+publisher:"University of Illinois – Urbana-Champaign" +contributor:("Schulten, Klaus J.")

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 01, 2021. http://hdl.handle.net/2142/18378.

MLA Handbook (7^th Edition):

Khalili Araghi, Fatemeh. “Voltage-Gating Mechanism in Potassium Channels.” 2011. Web. 01 Mar 2021.

Vancouver:

Khalili Araghi F. Voltage-Gating Mechanism in Potassium Channels. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 01]. 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. Brenner, Michael. Force manipulation and single molecule FRET of transcriptional regulatory factors.

Degree: PhD, 0335, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/42145

► Mechanical tension plays a large role in cell development ranging from morphology to gene expression. On the molecular level, the effects of tension can be… (more)

▼ Mechanical tension plays a large role in cell development ranging from morphology to gene expression. On the molecular level, the effects of tension can be seen in the dynamic arrangement of membrane proteins as well as the recruitment and activation of intracellular proteins leading to downstream signaling cascades regulating transcription. Forces applied to biopolymers during in vitro force measurements offer greater understanding of the effects of tension on molecules in live cells, and experimental techniques in test tubes and live cells can often overlap. Indeed, when forces exerted on cellular components can be calibrated ex vivo with force spectroscopy, a powerful tool is available for researchers in probing cellular mechanotransduction on the molecular scale. Here we report the effect of peptide length on the tension sensing properties of GPGGA peptide repeats using single-molecule fluorescence-force spectroscopy. Additionally, we report on the mechanical properties of IκBα, a transcriptional regulator, and the C-terminal domain of RNA polymerase II. Modification of proteins and peptides for single-molecule studies was extended to incorporation of unnatural amino acids into a DNA helicase. Chemical modification of RNA was performed to enable total-internal reflection microscopy of single molecules of the guanine riboswitch aptamer domain, which is involved in transcription termination. The combined FRET data support a model in which the unfolded state of the aptamer domain has a highly dynamic P2 helix that switches rapidly between two orientations relative to nondynamic P1 and P3. At <<1 mM Mg2+ (in the presence of saturating guanine) or 1 mM Mg2+ (in the absence of guanine), the riboswitch starts to adopt a folded conformation in which loop-loop interactions lock P2 and P3 into place. Another transcription terminator, Rho helicase, was studied using single molecule techniques. Our observations confirm the tethered-tracking model for RNA-directed Rho motion and suggest a repetitive translocation mechanism involving reversible, step-wise threading of RNA through the central Rho cavity in discrete steps, leading to loop formation at the exit side of the cavity. Our data reveal that secondary structure and lower UC content of RNA impedes processive translocation and results in more backwards motion of Rho helicase. We propose a global model for Rho dynamics. Furthermore, these results provide general insights into the mechanisms of RecA-family helicases and ring-shaped ATPases. Preliminary studies with the human Argonaute2 nuclease will also be presented. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (advisor), Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (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%22Katzenellenbogen%2C%20John%20A.%22%29&pagesize-30">Katzenellenbogen, John A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Selvin%2C%20Paul%20R.%22%29&pagesize-30">Selvin, Paul R. (committee member).

Subjects/Keywords: transcription; single-molecule; optical tweezers; Förster Resonance Energy Transfer (FRET); biophysics

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

APA (6^th Edition):

Brenner, M. (2013). Force manipulation and single molecule FRET of transcriptional regulatory factors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/42145

Chicago Manual of Style (16^th Edition):

Brenner, Michael. “Force manipulation and single molecule FRET of transcriptional regulatory factors.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/42145.

MLA Handbook (7^th Edition):

Brenner, Michael. “Force manipulation and single molecule FRET of transcriptional regulatory factors.” 2013. Web. 01 Mar 2021.

Vancouver:

Brenner M. Force manipulation and single molecule FRET of transcriptional regulatory factors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/42145.

