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<p dir="ltr">In life sciences, the determination of macromolecular structures and their functions, particularly proteins and protein complexes, is of paramount importance, as these molecules play critical roles within cells. The specific physical interactions of macromolecules govern molecular and cellular functions, making the 3D structure elucidation of these entities essential for comprehending the mechanisms underlying life processes, diseases, and drug discovery. Cryo-electron microscopy (cryo-EM) has emerged as a promising experimental technique for obtaining 3D macromolecular structures. In the course of my research, I proposed CryoREAD, an innovative AI-based method for <i>de nov</i>o DNA/RNA structure modeling. This novel approach represents the first fully automated solution for DNA/RNA structure modeling from cryo-EM maps at near-atomic resolution. However, as the resolution decreases, structure modeling becomes significantly more challenging. To address this challenge, I introduced Emap2sec+, a 3D deep convolutional neural network designed to identify protein secondary structures, RNA, and DNA information from cryo-EM maps at intermediate resolutions ranging from 5-10 Å. Additionally, I presented Alpha-EM-Multimer, a groundbreaking method for automatically building full protein complexes from cryo-EM maps at intermediate resolution. Alpha-EM-Multimer employs a diffusion model to trace the protein backbone and subsequently fits the AlphaFold predicted single-chain structure to construct the complete protein complex. Notably, this method stands as the first to enable the modeling of protein complexes with more than 10,000 residues for cryo-EM maps at intermediate resolution, achieving an average TM-Score of predicted protein complexes above 0.8, which closely approximates the native structure. Furthermore, I addressed the recognition of local structural errors in predicted and experimental protein structures by proposing DAQ, an evaluation approach for experimental protein structure quality that utilizes detection probabilities derived from cryo-EM maps via a pretrained multi-task neural network. In the pursuit of evaluating protein complexes generated through computational methods, I developed GNN-DOVE and DOVE, leveraging convolutional neural networks and graph neural networks to assess the accuracy of predicted protein complex structures. These advancements in cryo-EM-based structural modeling and evaluation methodologies hold significant promise for advancing our understanding of complex macromolecular systems and their biological implications.</p>

<p>  </p> <p>The investigation of laser-matter interactions has gained interest over the years due to the importance of these interactions in materials synthesis, diagnostics, electronics, and photonics. In-situ transmission electron microscopy (TEM) techniques are invaluable for real-time monitoring of dynamic processes in these systems at the nanoscale. In this work, the effect of pulsed laser heating on the reactions of energetic materials, plasmonic structures, and multilayer thin films has been studied by utilizing ultrafast transmission electron microscopy (UTEM) techniques. Heat transfer and electric field calculations have been carried out to compare and support the experimental findings. </p> <p>The photothermal reaction of an aluminum-fluoropolymer composite is studied to show the effect of pulsed laser heating on reactions of reactive materials. An aluminum nanoparticle - THV (terpolymer of tetrafluoroethylene, hexafluoropropylene, and vinylidene fluoride) sample is subjected to rapid heating and cooling cycles by employing the integrated laser system of an UTEM. TEM images and real-time movies (30 frame/s) are acquired to reveal the changes during the reaction. Heat transfer simulations proved that the temperature of the sample was high enough to trigger the decomposition of THV and start its reaction with Al nanoparticles. Electron diffraction patterns revealed that the reaction product was the rare and metastable η-phase aluminum fluoride (AlF3). The experimental and theoretical results showed that rapid pulsed laser heating and subsequent cooling of a nanoscale sample influences the phases that can form and be utilized to investigate other systems.</p> <p>Pulsed laser-assisted merging and alloying of noble metals are also studied to explore the fabrication of beaded gold-silver nanowires with a variety of morphology and composition. In-situ laser heating of plasmonic silver nanowire (Ag NW) - gold nanoparticle (Au NP) couples are performed inside an UTEM, and direct visualization of the evolution process gives insights into the formation mechanism. Experimental results show that silver melts at the surface to bridge the nanometer-sized gap between the NP and the NW, forming a cup-like morphology underneath the Au NP via capillary action. Progressive laser irradiation leads to wetting of the Au NP and the formation of a valley in the Ag NW around the NP, which flattens gradually by partial embedding of the NP. Inter-diffusion of Au into Ag and vice versa sets in at this stage, leading to depletion of Au from the Au-rich NP region. Prolonged irradiation and heating lead to gradual inter-mixing of Au-Ag, forming a beaded Au-doped Ag nanowire with homogeneous composition. Such a step-by-step understanding of the merging and alloying process has implications in nanowelding, which holds a future in designing efficient, transparent conductors and printed electronics. Numerical simulations are performed to calculate the electromagnetic enhancement at the interface of adjacent NPs and NWs and provide information on heat generation rates in NP-NW couples at the early stages of the nanowelding process. </p> <p>In the third chapter, laser-induced irreversible dynamics in electron beam sensitive organic energetic crystals and ultrathin multilayer films are studied by single-shot UTEM imaging. After various sample preparation methods are developed and compared for the well-controlled synthesis of nanoscale ammonium perchlorate samples on TEM grids, decomposition dynamics of ammonium perchlorate crystals are captured via single-shot imaging. The experimental data showed that the sublimation and decomposition are visible ~30 ns after the sample excitation laser in crystals smaller than 5 µm. Dependency of decomposition to crystal porosity and thickness is also observed with crack formation in some cases. In the following section, pulsed-laser irradiation is utilized to realize deformation in thin multilayer films under high temperatures, and triggered dynamic processes are investigated through single-shot imaging. Laser-assisted periodic wrinkle formation is demonstrated on SiN membranes coated with Ti/Ni bilayers. The resulting structures showed periodic wrinkling of the SiN membrane and corrugated surface formation on both sides of the film. Overall, the dissertation highlights the potential of ultrafast transmission electron microscopy in discovering fundamental processes related to, but not limited to, reactive materials, plasmonic nanomaterials, and ultrathin multilayer films. </p>

