Extension of The Improved Upper-Bound Pushover Analysis For Seismic Assessment of Steel Moment Resisting Frames With Setbacks

Pushover analysis technique is a key tool for the performance-based seismic design that has been largely adopted in the new generation of seismic codes. Therefore, more precise and reliable performance predictions are highly demanded. Improved upper-bound (IUB) pushover analysis is one of the advanced nonlinear static procedures (NSPs) that has been recently developed. This procedure estimates adequately the response of regular and tall buildings. In this study, IUB is extended to assess the seismic response of irregular buildings with setbacks. To this end, an adjustment of the IUB lateral load distribution is implemented by integrating a third mode of vibration to control the response of these complex buildings. Fifteen multi-storey steel frames with different types of setbacks including a reference structure are used to test the accuracy of the proposed procedure by comparing its results to those from other NSPs and the nonlinear time history analysis (NLHA). The findings show the superior capacity of the extended IUB in predicting the seismic response of buildings with different levels and types of setbacks.

A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis

Methods that use a linear genome reference for genome sequencing data analysis are reference biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. While pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe (Sirén et al. 2021) and the variant-calling tool DeepTrio (Kolesnikov et al. 2021) using a specially-trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (INDEL) variants over those produced by alignments created using BWA MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded the deleterious-variant (DV) detecting methods and programs of Gu et al. into a streamlined workflow (Gu et al. 2019). We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the mendelian models covered by the previously published Gu et al. methods were recapitulated by these workflows. The results of these experiments indicate a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.

Development of a fiber optic sensor for hydrogen monitoring in transformers

<p>Electric vehicles and photovoltaic power generation are two of factors that are increasing the demands on the electrical grid. To cope with these challenges and to improve grid stability, the development of a transformer monitoring system as a fundamental part of the smart grid is necessary. Dissolved hydrogen in the transformer oil can serve as a primary indicator of the transformer health. Depending on the hydrogen concentration and rate of increase the transformer can be diagnosed. The goal of this thesis was to develop a highly sensitive hydrogen sensor for online health monitoring of transformers. The developed sensors are based on palladium and fiber Bragg gratings (FBG). Palladium expands with hydrogen absorption and this expansion is measured with an FBG. Detailed guidance for optimizing the sensor design is given. First, the selection of the working temperature is discussed. Second, the influence of the palladium geometry on the sensitivity is elaborated: by varying the cross-sectional area ratio of palladium to fiber the sensitivity can be tuned. Two different options to attach palladium are discussed: vapour deposition of palladium and adhesive bonding of palladium foils. The sensitivity of the palladium foil sensors was improved by improved manufacturing processes. The foil sensor have a sensitivity of up to 295 pm/% hydrogen and a resolution of 0.006% hydrogen in gas atmosphere at 90◦C and 1060 mbar. To further increase the hydrogen sensitivity two concepts for amplification of the signal are presented. One relies on palladium silver foils, which have an increased hydrogen solubility and therefore expansion compared to pure palladium, which achieved an increase in sensitivity of a factor of 17. This leads to sensitivity of over 4500 pm/% hydrogen, which is the most sensitive hydrogen sensor reported so far. The other concept relies on a novel concept for strain concentration using a pre-strained palladium foil and FBG, which achieved an amplification of a factor of 2.5. The sensors were characterised in gas and oil environment in a newly developed setup which is stable in pressure, temperature and gas concentration. In gas the sensors were tested at 60, 75, 90, 105, and 120◦C and for a hydrogen concentration range of 0.01 (100 ppm) to 5%. In oil the sensor was tested at 90◦C and for a hydrogen concentration range of 5- 4000 ppm dissolved hydrogen. Furthermore, the influence of carbon monoxide (CO) on the hydrogen sensitivity was examined. A slowed response could be observed, but CO had no impact on the precision of the sensor. Finally, the hydrogen calibration of the sensor is discussed by investigating the strain transfer between expanding palladium and fiber. Three different methods are elaborated to determine the coefficient of strain transfer: (a) via hydrogen measurement, (b) via temperature measurement, and (c) via strain measurement. Methods (a) and (b) were applied directly on the hydrogen sensor, and gave similar results. Method (c) was applied on a reference structure and used to verify method (b). A hydrogen sensor suitable for transformer health monitoring has been developed and characterised, and is currently being implemented in a transformer in the New Zealand network.</p>

