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Unsteady Aerodynamics and Optimal Control of an Airfoil at Low Reynolds Number
Get PDFAs opposed to conventional air vehicles that have fixed wings, small birds and insects are known to flap their wings at higher angles of attack. The vortex produced at the tip of the wing, known as the leading-edge vortex (LEV), plays an important role to enhance lift during its flight. In this thesis, we analyze the influence of these vortices on aerodynamic forces that could be beneficial to micro-air vehicle performance and efficiency. The flow structures associated with simple harmonic motions of an airfoil are first investigated. The characteristics of the time-averaged and fluctuating forces are explained by analyzing vortical flow features, such as vortex lock-in, leading-edge vortex synchronization, and vortex formation time. Specific frequency regions where the wake instability locks in to the unsteady motion of the airfoil are identified, and these lead to significant changes in the mean forces. A detailed study of the flow structures associated with the LEV acting either in- or out-of-phase with the quasi-steady component of the forces is performed to quantify the amplification and attenuation behavior of the fluctuating forces. An inherent time scale of the LEV associated with its formation and detachment (LEV formation time) is shown to control the time-averaged forces. With these results, several optimal flow control problems are formulated. Adjoint-based optimal control is applied to an airfoil moving at a constant velocity and also to a reciprocating airfoil with no forward velocity. In both cases, we maximize lift by controlling the pitch rate of the airfoil. For the former case, the static map of lift at various angles of attack is additionally examined to find the static angle that provides maximum lift and also to confirm whether the optimizations perform according to the static map. For the latter case, we obtain a solution of the optimized motion of the flapping airfoil which resembles that of a hovering insect
Resolution of the Band Gap Prediction Problem for Materials Design
Get PDFAn important property with any new material is the band gap. In order to design new materials in silico, it is critical to have an accurate and computationally inexpensive tool for predicting band gaps. Standard density functional theory (DFT) methods are computationally efficient, but grossly underestimate band gaps. Hybrid density functionals are known to improve band gap predictions, but the computational cost in the overwhelmingly popular plane-wave basis set codes used for solids is a serious drawback. Exact exchange can be evaluated much more efficiently using localized Gaussian basis functions; however, the most readily available Gaussian basis periodic quantum chemistry code lacked spin-orbit coupling. This seriously limited the range of compounds that can be studies. In this thesis, spin-orbit coupling was implemented in the periodic, Gaussian basis set code CRYSTAL. Using the modified code, band gaps were computed using the B3PW91 hybrid density functional for 70 compounds spanning the entire periodic table and a factor of 500 in band gap (0.014 - 15 eV). To benchmark the quality of the hybrid method, we compared to the rigorous GW many-body perturbation theory method. Surprisingly, the MAD for B3PW91 is about 1.5 times smaller than the MAD for GW. Furthermore, B3PW91 is three to four orders of magnitude faster computationally. We also show that increasing (decreasing) the amount of exact exchange compared to B3PW91 leads to systematic overestimates (underestimates) of band gaps. Finally, we show that the pathological vanishing of the density of states at the Fermi level of a metal cannot be observed in practical calculations of real metals. Thus, we believe that B3PW91 is a practical tool for predicting the band gaps of materials before they are synthesized while being computationally efficient enough for high-throughput applications and represents a solution to the band gap prediction problem for materials design
Programming Molecular Association and Viscoelastic Behavior in Protein Hydrogels
Get PDFRecombinant artificial proteins contain genetically encoded information that specifies their assembly into higher order structures by physical or chemical cross-linking as well as elastic behavior and biological or chemical function. This thesis describes the use of artificial proteins to construct molecular networks containing covalent cross-links involving the thiol side chain of cysteine residues and physical cross-links involving the association of helical domains as coiled coils. The goal of this work was to demonstrate how the viscoelastic properties of protein hydrogels could be encoded within an artificial protein sequence.
Using genetic engineering methods, a telechelic protein denoted ERE was designed from elastin- and fibronectin-derived repeating units and expressed in Escherichia coli. ERE was end-linked by the reaction of terminal cysteine residues with tetrakis-vinyl sulfone-functionalized 4-arm star PEG to form hydrogel networks. The effects of varying the precursor concentration and cross-linker stoichiometry on the swelling ratio and mechanical properties of the hydrogels were studied in detail in Chapter 2. The capacity for ERE hydrogels to serve as an artificial extracellular matrix was also assessed by the encapsulation of mouse fibroblasts, which survived the cross-linking reaction and exhibited a spread morphology within the gel.
