Interplay of martensitic phase transformation and plastic slip in polycrystals

Inspired by key experimental and analytical results regarding Shape Memory Alloys (SMAs), we propose a modelling framework to explore the interplay between martensitic phase transformations and plastic slip in polycrystalline materials, with an eye towards computational efficiency. The resulting framework uses a convexified potential for the internal energy density to capture the stored energy associated with transformation at the meso-scale, and introduces kinetic potentials to govern the evolution of transformation and plastic slip. The framework is novel in the way it treats plasticity on par with transformation.

We implement the framework in the setting of anti-plane shear, using a staggered implicit/explict update: we first use a Fast-Fourier Transform (FFT) solver based on an Augmented Lagrangian formulation to implicitly solve for the full-field displacements of a simulated polycrystal, then explicitly update the volume fraction of martensite and plastic slip using their respective stick-slip type kinetic laws. We observe that, even in this simple setting with an idealized material comprising four martensitic variants and four slip systems, the model recovers a rich variety of SMA type behaviors. We use this model to gain insight into the isothermal behavior of stress-stabilized martensite, looking at the effects of the relative plastic yield strength, the memory of deformation history under non-proportional loading, and several others.

We extend the framework to the generalized 3-D setting, for which the convexified potential is a lower bound on the actual internal energy, and show that the fully implicit discrete time formulation of the framework is governed by a variational principle for mechanical equilibrium. We further propose an extension of the method to finite deformations via an exponential mapping. We implement the generalized framework using an existing Optimal Transport Mesh-free (OTM) solver. We then model the $\alpha$--$\gamma$ and $\alpha$--$\varepsilon$ transformations in pure iron, with an initial attempt in the latter to account for twinning in the parent phase. We demonstrate the scalability of the framework to large scale computing by simulating Taylor impact experiments, observing nearly linear (ideal) speed-up through 256 MPI tasks. Finally, we present preliminary results of a simulated Split-Hopkinson Pressure Bar (SHPB) experiment using the $\alpha$--$\varepsilon$ model.

Characterization of diverse megathrust fault behavior related to seismic supercycles, Mentawai Islands, Sumatra

Long paleoseismic histories are necessary for understanding the full range of behavior of faults, as the most destructive events often have recurrence intervals longer than local recorded history. The Sunda megathrust, the interface along which the Australian plate subducts beneath Southeast Asia, provides an ideal natural laboratory for determining a detailed paleoseismic history over many seismic cycles. The outer-arc islands above the seismogenic portion of the megathrust cyclically rise and subside in response to processes on the underlying megathrust, providing uncommonly good illumination of megathrust behavior. Furthermore, the growth histories of coral microatolls, which record tectonic uplift and subsidence via relative sea level, can be used to investigate the detailed coseismic and interseismic deformation patterns. One particularly interesting area is the Mentawai segment of the megathrust, which has been shown to characteristically fail in a series of ruptures over decades, rather than a single end-to-end rupture. This behavior has been termed a seismic “supercycle.” Prior to the current rupture sequence, which began in 2007, the segment previously ruptured during the 14th century, the late 16th to late 17th century, and most recently during historical earthquakes in 1797 and 1833. In this study, we examine each of these previous supercycles in turn.

First, we expand upon previous analysis of the 1797–1833 rupture sequence with a comprehensive review of previously published coral microatoll data and the addition of a significant amount of new data. We present detailed maps of coseismic uplift during the two great earthquakes and of interseismic deformation during the periods 1755–1833 and 1950–1997 and models of the corresponding slip and coupling on the underlying megathrust. We derive magnitudes of Mw 8.7–9.0 for the two historical earthquakes, and determine that the 1797 earthquake fundamentally changed the state of coupling on the fault for decades afterward. We conclude that while major earthquakes generally do not involve rupture of the entire Mentawai segment, they undoubtedly influence the progression of subsequent ruptures, even beyond their own rupture area. This concept is of vital importance for monitoring and forecasting the progression of the modern rupture sequence.

