Formation of Single and Multiple Deformation Twins in Nanocrystalline fcc Metals

Deformation twins are often observed to meet each other to form multi-fold twins in nanostructured face-centered cubic (fcc) metals.Here we propose two types of mechanism for the nucleation and growth of four different single and multiple twins. These mechanisms provide continuous generation of twinning partials for the growth of the twins after ucleation. A relatively high stress or high strain rate is needed to activate these mechanisms, making them more prevalent in nanocrystalline materials than in their coarse-grained counterparts.Experimental observations that support the proposed mechanisms are presented.

Vortex dislocations in wake-type flow induced by spanwise disturbances

Vortex dislocations in wake-type flow induced by three types of spanwise disturbances superimposed on an upstream velocity profile are investigated by direct numerical simulations. Three distinct modes of vortex dislocations and flow transitions have been found. A local spanwise exponential decay disturbance leads to the appearance of a twisted chainlike mode of vortex dislocation. A stepped spanwise disturbance causes a streamwise periodic spotlike mode of vortex dislocation. A spanwise sinusoidal wavy disturbance with a moderate waviness causes a strong unsteadiness of wake behavior. This unsteadiness starts with a systematic periodic mode of vortex dislocation in the spanwise direction followed by the spanwise vortex shedding suppressed completely with increased time and the near wake becoming a steady shear flow. Characteristics of these modes of vortex dislocation and complex vortex linkages over the dislocation, as well as the corresponding dynamic processes related to the appearance of dislocations, are described by examining the variations of vortex lines and vorticity distribution. The nature of the vortex dislocation is demonstrated by the substantial vorticity modification of the spanwise vortex from the original spanwise direction to streamwise and vertical directions, accompanied by the appearance of noticeable vortex branching and complex vortex linking, all of which are produced at the locations with the biggest phase difference or with a frequency discontinuity between shedding cells. The effect of vortex dislocation on flow transition, either to an unsteady irregular vortex flow or suppression of the Kaacutermaacuten vortex shedding making the wake flow steady state, is analyzed. Distinct similarities are found in the mechanism and main flow phenomena between the present numerical results obtained in wake-type flows and the experimental-numerical results of cylinder wakes reported in previous studies.

Physical investigations of small particles : (I) aerosol particle charging and flux enhancement and (II) whispering gallery mode sensing

Part I

Particles are a key feature of planetary atmospheres. On Earth they represent the greatest source of uncertainty in the global energy budget. This uncertainty can be addressed by making more measurement, by improving the theoretical analysis of measurements, and by better modeling basic particle nucleation and initial particle growth within an atmosphere. This work will focus on the latter two methods of improvement.

Uncertainty in measurements is largely due to particle charging. Accurate descriptions of particle charging are challenging because one deals with particles in a gas as opposed to a vacuum, so different length scales come into play. Previous studies have considered the effects of transition between the continuum and kinetic regime and the effects of two and three body interactions within the kinetic regime. These studies, however, use questionable assumptions about the charging process which resulted in skewed observations, and bias in the proposed dynamics of aerosol particles. These assumptions affect both the ions and particles in the system. Ions are assumed to be point monopoles that have a single characteristic speed rather than follow a distribution. Particles are assumed to be perfect conductors that have up to five elementary charges on them. The effects of three body interaction, ion-molecule-particle, are also overestimated. By revising this theory so that the basic physical attributes of both ions and particles and their interactions are better represented, we are able to make more accurate predictions of particle charging in both the kinetic and continuum regimes.

The same revised theory that was used above to model ion charging can also be applied to the flux of neutral vapor phase molecules to a particle or initial cluster. Using these results we can model the vapor flux to a neutral or charged particle due to diffusion and electromagnetic interactions. In many classical theories currently applied to these models, the finite size of the molecule and the electromagnetic interaction between the molecule and particle, especially for the neutral particle case, are completely ignored, or, as is often the case for a permanent dipole vapor species, strongly underestimated. Comparing our model to these classical models we determine an “enhancement factor” to characterize how important the addition of these physical parameters and processes is to the understanding of particle nucleation and growth.

