I. Exact solution of some nonlinear evolution equations. II. The similarity solution for the Korteweg-De Vries equation and the related Painleve Transcendent

In Part I, a method for finding solutions of certain diffusive dispersive nonlinear evolution equations is introduced. The method consists of a straightforward iteration procedure, applied to the equation as it stands (in most cases), which can be carried out to all terms, followed by a summation of the resulting infinite series, sometimes directly and other times in terms of traces of inverses of operators in an appropriate space.

We first illustrate our method with Burgers' and Thomas' equations, and show how it quickly leads to the Cole-Hopft transformation, which is known to linearize these equations.

We also apply this method to the Korteweg and de Vries, nonlinear (cubic) Schrödinger, Sine-Gordon, modified KdV and Boussinesq equations. In all these cases the multisoliton solutions are easily obtained and new expressions for some of them follow. More generally we show that the Marcenko integral equations, together with the inverse problem that originates them, follow naturally from our expressions.

Only solutions that are small in some sense (i.e., they tend to zero as the independent variable goes to ∞) are covered by our methods. However, by the study of the effect of writing the initial iterate u_1 = u_(1)(x,t) as a sum u_1 = ^∼/u_1 + ^≈/u_1 when we know the solution which results if u_1 = ^∼/u_1, we are led to expressions that describe the interaction of two arbitrary solutions, only one of which is small. This should not be confused with Backlund transformations and is more in the direction of performing the inverse scattering over an arbitrary “base” solution. Thus we are able to write expressions for the interaction of a cnoidal wave with a multisoliton in the case of the KdV equation; these expressions are somewhat different from the ones obtained by Wahlquist (1976). Similarly, we find multi-dark-pulse solutions and solutions describing the interaction of envelope-solitons with a uniform wave train in the case of the Schrodinger equation.

Other equations tractable by our method are presented. These include the following equations: Self-induced transparency, reduced Maxwell-Bloch, and a two-dimensional nonlinear Schrodinger. Higher order and matrix-valued equations with nonscalar dispersion functions are also presented.

In Part II, the second Painleve transcendent is treated in conjunction with the similarity solutions of the Korteweg-de Vries equat ion and the modified Korteweg-de Vries equation.

Invariants, Lie-Bäcklund operators and Bäcklund transformations

This thesis is mainly concerned with the application of groups of transformations to differential equations and in particular with the connection between the group structure of a given equation and the existence of exact solutions and conservation laws. In this respect the Lie-Bäcklund groups of tangent transformations, particular cases of which are the Lie tangent and the Lie point groups, are extensively used.

In Chapter I we first review the classical results of Lie, Bäcklund and Bianchi as well as the more recent ones due mainly to Ovsjannikov. We then concentrate on the Lie-Bäcklund groups (or more precisely on the corresponding Lie-Bäcklund operators), as introduced by Ibragimov and Anderson, and prove some lemmas about them which are useful for the following chapters. Finally we introduce the concept of a conditionally admissible operator (as opposed to an admissible one) and show how this can be used to generate exact solutions.

In Chapter II we establish the group nature of all separable solutions and conserved quantities in classical mechanics by analyzing the group structure of the Hamilton-Jacobi equation. It is shown that consideration of only Lie point groups is insufficient. For this purpose a special type of Lie-Bäcklund groups, those equivalent to Lie tangent groups, is used. It is also shown how these generalized groups induce Lie point groups on Hamilton's equations. The generalization of the above results to any first order equation, where the dependent variable does not appear explicitly, is obvious. In the second part of this chapter we investigate admissible operators (or equivalently constants of motion) of the Hamilton-Jacobi equation with polynornial dependence on the momenta. The form of the most general constant of motion linear, quadratic and cubic in the momenta is explicitly found. Emphasis is given to the quadratic case, where the particular case of a fixed (say zero) energy state is also considered; it is shown that in the latter case additional symmetries may appear. Finally, some potentials of physical interest admitting higher symmetries are considered. These include potentials due to two centers and limiting cases thereof. The most general two-center potential admitting a quadratic constant of motion is obtained, as well as the corresponding invariant. Also some new cubic invariants are found.

