Data based identification and prediction of nonlinear and complex dynamical systems

We thank Dr. R. Yang (formerly at ASU), Dr. R.-Q. Su (formerly at ASU), and Mr. Zhesi Shen for their contributions to a number of original papers on which this Review is partly based. This work was supported by ARO under Grant No. W911NF-14-1-0504. W.-X. Wang was also supported by NSFC under Grants No. 61573064 and No. 61074116, as well as by the Fundamental Research Funds for the Central Universities, Beijing Nova Programme.Peer reviewedPostprin

Assessment of the Structural and Thermal Behavior of Concrete Masonry Construction via Experimentally Informed Numerical Models

This dissertation aims at describing and examining the compressive and out-of-plane behavior and failure patterns of mortarless masonry prisms and walls through experimental tests and numerical models. In addition, the thermal performance of various masonry units is investigated through detailed thermo-fluid dynamic models to contribute to the masonry construction knowledge base. Studies on the behavior of masonry systems are fundamental to understanding their structural and thermal performance. One of the variations of this type of construction is dry-stack masonry, i.e., units laid without mortar between the joints. Despite reducing the time and cost of construction, mortarless construction has not gained widespread acceptance as a viable alternative to mortared masonry because the mechanical behavior of the mortarless system is not yet fully understood. To address this knowledge gap, this research developed numerical models to compare their response under compressive and out-of-plane loads with experimental tests. The validated structural numerical models of mortarless masonry prisms and reinforced mortarless walls are then used to predict and thoroughly examine the effects of design parameters. The mortarless prisms in these models included variations in the surface roughness between the units. These models revealed that both the stress distribution and failure pattern depended on the unit strength, the condition of the surface in contact between the units, and the grout strength for grouted prisms. The mortarless walls studied here included grout and steel reinforcement within the cells. In these walls, the load-carrying capacity, the displacement ductility, and the failure patterns were examined based on variations in the unit and grout compressive strength, yield strength, and reinforcement and grouting ratios. The thermal response of masonry units also merits further study to better understand the behavior of standard units as well as thermally efficient unit configurations. In this research, validated numerical models were used to evaluate the heat flow path, the distribution of temperatures, and the air velocities within the units. The results revealed the importance of including the three heat transfer mechanisms and the air flow within the cells of masonry units to better approximate the experimental thermal performance

Investigation of key challenges facing aerogel composites development through multiscale approach

