Dynamic Response Research Articles

A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs.

Transient protein-protein interactions play key roles in controlling dynamic cellular responses. Many examples involve globular protein domains that bind to peptide sequences known as Short Linear Motifs (SLiMs), which are enriched in intrinsically disordered regions of proteins. Here we describe a novel functional assay for measuring SLiM binding, called Systematic Intracellular Motif Binding Analysis (SIMBA). In this method, binding of a foreign globular domain to its cognate SLiM peptide allows yeast cells to proliferate by blocking a growth arrest signal. A high-throughput application of the SIMBA method involving competitive growth and deep sequencing provides rapid quantification of the relative binding strength for thousands of SLiM sequence variants, and a comprehensive interrogation of SLiM sequence features that control their recognition and potency. We show that multiple distinct classes of SLiM-binding domains can be analyzed by this method, and that the relative binding strength of peptides in vivo correlates with their biochemical affinities measured in vitro. Deep mutational scanning provides high-resolution definitions of motif recognition determinants and reveals how sequence variations at non-core positions can modulate binding strength. Furthermore, mutational scanning of multiple parent peptides that bind human tankyrase ARC or YAP WW domains identifies distinct binding modes and uncovers context effects in which the preferred residues at one position depend on residues elsewhere. The findings establish SIMBA as a fast and incisive approach for interrogating SLiM recognition via massively parallel quantification of protein-peptide binding strength in vivo.

Structural and Dynamical Response of Lipid Bilayers to Solvation of an Amphiphilic Anesthetic.

The structural response of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC)/water bilayers to addition and subsequent solvation of a small amphiphilic molecule - an anesthetic benzyl alcohol - was studied by means of solid-state NMR (2H NMR, 31P NMR) spectroscopy and low-angle X-ray diffraction. The sites of binding of this solute molecule within the bilayer were determined - the solute was shown to partition between several sites in the bilayer and the equilibrium was shown to be dynamic and dependent on the level of hydration and temperature. At the same time, it was shown that solubilization of benzyl alcohol reached a solubility limit and was terminated when the ordering profile of DMPC hydrocarbon chains adopted finite limiting values throughout the whole chain. Such findings were made probably for the first time for any lipid bilayer system and possibly have more general implications for dissolution of other small-molecule amphiphilic solutes in lipid bilayer systems other than DMPC. The limit to the hydrocarbon chain profile is probably a more general property and corresponds to the balance of intrabilayer and interbilayer forces established in combination with the elastic properties of the bilayer system that still consists of one single phase just before the solute forms an excess phase. It is not necessary to quantify the contribution of each individual intrabilayer and interbilayer force acting within such a bilayer system. A model of the dependence of surface density of lipid chains on the chain segment order parameter was also developed - an empirical mathematical model based on experimental data was derived and it was proposed to represent a relationship between intrinsic bilayer forces and bilayer deformation characteristics and might be proven to be of more general significance in the future.

Evolutionary characteristics and influencing mechanisms of green development efficiency in Chinese urban agglomerations: Analysis of the Yangtze River Delta urban agglomeration.

Urban agglomerations are central to global economic growth and the shift towards green development, particularly in developing countries. This study examines regional comparisons and variations in green development mechanisms within urban agglomerations to better understand their spatiotemporal patterns. An input-output indicator system was developed, accounting for social benefits and carbon emissions. Using the Yangtze River Delta urban agglomeration (YRDUA) as a case, this study measured green development efficiency (GDE) from 2003 to 2022 with the SBM-Undesirable model. It also employed the coefficient of variation (CV) method and Markov chain model to analyze the spatiotemporal variability and dynamic transformation law of GDE. Additionally, a panel quantile regression model was used to identify the dynamic response of key controlling factors, based on the GDE stages of each city. The findings reveal: (1) Cities in the central YRDUA area have higher GDE levels compared to those in non-central areas, with increasing disparity over time. (2) The green development level of a city influences its neighbors, enhancing or degrading their GDE stability and type. (3) Economic growth, foreign direct investment, industrial structure, and technological innovation significantly impact YRDUA's GDE. (4) In cities with low green development, economic growth strongly promotes GDE, while government regulation most restricts it. In medium-level cities, industrial structure advancements have the largest promotional effect, whereas technological innovation is the most limiting factor. In high-level cities, foreign investment intensity is the main inhibitor, while government regulation supports GDE. Marketization and environmental regulation effects on GDE remain consistent across different city levels. These findings provide targeted guidance for the green transition of urban agglomerations in China and other developing nations.

