+publisher:"University of Illinois – Urbana-Champaign" +contributor:("Clegg, Robert M.")

University of Illinois – Urbana-Champaign

1. Khalili Araghi, Fatemeh. Voltage-Gating Mechanism in Potassium Channels.

Degree: PhD, 0240, 2011, University of Illinois – Urbana-Champaign

► Voltage-gated potassium channels are membrane proteins that regulate the ???ow of K+ ions across the cell membrane. These channels respond to changes in electrostatic potential… (more)

▼ Voltage-gated potassium channels are membrane proteins that regulate the ???ow of K+ ions across the cell membrane. These channels respond to changes in electrostatic potential across the cell membrane, and allow passage of K+ ions through their conduction pore. In excitable cells, an interplay of voltage-gated K+, Na+, and Ca2+ channels results in generation of electrical signals, known as action potential, that are propagated along the cell membrane. The crystal structure of Kv1.2, a voltage-gated potassium channel from rat brain, provided the ???rst atomic-resolution structure of a voltage-gated potassium channel, in which the ion conduction gate is open. The studies presented in this dissertation use molecular dynamics simulations to investigate the ion permeation, as well as the gating mechanism of voltage-gated potassium channels. The atomic- resolution structures of Kv1.2 in the active and resting state conformations are re???ned in an explicit representation of the membrane environment. The gating charge of the Kv1.2 channel was calculated from all-atom molecular dynamics simulation. The residue-based decomposition of the gating charge revealed that the initial model of the closed state of Kv1.2 represents an intermediate conformation of the channel that precedes the resting state conformation. Electrostatic calculations revealed a highly-focused electric ???eld within the protein, inside membrane. The calculations showed how a rather small movement of gating residues within this highly focused ???eld is su???cient to provide enough energy to open and close the ion conduction pore. In addition, permeation of K+ ions through potassium channels was investigated. The simulations provided the ???rst tra jectories of ion conduction through the selectivity ???lter of potassium channels, con???rming the notion of ???knock-on??? mechanism suggested more than 50 years ago by Hodgkin and Katz. The simulations revealed the sequence of multi-ion con???gurations involved in permeation and the jump of ions between previously identi???ed binding sites. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Makri%2C%20Nancy%22%29&pagesize-30">Makri, Nancy (committee member), Champaign%22%20%2Bcontributor%3A%28%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (committee member).

Subjects/Keywords: Voltage-gating; potassium channels

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APA (6^th Edition):

Khalili Araghi, F. (2011). Voltage-Gating Mechanism in Potassium Channels. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/18378

Chicago Manual of Style (16^th Edition):

Khalili Araghi, Fatemeh. “Voltage-Gating Mechanism in Potassium Channels.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/18378.

MLA Handbook (7^th Edition):

Khalili Araghi, Fatemeh. “Voltage-Gating Mechanism in Potassium Channels.” 2011. Web. 05 Mar 2021.

Vancouver:

Khalili Araghi F. Voltage-Gating Mechanism in Potassium Channels. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/18378.

Council of Science Editors:

Khalili Araghi F. Voltage-Gating Mechanism in Potassium Channels. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/18378

University of Illinois – Urbana-Champaign

2. Simonson, Paul D. Using photo-instability to quantify fluorophores and achieve super-resolution imaging.

Degree: PhD, 0240, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/18590

► This dissertation presents techniques for localizing and quantifying fluorophores in biological imaging applications. Fluorophore photobleaching, blinking, binding, etc., is exploited to quantify and localize single… (more)

▼ This dissertation presents techniques for localizing and quantifying fluorophores in biological imaging applications. Fluorophore photobleaching, blinking, binding, etc., is exploited to quantify and localize single fluorophores, even when their fluorescent images overlap those of nearby fluorophores. In the first technique, we image single, membrane-bound receptors labeled with fluorophores and count the stepwise drops in fluorescence intensity to determine the number of ligand binding sites. Results from single α7 and neuromuscular junction nicotinic acetylcholine receptors in mammalian cell membranes are shown. The results indicate that there are two bungarotoxin binding sites in neuromuscular junction (NMJ) receptors, as expected, and five in α7 receptors, clarifying previous uncertainty. The other techniques are associated with super resolution imaging. Super-resolution imaging is achieved by localizing diffraction-limited spots corresponding to single fluorophores with high accuracy. In photobleaching and intermittency localization microscopy (PhILM), fluorophore transitions between dark and bright states (compatible with binding, photobleaching, photo-activation, blinking, etc.) are localized. We show that standard photobleaching and blinking movies can be used to create super-resolution images. We also explain how PhILM can be combined with another technique to image chromosomal DNA inside cells. In PAINT (point accumulation for imaging in nanoscale topography), the accumulated, stochastic binding events of fluorescent labels to an imaging target are localized. Combining PhILM and PAINT results in a robust microscopy that is faster than PAINT alone, requires less optimization, and corrects for cell autofluorescence. We used nanomolar concentrations of SYTO (which shows >40x fluorescence enhancement upon binding to DNA) to image chromosomal DNA in fixed cells. We found an average single-fluorophore localization error of 24 nm. We similarly imaged microtubules using fluorescent paclitaxel and streptavidin-based labeling to find 10 and 18 nm errors, respectively. Future work will involve simultaneous imaging of DNA, microtubules, and other proteins to answer important biological questions. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Selvin%2C%20Paul%20R.%22%29&pagesize-30">Selvin, Paul R. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (committee member), Champaign%22%20%2Bcontributor%3A%28%22Selvin%2C%20Paul%20R.%22%29&pagesize-30">Selvin, Paul R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22DeMarco%2C%20Brian%20L.%22%29&pagesize-30">DeMarco, Brian L. (committee member).

Subjects/Keywords: single molecule; acetylcholine receptors; bungarotoxin; photobleaching; super-resolution; image analysis; microtubules; Deoxyribonucleic Acid (DNA); photobleaching and intermittency localization microscopy (PhILM); transient labeling

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Simonson, P. D. (2011). Using photo-instability to quantify fluorophores and achieve super-resolution imaging. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/18590

Chicago Manual of Style (16^th Edition):

Simonson, Paul D. “Using photo-instability to quantify fluorophores and achieve super-resolution imaging.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/18590.

MLA Handbook (7^th Edition):

Simonson, Paul D. “Using photo-instability to quantify fluorophores and achieve super-resolution imaging.” 2011. Web. 05 Mar 2021.

Vancouver:

Simonson PD. Using photo-instability to quantify fluorophores and achieve super-resolution imaging. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/18590.