Turning our attention to the 14th century, we present evidence of a shallow slip event in approximately A.D. 1314, which preceded the “conventional” megathrust rupture sequence. We calculate a suite of slip models, slightly deeper and/or larger than the 2010 Pagai Islands earthquake, that are consistent with the large amount of subsidence recorded at our study site. Sea-level records from older coral microatolls suggest that these events occur at least once every millennium, but likely far less frequently than their great downdip neighbors. The revelation that shallow slip events are important contributors to the seismic cycle of the Mentawai segment further complicates our understanding of this subduction megathrust and our assessment of the region’s exposure to seismic and tsunami hazards.

Finally, we present an outline of the complex intervening rupture sequence that took place in the 16th and 17th centuries, which involved at least five distinct uplift events. We conclude that each of the supercycles had unique features, and all of the types of fault behavior we observe are consistent with highly heterogeneous frictional properties of the megathrust beneath the south-central Mentawai Islands. We conclude that the heterogeneous distribution of asperities produces terminations and overlap zones between fault ruptures, resulting in the seismic “supercycle” phenomenon.

Role of feedback and dynamics in a gene regulatory network

Cells exhibit a diverse repertoire of dynamic behaviors. These dynamic functions are implemented by circuits of interacting biomolecules. Although these regulatory networks function deterministically by executing specific programs in response to extracellular signals, molecular interactions are inherently governed by stochastic fluctuations. This molecular noise can manifest as cell-to-cell phenotypic heterogeneity in a well-mixed environment. Single-cell variability may seem like a design flaw but the coexistence of diverse phenotypes in an isogenic population of cells can also serve a biological function by increasing the probability of survival of individual cells upon an abrupt change in environmental conditions. Decades of extensive molecular and biochemical characterization have revealed the connectivity and mechanisms that constitute regulatory networks. We are now confronted with the challenge of integrating this information to link the structure of these circuits to systems-level properties such as cellular decision making. To investigate cellular decision-making, we used the well studied galactose gene-regulatory network in \textit{Saccharomyces cerevisiae}. We analyzed the mechanism and dynamics of the coexistence of two stable on and off states for pathway activity. We demonstrate that this bimodality in the pathway activity originates from two positive feedback loops that trigger bistability in the network. By measuring the dynamics of single-cells in a mixed sugar environment, we observe that the bimodality in gene expression is a transient phenomenon. Our experiments indicate that early pathway activation in a cohort of cells prior to galactose metabolism can accelerate galactose consumption and provide a transient increase in growth rate. Together these results provide important insights into strategies implemented by cells that may have been evolutionary advantageous in competitive environments.

Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

Investigation of hypervelocity impact phenomena using real-time concurrent diagnostics

Hypervelocity impact of meteoroids and orbital debris poses a serious and growing threat to spacecraft. To study hypervelocity impact phenomena, a comprehensive ensemble of real-time concurrently operated diagnostics has been developed and implemented in the Small Particle Hypervelocity Impact Range (SPHIR) facility. This suite of simultaneously operated instrumentation provides multiple complementary measurements that facilitate the characterization of many impact phenomena in a single experiment. The investigation of hypervelocity impact phenomena described in this work focuses on normal impacts of 1.8 mm nylon 6/6 cylinder projectiles and variable thickness aluminum targets. The SPHIR facility two-stage light-gas gun is capable of routinely launching 5.5 mg nylon impactors to speeds of 5 to 7 km/s. Refinement of legacy SPHIR operation procedures and the investigation of first-stage pressure have improved the velocity performance of the facility, resulting in an increase in average impact velocity of at least 0.57 km/s. Results for the perforation area indicate the considered range of target thicknesses represent multiple regimes describing the non-monotonic scaling of target perforation with decreasing target thickness. The laser side-lighting (LSL) system has been developed to provide ultra-high-speed shadowgraph images of the impact event. This novel optical technique is demonstrated to characterize the propagation velocity and two-dimensional optical density of impact-generated debris clouds. Additionally, a debris capture system is located behind the target during every experiment to provide complementary information regarding the trajectory distribution and penetration depth of individual debris particles. The utilization of a coherent, collimated illumination source in the LSL system facilitates the simultaneous measurement of impact phenomena with near-IR and UV-vis spectrograph systems. Comparison of LSL images to concurrent IR results indicates two distinctly different phenomena. A high-speed, pressure-dependent IR-emitting cloud is observed in experiments to expand at velocities much higher than the debris and ejecta phenomena observed using the LSL system. In double-plate target configurations, this phenomena is observed to interact with the rear-wall several micro-seconds before the subsequent arrival of the debris cloud. Additionally, dimensional analysis presented by Whitham for blast waves is shown to describe the pressure-dependent radial expansion of the observed IR-emitting phenomena. Although this work focuses on a single hypervelocity impact configuration, the diagnostic capabilities and techniques described can be used with a wide variety of impactors, materials, and geometries to investigate any number of engineering and scientific problems.

