Internal deformation and kinematic indicators within a tripartite Mass Transport Deposit, NW Argentina

Acknowledgments This work was carried out with support from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) – Brazil, BG-Brazil and the University of Aberdeen. We would like to thank the following geologists for their support, camaraderie and countless hours of fieldwork: Claus Fallgatter, Victoria Valdez, Carla Puigdomenech, Guilherme Bozetti, Roberto Noll Filho and Arthur Giovannini, and we thank Lorena Moscardelli and an anonymous reviewer, whose constructive comments helped to improve the manuscript.

A minimal model of partial synchrony

Acknowledgement We wish to acknowledge A. Pikovsky and M. Zaks for useful discussions. This work has been financially supported by the EU project COSMOS (642563).

Basement-cover tectonics, structural inheritance and deformation migration in the outer parts of orogenic belts : A view from the western Alps

Postprint

A minimal model of partial synchrony

We wish to acknowledge A Pikovsky and M Zaks for useful discussions. This work has been financially supported by the EU project COSMOS (642563).

Visualization and prediction of spatial deformation using thin-plate splines in the context of scoliosis

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Stochastically forced dislocation density distribution in plastic deformation

The dynamical evolution of dislocations in plastically deformed metals is controlled by both deterministic factors arising out of applied loads and stochastic effects appearing due to fluctuations of internal stress. Such type of stochastic dislocation processes and the associated spatially inhomogeneous modes lead to randomness in the observed deformation structure. Previous studies have analyzed the role of randomness in such textural evolution but none of these models have considered the impact of a finite decay time (all previous models assumed instantaneous relaxation which is "unphysical") of the stochastic perturbations in the overall dynamics of the system. The present article bridges this knowledge gap by introducing a colored noise in the form of an Ornstein-Uhlenbeck noise in the analysis of a class of linear and nonlinear Wiener and Ornstein-Uhlenbeck processes that these structural dislocation dynamics could be mapped on to. Based on an analysis of the relevant Fokker-Planck model, our results show that linear Wiener processes remain unaffected by the second time scale in the problem but all nonlinear processes, both Wiener type and Ornstein-Uhlenbeck type, scale as a function of the noise decay time τ. The results are expected to ramify existing experimental observations and inspire new numerical and laboratory tests to gain further insight into the competition between deterministic and random effects in modeling plastically deformed samples.

Acoustic and Magnetic Techniques for the Isolation and Analysis of Cells in Microfluidic Platforms

Cancer comprises a collection of diseases, all of which begin with abnormal tissue growth from various stimuli, including (but not limited to): heredity, genetic mutation, exposure to harmful substances, radiation as well as poor dieting and lack of exercise. The early detection of cancer is vital to providing life-saving, therapeutic intervention. However, current methods for detection (e.g., tissue biopsy, endoscopy and medical imaging) often suffer from low patient compliance and an elevated risk of complications in elderly patients. As such, many are looking to “liquid biopsies” for clues into presence and status of cancer due to its minimal invasiveness and ability to provide rich information about the native tumor. In such liquid biopsies, peripheral blood is drawn from patients and is screened for key biomarkers, chiefly circulating tumor cells (CTCs). Capturing, enumerating and analyzing the genetic and metabolomic characteristics of these CTCs may hold the key for guiding doctors to better understand the source of cancer at an earlier stage for more efficacious disease management.

The isolation of CTCs from whole blood, however, remains a significant challenge due to their (i) low abundance, (ii) lack of a universal surface marker and (iii) epithelial-mesenchymal transition that down-regulates common surface markers (e.g., EpCAM), reducing their likelihood of detection via positive selection assays. These factors potentiate the need for an improved cell isolation strategy that can collect CTCs via both positive and negative selection modalities as to avoid the reliance on a single marker, or set of markers, for more accurate enumeration and diagnosis.