Council of Science Editors:

Brenner M. Force manipulation and single molecule FRET of transcriptional regulatory factors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/42145

University of Illinois – Urbana-Champaign

3. Enkavi, Giray. Mechanism and energetics of membrane transporters and channels.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/46912

► Living cells have evolved specialized transport proteins called membrane transporters and channels that catalyze exchange of materials across the cell membrane. Membrane trans- porters couple… (more)

▼ Living cells have evolved specialized transport proteins called membrane transporters and channels that catalyze exchange of materials across the cell membrane. Membrane trans- porters couple the active transport of their specific substrates against their electrochemical gradient. On the other hand, membrane channels facilitate passive diffusion of polar or charged molecules down their electrochemical gradient. We present here molecular dy- namics (MD) investigation of a membrane transporter, glycerol-3 phosphate transporter (GlpT) and two membrane channels, urea transporter (UT) and aquaporin (Aqp1). Each simulations presented here provided a dynamical and atomistic picture of the protein of interest in a collaborative effort with an experimental lab. Membrane transporters use various source of cellular energy, e.g., ATP binding and hydrolysis in primary active transporters, and pre-established electrochemical gradient of molecular species other than their substrate in the case of secondary active trans- porters. All membrane transporters use the widely-accepted "alternating-access mecha- nism", which ensures that the substrate is only accessible from one side of the membrane at a given time, and relies on complex protein conformational changes between outward- facing (OF) and inward-facing (IF) states, going through several intermediate states. The first system that we investigated is the glycerol-3-phosphate transporter (GlpT), an antiporter member of the MFS. GlpT transports glycerol-3-phosphate (G3P) into the cell in exchange for inorganic phosphate (Pi ). Major facilitator superfamily (MFS) is the largest superfamily of secondary active transporters and catalyze the transport of an enormous variety of small solute molecules across biological membranes. Individual MFS members, despite their architectural similarities, exhibit strict specificity toward the substrates that they transport. The structural basis of this specificity, however, is poorly understood. Our collaborators, Da-Neng Wang Lab (New York University, NY) performed mutagenesis studies and transport assays, while we performed equilibrium sim- ulations of wild-type GlpT and several of its mutant forms in membrane in the presence of all physiologically relevant substrates (Pi , Pi2 , G3P , and G3P 2 ) to characterize the determinants of substrate selectivity and conformational response of the protein to substrate binding. The positive electrostatic potential of the lumen of GlpT recruits substrate and drives binding. Only a few amino acid residues that line the transporter lumen act as specificity determinants. The phosphate moiety of Pi and G3P bind to a common binding site and residues involved solely in recognition of the glycerol moiety of G3P confers it a higher binding affinity. Furthermore, the simulations characterized the process and mechanism of substrate binding, and the protein's initial conformational re- sponse. All substrate-bound systems resulted in partial closing of the cytoplasmic… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (advisor), Champaign%22%20%2Bcontributor%3A%28%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (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%22Gennis%2C%20Robert%20B.%22%29&pagesize-30">Gennis, Robert B. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Nair%2C%20Satish%20K.%22%29&pagesize-30">Nair, Satish K. (committee member).

Subjects/Keywords: membrane transporters; membrane channels; major facilitator superfamily; antiporter; urea; aquaporin

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

APA (6^th Edition):

Enkavi, G. (2014). Mechanism and energetics of membrane transporters and channels. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46912

Chicago Manual of Style (16^th Edition):

Enkavi, Giray. “Mechanism and energetics of membrane transporters and channels.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/46912.

MLA Handbook (7^th Edition):

Enkavi, Giray. “Mechanism and energetics of membrane transporters and channels.” 2014. Web. 01 Mar 2021.

Vancouver:

Enkavi G. Mechanism and energetics of membrane transporters and channels. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/46912.