Effects of particle size ratio on single particle motion in colloidal dispersions

The motion of a single Brownian particle of arbitrary size through a dilute colloidal dispersion of neutrally buoyant bath spheres of another characteristic size in a Newtonian solvent is examined in two contexts. First, the particle in question, the probe particle, is subject to a constant applied external force drawing it through the suspension as a simple model for active and nonlinear microrheology. The strength of the applied external force, normalized by the restoring forces of Brownian motion, is the Péclet number, Pe. This dimensionless quantity describes how strongly the probe is upsetting the equilibrium distribution of the bath particles. The mean motion and fluctuations in the probe position are related to interpreted quantities of an effective viscosity of the suspension. These interpreted quantities are calculated to first order in the volume fraction of bath particles and are intimately tied to the spatial distribution, or microstructure, of bath particles relative to the probe. For weak Pe, the disturbance to the equilibrium microstructure is dipolar in nature, with accumulation and depletion regions on the front and rear faces of the probe, respectively. With increasing applied force, the accumulation region compresses to form a thin boundary layer whose thickness scales with the inverse of Pe. The depletion region lengthens to form a trailing wake. The magnitude of the microstructural disturbance is found to grow with increasing bath particle size -- small bath particles in the solvent resemble a continuum with effective microviscosity given by Einstein's viscosity correction for a dilute dispersion of spheres. Large bath particles readily advect toward the minimum approach distance possible between the probe and bath particle, and the probe and bath particle pair rotating as a doublet is the primary mechanism by which the probe particle is able to move past; this is a process that slows the motion of the probe by a factor of the size ratio. The intrinsic microviscosity is found to force thin at low Péclet number due to decreasing contributions from Brownian motion, and force thicken at high Péclet number due to the increasing influence of the configuration-averaged reduction in the probe's hydrodynamic self mobility. Nonmonotonicity at finite sizes is evident in the limiting high-Pe intrinsic microviscosity plateau as a function of bath-to-probe particle size ratio. The intrinsic microviscosity is found to grow with the size ratio for very small probes even at large-but-finite Péclet numbers. However, even a small repulsive interparticle potential, that excludes lubrication interactions, can reduce this intrinsic microviscosity back to an order one quantity. The results of this active microrheology study are compared to previous theoretical studies of falling-ball and towed-ball rheometry and sedimentation and diffusion in polydisperse suspensions, and the singular limit of full hydrodynamic interactions is noted.

Second, the probe particle in question is no longer subject to a constant applied external force. Rather, the particle is considered to be a catalytically-active motor, consuming the bath reactant particles on its reactive face while passively colliding with reactant particles on its inert face. By creating an asymmetric distribution of reactant about its surface, the motor is able to diffusiophoretically propel itself with some mean velocity. The effects of finite size of the solute are examined on the leading order diffusive microstructure of reactant about the motor. Brownian and interparticle contributions to the motor velocity are computed for several interparticle interaction potential lengths and finite reactant-to-motor particle size ratios, with the dimensionless motor velocity increasing with decreasing motor size. A discussion on Brownian rotation frames the context in which these results could be applicable, and future directions are proposed which properly incorporate reactant advection at high motor velocities.

Ordinary mod p representations of the metaplectic cover of p-adic SL_2

We classify the genuine ordinary mod p representations of the metaplectic group SL(2,F)-tilde, where F is a p-adic field, and compute its genuine mod p spherical and Iwahori Hecke algebras. The motivation is an interest in a possible correspondence between genuine mod p representations of SL(2,F)-tilde and mod p representations of the dual group PGL(2,F), so we also compare the two Hecke algebras to the mod p spherical and Iwahori Hecke algebras of PGL(2,F). We show that the genuine mod p spherical Hecke algebra of SL(2,F)-tilde is isomorphic to the mod p spherical Hecke algebra of PGL(2,F), and that one can choose an isomorphism which is compatible with a natural, though partial, correspondence of unramified ordinary representations via the Hecke action on their spherical vectors. We then show that the genuine mod p Iwahori Hecke algebra of SL(2,F)-tilde is a subquotient of the mod p Iwahori Hecke algebra of PGL(2,F), but that the two algebras are not isomorphic. This is in contrast to the situation in characteristic 0, where by work of Savin one can recover the local Shimura correspondence for representations generated by their Iwahori fixed vectors from an isomorphism of Iwahori Hecke algebras.

