Structural Dynamic Properties Research Articles

Local atomic configuration and dynamic properties of liquid Ag-Si eutectic alloy by ab initio molecular dynamics

The structural evolution and dynamic properties of liquid Ag89Si11 eutectic alloy during rapid cooling were explored by ab initio molecular dynamics. The calculated pair distribution functions and structure factors at 1173 K agree well with the experimental reference data. The comprehensive analyses including Honeycutt-Andersen index, Voronoi tessellation, and atomistic cluster alignment reveal a gradual enhancement of chemical short-range order with the decreasing temperature and a dominant structural shifting towards perfect and distorted icosahedra. Additionally, the dynamic properties of liquid Ag89Si11 eutectic alloy were obtained and the diffusion coefficients follow Arrhenius relationship.

Investigating the Effect of Chemical Modifications on the Ribose Sugar Conformation, Watson-Crick Base Pairing, and Intrastrand Stacking Interactions: A Theoretical Approach.

Over the last few decades, chemically modified sugars have been incorporated into nucleic acid-based therapeutics to improve their pharmacological potential. Chemical modification can influence the sugar conformation, Watson-Crick hydrogen (W-C) bonding, and nucleobase stacking interactions, which play major roles in the structural integrity and dynamic properties of nucleic acid duplexes. In this study, we categorized 33 uridine (U*) and cytidine (C*) sugar modifications and calculated their sugar conformational parameters. We also calculated the Watson-Crick hydrogen bond energies of the modified RNA-type base pairs (U*:A and C*:G) using DFT and sSAPT0 methods. The W-C base pairing energy calculations suggested that the South-type modified sugar strengthens the C*:G base pair and weakens the U*:A base pair compared to the unmodified one. In contrast, the North-type sugar modifications form weaker C*:G base pair and marginally stronger U*:A base pair compared to the South-type modified sugars. Moreover, intrastrand base stacking energies were calculated for 15 modifications incorporated at the fourth position in 7-mer non-self-complementary RNA duplexes [(GCAU*GAC)2 and (GCAC*GAC)2], utilizing molecular dynamics simulation and quantum mechanical (DFT and sSAPT0) methods. The sugar modifications were found to have minimal effect on the intrastrand base-stacking interactions. However, the glycol nucleic acid modification disturbs the intrastrand base-stacking significantly, corroborating the experimental data.

Improvement to dynamic condensation of structural systems using an innovative virtual model reduction

Model reduction methods have primarily been used in the field of the structural dynamic analysis to reduce the computational time. However, it has progressively been extending to other engineering practices like the damage detection to extract the structural response by means of limited monitored degrees-of-freedom. This paper aims to improve the iterative dynamic condensation method, as a convenient method of the model reduction, for better assessment of the structural dynamic properties. The improvement consists of: (1) Capturing different modal frequencies by applying an iterative perturbation near the frequency obtained from the static condensation. The perturbation is evaluated in a manner that there is no need to solve eigenvalue problem successively; (2) Developing virtual dynamic condensation (VDC) procedure to generalize unique reduced stiffness and mass matrices, reflecting the influence of all modes of vibration, needed for a complete dynamic analysis. Finally, the accuracy of the proposed VDC method was proved by solving three examples.

The Possibility of Detrimental Effects on Soil–Structure Interaction in Seismic Design Due to a Shift in System Frequency

Soil–structure interaction (SSI) leads to a modification in the dynamic properties of structure, but due to the complexity of analysis, it is traditionally assumed in seismic designs that the structure is fixed-supported on the ground, which brings about potential risks to the seismic performances of structure. The study works on the possibility of SSI having detrimental effects by comparing the dynamic responses of the SSI system to a fixed-base structure, and presents charts for an evaluation of the system frequency of SSI for the purpose of engineering practice. In order to reveal the physical nature, the SSI model is reduced to its simplest form, consisting of a SDOF oscillator, a three-dimensional rectangular foundation, and a multi-layered half-space. The energy dissipation in the soil is achieved by foundation impedances and the substructure method. Previously, the foundation impedances are usually acquired by two-dimensional or axisymmetric three-dimensional models in uniform half-space to avoid the high cost of the more realistic, fully 3D models, while a high-precision indirect boundary element method is employed, combined with the non-singular Green’s functions of distributed loads to calculate the foundation impedances. Although SSI dampens the peak amplitude of structure response in the frequency domain, case studies on four buildings’ responses to 42 earthquakes in the time history show a possibility of 15–20% that SSI amplifies the dynamic responses of structures, such as the maximum and the mean values in the time history, depending on the properties of the structures and the site, as well as the frequency component of incident waves.