Chapter 3 describes a set of recombinant artificial proteins that can be cross-linked by covalent bonds, by association of helical domains, or by both mechanisms. These proteins were used to construct chemical, physical, and chemical-physical hydrogel networks in which the mechanism of cross-linking determines whether the material response to mechanical deformation is elastic or viscoelastic. In viscoelastic networks, stress relaxation and energy dissipation could be tuned by controlling the ratio of physical cross-linking to chemical cross-linking, and the physical cross-links could be disrupted either by protein denaturation or by mutation of the primary sequence.
Network dynamics control the viscoelasticity and erosion rate of materials and influence biological processes at multiple length scales.In Chapter 4, variation of the protein sequence was explored as a strategy to tune the characteristic relaxation timescale of protein networks. Single point mutations to coiled-coil physical cross-linking domains in chemical-physical hydrogels altered the characteristic relaxation time over five orders of magnitude. Using a pair of orthogonal coiled-coil physical cross-linking domains, networks with two distinct relaxation timescales were also engineered.
The dynamic properties of protein hydrogels can also be controlled by interactions between protein domains and small molecule ligands. In Chapter 5, the viscoelastic behavior of chemical-physical protein gels was tuned by swelling the gels with small hydrophobic molecules including vitamin D3 and fatty acids. The proposed mechanism for this effect involves binding of the ligands within the hydrophobic pore or channel created by a coiled-coil physical cross-link. Exploiting natural and designed protein-ligand interactions represents a new approach to developing hydrogel “formulations” in which the viscoelastic properties of the material can be engineered to meet specific design criteria.
In addition to exhibiting interesting dynamic properties, polymeric hydrogels containing permanent covalent cross-links and reversible physical cross-links often display enhanced toughness and extensibility. Protein hydrogels cross-linked by covalent thioether bonds and physical coiled coils could be extended further than control covalent hydrogels and exhibited a greater work of extension, which is considered a measure of material toughness. These results demonstrate progress toward engineering tougher, more extensible protein-based materials by the incorporation of coiled-coil physical cross-links within a covalent hydrogel network.</p
Biochemical and Genetic Studies of the N-End Rule Pathway in Yeast and Mammals
Get PDFRegulation of the in vivo half-lives of intracellular proteins is an important cellular process. Many intracellular proteins are short-lived, owing to their regulated and processive degradation by the Ubiquitin (Ub)-Proteasome System (UPS). In eukaryotes, the N-end rule pathway is one specific pathway within the UPS. The N-end rule pathway relates the identity of the N-terminal residue of a protein, or a protein fragment, to its in vivo half-life. Substrates of the N-end rule pathway are recognized by the presence of degradation signals, termed N-degrons. Recognition components of the N-end rule pathway are E3 ubiquitin ligases that are capable of binding to N-degrons. The N-end rule pathway consists of two distinct branches: the Arg/N-end rule pathway and the Ac/N-end rule pathway.
In the present studies, we demonstrate a complementary targeting of the rat serotonin N-acetyltransferase (AANAT), an important mediator of circadian physiology, by both branches of the N-end rule pathway. The co-targeting results from incomplete N-terminal (Nt-) acetylation of a Met-Ф motif at the N-terminus of AANAT in vivo. In the same study, we demonstrate that human AANAT is substantially longer-lived than its rat counterpart, owing to differences in their N-terminal sequences. This molecular genetic investigation of the degradation of a physiological N-end rule substrate followed an analogous earlier study, in which we reported that a clinically-relevant (blood pressure-increasing) Q2L mutant of human RGS2 (termed ML-RGS2), a regulator of G proteins, could likewise be co-targeted by both branches of the N-end rule pathway. Together, AANAT and RGS2 are the first identified and characterized physiological substrates of the Ac/N-end rule pathway in mammals.