Council of Science Editors:

Simonson PD. Using photo-instability to quantify fluorophores and achieve super-resolution imaging. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/18590

University of Illinois – Urbana-Champaign

3. Carr, Rogan C. Modeling the interface between biological and synthetic components in hybrid nanosystems.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29413

► The fusion of biology and nanotechnology holds amazing promise for revolutionizing medicine and personal technology. In order to take advantage of the great feats of… (more)

▼ The fusion of biology and nanotechnology holds amazing promise for revolutionizing medicine and personal technology. In order to take advantage of the great feats of engineering coming out of these fields, there needs to be theories and computational tools capable of describing the interface between the pristine and ordered world of precision electronics and the hot, wet, and stochastic world of biology. The success of these technologies will depend on our abilities to design and optimize interactions of biomolecules and solid-state materials down to the atomic scale. In my research at the University of Illinois, I have used molecular dynamics (MD) as a tool to describe the atomic-scale interactions driving the function of biomolecules and their interface with solid-state devices, and I have sought to use it as a starting point to create new methods for modeling, designing, and optimizing these interactions. In my dissertation, I show the methodologies that I use in my work and the range of possibilities that they present for researchers in the ???eld, and I present my research on the modeling of the interface between biological and synthetic materials in (1) immunosurfaces used for detection of live bacteria; (2) protein transport through a nanochannel; (3) deriving the Langmuir constant for adsorption for small, organic molecules on synthetic surfaces; (4) creating a multiscale model for transport in micro- and nanofluidic devices; (5) synthetic analogs of biological ion channels. It is my hope that the research that I have performed in my doctoral studies here at the University of Illinois at Urbana-Champaign will be a template for future research and interdisciplinary science. The work I have done here has shown the possibilities of the MD method for studying the physical interface of biological and synthetic components, and I have developed new techniques that can be used by researchers in field to further the science and engineering of bionanotechnology and nanobiotechnology. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (committee member), Champaign%22%20%2Bcontributor%3A%28%22Olson%2C%20Luke%20N.%22%29&pagesize-30">Olson, Luke N. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stack%2C%20John%20D.%22%29&pagesize-30">Stack, John D. (committee member).

Subjects/Keywords: Molecular Dynamics; Bionanotechnology; Nanobiotechnology; Nanofluidics; Adsorption; Langmuir Isotherm; Nanochannel; Polyoxometalates; Immunosurfaces

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Carr, R. C. (2012). Modeling the interface between biological and synthetic components in hybrid nanosystems. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29413

Chicago Manual of Style (16^th Edition):

Carr, Rogan C. “Modeling the interface between biological and synthetic components in hybrid nanosystems.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/29413.

MLA Handbook (7^th Edition):

Carr, Rogan C. “Modeling the interface between biological and synthetic components in hybrid nanosystems.” 2012. Web. 05 Mar 2021.

Vancouver:

Carr RC. Modeling the interface between biological and synthetic components in hybrid nanosystems. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/29413.

Council of Science Editors:

Carr RC. Modeling the interface between biological and synthetic components in hybrid nanosystems. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29413

University of Illinois – Urbana-Champaign

4. Aggen, David H. Engineering human single-chain T cell receptors.

Degree: PhD, 0318, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/18585

► The alpha-beta T cell receptor (TCR) is responsible for mediating T cell recognition of self and non-self tissues, through recognition between a complex of a… (more)

▼ The alpha-beta T cell receptor (TCR) is responsible for mediating T cell recognition of self and non-self tissues, through recognition between a complex of a peptide and a product of the major histocompatibility complex (pepMHC) on target cells. In the immune response to cancerous tissue, the immune repertoire of T cells is often insufficient to target pepMHC complexes associated with cancer cells, as these tumor antigens have often induced tolerance or the tumor microenvironment promotes immunosuppression of T cells. To improve the response to tumors, gene therapy with tumor specific T cell receptors provides an attractive approach to effectively arm patient???s T cells for cancer cell destruction. An inherent difficulty, however, is generation of T cell receptors of sufficient affinity to redirect both CD4+ and CD8+ T cells. This thesis describes the development of engineering strategies for human single-chain T cell receptor variable fragments (scTv), with the goal of understanding the properties that allow scTv to be expressed and deployed in a therapeutic mode. Stable scTv receptors can be used to generate high-affinity TCRs specific for disease-associated pepMHC complexes and produced in soluble expression systems for subsequent biochemical and biophysical characterization. This work also develops scTv and scFv (antibody variable fragments) as fusion proteins, collectively called chimeric antigen receptors, for cell mediated therapies to redirect T cells to specific antigens In chapter 2, two human Valpha2+ T cell receptors specific for human immunodeficiency virus and human T cell lymphotrophic virus derived pepMHC complexes were engineered for improved stability as scTv proteins, consisting of only the variable domains of the T cell receptor attached by a flexible linker. High-affinity, stabilized scTv proteins could be expressed as soluble proteins in E. coli and used for detection of low levels of HIV pepMHC antigens, suggesting that these receptors have potential diagnostic applications for the detection of HIV infected cells. Finally, the results suggest that other V???2+ TCRs with different specificities can be engineered for enhanced affinity by yeast display. Chapter 3 describes the development of chimeric antigen receptors, that consist of scTv-fusion proteins, for T cell targeting of tumor antigens. scTv proteins engineered for improved stability by yeast display were fused to the intracellular signaling domains of CD28,CD3zeta, and LCK and introduced into murine T cells. The high affinity scTv, called m33, that is specific for the pepMHC SIY/Kb was used to redirect T cells with similar antigen sensitivity to the full-length m33 TCR. An inherent problem with full-length TCR gene therapy is the generation of receptors of unknown specificity through mispairing between introduced and endogenous TCR, leading to graft versus host disease or autoimmunity. I show that the scTv-fusions avoided mispairing with endogenous alpha-beta TCRs and allowed for endogenous TCR surface expression at high… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Kranz%2C%20David%20M.%22%29&pagesize-30">Kranz, David M. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Kranz%2C%20David%20M.%22%29&pagesize-30">Kranz, David M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Wraight%2C%20Colin%20A.%22%29&pagesize-30">Wraight, Colin A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Fratti%2C%20Rutilio%20A.%22%29&pagesize-30">Fratti, Rutilio A. (committee member).

Subjects/Keywords: T Cell Receptors; Protein Engineering; Yeast Display; Adoptive T Cell Therapy; Gene Therapy; Single-Chain Fragment Variable (scFv); Single-Chain T Cell Receptor Variable (scTv)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Aggen, D. H. (2011). Engineering human single-chain T cell receptors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/18585

Chicago Manual of Style (16^th Edition):

Aggen, David H. “Engineering human single-chain T cell receptors.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/18585.

MLA Handbook (7^th Edition):

Aggen, David H. “Engineering human single-chain T cell receptors.” 2011. Web. 05 Mar 2021.

Vancouver:

Aggen DH. Engineering human single-chain T cell receptors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/18585.

