Matching Items (41)
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
The Physics and Chemistry of Surfaces and Interfaces conference has maintained a focus on the interfacial and surface properties of materials since its initiation in 1974. The conference continues to be a major force in this field, bringing together scientists from a variety of disciplines to focus upon the science of interfaces and surfaces. Here, a historical view of the development of the conference and a discussion of some of the themes that have been focal points for many years are presented.
ContributorsFerry, David (Author) / Ira A. Fulton Schools of Engineering (Contributor) / School of Electrical, Computer and Energy Engineering (Contributor)
Created2013
Description
X-ray Free Electron Lasers (XFELs) are used for diffractive x-ray imaging of the structure of many biological particles, such as viruses and proteins. The ultimate goal for XFEL-based microscopy is atomic resolution images of non-crystalline particles. However, data collection efficiency as well as the limited amount of measurement time given annually to researchers, such high-resolution images are presently impossible to attain. Here, we consider two potential solutions to the single-particle hit rate problem; the first looks at applying static electric fields to existing aerodynamic particle injectors, and the second looks at the viability of using time-varying electric fields associated with ion traps to create high-density regions of particles. For the static solution, we looked at applying a constant electric potential to the nozzle, as well as applying a high voltage to a ring electrode in close proximity to a grounded nozzle. We considered the breakdown field strength of the helium gas used to determine how closely the ring electrode could be placed without creating an arc that could potentially destroy expensive equipment. Then, we considered the possibility of using electrodynamic ion traps to increase particle densities. We first characterized how charged particles behave in oscillating electric fields using a simple electrode geometry. Using the general results from this, we then constructed a rudimentary ion trap to test if our experiment agreed with the theory. Finally, we conducted a literature review to determine what particle densities other scientists have been able to measure using ion traps. We then compared existing ion traps to what we expect from the nozzle injectors to determine which method may be the better solution.
ContributorsBradshaw, Layne Nicholas (Author) / Kirian, Richard (Thesis director) / Weierstall, Uwe (Committee member) / Department of Physics (Contributor, Contributor) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
A time-dependent semiclassical formalism is developed for the theory of incoherentdiffractive imaging (IDI), an atomically-precise imaging technique based on the principles of
intensity interferometry. The technique is applied to image inner-shell X-ray fluorescence
from heavy atoms excited by the femtosecond pulses of an X-ray free-electron laser (XFEL).
Interference between emission from different atoms is expected when the XFEL pulse duration
is shorter than the fluorescence lifetime. Simulations for atoms at the vertices of a simple
icosahedral virus capsid are used to generate mock IDI diffraction patterns. These are then
used to reconstruct the geometry by phase retrieval of the intensity correlation function between
photons emitted independently from many different atoms at two different detector
pixels. The dependence of the intensity correlation function on fluorescence lifetime relative
to XFEL pulse duration is computed, and a simple expression for the visibility (or contrast)
of IDI speckle as well as an upper bound on the IDI signal-to-noise ratio are obtained as a
function of XFEL flux and lifetime. This indicates that compact XFELs, with reduced flux
but attosecond pulses, should be ideally suited to 3D, atomic-resolution mapping of heavy
atoms in materials science, chemistry, and biology. As IDI is a new technique, not much has
yet been written about it in the literature. The current theoretical and experimental results
are reviewed, including a discussion of signal-to-noise issues that have been raised regarding
the idea that IDI is suitable for structural biology.
ContributorsShevchuk, Andrew Stewart Hegeman (Author) / Kirian, Richard A (Thesis advisor) / Schmidt, Kevin E (Committee member) / Weierstall, Uwe (Committee member) / Graves, William S (Committee member) / Arizona State University (Publisher)
Created2022
Description
Moore's law has been the most important driving force for the tremendous progress of semiconductor industry. With time the transistors which form the fundamental building block of any integrated circuit have been shrinking in size leading to smaller and faster electronic devices.As the devices scale down thermal effects and the short channel effects become the important deciding factors in determining transistor architecture.SOI (Silicon on Insulator) devices have been excellent alternative to planar MOSFET for ultimate CMOS scaling since they mitigate short channel effects. Hence as a part of thesis we tried to study the benefits of the SOI technology especially for lower technology nodes when the channel thickness reduces down to sub 10nm regime. This work tries to explore the effects of structural confinement due to reduced channel thickness on the electrostatic behavior of DG SOI MOSFET. DG SOI MOSFET form the Qfinfet which is an alternative to existing Finfet structure. Qfinfet was proposed and patented by the Finscale Inc for sub 10nm technology nodes.