Development of a fiber optic sensor for hydrogen monitoring in transformers

<p>Electric vehicles and photovoltaic power generation are two of factors that are increasing the demands on the electrical grid. To cope with these challenges and to improve grid stability, the development of a transformer monitoring system as a fundamental part of the smart grid is necessary. Dissolved hydrogen in the transformer oil can serve as a primary indicator of the transformer health. Depending on the hydrogen concentration and rate of increase the transformer can be diagnosed. The goal of this thesis was to develop a highly sensitive hydrogen sensor for online health monitoring of transformers. The developed sensors are based on palladium and fiber Bragg gratings (FBG). Palladium expands with hydrogen absorption and this expansion is measured with an FBG. Detailed guidance for optimizing the sensor design is given. First, the selection of the working temperature is discussed. Second, the influence of the palladium geometry on the sensitivity is elaborated: by varying the cross-sectional area ratio of palladium to fiber the sensitivity can be tuned. Two different options to attach palladium are discussed: vapour deposition of palladium and adhesive bonding of palladium foils. The sensitivity of the palladium foil sensors was improved by improved manufacturing processes. The foil sensor have a sensitivity of up to 295 pm/% hydrogen and a resolution of 0.006% hydrogen in gas atmosphere at 90◦C and 1060 mbar. To further increase the hydrogen sensitivity two concepts for amplification of the signal are presented. One relies on palladium silver foils, which have an increased hydrogen solubility and therefore expansion compared to pure palladium, which achieved an increase in sensitivity of a factor of 17. This leads to sensitivity of over 4500 pm/% hydrogen, which is the most sensitive hydrogen sensor reported so far. The other concept relies on a novel concept for strain concentration using a pre-strained palladium foil and FBG, which achieved an amplification of a factor of 2.5. The sensors were characterised in gas and oil environment in a newly developed setup which is stable in pressure, temperature and gas concentration. In gas the sensors were tested at 60, 75, 90, 105, and 120◦C and for a hydrogen concentration range of 0.01 (100 ppm) to 5%. In oil the sensor was tested at 90◦C and for a hydrogen concentration range of 5- 4000 ppm dissolved hydrogen. Furthermore, the influence of carbon monoxide (CO) on the hydrogen sensitivity was examined. A slowed response could be observed, but CO had no impact on the precision of the sensor. Finally, the hydrogen calibration of the sensor is discussed by investigating the strain transfer between expanding palladium and fiber. Three different methods are elaborated to determine the coefficient of strain transfer: (a) via hydrogen measurement, (b) via temperature measurement, and (c) via strain measurement. Methods (a) and (b) were applied directly on the hydrogen sensor, and gave similar results. Method (c) was applied on a reference structure and used to verify method (b). A hydrogen sensor suitable for transformer health monitoring has been developed and characterised, and is currently being implemented in a transformer in the New Zealand network.</p>

Delineation guidelines for the lymphatic target volumes in ‘prone crawl’ radiotherapy treatment position for breast cancer patients

Our recently developed prone crawl position (PCP) for radiotherapy of breast cancer patients with lymphatic involvement showed promising preliminary data and it is being optimized for clinical use. An important aspect in this process is making new, position specific delineation guidelines to ensure delineation (for treatment planning) is uniform across different centers. The existing ESTRO and PROCAB guidelines for supine position (SP) were adapted for PCP. Nine volunteers were MRI scanned in both SP and PCP. Lymph node regions were delineated in SP using the existing ESTRO and PROCAB guidelines and were then translated to PCP, based on the observed changes in reference structure position. Nine PCP patient CT scans were used to verify if the new reference structures were consistently identified and easily applicable on different patient CT scans. Based on these data, a team of specialists in anatomy, CT- and MRI radiology and radiation oncology postulated the final guidelines. By taking the ESTRO and PROCAB guidelines for SP into account and by using a relatively big number of datasets, these new PCP specific guidelines incorporate anatomical variability between patients. The guidelines are easily and consistently applicable, even for people with limited previous experience with delineations in PCP.

Modification of Variance-Based Sensitivity Indices for Stochastic Evaluation of Monitoring Measures

In complex engineering models, various uncertain parameters affect the computational results. Most of them can only be estimated or assumed quite generally. In such a context, measurements are interesting to determine the most decisive parameters accurately. While measurements can reduce parameters’ variance, structural monitoring might improve general assumptions on distributions and their characteristics. The decision on variables being measured often relies on experts’ practical experience. This paper introduces a method to stochastically estimate the potential benefits of measurements by modified sensitivity indices. They extend the established variance-based sensitivity indices originally suggested by Sobol’. They do not quantify the importance of a variable but the importance of its variance reduction. The numerical computation is presented and exemplified on a reference structure, a 50-year-old pre-stressed concrete bridge in Germany, where the prediction of the fatigue lifetime of the pre-stressing steel is of concern. Sensitivity evaluation yields six important parameters (e.g., shape of the S–N curve, temperature loads, creep, and shrinkage). However, taking into account individual monitoring measures and suited measurements identified by the modified sensitivity indices, creep and shrinkage, temperature loads, and the residual pre-strain of the tendons turn out to be most efficient. They grant the highest gains of accuracy with respect to the lifetime prediction.