The technologies proposed herein offer a unique set of strategies to focus, sort and template cells in three independent microfluidic modules. The first module exploits ultrasonic standing waves and a class of elastomeric particles for the rapid and discriminate sequestration of cells. This type of cell handling holds promise not only in sorting, but also in the isolation of soluble markers from biofluids. The second module contains components to focus (i.e., arrange) cells via forces from acoustic standing waves and separate cells in a high throughput fashion via free-flow magnetophoresis. The third module uses a printed array of micromagnets to capture magnetically labeled cells into well-defined compartments, enabling on-chip staining and single cell analysis. These technologies can operate in standalone formats, or can be adapted to operate with established analytical technologies, such as flow cytometry. A key advantage of these innovations is their ability to process erythrocyte-lysed blood in a rapid (and thus high throughput) fashion. They can process fluids at a variety of concentrations and flow rates, target cells with various immunophenotypes and sort cells via positive (and potentially negative) selection. These technologies are chip-based, fabricated using standard clean room equipment, towards a disposable clinical tool. With further optimization in design and performance, these technologies might aid in the early detection, and potentially treatment, of cancer and various other physical ailments.

Behavior Genetics and Post Genomics

The science of genetics is undergoing a paradigm shift. Recent discoveries, including the activity of retrotransposons, the extent of copy number variations, somatic and chromosomal mosaicism, and the nature of the epigenome as a regulator of DNA expressivity, are challenging a series of dogmas concerning the nature of the genome and the relationship between genotype and phenotype. DNA, once held to be the unchanging template of heredity, now appears subject to a good deal of environmental change; considered to be identical in all cells and tissues of the body, there is growing evidence that somatic mosaicism is the normal human condition; and treated as the sole biological agent of heritability, we now know that the epigenome, which regulates gene expressivity, can be inherited via the germline. These developments are particularly significant for behavior genetics for at least three reasons: First, these phenomena appear to be particularly prevalent in the human brain, and likely are involved in much of human behavior; second, they have important implications for the validity of heritability and gene association studies, the methodologies that largely define the discipline of behavior genetics; and third, they appear to play a critical role in development during the perinatal period, and in enabling phenotypic plasticity in offspring in particular. I examine one of the central claims to emerge from the use of heritability studies in the behavioral sciences, the principle of “minimal shared maternal effects,” in light of the growing awareness that the maternal perinatal environment is a critical venue for the exercise of adaptive phenotypic plasticity. This consideration has important implications for both developmental and evolutionary biology

Levi-flat Minimal Hypersurfaces in Two-dimensional Complex Space Forms

The purpose of this article is to classify the real hypersurfaces in complex space forms of dimension 2 that are both Levi-flat and minimal. The main results are as follows: When the curvature of the complex space form is nonzero, there is a 1-parameter family of such hypersurfaces. Specifically, for each one-parameter subgroup of the isometry group of the complex space form, there is an essentially unique example that is invariant under this one-parameter subgroup. On the other hand, when the curvature of the space form is zero, i.e., when the space form is complex 2-space with its standard flat metric, there is an additional `exceptional' example that has no continuous symmetries but is invariant under a lattice of translations. Up to isometry and homothety, this is the unique example with no continuous symmetries.

Active Surface Deformation Technology for Management of Marine Biofouling

Biofouling, the accumulation of biomolecules, cells, organisms and their deposits on submerged and implanted surfaces, is a ubiquitous problem across various human endeavors including maritime operations, medicine, food industries and biotechnology. Since several decades, there have been substantial research efforts towards developing various types of antifouling and fouling release approaches to control bioaccumulation on man-made surfaces. In this work we hypothesized, investigated and developed dynamic change of the surface area and topology of elastomers as a general approach for biofouling management. Further, we combined dynamic surface deformation of elastomers with other existing antifouling and fouling-release approaches to develop multifunctional, pro-active biofouling control strategies.

This research work was focused on developing fundamental, new and environment-friendly approaches for biofouling management with emphasis on marine model systems and applications, but which also provided fundamental insights into the control of infectious biofilms on biomedical devices. We used different methods (mechanical stretching, electrical-actuation and pneumatic-actuation) to generate dynamic deformation of elastomer surfaces. Our initial studies showed that dynamic surface deformation methods are effective in detaching laboratory grown bacterial biofilms and barnacles. Further systematic studies revealed that a threshold critical surface strain is required to debond a biofilm from the surface, and this critical strain is dependent on the biofilm mechanical properties including adhesion energy, thickness and modulus. To test the dynamic surface deformation approach in natural environment, we conducted field studies (at Beaufort, NC) in natural seawater using pneumatic-actuation of silicone elastomer. The field studies also confirmed that a critical substrate strain is needed to detach natural biofilm accumulated in seawater. Additionally, the results from the field studies suggested that substrate modulus also affect the critical strain needed to debond biofilms. To sum up, both the laboratory and the field studies proved that dynamic surface deformation approach can effectively detach various biofilms and barnacles, and therefore offers a non-toxic and environmental friendly approach for biofouling management.

