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Description
Transient receptor potential vanilloid member 1 (TRPV1) is a membrane protein ion channel that functions as a heat and capsaicin receptor. In addition to activation by hot temperature and vanilloid compounds such as capsaicin, TRPV1 is modulated by various stimuli including acidic pH, endogenous lipids, diverse biological and synthetic chemical ligands, and modulatory proteins. Due to its sensitivity to noxious stimuli such as high temperature and pungent chemicals, there has been significant evidence that TRPV1 participates in a variety of human physiological and pathophysiological pathways, raising the potential of TRPV1 as an attractive therapeutic target. However, the polymodal nature of TRPV1 function has complicated clinical application because the TRPV1 activation mechanisms from different modes have generally been enigmatic. Consequently, tremendous efforts have put into dissecting the mechanisms of different activation modes, but numerous questions remain to be answered.
The studies conducted in this dissertation probed the role of the S1-S4 membrane domain in temperature and ligand activation of human TRPV1. Temperature-dependent solution nuclear magnetic resonance (NMR) spectroscopy for thermodynamic and mechanistic studies of the S1-S4 domain. From these results, a potential temperature sensing mechanism of TRPV1, initiated from the S1-S4 domain, was proposed. Additionally, direct binding of various ligands to the S1-S4 domain were used to ascertain the interaction site and the affinities (Kd) of various ligands to this domain. These results are the first to study the isolated S1-S4 domain of human TRPV1 and many results indicate that the S1-S4 domain is crucial for both temperature-sensing and is the general receptor binding site central to chemical activation.
The studies conducted in this dissertation probed the role of the S1-S4 membrane domain in temperature and ligand activation of human TRPV1. Temperature-dependent solution nuclear magnetic resonance (NMR) spectroscopy for thermodynamic and mechanistic studies of the S1-S4 domain. From these results, a potential temperature sensing mechanism of TRPV1, initiated from the S1-S4 domain, was proposed. Additionally, direct binding of various ligands to the S1-S4 domain were used to ascertain the interaction site and the affinities (Kd) of various ligands to this domain. These results are the first to study the isolated S1-S4 domain of human TRPV1 and many results indicate that the S1-S4 domain is crucial for both temperature-sensing and is the general receptor binding site central to chemical activation.
ContributorsKim, Minjoo (Author) / Van Horn, Wade D (Thesis advisor) / Wang, Xu (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2019
Description
This thesis intends to cover the experimental investigation of the propagation of laser-generated optoacoustic waves in structural materials and how they can be utilized for damage detection. Firstly, a system for scanning a rectangular patch on the sample is designed. This is achieved with the help of xy stages which are connected to the laser head and allow it to move on a plane. Next, a parametric study was designed to determine the optimum testing parameters of the laser. The parameters so selected were then used in a series of tests which helped in discerning how the Ultrasound Waves behave when damage is induced in the sample (in the form of addition of masses). The first test was of increasing the mases in the sample. The second test was a scan of a rectangular area of the sample with and without damage to find the effect of the added masses. Finally, the data collected in such a manner is processed with the help of the Hilbert-Huang transform to determine the time of arrival. The major benefits from this study are the fact that this is a Non-Destructive imaging technique and thus can be used as a new method for detection of defects and is fairly cheap as well.
ContributorsRavi Narayanan, Venkateshwaran (Author) / Liu, Yongming (Thesis advisor) / Zhuang, Houlong (Committee member) / Nian, Qiong (Committee member) / Arizona State University (Publisher)
Created2019
Description
Droplet-structure interactions play a pivotal role in many engineering applications as droplet-based solutions are evolving. This work explores the physical understanding of these interactions through systematic research leading to improvements in thermal management via dropwise condensation (DWC), and breathable protective wearables against chemical aerosols for better thermoregulation.
