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First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance.
Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence.
Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking are found to be more responsive to modulation than purine-pyrimidine sequences. This sensitivity is attributed to the perturbation of &pi-&pi stacking interactions and resulting effects on the activation energy and electronic coupling for the end base pairs.
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(XFEL) allows it to outrun radiation damage in coherent diffractive imaging since elastic scattering terminates before photoelectron cascades commences. This “diffract-before-destroy” feature of XFEL opened up new opportunities for biological macromolecule imaging and structure studies by breaking the limit to spatial resolution imposed by the maximum dose that is allowed before radiation damage. However, data collection in serial femto-second crystallography (SFX) using XFEL is affected by a bunch of stochastic factors, which pose great challenges to the data analysis in SFX. These stochastic factors include crystal size, shape, random orientation, X-ray photon flux, position and energy spectrum. Monte-Carlo integration proves effective and successful in extracting the structure factors by merging all diffraction patterns given that the data set is sufficiently large to average out all stochastic factors. However, this approach typically requires hundreds of thousands of patterns collected from experiments. This dissertation explores both experimental and algorithmic methods to eliminate or reduce the effect of stochastic factors in data acquisition and analysis. Coherent convergent X-ray beam diffraction (CCB) is discussed for possibilities of obtaining single-shot angular-integrated rocking curves. It is also shown the interference between Bragg disks helps ab-initio phasing. Two-color diffraction scheme is proposed for time-resolved studies and general data collection strategies are discussed based on error metrics. A new auto-indexing algorithm for sparse patterns is developed and demonstrated for both simulated and experimental data. Statistics show that indexing rate is increased by 3 times for I3C data set collected from beam time LJ69 at Linac coherent light source (LCLS). Finally, dynamical inversion from electron diffraction is explored as an alternative approach for structure determination.
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It starts with establishing the limitations of traditional electron diffraction coupled with molecular replacement to study biomolecular structure and proceeds to suggest a pulsed electron source Hollow-Cone Transmission Electron Microscope as an alternative scheme to pursue ultrafast biomolecular imaging. In frequency domain, the use of Electron Energy Loss Spectroscopy as a tool to access ultrafast nuclear dynamics in the steady state, is detailed with the new monochromated NiON UltraSTEM and examples demonstrating this instrument’s capability are provided.
Ultrafast X-ray spectroscopy as a tool to elucidate biomolecular dynamics is presented in studying X-ray as a probe, with the study of the photolysis of Methylcobalamin using time-resolved laser pump – X-ray probe absorption spectroscopy. The analysis in comparison to prior literature as well as DFT based XAS simulations offer good agreement and understanding to the steady state spectra but are so far inadequate in explaining the time-resolved data. However, the trends in the absorption simulations for the transient intermediates show a strong anisotropic dependence on the axial ligation, which would define the direction for future studies on this material to achieve a solution.
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A 3-D technology computer aided design (TCAD) device simulation is done to compare the performance of FinFET and GAA nanowire structures with vertically stacked horizontal nanowires. Subthreshold slope, DIBL & saturation current are measured and compared between these devices. The FinFET’s device performance has been matched with the ASAP7 compact model with the impact of tensile and compressive strain on NMOS & PMOS respectively. Metal work function is adjusted for the desired current drive. The nanowires have shown better electrostatic performance over FinFETs with excellent improvement in DIBL and subthreshold slope. This proves that horizontal nanowires can be the potential candidate for 5 nm technology node. A GAA nanowire structure for 5 nm tech node is characterized with a gate length of 15 nm. The structure is scaled down from 7 nm node to 5 nm by using a scaling factor of 0.7.
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The coupled electro-thermal approach, initially developed for individual n-channel MOSFET (NMOS) devices, now allows multiple devices in tandem providing a platform for better comparison with heater-sensor experiments. The latest electro-thermal solver allows simulation of multiple NMOS and p-channel MOSFET (PMOS) devices, providing a platform for the study of complementary MOSFET (CMOS) circuit behavior. Modeling PMOS devices necessitates the inclusion of hole transport and hole-phonon interactions. The analysis of CMOS circuits uses the electro-thermal device simulation methodology alongside parametric iteration to ensure current continuity. Simulating a CMOS inverter and analyzing the extracted voltage transfer characteristics verifies the efficacy of this methodology. This work demonstrates the effectiveness of the dual-carrier electro-thermal solver in simulating thermal effects in CMOS circuits.
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This study explores the capabilities of the Coherent X-ray Imaging Instrument at the Linac Coherent Light Source to image small biological samples. The weak signal from small samples puts a significant demand on the experiment. Aerosolized Omono River virus particles of ∼40 nm in diameter were injected into the submicrometre X-ray focus at a reduced pressure. Diffraction patterns were recorded on two area detectors. The statistical nature of the measurements from many individual particles provided information about the intensity profile of the X-ray beam, phase variations in the wavefront and the size distribution of the injected particles. The results point to a wider than expected size distribution (from ∼35 to ∼300 nm in diameter). This is likely to be owing to nonvolatile contaminants from larger droplets during aerosolization and droplet evaporation. The results suggest that the concentration of nonvolatile contaminants and the ratio between the volumes of the initial droplet and the sample particles is critical in such studies. The maximum beam intensity in the focus was found to be 1.9 × 1012 photons per µm2 per pulse. The full-width of the focus at half-maximum was estimated to be 500 nm (assuming 20% beamline transmission), and this width is larger than expected. Under these conditions, the diffraction signal from a sample-sized particle remained above the average background to a resolution of 4.25 nm. The results suggest that reducing the size of the initial droplets during aerosolization is necessary to bring small particles into the scope of detailed structural studies with X-ray lasers.
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