Council of Science Editors:

Enkavi G. Mechanism and energetics of membrane transporters and channels. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46912

University of Illinois – Urbana-Champaign

4. Girdhar, Anuj. Quantum transport in graphene nanotransistors.

Degree: PhD, Physics, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/78634

► Over the past decade, interest in using graphene in condensed-matter physics and materials science applications has exploded, owing to its unique electrical properties. Narrow strips… (more)

▼ Over the past decade, interest in using graphene in condensed-matter physics and materials science applications has exploded, owing to its unique electrical properties. Narrow strips of graphene, called graphene nanoribbons, also display exotic behavior. A nanoribbon’s edge geometry determines its electronic transport properties, and the rich behavior of conductance of nanoribbons in response to external potentials makes them ideal for use within transistors. In this thesis, we work towards creating an accurate model of graphene nanoribbon transistors, and we asses two possible applications which exploit their amazing potential. We begin by outlining the basic theoretical and computational framework for the model developed in this work. We then demonstrate the capability of graphene nanoribbon transistors, with nanopores, to electronically detect, characterize, and manipulate translocating DNA strands. Specifically, we explore the tunability of such devices, by examining the role of lattice geometry, such as a quantum point contact constriction, on their performance. We perform a demonstration of the ability to detect the passage of double and single-stranded DNA, through molecular dynamics simulations. The transistors presented are capable of sensing the helical shape of double-stranded DNA molecules, the unraveling of a DNA helix into a planar-zipper form, and the passage of individual nucleotides of a single strand of DNA through the nanopore. We outline a preliminary analysis on the proper design of a multilayer transistor stack to control both the electronic properties of the conducting membrane, as well as the motion of the DNA. Lastly, we present another type of nanoribbon device, an all-carbon spintronic transistor for use in cascaded logic circuits. A thorough analysis of the transport properties of zigzag nanoribbon transistors in magnetic fields, in addition to the design and construction of logic gate circuits containing these spintronic transistors, is presented. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Leburton%2C%20Jean-Pierre%22%29&pagesize-30">Leburton, Jean-Pierre (advisor), Champaign%22%20%2Bcontributor%3A%28%22Mason%2C%20Nadya%22%29&pagesize-30">Mason, Nadya (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%22Bashir%2C%20Rashid%22%29&pagesize-30">Bashir, Rashid (committee member).

Subjects/Keywords: graphene; quantum; transport; nanoribbon; Deoxyribonucleic Acid (DNA); sequencing; transistor; nanopore; sensing; genome; monolayer; gate

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

APA (6^th Edition):

Girdhar, A. (2015). Quantum transport in graphene nanotransistors. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/78634

Chicago Manual of Style (16^th Edition):

Girdhar, Anuj. “Quantum transport in graphene nanotransistors.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/78634.

MLA Handbook (7^th Edition):

Girdhar, Anuj. “Quantum transport in graphene nanotransistors.” 2015. Web. 01 Mar 2021.

Vancouver:

Girdhar A. Quantum transport in graphene nanotransistors. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/78634.

Council of Science Editors:

Girdhar A. Quantum transport in graphene nanotransistors. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/78634

University of Illinois – Urbana-Champaign

5. Yu, Jitong. Some effects of dimensionality and defects on superconductivity.

Degree: PhD, Physics, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/87980

► This thesis reports some theoretical studies of superconductivity with reduced dimensions. After an intro- duction to the physics of superconductivity with reduced dimensions, we reports… (more)

Subjects/Keywords: superconductor; superconducting; dimensionality; defect; nanowire; Langer–Ambegaokar–McCumber–Halperin (LAMH); resistance; planar defects; Sr2RuO4; vortex pinning; critical current

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

APA (6^th Edition):

Yu, J. (2015). Some effects of dimensionality and defects on superconductivity. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/87980

Chicago Manual of Style (16^th Edition):

Yu, Jitong. “Some effects of dimensionality and defects on superconductivity.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/87980.

MLA Handbook (7^th Edition):

Yu, Jitong. “Some effects of dimensionality and defects on superconductivity.” 2015. Web. 01 Mar 2021.

Vancouver:

Yu J. Some effects of dimensionality and defects on superconductivity. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/87980.