<p>Research in the area of improving the efficiency and manufacturability of alternative energy technologies has been of high interest due to the growing environmental concerns of energy resources. Group III-antimonide-based compound semiconductors have been sought after as excellent candidates for photovoltaic conversion of infrared radiation, outside the spectral range absorbed by the currently available crystalline Si solar cells. The major challenge is the GaSb/Si interface is highly lattice mismatched, and inherently heterovalent. This leads to a high density of structural defects, many of which have not been investigated fully. Both optical and electrical properties of such heteroepitaxy thin films are strongly dependent on the periodicity of the crystal lattice, and the presence of extended defects cause perturbations in the lattice periodicity. Therefore the nature of such extended defects must be understood, in order to better manipulate the growth process to minimize their presence. This thesis demonstrates that through the use of conventional transmission electron microscopy, further insight can be gained into understanding the origin, distribution, propagation, and interaction of various extended defects. From this, a couple of ways to systematically suppress some of the defects have also been implemented, and the mechanism by which they induce such a suppression is also discussed.</p> / Master of Applied Science (MASc)

<p>InP nanowires with short InAs segments were grown on InP (111)B substrates by Au assisted vapour-liquid-solid growth in a gas source molecular beam epitaxy system. Nanowire crystal structure and morphology were investigated by transmission electron microscopy as a function of temperature, growth rate, and V/III flux ratio. At 370C predominantly kinked nanowires with random morphology and low areal density were observed with a rough parasitic 2D film. At 440C, nanowire density was also reduced but the 2D film growth was smoother and nanowires grew straight without kinking. An optimum temperature of 400C maximized areal density with uniform nanowire morphology. At the optimum temperature of 400C, an increase in V/III flux ratio changed the nanowire morphology from rod-shaped to pencil like indicating increased radial growth. Growth rate did not affect the crystal structure of InP nanowires. For InAs nanowires, changing the growth rate from 1 to 0.5 μm/hr reduced the presence of stacking faults to as low as one per nanowire. Short InAs segments in InP nanowires were found to grow through two mechanisms for nanowires of length L and diameter D. The first mechanism described the supply of In to the growth front via purging of In from the Au droplet where L was proportional to D. The second mechanism involved direct deposition of adatoms on the nanowire sidewall and subsequent diffusion to the growth front where L was proportional to 1/D. For intermediate growth durations, a transition between these two mechanisms was observed. For InP and InAs nanowires, the growth mode was varied from axial to radial through the inclusion of Al to form a core shell structure. Al_xIn_1-xAs(P) shells were grown on InAs cores with Al alloy fractions between 0.53 and 0.2. These nanowires were examined by transmission electron microscopy and it was found, for all values of x in InAs-Al_xIn_1-xP structures, that relaxation had occurred through the introduction of dislocations. For InAs-Al_xIn_1-xAs structures, all values except x=0.2 had relaxed through dislocation formation. A critical thickness model was developed to determine the core-shell coherency limits which confirmed the experimental observation of strain relaxation. The effects of passivation on the electronic transport and the optical properties were examined as a function of structural core-shell passivation and chemical passivation. The mechanisms for the observed improvement in mobility for core-shell versus bare InAs nanowires was due to the reduction in ionized impurity scattering from surface states. Similarly an increase in photoluminescence intensity after ammonium sulfide passivation was explained by the reduction of donor type surface states.</p> / Doctor of Philosophy (PhD)