Part II

Whispering gallery mode (WGM) optical biosensors are capable of extraordinarily sensitive specific and non-specific detection of species suspended in a gas or fluid. Recent experimental results suggest that these devices may attain single-molecule sensitivity to protein solutions in the form of stepwise shifts in their resonance wavelength, \lambda_{R}, but present sensor models predict much smaller steps than were reported. This study examines the physical interaction between a WGM sensor and a molecule adsorbed to its surface, exploring assumptions made in previous efforts to model WGM sensor behavior, and describing computational schemes that model the experiments for which single protein sensitivity was reported. The resulting model is used to simulate sensor performance, within constraints imposed by the limited material property data. On this basis, we conclude that nonlinear optical effects would be needed to attain the reported sensitivity, and that, in the experiments for which extreme sensitivity was reported, a bound protein experiences optical energy fluxes too high for such effects to be ignored.

Earthquakes of the Nepal Himalaya : towards a physical model of the seismic cycle

Home to hundreds of millions of souls and land of excessiveness, the Himalaya is also the locus of a unique seismicity whose scope and peculiarities still remain to this day somewhat mysterious. Having claimed the lives of kings, or turned ancient timeworn cities into heaps of rubbles and ruins, earthquakes eerily inhabit Nepalese folk tales with the fatalistic message that nothing lasts forever. From a scientific point of view as much as from a human perspective, solving the mysteries of Himalayan seismicity thus represents a challenge of prime importance. Documenting geodetic strain across the Nepal Himalaya with various GPS and leveling data, we show that unlike other subduction zones that exhibit a heterogeneous and patchy coupling pattern along strike, the last hundred kilometers of the Main Himalayan Thrust fault, or MHT, appear to be uniformly locked, devoid of any of the “creeping barriers” that traditionally ward off the propagation of large events. The approximately 20 mm/yr of reckoned convergence across the Himalaya matching previously established estimates of the secular deformation at the front of the arc, the slip accumulated at depth has to somehow elastically propagate all the way to the surface at some point. And yet, neither large events from the past nor currently recorded microseismicity nearly compensate for the massive moment deficit that quietly builds up under the giant mountains. Along with this large unbalanced moment deficit, the uncommonly homogeneous coupling pattern on the MHT raises the question of whether or not the locked portion of the MHT can rupture all at once in a giant earthquake. Univocally answering this question appears contingent on the still elusive estimate of the magnitude of the largest possible earthquake in the Himalaya, and requires tight constraints on local fault properties. What makes the Himalaya enigmatic also makes it the potential source of an incredible wealth of information, and we exploit some of the oddities of Himalayan seismicity in an effort to improve the understanding of earthquake physics and cipher out the properties of the MHT. Thanks to the Himalaya, the Indo-Gangetic plain is deluged each year under a tremendous amount of water during the annual summer monsoon that collects and bears down on the Indian plate enough to pull it away from the Eurasian plate slightly, temporarily relieving a small portion of the stress mounting on the MHT. As the rainwater evaporates in the dry winter season, the plate rebounds and tension is increased back on the fault. Interestingly, the mild waggle of stress induced by the monsoon rains is about the same size as that from solid-Earth tides which gently tug at the planets solid layers, but whereas changes in earthquake frequency correspond with the annually occurring monsoon, there is no such correlation with Earth tides, which oscillate back-and-forth twice a day. We therefore investigate the general response of the creeping and seismogenic parts of MHT to periodic stresses in order to link these observations to physical parameters. First, the response of the creeping part of the MHT is analyzed with a simple spring-and-slider system bearing rate-strengthening rheology, and we show that at the transition with the locked zone, where the friction becomes near velocity neutral, the response of the slip rate may be amplified at some periods, which values are analytically related to the physical parameters of the problem. Such predictions therefore hold the potential of constraining fault properties on the MHT, but still await observational counterparts to be applied, as nothing indicates that the variations of seismicity rate on the locked part of the MHT are the direct expressions of variations of the slip rate on its creeping part, and no variations of the slip rate have been singled out from the GPS measurements to this day. When shifting to the locked seismogenic part of the MHT, spring-and-slider models with rate-weakening rheology are insufficient to explain the contrasted responses of the seismicity to the periodic loads that tides and monsoon both place on the MHT. Instead, we resort to numerical simulations using the Boundary Integral CYCLes of Earthquakes algorithm and examine the response of a 2D finite fault embedded with a rate-weakening patch to harmonic stress perturbations of various periods. We show that such simulations are able to reproduce results consistent with a gradual amplification of sensitivity as the perturbing period get larger, up to a critical period corresponding to the characteristic time of evolution of the seismicity in response to a step-like perturbation of stress. This increase of sensitivity was not reproduced by simple 1D-spring-slider systems, probably because of the complexity of the nucleation process, reproduced only by 2D-fault models. When the nucleation zone is close to its critical unstable size, its growth becomes highly sensitive to any external perturbations and the timings of produced events may therefore find themselves highly affected. A fully analytical framework has yet to be developed and further work is needed to fully describe the behavior of the fault in terms of physical parameters, which will likely provide the keys to deduce constitutive properties of the MHT from seismological observations.