Deformable elastomer systems used in our studies are easy to fabricate and can be used as complementary approach for existing commercial strategies for biofouling control. To this end, we aimed towards developed proactive multifunctional surfaces and proposed two different approaches: (i) modification of elastomers with antifouling polymers to produce multifunctional, and (ii) incorporation of silicone-oil additives into the elastomer to enhance fouling-release performance.

In approach (i), we modified poly(vinylmethylsiloxane) elastomer surfaces with zwitterionic polymers using thiol-ene click chemistry and controlled free radical polymerization. These surfaces exhibited both fouling resistance and triggered fouling-release functionalities. The zwitterionic polymers exhibited fouling resistance over short-term (∼hours) exposure to bacteria and barnacle cyprids. The biofilms that eventually accumulated over prolonged-exposure (∼days) were easily detached by applying mechanical strain to the elastomer substrate. In approach (ii), we incorporated silicone-oil additives in deformable elastomer and studied synergistic effect of silicone-oils and surface strain on barnacle detachment. We hypothesized that incorporation of silicone-oil additive reduces the amount of surface strain needed to detach barnacles. Our experimental results supported the above hypothesis and suggested that surface-action of silicone-oils plays a major role in decreasing the strain needed to detach barnacles. Further, we also examined the effect of change in substrate modulus and showed that stiffer substrates require lower amount of strain to detach barnacles.

In summary, this study shows that (1) dynamic surface deformation can be used as an effective, environmental friendly approach for biofouling control (2) stretchable elastomer surfaces modified with anti-fouling polymers provides a pro-active, dual-mode approach for biofouling control, and (3) incorporation of silicone-oils additives into stretchable elastomers improves the fouling-release performance of dynamic surface deformation technology. Dynamic surface deformation by itself and as a supplementary approach can be utilized biofouling management in biomedical, industrial and marine applications.

Visualization and prediction of spatial deformation using thin-plate splines in the context of scoliosis

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Synthesis, Modification, and Application of Siloxane Materials for Environmental Sensing

As human populations and resource consumption increase, it is increasingly important to monitor the quality of our environment. While laboratory instruments offer useful information, portable, easy to use sensors would allow environmental analysis to occur on-site, at lower cost, and with minimal operator training. We explore the synthesis, modification, and applications of modified polysiloxane in environmental sensing. Multiple methods of producing modified siloxanes were investigated. Oligomers were formed by using functionalized monomers, producing siloxane materials containing silicon hydride, methyl, and phenyl side chains. Silicon hydride-functionalized oligomers were further modified by hydrosilylation to incorporate methyl ester and naphthyl side chains. Modifications to the siloxane materials were also carried out using post-curing treatments. Methyl ester-functionalized siloxane was incorporated into the surface of a cured poly(dimethylsiloxane) film by siloxane equilibration. The materials containing methyl esters were hydrolyzed to reveal carboxylic acids, which could later be used for covalent protein immobilization. Finally, the siloxane surfaces were modified to incorporate antibodies by covalent, affinity, and adsorption-based attachment. These modifications were characterized by a variety of methods, including contact angle, attenuated total reflectance Fourier transform infrared spectroscopy, dye labels, and 1H nuclear magnetic resonance spectroscopy. The modified siloxane materials were employed in a variety of sensing schemes. Volatile organic compounds were detected using methyl, phenyl, and naphthyl-functionalized materials on a Fabry-Perot interferometer and a refractometer. The Fabry-Perot interferometer was found to detect the analytes upon siloxane extraction by deformation of the Bragg reflectors. The refractometer was used to determine that naphthyl-functionalized siloxanes had elevated refractive indices, rendering these materials more sensitive to some analytes. Antibody-modified siloxanes were used to detect biological analytes through a solid phase microextraction-mediated enzyme linked immunosorbent assay (SPME ELISA). The SPME ELISA was found to have higher analyte sensitivity compared to a conventional ELISA system. The detection scheme was used to detect Escherichia coli at 8500 CFU/mL. These results demonstrate the variety of methods that can be used to modify siloxanes and the wide range of applications of modified siloxanes has been demonstrated through chemical and biological sensing schemes.