Error on title page. Date of award is 2022The aerogel particulate and fibre reinforced composites are becoming more and more popular due to their exceptional properties, nevertheless, they do face a range of challenges that need to be overcome for wider applications. The main ones include a lack of understanding of the interactions between aerogels and reinforcing fibre materials, lack of appropriate models to predict their performance, and finally, lack of property database, allowing for an informative selection of aerogel composites as a viable alternative to other materials. The primary goal of this work is to tackle those challenges and provide a better fundamental understanding of some cases of aerogel composites. In order to fulfil the thesis' goals, the aerogel influence on the various thermal and mechanical properties of epoxy and vinyl ester polymers were investigated. By incorporating various weight contents and sizes of silica and polyimide aerogel particles into these polymers, their thermal conductivity, compressive properties, and other thermomechanical properties in these particle-filled polymers have been evaluated. Overall, created composites presented a significant decrease in thermal conductivity, while the introduction of porous particles deteriorated composite mechanical response. Additionally, micromechanical testing of the interface between aerogel and fibre reinforcement has been performed for the first time to understand their bonding ability. By designing a method to deposit an aerogel droplet surrounding the fibre, the microbond tests were enabled, and the results revealed poor adhesion between aerogel and selected fibre type in general. In addition to the experimental part, this study also focused on modelling aerogels and aerogel composites, which provided insight into the interactions between aerogels and most common reinforcement materials using a multiscale approach. As a result, the nanoscale analysis using molecular dynamics allowed to estimate thermal and mechanical properties of low density silica and polyimide. What is more, the aerogel-fibre interfacial properties values have also been obtained though modelling. Finally, the microscale model was used to model the thermal and mechanical properties of epoxy composites. A close match between experimental and modelled thermal conductivity and compressive modulus of epoxy combined with low density silica or polyimide particles has been achieved by incorporating the nanoscale properties into the micromechanical model.The aerogel particulate and fibre reinforced composites are becoming more and more popular due to their exceptional properties, nevertheless, they do face a range of challenges that need to be overcome for wider applications. The main ones include a lack of understanding of the interactions between aerogels and reinforcing fibre materials, lack of appropriate models to predict their performance, and finally, lack of property database, allowing for an informative selection of aerogel composites as a viable alternative to other materials. The primary goal of this work is to tackle those challenges and provide a better fundamental understanding of some cases of aerogel composites. In order to fulfil the thesis' goals, the aerogel influence on the various thermal and mechanical properties of epoxy and vinyl ester polymers were investigated. By incorporating various weight contents and sizes of silica and polyimide aerogel particles into these polymers, their thermal conductivity, compressive properties, and other thermomechanical properties in these particle-filled polymers have been evaluated. Overall, created composites presented a significant decrease in thermal conductivity, while the introduction of porous particles deteriorated composite mechanical response. Additionally, micromechanical testing of the interface between aerogel and fibre reinforcement has been performed for the first time to understand their bonding ability. By designing a method to deposit an aerogel droplet surrounding the fibre, the microbond tests were enabled, and the results revealed poor adhesion between aerogel and selected fibre type in general. In addition to the experimental part, this study also focused on modelling aerogels and aerogel composites, which provided insight into the interactions between aerogels and most common reinforcement materials using a multiscale approach. As a result, the nanoscale analysis using molecular dynamics allowed to estimate thermal and mechanical properties of low density silica and polyimide. What is more, the aerogel-fibre interfacial properties values have also been obtained though modelling. Finally, the microscale model was used to model the thermal and mechanical properties of epoxy composites. A close match between experimental and modelled thermal conductivity and compressive modulus of epoxy combined with low density silica or polyimide particles has been achieved by incorporating the nanoscale properties into the micromechanical model

Characterisation of cement-treated crushed rock basecourse for Western Australian roads

Cement treatment for pavement basecourse materials results in the creation of cement treated basecourse which is either classified as "modified" or "stabilised". The two classifications perform differently in service, with susceptibility to fatigue being the most obvious characteristic delineating the two. This classification methodology is currently quantified based on Unconfined Compressive Strength (UCS) ranges.Throughout the 1990s to the early 2000s, Main Roads Western Australia (MRWA) has investigated various basecourse products created by adding cement. However, due to unexpected behaviour when applying the cement treated basecourse materials, MRWA sanctioned restrictions of its use in Western Australia. "Stabilised" basecourse were not to be used on roads and strength gained from "modified" basecourse is to be ignored. This is quantified by measuring the UCS gained from the cement treatment.Nevertheless, using UCS to classify cement treated crushed rock is injudicious and does not portray the insitu behaviour and characteristics of cement treated crushed rock basecourse. This dissertation therefore investigates the characteristics of cement treated crushed rock basecourse for Western Australian roads. This is to determine a better method to quantify the various classification of cement treated basecourse and understand its insitu behaviour. Subsequently, the result provides encouragement to reintroduce the use of cement treated crushed rocks in Western Australia.Amongst the characteristics investigated are strength, fatigue, shrinkage, durability and erodibility. These characteristics are assessed against varying cement content. The dissertation combines known standard testing methods along with uniquely developed testing methods to establish numerical models for characterising the materials. This includes the application of the Four Point Bending Test for fatigue, Tube Suction Test for durability, Nitrogen Adsoprtion for shrinkage, and Wheel Tracking Test for erodibility. A finite element model is also created to validate the results for fatigue.This dissertation has improved the understanding of the cement treated crushedrock materials. It proposes a new numerical fatigue model and provides an alternative classification methodology by incorporating the other key characteristics studied by this paper

Unveiling human interactions : approaches and techniques toward the discovery and representation of interactions in networks