Towards conditional RNAi : shape and sequence transduction with small conditional RNAs

RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement “conditional RNAi.” Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.

To implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.

We demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.

A Study on iron-based amorphous alloys : alloy development, thermodynamics and soft magnetism

Metallic glass has since its debut been of great research interest due to its profound scientific significance. Magnetic metallic glasses are of special interest because of their promising technological applications. In this thesis, we introduced a novel series of Fe-based alloys and offer a holistic review of the physics and properties of these alloys. A systematic alloy development and optimization method was introduced, with experimental implementation on transition metal based alloying system. A deep understanding on the influencing factors of glass forming ability was brought up and discussed, based on classical nucleation theory. Experimental data of the new Fe-based amorphous alloys were interpreted to further analyze those influencing factors, including reduced glass transition temperature, fragility, and liquid-crystal interface free energy. Various treatments (fluxing, overheating, etc.) were discussed for their impacts on the alloying systems' thermodynamics and glass forming ability. Multiple experimental characterization methods were discussed to measure the alloys' soft magnetic properties. In addition to theoretical and experimental investigation, we also gave a detailed numerical analysis on the rapid-discharge-heating-and-forming platform. It is a novel experimental system which offers extremely fast heating rate for calorimetric characterization and alloy deformation.

Interaction of aqueous inorganic orthophosphate and phosphate rock

An experimental study was made of the interaction of phosphate rock and aqueous inorganic orthophosphate, calcium, and hydroxyl ions. A model of the reaction was developed by observing electron diffraction patterns in conjunction with concentration changes of chemical components. The model was applied in explaining the performance of batch suspensions of powdered phosphate rock and packed columns of granular phosphate rock. In both cases the reaction consisted initially of a rapid nucleation phase that occurred in a time period of minutes. In the batch system the calcium phosphate nuclei then ripened into larger micro-crystals of hydroxyapatite, which eventually became indistinguishable from the original phosphate rock surface. During column operation the high supersaturation ratio that existed after the rapid nucleation phase resulted in a layer of small nuclei that covered a slowly growing hydroxyapatite crystal.

The column steady-state rate constant was found to increase with increasing temperature, pH, and fluoride concentration, and to decrease with increasing concentrations of magnesium sulfate, ammonium chloride, and bicarbonate ion.

An engineering feasibility study indicated that, based on economic considerations, nucleation of apatite on phosphate rock ore has a potential use as a wastewater phosphate removal treatment process.