As part of MS Thesis we developed electrostatic simulator for DG SOI devices by implementing the self consistent full band Schrodinger Poisson solver. We used the Empirical Pseudopotential method in conjunction with supercell approach to solve the Schrodinger Equation. EPM was chosen because it has few empirical parameters which give us good accuracy for experimental results. Also EPM is computationally less expensive as compared to the atomistic methods like DFT(Density functional theory) and NEGF (Non-equilibrium Green's function). In our workwe considered two crystallographic orientations of Si,namely [100] and [110].
As part of MS Thesis we developed electrostatic simulator for DG SOI devices by implementing the self consistent full band Schrodinger Poisson solver. We used the Empirical Pseudopotential method in conjunction with supercell approach to solve the Schrodinger Equation. EPM was chosen because it has few empirical parameters which give us good accuracy for experimental results. Also EPM is computationally less expensive as compared to the atomistic methods like DFT(Density functional theory) and NEGF (Non-equilibrium Green's function). In our workwe considered two crystallographic orientations of Si,namely [100] and [110].
ContributorsLaturia, Akash (Author) / Vasileska, Dragica (Thesis advisor) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2016
Description
Thermal effects in nano-scaled devices were reviewed and modeling methodologies to deal with this issue were discussed. The phonon energy balance equations model, being one of the important previous works regarding the modeling of heating effects in nano-scale devices, was derived. Then, detailed description was given on the Monte Carlo (MC) solution of the phonon Boltzmann Transport Equation. The phonon MC solver was developed next as part of this thesis. Simulation results of the thermal conductivity in bulk Si show good agreement with theoretical/experimental values from literature.
ContributorsYoo, Seung Kyung (Author) / Vasileska, Dragica (Thesis advisor) / Ferry, David (Committee member) / Goodnick, Stephen (Committee member) / Arizona State University (Publisher)
Created2015
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 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.
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
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 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.
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
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 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.
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
Description
ABSTRACT
X-Ray crystallography and NMR are two major ways of achieving atomic
resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning radiation damage with ultra high brightness femtosecond X-ray pulses, which is so short in time that the pulse terminates before atomic motion starts. A variety of experimental techniques for structure determination of macro biomolecules is now available including imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide- angle x-ray scattering (WAXS) from molecules in solution. However, due to the nature of the "diffract-then-destroy" process, each protein crystal would be destroyed once
probed. Hence a new sample delivery system is required to replenish the target crystal at a high rate. In this dissertation, the sample delivery systems for the application of XFELs to biomolecular imaging will be discussed and the severe challenges related to the delivering of macroscopic protein crystal in a stable controllable way with minimum waste of sample and maximum hit rate will be tackled with several different development of injector designs and approaches. New developments of the sample delivery system such as liquid mixing jet also opens up new experimental methods which gives opportunities to study of the chemical dynamics in biomolecules in a molecular structural level. The design and characterization of the system will be discussed along with future possible developments and applications. Finally, LCP injector will be discussed which is critical for the success in various applications.
X-Ray crystallography and NMR are two major ways of achieving atomic
resolution of structure determination for macro biomolecules such as proteins. Recently, new developments of hard X-ray pulsed free electron laser XFEL opened up new possibilities to break the dilemma of radiation dose and spatial resolution in diffraction imaging by outrunning radiation damage with ultra high brightness femtosecond X-ray pulses, which is so short in time that the pulse terminates before atomic motion starts. A variety of experimental techniques for structure determination of macro biomolecules is now available including imaging of protein nanocrystals, single particles such as viruses, pump-probe experiments for time-resolved nanocrystallography, and snapshot wide- angle x-ray scattering (WAXS) from molecules in solution. However, due to the nature of the "diffract-then-destroy" process, each protein crystal would be destroyed once
probed. Hence a new sample delivery system is required to replenish the target crystal at a high rate. In this dissertation, the sample delivery systems for the application of XFELs to biomolecular imaging will be discussed and the severe challenges related to the delivering of macroscopic protein crystal in a stable controllable way with minimum waste of sample and maximum hit rate will be tackled with several different development of injector designs and approaches. New developments of the sample delivery system such as liquid mixing jet also opens up new experimental methods which gives opportunities to study of the chemical dynamics in biomolecules in a molecular structural level. The design and characterization of the system will be discussed along with future possible developments and applications. Finally, LCP injector will be discussed which is critical for the success in various applications.
ContributorsWang, Dingjie (Author) / Spence, John CH (Thesis advisor) / Weierstall, Uwe (Committee member) / Schmidt, Kevin (Committee member) / Fromme, Petra (Committee member) / Ozkan, Banu (Committee member) / Arizona State University (Publisher)
Created2014