Council of Science Editors:

Yu J. Some effects of dimensionality and defects on superconductivity. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/87980

University of Illinois – Urbana-Champaign

6. Li, Jing. Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/49738

► Membrane transporters are specialized molecular machinery for selective, regulable, efficient, and more importantly, active transport of diverse chemical species, e.g., nutrients, reaction precursors and products,… (more)

▼ Membrane transporters are specialized molecular machinery for selective, regulable, efficient, and more importantly, active transport of diverse chemical species, e.g., nutrients, reaction precursors and products, and chemicals transmitting signals, across the cellular membrane. As a major class of membrane transporters, secondary active transporters couple vectorial translocation of one solute, typically Na+ or H+ ions, along its electrochemical gradient to uphill transport of their substrates. To fulfill its function, transporter operates via an alternating-access mechanism, in which it undergoes structural transitions between outward-facing (OF) and inward-facing (IF) states, to translocate substrate from one to the other side of the membrane. The alternating access mechanism has received substantial supports from recent structural studies. However, as an inherently dynamic process, several critical aspects of alternating access mechanism remain poorly understood solely on the basis of limited static snapshots of the transport cycle. To address several key questions of alternating access model and to elucidate the underlying molecular mechanism at atomic level, we conducted computational studies mainly using molecular dynamics (MD) simulations on two secondary active transporters, i.e., bacterial Na+–coupled glucose transporter (vSGLT), and the benzyl-hydantoin transporter (Mhp1). vSGLT presents the first IF structural state of a LeuT-fold transporter, and Mhp1 is the first secondary active transporter structurally resolved in both OF and IF states. Both of vSGLT and Mhp1 provided crucial information toward better characterization of the alternating–access mechanism. Based on the crystal structures of these two transporters, the computational studies elucidated several key functional molecular events in the transport cycle, and provided deeper insights of the underlying molecular mechanism of alternating access model. My early study on vSGLT identified the first ion-releasing state in the secondary active transporters. The crystal structure of vSGLT reports the transporter in its substrate-bound state, with a Na+ ion modeled in a binding site corresponding to that of a homologous protein, leucine transporter (LeuT). In repeated MD simulations, however, the Na+ ion is found instable, invariably and spontaneously diffusing out of the transporter through a pathway lined by D189, which appears to facilitate the diffusion of the ion toward the cytoplasm. Further analysis of the trajectories and close structural examination, in particular comparison of the Na+-binding sites of vSGLT and LeuT, strongly indicates that the crystal structure of vSGLT actually represents an ion-releasing state of the transporter. Structural comparison of LeuT-fold transporters provides the first example in which we clearly see how global structural changes (tilting and shift of the helices) that take place during the transition between the IF and OF states, propagate into specific binding site of the ion (expansion of the site), thus,… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (advisor), Champaign%22%20%2Bcontributor%3A%28%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (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%22Leckband%2C%20Deborah%20E.%22%29&pagesize-30">Leckband, Deborah E. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Grosman%2C%20Claudio%20F.%22%29&pagesize-30">Grosman, Claudio F. (committee member).

Subjects/Keywords: Secondary active transporter; Alternating access mechanism; Molecular dynamics simulations; Ion-coupling mechanism; Water-conducting state; Ion release; Substrate release; LeuT-fold transporters

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APA (6^th Edition):

Li, J. (2014). Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/49738

Chicago Manual of Style (16^th Edition):

Li, Jing. “Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/49738.

MLA Handbook (7^th Edition):

Li, Jing. “Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations.” 2014. Web. 01 Mar 2021.

Vancouver:

Li J. Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/49738.

Council of Science Editors:

Li J. Molecular insights into alternating access mechanism of secondary active transporters from molecular dynamics simulations. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/49738

University of Illinois – Urbana-Champaign

7. Chen, Ke. Evolution and assembly of the ribosome.

Degree: PhD, 0319, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/46886

► The ribosome is a large macromolecular assembly responsible for protein synthesis in all living cells. A typical bacterial ribosome consists of three ribosomal RNA (rRNA)… (more)