Crystals that count! Physical principles and experimental investigations of DNA tile self-assembly

Algorithmic DNA tiles systems are fascinating. From a theoretical perspective, they can result in simple systems that assemble themselves into beautiful, complex structures through fundamental interactions and logical rules. As an experimental technique, they provide a promising method for programmably assembling complex, precise crystals that can grow to considerable size while retaining nanoscale resolution. In the journey from theoretical abstractions to experimental demonstrations, however, lie numerous challenges and complications.

In this thesis, to examine these challenges, we consider the physical principles behind DNA tile self-assembly. We survey recent progress in experimental algorithmic self-assembly, and explain the simple physical models behind this progress. Using direct observation of individual tile attachments and detachments with an atomic force microscope, we test some of the fundamental assumptions of the widely-used kinetic Tile Assembly Model, obtaining results that fit the model to within error. We then depart from the simplest form of that model, examining the effects of DNA sticky end sequence energetics on tile system behavior. We develop theoretical models, sequence assignment algorithms, and a software package, StickyDesign, for sticky end sequence design.

As a demonstration of a specific tile system, we design a binary counting ribbon that can accurately count from a programmable starting value and stop growing after overflowing, resulting in a single system that can construct ribbons of precise and programmable length. In the process of designing the system, we explain numerous considerations that provide insight into more general tile system design, particularly with regards to tile concentrations, facet nucleation, the construction of finite assemblies, and design beyond the abstract Tile Assembly Model.

Finally, we present our crystals that count: experimental results with our binary counting system that represent a significant improvement in the accuracy of experimental algorithmic self-assembly, including crystals that count perfectly with 5 bits from 0 to 31. We show some preliminary experimental results on the construction of our capping system to stop growth after counters overflow, and offer some speculation on potential future directions of the field.

An experimental study of the mobility of edge dislocations in pure copper single crystals

The velocity of selectively-introduced edge dislocations in 99.999 percent pure copper crystals has been measured as a function of stress at temperatures from 66°K to 373°K by means of a torsion technique. The range of resolved shear stress was 0 to 15 megadynes/ cm^2 for seven temperatures (66°K, 74°K, 83°K, 123°K, 173°K, 296°K, 296°K, 373°K.

Dislocation mobility is characterized by two distinct features; (a) relatively high velocity at low stress (maximum velocities of about 9000 em/sec were realized at low temperatures), and (b) increasing velocity with decreasing temperature at constant stress.

The relation between dislocation velocity and resolved shear stress is:

v = v_o(τ_r/τ_o)^n

where v is the dislocation velocity at resolved shear stress τ_r, v_o is a constant velocity chosen equal to 2000 cm/ sec, τ_o is the resolved shear stress required to maintain velocity v_o, and n is the mobility coefficient. The experimental results indicate that τ_o decreases from 16.3 x 10^6 to 3.3 x 10^6 dynes/cm^2 and n increases from about 0.9 to 1.1 as the temperature is lowered from 296°K to 66°K.

The experimental dislocation behavior is consistent with an interpretation on the basis of phonon drag. However, the complete temperature dependence of dislocation mobility could not be closely approximated by the predictions of one or a combination of mechanisms.

Radio frequency studies of surface resistance and critical magnetic field of type I and type II superconductors

The surface resistance and the critical magnetic field of lead electroplated on copper were studied at 205 MHz in a half-wave coaxial resonator. The observed surface resistance at a low field level below 4.2°K could be well described by the BCS surface resistance with the addition of a temperature independent residual resistance. The available experimental data suggest that the major fraction of the residual resistance in the present experiment was due to the presence of an oxide layer on the surface. At higher magnetic field levels the surface resistance was found to be enhanced due to surface imperfections.

