Characterization Of Structural Dynamics Research Articles

Structural Dynamic Characterization of a Modular Morphing Wing Exploiting Finite Elements and Taguchi Methodology

Detrimental environmental impacts due to the increasing demands of the aviation industry have gained tremendous global attention. With a potential fuel saving, along with high aerodynamic performance and maneuverability during different phases of a flight, adaptable wing design has become a viable alternative to its fixed-shape counterpart. A morphing wing design embraces, and can respond accordingly to, most of the flight condition variations effectively and efficiently. Despite these prospects, morphing wing design comes with some challenges due to its inherent complexity caused by an increased number of degrees of freedom. With the availability of various morphing parameters, the vibration signature of a morphing wing design plays a vital role in terms of its structural as well as aeroelastic characteristics. In the present paper, the dynamic characteristics of a re-configurable modular morphing wing developed in-house by a research team at Toronto Metropolitan University are investigated. This modular morphing wing, developed based on the idea of a parallel robot, consists of a number of structural elements connected to each other and to the wing ribs through eyebolt joints. Timoshenko bending beam theories, in conjunction with finite element methodology, are exploited. The free vibration of un-morphed (original) and morphed configurations undergoing multiple levels of sweep and spanwise morphing is presented through a design of experiment methodology.

Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.

Robust Synchronization of Ambient Vibration Time Histories Based on Phase Angle Compensations and Kernel Density Function.

The output-only modal analysis is ubiquitously used for structural health monitoring of civil engineering systems. The measurements for such applications require the use of multiple data acquisition systems (DAS) to avoid complicated meshes of cables in high-rise buildings, avoid traffic constriction on a bridge during measurements, or to avoid having limited channels in a single DAS. Nevertheless, such requirements introduce time synchronization problems which potentially lead to erroneous structural dynamic characterization and hence misleading or inconclusive structural health monitoring results. This research aims at proposing a system-identification-based time synchronization algorithm for output-only modal analysis using multiple DAS. A new procedure based on the compensation of the phase angle shifts is proposed to identify and address the time synchronization issue in ambient vibration data measured through multiple DAS. To increase the robustness of the proposed algorithm to the inherent inconsistencies in these datasets, the kernel density function is applied to rank multiple time-shift estimates that are sometimes detected by the algorithm when inaccuracies exist in the data arising from low signal-to-noise ratio and/or presence of colored noise in the ambient excitations. First, the synchronized ambient vibration dataset of a full-scale bridge is artificially de-synchronized and used to present a proof of concept for the proposed algorithm. Next, the algorithm is applied to ambient vibration data of a 30-story, reinforced concrete building, where the synchronization of the data could not be achieved using two DAS despite best efforts. The application of the proposed time synchronization algorithm is shown to both detect and correct the time synchronization discrepancies in the output-only modal analysis.

Affinity propagation clustering of full-field, high-spatial-dimensional measurements for robust output-only modal identification: A proof-of-concept study

Determination of the model order is a challenging problem in system identification, especially in output-only or operational modal identification where some modes are weakly excited. Although existing methods such as the stabilization diagram method (spectral information) are effective, they do not scale to high-dimensional data, which is usually needed for high-fidelity characterization of structural dynamics and has been made available in the emerging full-field measurement techniques using optical methods such as photogrammetry and laser vibrometers.In this proof-of-concept study we present a new non-parametric, data-driven approach for robust output-only identification of high-spatial-dimensional modal parameters of basic structures by efficiently processing and interactively exploiting the full-field measurement (i.e., very dense spatial measurement points). Specifically, we first over-estimate the system model once, producing a pool of candidate modes associated with their modal frequencies and full-field, high-spatial-dimensional mode shapes. This is accomplished by a data-driven method termed affinity propagation clustering (APC), where the active clusters, which are the active modes in our formulations, emerge from the “message-passing” procedure and does not require a pre-determination of the cluster number (mode or model order). Next, rather than using the spectral information to distinguish the physical and spurious modes in the stabilization diagram method, we exploit and visualize the spatial, full-field mode shape associated with each candidate mode to do so. We conduct extensive experiments on basic structural models with comparisons to a few existing methods. The results indicate that the new method is computationally efficient for identifying high-spatial-dimensional modal parameters, and robust to identify weak modes by exploiting the full-field measurement. We also discuss its applicability and limitations for structures with complex geometry (shapes).

Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins.

Intrinsically disordered proteins and regions (IDPs and IDRs) have attracted increasing interest with their abundance in the human proteome and critical roles in various human diseases. However, the characterization of structural dynamics of IDPs presents a challenge to general experimental methods due to their highly heterogeneous ensembles. Molecular dynamics (MD) simulation has been an alternative method with recent advances in computation power. Nevertheless, it is imperative that eligible predictions are determined by a highly precise force field, but traditional force fields sometimes give a collapsed disorder structure and overestimate the stability of IDPs. Here, we present a novel residue-specific force field, OPLSIDPSFF, to correct backbone dihedral terms for all 20 natural amino acids based on OPLS-AA/L. Extensive tests of 11 IDPs and two short peptides show that the simulated chemical shifts and J-coupling with the OPLSIDPSFF force field are in quantitative agreement with those from NMR experimental observables and are more accurate than the base generic force field. The influences of solvent models were also investigated, and it was found that TIP4P-D water had positive effects on limited observables. Furthermore, OPLSIDPSFF can still be used to model structural and dynamic properties of two tested folded proteins and fast-folding proteins. These findings confirm that the newly developed residue-specific force field OPLSIDPSFF can improve the conformer sampling of intrinsically disordered and folded proteins.