▼ The ribosome is a large macromolecular assembly responsible for protein synthesis in all living cells. A typical bacterial ribosome consists of three ribosomal RNA (rRNA) molecules and approximately fifty ribosomal proteins (r-proteins), which are arranged into two subunits of unequal size and distinct function. The large subunit promotes formation of the peptide bond, and the small subunit enforces the recognition between the mRNA codons and the tRNA anticodons. With the availability of the ribosome crystal structure, it becomes clear that the two major functions, peptide bond formation and decoding, are performed within an entire RNA environment devoid of proteins. Combining with the fact that the majority of the ribosomal components are conserved across all three domains of life, it is believed that the ribosome has its origin deep in the RNA world before the last universal common ancestor (LUCA). Further evolutionary studies lead to the hypothesis that the evolution of the ribosome begins with a prototype ribozyme that catalyzes peptidyl-transferase reaction. Structural and sequence analysis suggests that the small ribozyme capable of catalyzing formation of short peptides may still exist in the core of the modern ribosome. Accordingly, a proto-ribosome model is constructed computationally using RNA fragments near the peptidyl-transferase center (PTC), and is proven to be stable throughout the micro-second molecular dynamics (MD) simulations. The model is capable of incorporating freely diffusing substrates spontaneously into its binding site, and holds them in both pockets long enough to reach a transition intermediate favorable for peptide bond formation. This in silico designed proto-ribosome is then subjected to experimental investigations to test its ability to assemble and bind potential substrates in solution. The successful design of the proto-ribosome presents a possible scenario for the initial development of the early translation apparatus. The proto-ribosome coupled with the probable parallel evolution of ancient tRNAs might have driven the emergence of the oldest coded protein shortly afterwards. The universally conserved r-protein S4 is likely an ancient protein due to its role in the initiation of the 30S assembly, control of the translational accuracy, and regulation of the conserved operon. However, the N-terminal domain of S4 is identified as a “molecular signature” that distinguishes between Bacteria and Archaea, and hence might be a newer addition to the protein. The presence of both an old and a new component in the same protein makes it an extremely interesting case to study for the ribosomal evolution. Therefore, we perform phylogenetic analysis of S4 in relation to a broad sharing of zinc/non-zinc binding sequence in the N-terminal domain of the protein, and study the scope of horizontal gene transfer (HGT) of S4 during bacterial evolution. The complex history presented for “core” protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Martin%20Gruebele%22%29&pagesize-30">Martin Gruebele (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member).

Subjects/Keywords: the RNA world; last universal common ancestor (LUCA); ribosomal evolution; ribosomal signature; ribosomal assembly; ribosomal RNA (rRNA); r-proteins; r-protein S4; RNA folding; protein binding; ligand binding; fly-casting mechanism; single-molecule Förster resonance energy transfer (smFRET); selective 20-hydroxyl acylation analyzed by primer extension (SHAPE); footprinting; molecular dynamics simulation; structure-based Go potential; micro-second simulation

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

APA (6^th Edition):

Chen, K. (2014). Evolution and assembly of the ribosome. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/46886

Chicago Manual of Style (16^th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/46886.

MLA Handbook (7^th Edition):

Chen, Ke. “Evolution and assembly of the ribosome.” 2014. Web. 01 Mar 2021.

Vancouver:

Chen K. Evolution and assembly of the ribosome. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/46886.

Council of Science Editors:

Chen K. Evolution and assembly of the ribosome. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/46886

University of Illinois – Urbana-Champaign

8. Mathew, Damien C. Computational studies of origins of life scenarios.

Degree: PhD, 0319, 2011, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/18307

► Understanding the origins of life on Earth is one of the most intriguing problems facing science today. In the research presented here, we apply computational… (more)