The attainable rf critical magnetic field between 2.2°K and T_c of lead was found to be limited not by the thermodynamic critical field but rather by the superheating field predicted by the one-dimensional Ginzburg-Landau theory. The observed rf critical field was very close to the expected superheating field, particularly in the higher reduced temperature range, but showed somewhat stronger temperature dependence than the expected superheating field in the lower reduced temperature range.

The rf critical magnetic field was also studied at 90 MHz for pure tin and indium, and for a series of SnIn and InBi alloys spanning both type I and type II superconductivity. The samples were spherical with typical diameters of 1-2 mm and a helical resonator was used to generate the rf magnetic field in the measurement. The results of pure samples of tin and indium showed that a vortex-like nucleation of the normal phase was responsible for the superconducting-to-normal phase transition in the rf field at temperatures up to about 0.98-0.99 T_c' where the ideal superheating limit was being reached. The results of the alloy samples showed that the attainable rf critical fields near T_c were well described by the superheating field predicted by the one-dimensional GL theory in both the type I and type II regimes. The measurement was also made at 300 MHz resulting in no significant change in the rf critical field. Thus it was inferred that the nucleation time of the normal phase, once the critical field was reached, was small compared with the rf period in this frequency range.

Análise de fadiga em pontes rodoviárias de concreto armado

As pontes rodoviárias de concreto armado estão sujeitas às ações dinâmicas variáveis devido ao tráfego de veículos sobre o tabuleiro. Estas ações dinâmicas podem gerar o surgimento das fraturas ou mesmo a sua propagação na estrutura. A correta consideração destes aspectos objetivou o desenvolvimento de um estudo, de forma a avaliar os esforços do tráfego de veículos pesados sobre o tabuleiro. As técnicas para a contagem de ciclos de esforços e a aplicação das regras de dano acumulado foram analisadas através das curvas S-N de diversas normas estudadas. A ponte rodoviária investigada é constituída por quatro vigas longitudinais, três transversinas e por um tabuleiro de concreto armado. O modelo computacional, desenvolvido para a análise dinâmica da ponte, foi concebido com base no emprego de técnicas usuais de discretização através do método dos elementos finitos. O modelo estrutural da obra de arte rodoviária estudada foi simulado com base no emprego de elementos finitos sólidos tridimensionais. Os veículos são representados a partir de sistemas massa-mola-amortecedor. O tráfego dessas viaturas é considerado mediante a simulação de comboios semi-infinitos, deslocando-se com velocidade constante sobre o tabuleiro da ponte. As conclusões deste trabalho versam acerca da vida útil de serviço dos elementos estruturais de pontes rodoviárias de concreto armado submetidas às ações dinâmicas provenientes do tráfego de veículos pesados sobre o tabuleiro.

Micromechanical damage and fracture in elastomeric polymers

This thesis aims at a simple one-parameter macroscopic model of distributed damage and fracture of polymers that is amenable to a straightforward and efficient numerical implementation. The failure model is motivated by post-mortem fractographic observations of void nucleation, growth and coalescence in polyurea stretched to failure, and accounts for the specific fracture energy per unit area attendant to rupture of the material.

Furthermore, it is shown that the macroscopic model can be rigorously derived, in the sense of optimal scaling, from a micromechanical model of chain elasticity and failure regularized by means of fractional strain-gradient elasticity. Optimal scaling laws that supply a link between the single parameter of the macroscopic model, namely the critical energy-release rate of the material, and micromechanical parameters pertaining to the elasticity and strength of the polymer chains, and to the strain-gradient elasticity regularization, are derived. Based on optimal scaling laws, it is shown how the critical energy-release rate of specific materials can be determined from test data. In addition, the scope and fidelity of the model is demonstrated by means of an example of application, namely Taylor-impact experiments of polyurea rods. Hereby, optimal transportation meshfree approximation schemes using maximum-entropy interpolation functions are employed.