<p>Heteroepitaxial films of group III-antimonide-based semiconductor compounds on Si are amongst the most appealing candidates for solar applications because of the well-established Si platform and also for offering band-gap energies beyond the silicon road map. Nonetheless, high lattice mismatch between GaSb and Si as well as ambiguous nucleation of GaSb on Si are major drawbacks in manufacturing of heteroepitaxial GaSb/Si films because they can generate various defects in films. Atomic-level detection of these defects and delving into their origin, orientation, distribution, propagation, and interaction with each other will therefore provide an insight into inhibiting their formation or reducing their severity. State-of-the-art aberration-corrected transmission electron microscopes have marked a new era in the investigation of interfaces and defects. With sub-angstrom electron probes in scanning transmission electron microscopes, it is possible to pinpoint the individual atomic columns at interfaces and defects.</p> <p>In this thesis, GaSb epilayers grown with molecular beam epitaxy on Si substrates were studied through aberration-corrected scanning transmission electron microscopy. The strain-relief mechanism of the epitaxial GaSb through formation of interfacial misfit dislocations was investigated and the strain distribution in the vicinity of dislocation cores as well as epitaxial layer was analyzed. The specific atomic-number dependent contrast mechanism of the high-angle annular dark-field technique enabled the unprecedented direct observation of anti-phase boundaries, the extended defects of highest interest in polar-on-nonpolar growths. This observation unraveled the ambiguity of nucleation of GaSb at interface regardless of preferential deposition of atomic species during growth procedure. The growth of GaSb at the initial stage of deposition was further investigated to understand the role of an AlSb buffer layer and growth mechanism of GaSb precisely. This investigation showed that AlSb and GaSb epilayers occur by Volmer-Weber growth mode and AlSb islands provide energetically favorable nucleation sites for GaSb film. Furthermore, taking advantage of atomic-resolution detection capability of high-angle annular dark-field in scanning transmission electron microscopy a novel mechanism of strain relief through multiple twining resulting in a lattice-registered growth of GaSb on Si(211) was elucidated. This contribution demonstrates that aberration-corrected scanning transmission electron microscopy provides profound insight into the polar-on-nonpolar growth which can be exploited to suppress the formation of structural defects.</p> / Doctor of Philosophy (PhD)

The work presented in this thesis centers on the application of atomic-resolution transmission electron microscopy to study Platinum-alloy nanoparticles. In particular, the thesis focusses on the platinum-iron and platinum-gold systems. Additionally, few other complementary structures based on Pt thin films and nanowires are also characterized. These materials are studied in the context of their catalytic application towards the oxygen reduction reaction in polymer electrolyte membrane fuel cells (PEMFCs). Here we report on the detailed investigation of many structural and compositional aspects of these catalyst nanoparticles including lattice strain, the surface and bulk atomic-structure, the surface/bulk chemical composition, surface segregation, and atomic ordering. In some cases we have even looked beyond the traditional characterization approaches. For instance, instead of observing the particle structures before and after a particular treatment (e.g., heating and degradation tests), we have captured the dynamics of structural evolution over the entire course of such treatments. These investigations were useful in interpreting their catalytic performances, which opened new perspectives towards further optimization of their material structure on the atomic-level. / Thesis / Doctor of Philosophy (PhD)

Ternary InGaN and AlGaN alloys have been sought after for the application of various optoelectronic devices spanning a large spectral range between the deep ultraviolet and infrared, including light-emitting diodes, and laser diodes. Their non-ideal alloy mixing, and differences in bond energy and in adatom diffusion are established as the cause for various types of nanoscale compositional inhomogeneity commonly observed in nitride thin films. Growth in a nanowire geometry can overcome the phase separation, surface segregation, and chemical ordering by providing enhanced strain relaxation of the large lattice mismatch at the free surfaces. In this dissertation, the spectral and spatial luminescence distributions of ternary III-N alloy nanowire heterostructures are investigated and correlated to structural and chemical properties with scanning transmission electron microscopy. Quantitative elemental mapping of InGaN/GaN dot-in-a-wire structures using electron energy-loss spectroscopy revealed compositional non-uniformity between successive quantum dots. Local strain mapping of the heterostructure showed a dependence of the incorporation of indium on the magnitude of the out-of-plane compressive strain within the underlying GaN barrier layer. Cathodoluminescence spectroscopy on individual nanowires presented diverse emission properties, nevertheless, the In-content variability could be directly correlated to the broad range of peak emission energies. Atomic-level chemical ordering within the InGaN was then reported, and attributed to the faceted growth surface in nanowires that promotes preferential site incorporation by In-atoms that allows for better strain relaxation. Distinct atomic-scale alloy inhomogeneities were also investigated in AlGaN nanowires, which evidenced spatial localization of carriers taking place at the resulting energy band fluctuations. A high spectral density of narrow emission lines arose from such compositional modulations, whose luminescence behaviours exhibit a dependence on the nature of the compositional fluctuations from which they originate. / Thesis / Doctor of Philosophy (PhD)