Charles I : unhero of royalist poetry

During the English Civil War, Charles I appeared as a character in Royalist poetry, both directly and allegorically. These depictions drew on ancient Roman epic poems, particularly Lucan’s De Bello Civili, in their treatment of the subject matter of civil war and Charles as an epic hero. Though the authors of these poems supported Charles, their depictions of him and his reign reveal anxiety about his weakness as a ruler. In comparison to the cults of personality surrounding his predecessors and the heroes of De Bello Civili, his cult appears bland and forced. The lack of enthusiasm surrounding Charles I may help to explain his downfall at the hands of his Parliamentarian opponents.  

Quantum simulation of enzyme catalysis

Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation.

Constraints on the carbon cycle and climate during the early evolution of animals

One of the greatest challenges in science lies in disentangling causality in complex, coupled systems. This is illustrated no better than in the dynamic interplay between the Earth and life. The early evolution and diversification of animals occurred within a backdrop of global change, yet reconstructing the potential role of the environment in this evolutionary transition is challenging. In the 200 million years from the end-Cryogenian to the Ordovician, enigmatic Ediacaran fauna explored body plans, animals diversified and began to biomineralize, forever changing the ocean's chemical cycles, and the biological community in shallow marine ecosystems transitioned from a microbial one to an animal one.

In the following dissertation, a multi-faceted approach combining macro- and micro-scale analyses is presented that draws on the sedimentology, geochemistry and paleontology of the rocks that span this transition to better constrain the potential environmental changes during this interval.

In Chapter 1, the potential of clumped isotope thermometry in deep time is explored by assessing the importance of burial and diagenesis on the thermometer. Eocene- to Precambrian-aged carbonates from the Sultanate of Oman were analyzed from current burial depths of 350-5850 meters. Two end-member styles of diagenesis independent of burial depth were observed.

Chapters 2, 3 and 4 explore the fallibility of the Ediacaran carbon isotope record and aspects of the sedimentology and geochemistry of the rocks preserving the largest negative carbon isotope excursion on record---the Shuram Excursion. Chapter 2 documents the importance of temperature, fluid composition and mineralogy on the delta 18-O min record and interrogates the bulk trace metal signal. Chapter 3 explores the spatial variability in delta 13-C recorded in the transgressive Johnnie Oolite and finds a north-to-south trend recording the onset of the excursion. Chapter 4 investigates the nature of seafloor precipitation during this excursion and more broadly. We document the potential importance of microbial respiratory reactions on the carbonate chemistry of the sediment-water interface through time.

Chapter 5 investigates the latest Precambrian sedimentary record in carbonates from the Sultanate of Oman, including how delta 13-C and delta 34-S CAS vary across depositional and depth gradients. A new model for the correlation of the Buah and Ara formations across Oman is presented. Isotopic results indicate delta 13-C varies with relative eustatic change and delta 34-S CAS may vary in absolute magnitude across Oman.

Chapter 6 investigates the secular rise in delta 18-Omin in the early Paleozoic by using clumped isotope geochemistry on calcitic and phosphatic fossils from the Cambrian and Ordovician. Results do not indicate extreme delta 18-O seawater depletion and instead suggest warmer equatorial temperatures across the early Paleozoic.

Palladium-catalyzed asymmetric allylic alkylation: insights, application toward cyclopentanoid and cycloheptanoid molecules, and the total synthesis of several daucane sesquiterpenes

The asymmetric construction of quaternary stereocenters is a topic of great interest in the organic chemistry community given their prevalence in natural products and biologically active molecules. Over the last decade, the Stoltz group has pursued the synthesis of this challenging motif via a palladium-catalyzed allylic alkylation using chiral phosphinooxazoline (PHOX) ligands. Recent results indicate that the alkylation of lactams and imides consistently proceeds with enantioselectivities substantially higher than any other substrate class previously examined in this system. This observation prompted exploration of the characteristics that distinguish these molecules as superior alkylation substrates, resulting in newfound insights and marked improvements in the allylic alkylation of carbocyclic compounds.