L'abstract è presente nell'allegato / the abstract is in the attachmen

A platform to restore intra-tissue flow in live explant assays

Tissue resection during first-line surgery is a standard strategy in the clinic for several life-threatening diseases, such as cancer. In case of malignancy, despite the benefits from surgery, cancer often becomes treatment-resistant and metastasises, limiting therapeutic options and patient survival. Due to tumour heterogeneity, treatment personalisation can improve patient outcomes, however tools based on native tissue samples, used for patient-specific drug screening remain very limited. This is primarily due to the diffusion-limited mass transport in static culture conditions, where tissue viability is rapidly reduced due to ischemia. Our aim is to develop a platform that restores intra-tissue flow through native tissue specimens to prolong their preservation ex vivo. Flow of culture media around tissue specimens has been commonly used for sample preservation. However, the efficacy of most currently available platforms has been limited, as ex vivo specimen perfusion is not facilitated in these technologies. As fluid is allowed to travel around specimen periphery, intra-tissue flow is hydraulically disadvantaged and benefits from culture media renewal only affect cells within 200 μm from explant surface. In this thesis, a novel system is presented that comprises a channel-based device with a suitably-designed constriction to block peri-fusion (i.e. flow around the tissue) and facilitate specimen entrapment and perfusion. Using a syringe pump, device efficacy to facilitate intra-tissue flow was investigated, showing that the induced perfusion occurred through both the vasculature and the interstitium. The effects of perfusion on specimen maintenance and function were also investigated. It was showed that healthy mouse liver and cancerous mouse and human omental specimens were better preserved under perfused conditions in the developed apparatus for 48h. Intra-tissue flow was also effective to inhibit cell metabolism after a 2h-specimen perfusion with a metabolic poison, suggesting this system may have great potential for predictive, live explant assays.Open Acces

Bone fracture incidence, measurement and adaptation: An exploration through the continuum from incidence to measurement and adaptation

This research encompasses four studies exploring bone adaptation, fracture incidence, and preventative measures to decrease fracture risk and increase bone health. Study one was a clinical audit exploring incidence rates for appendicular fractures in children in Western Australia over ten years. Diagnostic and remedial approaches were explored in studies two, three and four by examining the between-day reliability of upper limb scans; reliability of the osteogenic index (OI) for upper-body strength and power exercises; and the diagnostic value or utility of using pQCT in disease profiling, respectively. Fracture rates in the limbs of children were found to be increasing each year, particularly in the forearm, and regardless of gender, between 2005 and 2015, similar to international trend data. pQCT was established as a reliable tool for quantifying upper limb diaphyseal measurements. The OI had varying reliability depending on the equation used, exercise type and exercise intensity when measured using accelerometers at multiple locations. Lastly, paediatric populations with low motor competence and/or neuromuscular disorders were disease profiles which had a measurably negative influence on bone when compared to unaffected controls. The increase in fracture incidence in Western Australia is a concerning trend for bone health in children and adolescents that requires lifestyle and population-based interventions to arrest this incremental problem. pQCT may be a valuable tool for disease profiling with area measurements for bone and some muscle variables more reliable than volumetric measurements in the upper limbs. The OI is a more reliable tool when measuring strength exercises than power exercises; and individuals with a greater risk of weaker bones should apply more daily load to increase their overall bone health. Interventions should be put into place to rehabilitate individuals with already weaker bones, such as targeted and well-designed exercise programs supported by good nutritional practices

Research opportunities in bone demineralization, phase 3

Bone demineralization, calcium responses to weightlessness, endocrine responses to weightlessness, mechanisms of bone loss, biomedical research, pathogenesis, and endocrine effects are discussed

Shining light on T6SS mode of action and function within single cells and bacterial communities