Council of Science Editors:

Aggen DH. Engineering human single-chain T cell receptors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/18585

University of Illinois – Urbana-Champaign

5. Hsieh, Wen-Pin. Testing theories for thermal transport using high pressure.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29643

► This dissertation focuses on experimental studies of thermal transport in various materials, such as heat transfer in crystals and amorphous polymers, and across interfaces, using… (more)

▼ This dissertation focuses on experimental studies of thermal transport in various materials, such as heat transfer in crystals and amorphous polymers, and across interfaces, using an ultrafast pump-probe method, time-domain thermoreflectance (TDTR), combined with gem anvil cell techniques. I demonstrated that pressure tuning of physical properties of materials is an elegant approach to test the validity of theories for thermal transport. Pressure dependence of the cross-plane thermal conductivity ??(P) of a layered muscovite mica crystal was measured by TDTR combined with diamond anvil cell techniques. Under a simple relaxation time approximation, most of the ??(P) of muscovite mica can be described by the pressure dependence of the cross-plane sound velocity, indicating that the cross-plane sound velocity plays an important role in the thermal transport in a layered crystal. The validity of the minimum thermal conductivity model for amorphous polymers was verified by the good agreement between my measurements of the pressure dependent thermal conductivity of poly(methyl methacrylate) (PMMA) and the model prediction. The thermal energy exchange between non-propagating vibrational modes is the dominant mechanism of thermal transport in amorphous polymers. I also used high pressure to demonstrate the importance of interface stiffness on the interfacial thermal transport. By measuring the pressure dependence of thermal conductance G(P) of clean and modified Al/SiC interfaces, I found that G(P) of a clean interface with high interface stiffness is weakly dependent on pressure and can be well accounted for by the diffuse mismatch model (DMM). By contrast, G(P) of modified interfaces with low interface stiffness initially increase rapidly with pressure; as the interface stiffness is increased to be comparable to the stiffness of chemical bonds, G(P) saturate at the value for the clean interface and value predicted by the DMM. In order to extend the TDTR measurements to high pressures and high temperatures, I studied the pressure dependent thermoreflectance and piezo-optical coefficient of metal film transducers???Al, Ta, and Au(Pd) alloy (???5 at. % Pd) at a laser wavelength of 785 nm. The thermoreflectance of Ta and Au(Pd) are comparable to that of Al at ambient conditions and independent of pressure in the range 0<P<10 GPa. Ta and Au(Pd) also present strong acoustic echo strengths in this pressure range. I conclude that Ta and Au(Pd) films can replace Al as metal transducers and extend TDTR to higher pressures and temperatures. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Cahill%2C%20David%20G.%22%29&pagesize-30">Cahill, David G. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Cooper%2C%20S.%20Lance%22%29&pagesize-30">Cooper, S. Lance (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Cahill%2C%20David%20G.%22%29&pagesize-30">Cahill, David G. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Trinkle%2C%20Dallas%20R.%22%29&pagesize-30">Trinkle, Dallas R. (committee member).

Subjects/Keywords: Thermal transport; pressure; thermoreflectance

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Hsieh, W. (2012). Testing theories for thermal transport using high pressure. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29643

Chicago Manual of Style (16^th Edition):

Hsieh, Wen-Pin. “Testing theories for thermal transport using high pressure.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/29643.

MLA Handbook (7^th Edition):

Hsieh, Wen-Pin. “Testing theories for thermal transport using high pressure.” 2012. Web. 05 Mar 2021.

Vancouver:

Hsieh W. Testing theories for thermal transport using high pressure. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/29643.

Council of Science Editors:

Hsieh W. Testing theories for thermal transport using high pressure. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29643

University of Illinois – Urbana-Champaign

6. Ma, Hyungjin. An experimental study of light-material interaction at subwavelength scale.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29744

► The recent emergence of nanotechnology offers a new perspective in the field of optics. The study of light-material interaction has evolved into a nanoscale regime… (more)

▼ The recent emergence of nanotechnology offers a new perspective in the field of optics. The study of light-material interaction has evolved into a nanoscale regime with its dimension smaller than the wavelength of light. While there are pressing needs of optical applications with higher resolution and efficiency, one important hurdle is the so-called diffraction limit that originates from light???s inherent wave nature. Based on the localized electromagnetic field generation due to the resonant oscillation of electron plasma in metal, plasmonics offers new opportunities for manipulating light at the subwavelength scale. This dissertation investigates the effects of electromagnetic field confinement on light-material interaction inside nanoscale metal-dielectric composite structures. One of the simplest structures is a subwavelength hole perforated on a thin metal film. The scalar diffraction theory by Kirchhoff fails to explain the nature of light at nanoscale. Later, it was pointed out by Bethe that light in a small hole can be represented by the electric and magnetic dipole fields which satisfy the boundary conditions at the screen. Using near-field scanning optical microscope (NSOM), I have experimentally studied light transmission through a subwavelength hole, and found an unusually large amount of phase shift in the transmitted light contradicting Bethe???s theory. Such effect is explained by the strong contribution of in-plane electric dipole field due to the excitation of surface plasmon wave. An important challenge to the study of a localized light field is the requirement of non-traditional optical tools that can probe the near-field of light with subwavelength resolution. The cathodoluminescence (CL) microscope, which is a variation of the electron microscope (that has an imaging resolution better than 10nm), is employed to generate a point-like dipole light source using an electron beam in a controlled way. By using CL to excite local plasmonic modes in a nanoscale metal-air-semiconductor bubbles, I demonstrate an ultrasmall mode volume and cavity-enhanced luminescence from a plasmonic structure. Numerical calculation based on a point dipole model indicates that such an effect is a result of increased local optical density of states (LDOS) due to a strong localized field. This device enables a way to generate localized light from a continuous active medium with high quantum efficiency, which is potentially useful for on-chip subwavelength optoelectric applications. Active optical devices sometimes involve an interaction between a plane electromagnetic wave and an active optical medium, which interaction can be modulated by an external stimulus, such as optical or electric pumping. The optical non-linearity of active media available in nature is, in general, extremely weak. Therefore, either bulky or highly resonant structures are required to build an effective, active optical device. Artificially engineered material, sometimes referred as a ???metamaterials,??? can have optical properties that are… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Fang%2C%20Nicholas%20X.%22%29&pagesize-30">Fang, Nicholas X. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Kwiat%2C%20Paul%20G.%22%29&pagesize-30">Kwiat, Paul G. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Fang%2C%20Nicholas%20X.%22%29&pagesize-30">Fang, Nicholas X. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Eden%2C%20James%20G.%22%29&pagesize-30">Eden, James G. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member).

Subjects/Keywords: plasmonics; surface plasmon; metamaterial; optical modulator; nano-bubble; extraordinary transmission; cathodoluminescence; near field scanning optical microscope; near-field scanning optical microscope (NSOM)

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Ma, H. (2012). An experimental study of light-material interaction at subwavelength scale. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29744

Chicago Manual of Style (16^th Edition):

Ma, Hyungjin. “An experimental study of light-material interaction at subwavelength scale.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/29744.

MLA Handbook (7^th Edition):

Ma, Hyungjin. “An experimental study of light-material interaction at subwavelength scale.” 2012. Web. 05 Mar 2021.

Vancouver:

Ma H. An experimental study of light-material interaction at subwavelength scale. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/29744.