The Resistance of Sandwich Cylinders With Density-Graded Foam Cores to Internal Blast Loadings

Abstract The resistance of sandwich cylinders with density-graded foam cores to internal blast loadings is investigated theoretically and numerically. Four kinds of density-graded foam core are designed, such as positive, negative, middle–high, and middle–low gradients. The deformation process of the sandwich cylinders is assumed to be split into three phases, i.e., fluid–structure interaction, combined deformation of core and inner wall, and sandwich stage of motion. Employing a rigid perfectly-plastic locking model of density-graded foam core, analytical models are proposed to predict the dynamic response of gradient sandwich cylinders. Finite element simulations of gradient sandwich cylinders subjected to internal blast loadings are carried out and agree well with the analytical predictions. Furthermore, the effects of the core density gradients and the wall thickness distributions on the blast resistance are explored and identified. It is shown that the thicker inner wall design can enhance the blast resistance of sandwich cylinders with the same mass.

Adaptive weight adjustment technology for reinforcement learning reward indicators based on the new-type power system

Current RL-based scheduling methods struggle with designing effective reward functions that balance cost reduction, safety and renewable energy integration. To tackle these issues, this paper proposes a novel hybrid optimization framework that combines Particle Swarm Optimization and Reinforcement Learning (PSO-RL), focusing on three key aspects: (1) Minimizing Generation Costs: Systematically reducing operational costs for economic efficiency. (2) Enhancing System Safety: Improving reliability by incorporating operational constraints. (3) Increasing Renewable Energy Proportion: Emphasizing the integration of renewable energy sources. The comprehensive mathematical model encapsulates intricate constraints and multi-objective characteristics of the new-type power system, featuring reward functions tailored for dynamic responsiveness. Empirical validations using the Grid2Op scheduler affirm the efficacy of our framework. Results highlight superior convergence speed and optimization precision of the PSO-RL approach over traditional RL methods. In summary, this study advances scheduling methodologies for the new-type power system, fostering renewable integration and smart grid technology evolution.

Analysis of the dynamic response of a model of an oyster farming structure

ABSTRACT Encouraged by the increase in oyster consumption, allied to the growth in the use of coastal marine areas, the development of oyster farming in open sea areas involves the joint efforts of different areas of knowledge. This interdisciplinarity is needed, given that the vibrations and hydrodynamics of structures can affect the distribution of food, the filtering capacity and hence the growth of these organisms. In this context, the article discusses the dynamic response of a hanging oyster farming structure subjected to the influence of different waves. The quantification of the relative velocity between the body and the fluid indicates that the oyster shells probably close part of the time. Lastly, by increasing the length of the cable supporting the cultivation line, an attenuation of approximately 60% can be achieved in the horizontal movement as a result of the distance from the system's natural frequency to that of excitation.

Reducing undesirable effects of revolute joint clearances on the dynamic performance of spatial parallel mechanism

To mitigate the adverse effects of joint clearances on the dynamic performance of mechanisms, it is essential to investigate the dynamic optimization design of spatial parallel mechanisms with clearances. Currently, there are many studies on the dynamic characteristics of mechanisms with clearances, but there are few studies on dynamic optimization design of mechanisms with clearances, especially on the optimization design of parallel mechanisms with clearances. Therefore, the dynamic optimization design of 3-RRPaR (R stands for revolute joint, Pa stands for quadrilateral structure) parallel mechanism with dry friction clearance of revolute joints is studied. The dynamic model of the parallel mechanism with revolute joint clearance is derived. On these grounds, the dynamic response of the end actuator, the contact collision force at the clearance joint, and their weighted combination are defined as objective functions, respectively. The mass and moment of inertia of the end actuator are taken as optimization variables. A mathematical model for the dynamic optimization design of the parallel mechanism considering dry friction clearances is developed, and the optimal mass and moment of inertia of the end actuator are obtained by G-MSRS method. This study comparatively analyzes the dynamic characteristics of parallel mechanisms with clearances before and after optimization. The results indicate that dynamic optimization significantly enhances the dynamic characteristics of the mechanism. This study lays a theoretical foundation for dynamic optimization design of parallel mechanisms with clearances.

Analysis on dynamic characteristics and control strategy of medium structure network converter in new energy medium voltage flexible interconnection project

Abstract In view of the possible voltage and current overshoot problems in the process of new energy grid connection, the dynamic characteristics analysis and control strategy of the network converter in the new medium voltage flexible interconnection project are proposed. Firstly, a synchronous control strategy based on voltage phase and amplitude compensation is proposed. Then, based on the characteristics of new AC-DC hybrid distribution network, the new energy medium voltage flexible interconnection network is analyzed. The simulation experiment reveals the dynamic response characteristics of the new energy grid converter under frequency interference and load change.

