Matching Items (56)
Description
Single molecules in a tunnel junction can now be interrogated reliably using chemically-functionalized electrodes. Monitoring stochastic bonding fluctuations between a ligand bound to one electrode and its target bound to a second electrode ("tethered molecule-pair" configuration) gives insight into the nature of the intermolecular bonding at a single molecule-pair level, and defines the requirements for reproducible tunneling data. Importantly, at large tunnel gaps, there exists a regime for many molecules in which the tunneling is influenced more by the chemical identity of the molecules than by variability in the molecule-metal contact. Functionalizing a pair of electrodes with recognition reagents (the "free analyte" configuration) can generate a distinct tunneling signal when an analyte molecule is trapped in the gap. This opens up a new interface between chemistry and electronics with immediate implications for rapid sequencing of single DNA molecules.
ContributorsChang, Shuai (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Zhang, Peiming (Committee member) / Tao, Nongjian (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2012
Description
CpG methylation is an essential requirement for the normal development of mammals, but aberrant changes in the methylation can lead to tumor progression and cancer. An in-depth understanding of this phenomenon can provide insights into the mechanism of gene repression. We present a study comparing methylated DNA and normal DNA wrt its persistence length and contour length. Although, previous experiments and studies show no difference between the physical properties of the two, the data collected and interpreted here gives a different picture to the methylation phenomena and its effect on gene silencing. The study was extended to the artificially reconstituted chromatin and its interactions with the methyl CpG binding proteins were also probed.
ContributorsKaur, Parminder (Author) / Lindsay, Stuart (Thesis advisor) / Ros, Robert (Committee member) / Tao, Nongjian (Committee member) / Vaiana, Sara (Committee member) / Beckenstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2012
Description
ABSTRACT Group III-nitride semiconductor materials have been commercially used in fabrication of light-emitting diodes (LEDs) and laser diodes (LDs) covering the spectral range from UV to visible and infrared, and exhibit unique properties suitable for modern optoelectronic applications. Great advances have recently happened in the research and development in high-power and high-efficiency blue-green-white LEDs, blue LDs and other optoelectronic applications. However, there are still many unsolved challenges with these materials. In this dissertation, several issues concerning structural, electronic and optical properties of III-nitrides have been investigated using a combination of transmission electron microscopy (TEM), electron holography (EH) and cathodoluminescence (CL) techniques. First, a trend of indium chemical inhomogeneity has been found as the indium composition increases for the InGaN epitaxial layers grown by hydride vapor phase epitaxy. Second, different mechanisms contributing to the strain relaxation have been studied for non-polar InGaN epitaxial layers grown on zinc oxide (ZnO) substrate. Third, various structural morphologies of non-polar InGaN epitaxial layers grown on free-standing GaN substrate have been investigated. Fourth, the effect of the growth temperature on the performance of GaN lattice-matched InAlN electron blocking layers has been studied. Finally, the electronic and optical properties of GaN nanowires containing a AlN/GaN superlattice structure have been investigated showing relatively small internal electric field and superlattice- and defect-related emissions along the nanowires.
ContributorsSun, Kewei (Author) / Ponce, Fernando (Thesis advisor) / Smith, David (Committee member) / Treacy, Michael (Committee member) / Drucker, Jeffery (Committee member) / Schmidt, Kevin (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation presents research findings regarding the exploitation of localized surface plasmon (LSP) of epitaxial Ag islands as a means to enhance the photoluminescence (PL) of Germanium (Ge) quantum dots (QDs). The first step of this project was to investigate the growth of Ag islands on Si(100). Two distinct families of Ag islands have been observed. “Big islands” are clearly faceted and have basal dimensions in the few hundred nm to μm range with a variety of basal shapes. “Small islands” are not clearly faceted and have basal diameters in the 10s of nm range. Big islands form via a nucleation and growth mechanism, and small islands form via precipitation of Ag contained in a planar layer between the big islands that is thicker than the Stranski-Krastanov layer existing at room-temperature.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
ContributorsKong, Dexin (Author) / Drucker, Jeffery (Thesis advisor) / Chen, Tingyong (Committee member) / Ros, Robert (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
Photosystem II (PSII) is a large protein-cofactor complex. The first step in
photosynthesis involves the harvesting of light energy from the sun by the antenna (made
of pigments) of the PSII trans-membrane complex. The harvested excitation energy is
transferred from the antenna complex to the reaction center of the PSII, which leads to a
light-driven charge separation event, from water to plastoquinone. This phenomenal
process has been producing the oxygen that maintains the oxygenic environment of our
planet for the past 2.5 billion years.