Finally, a different crazing model using full derivatives of the deformation gradient and a core cut-off is presented, along with a numerical non-local regularization model. The numerical model takes into account higher-order deformation gradients in a finite element framework. It is shown how the introduction of non-locality into the model stabilizes the effect of strain localization to small volumes in materials undergoing softening. From an investigation of craze formation in the limit of large deformations, convergence studies verifying scaling properties of both local- and non-local energy contributions are presented.

A variational framework for spectral discretization of the density matrix in Kohn Sham density functional theory

Kohn-Sham density functional theory (KSDFT) is currently the main work-horse of quantum mechanical calculations in physics, chemistry, and materials science. From a mechanical engineering perspective, we are interested in studying the role of defects in the mechanical properties in materials. In real materials, defects are typically found at very small concentrations e.g., vacancies occur at parts per million, dislocation density in metals ranges from $10^{10} m^{-2}$ to $10^{15} m^{-2}$, and grain sizes vary from nanometers to micrometers in polycrystalline materials, etc. In order to model materials at realistic defect concentrations using DFT, we would need to work with system sizes beyond millions of atoms. Due to the cubic-scaling computational cost with respect to the number of atoms in conventional DFT implementations, such system sizes are unreachable. Since the early 1990s, there has been a huge interest in developing DFT implementations that have linear-scaling computational cost. A promising approach to achieving linear-scaling cost is to approximate the density matrix in KSDFT. The focus of this thesis is to provide a firm mathematical framework to study the convergence of these approximations. We reformulate the Kohn-Sham density functional theory as a nested variational problem in the density matrix, the electrostatic potential, and a field dual to the electron density. The corresponding functional is linear in the density matrix and thus amenable to spectral representation. Based on this reformulation, we introduce a new approximation scheme, called spectral binning, which does not require smoothing of the occupancy function and thus applies at arbitrarily low temperatures. We proof convergence of the approximate solutions with respect to spectral binning and with respect to an additional spatial discretization of the domain. For a standard one-dimensional benchmark problem, we present numerical experiments for which spectral binning exhibits excellent convergence characteristics and outperforms other linear-scaling methods.

Effect of Microstructural Interfaces on the Mechanical Response of Crystalline Metallic Materials

Advances in nano-scale mechanical testing have brought about progress in the understanding of physical phenomena in materials and a measure of control in the fabrication of novel materials. In contrast to bulk materials that display size-invariant mechanical properties, sub-micron metallic samples show a critical dependence on sample size. The strength of nano-scale single crystalline metals is well-described by a power-law function, σαD^-n, where D is a critical sample size and n is a experimentally-fit positive exponent. This relationship is attributed to source-driven plasticity and demonstrates a strengthening as the decreasing sample size begins to limit the size and number of dislocation sources. A full understanding of this size-dependence is complicated by the presence of microstructural features such as interfaces that can compete with the dominant dislocation-based deformation mechanisms. In this thesis, the effects of microstructural features such as grain boundaries and anisotropic crystallinity on nano-scale metals are investigated through uniaxial compression testing. We find that nano-sized Cu covered by a hard coating displays a Bauschinger effect and the emergence of this behavior can be explained through a simple dislocation-based analytic model. Al nano-pillars containing a single vertically-oriented coincident site lattice grain boundary are found to show similar deformation to single-crystalline nano-pillars with slip traces passing through the grain boundary. With increasing tilt angle of the grain boundary from the pillar axis, we observe a transition from dislocation-dominated deformation to grain boundary sliding. Crystallites are observed to shear along the grain boundary and molecular dynamics simulations reveal a mechanism of atomic migration that accommodates boundary sliding. We conclude with an analysis of the effects of inherent crystal anisotropy and alloying on the mechanical behavior of the Mg alloy, AZ31. Through comparison to pure Mg, we show that the size effect dominates the strength of samples below 10 μm, that differences in the size effect between hexagonal slip systems is due to the inherent crystal anisotropy, suggesting that the fundamental mechanism of the size effect in these slip systems is the same.