Council of Science Editors:

Ma H. An experimental study of light-material interaction at subwavelength scale. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29744

University of Illinois – Urbana-Champaign

7. Frank, Daniel J. Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4.

Degree: PhD, 0318, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/24520

► Cytochrome P450 3A4 (CYP3A4) plays a central role in xenobiotic metabolism, and is of critical importance to both human health and the pharmaceutical industry. Its… (more)

▼ Cytochrome P450 3A4 (CYP3A4) plays a central role in xenobiotic metabolism, and is of critical importance to both human health and the pharmaceutical industry. Its ability to interact with multiple molecules of the same substrate, or multiple substrates, leads to complex non-Michaelis kinetics, called “homotropic” and “heterotropic” cooperativity respectively. Significant progress has been made towards understanding the enzyme’s complex kinetics by work in our laboratory to isolate the enzyme in Nanodiscs. This provides a homogenous, monodisperse, native-like environment, where the monomeric enzyme is biophysically characterized in the absence of detergent micellar mixtures or liposomal systems which are reported to lead to enzyme heterogeneity and obfuscate its kinetic behavior. Three distinct observable properties which CYP3A4 displays as a result of its reaction cycle are: heme iron spin state, NADPH oxidation rate, and product formation rate. Measuring these three observables as a function of substrate concentration and simultaneously fitting the data sets to a model results in a global analysis of the enzyme’s properties. It reveals the source of homotropic atypical kinetics is not due to any binding cooperativity between the substrates, but rather differences in magnitude of the functional properties from the various enzyme-substrate complexes in solution. To extend this analysis to better understand heterotropic interactions in the system, we generate an interaction surface based upon the linear combination of two substrates kinetic profiles, which corresponds to the absence of any specific heterotropic interactions between them. By comparing the observed behavior of the mixed substrate system to that of the model, we show how two commonly reported heterotropic substrates of CYP3A4 are actually not cooperative, and the observed cooperativity is due to differences in the amplitudes of the functional properties from the various binding intermediates in the system which give rise to the overall observed behavior of the enzyme. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Sligar%2C%20Stephen%20G.%22%29&pagesize-30">Sligar, Stephen G. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Sligar%2C%20Stephen%20G.%22%29&pagesize-30">Sligar, Stephen G. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Gerlt%2C%20John%20A.%22%29&pagesize-30">Gerlt, John A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Fratti%2C%20Rutilio%20A.%22%29&pagesize-30">Fratti, Rutilio A. (committee member).

Subjects/Keywords: cooperativity; cytochrome P450 3A4; drug-drug interactions

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APA (6^th Edition):

Frank, D. J. (2011). Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/24520

Chicago Manual of Style (16^th Edition):

Frank, Daniel J. “Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/24520.

MLA Handbook (7^th Edition):

Frank, Daniel J. “Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4.” 2011. Web. 05 Mar 2021.

Vancouver:

Frank DJ. Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/24520.

Council of Science Editors:

Frank DJ. Global deconvolution of heterotropic cooperativity in cytochrome P450 3A4. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/24520

University of Illinois – Urbana-Champaign

8. Pasienski, Matthew J. Disordered insulator in an optical lattice.

Degree: PhD, 0240, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/26044

► We experimentally studied the transport properties of ultracold bosonic atoms trapped in a disordered optical lattice|a system described by the disordered Bose-Hubbard model, which is… (more)

Subjects/Keywords: Optical Lattice; Disorder; Atomic Physics; Transport; Digital Holography

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APA (6^th Edition):

Pasienski, M. J. (2011). Disordered insulator in an optical lattice. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/26044

Chicago Manual of Style (16^th Edition):

Pasienski, Matthew J. “Disordered insulator in an optical lattice.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/26044.

MLA Handbook (7^th Edition):

Pasienski, Matthew J. “Disordered insulator in an optical lattice.” 2011. Web. 05 Mar 2021.

Vancouver:

Pasienski MJ. Disordered insulator in an optical lattice. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/26044.

Council of Science Editors:

Pasienski MJ. Disordered insulator in an optical lattice. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/26044

University of Illinois – Urbana-Champaign

9. Mantey, Kevin A. Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles.

Degree: PhD, 0240, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/26172

► Silicon particles are created via anodic or platinum catalyzed etching of bulk silicon. A peroxide and HF etchant provides uniform surface termination, and results in… (more)

▼ Silicon particles are created via anodic or platinum catalyzed etching of bulk silicon. A peroxide and HF etchant provides uniform surface termination, and results in discrete stable sizes for particles below 3 nm in size. The smallest of these are 1 nm silicon particles, which is amenable to rst principles quan- tum calculations of the structure, electronic levels, and ionic interactions. The vibrational modes of several candidate structures of the 1 nm particles are calculated at the Hartree-Fock level, and compared to previously acquired Raman spectra to determine the structure. The vibrational modes are also compared to the vibrational structure in low temperature photo-luminescence to indicate surface reconstruction bonds play a role in the uorescence. The uorescence mechanism is explored further with calculations of the excited state potential energy surface using time dependent density functional theory, which show radiative traps accessible via direct excitation at the band edge of the ground state geometry. The self-trapped excitons proposed by Lannoo et al. [1, 2] are found to be unstable for the Si29H24 structure, with the outer-well leading to non-radiative recombination via conical intersection of the excited state with the ground state. Absorption measurements indicate the silicon nanoparticles may form charge complexes with iron ions in aque- ous solutions. Calculations including solvation e ects provide a proposed structure for the complex, with a binding energy of 0.49 eV. The binding mechanism is quite general and suggests many other ions could form charge complexes with the silicon particles in aqueous solutions, potentially leading to new applications. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Nayfeh%2C%20Munir%20H.%22%29&pagesize-30">Nayfeh, Munir H. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Nayfeh%2C%20Munir%20H.%22%29&pagesize-30">Nayfeh, Munir H. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ceperley%2C%20David%20M.%22%29&pagesize-30">Ceperley, David M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stack%2C%20John%20D.%22%29&pagesize-30">Stack, John D. (committee member).

Subjects/Keywords: Silicon nanocrystal; Vibrational spectroscopy; Fluorescence; Metal ion complex

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APA (6^th Edition):

Mantey, K. A. (2011). Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/26172

Chicago Manual of Style (16^th Edition):

Mantey, Kevin A. “Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/26172.

MLA Handbook (7^th Edition):

Mantey, Kevin A. “Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles.” 2011. Web. 05 Mar 2021.

Vancouver:

Mantey KA. Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/26172.

Council of Science Editors:

Mantey KA. Structure, electronic levels, and ionic interactions of 1 nanometer silicon particles. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/26172

10. Gough, Dara V. Materials with engineered mesoporosity for programmed mass transport.

Degree: PhD, 0130, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/24198

► Transport in nanostructured materials is of great interest for scientists in various fields, including molecular sequestration, catalysis, artificial photosynthesis and energy storage. This thesis will… (more)