In Chapter III we first establish the group nature of all separable solutions of any linear, homogeneous equation. We then concentrate on the Schrodinger equation and look for an algorithm which generates a quantum invariant from a classical one. The problem of an isomorphism between functions in classical observables and quantum observables is studied concretely and constructively. For functions at most quadratic in the momenta an isomorphism is possible which agrees with Weyl' s transform and which takes invariants into invariants. It is not possible to extend the isomorphism indefinitely. The requirement that an invariant goes into an invariant may necessitate variants of Weyl' s transform. This is illustrated for the case of cubic invariants. Finally, the case of a specific value of energy is considered; in this case Weyl's transform does not yield an isomorphism even for the quadratic case. However, for this case a correspondence mapping a classical invariant to a quantum orie is explicitly found.

Chapters IV and V are concerned with the general group structure of evolution equations. In Chapter IV we establish a one to one correspondence between admissible Lie-Bäcklund operators of evolution equations (derivable from a variational principle) and conservation laws of these equations. This correspondence takes the form of a simple algorithm.

In Chapter V we first establish the group nature of all Bäcklund transformations (BT) by proving that any solution generated by a BT is invariant under the action of some conditionally admissible operator. We then use an algorithm based on invariance criteria to rederive many known BT and to derive some new ones. Finally, we propose a generalization of BT which, among other advantages, clarifies the connection between the wave-train solution and a BT in the sense that, a BT may be thought of as a variation of parameters of some. special case of the wave-train solution (usually the solitary wave one). Some open problems are indicated.

Most of the material of Chapters II and III is contained in [I], [II], [III] and [IV] and the first part of Chapter V in [V].

Palladium-Catalyzed Decarboxylative and Decarbonylative Transformations in the Synthesis of Fine and Commodity Chemicals

Decarboxylation and decarbonylation are important reactions in synthetic organic chemistry, transforming readily available carboxylic acids and their derivatives into various products through loss of carbon dioxide or carbon monoxide. In the past few decades, palladium-catalyzed decarboxylative and decarbonylative reactions experienced tremendous growth due to the excellent catalytic activity of palladium. Development of new reactions in this category for fine and commodity chemical synthesis continues to draw attention from the chemistry community.

The Stoltz laboratory has established a palladium-catalyzed enantioselective decarboxylative allylic alkylation of β-keto esters for the synthesis of α-quaternary ketones since 2005. Recently, we extended this chemistry to lactams due to the ubiquity and importance of nitrogen-containing heterocycles. A wide variety of α-quaternary and tetrasubstituted α-tertiary lactams were obtained in excellent yields and exceptional enantioselectivities using our palladium-catalyzed decarboxylative allylic alkylation chemistry. Enantioenriched α-quaternary carbonyl compounds are versatile building blocks that can be further elaborated to intercept synthetic intermediates en route to many classical natural products. Thus our chemistry enables catalytic asymmetric formal synthesis of these complex molecules.

In addition to fine chemicals, we became interested in commodity chemical synthesis using renewable feedstocks. In collaboration with the Grubbs group, we developed a palladium-catalyzed decarbonylative dehydration reaction that converts abundant and inexpensive fatty acids into value-added linear alpha olefins. The chemistry proceeds under relatively mild conditions, requires very low catalyst loading, tolerates a variety of functional groups, and is easily performed on a large scale. An additional advantage of this chemistry is that it provides access to expensive odd-numbered alpha olefins.

