Matching Items (28)
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Description
Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques.

The XFEL is characterized by high

Scientists have used X-rays to study biological molecules for nearly a century. Now with the X-ray free electron laser (XFEL), new methods have been developed to advance structural biology. These new methods include serial femtosecond crystallography, single particle imaging, solution scattering, and time resolved techniques.

The XFEL is characterized by high intensity pulses, which are only about 50 femtoseconds in duration. The intensity allows for scattering from microscopic particles, while the short pulses offer a way to outrun radiation damage. XFELs are powerful enough to obliterate most samples in a single pulse. While this allows for a “diffract and destroy” methodology, it also requires instrumentation that can position microscopic particles into the X-ray beam (which may also be microscopic), continuously renew the sample after each pulse, and maintain sample viability during data collection.

Typically these experiments have used liquid microjets to continuously renew sample. The high flow rate associated with liquid microjets requires large amounts of sample, most of which runs to waste between pulses. An injector designed to stream a viscous gel-like material called lipidic cubic phase (LCP) was developed to address this problem. LCP, commonly used as a growth medium for membrane protein crystals, lends itself to low flow rate jetting and so reduces the amount of sample wasted significantly.

This work discusses sample delivery and injection for XFEL experiments. It reviews the liquid microjet method extensively, and presents the LCP injector as a novel device for serial crystallography, including detailed protocols for the LCP injector and anti-settler operation.
ContributorsJames, Daniel (Author) / Spence, John (Thesis advisor) / Weierstall, Uwe (Committee member) / Kirian, Richard (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2015
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Description
From 2D planar MOSFET to 3D FinFET, the geometry of semiconductor devices is getting more and more complex. Correspondingly, the number of mesh grid points increases largely to maintain the accuracy of carrier transport and heat transfer simulations. By substituting the conventional uniform mesh with non-uniform mesh, one can reduce

From 2D planar MOSFET to 3D FinFET, the geometry of semiconductor devices is getting more and more complex. Correspondingly, the number of mesh grid points increases largely to maintain the accuracy of carrier transport and heat transfer simulations. By substituting the conventional uniform mesh with non-uniform mesh, one can reduce the number of grid points. However, the problem of how to solve governing equations on non-uniform mesh is then imposed to the numerical solver. Moreover, if a device simulator is integrated into a multi-scale simulator, the problem size will be further increased. Consequently, there exist two challenges for the current numerical solver. One is to increase the functionality to accommodate non-uniform mesh. The other is to solve governing physical equations fast and accurately on a large number of mesh grid points.

This research rst discusses a 2D planar MOSFET simulator and its numerical solver, pointing out its performance limit. By analyzing the algorithm complexity, Multigrid method is proposed to replace conventional Successive-Over-Relaxation method in a numerical solver. A variety of Multigrid methods (standard Multigrid, Algebraic Multigrid, Full Approximation Scheme, and Full Multigrid) are discussed and implemented. Their properties are examined through a set of numerical experiments. Finally, Algebraic Multigrid, Full Approximation Scheme and Full Multigrid are integrated into one advanced numerical solver based on the exact requirements of a semiconductor device simulator. A 2D MOSFET device is used to benchmark the performance, showing that the advanced Multigrid method has higher speed, accuracy and robustness.
ContributorsGuo, Xinchen (Author) / Vasileska, Dragica (Thesis advisor) / Goodnick, Stephen (Committee member) / Ferry, David (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically

Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically gated can be developed. This thesis demonstrates three examples of the unique electromechanical properties of single molecules.

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.
ContributorsBruot, Christopher, 1986- (Author) / Tao, Nongjian (Thesis advisor) / Lindsay, Stuart (Committee member) / Mujica, Vladimiro (Committee member) / Ferry, David (Committee member) / Arizona State University (Publisher)
Created2014
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Description
Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing the phase information. The measurement of amplitude alone is insufficient to solve the structure. Therefore, phase retrieval is essential to

Phase problem has been long-standing in x-ray diffractive imaging. It is originated from the fact that only the amplitude of the scattered wave can be recorded by the detector, losing the phase information. The measurement of amplitude alone is insufficient to solve the structure. Therefore, phase retrieval is essential to structure determination with X-ray diffractive imaging. So far, many experimental as well as algorithmic approaches have been developed to address the phase problem. The experimental phasing methods, such as MAD, SAD etc, exploit the phase relation in vector space. They usually demand a lot of efforts to prepare the samples and require much more data. On the other hand, iterative phasing algorithms make use of the prior knowledge and various constraints in real and reciprocal space. In this thesis, new approaches to the problem of direct digital phasing of X-ray diffraction patterns from two-dimensional organic crystals were presented. The phase problem for Bragg diffraction from two-dimensional (2D) crystalline monolayer in transmission may be solved by imposing a compact support that sets the density to zero outside the monolayer. By iterating between the measured stucture factor magnitudes along reciprocal space rods (starting with random phases) and a density of the correct sign, the complex scattered amplitudes may be found (J. Struct Biol 144, 209 (2003)). However this one-dimensional support function fails to link the rod phases correctly unless a low-resolution real-space map is also available. Minimum prior information required for successful three-dimensional (3D) structure retrieval from a 2D crystal XFEL diffraction dataset were investigated, when using the HIO algorithm. This method provides an alternative way to phase 2D crystal dataset, with less dependence on the high quality model used in the molecular replacement method.
ContributorsZhao, Yun (Author) / Spence, John C.H. (Thesis advisor) / Schmidt, Kevin (Committee member) / Weierstall, Uwe (Committee member) / Kirian, Richard (Committee member) / Zatsepin, Nadia (Committee member) / Arizona State University (Publisher)
Created2016
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Description
CMOS Technology has been scaled down to 7 nm with FinFET replacing planar MOSFET devices. Due to short channel effects, the FinFET structure was developed to provide better electrostatic control on subthreshold leakage and saturation current over planar MOSFETs while having the desired current drive. The FinFET structure has an