▼ Transport in nanostructured materials is of great interest for scientists in various fields, including molecular sequestration, catalysis, artificial photosynthesis and energy storage. This thesis will present work on the transport of molecular and ionic species in mesoporous materials (materials with pore sizes between 2 and 50 nm). Initially, discussion will focus on the synthesis of mesoporous ZnS nanorattles and the size selected mass transport of small molecules through the mesopores. Discussion will then shift of exploration of cation exchange and electroless plating of metals to alter the mesoporous hollow sphere (MHS) materials and properties. The focus of discussion will then shift to the transport of ions into and out of a hierarchically structured gold electrode. Finally, a model λ-bactiophage was developed to study the electromigration of charged molecules into and out of a confined geometry. A catalytically active biomolecular species was encapsulated within the central cavity of ZnS MHS. Both the activity of the encapsulated enzyme and the size-selective transport through the wall of the MHS were verified through the use of a common fluorogen, hydrogen peroxide, and sodium azide. Additionally, the protection of the enzyme was shown through size-selected blocking of a protease. The mesoporous hollow sphere system introduces size-selectivity to catalyzed chemical reactions; future work may include variations in pore sizes, and pore wall chemical functionalization. The pore size in ZnS mesoporous hollow spheres is controlled between 2.5 and 4.1 nm through swelling of the lyotropic liquid crystal template. The incorporation of a swelling agent is shown to linearly vary the hexagonal lyotropic liquid crystalline phase, which templates the mesopores, while allowing the high fidelity synthesis of mesoporous hollow spheres. Fluorescnently labeled ssDNA was utilized as a probe to explore the change in mesopore permeability afforded by the swollen template relative to the unswollen template. Electroless plating and cation exchange were explored as methods to vary the shell material of MHS. Mesoporous Ni MHS were obtained by the reduction of Ni2+ with dimethylamine borane onto a CML latex core. However, the resultant MHS were damaged due to core swelling during etch. To successfully obtain undeformed MHS, a silica core must be utilized; one possible route to explore, in order to reach this goal, is the surface chemistry/ligand effects on Ni2+. Cation exchange was performed in order to obtain CuS MHS; however, it proved an unsuccessful route to PbS, S and HgS. CdS-ZnS, Bi2S3 and Ag2S MHS were obtained only with significant defects. A novel hierarchically structured material, porous opal, was prepared using a colloidal crystal template and the dealloying of silver from gold and possed porosity on length scales range from 10s of nanometers (due to the colloidal crystal template) down to ca. 10 nm (due to dealloying). The transport properties of the material were studied using cyclic voltammetry and… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Braun%2C%20Paul%20V.%22%29&pagesize-30">Braun, Paul V. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Braun%2C%20Paul%20V.%22%29&pagesize-30">Braun, Paul V. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Dillon%2C%20Shen%20J.%22%29&pagesize-30">Dillon, Shen J. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Sottos%2C%20Nancy%20R.%22%29&pagesize-30">Sottos, Nancy R. (committee member).

Subjects/Keywords: mesoporous; Zinc sulfide (ZnS); porous gold; mass transport; lyotropic liquid crystal templating; self assembly

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APA (6^th Edition):

Gough, D. V. (2011). Materials with engineered mesoporosity for programmed mass transport. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/24198

Chicago Manual of Style (16^th Edition):

Gough, Dara V. “Materials with engineered mesoporosity for programmed mass transport.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/24198.

MLA Handbook (7^th Edition):

Gough, Dara V. “Materials with engineered mesoporosity for programmed mass transport.” 2011. Web. 05 Mar 2021.

Vancouver:

Gough DV. Materials with engineered mesoporosity for programmed mass transport. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/24198.

Council of Science Editors:

Gough DV. Materials with engineered mesoporosity for programmed mass transport. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/24198

11. Strumpfer, Johan. Computational investigation of light harvesting in purple photosynthetic bacteria.

Degree: PhD, 0319, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34275

► Purple photosynthetic bacteria achieve remarkably high light harvesting efficiency, thus reconciling multiple competing processes in the chromatophore. The first step in photosynthesis is the capture… (more)

▼ Purple photosynthetic bacteria achieve remarkably high light harvesting efficiency, thus reconciling multiple competing processes in the chromatophore. The first step in photosynthesis is the capture and transport of light energy in the form of short-lived electronic excitation called excitons. Rapid long-range exciton transport is key to the high light harvesting efficiency associated with purple bacteria. The light harvesting system of purple bacteria consists of light harvesting complex 2 (LH2), light harvesting complex 1 (LH1) and reaction center (RC) assembeled into a structure known as the chromatophore. The pigments embedded into the complexes in the chromatophore are placed close together and are tightly held by their surrounding proteins. Pigment excited states thus interact very strongly and are also strongly coupled to surrounding environmental fluctuation. Exciton dynamics in purple bacteria is thus described using the hierarchy equations of motion (HEOM) for open quantum systems, which does not rely on assumptions of relative interaction strengths and includes quantum coherence effects. An efficient implementation of the HEOM is developed and utilized to describe exciton dynamics in the light harvesting complexes of purple bacteria, and calculate excitation transfer between LH2-LH2, LH2-LH1 and LH1-RC pairs. It is shown that strong environmental coupling is reponsible for rapid exciton relaxation into equilibrium prior to inter- complex exciton transfer, thus allowing inter-complex transfer rates to be calculated with the much simpler generalized F ̈orster theory. The effect of intra-complex correlated environmental fluctuations is also examined and found to substantially affect inter-complex exciton transfer. Strong coupling between pigments within a complex results in inter-pigment quantum coherence that significantly improves the rate of inter-complex exciton transfer, vital to efficient light harvesting in purple bacteria. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Govindjee%22%29&pagesize-30">Govindjee (committee member), Champaign%22%20%2Bcontributor%3A%28%22Crofts%2C%20Antony%20R.%22%29&pagesize-30">Crofts, Antony R. (committee member).

Subjects/Keywords: Photosynthesis; Purple Bacteria; Excitation transfer; open quantum dynamics; hierarchy equations of motion; quantum coherence

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APA (6^th Edition):

Strumpfer, J. (2012). Computational investigation of light harvesting in purple photosynthetic bacteria. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34275

Chicago Manual of Style (16^th Edition):

Strumpfer, Johan. “Computational investigation of light harvesting in purple photosynthetic bacteria.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/34275.

MLA Handbook (7^th Edition):

Strumpfer, Johan. “Computational investigation of light harvesting in purple photosynthetic bacteria.” 2012. Web. 05 Mar 2021.

Vancouver:

Strumpfer J. Computational investigation of light harvesting in purple photosynthetic bacteria. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/34275.

Council of Science Editors:

Strumpfer J. Computational investigation of light harvesting in purple photosynthetic bacteria. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34275

12. Schmidt, Nathan. Deterministic design of peptide-membrane interactions.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29632

► Antimicrobial peptides (AMPs) are present in virtually every multi-cellular organism and comprise an important component of the innate host defense system. Collectively, AMPs have broad… (more)

▼ Antimicrobial peptides (AMPs) are present in virtually every multi-cellular organism and comprise an important component of the innate host defense system. Collectively, AMPs have broad spectrum and selective microbicidal effects. A general mechanism of AMP activity is destabilization of the physical integrity of cell plasma membranes leading to depolarization, leakage, and eventual cell death. This thesis provides a detailed molecular model how AMPs destabilize membranes specifically, based upon their fundamental structural motif: they are amphipathic and cationic. Generic electrostatic and hydrophobic interactions between a cationic, amphipathic AMP and a cell membrane lead to strong binding between the peptide and membrane and subsequent partial insertion of the peptide into the bilayer. The physical chemistry of AMPs leads to a whole taxonomy of local membrane distortions, specific combinations of which are topologically active and can lead to membrane destabilization. AMPs permeabilize model bacterial membranes but not model eukaryotic membranes by selectively generating topologically active saddle-splay ('negative Gaussian') curvature in membranes rich in negative curvature lipids and anionic lipids, compositions characteristic of bacterial cell membranes. A mechanism of action based on saddle-splay membrane curvature generation is broadly enabling, since it is a necessary condition for processes such as pore formation, blebbing, budding, vesicularization, all of which destabilize the barrier function of cell membranes. The topological requirement for saddle-splay curvature places constraints on the amino acid compositions of membrane disruptive peptides. In AMPs decreasing arginine content is offset by a simultaneous increase in lysine and hydrophobic content. This 'saddle-splay curvature design rule' is consistent with the amino acid compositions of 1,080 known cationic AMPs. Furthermore, good correspondence is observed between membrane curvature generation and the microbicidal profiles of prototypical AMPs, suggesting that curvature generation is an indicator of AMP activity. Finally, this thesis concludes with brief discussions on the possibility of other AMP design rules, as well as the presence of amphipathic domains in other curvature generating proteins which generate similar or distinct curvatures to AMPs depending on their structural motifs. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Wong%2C%20Gerard%20C.%20L.%22%29&pagesize-30">Wong, Gerard C. L. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Wong%2C%20Gerard%20C.%20L.%22%29&pagesize-30">Wong, Gerard C. L. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schweizer%2C%20Kenneth%20S.%22%29&pagesize-30">Schweizer, Kenneth S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member).