The Emergence of the Slc11 Clade MCbgut: A Parsimonious Hypothesis for the Dawn of Lactobacillales in the Gut of Early Vertebrates

The Lactobacillales (LB) stand apart among bacterial orders, using manganese (Mn) instead of iron to support their growth and swiftly ferment complex foods while acidifying their environment. The present work investigates whether a shift in the use of Mn could mark the origin of LB. Transmembrane carriers of the ubiquitous Slc11 family play key roles in LB physiology by catalyzing proton-dependent Mn import. In prior studies, the Slc11 clade found in LB (MntH Cb, MCb) showed both remarkable structural plasticity and highly efficient Mn uptake, and another Slc11 clade, MCg1, demonstrated divergent evolution coinciding with emergence of bacterial genera (e.g., Bordetella, Achromobacter). Herein, the Slc11 clade MCb is subdivided in sister groups: MCbie and MCbgut. MCbie derives directly from the Slc11 clade MCa, pointing an intermediate stage in the evolution of MCbgut. MCbie predominates in marine Bacillaceae, is more conserved than MCbgut, lacks the structural plasticity that typify MCbgut carriers, and responds differently to identical mutagenesis. Exchanging MCbie/MCbgut amino acid residues at sites that distinguish these clades showed conformation-dependent effects with both MCbie and MCbgut templates, and the 3D location of the targeted sites in the carrier structure together suggests that the mechanism to open the inner gate, and release Mn into the cytoplasm, differs between MCbie and MCbgut. Building on the established phylogeny for Enterococcus revealed that a pair of genes encoding MCbgut was present in the common ancestor of LB, as MCbgu1 and MCbgu2 templates exhibited distinct structural dynamics properties. These data are discussed when examining whether MCbgut+ LB could emerge in the upper gut of early vertebrates (ca. 540 mya), through genome contraction and evolution toward Mn-centrism, as they specialized as gastric aids favoring stomach establishment in jawed vertebrates through bi-directional communication with host nervous, endocrine and immune systems.

Photothermally Heated Asymmetric Thin Nanopores Suggest the Influence of Temperature on the Intermediate Conformational State of Cytochrome c in an Electric Field.

Nanopore sensing is a label-free single-molecule technique that enables the study of the dynamical structural properties of proteins. Here, we detect the translocation of cytochrome c (Cyt c) through an asymmetric thin nanopore with photothermal heating to evaluate the influence of temperature on Cyt c conformation during its translocation in an electric field. Before Cyt c translocates through an asymmetric thin SiNx nanopore, ∼1 ms trapping events occur due to electric field-induced denaturation. These trapping events were corroborated by a control analysis with a transmission electron microscopy-drilled pore and denaturant buffer. Cyt c translocation events exhibited markedly greater broad current blockade when the pores were photothermally heated. Collectively, our molecular dynamics simulation predicted that an increased temperature facilitates denaturation of the α-helical structure of Cyt c, resulting in greater blockade current during Cyt c trapping. Our photothermal heating method can be used to study the influence of temperature on protein conformation at the single-molecule level in a label-free manner.

Strain aided drastic reduction in lattice thermal conductivity and improved thermoelectric properties in Janus MXenes

Surface and strain engineering are among the cheaper ways to modulate structure property relations in materials. Due to their compositional flexibilities, MXenes, the family of two-dimensional materials, provide enough opportunity for surface engineering. In this work, we have explored the possibility of improving thermoelectric efficiency of MXenes through these routes. The Janus MXenes obtained by modifications of the transition metal constituents and the functional groups passivating their surfaces are considered as surface engineered materials on which bi-axial strain is applied in a systematic way. We find that in the three Janus compounds Zr2COS, ZrHfCO2and ZrHfCOS, tensile strain modifies the electronic and lattice thermoelectric parameters such that the thermoelectric efficiency can be maximised. A remarkable reduction in the lattice thermal conductivity due to increased anharmonicity and elevation in Seebeck coefficient are obtained by application of moderate tensile strain. With the help of first-principles electronic structure method and semi-classical Boltzmann transport theory we analyse the interplay of structural parameters, electronic and dynamical properties to understand the effects of strain and surface modifications on thermoelectric properties of these systems. Our detailed calculations and in depth analysis lead not only to the microscopic understanding of the influences of surface and strain engineering in these three systems, but also provide enough insights for adopting this approach and improve thermoelectric efficiencies in similar systems.

