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.

Quantifying Earthquake Collapse Risk of Tall Steel Moment Frame Buildings Using Rupture-to-Rafters Simulations

There is a sparse number of credible source models available from large-magnitude past earthquakes. A stochastic source model generation algorithm thus becomes necessary for robust risk quantification using scenario earthquakes. We present an algorithm that combines the physics of fault ruptures as imaged in laboratory earthquakes with stress estimates on the fault constrained by field observations to generate stochastic source models for large-magnitude (Mw 6.0-8.0) strike-slip earthquakes. The algorithm is validated through a statistical comparison of synthetic ground motion histories from a stochastically generated source model for a magnitude 7.90 earthquake and a kinematic finite-source inversion of an equivalent magnitude past earthquake on a geometrically similar fault. The synthetic dataset comprises of three-component ground motion waveforms, computed at 636 sites in southern California, for ten hypothetical rupture scenarios (five hypocenters, each with two rupture directions) on the southern San Andreas fault. A similar validation exercise is conducted for a magnitude 6.0 earthquake, the lower magnitude limit for the algorithm. Additionally, ground motions from the Mw7.9 earthquake simulations are compared against predictions by the Campbell-Bozorgnia NGA relation as well as the ShakeOut scenario earthquake. The algorithm is then applied to generate fifty source models for a hypothetical magnitude 7.9 earthquake originating at Parkfield, with rupture propagating from north to south (towards Wrightwood), similar to the 1857 Fort Tejon earthquake. Using the spectral element method, three-component ground motion waveforms are computed in the Los Angeles basin for each scenario earthquake and the sensitivity of ground shaking intensity to seismic source parameters (such as the percentage of asperity area relative to the fault area, rupture speed, and risetime) is studied.

Under plausible San Andreas fault earthquakes in the next 30 years, modeled using the stochastic source algorithm, the performance of two 18-story steel moment frame buildings (UBC 1982 and 1997 designs) in southern California is quantified. The approach integrates rupture-to-rafters simulations into the PEER performance based earthquake engineering (PBEE) framework. Using stochastic sources and computational seismic wave propagation, three-component ground motion histories at 636 sites in southern California are generated for sixty scenario earthquakes on the San Andreas fault. The ruptures, with moment magnitudes in the range of 6.0-8.0, are assumed to occur at five locations on the southern section of the fault. Two unilateral rupture propagation directions are considered. The 30-year probabilities of all plausible ruptures in this magnitude range and in that section of the fault, as forecast by the United States Geological Survey, are distributed among these 60 earthquakes based on proximity and moment release. The response of the two 18-story buildings hypothetically located at each of the 636 sites under 3-component shaking from all 60 events is computed using 3-D nonlinear time-history analysis. Using these results, the probability of the structural response exceeding Immediate Occupancy (IO), Life-Safety (LS), and Collapse Prevention (CP) performance levels under San Andreas fault earthquakes over the next thirty years is evaluated.

Furthermore, the conditional and marginal probability distributions of peak ground velocity (PGV) and displacement (PGD) in Los Angeles and surrounding basins due to earthquakes occurring primarily on the mid-section of southern San Andreas fault are determined using Bayesian model class identification. Simulated ground motions at sites within 55-75km from the source from a suite of 60 earthquakes (Mw 6.0 − 8.0) primarily rupturing mid-section of San Andreas fault are considered for PGV and PGD data.