Subjects/Keywords: antimicrobial peptide; lipid membrane; saddle-splay curvature; membrane curvature; amphipathic peptide; peptide-membrane interactions

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APA (6^th Edition):

Schmidt, N. (2012). Deterministic design of peptide-membrane interactions. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29632

Chicago Manual of Style (16^th Edition):

Schmidt, Nathan. “Deterministic design of peptide-membrane interactions.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/29632.

MLA Handbook (7^th Edition):

Schmidt, Nathan. “Deterministic design of peptide-membrane interactions.” 2012. Web. 05 Mar 2021.

Vancouver:

Schmidt N. Deterministic design of peptide-membrane interactions. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/29632.

Council of Science Editors:

Schmidt N. Deterministic design of peptide-membrane interactions. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29632

13. Yonet Tanyeri, Nihan. Polymers as directing agents for motions of chemical and biological species.

Degree: PhD, 0130, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/26235

► This thesis involves descriptions of solid surface modifications with various polymeric materials which were used as a guiding agent for motion of chemical and biological… (more)

▼ This thesis involves descriptions of solid surface modifications with various polymeric materials which were used as a guiding agent for motion of chemical and biological species. Quasi-two dimensional poly(oligoethylene glycol) acrylate polymer brush based molecular conduits have been designed with the goal of regulating and controlling the diffusive transport of molecular, e.g. organic dyes, and ionic species, e.g. AuCl4-, and Cu2+ ions, along predefined 2-D pathways. The transport of these chemical species has been examined by both fluorescence and dark field microscopy. The polymer brushes were formed through microcontact printing of an initiator, followed by surface-initiated Atom Transfer Radical Polymerization (SI-ATRP). SI-ATRP enables both 2-D patterning with a resolution of about 1 micrometer, and control over the resultant polymer brush thickness (which was varied from 10-100 nm). A hydrophilic poly(oligoethylene glycol) acrylate brushe was selected because of its potential to dissolve a wide range of hydrophilic species. The transport of fluorescent species can be directly followed. A non-lithographic fabrication method was developed for microfluidic devices used in the diffusion studies. Singular channel microfluidic device was utilized to study the directed organic dye diffusion. The AuCl4-, and Cu2+ ion transport was studied by designing molecular devices with two microfluidic channels. We have demonstrated that the various species of interest diffuse much more rapidly along the predefined pathway than along the bare (polymer brush free) regions of the substrate, demonstrating that diffusive conduits for molecular transport can indeed be formed. The protein resistance of poly(N-isopropylacrylamide) (PNIPAM) brushes grafted from silicon wafers was investigated as a function of the chain molecular weight, grafting density, and temperature. Above the lower critical solution temperature (LCST) of 32°C, the collapse of the water swollen chains, determined by ellipsometry, depends on the grafting density and molecular weight. Ellipsometry, radio assay, and fluorescence imaging demonstrated that, below the LCST, the brushes repel protein as effectively as oligoethylene oxide terminated monolayers. Above 32°C, very low levels of protein adsorb on densely grafted brushes, and the amounts of adsorbed protein increase with decreasing brush grafting densities. Brushes that do not exhibit a collapse transition also bind protein, even though the chains remain extended above the LCST. These findings suggest possible mechanisms underlying protein interactions with end-grafted PNIPAM brushes. 3D porous materials on solid surfaces were built to mimic the corneal basement membrane so that we can monitor direction of the corneal epithelia cells behaviors as the surface topography changes. We have used colloidal crystal templating approach to build the 3D porous structures. Polystyrene (PS) colloids were crystallized in a flow cell. The crystals were filled with acrylamide precursor (including photoinitiator, crosslinker)… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Braun%2C%20Paul%20V.%22%29&pagesize-30">Braun, Paul V. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Braun%2C%20Paul%20V.%22%29&pagesize-30">Braun, Paul V. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Lewis%2C%20Jennifer%20A.%22%29&pagesize-30">Lewis, Jennifer A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Cheng%2C%20Jianjun%22%29&pagesize-30">Cheng, Jianjun (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member).

Subjects/Keywords: Surface modification; polymeric materials; microcontact printing; microfluidics; directed surface diffusion; protein adsorption; biomaterials; porous hydrogels; surface topography-cell behavior interaction

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APA (6^th Edition):

Yonet Tanyeri, N. (2011). Polymers as directing agents for motions of chemical and biological species. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/26235

Chicago Manual of Style (16^th Edition):

Yonet Tanyeri, Nihan. “Polymers as directing agents for motions of chemical and biological species.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/26235.

MLA Handbook (7^th Edition):

Yonet Tanyeri, Nihan. “Polymers as directing agents for motions of chemical and biological species.” 2011. Web. 05 Mar 2021.

Vancouver:

Yonet Tanyeri N. Polymers as directing agents for motions of chemical and biological species. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/26235.

Council of Science Editors:

Yonet Tanyeri N. Polymers as directing agents for motions of chemical and biological species. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/26235

14. So, Lok-hang. Gene regulation in Escherichia coli beyond the "rate" approximation.

Degree: PhD, 0240, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/24231

► The blueprint of a living cell is inscribed in its DNA. A region of DNA encoding a protein is called a gene. The cell reads… (more)

▼ The blueprint of a living cell is inscribed in its DNA. A region of DNA encoding a protein is called a gene. The cell reads the DNA and makes molecular machines made up of proteins to carry out all cellular functions required for survival. All cells live in ever-changing environments, and have different needs at different times. The control of when and how often each protein is produced from a gene is called gene regulation. Transcription, the copying of a DNA sequence into a complementary mRNA molecule, is the first step in the information flow from DNA to proteins, and most regulation is already done at the transcription level to avoid the production of superfluous intermediates. A living cell takes environmental stimuli as input, and regulates the activity of genes through DNA-binding proteins called transcription factors. The activity of a gene is described by its time-series of discrete mRNA production events. The events constituting this transcriptional time-series are stochastic and exhibit intermittent, bursty behavior, in bacteria as well as higher organisms. Thus the transcriptional time-series cannot be fully described by a simple chemical “rate”—the probability per unit time of transcribing an mRNA molecule. An important consequence of this temporal complexity is that gene expression level can be tuned by varying different features of the time-series. It is then natural to ask: What modulation scheme is used by the cell to change expression levels of genes? Furthermore, if we look at the transcriptional time-series of multiple genes, would we see different modulation schemes for different genes, or a common modulation scheme shared by all genes? Last but not least, what is the molecular mechanism leading to bursty transcriptional time-series? What are the biophysical states that correspond to the active and inactive periods in a bursty transcriptional time-series? To answer these questions, I characterized the mRNA copy-number statistics from multiple promoters in the model organism Escherichia coli under various growth conditions using single-molecule fluorescence in situ hybridization. The kinetics of the underlying transcriptional time-series was then inferred using the two-state model, a simple stochastic mathematical model that describes bursty transcription time-series. I found that the degree of burstiness depends only on the gene expression level, while being independent of the details of gene regulation. The observed behavior is explained by the underlying variation in the duration of bursting events. At this stage, there is no mechanistic, molecular-level understanding of what gives rise to the bursty behavior of gene activity in bacteria. However, my finding here, that the properties of the transcriptional time-series are gene-independent rather than gene-specific, is contrary to the most common theoretical model used to explain bursty transcriptional time-series in bacteria, which involves the binding and unbinding of transcription factors at the promoter. My data suggests that the… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Golding%2C%20Ido%22%29&pagesize-30">Golding, Ido (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Golding%2C%20Ido%22%29&pagesize-30">Golding, Ido (committee member), Champaign%22%20%2Bcontributor%3A%28%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stack%2C%20John%20D.%22%29&pagesize-30">Stack, John D. (committee member).