In DWC, the heat transfer rate can be further increased by increasing the nucleation and by optimally ‘refreshing’ the surface via droplet shedding. Softening of surfaces favor the former while having an adverse effect on the latter. This optimization problem is addressed by investigating how mechanical properties of a substrate impact relevant droplet-surface interactions and DWC heat transfer rate. The results obtained by combining droplet induced surface deformation with finite element model show that softening of the substrates below a shear modulus of 500 kPa results in a significant reduction in the condensation heat transfer rate.
On the other hand, interactions between droplet and polymer leading to polymer swelling can be used to develop breathable wearables for use in chemically harsh environments. Chemical aerosols are hazardous and conventional protective measures include impermeable barriers which limit the thermoregulation. To solve this, a solution is proposed consisting of a superabsorbent polymer developed to selectively absorb these chemicals and closing the pores in the fabric. Starting from understanding and modeling the droplet induced swelling in elastomers, the extent and topological characteristic of swelling is shown to depend on the relative comparison of the polymer and aerosol geometries. Then, this modeling is extended to a customized polymer, through a simplified characterization paradigm. In that, a new method is proposed to measure the swelling parameters of the polymer-solvent pair and develop a validated model for swelling. Through this study, it is shown that for this polymer, the concentration-dependent diffusion coefficient can be measured through gravimetry and Poroelastic Relaxation Indentation, simplifying the characterization effort. Finally, this model is used to design composite fabric. Specifically, using model results, the SAP geometry, base fabric design, method of composition is optimized, and the effectiveness of the composite fabric highlighted in moderate-to-high concentrations over short durations.
In DWC, the heat transfer rate can be further increased by increasing the nucleation and by optimally ‘refreshing’ the surface via droplet shedding. Softening of surfaces favor the former while having an adverse effect on the latter. This optimization problem is addressed by investigating how mechanical properties of a substrate impact relevant droplet-surface interactions and DWC heat transfer rate. The results obtained by combining droplet induced surface deformation with finite element model show that softening of the substrates below a shear modulus of 500 kPa results in a significant reduction in the condensation heat transfer rate.
On the other hand, interactions between droplet and polymer leading to polymer swelling can be used to develop breathable wearables for use in chemically harsh environments. Chemical aerosols are hazardous and conventional protective measures include impermeable barriers which limit the thermoregulation. To solve this, a solution is proposed consisting of a superabsorbent polymer developed to selectively absorb these chemicals and closing the pores in the fabric. Starting from understanding and modeling the droplet induced swelling in elastomers, the extent and topological characteristic of swelling is shown to depend on the relative comparison of the polymer and aerosol geometries. Then, this modeling is extended to a customized polymer, through a simplified characterization paradigm. In that, a new method is proposed to measure the swelling parameters of the polymer-solvent pair and develop a validated model for swelling. Through this study, it is shown that for this polymer, the concentration-dependent diffusion coefficient can be measured through gravimetry and Poroelastic Relaxation Indentation, simplifying the characterization effort. Finally, this model is used to design composite fabric. Specifically, using model results, the SAP geometry, base fabric design, method of composition is optimized, and the effectiveness of the composite fabric highlighted in moderate-to-high concentrations over short durations.
ContributorsPhadnis, Akshay (Author) / Rykaczewski, Konrad (Thesis advisor) / Wang, Robert (Committee member) / Wang, Liping (Committee member) / Oswald, Jay (Committee member) / Burgin, Timothy (Committee member) / Arizona State University (Publisher)
Created2019
Description
Corrosion fatigue has been of prime concern in railways, aerospace, construction industries and so on. Even in the case of many medical equipment, corrosion fatigue is considered to be a major challenge. The fact that even high strength materials have lower resistance to corrosion fatigue makes it an interesting area for research. The analysis of propagation of fatigue crack growth under environmental interaction and the life prediction is significant to reduce the maintenance costs and assure structural integrity. Without proper investigation of the crack extension under corrosion fatigue, the scenario can lead to catastrophic disasters due to premature failure of a structure. An attempt has been made in this study to predict the corrosion fatigue crack growth with reasonable accuracy. Models that have been developed so far predict the crack propagation for constant amplitude loading (CAL). However, most of the industrial applications encounter random loading. Hence there is a need to develop models based on time scale. An existing time scale model that can predict the fatigue crack growth for constant and variable amplitude loading (VAL) in the Paris region is initially modified to extend the prediction to near threshold and unstable crack growth region. Extensive data collection was carried out to calibrate the model for corrosion fatigue crack growth (CFCG) based on the experimental data. The time scale model is improved to incorporate the effect of corrosive environments such as NaCl and dry hydrogen in the fatigue crack growth (FCG) by investigation of the trend in change of the crack growth. The time scale model gives the advantage of coupling the time phenomenon stress corrosion cracking which is suggested as a future work in this paper.