We also report on the development and use of in vitro N-terminal arginylation (Nt-arginylation) assays using CelluSpots peptide arrays, in conjunction with pulse-chase assays in rabbit reticulocyte extract, for the systematic investigation of the effects of N-terminus-proximal sequence context on the Nt-arginylation activity of the Ate1 arginyltransferase, a component of the Arg/N-end rule pathway. These experiments help to define the sequence requirements for efficient Nt-arginylation by Ate1. Finally, we demonstrate that Rec8, a subunit of the cohesin protein complex during meiosis, is a natural short-lived substrate of the mammalian Arg/N-end rule pathway.</p
Refining Sea Urchin Developmental Gene Regulatory Network Models by Incorporating Wnt Signaling and Information Processed at the hox11/13b Locus
Get PDFThe availability of advanced GRN models for sea urchin development presents a unique opportunity to address the function of signaling interactions in cell fate specification at a system-wide level. Here we take a global approach to investigate the regulatory functions of the Wnt signaling system during pre-gastrular development. We examine the embryonic specification processes in order to determine in which embryonic lineages and at what time specific Wnt signals are required. We show a functional divergence among individual Wnt ligands despite their similar and partially overlapped spatial expression. By studying TF activators, we show that expression of wnt genes is tightly controlled and is correlated with their respective functions. In particular Wnt1 and Wnt16, which regulate endodermal specification, are activated by the endoderm regulator Hox11/13b. Motivated by these results and in an effort to further enhance our understanding of endodermal specification, we conducted a cis-regulatory analysis of the hox11/13b gene across a range of developmental stages up to 60 hours post-fertilization. We identify Ets, Eve, and Tcf as direct regulators of hox11/13b, and we show that their combinatorial control drives the endoderm-specific and dynamic early expression of hox11/13b. Furthermore, we show that its late expression in the hindgut is controlled by an inter-modular AND logic gate, in which two separate regulatory modules are both required but neither alone is sufficient
Thermoelectric Properties of Bismuth Antimony Telluride Alloys
Get PDFCommonly used ozone-depleting refrigerants in refrigerators will be completely phased out in less than 15 years according to the Montreal Protocol. This imminent challenge can be tackled effectively by replacing the current vapor-compression cooling with environmentally sustainable thermoelectric cooling. P-type (Bi0.25Sb0.75)2Te3 alloys have been intensively studied over the past 50 years for cooling applications because of their high thermoelectric performance near room temperature. However, the electronic origin of the high thermoelectric efficiency of (Bi0.25Sb0.75)2Te3 alloys is often understated or ignored completely. In this thesis, the underlying physics of high electronic performance observed in the particular alloy composition, (Bi2Te3).25–(Sb2Te3).75, is investigated. It was demonstrated with two-band transport calculation that the convergence of bands occurred at (Bi2Te3).25–(Sb2Te3).75. A zT improvement of 17 % was also achieved in zone-levelled (Bi0.25Sb.75)2Te3 crystals by controlling their carrier concentration while using the two-band model as a guide. With the optimum electronic efficiency theoretically calculated and achieved experimentally, the thesis moves on to minimize lattice thermal conductivity of (Bi0.25Sb.75)2Te3 for the maximum zT. A new liquid compaction method was devised to produce dense arrays of dislocations in grain boundaries of nanostructured (Bi0.25Sb.75)2Te3. The grain boundary dislocations were found to be highly effective in scattering phonons and a substantial improvement in zT was possible (zT = 1.86 at 320 K). The understanding of phonon scattering by dislocations was in turn applied to phonon scattering at grain boundaries of polycrystalline materials. By demonstrating that the frequency-dependent dislocation scattering can replace the commonly used frequency-independent boundary scattering by Casimir, this thesis suggests that the grain boundary dislocation scattering may be responsible for the mechanism of phonon scattering at grain boundaries
Neural and Hormonal Systems Underlying Human Reward-Seeking Behavior
Get PDFOur evolutionary history has endowed us with biological systems for identifying those elements of the environment that contribute to our biological fitness and for modifying our behaviors to allow us to acquire them.
Theoretical propositions suggest that the ability to detect changes in the statistics underlying in the environment may be useful for rapidly adapting our behaviors. However, little is known about the neural representation of the quantity representing the evidence for a change point: unexpected uncertainty. In Chapter 2, I describe a study in which humans interact with an unstable reward environment while undergoing fMRI. Representations of unexpected uncertainty were found in multiple cortical areas, as well as the noradrenergic brainstem nucleus locus coeruleus. Other unique cortical regions were found to encode estimation uncertainty, or the uncertainty in one’s estimates of the reward contingencies, and risk, or one’s estimate of the stochasticity of the environment. Collectively, these findings support theoretical models in which uncertainty computations determine the speed of learning.