Finally, combining features of both projects, we applied a small-scale decarbonylative dehydration reaction to the synthesis of α-vinyl carbonyl compounds. Direct α-vinylation is challenging, and asymmetric vinylations are rare. Taking advantage of our decarbonylative dehydration chemistry, we were able to transform enantioenriched δ-oxocarboxylic acids into quaternary α-vinyl carbonyl compounds in good yields with complete retention of stereochemistry. Our explorations culminated in the catalytic enantioselective total synthesis of (–)-aspewentin B, a terpenoid natural product featuring a quaternary α-vinyl ketone. Both decarboxylative and decarbonylative chemistries found application in the late stage of the total synthesis.

Some generalizations of commutativity for linear transformations on a finite dimensional vector space

Let L be the algebra of all linear transformations on an n-dimensional vector space V over a field F and let A, B, ƐL. Let A_i+1 = A_iB - BA_i, i = 0, 1, 2,…, with A = A_o. Let f_k (A, B; σ) = A_2K+1 - ^σ1^A2K-1 ^{+ σ}2^A2K-3 -… +(-1)^Kσ_KA₁ where σ = (σ₁, σ₂,…, σ_K), σ_i belong to F and K = k(k-1)/2. Taussky and Wielandt [Proc. Amer. Math. Soc., 13(1962), 732-735] showed that f_n(A, B; σ) = 0 if σ_i is the i^th elementary symmetric function of (β₄- β_s)², 1 ≤ r ˂ s ≤ n, i = 1, 2, …, N, with N = n(n-1)/2, where β₄ are the characteristic roots of B. In this thesis we discuss relations involving f_k(X, Y; σ) where X, Y Ɛ L and 1 ≤ k ˂ n. We show: 1. If F is infinite and if for each X Ɛ L there exists σ so that f_k(A, X; σ) = 0 where 1 ≤ k ˂ n, then A is a scalar transformation. 2. If F is algebraically closed, a necessary and sufficient condition that there exists a basis of V with respect to which the matrices of A and B are both in block upper triangular form, where the blocks on the diagonals are either one- or two-dimensional, is that certain products X₁, X₂…X_r belong to the radical of the algebra generated by A and B over F, where X_i has the form f₂(A, P(A,B); σ), for all polynomials P(x, y). We partially generalize this to the case where the blocks have dimensions ≤ k. 3. If A and B generate L, if the characteristic of F does not divide n and if there exists σ so that f_k(A, B; σ) = 0, for some k with 1 ≤ k ˂ n, then the characteristic roots of B belong to the splitting field of g_k(w; σ) = w^2K+1 - σ₁w^2K-1 + σ₂w^2K-3 - …. +(-1)^K σ_Kw over F. We use this result to prove a theorem involving a generalized form of property L [cf. Motzkin and Taussky, Trans. Amer. Math. Soc., 73(1952), 108-114]. 4. Also we give mild generalizations of results of McCoy [Amer. Math. Soc. Bull., 42(1936), 592-600] and Drazin [Proc. London Math. Soc., 1(1951), 222-231].

Exact solutions and transformation properties of nonlinear partial differential equations from general relativity

Various families of exact solutions to the Einstein and Einstein-Maxwell field equations of General Relativity are treated for situations of sufficient symmetry that only two independent variables arise. The mathematical problem then reduces to consideration of sets of two coupled nonlinear differential equations.

The physical situations in which such equations arise include: a) the external gravitational field of an axisymmetric, uncharged steadily rotating body, b) cylindrical gravitational waves with two degrees of freedom, c) colliding plane gravitational waves, d) the external gravitational and electromagnetic fields of a static, charged axisymmetric body, and e) colliding plane electromagnetic and gravitational waves. Through the introduction of suitable potentials and coordinate transformations, a formalism is presented which treats all these problems simultaneously. These transformations and potentials may be used to generate new solutions to the Einstein-Maxwell equations from solutions to the vacuum Einstein equations, and vice-versa.

The calculus of differential forms is used as a tool for generation of similarity solutions and generalized similarity solutions. It is further used to find the invariance group of the equations; this in turn leads to various finite transformations that give new, physically distinct solutions from old. Some of the above results are then generalized to the case of three independent variables.