In situ characterization of structural dynamics in swelling hydrogels.

Characterizing the structural morphology and the local viscoelastic properties of soft complex systems raises significant challenges. Here we introduce a dynamic light scattering method capable of in situ, continuous monitoring of structural changes in evolving systems such as swelling gels. We show that the inherently non-stationary dynamics of embedded probes can be followed using partially coherent radiation, which effectively isolates only single scattering contributions even during the dramatic changes in the scattering regime. Using a simple and robust experimental setup, we demonstrate the ability to continuously monitor the structural dynamics of chitosan hydrogels formed by the Ag(+) ion-triggered gelation during their long-term swelling process. We demonstrate that both the local viscoelastic properties of the suspending medium and an effective cage size experienced by diffusing probe particles loaded into the hydrogel can be recovered and used to describe the structural dynamics of hydrogels with different levels of cross-linking. This characterization capability is critical for defining and controlling the hydrogel performance in different biomedical applications.

Laser Doppler Vibrometry for Structural Dynamic Characterization of Rotating Machinery

Laser Doppler Vibrometry (LDV) is a well established technique able to accurately measure vibration velocity of any kind of structure in remote, i.e. non-intrusive way, this allowing to overcome the problem of mass loading, typical of contact sensors as accelerometers and strain-gauges, which has strong influence in case of lightweight structures. Moreover, the possibility of driving automatically the laser beam, by means of moving mirrors controlled with galvanometer servo-actuators, permits to perform scanning measurements at different locations with high spatial resolution and reduced testing time and easily measure the operational deflection shapes (ODS) of the scanned surface. The exploitation of the moving mirrors has allowed to drive the laser beam in a continuous way making it to scan continuously over the structure surface and cover it completely. This way of operation, named Continuous Scanning LDV, permits to perform full-field measurements, the LDV output carrying simultaneously the time-and spatial-dependent information related to the structural vibration. A complementary strategy making use of the LDV coupled with moving mirrors is the so called Tracking LDV, where the laser beam is driven to follow a moving object whose trajectory must be known a priori or measured during operation (e.g. via an encoder in the case of rotating structures). In this paper some applications of the Tracking Laser Doppler Vibrometry (TLDV) and Continuous Scanning Laser Doppler Vibrometry (CSLDV) will be described they concerning, specifically modal and vibrational analysis of rotating structures.

Structural dynamic characterization of a vehicle seat coupled with human occupant

Predicting the responses of the combined human body–seat structure to vibration excitation is still a challenging task. This is mainly due to the complex dynamics behaviour of the seated human body in response to vibration. It is however essential to characterize and predict the critical frequencies and the corresponding vibration patterns of the seat when it is coupled with a human occupant. This study provides important knowledge to predict the structural resonant frequencies and corresponding vibration mode shapes of the vehicle seat coupled with occupant from the seat alone or seat bare-frame (seat without foam cushion). An experiment is designed to measure the frequency responses, resonant frequencies, and corresponding mode shapes of the three different selected vehicle seats when mounted on the test rig. Six volunteers have participated in the experiments. The experiment data for each of the seats were collected for the seat bare-frames, seat alone (seat with foam cushion), and seat with human occupant. The results indicate that the vehicle seat bare-frame, seat alone, and seat with occupant have similar main seatback lateral, seatback fore–aft, and seat twisting structural resonant frequencies below 80Hz. The coupling of the seated human body with the seat shows that the human occupant is not adding any new structural resonant frequency or mode shape to the seat below 80Hz. It is therefore possible to characterize and predict the key vibration attributes such as occupied seat structural resonant frequencies and mode shapes from their corresponding unoccupied seat or bare frame characteristics. This alleviates the need for complex modelling or detailed analysis of the human body structure itself.

Top-down hydrogen/deuterium exchange and ECD-stitched FTICR-MS for probing structural dynamics of a 29-kDa enzyme

Top-down hydrogen/deuterium exchange mass spectrometry (HDX-MS) is becoming a powerful tool for structural biology. Using gas-phase sequencing methods such as electron capture dissociation (ECD), “H/D scrambling free” top-down HDX measurements on proteins can be made with high resolution and full sequence coverage. Although it has clear advantages over traditional proteolysis- and liquid chromatography-based HDX-MS, its application has thus far been limited to small (<18kDa) proteins. The current study has extended the top-down approach to structural dynamics characterization of a nearly 30kDa protein, carbonic anhydrase II (CAII). Employing a novel “ECD-stitching” method, which combines two different ECD settings optimized for the observation of small and large fragments respectively, a total of 120 fragment ions were obtained with sufficient signal/noise for top-down HDX-MS analysis. These ions cover the whole sequence of the protein and provide an average resolution of 2 residues. The results have shown that the most protected region in CAII is the β-sheet motif located in the center of the enzyme, while α-helices located at the outer surface exhibit much less protection. A high degree of protection was also found in loops where solvent access is restricted. These observations are compatible with the structural features of CAII as provided by X-ray crystallographic studies. In addition, the drug-induced conformational transitions of CAII were also characterized. The ECD-stitching top-down approach should be readily applicable to other large proteins and protein complexes, and may give better insights into conformational changes and other solution-phase processes than can be obtained via crystallographic techniques.