▼ Understanding the origins of life on Earth is one of the most intriguing problems facing science today. In the research presented here, we apply computational methods to explore origins of life scenarios. In particular, we focus on the origins of the genetic code and the intersection between geochemistry and a primordial ``biochemistry" in which mononucleotides could form short oligoucleotide chains. We also apply quantum chemical methods to a modern biochemical reaction, the charging of tRNA by an aminoacyl-tRNA synthetase, in order to shed light on the possible chemistry one may want to consider in problems relating to the origins of life. The question of how codons came to be associated with specific amino acids in the present form of the genetic code is one fundamental part of gaining insight into the origins of life. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and nucleobases that may have played a role in establishing the genetic code. Through these experiments it was found that a property of amino acids called the polar requirement (PR) is correlated to the organization of the codon table. No other property of amino acids has been found that correlates with the codon table as well as PR, indicating that PR is uniquely related to the modern genetic code. Using molecular dynamics simulations of amino acids in solutions of water and dimethylpyridine used to experimentally measure PR, we show that variations in the partitioning between the two phases as described by radial distribution functions correlate well with the measured PRs. Partition coefficients based on probability densities of the amino acids in each phase have the linear behavior with base concentration as suggested by the PR experiments. We also investigate the possible roles of inorganic mineral surfaces in catalysis and stabilization of reactions essential for early forms of replicating systems that could have evolved into biochemical processes we know today. We study a proposed origins of life scenario involving the clay montmorillonite, as well as a generalized form of a charged surface, and their catalytic role in forming oligonucleotides from activated mononucleotides. Clay and mineral surfaces are important for concentrating the reactants and for promoting nucleotide polymerization reactions. Using classical molecular dynamics methods we provide atomic details of reactant conformations prior to polynucleotide formation, lending insight into previously reported experimental observations of this phenomenon. The simulations clarify the catalytic role of metal ions, demonstrate that reactions leading to correct linkages take place primarily in the interlayer, and explain the observed sequence selectivity in the elongation of the chain. The study comparing reaction probabilities involving L- and D- chiral forms of the reactants has found enhancement of homochiral over heterochiral products when catalyzed by montmorillonite. Finally, we shift our perspective on the… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Crofts%2C%20Antony%20R.%22%29&pagesize-30">Crofts, Antony R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Dunning%2C%20Thomas%20H.%22%29&pagesize-30">Dunning, Thomas H. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member).

Subjects/Keywords: origins of life; evolution; molecular dynamics; genetic code

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

APA (6^th Edition):

Mathew, D. C. (2011). Computational studies of origins of life scenarios. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/18307

Chicago Manual of Style (16^th Edition):

Mathew, Damien C. “Computational studies of origins of life scenarios.” 2011. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/18307.

MLA Handbook (7^th Edition):

Mathew, Damien C. “Computational studies of origins of life scenarios.” 2011. Web. 01 Mar 2021.

Vancouver:

Mathew DC. Computational studies of origins of life scenarios. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2011. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/18307.

Council of Science Editors:

Mathew DC. Computational studies of origins of life scenarios. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2011. Available from: http://hdl.handle.net/2142/18307

University of Illinois – Urbana-Champaign

9. Latinwo, Folarin. Fluctuation theorems and work relations for single polymer rheology.

Degree: PhD, 0300, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/49677

► Synthetic and biological polymeric materials are ubiquitous in nature and modern technology. The emergent properties afforded by these materials allows for wide a array of… (more)

▼ Synthetic and biological polymeric materials are ubiquitous in nature and modern technology. The emergent properties afforded by these materials allows for wide a array of applications as found in adhesives, coatings, and synthetic polymers for plastics. Importantly, the molecular properties of polymeric systems ultimately determine their bulk macroscopic response and behavior in equilibrium and highly nonequilibrium conditions. As a result, the field of single polymer rheology can play a key role in establishing a molecular level understanding of polymeric systems by investigating the dynamics of single chains. Single polymer rheology is now a well-established approach to study polymer dynamics from experimental and computational perspectives. In general, this approach allows for the determination of molecular subpopulations, relaxation, and polymer chain dynamics in a wide variety of flows. Despite recent progress, current methods in single polymer rheology do not allow for the determination of equilibrium and nonequilibrium thermodynamic properties of polymeric systems. Moreover, it is challenging to connect backbone dynamics to key macroscopic rheological phenomena. In this context, the impact of single polymer rheology has remained limited for the past two decades. In this thesis, we address these challenges by developing and applying fluctuation theorems and nonequilibrium work relations to the field of single polymer rheology. The discovery of thermodynamic identities known as nonequilibrium work relations (NWRs) and fluctuation theorems (FTs) has catalyzed recent advances in statistical mechanics. In general, work relations provide an unprecedented route to extract fundamental materials properties of equilibrium and nonequilibrium systems. Furthermore, these identities have uncovered a broad range of unexpected and remarkable thermodynamic phenomena, including molecular level violations to the second law of thermodynamics. In the context of rheology and fluid mechanics, thermodynamics plays a key role in the understanding and design of a wide array of processes, including flow-induced phase separation and crystallization. As a result, there is a strong need for new methods to analyze the dynamics of complex fluids. In this thesis, we apply the Jarzynski/Hatano/Sasa equality and Crooks fluctuation theorem to determine equilibrium and nonequilibrium properties of polymer solutions in fluid flow. In particular, we use a combination of single molecule polymer experiments and computer simulations to probe the application of these NWRs to polymer dynamics in shear and extensional flows. Using this approach, we determine the equilibrium linear and nonlinear elasticity, the nonequilibrium free energies, and entropies of flowing polymer solutions. Interestingly, we also find that fundamental thermodynamic quantities are related to well known rheological functions such as the longest polymer relaxation time, viscosity, and stress. Overall, NWRs appear to provide a simple and distinct framework that… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Schroeder%2C%20Charles%20M.%22%29&pagesize-30">Schroeder, Charles M. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Schroeder%2C%20Charles%20M.%22%29&pagesize-30">Schroeder, Charles M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Higdon%2C%20Jonathan%20J.L.%22%29&pagesize-30">Higdon, Jonathan J.L. (committee member), 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%22Schweizer%2C%20Kenneth%20S.%22%29&pagesize-30">Schweizer, Kenneth S. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ferguson%2C%20Andrew%22%29&pagesize-30">Ferguson, Andrew (committee member).