Although learning from direct experience in this way is vital to our survival, humans are also particularly adept at learning from conspecifics. However, it is not known whether differing computational strategies thought to support experiential learning, model-based and model-free learning, also support learning by observation. Chapter 3 describes a study in which human participants played a multi-armed bandit task that encouraged them to employ both experiential and observational learning while they underwent fMRI. Model-based learning signals are found during both observational and experiential learning in the intraparietal sulcus. However, unlike in experiential learning, model-free learning signals in the ventral striatum were not detectable during observational learning. These results provide insight into the flexibilty of the model-based learning system, and further suggest that the model-free learning system may be less flexible with regard to its involvement in observational learning.
While Chapters 2 and 3 are concerned with modifying reward-seeking behavior in reponse to changes in the external environment, Chapter 4 examines a modification of reward-seeking behavior in response to changes in the internal hormonal environment. Specifically, it describes how the behavior of human males in a simple economic game was influenced by the administration of testosterone. Although a popular view on the role of testosterone in human social behaviour proposes that it increases aggression, a recent theory states that it instead promotes behaviors that enhance social status. In a double-blind, placebo-controlled between-subjects design, administration of testosterone increased punishment of players who treat the participants unfairly but also increased reward of those who treat them generously. Our findings are inconsistent with the view that testosterone simply increases aggression and provides causal evidence for the social-status hypothesis in men.
In Chapter 5, I describe an investigation of the phenomenon of ‘choking under pressure’, in which reward-seeking behavior is compromised by the promise of high reward for successful performance. A novel approach to attenuating such 'choking under pressure' using cognitive reappraisal of the incentive is described and tested. When participants performed a demanding motor task under reappraisal, choking was indeed significantly reduced, with the magnitude of this reduction being predicted by the striatal BOLD response to incentive magnitude. In addition, application of the reappraisal strategy was associated with reduced sympathetic arousal during trials on which performance failed at high levels of incentive. These results suggest that reappraisal of the incentive is indeed a promising intervention for attenuating choking under pressure.</p
Advanced Applications of Nanoelectromechanical Systems
Get PDFNanoelectromechanical systems (NEMS) have advanced the technologies in a wide spectrum of fields, including nonlinear dynamics, sensors for force detection, mass spectrometry, inertial imaging, calorimetry, and charge sensing. Due to their low power consumption, fast response time, large dynamic range, high quality factor, and low mass, NEMS have achieved unprecedented measurement sensitivity. For optimized system functionalization and design, precise characterization of material properties at the nanoscale is essential. In this thesis, we will discuss three applications of NEMS: mechanical switches, using anharmonic nonlinearity to measure device and material properties, and mass spectrometry and inertial imaging.
The first application of NEMS we discuss is NEMS switches, switches with physical moving parts. Conventional electronics, based largely on silicon transistors, is reaching a physical limit in both size and power consumption. Mechanical switches provide a promising solution to surpass this limit by forcing a jump between the on and off states. Graphene, which is a single sheet of carbon atoms arranged in a hexagonal structure, has high mechanical strength and strong planar bonding, making it an ideal candidate for nanoelectromechanical switches. In addition, graphene is conductive, which decreases resistive heating at the contact area, therefore reducing bonding issues and subsequently reducing degradation. We demonstrate using exfoliated graphene to fabricate suspended graphene NEMS switches with successful switching.
The second application of NEMS we discuss in this thesis is the use of mechanical nonlinearity to measure device and material properties. While the nonlinear dynamics of NEMS have been used previously to investigate the longitudinal speed of sound of materials at nano- and micro-scales, we correct a previously attempted method that employs the anharmonicity of NEMS arising from deflection-dependent stress to interrogate the transport of RF acoustic phonons at nanometer scales. In contrast to existing approaches, this decouples intrinsic material properties, such as longitudinal speed of sound, from properties associated with linear dynamics, such as tension, of the structure. We demonstrate this approach through measurements of the longitudinal speed of sound in several NEMS devices composed of single crystal silicon along different crystal orientations. Good agreement with literature values is reported.
