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A hole-effect autocorrelation function is one that is non-monotonic or pseudo-periodic as defined in the geostatistics literature. This paper shows that such an autocorrelation function (AC...

The autocorrelation function (ACF) of the soil profile in some sites in Shandong province, China is studied using cone penetration test (CPT) data. This is done in the context of a random field modeling of the soil deposits. It is found that the different types of soil profile have different stochastic parameters, and there is no obvious trend along the depth of the soil profile. Thus, the soil profile is examined within each layer. Numerical values for three existing analytical (ACF) models are derived by the least squares fitting approach for the different types of soil. Further, comparisons of the autocorrelation function between the tip resistance and sleeve friction were examined. Based on the autocorrelation data analysis, a new autocorrelation model, named linear-exponential-cosine (LNCS), is considered with differentiability at the origin of the spatial lag axis, and alternating sign along this axis. For all of the four ACF models, a related integral equation is numerically solved for determining the associated Karhunen-Loeve (K-L) representation. In this regard, it is noted that the new model is not only more physics-consistent, but also yields quite good computational efficiency. In the end, the random field of the soil profile is modeled using a two-dimensional K-L expansion with the new model, assuming separability in two dimensions.

A stochastic model is developed to describe the fracture behaviour of concrete fibres at micro-level, and a probabilistic relation between the fibre strain and the concrete damage variable is estab...

A versatile approach for synthesizing non-stationary multicomponent ground motions compatible with a given target response spectrum is presented. In conjunction with performance-based structural design, the proposed approach combines a scenario-based procedure to select the target spectra of the three components of the motion, and a stochastic scheme, with an iterative wavelet-based method to generate the artificial time histories. In this context, the selection of an appropriate target spectrum is mandatory to synthesizing accelerograms with proper frequency content, input-energy, effective duration, and inelastic demand. In the scenario-based assessments, the target spectrum is derived directly from an earthquake scenario defined by seismic hazard disaggregation and strong ground-motion attenuation relationships. Firstly, the design spectrum specified by aseismic code provisions is replaced by a set of conditional mean spectra (CMS) for each of the ground motion components. Subsequently, an inverse stochastic dynamics problem, defined by a set of parametric evolutionary power spectra (EPS), is formulated and solved in a point-wise format for each CMS and for the three components of the motion. To improve the matching between the response spectrum of the simulated records and the CMS, an iterative procedure involving the family of harmonic wavelets is then employed. Post-processing for a proper baseline correction of the records is performed to synthesize ground-motions yielding realistic velocity and displacement traces. To illustrate the effectiveness of the approach, extensive numerical results pertaining to the Italian aseismic code provisions are included in this paper. In this regard, Monte Carlo simulations are undertaken to relate the CMSs to the evolutionary power spectrum. In particular, non-constant peak factor expressions via regression analysis are derived for various ground-motion durations. Finally, the nonlinear responses of elasto-plastic SDOF oscillators with different values of the yield strength reduction factor are considered. The oscillators subjected to artificially generated records and a set of natural unscaled and spectrum-compatible accelerograms, are examined in terms of ductility demand and equivalent number of yield cycles.

This paper studied the stochastic response and reliability of the tunnel system through modelling the elastic modulus and yield stress of the surrounding soil as a random field. A 3D tunnel-soil finite element model was established and the corresponding random field was simulated by the spectral representation method. The Wenchuan earthquake was chosen as input from the bottom in the perpendicular direction to the longitudinal axis. Results show that the peak values of the internal forces of the cross sections of the tunnel are not uniformly distributed and the hoop forces and bending moments are higher under the condition that the elastic modulus and yield stress of soil are both random fields (Case II) than only the elastic modulus of the soil is considered as random field (Case I). Using PDEM (probability density evolution method), the stochastic response of the tunnel indicates that the probability density function of the response is complex with two or more peaks. The design limit and ultimat...

The multicopper oxidase CueO is involved in copper homeostasis and copper (Cu) tolerance in Escherichia coli. The laccase activity of CueO G304K mutant is higher than wild-type CueO. To explain this increase in activity, we solved the crystal structure of G304K mutant at 1.49 Å. Compared with wild-type CueO, the G304K mutant showed dramatic conformational changes in methionine-rich helix and the relative regulatory loop (R-loop). We further solved the structure of Cu-soaked enzyme, and found that the addition of Cu ions induced further conformational changes in the R-loop and methionine-rich helix as a result of the new Cu-binding sites on the enzyme’s surface. We propose a mechanism for the enhanced laccase activity of the G304K mutant, where movements of the R-loop combined with the changes of the methionine-rich region uncover the T1 Cu site allowing greater access of the substrate. Two of the G304K double mutants showed the enhanced or decreased laccase activity, providing further evidence for the interaction between the R-loop and the methionine-rich region. The cuprous oxidase activity of these mutants was about 20% that of wild-type CueO. These structural features of the G304K mutant provide clues for designing specific substrate-binding mutants in the biotechnological applications.

The damages of tunnels under earthquakes showed that soil–rock deposits around a tunnel have significant effects on its response to earthquake excitations, caused by the spatial variability and correlation of the soil properties, which may properly be modelled as a random field. This paper studied these effects through modelling the surrounding soil as a random field on the response of a tunnel and made some comparisons with the corresponding deterministic analysis. A two-dimensional finite element model of the tunnel-soil system was examined, and the corresponding random field was simulated by the spectral representation method. The results revealed that the corners of the tunnel are the critical locations for the axial force and bending moment. The comparisons showed that the results of the deterministic analysis usually yield higher results than the corresponding random field results. The reliabilities of a tunnel for two limit-state functions were considered: one is defined as exceeding the design lim...