Dynamic stability and vibration isolation property of a foot-leg coupling bio-inspired vibration isolation structure

Dynamic stability and vibration isolation property of a foot-leg coupling bio-inspired vibration isolation structure

Dynamic behavior monitoring of twin supertall buildings during Super Typhoon Soksuri using social sensing data

This paper presents the dynamic behavior monitoring of the 300-m-tall Xiamen twin towers during Super Typhoon Soksuri by means of social sensing, which involves two individuals equipped with six smart devices to conduct acceleration measurement and video footage filming. The measured acceleration data are first corrected by the resampling technique since the sampling rate of smart-device-based measurement is unstable, and the corrected building acceleration obtained from different smart devices shows good consistency. Based on the corrected building acceleration responses, the amplitude-dependent and time-variant structural dynamic properties of the monitored twin towers are revealed by the random decrement technique and the Bayesian spectral density approach, respectively. The determined structural dynamic properties are further compared with seven existing prediction models to evaluate their accuracy. Moreover, by employing a computer-vision technique (i.e., the Kanade-Lucas-Tomasi optical-flow approach), the structural dynamic displacement was extracted from the video footage filmed during Soksuri, and its accuracy was further validated through comparison with direct acceleration measurements. This paper aims to demonstrate the feasibility and effectiveness of social sensing for dynamic behavior monitoring of supertall buildings.

Analysis of structural dynamic response of vertical sound barriers under natural wind and vehicle induced pulsating wind effects

Abstract Aiming at the influence of natural wind and vehicle-induced pulsating wind on vertical sound barriers, a finite element plug-in panel sound barrier is established based on the finite element method for dynamic response analysis. This paper establishes a sound barrier finite element analysis model based on finite element analysis software. It takes the 8-span vertical sound barrier as the basic working condition to analyze the dynamic response analysis of the sound barrier structure under the action of natural wind of different grades, i.e., the influence of pressure and displacement; the dynamic response of the sound barrier structure with a natural wind speed of 7 grades or more. In addition, it analyzes the dynamic properties of the sound barrier structure caused by train-induced pulsating wind pressure at speeds of more than 200 km/h, i.e., the influence of pressure and displacement, and investigates the dynamic characteristics of different vehicles with different wind speeds, pressure, and displacement. Furthermore, the response of the vertical sound barrier at different vehicle speeds is also explored, and the results are compared to examine its dynamic response. The research findings show that the sound barrier structure does not resonate during the self-resonance analysis, but the vibration of adjacent sound barrier panels affects each other. As natural wind speeds increase, the displacement of the steel column endpoints of the vertical sound barrier gradually increases; along the length of the sound barrier, the change of the peak pressure at the top of the steel columns and the top of the unit plate shows a symmetrical trend, and the displacements of the steel columns and the top of the unit plate show a trend of gradual increase in the travelling direction, and they both increase at the end of the column. The displacement of the top of the steel column and the top of the unit plate both show a trend of gradual increase along the direction of the vehicle, and both reach the maximum value at the end of the steel column and the unit plate. With the increase in vehicle speed, the overall peak displacement value also increases synchronously.

Strain-tunable electronic structure, optical and thermoelectric properties of BAs

Strain engineering stands as a reliable method for tailoring the physicochemical properties of materials to achieve desired performance. However, the effects of strain on the physicochemical properties of BAs remain unclear, impeding the comprehensive understanding of its practical performance. Here, employing first-principles calculations coupled with semiclassical Boltzmann transport theory, we investigate the dynamic stability, mechanical stability, electronic structure, and thermoelectric properties of cubic boron arsenide (BAs) under various strains. The results demonstrate that BAs maintains excellent stability throughout the triaxial strain range. The electronic structure of BAs is less affected by strain. Young’s modulus and Poisson’s ratio show a corresponding linear increase when the compression strain increases. The optical absorption coefficient in the visible region of BAs under tensile strain showed an overall increasing trend, and the optical absorption coefficient in the visible wavelength region of BAs under 5% tensile strain was as high as 2 × 105 cm−1. The thermoelectric properties of BAs under tensile strain have been improved, and the ZT value of BAs under 5% tensile strain at 1500 K has been increased to 0.6. The research findings address the gaps in understanding the properties of BAs under strain and provide theoretical support for its applications in the fields of thermoelectrics and optoelectronics.

Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy.

SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2.

Dynamic compressive behavior of functionally graded triply periodic minimal surface cellular structures

The Triply Periodic Minimal Surface (TPMS) structure is regarded as a porous structure used for impact protection due to its lightweight, high strength, and high specific energy absorption (SEA). This paper investigates the dynamic mechanical properties of the TPMS structure by Split Hopkinson Bar (SHPB) experiments and finite element analysis (FEA). We compare stress peak, SEA, strain rate effect, and deformation pattern for functionally graded Primitive (P), uniform P, and uniform Gyroid (G) structures. It is found that the increasing magnitude of peak stress in the TPMS structures becomes more evident under high-impact loads. As the relative density increases, the strain rate effect becomes more prominent. The uniform G structures exhibit higher plateau stress and SEA than uniform P structures. Besides, graded P structures exhibit a climbing phenomenon compared to uniform P structures in the platform section. The FEA results also demonstrate that higher SEA and plateau stresses are exhibited in the graded P structure. The graded design minimizes the strain rate effect compared to the corresponding uniform structures. It is essential to set a properly graded index to enhance the dynamic energy absorption capacity of the TPMS structure, as more fluctuations occur when the graded index increases.

Finite element model updating and response prediction of a frame structure based on optimal sensor placement

This paper proposes an approach for finite element (FE) model updating and response prediction of frame structures based on optimal sensor placement (OSP), which integrates sensor placement optimization, mode expansion, and model updating techniques. Firstly, sensor optimization layout and modal testing analysis are conducted on a bolted laboratory frame structure. The covariance-driven stochastic subspace identification (SSI-COV) method identifies the real-world structure’s natural frequencies, modal damping, and mode shapes. Secondly, the complete mode shapes are expanded using the measured incomplete modal data from the limited number of sensors. Thirdly, a multi-objective function based on frequency and mode shapes is established to adjust the parameters of the FE model. This ensures that the updated model accurately represents the dynamic properties of the actual structure within a specific frequency range. Finally, the Rayleigh damping of the frame structure is estimated, and the damping matrix is assembled to enhance the accuracy of dynamic response prediction in the updated model. By comparing the response prediction results of the updated FE model with and without considering the updated damping effects to the measurement data of the real-world structure, it is demonstrated that the proposed method considering updated damping effects can more effectively predict the structural response.

Adaptive semiactive control of structure with magnetorheological dampers using wavelet packet transform

Conventional active controllers generally adopt initial dynamic properties of intact structures to calculate optimal control force for magnetorheological damper, which eventually leads to ideal damping force of the device. Also, they cannot assure trade-off between damping force and response reduction under non-stationary excitations. To this end, an adaptive semiactive control algorithm for magnetorheological damper is proposed. Using wavelet packet transform, an improved control law determines optimal control forces in terms of resonant and non-resonant frequency bands in time interval. Both frequency bands are established based on natural frequency(ies) of structures, making damping force rely on actual structural properties and achieving trade-off under non-stationary disturbances. A refined clipped-optimal control algorithm is then deployed to convert optimal control force to the device’s voltage. A numerical study of a six-degree-of-freedom structure under four near- and far-fault ground accelerations reveals that the scheme outperforms existing controllers while attaining cost-effectiveness of damping force versus response alleviations.

An Experimental Study on the Dynamic Properties of 3D-Printed Structures with Different Layer Orientations

An Experimental Study on the Dynamic Properties of 3D-Printed Structures with Different Layer Orientations

Estimation of wind load on supertall buildings using partial output measurements

Supertall buildings possess distinctive characteristics such as high flexibility, low damping, and susceptibility to wind. The impact of the wind load and wind-induced responses plays a critical role in ensuring the safety and functionality of these structures. Consequently, investigating the wind load and wind-induced responses of supertall buildings has immense practical significance and engineering value to guarantee the secure operation of such buildings under strong wind conditions. However, the direct measurement of wind loads and wind-induced responses across all building floors presents substantial challenges, including considerable engineering workload and implementation difficulties. This study proposes a novel approach based on Kalman filtering to estimate wind loads and wind-induced responses in supertall buildings. This approach involves fusing partial acceleration and displacement measurements to estimate wind load and wind-induced response accurately. Additionally, optimized sensor placement was considered based on the iterative process of the effective independence method. Wind-induced responses were obtained through numerical testing and subsequently utilized to estimate the wind loads on a supertall building. Various factors, such as measurement noise, modeling errors of structural dynamic properties, sensor placement, and response synchronization, were thoroughly discussed to assess their impact on the overall analysis.