Numerical Analysis and Experimental Verification of Damage Identification Metrics for Smart Beam with MFC Elements to Support Structural Health Monitoring

This paper investigates damage identification metrics and their performance using a cantilever beam with a piezoelectric harvester for Structural Health Monitoring. In order to do this, the vibrations of three different beam structures are monitored in a controlled manner via two piezoelectric energy harvesters (PEH) located in two different positions. One of the beams is an undamaged structure recognized as reference structure, while the other two are beam structures with simulated damage in form of drilling holes. Subsequently, five different damage identification metrics for detecting damage localization and extent are investigated in this paper. Overall, each computational model has been designed on the basis of the modified First Order Shear Theory (FOST), considering an MFC element consisting homogenized materials in the piezoelectric fiber layer. Frequency response functions are established and five damage metrics are assessed, three of which are relevant for damage localization and the other two for damage extent. Experiments carried out on the lab stand for damage structure with control damage by using a modal hammer allowed to verify numerical results and values of particular damage metrics. In the effect, it is expected that the proposed method will be relevant for a wide range of application sectors, as well as useful for the evolving composite industry.

Low-Frequency Harmonic Perturbations Drive Protein Conformational Changes

Protein dynamics has been investigated since almost half a century, as it is believed to constitute the fundamental connection between structure and function. Elastic network models (ENMs) have been widely used to predict protein dynamics, flexibility and the biological mechanism, from which remarkable results have been found regarding the prediction of protein conformational changes. Starting from the knowledge of the reference structure only, these conformational changes have been usually predicted either by looking at the individual mode shapes of vibrations (i.e., by considering the free vibrations of the ENM) or by applying static perturbations to the protein network (i.e., by considering a linear response theory). In this paper, we put together the two previous approaches and evaluate the complete protein response under the application of dynamic perturbations. Harmonic forces with random directions are applied to the protein ENM, which are meant to simulate the single frequency-dependent components of the collisions of the surrounding particles, and the protein response is computed by solving the dynamic equations in the underdamped regime, where mass, viscous damping and elastic stiffness contributions are explicitly taken into account. The obtained motion is investigated both in the coordinate space and in the sub-space of principal components (PCs). The results show that the application of perturbations in the low-frequency range is able to drive the protein conformational change, leading to remarkably high values of direction similarity. Eventually, this suggests that protein conformational change might be triggered by external collisions and favored by the inherent low-frequency dynamics of the protein structure.

X-ray restrained extremely localized molecular orbitals for the embedding of quantum mechanical calculations

The X-ray restrained wavefunction (XRW) method is a quantum crystallographic technique that allows the calculation of molecular wavefunctions adapted to minimize the difference between computed and reference structure factor amplitudes. The latter result from experimental measurements on crystals or from advanced theoretical calculations with periodic boundary conditions, and are used as external restraints in a traditional least-squares structural refinement. Detailed investigations have shown that the technique is able to reliably capture the effects of the crystal field on the molecular electron density. In a recent application, electron distributions obtained from preliminary X-ray restrained wavefunction calculations have been employed in the framework of frozen density embedding theory to embed excited state computations of well defined subsystems. Inspired by these results, it was decided to test, for the first time, the X-ray restrained extremely localized molecular orbitals (XR-ELMOs) along with the recently developed quantum mechanics/extremely localized molecular orbital multiscale embedding approach. By exploiting XR-ELMOs obtained through XRW calculations that used structure factor amplitudes resulting from periodic ab initio computations, excited state calculations of acrylamide in an environment mimicking the one of the crystal structure were performed. In all these computations, the QM region coincides with the crystal asymmetric unit and the ELMO subsystem consisted of two other acrylamide molecules involved in direct hydrogen bonds with the reference unit. The shifts of the excitation energies with respect to the corresponding gas-phase values were evaluated as a function of different parameters on which the computations with XR-ELMOs depend. For instance, the dependence on the resolution of the sets of structure factors that were used to determine the embedding XR-ELMOs were assessed in particular. The results have shown that the use of XR-ELMOs slightly (but not negligibly) improves the description of excited states compared to the gas-phase ELMOs. Once again, these results demonstrate the efficiency of the XRW approach in incorporating environment effects into the calculated molecular orbitals and, hence, into the corresponding electron densities.