CMOS Technology has been scaled down to 7 nm with FinFET replacing planar MOSFET devices. Due to short channel effects, the FinFET structure was developed to provide better electrostatic control on subthreshold leakage and saturation current over planar MOSFETs while having the desired current drive. The FinFET structure has an undoped or fully depleted fin, which supports immunity from random dopant fluctuations (RDF – a phenomenon which causes a reduction in the threshold voltage and is prominent at sub 50 nm tech nodes due to lesser dopant atoms) and thus causes threshold voltage (Vth) roll-off by reducing the Vth. However, as the advanced CMOS technologies are shrinking down to a 5 nm technology node, subthreshold leakage and drain-induced-barrier-lowering (DIBL) are driving the introduction of new metal-oxide-semiconductor field-effect transistor (MOSFET) structures to improve performance. GAA field effect transistors are shown to be the potential candidates for these advanced nodes. In nanowire devices, due to the presence of the gate on all sides of the channel, DIBL should be lower compared to the FinFETs.

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.
ContributorsRana, Parshant (Author) / Clark, Lawrence (Thesis advisor) / Ferry, David (Committee member) / Brunhaver, John (Committee member) / Arizona State University (Publisher)
Created2017
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Description
Scaling of the Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET) towards shorter channel lengths, has lead to an increasing importance of quantum effects on the device performance. Until now, a semi-classical model based on Monte Carlo method for instance, has been sufficient to address these issues in silicon, and arrive at a

Scaling of the Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET) towards shorter channel lengths, has lead to an increasing importance of quantum effects on the device performance. Until now, a semi-classical model based on Monte Carlo method for instance, has been sufficient to address these issues in silicon, and arrive at a reasonably good fit to experimental mobility data. But as the semiconductor world moves towards 10nm technology, many of the basic assumptions in this method, namely the very fundamental Fermi’s golden rule come into question. The derivation of the Fermi’s golden rule assumes that the scattering is infrequent (therefore the long time limit) and the collision duration time is zero. This thesis overcomes some of the limitations of the above approach by successfully developing a quantum mechanical simulator that can model the low-field inversion layer mobility in silicon MOS capacitors and other inversion layers as well. It solves for the scattering induced collisional broadening of the states by accounting for the various scattering mechanisms present in silicon through the non-equilibrium based near-equilibrium Green’s Functions approach, which shall be referred to as near-equilibrium Green’s Function (nEGF) in this work. It adopts a two-loop approach, where the outer loop solves for the self-consistency between the potential and the subband sheet charge density by solving the Poisson and the Schrödinger equations self-consistently. The inner loop solves for the nEGF (renormalization of the spectrum and the broadening of the states), self-consistently using the self-consistent Born approximation, which is then used to compute the mobility using the Green-Kubo Formalism.
ContributorsJayaram Thulasingam, Gokula Kannan (Author) / Vasileska, Dragica (Thesis advisor) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Allee, David (Committee member) / Arizona State University (Publisher)
Created2017
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Description
This dissertation explores thermal effects and electrical characteristics in metal-oxide-semiconductor field effect transistor (MOSFET) devices and circuits using a multiscale dual-carrier approach. Simulating electron and hole transport with carrier-phonon interactions for thermal transport allows for the study of complementary logic circuits with device level accuracy in electrical characteristics and thermal

This dissertation explores thermal effects and electrical characteristics in metal-oxide-semiconductor field effect transistor (MOSFET) devices and circuits using a multiscale dual-carrier approach. Simulating electron and hole transport with carrier-phonon interactions for thermal transport allows for the study of complementary logic circuits with device level accuracy in electrical characteristics and thermal effects. The electrical model is comprised of an ensemble Monte Carlo solution to the Boltzmann Transport Equation coupled with an iterative solution to two-dimensional (2D) Poisson’s equation. The thermal model solves the energy balance equations accounting for carrier-phonon and phonon-phonon interactions. Modeling of circuit behavior uses parametric iteration to ensure current and voltage continuity. This allows for modeling of device behavior, analyzing circuit performance, and understanding thermal effects.