Modelling and Analysis of Multilayer Porous FG-GPRC Plates Using Zigzag Function and Cell-Based Smoothed-Discrete Shear Gap Method

An efficient computational approach is presented to analyze the structural responses of multilayer porous plates, incorporating the reinforcement of functionally graded graphene platelets (GPLs). The approach seamlessly integrates the Murakami function zigzag (MZZ) theory with a formulation based on the discrete shear gap technique and the cell-based smoothed finite element method (CS-DSG3). This study investigates the characteristics of porous nanocomposite plates, scrutinizing their responses under diverse conditions. It comprehensively analyzes static bending, free vibration, and dynamic responses of nanocomposite plates, taking into account variations in porosity distributions and GPL dispersion patterns across the thickness. The mechanical properties of the nanocomposites are scrutinized through micromechanical models. The prediction of Young’s modulus employs a modified Halpin–Tsai model, while Poisson’s ratio and density are calculated utilizing the rule of mixtures. Due to the precise nature and the demand for [Formula: see text]-continuity shape function, the Murakami zigzag theory is employed to enhance the computational efficiency of CS-DSG3 for the extensive evaluation of both conventional and functionally graded reinforced nanocomposite structures. Within the results section, the efficacy of the approach is demonstrated through comparisons with alternative numerical approaches. The analysis reveals accuracy and efficiency in predicting the responses of PFG-GPRC multilayer quadrilateral plates. These results offer valuable insights for optimizing practical engineering applications involving PFG-GPRC.

Regional-scale bridge health monitoring: survey of current methods and roadmap for future opportunities under changing climate

Climate-related extreme events are becoming increasingly frequent, posing significant threats to bridges, which are critical components of transportation infrastructure. This paper offers an overview of recent advancements in methodologies and technologies for conducting structural health monitoring (SHM) of bridges over large areas, where deploying sensors on every structure may be cost-prohibitive for local administrations. It specifically examines two approaches that have garnered interest in the past decade: indirect SHM, which involves instrumenting vehicles and analyzing their dynamic responses to infer information about bridges, and satellite interferometric radar data, which offer static displacement measurements for large regions and has recently been exploited for civil SHM purposes. Additionally, it reviews the recent developments in population-based SHM, which facilitates knowledge-sharing among structures with similar characteristics within a population. Through an analysis of the advantages and limitations of these three rapidly developing research areas, the paper outlines future opportunities and lays the roadmap for a comprehensive “regional-scale SHM” approach based on remote and/or crowdsourced data, supported by population-level analyses. Specific topics addressed include strategies for similarity assessment among monitored structures, available data sources, and feature extraction/integration approaches for different scenarios.

Influences of Feedback Gains on Vehicle–Bridge Coupled Vibration for a Mid-Mounted Maglev Train

Levitation control systems play a vital role in ensuring the operational performance of medium and low speed maglev trains. Improper gain values may induce excessive vibrations in vehicles and bridges, potentially leading to collisions. This research investigates the influence of feedback gains on the levitation subsystem and the vehicle-bridge coupled system, leveraging a newly designed maglev vehicle equipped with mid-mounted suspension and a state feedback control strategy. A dynamic model of the vehicle-bridge coupled system was developed, incorporating control strategies, track irregularities, and bridge flexibility, and was validated through experimental data. The dynamic responses of the bogie and bridge under varying gain values were analyzed in-depth. By examining pole locations and frequency responses, the mechanisms through which each gain impacts the coupled system were clarified. The study identifies that gains associated with acceleration, velocity, and displacement each have unique stability domains that interact with one another. To maintain system stability, the gains must adhere to the Routh-Hurwitz stability criterion while fulfilling specific bandwidth and damping requirements. Gains set too low or too high may result in levitation failures. Recommended ranges for these gains are as follows: acceleration (0.2–0.6), velocity (30–100), and displacement (5,000–10,000). These findings could provide valuable guidance for designing control systems that enhance the stability and safety of maglev train operations.

Ononin's Antagonistic Activity towards TRPV1: Insights from Molecular Dynamics and Capsaicin-Evoked Calcium Response in DRG Neurons.