Subjects/Keywords: Systems Biology; Quantitative Biology; Biophysics; Stochastic Gene Expression; Escherichia coli; Transcriptional Time-Series; Fluorescence in situ Hybridization; Single-Cell

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APA (6^th Edition):

So, L. (2011). Gene regulation in Escherichia coli beyond the "rate" approximation. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/24231

Chicago Manual of Style (16^th Edition):

So, Lok-hang. “Gene regulation in Escherichia coli beyond the "rate" approximation.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/24231.

MLA Handbook (7^th Edition):

So, Lok-hang. “Gene regulation in Escherichia coli beyond the "rate" approximation.” 2011. Web. 05 Mar 2021.

Vancouver:

So L. Gene regulation in Escherichia coli beyond the "rate" approximation. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/24231.

Council of Science Editors:

So L. Gene regulation in Escherichia coli beyond the "rate" approximation. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/24231

15. Wistrom, Mark. Imaging vortices in superconducting weakly coupled arrays.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/31039

► This thesis presents the direct observations of magnetic flux vortices in superconducting weakly coupled arrays. Real space images of vortices were obtained for various values… (more)

Subjects/Keywords: Scanning SQUID Microscope; Superconducting arrays

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APA (6^th Edition):

Wistrom, M. (2012). Imaging vortices in superconducting weakly coupled arrays. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31039

Chicago Manual of Style (16^th Edition):

Wistrom, Mark. “Imaging vortices in superconducting weakly coupled arrays.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/31039.

MLA Handbook (7^th Edition):

Wistrom, Mark. “Imaging vortices in superconducting weakly coupled arrays.” 2012. Web. 05 Mar 2021.

Vancouver:

Wistrom M. Imaging vortices in superconducting weakly coupled arrays. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/31039.

Council of Science Editors:

Wistrom M. Imaging vortices in superconducting weakly coupled arrays. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31039

16. Wells, David. Nanoscale control in biological and synthetic systems.

Degree: PhD, 0240, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/34407

► The ability to control a system is at the heart of experimental science. Modern experimental methods have pushed the length scale at which control is… (more)

Subjects/Keywords: molecular dynamics; simulation; Grid-Steered Molecular Dynamics (g-smd); Deoxyribonucleic acid (dna); graphene; microtubule

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APA (6^th Edition):

Wells, D. (2012). Nanoscale control in biological and synthetic systems. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/34407

Chicago Manual of Style (16^th Edition):

Wells, David. “Nanoscale control in biological and synthetic systems.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/34407.

MLA Handbook (7^th Edition):

Wells, David. “Nanoscale control in biological and synthetic systems.” 2012. Web. 05 Mar 2021.

Vancouver:

Wells D. Nanoscale control in biological and synthetic systems. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/34407.

Council of Science Editors:

Wells D. Nanoscale control in biological and synthetic systems. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/34407

University of Illinois – Urbana-Champaign

17. Chen, Yi-Chun. Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis.

Degree: PhD, 0408, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/17035

► Development of instrumentation and image analysis methods for the fluorescence lifetime-resolved imaging microscopy (FLIM) were carried out in this thesis. With the new instrument setup… (more)

▼ Development of instrumentation and image analysis methods for the fluorescence lifetime-resolved imaging microscopy (FLIM) were carried out in this thesis. With the new instrument setup and imaging processing algorithms, valuable information has been provided for studying in vivo photosynthesis activities. Chapter 1 introduces the physics of fluorescence lifetimes and different techniques of FLIM measurements. It also provides practical considerations for successfully acquiring fluorescence lifetime imaging data, especially with in vivo samples. Chapter 2 discusses the image analysis algorithms essential for quantitative analysis of high through-put FLIM data. The advantages of the polar plot, a model-free analysis for fluorescence lifetime data, will be described in detail. The denoising procedure, variance-stabilizing-transform translation-invariant Harr wavelet, and the multi-scale edge detection algorithm, wavelet transform, were applied to improve the precision of lifetime resolution in the images, and to select features at the desired spatial frequency, respectively. K-means cluster analysis was used to analyze a polymer brush microfluid device and the Chlorophyll (Chl) a fluorescence transient of Chlamydomonas reinhardtii cells. It will be shown that additional information is provided by the cluster analysis, which would otherwise be hidden in the large quantity of data. Chapter 3 discusses the instrumentation and image analysis methods for the spectrally-resolved FLIM (Spectral-FLIM), which was developed to overcome problems of separating lifetime components in complex environments, especially for fluorescence signals from fluorophores with very low intensity (< 2% of the background). Spectral-FLIM also allows a more detailed and accurate analysis of F??rster resonance energy transfer (FRET) measurements. It will be shown in Chapter 3 that a single measurement of Spectral-FLIM can resolve three fluorescence signals (donor undergoing FRET to the acceptor, acceptor excited by FRET, and directly excited acceptor) on the polar plot. Chapter 4 describes FLIM applications in photosynthesis studies. FLIM data of Chlamydomonas reinhardtii could distinguish the Chl a signals undergoing two different non-photochemical quenching pathways, energy-dependent quenching and state transitions. Spectral-FLIM measurements of avocado leaves (Persea americana Mill.) during the slow phase of Chl a fluorescence transient were also carried out. The data show that the red- and far-red regions of the spectrum have different kinetics and lifetimes, which might suggest that there are two separate locations for xanthophyll molecules. Chapter 5 describes experiments to study the lutein-epoxide and violaxanthin cycles operating in parallel in avocado leaves. A good correlation of the fluorescence intensity and Chlorophyll a lifetimes is shown by FLIM measurements, indicating two different quenching states; therefore, the FLIM measurements provide evidence that both cycles are energy-dependent quenching pathways. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Govindjee%22%29&pagesize-30">Govindjee (committee member), Champaign%22%20%2Bcontributor%3A%28%22Wang%2C%20Yingxiao%22%29&pagesize-30">Wang, Yingxiao (committee member), Champaign%22%20%2Bcontributor%3A%28%22Toussaint%2C%20Kimani%20C.%22%29&pagesize-30">Toussaint, Kimani C. (committee member).