Subjects/Keywords: Thermodynamics; Rheology; Work Relations; Polymers

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

APA (6^th Edition):

Latinwo, F. (2014). Fluctuation theorems and work relations for single polymer rheology. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/49677

Chicago Manual of Style (16^th Edition):

Latinwo, Folarin. “Fluctuation theorems and work relations for single polymer rheology.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/49677.

MLA Handbook (7^th Edition):

Latinwo, Folarin. “Fluctuation theorems and work relations for single polymer rheology.” 2014. Web. 01 Mar 2021.

Vancouver:

Latinwo F. Fluctuation theorems and work relations for single polymer rheology. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/49677.

Council of Science Editors:

Latinwo F. Fluctuation theorems and work relations for single polymer rheology. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/49677

University of Illinois – Urbana-Champaign

10. Comellas Canal, Gemma. Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils.

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

URL: http://hdl.handle.net/2142/31996

► In my thesis, I have focused on new methodology development combined with state-of-the-art solid-state nuclear magnetic resonance (NMR) experiments with scanning transmission electron microscopy (STEM)… (more)

▼ In my thesis, I have focused on new methodology development combined with state-of-the-art solid-state nuclear magnetic resonance (NMR) experiments with scanning transmission electron microscopy (STEM) to obtain atomic level structural information of the alpha-synuclein (AS) fibrils and the mechanism of their formation; We first investigated the effect of protein deuteration and 1H decoupling optimization to maximize the resolution and sensitivity of biomolecular solid-state NMR; We then applied state-of-the-art solid-state NMR experiments to do a detailed structural characterization and conformational dynamics of AS fibrils using improved sample preparation and labeling schemes; These results show that the core of the fibrils extends for about 70 residues with a repeated secondary structure motif; Additionally, it demonstrates that the three mutation sites (A30P, E46K, A53T) are located in structured regions of the fibrils; Upon mutation, we have shown that the structure suffers major and minor perturbations by E46K and A53T, respectively; while the structure is unaltered by A30P; The fibril formation has also been investigated by capturing the transition from α-helical to β-sheet at the atomic level using solid-state NMR; Additionally, to investigate the AS fold, the mass-per-length (MPL) measurement of the fibrils has been obtained using STEM that together with solid-state NMR restraints have been used to propose possible models of how the fibrils arrange; Finally, initial results for solving 3D high-resolution structures of large proteins with new computational methods have been investigated. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Rienstra%2C%20Chad%20M.%22%29&pagesize-30">Rienstra, Chad M. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Rienstra%2C%20Chad%20M.%22%29&pagesize-30">Rienstra, Chad M. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22George%2C%20Julia%20M.%22%29&pagesize-30">George, Julia M. (committee member), 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%22Martin%2C%20Gruebele%20H.%22%29&pagesize-30">Martin, Gruebele H. (committee member).