Nonlinear oscillations in discrete and continuous systems

The first thesis topic is a perturbation method for resonantly coupled nonlinear oscillators. By successive near-identity transformations of the original equations, one obtains new equations with simple structure that describe the long time evolution of the motion. This technique is related to two-timing in that secular terms are suppressed in the transformation equations. The method has some important advantages. Appropriate time scalings are generated naturally by the method, and don't need to be guessed as in two-timing. Furthermore, by continuing the procedure to higher order, one extends (formally) the time scale of valid approximation. Examples illustrate these claims. Using this method, we investigate resonance in conservative, non-conservative and time dependent problems. Each example is chosen to highlight a certain aspect of the method.

The second thesis topic concerns the coupling of nonlinear chemical oscillators. The first problem is the propagation of chemical waves of an oscillating reaction in a diffusive medium. Using two-timing, we derive a nonlinear equation that determines how spatial variations in the phase of the oscillations evolves in time. This result is the key to understanding the propagation of chemical waves. In particular, we use it to account for certain experimental observations on the Belusov-Zhabotinskii reaction.

Next, we analyse the interaction between a pair of coupled chemical oscillators. This time, we derive an equation for the phase shift, which measures how much the oscillators are out of phase. This result is the key to understanding M. Marek's and I. Stuchl's results on coupled reactor systems. In particular, our model accounts for synchronization and its bifurcation into rhythm splitting.

Finally, we analyse large systems of coupled chemical oscillators. Using a continuum approximation, we demonstrate mechanisms that cause auto-synchronization in such systems.

Part I. On the breaking of nonlinear dispersive waves. Part II. Variational principles in continuum mechanics

A model equation for water waves has been suggested by Whitham to study, qualitatively at least, the different kinds of breaking. This is an integro-differential equation which combines a typical nonlinear convection term with an integral for the dispersive effects and is of independent mathematical interest. For an approximate kernel of the form e^(-b|x|) it is shown first that solitary waves have a maximum height with sharp crests and secondly that waves which are sufficiently asymmetric break into "bores." The second part applies to a wide class of bounded kernels, but the kernel giving the correct dispersion effects of water waves has a square root singularity and the present argument does not go through. Nevertheless the possibility of the two kinds of breaking in such integro-differential equations is demonstrated.

Difficulties arise in finding variational principles for continuum mechanics problems in the Eulerian (field) description. The reason is found to be that continuum equations in the original field variables lack a mathematical "self-adjointness" property which is necessary for Euler equations. This is a feature of the Eulerian description and occurs in non-dissipative problems which have variational principles for their Lagrangian description. To overcome this difficulty a "potential representation" approach is used which consists of transforming to new (Eulerian) variables whose equations are self-adjoint. The transformations to the velocity potential or stream function in fluids or the scaler and vector potentials in electromagnetism often lead to variational principles in this way. As yet no general procedure is available for finding suitable transformations. Existing variational principles for the inviscid fluid equations in the Eulerian description are reviewed and some ideas on the form of the appropriate transformations and Lagrangians for fluid problems are obtained. These ideas are developed in a series of examples which include finding variational principles for Rossby waves and for the internal waves of a stratified fluid.

Olefin cyclopropanation and carbon-hydrogen amination via carbene and nitrene transfers catalyzed by engineered cytochrome P450 enzymes