Soil parameters are spatially random variables. Thus, the spatial correlation relationship, besides the mean and variance, of a specific soil site is needed for any realistic stochastic modeling. In this regard, an improved autocorrelation model involving a linear, an exponential and cosine terms, named linear-exponential-cosine (LNCS), is adopted here to capture the spatial properties of the soil deposits. Further, a random field of the soil deposit is simulated using a two-dimensional Karhunen–Loeve expansion based on the new autocorrelation model. Furthermore, two cases for the soil settlement are calculated with the random field of the soil deposits. One case is the stochastic settlement from a reference paper. Some comparisons are undertaken, and it is found that the mean value agrees well with the reference. The other case involves the differential settlement analysis of a real engineering project. The settlement is calculated with the random field, the uniform field respectively, and is compared with the on-site measured values. The results show that the random field model can capture the differential settlement better than the corresponding uniform field model.

Of the 20 common amino acids, 18 are encoded by multiple synonymous codons. These synonymous codons are not redundant; in fact, all of codons contribute substantially to protein expression, structure and function. In this study, the codon usage pattern of genes in the E. coli was learned from the sequenced genomes of E. coli. A machine learning based method, Presyncodon was proposed to predict synonymous codon selection in E. coli based on the learned codon usage patterns of the residue in the context of the specific fragment. The predicting results indicate that Presycoden could be used to predict synonymous codon selection of the gene in the E. coli with the high accuracy. Two reporter genes (egfp and mApple) were designed with a combination of low- and high-frequency-usage codons by the method. The fluorescence intensity of eGFP and mApple expressed by the (egfp and mApple) designed by this method was about 2.3- or 1.7- folds greater than that from the genes with only high-frequency-usage codons in E. coli. Therefore, both low- and high-frequency-usage codons make positive contributions to the functional expression of the heterologous proteins. This method could be used to design synthetic genes for heterologous gene expression in biotechnology.

Additional file 2: Figure S1. Sodium dodecyl sulfateâ polyacrylamide gel electrophoresis of recombinant CueO and its mutants produced in E. coli BL21(DE3). Lane 1 The wild-type CueO. Lane 2 The mutant G276R. Lane 3 The mutant G276K. Lane 4 The mutant G276Y. Lane 5 The mutant G276N, the proteins were purified through the Ni-chelating affinity chromatography.

The modeling methodologies and calculation of dynamic response of underground structure under Rayleigh waves is investigated in this paper. First the free field responses under Rayleigh waves are analyzed and the numerical results agree well with the theoretical results. Then, the approximate Rayleigh waves are put forward based on the preliminary research, and Rayleigh wave field is obtained through fast Fourier transform technique. Taking a utility tunnel as an example, its dynamic responses under Rayleigh waves is calculated by ABAQUS. The results demonstrate that bending deformation is the main component of structural deformation and the deformation at the top of the structure is about twice as much as that at bottom of the structure. The effect of soil-structure interface and the buried depth of underground structure are also investigated via parameter analysis. For the shallow buried underground structures, Rayleigh waves can be the key factor to control the responses and damage of the structure.

Summary Underpinning is a key component in the structural moving process, especially for high-rise buildings with gravitational loads. In this paper, a most commonly used 4-sided wrapped underpinning joint with 2 underpinning beams and 2 coupling beams for the frame structures was investigated. Sixteen prototypes were tested considering different shear span-to-depth ratios, underpinning joint heights, reinforcement ratios, and so forth. The experimental results showed that the underpinning beams can fail in shear or flexure-shear. The interface between the column and the beam is also prone to failure during the loading. Further, the bearing capacity can be greatly improved with decreasing of the shear span-to-depth ratio, whereas more damage may occur within the interface domain. In the numerical simulations, a damage–plasticity constitutive model was adopted, and the cohesive elements were used to model the old-to-new concrete interface between the column and beams. It was found that the numerical results agreed quite well with the experimental results. Thus, the proposed approach can be a useful basis for further analysis and optimized design of underpinning joints.

Free-Field responses of soil in a large-scale shaking table test is simulated by a three-dimensional numerical model using FEM software ABAQUS as a platform. The Drucker-Prager model is adopted for the soil modeling and the shell elements are used for the box with a mass representing the effect of inertia force caused by the frame of laminar shear box. The feasibility and efficiency of the proposed FEM model is validated by comparing the predicted responses with experimental measurements in terms of time history and soil acceleration amplification factors. The results demonstrate that the proposed analytical model can predict deformational characteristics, within acceptable accuracy, of the test soil, and the response of the utility tunnel was also calculated and compared with the test results. The results agree well.

The research of soil-structure interaction is a hot point in earthquake engineering. Large-scale shaking table tests are widely employed to verify and modify the current available theoretical models and explore the internal mechanism of the interaction. The rationality of experimental foundation model designs greatly influences the reliability of test results. This paper investigates some previous shaking table tests considering soil-structure interaction and analyzes the major factors influencing the foundation model design. The obtained results will be very helpful for the future similar test design.