General routes to cyclopentanoid and cycloheptanoid core structures have been developed that incorporate the palladium-catalyzed allylic alkylation as a key transformation. The unique reactivity of α-quaternary vinylogous esters upon addition of hydride or organometallic reagents enables divergent access to γ-quaternary acylcyclopentenes or cycloheptenones through respective ring contraction or carbonyl transposition pathways. Derivatization of the resulting molecules provides a series of mono-, bi-, and tricyclic systems that can serve as valuable intermediates for the total synthesis of complex natural products.

The allylic alkylation and ring contraction methodology has been employed to prepare variably functionalized bicyclo[5.3.0]decane molecules and enables the enantioselective total syntheses of daucene, daucenal, epoxydaucenal B, and 14-p-anisoyloxydauc-4,8-diene. This route overcomes the challenge of accessing β-substituted acylcyclopentenes by employing a siloxyenone to effect the Grignard addition and ring opening in a single step. Subsequent ring-closing metathesis and aldol reactions form the hydroazulene core of these targets. Derivatization of a key enone intermediate allows access to either the daucane sesquiterpene or sphenobolane diterpene carbon skeletons, as well as other oxygenated scaffolds.

Sound velocities and equation of state of iron-rich (Mg,Fe)O

Ultralow-velocity zones (ULVZs) are small structures at the base of the mantle characterized by sound velocities up to 30% lower than those of surrounding mantle. In this thesis, we propose that iron-rich (Mg,Fe)O plays a key role in the observed sound velocities, and argue that chemically distinct, iron-enriched structures are consistent with both the low sound velocities and the measured shapes of ULVZs.

Probing the thermodynamic properties of mantle rocks in solid and liquid states

Our understanding of the structure and evolution of the deep Earth is strongly linked to knowledge of the thermodynamic properties of rocky materials at extreme temperatures and pressures. In this thesis, I present work that helps constrain the equation of state properties of iron-bearing Mg-silicate perovskite as well as oxide-silicate melts. I use a mixture of experimental, statistical, and theoretical techniques to obtain knowledge about these phases. These include laser-heated diamond anvil cell experiments, Bayesian statistical analysis of powder diffraction data, and the development of a new simplified model for understanding oxide and silicate melts at mantle conditions. By shedding light on the thermodynamic properties of such ubiquitous Earth-forming materials, I hope to aid our community’s progress toward understanding the large-scale processes operating in the Earth’s mantle, both in the modern day and early in Earth’s history.

Planar reflection of gaseous detonations

Pipes containing flammable gaseous mixtures may be subjected to internal detonation. When the detonation normally impinges on a closed end, a reflected shock wave is created to bring the flow back to rest. This study built on the work of Karnesky (2010) and examined deformation of thin-walled stainless steel tubes subjected to internal reflected gaseous detonations. A ripple pattern was observed in the tube wall for certain fill pressures, and a criterion was developed that predicted when the ripple pattern would form. A two-dimensional finite element analysis was performed using Johnson-Cook material properties; the pressure loading created by reflected gaseous detonations was accounted for with a previously developed pressure model. The residual plastic strain between experiments and computations was in good agreement.

During the examination of detonation-driven deformation, discrepancies were discovered in our understanding of reflected gaseous detonation behavior. Previous models did not accurately describe the nature of the reflected shock wave, which motivated further experiments in a detonation tube with optical access. Pressure sensors and schlieren images were used to examine reflected shock behavior, and it was determined that the discrepancies were related to the reaction zone thickness extant behind the detonation front. During these experiments reflected shock bifurcation did not appear to occur, but the unfocused visualization system made certainty impossible. This prompted construction of a focused schlieren system that investigated possible shock wave-boundary layer interaction, and heat-flux gauges analyzed the boundary layer behind the detonation front. Using these data with an analytical boundary layer solution, it was determined that the strong thermal boundary layer present behind the detonation front inhibits the development of reflected shock wave bifurcation.