Synthetic biology promises to transform organic synthesis by enabling artificial catalysis in living cells. I start by reviewing the state of the art in this young field and recognizing that new approaches are required for designing enzymes that catalyze nonnatural reactions, in order to expand the scope of biocatalytic transformations. Carbene and nitrene transfers to C=C and C-H bonds are reactions of tremendous synthetic utility that lack biological counterparts. I show that various heme proteins, including cytochrome P450BM3, will catalyze promiscuous levels of olefin cyclopropanation when provided with the appropriate synthetic reagents (e.g., diazoesters and styrene). Only a few amino acid substitutions are required to install synthetically useful levels of stereoselective cyclopropanation activity in P450BM3. Understanding that the ferrous-heme is the active species for catalysis and that the artificial reagents are unable to induce a spin-shift-dependent increase in the redox potential of the ferric P450, I design a high-potential serine-heme ligated P450 (P411) that can efficiently catalyze cyclopropanation using NAD(P)H. Intact E. coli whole-cells expressing P411 are highly efficient asymmetric catalysts for olefin cyclopropanation. I also show that engineered P450s can catalyze intramolecular amination of benzylic C-H bonds from arylsulfonyl azides. Finally, I review other examples of where synthetic reagents have been used to drive the evolution of novel enzymatic activity in the environment and in the laboratory. I invoke preadaptation to explain these observations and propose that other man-invented reactions may also be transferrable to natural enzymes by using a mechanism-based approach for choosing the enzymes and the reagents. Overall, this work shows that existing enzymes can be readily adapted for catalysis of synthetically important reactions not previously observed in nature.

Responses to auditory stimuli in macaque lateral intraparietal area

The lateral intraparietal area (LIP) of macaque posterior parietal cortex participates in the sensorimotor transformations underlying visually guided eye movements. Area LIP has long been considered unresponsive to auditory stimulation. However, recent studies have shown that neurons in LIP respond to auditory stimuli during an auditory-saccade task, suggesting possible involvement of this area in auditory-to-oculomotor as well as visual-to-oculomotor processing. This dissertation describes investigations which clarify the role of area LIP in auditory-to-oculomotor processing.

Extracellular recordings were obtained from a total of 332 LIP neurons in two macaque monkeys, while the animals performed fixation and saccade tasks involving auditory and visual stimuli. No auditory activity was observed in area LIP before animals were trained to make saccades to auditory stimuli, but responses to auditory stimuli did emerge after auditory-saccade training. Auditory responses in area LIP after auditory-saccade training were significantly stronger in the context of an auditory-saccade task than in the context of a fixation task. Compared to visual responses, auditory responses were also significantly more predictive of movement-related activity in the saccade task. Moreover, while visual responses often had a fast transient component, responses to auditory stimuli in area LIP tended to be gradual in onset and relatively prolonged in duration.

Overall, the analyses demonstrate that responses to auditory stimuli in area LIP are dependent on auditory-saccade training, modulated by behavioral context, and characterized by slow-onset, sustained response profiles. These findings suggest that responses to auditory stimuli are best interpreted as supramodal (cognitive or motor) responses, rather than as modality-specific sensory responses. Auditory responses in area LIP seem to reflect the significance of auditory stimuli as potential targets for eye movements, and may differ from most visual responses in the extent to which they arc abstracted from the sensory parameters of the stimulus.

Lattice quantum codes and exotic topological phases of matter

This thesis addresses whether it is possible to build a robust memory device for quantum information. Many schemes for fault-tolerant quantum information processing have been developed so far, one of which, called topological quantum computation, makes use of degrees of freedom that are inherently insensitive to local errors. However, this scheme is not so reliable against thermal errors. Other fault-tolerant schemes achieve better reliability through active error correction, but incur a substantial overhead cost. Thus, it is of practical importance and theoretical interest to design and assess fault-tolerant schemes that work well at finite temperature without active error correction.

In this thesis, a three-dimensional gapped lattice spin model is found which demonstrates for the first time that a reliable quantum memory at finite temperature is possible, at least to some extent. When quantum information is encoded into a highly entangled ground state of this model and subjected to thermal errors, the errors remain easily correctable for a long time without any active intervention, because a macroscopic energy barrier keeps the errors well localized. As a result, stored quantum information can be retrieved faithfully for a memory time which grows exponentially with the square of the inverse temperature. In contrast, for previously known types of topological quantum storage in three or fewer spatial dimensions the memory time scales exponentially with the inverse temperature, rather than its square.