The search for effective painkillers has led to intensive research, with a particular focus on the transient receptor potential vanilloid-1 (TRPV1) channel as a possible target. One promising candidate is ononin, which is investigated for its binding with TRPV1 through a 200-ns molecular dynamic simulation and analysed via root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), hydrogen-bond interactions, radius of gyration (RadGyr), and MM-PBSA energy calculations. The results were further validated experimentally via calcium imaging studies. Molecular dynamics revealed that the ononin-TRPV1 complex achieved stable binding within a remarkably short time of approximately 38 ns while maintaining the degree of compactness of the receptor throughout a 200 ns simulation period. In contrast, the capsazepine-TRPV1 complex displayed more significant structural deviations during the whole simulation. Moreover, MM-PBSA energy calculations showed a relatively strong binding affinity between ononin and TRPV1, mainly attributed to favourable hydrophobic interactions. Pre-incubation of dorsal root ganglia (DRG) neurons with ononin (1 and 10 μM) or capsazepine (10 μM) for 4 min prior to stimulation with capsaicin significantly reduced capsaicin-evoked calcium responses. No significant difference between capsazepine and ononin was found at a concentration of 10 μM. Overall, this research demonstrates the potential of ononin as a potential antagonist for developing analgesics targeting TRPV1. Hence, and to our best knowledge, this study represents the first report of ononin's antagonistic activity towards TRPV1.

Fast vocal-motor tracking of escaping prey in echolocating bats

BackgroundEcholocating bats face an intense arms race with insect prey that can detect bat calls and initiate evasive maneuvers. Their high closing speeds and short biosonar ranges leave bats with only a few 100 ms between detection and capture, suggesting a reactive sensory-motor operation that might preclude tracking of escaping prey. Here we test this hypothesis using greater mouse-eared bats (Myotis myotis) as a model species. With high-resolution biologging tags, we recorded bats hunting aerial prey in the wild and we also collected data from trained conspecifics in the laboratory facing simulated prey escapes of various speeds and distances.ResultsWe show that wild bats employed flexible buzz durations during hunting. In the laboratory, such dynamic vocal responses were driven by moving targets, where faster and longer movements led to longer buzzes. During these buzzes, the bats engaged in acute vocal-motor tracking via increased call intervals within 240 ms of evasive prey maneuvers.ConclusionsEcholocating bats can track evasive prey via a fast vocal-motor feedback loop allowing them to expand their acoustic depth of field. This echo-guided sensory adjustment contributes to the hunting superiority of bats as the most formidable insectivorous predator of the night skies.

Extracting rates and activation free energies of martensitic transitions using nanomechanical force statistics: theory, models, and analysis

Nanomechanical responses (force-time profiles) of crystal lattices under deformation exhibit random critical jumps, reflecting the underlying structural transition processes. Despite extensive data collection, interpreting dynamic critical responses and their underlying mechanisms remains a significant challenge. This study explores a microscopic theoretical approach to analyse critical force fluctuations in martensitic transitions. Extensive sampling of the critical forces was performed using nonequilibrium molecular dynamics simulations of an atomic model of single-crystalline titanium nickel. We demonstrate that a framework of nonequilibrium statistical mechanics offers a principled explanation of the relationship between strain rate and the critical force distribution as well as its mean. The martensitic transition is represented on a free energy landscape, taking into account the thermally activated evolution of atomic arrangements over a barrier during its time-dependent deformation. The framework enables consistent inference of the relevant fundamental properties (e.g., intrinsic rate, activation free energy) that define the rate process of structural transition. The study demonstrates how the statistical characterisation of nanomechanical response-stimulus patterns can offer microscopic insights into the deformation behaviours of crystalline materials.

A Comparative Study of the Modal Response of Additively and Subtractively Manufactured Thin Plates After Thermal Loading

Abstract Background Additively-manufactured parts contain residual stresses induced by manufacturing. These residual stresses can be relaxed or redistributed by thermal loading. The presence of internal stress influences the dynamic response of parts, and this is of particular interest in thin plates subject to thermoacoustic loading in hypersonic vehicles and fusion reactors. Objective To measure the changes in shape and modal frequencies caused by thermal loading of geometrically-reinforced thin plates that were additively manufactured in Inconel 625. Methods Plates were additively-manufactured in landscape and portrait orientations using laser powder bed fusion. The plates were heated to a nominal temperature of 820 ̊C, which was expected to alleviate the residual stress from the build process. Pre- and post-heating, their modal frequencies were found experimentally and pulsed-laser stereo (3D) digital image correlation was used to evaluate their modal shapes. The resultant modal frequencies and shapes were compared with those from a subtractively-manufactured plate. Results It was found that the heat cycle changed the shape of the plates relative to their as-manufactured state in addition to changing their natural frequencies and modal shapes. Conclusions The change in shape induced by heating caused shifts in the natural frequencies and changes in the corresponding modal shapes. The results show quantitatively for the first time the important role that residual stresses can play in the dynamic response of geometrically-reinforced thin plates manufactured by additive and subtractive processes.

