Physical Sciences and Mathematics Commons^™

Structure And Function Of Proteins Investigated By Crystallographic And Spectroscopic Time-Resolved Methods, Namrta Purwar

Theses and Dissertations

Biomolecules play an essential role in performing the necessary functions for life. The goal of this thesis is to contribute to an understanding of how biological systems work on the molecular level. We used two biological systems, beef liver catalase (BLC) and photoactive yellow protein (PYP). BLC is a metalloprotein that protects living cells from the harmful effects of reactive oxygen species by converting H2O2 into water and oxygen. By binding nitric oxide (NO) to the catalase, a complex was generated that mimics the Cat-H2O2 adduct, a crucial intermediate in the reaction promoted by the catalase. The Cat-NO complex is …

Extracting The Structure And Conformations Of Biological Entities From Large Datasets, Ali Dashti

Theses and Dissertations

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging "diffract & destroy" X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of "unsorted" snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive.

It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms …

Beyond The Standard Model: Lhc Phenomenology, Cosmology From Post-Inflationary Sources, And Dark Matter Physics, Brian J. Vlcek

Theses and Dissertations

It is the goal of this dissertation to demonstrate that beyond the standard model, certain theories exist which solve conflicts between observation and theory -- conflicts such as massive neutrinos, dark matter, unstable Higgs vacuum, and recent Planck observations of excess relativistic degrees of freedom in the early universe. Theories explored include a D-brane inspired construct of U(3) × Sp(1) × U(1) × U(1) extension of the standard model, in which we demonstrate several possible observables that may be detected at the LHC, and an ability to stabilize the Higgs mechanism. The extended model can also explain recent Planck data …

Protein Association In Living Cells Using Fret Spectrometry: Application To G-Protein Coupled Receptors, Suparna Patowary

Theses and Dissertations

Recent advancements in fluorescence microscopy coupled with newly developed fluorescent tags have transformed Fluorescence (Förster) Resonance Energy Transfer (FRET) into a powerful tool studying in vivo molecular interactions with improved spatial (angstrom) resolution. Though widely used to study protein-protein interactions, generalizing and testing the FRET theory for oligomeric complexes containing multiple donors and acceptors has only become possible in recent years. Therefore, many aspects of it are yet unexplored.

In this work, we tested the kinetic theory of FRET using linked fluorescent proteins located in the cytoplasm or at the plasma membrane. We used a novel method developed in our …

Growth Of Zno Thin Films On Polar Oxide Surfaces By Atomic Layer Deposition, Kallol Pradhan

Theses and Dissertations

Polar heterointerfaces of MgO(111) and the II-VI semiconductor ZnO are of technological interest for transparent conducting electrode applications. Growth and structure of thin films on polar surfaces can be different than on non-polar surfaces due to the large surface energy of polar surfaces. We have grown ZnO on unreconstructed MgO(111)-(1x1)-OH terminated and reconstructed MgO(111)-(√3x√3)R30° polar oxide surfaces using atomic layer deposition. A homemade UHV-interfaced viscous-flow atomic layer deposition (ALD) reactor with in-situ quartz crystal monitor was used to grow ZnO thin films on the MgO(111) substrates. Surface morphology studies revealed that the surface roughness increases with ZnO film thickness and …

Solving Virus Structures From Xfel Diffraction Patterns Of Random Particle Orientations Using Angular Correlations Of Intensities, Miraj Uddin

Theses and Dissertations

The world's first x-ray free electron laser (XFEL), the Linac Coherent Light Source (LCLS) at the Stanford Linear Accelerator Center (SLAC) is now creating X-ray pulses not only of unprecendented brilliance; (a billion times brighter than the most powerful previous sources [8]) but also of ex- tremely short duration. Amongst the promised capabilities of this fourth- generation x-ray sources is the ability to record diffraction patterns from individual bio-molecules. The very first XFEL ''diffract and destroy'' exper- iments are being performed on relatively large objects such as viruses. To quote from Caspar and Klug[2], ''there are only a limited number …

Probing Bonding And Dynamics At Heterogeneous Adsorbate/Graphene Interfaces, Eric Charles Mattson

Theses and Dissertations

Graphene-based materials are becoming an astoundingly promising choice for many relevant technological and environmental applications. Deriving graphene from the reduction of graphene oxide (GO) is becoming a popular and inexpensive route toward the synthesis of these materials. While the desired product from GO reduction is pristine graphene, defects and residual oxygen functional groups inherited from the parent GO render reduced graphene oxide (RGO) distinct from graphene. In this work, the structure and bonding for GO and RGO is investigated to the end of a working understanding of the composition and properties of these materials. In situ selected area electron diffraction …

Multimessenger Approach To Search For Cosmic Ray Anisotropies, Larry David Buroker

Theses and Dissertations

The origin of the highest energy cosmic rays is still unknown. The discovery of their sources will reveal the workings of the most energetic astrophysical accelerators in the universe. Recent international efforts have brought us closer to unveiling this mystery. Possible ultra-high energy cosmic ray sources have been narrowed down with the confirmation of an "ankle" and the GZKlike spectral feature at the high-end of the energy spectrum. A clear resolution of the ultra-high energy mystery calls for the search of anisotropies in the distribution of arrival directions of cosmic rays. In this thesis, we adopt the so-called "multi-messenger" approach …

How To Think About Indiscernible Particles, Daniel Joseph Giglio

Theses and Dissertations

Permutation symmetries which arise in quantum mechanics pose an intriguing problem. It is not clear that particles which exhibit permutation symmetries (i.e. particles which are indiscernible, meaning that they can be swapped with each other without this yielding a new physical state) qualify as "objects" in any reasonable sense of the term. One solution to this puzzle, which I attribute to W.V. Quine, would have us eliminate such particles from our ontology altogether in order to circumvent the metaphysical vexations caused by permutation symmetries. In this essay I argue that Quine's solution is too rash, and in its place I …