Structural and clumped-isotope constraints on the mechanisms of displacement along low-angle detachments

Despite years of research on low-angle detachments, much about them remains enigmatic. This thesis addresses some of the uncertainty regarding two particular detachments, the Mormon Peak detachment in Nevada and the Heart Mountain detachment in Wyoming and Montana.

Constraints on the geometry and kinematics of emplacement of the Mormon Peak detachment are provided by detailed geologic mapping of the Meadow Valley Mountains, along with an analysis of structural data within the allochthon in the Mormon Mountains. Identifiable structures well suited to constrain the kinematics of the detachment include a newly mapped, Sevier-age monoclinal flexure in the hanging wall of the detachment. This flexure, including the syncline at its base and the anticline at its top, can be readily matched to the base and top of the frontal Sevier thrust ramp, which is exposed in the footwall of the detachment to the east in the Mormon Mountains and Tule Springs Hills. The ~12 km of offset of these structural markers precludes the radial sliding hypothesis for emplacement of the allochthon.

The role of fluids in the slip along faults is a widely investigated topic, but the use of carbonate clumped-isotope thermometry to investigate these fluids is new. Faults rocks from within ~1 m of the Mormon Peak detachment, including veins, breccias, gouges, and host rocks, were analyzed for carbon, oxygen, and clumped-isotope measurements. The data indicate that much of the carbonate breccia and gouge material along the detachment is comminuted host rock, as expected. Measurements in vein material indicate that the fluid system is dominated by meteoric water, whose temperature indicates circulation to substantial depths (c. 4 km) in the upper crust near the fault zone.

Slip along the subhorizontal Heart Mountain detachment is particularly enigmatic, and many different mechanisms for failure have been proposed, predominantly involving catastrophic failure. Textural evidence of multiple slip events is abundant, and include multiple brecciation events and cross-cutting clastic dikes. Footwall deformation is observed in numerous exposures of the detachment. Stylolitic surfaces and alteration textures within and around “banded grains” previously interpreted to be an indicator of high-temperature fluidization along the fault suggest their formation instead via low-temperature dissolution and alteration processes. There is abundant textural evidence of the significant role of fluids along the detachment via pressure solution. The process of pressure solution creep may be responsible for enabling multiple slip events on the low-angle detachment, via a local rotation of the stress field.

Clumped-isotope thermometry of fault rocks associated with the Heart Mountain detachment indicates that despite its location on the flanks of a volcano that was active during slip, the majority of carbonate along the Heart Mountain detachment does not record significant heating above ambient temperatures (c. 40-70°C). Instead, cold meteoric fluids infiltrated the detachment breccia, and carbonate precipitated under ambient temperatures controlled by structural depth. Locally, fault gouge does preserve hot temperatures (>200°C), as is observed in both the Mormon Peak detachment and Heart Mountain detachment areas. Samples with very hot temperatures attributable to frictional shear heating are present but rare. They appear to be best preserved in hanging wall structures related to the detachment, rather than along the main detachment.

Evidence is presented for the prevalence of relatively cold, meteoric fluids along both shallow crustal detachments studied, and for protracted histories of slip along both detachments. Frictional heating is evident from both areas, but is a minor component of the preserved fault rock record. Pressure solution is evident, and might play a role in initiating slip on the Heart Mountain fault, and possibly other low-angle detachments.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Dynamic characterization of micro-particle systems

Ordered granular systems have been a subject of active research for decades. Due to their rich dynamic response and nonlinearity, ordered granular systems have been suggested for several applications, such as solitary wave focusing, acoustic signals manipulation, and vibration absorption. Most of the fundamental research performed on ordered granular systems has focused on macro-scale examples. However, most engineering applications require these systems to operate at much smaller scales. Very little is known about the response of micro-scale granular systems, primarily because of the difficulties in realizing reliable and quantitative experiments, which originate from the discrete nature of granular materials and their highly nonlinear inter-particle contact forces.