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.
ContributorsDaugherty, Robin (Author) / Vasileska, Dragica (Thesis advisor) / Aberle, James T., 1961- (Committee member) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2019
Description

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth’s oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the ‘dangler’ Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

ContributorsKupitz, Christopher (Author) / Basu, Shibom (Author) / Grotjohann, Ingo (Author) / Fromme, Raimund (Author) / Zatsepin, Nadia (Author) / Rendek, Kimberly (Author) / Hunter, Mark (Author) / Shoeman, Robert L. (Author) / White, Thomas A. (Author) / Wang, Dingjie (Author) / James, Daniel (Author) / Yang, Jay-How (Author) / Cobb, Danielle (Author) / Reeder, Brenda (Author) / Sierra, Raymond G. (Author) / Liu, Haiguang (Author) / Barty, Anton (Author) / Aquila, Andrew L. (Author) / Deponte, Daniel (Author) / Kirian, Richard (Author) / Bari, Sadia (Author) / Bergkamp, Jesse (Author) / Beyerlein, Kenneth R. (Author) / Bogan, Michael J. (Author) / Caleman, Carl (Author) / Chao, Tzu-Chiao (Author) / Conrad, Chelsie (Author) / Davis, Katherine M. (Author) / Department of Chemistry and Biochemistry (Contributor)
Created2014-09-11
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Description
Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A[subscript 2A] adenosine receptor (A[subscript 2A]AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A[subscript 2A]AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A[subscript 2A]AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. These developments will enable structure determination from smaller and/or weakly diffracting microcrystals.
ContributorsMartin Garcia, Jose Manuel (Author) / Conrad, Chelsie (Author) / Nelson, Garrett (Author) / Stander, Natasha (Author) / Zatsepin, Nadia (Author) / Zook, James (Author) / Zhu, Lan (Author) / Geiger, James (Author) / Chun, Eugene (Author) / Kissick, David (Author) / Hilgart, Mark C. (Author) / Ogata, Craig (Author) / Ishchenko, Andrii (Author) / Nagaratnam, Nirupa (Author) / Roy Chowdhury, Shatabdi (Author) / Coe, Jesse (Author) / Subramanian, Ganesh (Author) / Schaffer, Alexander (Author) / James, Daniel (Author) / Ketwala, Gihan (Author) / Venugopalan, Nagarajan (Author) / Xu, Shenglan (Author) / Corcoran, Stephen (Author) / Ferguson, Dale (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Cherezov, Vadim (Author) / Fromme, Petra (Author) / Fischetti, Robert F. (Author) / Liu, Wei (Author) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / Department of Physics (Contributor)
Created2017-05-24
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Description
CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli. The first variant contained a flexible GPGP linker between CTB and MPR, and yielded crystals that diffracted to a resolution of 2.3 Å, but only the CTB region was detected in the electron-density map. A second variant, in which the CTB was directly attached to MPR, was shown to destabilize pentamer formation. A third construct containing a polyalanine linker between CTB and MPR proved to stabilize the pentameric form of the protein during purification. The purification procedure was shown to produce a homogeneously pure and monodisperse sample for crystallization. Initial crystallization experiments led to pseudo-crystals which were ordered in only two dimensions and were disordered in the third dimension. Nanocrystals obtained using the same precipitant showed promising X-ray diffraction to 5 Å resolution in femtosecond nanocrystallography experiments at the Linac Coherent Light Source at the SLAC National Accelerator Laboratory. The results demonstrate the utility of femtosecond X-ray crystallography to enable structural analysis based on nano/microcrystals of a protein for which no macroscopic crystals ordered in three dimensions have been observed before.
ContributorsLee, Ho-Hsien (Author) / Cherni, Irene (Author) / Yu, HongQi (Author) / Fromme, Raimund (Author) / Doran, Jeffrey (Author) / Grotjohann, Ingo (Author) / Mittman, Michele (Author) / Basu, Shibom (Author) / Deb, Arpan (Author) / Dorner, Katerina (Author) / Aquila, Andrew (Author) / Barty, Anton (Author) / Boutet, Sebastien (Author) / Chapman, Henry N. (Author) / Doak, R. Bruce (Author) / Hunter, Mark (Author) / James, Daniel (Author) / Kirian, Richard (Author) / Kupitz, Christopher (Author) / Lawrence, Robert (Author) / Liu, Haiguang (Author) / Nass, Karol (Author) / Schlichting, Ilme (Author) / Schmidt, Kevin (Author) / Seibert, M. Marvin (Author) / Shoeman, Robert L. (Author) / Spence, John (Author) / Stellato, Francesco (Author) / Weierstall, Uwe (Author) / Williams, Garth J. (Author) / Yoon, Chun Hong (Author) / Wang, Dingjie (Author) / Zatsepin, Nadia (Author) / Hogue, Brenda (Author) / Matoba, Nobuyuki (Author) / Fromme, Petra (Author) / Mor, Tsafrir (Author) / ASU Biodesign Center Immunotherapy, Vaccines and Virotherapy (Contributor) / Department of Chemistry and Biochemistry (Contributor) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / Biodesign Institute (Contributor) / Infectious Diseases and Vaccinology (Contributor) / Department of Physics (Contributor)
Created2014-08-20