The third application of NEMS we discuss is mass spectrometry and inertial imaging. Currently, only doubly clamped beams and cantilevers have been experimentally demonstrated for mass spectrometry. We extend the one-dimension model for mass spectrometry to a novel method for inertial imaging. We further extend the theory of mass spectrometry and inertial imaging to two dimensions by using a plate geometry. We show that the mode shape is critical in performing NEMS mass spectrometry and inertial imaging, and that the mode shapes in plates deviate from the ideal scenario with isotropic stress. We experiment with various non-ideal conditions to match non-ideal mode shape observed.</p
Dynamic Characterization of Micro-Particle Systems
Get PDFOrdered granular systems have been a subject of active research for decades. Due to their rich dynamic response and nonlinearity, ordered granular systems have been suggested for several applications, such as solitary wave focusing, acoustic signals manipulation, and vibration absorption. Most of the fundamental research performed on ordered granular systems has focused on macro-scale examples. However, most engineering applications require these systems to operate at much smaller scales. Very little is known about the response of micro-scale granular systems, primarily because of the difficulties in realizing reliable and quantitative experiments, which originate from the discrete nature of granular materials and their highly nonlinear inter-particle contact forces.
In this work, we investigate the physics of ordered micro-granular systems by designing an innovative experimental platform that allows us to assemble, excite, and characterize ordered micro-granular systems. This new experimental platform employs a laser system to deliver impulses with controlled momentum and incorporates non-contact measurement apparatuses to detect the particles’ displacement and velocity. We demonstrated the capability of the laser system to excite systems of dry (stainless steel particles of radius 150 micrometers) and wet (silica particles of radius 3.69 micrometers, immersed in fluid) micro-particles, after which we analyzed the stress propagation through these systems.
We derived the equations of motion governing the dynamic response of dry and wet particles on a substrate, which we then validated in experiments. We then measured the losses in these systems and characterized the collision and friction between two micro-particles. We studied wave propagation in one-dimensional dry chains of micro-particles as well as in two-dimensional colloidal systems immersed in fluid. We investigated the influence of defects to wave propagation in the one-dimensional systems. Finally, we characterized the wave-attenuation and its relation to the viscosity of the surrounding fluid and performed computer simulations to establish a model that captures the observed response.
The findings of the study offer the first systematic experimental and numerical analysis of wave propagation through ordered systems of micro-particles. The experimental system designed in this work provides the necessary tools for further fundamental studies of wave propagation in both granular and colloidal systems.</p
Force Chains, Friction, and Flow: Behavior of Granular Media across Length Scales
Get PDFWe study the behavior of granular materials at three length scales. At the smallest length scale, the grain-scale, we study inter-particle forces and "force chains". Inter-particle forces are the natural building blocks of constitutive laws for granular materials. Force chains are a key signature of the heterogeneity of granular systems. Despite their fundamental importance for calibrating grain-scale numerical models and elucidating constitutive laws, inter-particle forces have not been fully quantified in natural granular materials. We present a numerical force inference technique for determining inter-particle forces from experimental data and apply the technique to two-dimensional and three-dimensional systems under quasi-static and dynamic load. These experiments validate the technique and provide insight into the quasi-static and dynamic behavior of granular materials.
At a larger length scale, the mesoscale, we study the emergent frictional behavior of a collection of grains. Properties of granular materials at this intermediate scale are crucial inputs for macro-scale continuum models. We derive friction laws for granular materials at the mesoscale by applying averaging techniques to grain-scale quantities. These laws portray the nature of steady-state frictional strength as a competition between steady-state dilation and grain-scale dissipation rates. The laws also directly link the rate of dilation to the non-steady-state frictional strength.
At the macro-scale, we investigate continuum modeling techniques capable of simulating the distinct solid-like, liquid-like, and gas-like behaviors exhibited by granular materials in a single computational domain. We propose a Smoothed Particle Hydrodynamics (SPH) approach for granular materials with a viscoplastic constitutive law. The constitutive law uses a rate-dependent and dilation-dependent friction law. We provide a theoretical basis for a dilation-dependent friction law using similar analysis to that performed at the mesoscale. We provide several qualitative and quantitative validations of the technique and discuss ongoing work aiming to couple the granular flow with gas and fluid flows.</p