ContributorsKurian, Bianca (Author) / Liu, Yongming (Thesis advisor) / Nian, Qiong (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2019
Description
Shock loading produces a compressive stress pulse with steep gradients in density, temperature, and pressure that are also often modeled as discontinuities. When a material is subject to these dynamic (shock) loading conditions, fracture and deformation patterns due to spall damage can arise. Spallation is a dynamic material failure that is caused by the nucleation, growth, and coalescence of voids, with possible ejection of the surface of the material. Intrinsic defects, such as grain boundaries are the preferred initiation sites of spall damage in high purity materials. The focus of this research is to study the phenomena that cause void nucleation and growth at a particular grain boundary (GB), chosen to maximize spall damage localization.
Bicrystal samples were shock loaded using flyer-plates via light gas gun and direct laser ablation. Stress, pulse duration, and crystal orientation along the shock direction were varied for a fixed boundary misorientation to determine thresholds for void nucleation and coalescence as functions of these parameters. Pressures for gas gun experiments ranged from 2 to 5 GPa, while pressures for laser ablation experiments varied from 17 to 25 GPa. Samples were soft recovered to perform damage characterization using electron backscattering diffraction (EBSD) and Scanning Electron Microscopy (SEM). Results showed a 14% difference in the thresholds for void nucleation and coalescence between samples with different orientations along the shock direction, which were affected by pulse duration and stress level. Fractography on boundaries with strong damage localization showed many small voids, indicating they experience rapid nucleation, causing early coalescence. Composition analysis was also performed to determine the effect of impurities on damage evolution. Results showed that higher levels of impurities led to more damage. ABAQUS/Explicit models were developed to simulate flyer-plate impact and void growth with the same crystal orientations and experimental conditions. Results are able to match the damage seen in each grain of the target experimentally. The Taylor Factor mismatch at the boundary can also be observed in the model with the higher Taylor Factor grain exhibiting more damage.
Bicrystal samples were shock loaded using flyer-plates via light gas gun and direct laser ablation. Stress, pulse duration, and crystal orientation along the shock direction were varied for a fixed boundary misorientation to determine thresholds for void nucleation and coalescence as functions of these parameters. Pressures for gas gun experiments ranged from 2 to 5 GPa, while pressures for laser ablation experiments varied from 17 to 25 GPa. Samples were soft recovered to perform damage characterization using electron backscattering diffraction (EBSD) and Scanning Electron Microscopy (SEM). Results showed a 14% difference in the thresholds for void nucleation and coalescence between samples with different orientations along the shock direction, which were affected by pulse duration and stress level. Fractography on boundaries with strong damage localization showed many small voids, indicating they experience rapid nucleation, causing early coalescence. Composition analysis was also performed to determine the effect of impurities on damage evolution. Results showed that higher levels of impurities led to more damage. ABAQUS/Explicit models were developed to simulate flyer-plate impact and void growth with the same crystal orientations and experimental conditions. Results are able to match the damage seen in each grain of the target experimentally. The Taylor Factor mismatch at the boundary can also be observed in the model with the higher Taylor Factor grain exhibiting more damage.