A consumption-based term structure model of bonds and equity

In this study, I propose a consumption-based asset pricing model to capture the dynamic properties of term structures of bonds and equity. I extend the long-run risks model by introducing a mean-reversion of dividend growth and the external habit formation of a representative agent. The mean-reverting dividend growth generates a negative equity term premium, while the habit formation augments the equity premium and renders an upward-sloping bond yield curve, on average. In addition, fluctuations in the surplus consumption ratio and the conditional variance of consumption growth allow the model to reproduce pro-cyclical variations in bond and equity yield spreads and counter-cyclical variations in bond and equity term premiums, as observed in the U.S. data.

The influence of anions in the ionic liquid-water mixtures on the conformational structures of emeraldine base and emeraldine salt form of polyaniline

The development of antifouling membranes for water filtration applications is challenging. Conducting polymers can show enhanced antifouling characteristics by blending with various polymers, nanomaterials, and Ionic liquids (ILs). In this paper, we perform an all-atom molecular dynamics simulation on a conducting polymer polyaniline (PANI) immersed in IL-water mixtures. Two forms of PANI were considered, namely Emeraldine base (EB) and Emeraldine salt (ES) as well as two different water-mixed ILs are considered namely (a) 1-ethyl-3-methyl imidazolium [EMIM]+ hexafluorophosphate [PF6]- and (b) 1-ethyl-3-methyl imidazolium [EMIM]+ tetra-fluoroborate [BF4]-. We present various intra- and inter-molecular structural properties, solvation thermodynamics, and dynamic properties. We observe that with an increase in IL concentration, the radius of gyration (Rg) value shows a decrease for ES in pure state in both ILs; on the other hand, we see a minimal increase in the Rg values of EB in both ILs. The dihedral angle distribution analysis shows a combination of gauche and trans state for ES, whereas trans state is more pronounced for the case of EB in both water-IL mixtures. The radial distribution function (RDF) analysis between the ortho, meta carbons of the benzene rings, and the amine groups on ES with [BF4]- and [PF6]- show significant structural peaks. On the other hand, EB and ES show lower interaction with the water molecules. The number of hydrogen bonds (h-bonds) between polymer and water is higher for EB than ES in both IL-water mixtures. The hydrogen bond lifetime (τ) values show one-fold higher values for EB than ES. The self-diffusion coefficient (D) values of water show a decrease with an increase in IL concentration. The thermodynamic properties solvation enthalpy (ΔH) and excess molar volume (VmE) for both ES and EB show a more favorable solvation in [EMIM]+[BF4]- when compared to [EMIM]+[PF6]- with an increase in IL concentration. These observations are crucial for selecting ILs and designing sustainable polymers for antifouling membranes.

Exploration and Characterization of Dynamic Properties for Cultural Heritage Conservation: A Case Study for Historical Stone Masonry Buildings in Zanzibar

Ancient civilizations have imprinted their legacy on Zanzibar Stone Town through the construction of revered stone masonry buildings, which are experiencing rapid deterioration due to severe ambient environmental impacts. In response to these challenges, this study presents a comprehensive field exploration through the ambient vibration test (AVT) and numerical prediction of historical stone masonry buildings in Zanzibar Stone Town to analyze the dynamic characteristics. The ambient vibration test (AVT) reveals structural dynamic properties in terms of peak resonance frequencies (fr(avg)), mode shape, and damping ratio, in conjunction with the development of correlation with the geometric parameters of the building. The results reveal fr(avg) ranges between 2.8 and 5.3 Hz for investigated structures, non-uniform deformed mode shapes, and damping ratio ranges between 1.35% and 4.45% at various orientation axes of the understudy buildings. However, the relationship between natural frequencies indicates a higher association with the geometrical parameters of the building, yielding a correlation coefficient (R2) between 0.85 and 0.99. Moreover, the numerical prediction via eigenvalue analysis (EVA) yields a considerable association with the investigated data, quantified by root mean square error (RMSE), mean absolute error (MAE) ranged between 0.29 and 0.3, with Nash–Sutcliffe efficiency (NSE) and R2 between 0.81 and 0.99, respectively. Furthermore, conservation work guidelines were also developed to assist the structural engineer and conservationist in adopting targeted conservation strategies for the efficient preservation of the historical integrity in Stone Town.