Sequence Evolution Correlates with Structural Dynamics

Biochemical activity and core stability are essential properties of proteins, maintained usually by conserved amino acids. Structural dynamics emerged in recent years as another essential aspect of protein functionality. Structural dynamics enable the adaptation of the protein to binding substrates and to undergo allosteric transitions, while maintaining the native fold. Key residues that mediate structural dynamics would thus be expected to be conserved or exhibit coevolutionary patterns at least. Yet, the correlation between sequence evolution and structural dynamics is yet to be established. With recent advances in efficient characterization of structural dynamics, we are now in a position to perform a systematic analysis. In the present study, a set of 34 enzymes representing various folds and functional classes is analyzed using information theory and elastic network models. Our analysis shows that the structural regions distinguished by their coevolution propensity as well as high mobility are predisposed to serve as substrate recognition sites, whereas residues acting as global hinges during collective dynamics are often supported by conserved residues. We propose a mobility scale for different types of amino acids, which tends to vary inversely with amino acid conservation. Our findings suggest the balance between physical adaptability (enabled by structure-encoded motions) and chemical specificity (conferred by correlated amino acid substitutions) underlies the selection of a relatively small set of versatile folds by proteins.

NMR Chromatography: Molecular Diffusion in the Presence of Pulsed Field Gradients in Analytical Chemistry Applications

Nuclear magnetic resonance (NMR) spectroscopy is an excellent analytical tool for precise structural characterization of organic and bio-molecules. Though NMR is often used to characterize a single compound in solution, emerging experimental methods using pulsed-field-gradients (PFGs) allow structural dynamic characterization of several compounds, simultaneously in the same solution. NMR as a chromatography tool is often an overlooked application by analytical chemists. Therefore, in this article we introduce the concept of NMR based diffusion measurements, basic operational methods and novel applications. We expect this article to increase the overall use and appreciation of NMR-based diffusion measurements in general and in particular, in analytical chemistry applications.

Mass spectrometric characterization of conformational preludes to β 2-microglobulin aggregation

Characterization of protein folding and unfolding is an important issue for basic biological science, for understanding the devastating amyloid diseases, and for the manufacture and use of biological therapeutics. Unlike nuclear magnetic resonance spectroscopy, the use of mass spectrometry to monitor amide hydrogen ( 1H/ 2H) exchange kinetics (HX-MS) allows characterization of structural dynamics even when only limited amounts of protein is available. As an adjunct technique, requiring even less material and very well suited for serial monitoring of folding phenomena in a single solution under native conditions capillary electrophoresis may also be very informative. These approaches are here used to examine the small (99 amino acid residues) protein β 2-microglobulin (β 2m) which is prone to amyloidogenic unfolding especially after cleavage at its lysine-58 residue. The propensity for unfolding of native, non-cleaved β 2m and lysine-58 cleaved β 2m variants as well as the effect of acetonitrile on the conformational equilibria could be addressed by these approaches. At physiological conditions, intact β 2m and the lysine-58 cleaved variants undergo a transient unfolding that exhibit an EX1 type hydrogen exchange behaviour. We have measured the unfolding rate constants for the cleaved variant where Lys-58 is removed (ΔK58-β 2m) and the cleaved variant where this residue is preserved (cK58-β 2m) at various temperatures. Below 37 °C, the variant devoid of Lys-58 (ΔK58-β 2m) has a higher unfolding rate than cK58-β 2m and this correlates with the observation that ΔK58-β 2m has a higher propensity to aggregate. The results of our studies provide valuable insight into the early conformational perturbations involved in rendering this protein insoluble and amyloidogenic. The approaches used in this study should be useful also for the characterization of other conformationally unstable proteins.

511 EXPERIMENTAL CHARACTERIZATION OF STRUCTURAL DYNAMICS OF MICRO/MESO-SCALE MACHINE TOOL (mMT)

A miniaturized machine tool-referred to as Micro/Meso-Scale Machine Tool (mMT)-is studied by the characterization of structural dynamics in this paper. The scaling effect of the dynamics of machine structures of a conventional machine tool and the prototype of a mMT is investigated through the finite element analysis (FEA) and the experimental modal analysis. The results of experimental modal analysis reveal that the fundamental natural frequency of the prototype of mMT (148.6 Hz) is much lower than that obtained by the dynamic scaling analysis via FEA (250 Hz approximately). The effect of joint conditions between machine components on the dynamic behaviors of the machine structure is shown to be a significant factor.