The oxygen molecule formation involves the light-driven extraction of 4 electrons
and protons from two water molecules through a multistep reaction, in which the Oxygen
Evolving Center (OEC) of PSII cycles through 5 different oxidation states, S0 to S4.
Unraveling the water-splitting mechanism remains as a grant challenge in the field of
photosynthesis research. This requires the development of an entirely new capability, the
ability to produce molecular movies. This dissertation advances a novel technique, Serial
Femtosecond X-ray crystallography (SFX), into a new realm whereby such time-resolved
molecular movies may be attained. The ultimate goal is to make a “molecular movie” that
reveals the dynamics of the water splitting mechanism using time-resolved SFX (TRSFX)
experiments and the uniquely enabling features of X-ray Free-Electron Laser
(XFEL) for the study of biological processes.
This thesis presents the development of SFX techniques, including development of
new methods to analyze millions of diffraction patterns (~100 terabytes of data per XFEL
experiment) with the goal of solving the X-ray structures in different transition states.
ii
The research comprises significant advancements to XFEL software packages (e.g.,
Cheetah and CrystFEL). Initially these programs could evaluate only 8-10% of all the
data acquired successfully. This research demonstrates that with manual optimizations,
the evaluation success rate was enhanced to 40-50%. These improvements have enabled
TR-SFX, for the first time, to examine the double excited state (S3) of PSII at 5.5-Å. This
breakthrough demonstrated the first indication of conformational changes between the
ground (S1) and the double-excited (S3) states, a result fully consistent with theoretical
predictions.
The power of the TR-SFX technique was further demonstrated with proof-of principle
experiments on Photoactive Yellow Protein (PYP) micro-crystals that high
temporal (10-ns) and spatial (1.5-Å) resolution structures could be achieved.
In summary, this dissertation research heralds the development of the TR-SFX
technique, protocols, and associated data analysis methods that will usher into practice a
new era in structural biology for the recording of ‘molecular movies’ of any biomolecular
process.
photosynthesis involves the harvesting of light energy from the sun by the antenna (made
of pigments) of the PSII trans-membrane complex. The harvested excitation energy is
transferred from the antenna complex to the reaction center of the PSII, which leads to a
light-driven charge separation event, from water to plastoquinone. This phenomenal
process has been producing the oxygen that maintains the oxygenic environment of our
planet for the past 2.5 billion years.
The oxygen molecule formation involves the light-driven extraction of 4 electrons
and protons from two water molecules through a multistep reaction, in which the Oxygen
Evolving Center (OEC) of PSII cycles through 5 different oxidation states, S0 to S4.
Unraveling the water-splitting mechanism remains as a grant challenge in the field of
photosynthesis research. This requires the development of an entirely new capability, the
ability to produce molecular movies. This dissertation advances a novel technique, Serial
Femtosecond X-ray crystallography (SFX), into a new realm whereby such time-resolved
molecular movies may be attained. The ultimate goal is to make a “molecular movie” that
reveals the dynamics of the water splitting mechanism using time-resolved SFX (TRSFX)
experiments and the uniquely enabling features of X-ray Free-Electron Laser
(XFEL) for the study of biological processes.
This thesis presents the development of SFX techniques, including development of
new methods to analyze millions of diffraction patterns (~100 terabytes of data per XFEL
experiment) with the goal of solving the X-ray structures in different transition states.
ii
The research comprises significant advancements to XFEL software packages (e.g.,
Cheetah and CrystFEL). Initially these programs could evaluate only 8-10% of all the
data acquired successfully. This research demonstrates that with manual optimizations,
the evaluation success rate was enhanced to 40-50%. These improvements have enabled
TR-SFX, for the first time, to examine the double excited state (S3) of PSII at 5.5-Å. This
breakthrough demonstrated the first indication of conformational changes between the
ground (S1) and the double-excited (S3) states, a result fully consistent with theoretical
predictions.