This spin model exhibits a previously unexpected topological quantum order, in which ground states are locally indistinguishable, pointlike excitations are immobile, and the immobility is not affected by small perturbations of the Hamiltonian. The degeneracy of the ground state, though also insensitive to perturbations, is a complicated number-theoretic function of the system size, and the system bifurcates into multiple noninteracting copies of itself under real-space renormalization group transformations. The degeneracy, the excitations, and the renormalization group flow can be analyzed using a framework that exploits the spin model's symmetry and some associated free resolutions of modules over polynomial algebras.

Fracture of materials undergoing solid-solid phase transformation

A large number of technologically important materials undergo solid-solid phase transformations. Examples range from ferroelectrics (transducers and memory devices), zirconia (Thermal Barrier Coatings) to nickel superalloys and (lithium) iron phosphate (Li-ion batteries). These transformations involve a change in the crystal structure either through diffusion of species or local rearrangement of atoms. This change of crystal structure leads to a macroscopic change of shape or volume or both and results in internal stresses during the transformation. In certain situations this stress field gives rise to cracks (tin, iron phosphate etc.) which continue to propagate as the transformation front traverses the material. In other materials the transformation modifies the stress field around cracks and effects crack growth behavior (zirconia, ferroelectrics). These observations serve as our motivation to study cracks in solids undergoing phase transformations. Understanding these effects will help in improving the mechanical reliability of the devices employing these materials.

In this thesis we present work on two problems concerning the interplay between cracks and phase transformations. First, we consider the directional growth of a set of parallel edge cracks due to a solid-solid transformation. We conclude from our analysis that phase transformations can lead to formation of parallel edge cracks when the transformation strain satisfies certain conditions and the resulting cracks grow all the way till their tips cross over the phase boundary. Moreover the cracks continue to grow as the phase boundary traverses into the interior of the body at a uniform spacing without any instabilities. There exists an optimal value for the spacing between the cracks. We ascertain these conclusion by performing numerical simulations using finite elements.

Second, we model the effect of the semiconducting nature and dopants on cracks in ferroelectric perovskite materials, particularly barium titanate. Traditional approaches to model fracture in these materials have treated them as insulators. In reality, they are wide bandgap semiconductors with oxygen vacancies and trace impurities acting as dopants. We incorporate the space charge arising due the semiconducting effect and dopant ionization in a phase field model for the ferroelectric. We derive the governing equations by invoking the dissipation inequality over a ferroelectric domain containing a crack. This approach also yields the driving force acting on the crack. Our phase field simulations of polarization domain evolution around a crack show the accumulation of electronic charge on the crack surface making it more permeable than was previously believed so, as seen in recent experiments. We also discuss the effect the space charge has on domain formation and the crack driving force.

Conformal geometry processing

This thesis introduces fundamental equations and numerical methods for manipulating surfaces in three dimensions via conformal transformations. Conformal transformations are valuable in applications because they naturally preserve the integrity of geometric data. To date, however, there has been no clearly stated and consistent theory of conformal transformations that can be used to develop general-purpose geometry processing algorithms: previous methods for computing conformal maps have been restricted to the flat two-dimensional plane, or other spaces of constant curvature. In contrast, our formulation can be used to produce---for the first time---general surface deformations that are perfectly conformal in the limit of refinement. It is for this reason that we commandeer the title Conformal Geometry Processing.

The main contribution of this thesis is analysis and discretization of a certain time-independent Dirac equation, which plays a central role in our theory. Given an immersed surface, we wish to construct new immersions that (i) induce a conformally equivalent metric and (ii) exhibit a prescribed change in extrinsic curvature. Curvature determines the potential in the Dirac equation; the solution of this equation determines the geometry of the new surface. We derive the precise conditions under which curvature is allowed to evolve, and develop efficient numerical algorithms for solving the Dirac equation on triangulated surfaces.