ContributorsFortin, Elizabeth Victoria (Author) / Peralta, Pedro (Thesis advisor) / Mignolet, Marc (Committee member) / Loomis, Eric (Committee member) / Oswald, Jay (Committee member) / Solanki, Kiran (Committee member) / Arizona State University (Publisher)
Created2020
Description
Phononic crystals are artificially engineered materials that can forbid phonon propagation in a specific frequency range that is referred to as a “phononic band gap.” Phononic crystals that have band gaps in the GHz to THz range can potentially enable sophisticated control over thermal transport with “phononic devices”. Calculations of the phononic band diagram are the standard method of determining if a given phononic crystal structure has a band gap. However, calculating the phononic band diagram is a computationally expensive and time-consuming process that can require sophisticated modeling and coding. In addition to this computational burden, the inverse process of designing a phononic crystal with a specific band gap center frequency and width is a challenging problem that requires extensive trial-and-error work.
In this dissertation, I first present colloidal nanocrystal superlattices as a new class of three-dimensional phononic crystals with periodicity in the sub-20 nm size regime using the plane wave expansion method. These calculations show that colloidal nanocrystal superlattices possess phononic band gaps with center frequencies in the 102 GHz range and widths in the 101 GHz range. Varying the colloidal nanocrystal size and composition provides additional opportunities to fine-tune the phononic band gap. This suggests that colloidal nanocrystal superlattices are a promising platform for the creation of high frequency phononic crystals.
For the next topic, I explore opportunities to use supervised machine learning for expedited discovery of phononic band gap presence, center frequency and width for over 14,000 two-dimensional phononic crystal structures. The best trained model predicts band gap formation, center frequencies and band gap widths, with 94% accuracy and coefficients of determination (R2) values of 0.66 and 0.83, respectively.
Lastly, I expand the above machine learning approach to use machine learning to design a phononic crystal for a given set of phononic band gap properties. The best model could predict elastic modulus of host and inclusion, density of host and inclusion, and diameter-to-lattice constant ratio for target center and width frequencies with coefficients of determinations of 0.94, 0.98, 0.94, 0.71, and 0.94 respectively. The high values coefficients of determination represents great opportunity for phononic crystal design.
In this dissertation, I first present colloidal nanocrystal superlattices as a new class of three-dimensional phononic crystals with periodicity in the sub-20 nm size regime using the plane wave expansion method. These calculations show that colloidal nanocrystal superlattices possess phononic band gaps with center frequencies in the 102 GHz range and widths in the 101 GHz range. Varying the colloidal nanocrystal size and composition provides additional opportunities to fine-tune the phononic band gap. This suggests that colloidal nanocrystal superlattices are a promising platform for the creation of high frequency phononic crystals.
For the next topic, I explore opportunities to use supervised machine learning for expedited discovery of phononic band gap presence, center frequency and width for over 14,000 two-dimensional phononic crystal structures. The best trained model predicts band gap formation, center frequencies and band gap widths, with 94% accuracy and coefficients of determination (R2) values of 0.66 and 0.83, respectively.
Lastly, I expand the above machine learning approach to use machine learning to design a phononic crystal for a given set of phononic band gap properties. The best model could predict elastic modulus of host and inclusion, density of host and inclusion, and diameter-to-lattice constant ratio for target center and width frequencies with coefficients of determinations of 0.94, 0.98, 0.94, 0.71, and 0.94 respectively. The high values coefficients of determination represents great opportunity for phononic crystal design.