Subjects/Keywords: fluorescence lifetime imaging microscopy (FLIM); F??rster resonance energy transfer (FRET); Spectral-FLIM; fluorescence spectrum; linear unmixing; polar plot; Chlorophyll a fluorescence transient; lutein epoxide cycle; non-photochemical quenching; violaxanthin cycle; chlamydomonas reinhardtii

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APA (6^th Edition):

Chen, Y. (2010). Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/17035

Chicago Manual of Style (16^th Edition):

Chen, Yi-Chun. “Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/17035.

MLA Handbook (7^th Edition):

Chen, Yi-Chun. “Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis.” 2010. Web. 05 Mar 2021.

Vancouver:

Chen Y. Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/17035.

Council of Science Editors:

Chen Y. Fluorescence lifetime-resolved imaging microscopy studies: quantitative image analysis, spectral-FLIM, and photosynthesis. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/17035

University of Illinois – Urbana-Champaign

18. Denos, Sharlene. Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science.

Degree: PhD, 0319, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/14567

► This work deals with three important problems in membrane protein folding studies, namely the preparation and storage of homogeneous small unilamellar vesicles (SUV), the development… (more)

Subjects/Keywords: Proteins; Protein Folding; Crowding; Science Education; Science Outreach; Membrane Proteins; Peptide Design

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APA (6^th Edition):

Denos, S. (2010). Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/14567

Chicago Manual of Style (16^th Edition):

Denos, Sharlene. “Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/14567.

MLA Handbook (7^th Edition):

Denos, Sharlene. “Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science.” 2010. Web. 05 Mar 2021.

Vancouver:

Denos S. Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/14567.

Council of Science Editors:

Denos S. Studies of protein folding on membranes and in crowded environments and bridging the research-teaching gap in K-12 science. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/14567

University of Illinois – Urbana-Champaign

19. Heller, Daniel. Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes.

Degree: PhD, 0335, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/16052

► Single-walled carbon nanotubes (SWNT) have unique photo-physical properties which, through the work in this dissertation, are investigated and harnessed to produce optical sensors with unique… (more)

▼ Single-walled carbon nanotubes (SWNT) have unique photo-physical properties which, through the work in this dissertation, are investigated and harnessed to produce optical sensors with unique capabilities. Early studies of the modulation of SWNT optical properties???both photoluminescence and resonance Raman scattering???demonstrate their tunable nature. Solution dispersed SWNT are sorted by length and the photoluminescence quantum yield is shown to increase nonlinearly with length, suggesting that SWNT ends quench the exciton. The change in Raman scattering cross section and resonant window is mapped as a function of SWNT aggregation, as well as sonochemical effects on photoluminescence. Nanotube photoluminescence and scattering are then detected, via imaging and spectrometry, from within live murine macrophage cells, and shown to be extremely resilient, demonstrating the potential of nanotube-based molecular probes and biosensors. The work culminates in several major findings in optical sensing. We show that a nanotube-ds(GT)15 DNA complex can detect genotoxic analytes by solvatochromism, and measure this from within live cells and tissues in real-time. We find that such optical signals can be multiplexed, resulting in analyte fingerprinting, and a bioanalyte can be detected at the single-molecule level stochastic operation of such sensors. These concepts are employed to detect, identify, and measure bioanalytes, such as reactive oxygen species, as well as explosives, such as TNT and RDX, with single-molecule sensitivity. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Strano%2C%20Michael%20S.%22%29&pagesize-30">Strano, Michael S. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Sligar%2C%20Stephen%20G.%22%29&pagesize-30">Sligar, Stephen G. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Strano%2C%20Michael%20S.%22%29&pagesize-30">Strano, Michael S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Gennis%2C%20Robert%20B.%22%29&pagesize-30">Gennis, Robert B. (committee member).

Subjects/Keywords: Nanotechnology; Carbon nanotubes; Biosensors; Photoluminescence; Near-infrared; Optical sensors; Fluorescence; Single-molecule detection; Spectroscopy

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APA (6^th Edition):

Heller, D. (2010). Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/16052

Chicago Manual of Style (16^th Edition):

Heller, Daniel. “Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/16052.

MLA Handbook (7^th Edition):

Heller, Daniel. “Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes.” 2010. Web. 05 Mar 2021.

Vancouver:

Heller D. Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/16052.

Council of Science Editors:

Heller D. Biopolymer-mediated analyte detection via photoluminescence modulation of single-walled carbon nanotubes. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/16052

University of Illinois – Urbana-Champaign

20. Trabuco, Leonardo G. Investigating the mechanisms of protein synthesis using multi-resolution structural data.

Degree: PhD, 0319, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/16525

► The ribosome is a complex, dynamic molecular machine responsible for protein synthesis in all cells according to the genetic information. Recent breakthroughs in ribosome crystallography… (more)

▼ The ribosome is a complex, dynamic molecular machine responsible for protein synthesis in all cells according to the genetic information. Recent breakthroughs in ribosome crystallography culminated with the 2009 Nobel Prize in Chemistry. Concomitantly, advances in cryo-electron microscopy (cryo-EM) enabled the determination of images of the ribosome trapped in functional states at ever increasing resolution. In order to study different aspects of ribosome function at the atomic level, we developed the molecular dynamics flexible fitting (MDFF) method that combines X-ray and cryo-EM data, furnishing atomic models of the ribosome corresponding to functional intermediates. The MDFF-derived atomic models, combined with molecular dynamics simulations and other computational techniques, allowed us to address different research questions presented in this thesis. First, we found how ribosome-induced changes in the structure of elongation factor Tu leads to its GTPase activation, a crucial step in the decoding of genetic information. Next, we investigated structural and regulatory aspects of ribosomes in complex with a protein-conducting channel, which transports certain nascent proteins across or into membranes. Another area of investigation was the recognition of a regulatory nascent chain by the ribosome, as well as the mechanism by which it leads to translational stalling. Finally, we studied intermediate states of translocation of messenger and transfer RNAs through the ribosome, reconciling data from cryo-EM and single-molecule experiments. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Baranger%2C%20Anne%20M.%22%29&pagesize-30">Baranger, Anne M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Clegg%2C%20Robert%20M.%22%29&pagesize-30">Clegg, Robert M. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member).

Subjects/Keywords: ribosome; molecular dynamics flexible fitting; Cryo-electron microscopy (cryo-EM); Elongation factor Tu (EF-Tu); SecY; TnaC; L1 stalk

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6^th Edition):

Trabuco, L. G. (2010). Investigating the mechanisms of protein synthesis using multi-resolution structural data. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/16525

Chicago Manual of Style (16^th Edition):

Trabuco, Leonardo G. “Investigating the mechanisms of protein synthesis using multi-resolution structural data.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 05, 2021. http://hdl.handle.net/2142/16525.

MLA Handbook (7^th Edition):

Trabuco, Leonardo G. “Investigating the mechanisms of protein synthesis using multi-resolution structural data.” 2010. Web. 05 Mar 2021.

Vancouver:

Trabuco LG. Investigating the mechanisms of protein synthesis using multi-resolution structural data. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 05]. Available from: http://hdl.handle.net/2142/16525.

Council of Science Editors:

Trabuco LG. Investigating the mechanisms of protein synthesis using multi-resolution structural data. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/16525

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