Stress Inversion Using LiDAR Tunnel Deformation Measurements

Far-field stresses are those present in a volume of rock prior to excavations being created. Estimates of the orientation and magnitude of far-field stresses, often used in mine design, are generally obtained by single-point measurements of stress, or large-scale, regional trends. Point measurements can be a poor representation of far-field stresses as a result of excavation-induced stresses and geological structures. For these reasons, far-field stress estimates can be associated with high levels of uncertainty. The purpose of this thesis is to investigate the practical feasibility, applications, and limitations of calibrating far-field stress estimates through tunnel deformation measurements captured using LiDAR imaging. A method that estimates the orientation and magnitude of excavation-induced principal stress changes through back-analysis of deformation measurements from LiDAR imaged tunnels was developed and tested using synthetic data. If excavation-induced stress change orientations and magnitudes can be accurately estimated, they can be used in the calibration of far-field stress input to numerical models. LiDAR point clouds have been proven to have a number of underground applications, thus it is desired to explore their use in numerical model calibration. The back-analysis method is founded on the superposition of stresses and requires a two-dimensional numerical model of the deforming tunnel. Principal stress changes of known orientation and magnitude are applied to the model to create calibration curves. Estimation can then be performed by minimizing squared differences between the measured tunnel and sets of calibration curve deformations. In addition to the back-analysis estimation method, a procedure consisting of previously existing techniques to measure tunnel deformation using LiDAR imaging was documented. Under ideal conditions, the back-analysis method estimated principal stress change orientations within ±5° and magnitudes within ±2 MPa. Results were comparable for four different tunnel profile shapes. Preliminary testing using plastic deformation, a rough tunnel profile, and profile occlusions suggests that the method can work under more realistic conditions. The results from this thesis set the groundwork for the continued development of a new, inexpensive, and efficient far-field stress estimate calibration method.

THE MICROSTRUCTURES OF ZR-EXCEL ALLOY: EFFECTS OF HEAVY ION IRRADIATION, PLASTIC DEFORMATION, THERMAL TREATMENT AND IN-SITU HEATING

Zr-Excel alloy (Zr-3.5Sn-0.8Nb-0.8Mo) is a dual phase (α + β) alloy in the as-received pressure tube condition. It has been proposed to be the pressure tube candidate material for the Generation-IV CANDU-Supercritical Water Reactor (CANDU-SCWR). In this dissertation, the effects of heavy ion irradiation, deformation and heat treatment on the microstructures of the alloy were investigated to enable us to have a better understanding of the potential in-reactor performance of this alloy. In-situ heavy ion (1 MeV) irradiation was performed to study the nucleation and evolution of dislocation loops in both α- and β-Zr. Small and dense type dislocation loops form under irradiation between 80 and 450 °C. The number density tends to saturate at ~ 0.1 dpa. Compared with the α-Zr, the defect yield is much lower in β-Zr. The stabilities of the metastable phases (β-Zr and ω-Zr) and the thermal-dynamically equilibrium phase, fcc Zr(Mo, Nb)2, under irradiation were also studied at different temperatures. Chemi-STEM elemental mapping was carried out to study the elemental redistribution caused by irradiation. The stability of these phases and the elemental redistribution are strongly dependent on irradiation temperature. In-situ time-of-flight neutron diffraction tensile and compressive tests were carried out at different temperatures to monitor lattice strain evolutions of individual grain families during these tests. The β-Zr is the strengthening phase in this alloy in the as-received plate material. Load is transferred to the β-Zr after yielding of the α-Zr grains. The temperature dependence of static strain aging and the yielding sequence of the individual grain families were discussed. Strong tensile/compressive asymmetry was observed in the {0002} grain family at room temperature. The microstructures of the sample deformed at 400 °C and the samples only subjected to heat treatment at the same temperature were characterized with TEM. Concentration of β phase stabilizers in the β grain and the morphology of β grain have significant effect on the stability of β- and ω-Zr under thermal treatment. Applied stress/strain enhances the decomposition of isothermal ω phase but suppresses α precipitation inside the β grains at high temperature. An α → ω/ZrO phase transformation was observed in the thin foils of Zr-Excel alloy and pure Zr during in-situ heating at 700 °C in TEM.