ContributorsSadat, Seid Mohamadali (Author) / Wang, Robert Y (Thesis advisor) / Huang, Huei-Ping (Committee member) / Ankit, Kumar (Committee member) / Wang, Liping (Committee member) / Phelan, Patrick (Committee member) / Arizona State University (Publisher)
Created2020
Description
The fundamental building blocks for constructing complex synthetic gene networks are effective biological parts with wide dynamic range, low crosstalk, and modularity. RNA-based components are promising sources of such parts since they can provide regulation at the level of transcription and translation and their predictable base pairing properties enable large libraries to be generated through in silico design. This dissertation studies two different approaches for initiating interactions between RNA molecules to implement RNA-based components that achieve translational regulation. First, single-stranded domains known as toeholds were employed for detection of the highly prevalent foodborne pathogen norovirus. Toehold switch riboregulators activated by trigger RNAs from the norovirus RNA genome are designed, validated, and coupled with paper-based cell-free transcription-translation systems. Integration of paper-based reactions with synbody enrichment and isothermal RNA amplification enables as few as 160 copies/mL of norovirus from clinical samples to be detected in reactions that do not require sophisticated equipment and can be read directly by eye. Second, a new type of riboregulator that initiates RNA-RNA interactions through the loop portions of RNA stem-loop structures was developed. These loop-initiated RNA activators (LIRAs) provide multiple advantages compared to toehold-based riboregulators, exhibiting ultralow signal leakage in vivo, lacking any trigger RNA sequence constraints, and appending no additional residues to the output protein. Harnessing LIRAs as modular parts, logic gates that exploit loop-mediated control of mRNA folding state to implement AND and OR operations with up to three sequence-independent input RNAs were constructed. LIRA circuits can also be ported to paper-based cell-free reactions to implement portable systems with molecular computing and sensing capabilities. LIRAs can detect RNAs from a variety of different pathogens, such as HIV, Zika, dengue, yellow fever, and norovirus, and after coupling to isothermal amplification reactions, provide visible test results down to concentrations of 20 aM (12 RNA copies/µL). And the logic functionality of LIRA circuits can be used to specifically identify different HIV strains and influenza A subtypes. These findings demonstrate that toehold- and loop-mediated RNA-RNA interactions are both powerful strategies for implementing RNA-based computing systems for intracellular and diagnostic applications.
ContributorsMA, DUO (Author) / Green, Alexander (Thesis advisor) / Mangone, Marco (Committee member) / Liu, Yan (Committee member) / Arizona State University (Publisher)
Created2019
Description
Serial femtosecond crystallography (SFX) uses diffraction patterns from crystals delivered in a serial fashion to an X-Ray Free Electron Laser (XFEL) for structure determination. Typically, each diffraction pattern is a snapshot from a different crystal. SFX limits the effect of radiation damage and enables the use of nano/micro crystals for structure determination. However, analysis of SFX data is challenging since each snapshot is processed individually.
Many photosystem II (PSII) dataset have been collected at XFELs, several of which are time-resolved (containing both dark and laser illuminated frames). Comparison of light and dark datasets requires understanding systematic errors that can be introduced during data analysis. This dissertation describes data analysis of PSII datasets with a focus on the effect of parameters on later results. The influence of the subset of data used in the analysis is also examined and several criteria are screened for their utility in creating better subsets of data. Subsets are compared with Bragg data analysis and continuous diffuse scattering data analysis.
A new tool, DatView aids in the creation of subsets and visualization of statistics. DatView was developed to improve the loading speed to visualize statistics of large SFX datasets and simplify the creation of subsets based on the statistics. It combines the functionality of several existing visualization tools into a single interface, improving the exploratory power of the tool. In addition, it has comparison features that allow a pattern-by-pattern analysis of the effect of processing parameters. \emph{DatView} improves the efficiency of SFX data analysis by reducing loading time and providing novel visualization tools.
Many photosystem II (PSII) dataset have been collected at XFELs, several of which are time-resolved (containing both dark and laser illuminated frames). Comparison of light and dark datasets requires understanding systematic errors that can be introduced during data analysis. This dissertation describes data analysis of PSII datasets with a focus on the effect of parameters on later results. The influence of the subset of data used in the analysis is also examined and several criteria are screened for their utility in creating better subsets of data. Subsets are compared with Bragg data analysis and continuous diffuse scattering data analysis.
A new tool, DatView aids in the creation of subsets and visualization of statistics. DatView was developed to improve the loading speed to visualize statistics of large SFX datasets and simplify the creation of subsets based on the statistics. It combines the functionality of several existing visualization tools into a single interface, improving the exploratory power of the tool. In addition, it has comparison features that allow a pattern-by-pattern analysis of the effect of processing parameters. \emph{DatView} improves the efficiency of SFX data analysis by reducing loading time and providing novel visualization tools.