Bacteria are ubiquitously found in the environment and form the basis for all known ecosystems on our planet. Most bacterial cells reside in complex multi-species bacterial communities, which are often associated with a host, such as the human microbiota. These bacterial communities are shaped by cooperative and competitive interactions amongst their members. Like higher animals, bacteria also compete with their conspecifics for nutrients and space. This evolutionary arms race resulted in a diverse set of strategies for microbial competition. In particular, bacteria residing on solid surfaces can compete with their neighbors through the use of specialized nanomachines, called secretion systems, enabling the direct delivery of toxic effector molecules into by-standing target cells. The most commonly used weapon for contact-dependent antagonism is the bacterial Type VI secretion system (T6SS). The T6SS belongs to the family of contractile injection systems (CISs). All CISs are structurally and functionally related to contractile bacteriophages (e.g. phage T4) and translocate proteins into target cells by means of physical force, which is generated by rapid sheath contraction. This results in the ejection of the inner tube associated with a sharp tip and effector proteins at its end. Effector translocation leads ultimately to target cell death. Importantly, the T6SS is capable translocating effectors across broad ranges of biological membranes making it a powerful weapon in microbial warfare as well as potent virulence mechanism towards eukaryotic host cells. Our current understanding of T6SS mode of action is primarily based on the combination of structural biology and fluorescence live-cell microscopy studies. While in particular cryo-electron microscopy (cryo-EM) revealed the detailed architecture of the T6SS in situ and of isolated subassemblies, fluorescence live-cell microscopy uncovered the remarkable dynamics of T6SS biogenesis. However, a complete understanding of T6SS dynamics is hampered in standard fluorescent microscopy due to: (i) the spatial and temporal resolution limit, (ii) the inability to efficiently label secreted components of the machinery, (iii) the weak signals due to low protein abundance and rapid photobleaching, (iv) the difficulty to perform long-term co-incubation experiments as well as (v) the inability to precisely control spatial and chemical environment. My doctoral thesis aimed to overcome these limitations to allow novel insights into dynamics of the T6SSs of Vibrio cholerae, Pseudomonas aeruginosa and Acinetobacter baylyi. Specifically sheath assembly, initiation of sheath contraction, T6SS mediated protein translocation in to sister cells as well as strategies for prey cell inhibition were studied in this thesis. First, I studied sheath assembly in ampicillin induced V. cholerae spheroplasts. These enlarged cells assemble T6SS sheaths which are up to 10x longer as compared to rod shaped cells. This allowed us to photobleach an assembling sheath structure and demonstrate that new sheath subunits are added to the growing sheath polymer at the distal end opposite the baseplate. Importantly, this was the first direct observation made for any contractile machines studied to date. Moreover, I showed that unlike for all other CISs, T6SS sheath length is not regulated and correlates with cell size. In order to monitor protein translocation into target cells, we developed a T6SS dependent interbacterial protein complementation assay, enabling the indirect detection of translocated T6SS components into the cytosol of recipient cells. This allowed us to demonstrate that secreted T6SS components are exchanged among by-standing sister cells within minutes upon initial cell contact. Importantly, these results were the first experimental indication that T6SS is capable of translocating its components into the cytosol of Gram-negative target cells. Furthermore, we showed that the amount and the composition of the secreted tip influences the number of T6SS assemblies per cell, whereas different concentration of the tube protein influenced sheath length. We also provided evidence that precise aiming of T6SS assemblies through posttranslational regulation in P. aeruginosa increases the efficiency of substrate delivery. In addition, together with two Nanoscience master students we have also been implementing microfluidics in the Basler laboratory. This powerful technology enabled us to control the spatial arrangements of aggressor and prey populations and to follow these populations at single-cell level over time scales of several hours. In collaboration with Prof. Kevin Forster, University of Oxford, we demonstrated that the rate of target cell lysis heavily influences the outcome of contact-dependent T6SS killing and thus drives evolution of lytic effectors. Moreover, microfluidics allows for the dynamic change of the chemical microenvironment during imaging experiments. By following the T6SS dynamics in response to hyperosmotic shocks resulting in a rapid cell volume reduction, we found that physical pressure from the collapsing cell envelope could trigger sheath contraction. This led us to propose a model for sheath contraction under steady-state conditions where continued sheath polymerization against membrane contact site leads to a gradual increase in pressure applied to the assembled sheath. We propose that this could be potentially sensed by the baseplate, which in turn would trigger sheath contraction