a ground structure. In the numerical analysis, saturated sand is simulated using a plasticity constitutive model for large post-liquefaction deformation of sand. The numerical analysis method is first validated based on a centrifuge shaking table test for a ground structure-underground structure system in liquefiable sand, and then applied to reveal the influence of ground structures on nearby underground structure seismic behavior. Results show that nearby ground structures significantly affect the underground structure's seismic response in saturated sand. A ground structure directly above an underground structure can amplify the underground structure's dynamic internal forces and restrict its uplift, whereas a ground structure to the side can amplify the underground structure's deformation and cause rotation. Factors including relative structure positions, ground structure characteristics, and ground motion properties influence the ground structure's effects on the underground structure's seismic response.
•Ground structure-underground structure system seismic response in liquefiable soil.•Plasticity model for liquefaction behavior of sand used in numerical analysis.•Ground structure directly above amplifies underground structure's internal forces.•Ground structure to the side amplifies underground structure's racking deformation.•Ground structure restricts underground structure's uplift and may cause rotation.
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•Cellular ceramic structures have been extensively applied in catalysis supports, concentrated solar energy, thermal protection or thermal storage, heat exchangers, radiant burners, ...nuclear fusion, gas streams, and biomedical implants.•Additive manufacturing technologies based on stereolithography, extrusion free-forming, two-photo lithography have been extensively adopted to fabricate cellular ceramic structures.•Structural additively manufactured cellular ceramic lattices, as well as structure–function integrated additively manufactured cellular ceramic lattices, were comprehensively summarized.•Smart and flexible cellular ceramic structures may be the future trend in this field.
Cellular ceramic structures (CCSs) have promising application perspectives in various fields. Recently, additive manufacturing (AM), usually known as three-dimensional printing (3D printing), has been increasingly adopted to produce CCSs. Usually, the structural properties of additively manufactured cellular ceramic structures (AM-CCSs), i.e., lightweight characteristics, load-bearing capacity, toughness, unconventional properties, are traditionally investigated. Interestingly, AM technologies have a significant advantage in achieving the structure–function integration for CCSs. Functional properties, e.g., electromagnetic property, acoustic property, thermal property, of CCSs can be achieved during the structural design synchronously. In this review, firstly, the AM technologies for CCSs are comparatively introduced. Then, structural AM-CCSs are summarized. After that, structure–function integrated AM-CCSs are further introduced in detail. Finally, challenges and opportunities towards structure–function integrated AM-CCSs are forecasted. This review is believed to give some guidance for the research and development of CCSs.
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