ContributorsStander, Natasha (Author) / Fromme, Petra (Thesis advisor) / Zatsepin, Nadia (Thesis advisor) / Kirian, Richard (Committee member) / Liu, Wei (Committee member) / Arizona State University (Publisher)
Created2019
Description
This work aims to characterize protein-nanoparticle interactions through the application of experimental techniques to aid in controlled nanoparticle production for various applications from manufacturing through medical to defense. It includes multiple steps to obtain purified and characterized protein and then the production of nanoparticles using the protein. This application of protein requires extremely pure homogenous solution of the protein that was achieved using numerous protein separation techniques which were experimented with. Crystallization conditions, protein separation methods and protein characterization methods were all investigated along with the protein-nanoparticle interaction studies. The main protein of study here is GroEL and the inorganic nanoparticle used is platinum. Some studies on MBP producing gold nanoparticles from an ionic gold precursor were also conducted to get a better perspective on nanoparticle formation. Protein purification methods, crystallization conditions, Car-9 tag testing and protein characterization methods were all investigated along with the focus of this work. It was concluded that more Car9 studies need to be carried out before being used as in the form of a loop in the protein. The nanoparticle experiments were successful and platinum nanoparticles were successfully synthesized using GroEL. The direction of further research in protein-nanoparticle studies are outlined towards the end of the thesis.
ContributorsSirajudeen, Luqmanal Hakim (Author) / Nannenga, Brent L. (Thesis advisor) / Acharya, Abhinav P (Committee member) / Mills, Jeremy H (Committee member) / Arizona State University (Publisher)
Created2019
Description
This dissertation aimed to evaluate the effectiveness and drawbacks of promising fall prevention strategies in individuals with stroke by rigorously analyzing the biomechanics of laboratory falls and compensatory movements required to prevent a fall. Ankle-foot-orthoses (AFOs) and functional electrical stimulators (FESs) are commonly prescribed to treat foot drop. Despite well-established positive impacts of AFOs and FES devices on balance and gait, AFO and FES users fall at a high rate. In chapter 2 (as a preliminary study), solely mechanical impacts of a semi-rigid AFO on the compensatory stepping response of young healthy individuals following trip-like treadmill perturbations were evaluated. It was found that a semi-rigid AFO on the stepping leg diminished the propulsive impulse of the compensatory step which led to decreased trunk movement control, shorter step length, and reduced center of mass (COM) stability. These results highlight the critical role of plantarflexors in generating an effective compensatory stepping response. In chapter 3, the underlying biomechanical mechanisms leading to high fall risk in long-term AFO and FES users with chronic stroke were studied. It was found that AFO and FES users fall more than Non-users because they have a more impaired lower limb that is not fully addressed by AFO/FES, therefore leading to a more impaired compensatory stepping response characterized by increased inability to generate a compensatory step with paretic leg and decreased trunk movement control. An ideal future AFO that provides dorsiflexion assistance during the swing phase and plantarflexion assistance during the push-off phase of gait is suggested to enhance the compensatory stepping response and reduce more falls. In chapter 4, the effects of a single-session trip-specific training on the compensatory stepping response of individuals with stroke were evaluated. Trunk movement control was improved after a single session of training suggesting that this type of training is a viable option to enhance compensatory stepping response and reduce falls in individuals with stroke. Finally, a future powered AFO with plantarflexion assistance complemented by a trip-specific training program is suggested to enhance the compensatory stepping response and decrease falls in individuals with stroke.
ContributorsNevisipour, Masood (Author) / Honeycutt, Claire (Thesis advisor) / Sugar, Thomas (Thesis advisor) / Artemiadis, Panagiotis (Committee member) / Abbas, James (Committee member) / Lee, Hyunglae (Committee member) / Arizona State University (Publisher)
Created2019