The power of the TR-SFX technique was further demonstrated with proof-of principle
experiments on Photoactive Yellow Protein (PYP) micro-crystals that high
temporal (10-ns) and spatial (1.5-Å) resolution structures could be achieved.
In summary, this dissertation research heralds the development of the TR-SFX
technique, protocols, and associated data analysis methods that will usher into practice a
new era in structural biology for the recording of ‘molecular movies’ of any biomolecular
process.
ContributorsBasu, Shibom, 1988- (Author) / Fromme, Petra (Thesis advisor) / Spence, John C.H. (Committee member) / Wolf, George (Committee member) / Ros, Robert (Committee member) / Fromme, Raimund (Committee member) / Arizona State University (Publisher)
Created2015
Description
Bio-molecules and proteins are building blocks of life as is known, and understanding
their dynamics and functions are necessary to better understand life and improve its
quality. While ergodicity and fluctuation dissipation theorem (FDT) are fundamental
and crucial concepts regarding study of dynamics of systems in equilibrium, biological
function is not possible in equilibrium.
In this work, dynamical and orientational structural crossovers in low-temperature
glycerol are investigated. A sudden and notable increase in the orientational Kirk-
wood factor and the dielectric constant is observed, which appears in the same range
of temperatures that dynamic crossover of translational and rotational dynamics oc-
cur.
Theory and electrochemistry of cytochrome c is also investigated. The seeming
discrepancy in reorganization energies of protein electron transfer produced by atom-
istic simulations and those reported by protein electrochemistry (which are smaller)
is resolved. It is proposed in this thesis that ergodicity breaking results in an effective
reorganization energy (0.57 eV) consistent with experiment.
Ergodicity breaking also affects the iron displacement in heme proteins. A model
for dynamical transition of atomic displacements in proteins is provided. Different
temperatures for rotational and translational crossovers of water molecules are re-
ported, which all are ergodicity breaking transitions depending on the corresponding
observation windows. The comparison with Mössbauer spectroscopy is presented.
Biological function at low temperatures and its termination is also investigated in
this research. Here, it is proposed that ergodicity breaking gives rise to the violation
of the FDT, and this violation is maintained in the entire range of physiological
temperatures for cytochrome c. Below the crossover temperature, the protein returns
to the FDT, which leads to a sudden jump in the activation barrier for electron
itransfer.
Finally the interaction of charges in dielectric materials is discussed. It is shown
that the potential of mean force between ions in polar liquids becomes oscillatory at
short distances.
their dynamics and functions are necessary to better understand life and improve its
quality. While ergodicity and fluctuation dissipation theorem (FDT) are fundamental
and crucial concepts regarding study of dynamics of systems in equilibrium, biological
function is not possible in equilibrium.
In this work, dynamical and orientational structural crossovers in low-temperature
glycerol are investigated. A sudden and notable increase in the orientational Kirk-
wood factor and the dielectric constant is observed, which appears in the same range
of temperatures that dynamic crossover of translational and rotational dynamics oc-
cur.
Theory and electrochemistry of cytochrome c is also investigated. The seeming
discrepancy in reorganization energies of protein electron transfer produced by atom-
istic simulations and those reported by protein electrochemistry (which are smaller)
is resolved. It is proposed in this thesis that ergodicity breaking results in an effective
reorganization energy (0.57 eV) consistent with experiment.
Ergodicity breaking also affects the iron displacement in heme proteins. A model
for dynamical transition of atomic displacements in proteins is provided. Different
temperatures for rotational and translational crossovers of water molecules are re-
ported, which all are ergodicity breaking transitions depending on the corresponding
observation windows. The comparison with Mössbauer spectroscopy is presented.
Biological function at low temperatures and its termination is also investigated in
this research. Here, it is proposed that ergodicity breaking gives rise to the violation
of the FDT, and this violation is maintained in the entire range of physiological
temperatures for cytochrome c. Below the crossover temperature, the protein returns
to the FDT, which leads to a sudden jump in the activation barrier for electron
itransfer.
Finally the interaction of charges in dielectric materials is discussed. It is shown
that the potential of mean force between ions in polar liquids becomes oscillatory at
short distances.