In this work, we investigate the physics of ordered micro-granular systems by designing an innovative experimental platform that allows us to assemble, excite, and characterize ordered micro-granular systems. This new experimental platform employs a laser system to deliver impulses with controlled momentum and incorporates non-contact measurement apparatuses to detect the particles’ displacement and velocity. We demonstrated the capability of the laser system to excite systems of dry (stainless steel particles of radius 150 micrometers) and wet (silica particles of radius 3.69 micrometers, immersed in fluid) micro-particles, after which we analyzed the stress propagation through these systems.

We derived the equations of motion governing the dynamic response of dry and wet particles on a substrate, which we then validated in experiments. We then measured the losses in these systems and characterized the collision and friction between two micro-particles. We studied wave propagation in one-dimensional dry chains of micro-particles as well as in two-dimensional colloidal systems immersed in fluid. We investigated the influence of defects to wave propagation in the one-dimensional systems. Finally, we characterized the wave-attenuation and its relation to the viscosity of the surrounding fluid and performed computer simulations to establish a model that captures the observed response.

The findings of the study offer the first systematic experimental and numerical analysis of wave propagation through ordered systems of micro-particles. The experimental system designed in this work provides the necessary tools for further fundamental studies of wave propagation in both granular and colloidal systems.

On the added mass of sphere in a circular cylinder considering real fluid effects

An experimental method combined with boundary layer theory is given for evaluating the added mass of a sphere moving along the axis of a circular cylinder filled with water or oil. The real fluid effects are separated from ideal fluid effects.

The experimental method consists essentially of a magnetic steel sphere propelled from rest by an electromagnetic coil in which the current is accurately controlled so that it only supplies force for a short time interval which is within the laminar flow regime of the fluid. The motion of the sphere as a function of time is recorded on single frame photographs using a short-arc multiple flash lamp with accurately controlled time intervals between flashes.

A concept of the effect of boundary layer displacement on the fluid flow around a sphere is introduced to evaluate the real fluid effects on the added mass. Surprisingly accurate agreement between experiment and theory is achieved.

Using Earth Deformation Caused by Surface Mass Loading to Constrain the Elastic Structure of the Crust and Mantle

Surface mass loads come in many different varieties, including the oceans, atmosphere, rivers, lakes, glaciers, ice caps, and snow fields. The loads migrate over Earth's surface on time scales that range from less than a day to many thousand years. The weights of the shifting loads exert normal forces on Earth's surface. Since the Earth is not perfectly rigid, the applied pressure deforms the shape of the solid Earth in a manner controlled by the material properties of Earth's interior. One of the most prominent types of surface mass loading, ocean tidal loading (OTL), comes from the periodic rise and fall in sea-surface height due to the gravitational influence of celestial objects, such as the moon and sun. Depending on geographic location, the surface displacements induced by OTL typically range from millimeters to several centimeters in amplitude, which may be inferred from Global Navigation and Satellite System (GNSS) measurements with sub-millimeter precision. Spatiotemporal characteristics of observed OTL-induced surface displacements may therefore be exploited to probe Earth structure. In this thesis, I present descriptions of contemporary observational and modeling techniques used to explore Earth's deformation response to OTL and other varieties of surface mass loading. With the aim to extract information about Earth's density and elastic structure from observations of the response to OTL, I investigate the sensitivity of OTL-induced surface displacements to perturbations in the material structure. As a case study, I compute and compare the observed and predicted OTL-induced surface displacements for a network of GNSS receivers across South America. The residuals in three distinct and dominant tidal bands are sub-millimeter in amplitude, indicating that modern ocean-tide and elastic-Earth models well predict the observed displacement response in that region. Nevertheless, the sub-millimeter residuals exhibit regional spatial coherency that cannot be explained entirely by random observational uncertainties and that suggests deficiencies in the forward-model assumptions. In particular, the discrepancies may reveal sensitivities to deviations from spherically symmetric, non-rotating, elastic, and isotropic (SNREI) Earth structure due to the presence of the South American craton.