Fluid-induced vibration response characteristics of the oxygen pump volute

The oxygen pump constitutes a crucial and intricate component within liquid rocket engines, serving as a primary source of engine vibration. This study delves into the unsteady fluid-induced excitation loading, considering the interplay between gap flow and main flow. The findings are validated through testing on a liquid rocket engine. Modal characteristics of the oxygen pump under varying liquid mediums are examined. The Rayleigh damping parameter is determined, accounting for the frequency characteristics of fluid-induced excitation, thereby establishing a comprehensive transient dynamic model. Subsequently, the transient dynamic response of the volute in an oxygen pump to unsteady fluid-induced excitation is analyzed, unveiling both time-domain and frequency-domain vibration response characteristics. The analysis methodology is corroborated through comparison with the statistical distribution of test results. Notably, the vibration response of the oxygen pump volute predominantly exhibits frequency doubling of rotational speed, with prominent occurrences observed at the 12X and 18X frequencies.

GOLD Observations of Thermospheric Neutral Temperature Variability During the 14 October 2023 Annular Solar Eclipse

AbstractThe 14 October 2023 annular solar eclipse was visible from the US Pacific coast to Brazil's east coast. NASA's Global‐scale Observations of Limb and Disk (GOLD) mission observed the first synoptic thermospheric temperature changes from a geo‐stationary orbit above 47.5°W longitude between 17 and 20 UT during the eclipse. These daytime thermospheric changes were derived using GOLD's disk far ultraviolet (FUV) measurements. A significant decrease in the daytime disk temperatures (∼100 K) was seen near the peak annularity compared to the day before (baseline). The temperature reduction's spatial morphology is also like that of the eclipse shadow. Previous modeling studies of other eclipses typically show a much smaller temperature decrease (∼30–40 K; a factor of 2–3 lower) compared to GOLD observations. These first of kind results provide new insight into the dynamic response of the coupled thermosphere and ionosphere system to transient solar events, including eclipses.

Dynamic Response of Train–Ballastless Track Caused by Failure in Cement–Asphalt Mortar Layer

Dynamic Response of Train–Ballastless Track Caused by Failure in Cement–Asphalt Mortar Layer

Eumelanin & keratin sourced from waste: unraveling criss-cross functionalities for green electronic applications

Abstract In the framework of the Circular Economy this study provides a detailed analysis of water-based suspensions of two biopolymers derived by sustainable processes: eumelanin from insect farming and keratin from chicken feathers. The latter material was obtained via two different extraction procedures. Colloidal-like suspensions were produced in water either as a single component system or a mixture of both in selected ratios, taking advantage of their high solubility. The suspensions were examined using a comprehensive set of chemical, structural and dielectric techniques to gather information on their properties. Small-Angle x-ray Scattering results provided insights into the elemental polymer sections within the suspension, while Transmission Electron Microscopy images indicate that keratin is the component driving the shape of the aggregation structure in a colloidal environment, and, in some cases, eumelanin internalization. Furthermore, the co-presence of both polymers in water determines the aggregation dimensions and shapes. The discussion focuses on the influence of the aggregation on the dielectric proper-ties by comparing the former to the AC dynamic response returned by Broadband Dielectric Spectroscopy (BDS). Within the BDS framework various items are highlighted including dielectric relaxations, screening effects, counterion condensation and ionic charge transport. The results shown in this work let to foresee the adoption of water or biofriendly aqueous BSF-EuM:Keratin suspensions in the production of devices and sensors with low environmental impact.

Seismic Behaviors of Historic Timber Buildings Considering the Looseness of Mortise-Tenon Connections

ABSTRACT Due to the effects of the long-term loads, earthquakes, as well as aging and decay of the wood, existing historic timber buildings (HTBs) are inevitably damaged, especially by mortise–tenon loosening. Therefore, this paper aimed to investigate the seismic behaviors of HTBs considering the looseness of mortise–tenon connections. Shaking table tests were conducted on a 1/3.52 scale model of an intact HTB made by the Engineering Code of the Qing Dynasty to simulate seismic loads and study the seismic response of HTBs. The deformation characteristics, failure modes, and dynamic response of the test model were all studied. Furthermore, the modal and dynamic response analyses of all finite element models (FEMs) were used to investigate the influence of looseness on seismic behaviors of HTBs. The results show that with a larger damaged degree than 13.3%, the inter-story drift ratio (IDR) θ of the damaged model with looseness mortise–tenon connections resulted from earthquakes, is more than the IDR limit of 1/30 under an 8-degree rare earthquake, indicating that the HTBs must be strengthened and retrofitted immediately.