ContributorsSeyedi, seyed salman (Author) / Matyushov, Dmitry V (Thesis advisor) / Beckstein, Oliver (Committee member) / Vaiana, Sara M (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2018
Description
This dissertation describes the characterization of optoelectronic and electronic materials being considered for next generation semiconductor devices, primarily using electron microscopy techniques. The research included refinement of growth parameters for optimizing material quality, and investigation of heterostructured interfaces. The results provide better understanding of the fundamental materials science and should lead to future improvements in device applications.
A microstructural study of tin selenide and tin manganese selenide thin films grown by molecular beam epitaxy (MBE) on GaAs (111)B substrates with different Se:Sn flux ratios and Mn concentrations was carried out. Low flux ratios lead to highly defective films, mostly consisting of SnSe, whereas higher flux ratios gave higher quality, single-phase SnSe2. The ternary (Sn,Mn)Se films evolved quasi-coherently, as the Mn concentration increased, from SnSe2 into a complex lattice, and then into MnSe with 3D rock-salt structure. These structural transformations should underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.
II-VI/III-V compound semiconductor heterostructures have been characterized for growth in both single- and dual-chamber MBE systems. Three groups of lattice-matched materials have been investigated: i) 5.65Å materials based on GaAs, ii) 6.1Å materials based on InAs or GaSb, and iii) 6.5Å materials based on InSb. High quality II-VI materials grown on III-V substrates were demonstrated for ZnTe/GaSb and CdTe/InSb. III-V materials grown on II-VI buffer layers present additional challenges and were grown with varying degrees of success. InAsSb quantum wells in between ZnTe barriers were nearly defect-free, but showed 3D island growth. All other materials demonstrated flat interfaces, despite low growth temperature, but with stacking faults in the II-VI materials.
Femtosecond laser-induced defects (LIDs) in silicon solar cells were characterized using a variety of electron microscopy techniques. Scanning electron microscope (SEM) images showed that the intersections of laser lines, finger and busbar intersections, exhibited LIDs with the potential to shunt the contacts. SEM and transmission electron microscope (TEM) images correlated these LIDs with ablated c-Si and showed these defects to come in two sizes ~40nm and ~.5µm. The elemental profiles across defective and non-defective regions were found using energy dispersive x-ray spectroscopy.
A microstructural study of tin selenide and tin manganese selenide thin films grown by molecular beam epitaxy (MBE) on GaAs (111)B substrates with different Se:Sn flux ratios and Mn concentrations was carried out. Low flux ratios lead to highly defective films, mostly consisting of SnSe, whereas higher flux ratios gave higher quality, single-phase SnSe2. The ternary (Sn,Mn)Se films evolved quasi-coherently, as the Mn concentration increased, from SnSe2 into a complex lattice, and then into MnSe with 3D rock-salt structure. These structural transformations should underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.
II-VI/III-V compound semiconductor heterostructures have been characterized for growth in both single- and dual-chamber MBE systems. Three groups of lattice-matched materials have been investigated: i) 5.65Å materials based on GaAs, ii) 6.1Å materials based on InAs or GaSb, and iii) 6.5Å materials based on InSb. High quality II-VI materials grown on III-V substrates were demonstrated for ZnTe/GaSb and CdTe/InSb. III-V materials grown on II-VI buffer layers present additional challenges and were grown with varying degrees of success. InAsSb quantum wells in between ZnTe barriers were nearly defect-free, but showed 3D island growth. All other materials demonstrated flat interfaces, despite low growth temperature, but with stacking faults in the II-VI materials.
Femtosecond laser-induced defects (LIDs) in silicon solar cells were characterized using a variety of electron microscopy techniques. Scanning electron microscope (SEM) images showed that the intersections of laser lines, finger and busbar intersections, exhibited LIDs with the potential to shunt the contacts. SEM and transmission electron microscope (TEM) images correlated these LIDs with ablated c-Si and showed these defects to come in two sizes ~40nm and ~.5µm. The elemental profiles across defective and non-defective regions were found using energy dispersive x-ray spectroscopy.