From a practical perspective, this theory has a variety of benefits: conformal maps are desirable in geometry processing because they do not exhibit shear, and therefore preserve textures as well as the quality of the mesh itself. Our discretization yields a sparse linear system that is simple to build and can be used to efficiently edit surfaces by manipulating curvature and boundary data, as demonstrated via several mesh processing applications. We also present a formulation of Willmore flow for triangulated surfaces that permits extraordinarily large time steps and apply this algorithm to surface fairing, geometric modeling, and construction of constant mean curvature (CMC) surfaces.

The intramolecular Buchner reaction of α-diazo-β-ketonitriles : development and application to the total synthesis of (+)-Salvileucalin B

Since its discovery in 1896, the Buchner reaction has fascinated chemists for more than a century. The highly reactive nature of the carbene intermediates allows for facile dearomatization of stable aromatic rings, and provides access to a diverse array of cyclopropane and seven-membered ring architectures. The power inherent in this transformation has been exploited in the context of a natural product total synthesis and methodology studies.

The total synthesis work details efforts employed in the enantioselective total synthesis of (+)-salvileucalin B. The fully-substituted cyclopropane within the core of the molecule arises from an unprecedented intramolecular Buchner reaction involving a highly functionalized arene and an α-diazo-β-ketonitrile. An unusual retro-Claisen rearrangement of a complex late-stage intermediate was discovered on route to the natural product.

The unique reactivity of α-diazo-β-ketonitriles toward arene cyclopropanation was then investigated in a broader methodological study. This specific di-substituted diazo moiety possesses hitherto unreported selectivity in intramolecular Buchner reactions. This technology was enables the preparation of highly functionalized norcaradienes and cyclopropanes, which themselves undergo various ring opening transformations to afford complex polycyclic structures.

Finally, an enantioselective variant of the intramolecular Buchner reaction is described. Various chiral copper and dirhodium catalysts afforded moderate stereoinduction in the cyclization event.

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.

Flight dynamics in Drosophila through a dynamically-scaled robotic approach

Flies are particularly adept at balancing the competing demands of delay tolerance, performance, and robustness during flight, which invites thoughtful examination of their multimodal feedback architecture. This dissertation examines stabilization requirements for inner-loop feedback strategies in the flapping flight of Drosophila, the fruit fly, against the backdrop of sensorimotor transformations present in the animal. Flies have evolved multiple specializations to reduce sensorimotor latency, but sensory delay during flight is still significant on the timescale of body dynamics. I explored the effect of sensor delay on flight stability and performance for yaw turns using a dynamically-scaled robot equipped with a real-time feedback system that performed active turns in response to measured yaw torque. The results show a fundamental tradeoff between sensor delay and permissible feedback gain, and suggest that fast mechanosensory feedback provides a source of active damping that compliments that contributed by passive effects. Presented in the context of these findings, a control architecture whereby a haltere-mediated inner-loop proportional controller provides damping for slower visually-mediated feedback is consistent with tethered-flight measurements, free-flight observations, and engineering design principles. Additionally, I investigated how flies adjust stroke features to regulate and stabilize level forward flight. The results suggest that few changes to hovering kinematics are actually required to meet steady-state lift and thrust requirements at different flight speeds, and the primary driver of equilibrium velocity is the aerodynamic pitch moment. This finding is consistent with prior hypotheses and observations regarding the relationship between body pitch and flight speed in fruit flies. The results also show that the dynamics may be stabilized with additional pitch damping, but the magnitude of required damping increases with flight speed. I posit that differences in stroke deviation between the upstroke and downstroke might play a critical role in this stabilization. Fast mechanosensory feedback of the pitch rate could enable active damping, which would inherently exhibit gain scheduling with flight speed if pitch torque is regulated by adjusting stroke deviation. Such a control scheme would provide an elegant solution for flight stabilization across a wide range of flight speeds.