ContributorsTracy, Brian David (Author) / Smith, David J. (Thesis advisor) / Bennett, Peter A (Committee member) / Drucker, Jeffery (Committee member) / Mccartney, Martha R (Committee member) / Zhang, Yong-Hang (Committee member) / Arizona State University (Publisher)
Created2018
Description
In this project, we introduce a type of microscopy which produces correlated topography and fluorescence lifetime images with nanometer resolution. This technique combines atomic force microscopy (AFM) and time resolved confocal fluorescence microscopy to conduct biological and materials research. This method is used to investigate nanophotonic effects on single fluorophores, including quantum dots and fluorescent molecules. For single fluorescent molecules, we investigate the effects of quenching of fluorescence with the probe of an atomic force microscope which is combined and synchronized with a confocal fluorescence lifetime microscope. For quantum dots, we investigate the correlation between the topographic and fluorescence data. With this method of combining an atomic force microscope with a confocal microscope, it is anticipated that there will be applications in nanomaterial characterization and life sciences; such as the determination of the structure of small molecular systems on surfaces, molecular interactions, as well as the structure and properties of fluorescent nanomaterials.
ContributorsWard, Alex Mark (Author) / Ros, Robert (Thesis director) / Shumway, John (Committee member) / Schulz, Olaf (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2013-05
Description
Proteins continually and naturally incur evolutionary selection through mutagenesis that optimizes their fitness, which is primarily determined by their function. It is known that allosteric regulation alters a protein's conformational dynamics leading to functional changes. We have computationally introduced a mutation at a predicted regulatory site of a short, 46 residue-long, protein interaction module composed of a WW domain and corresponding polyproline ligand (PDB id: 1k9r). The dynamic flexibility index (DFI) was computed for the binding site of the wild type and mutant WW domains to quantify the mutations effect on the rigidity of the binding pocket. DFI is used as a metric to quantify the resilience of a given position to perturbation along the chain. Using steered molecular dynamics (SMD), we also measure the effect of the point mutation on allosteric regulation by approximating the binding free energy of the system calculated using Jarzynski's Equality. Calculation of the DFI shows that the overall flexibility of the protein complex increases as a result of the distal point mutation. Total change in DFI percentile of the binding site showed a 0.067 increase suggesting an allosteric, loss of function mutation. Furthermore, we see that the change in the binding free energy is greater for that of the mutated complex supporting the idea that an increase in flexibility is correlated to a decrease in proteinlig and binding affinity. We show that sequence mutation of an allosteric site affects the mechanical stability and functionality of the binding pocket.
ContributorsMarianchuk, Tegan (Author) / Ozkan, Sefika (Thesis director) / Ros, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Physics (Contributor)
Created2018-05
Description
The atomic force microscope (AFM) is capable of directly probing the mechanics of samples with length scales from single molecules to tissues and force scales from pico to micronewtons. In particular, AFM is widely used as a tool to measure the elastic modulus of soft biological samples by collecting force-indentation relationships and fitting these to classic elastic contact models. However, the analysis of raw force-indentation data may be complicated by mechanical heterogeneity present in biological systems. An analytical model of an elastic indentation on a bonded two-layer sample was solved. This may be used to account for substrate effects and more generally address experimental design for samples with varying elasticity. This model was applied to two mechanobiology systems of interest. First, AFM was combined with confocal laser scanning fluorescence microscopy and finite element analysis to examine stiffness changes during the initial stages of invasion of MDA-MB-231 metastatic breast cells into bovine collagen I matrices. It was determined that the cells stiffen significantly as they invade, the amount of stiffening is correlated with the elastic modulus of the collagen gel, and inhibition of Rho-associated protein kinase reduces the elastic modulus of the invading cells. Second, the elastic modulus of cancer cell nuclei was investigated ex situ and in situ. It was observed that inhibition of histone deacetylation to facilitate chromatin decondenstation result in significantly more morphological and stiffness changes in cancerous cells compared to normal cells. The methods and results presented here offer novel strategies for approaching biological systems with AFM and demonstrate its applicability and necessity in studying cellular function in physiologically relevant environments.
ContributorsDoss, Bryant Lee (Author) / Ros, Robert (Thesis advisor) / Lindsay, Stuart (Committee member) / Nikkhah, Mehdi (Committee member) / Beckstein, Oliver (Committee member) / Arizona State University (Publisher)
Created2015