Subjects/Keywords: Nuclear magnetic resonance (NMR); magic-angle spinning (MAS); protein structure; alpha-synuclein (AS)

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

APA (6^th Edition):

Comellas Canal, G. (2012). Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31996

Chicago Manual of Style (16^th Edition):

Comellas Canal, Gemma. “Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/31996.

MLA Handbook (7^th Edition):

Comellas Canal, Gemma. “Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils.” 2012. Web. 01 Mar 2021.

Vancouver:

Comellas Canal G. Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/31996.

Council of Science Editors:

Comellas Canal G. Structure, conformational dynamics and formation of large amyloids: the case of alpha-synuclein fibrils. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31996

University of Illinois – Urbana-Champaign

11. Sanghi, Tarun. Multiscale models for structure and dynamics of confined fluids.

Degree: PhD, Mechanical Engineering, 2016, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/92711

► In this dissertation, using systematic coarse-graining, we develop multiscale models to study structural and dynamical properties of confined fluids. With the advent of nanofluidics and… (more)

▼ In this dissertation, using systematic coarse-graining, we develop multiscale models to study structural and dynamical properties of confined fluids. With the advent of nanofluidics and nanobiotechnology, fluids confined inside nanometer scale geometries have become a subject of both fundamental investigation and applied research. An understanding of the structural and dynamical properties of fluids at nanoscale is essential for designing novel engineering applications such as nanofiltration, carbon-dioxide sequestration, single-file transport, nanomedicine and many others. Our structural model is based on an empirical potential based quasi-continuum theory (EQT). EQT is a multiscale theory that seamlessly integrates the interatomic potentials describing various atomic interactions into a continuum framework to obtain the equilibrium density and potential profiles of confined fluids in a self-consistent manner. The density and potential profiles obtained from it are comparable in accuracy with those obtained from particle-based methods such as molecular dynamics (MD) simulations. Also, being a continuum approach, EQT is very simple to implement and is computationally several orders of magnitude faster than MD simulations. The central task in EQT is the development of quasi-continuum potential models that accurately describe the wall-fluid and fluid-fluid interactions in confined fluids. Using systematic coarse-graining, we discuss the development of coarse-grained single-site (CGSS) pair-potentials and quasi-continuum potential models for poly-atomic fluids. Proposed potential models systematically incorporate the effect of size, geometric shape and orientation of poly-atomic fluids to predict the correct microstructure in confined environments. We take carbon-dioxide as an example fluid and demonstrate the applicability of the potentials models in EQT as well as coarse-grained MD (CG-MD) simulations to predict the center-of-mass (COM) density and potential profiles of carbon-dioxide inside slit-shape graphite nanochannels at several high and low pressure confinements. The results obtained from EQT and CG-MD simulations are found in good agreement with those obtained from all-atom MD (AA-MD) simulations. To develop dynamical models, one fundamental question is to understand the role of thermal noise in nanofluidic dynamics and transport. We discuss a combined memory function equation (MFE) and generalized Langevin equation (GLE) based approach (referred to as MFE/GLE formulation) to characterize thermal noise in molecular fluids. Using MFE/GLE formulation in conjunction with MD simulation, we extract and analyze the statistical properties of thermal noise in confined fluids. We find that the thermal noise correlation time of the confined fluid does not vary significantly across the confinement and is quite similar to that of the corresponding reference bulk state fluid. We show that it is the cross-correlation of the mean force with the molecular velocity that gives rise to the spatial anisotropy in the… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Aluru%2C%20Narayana%20R%22%29&pagesize-30">Aluru, Narayana R (advisor), Champaign%22%20%2Bcontributor%3A%28%22Aluru%2C%20Narayana%20R%22%29&pagesize-30">Aluru, Narayana R (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%22Schweizer%2C%20Kenneth%20S%22%29&pagesize-30">Schweizer, Kenneth S (committee member), Champaign%22%20%2Bcontributor%3A%28%22Ferguson%2C%20Andrew%20L%22%29&pagesize-30">Ferguson, Andrew L (committee member).

Subjects/Keywords: Multiscale modes; Structure and Dynamics of Confined fluids; Generalized Langevin Equation; Thermal noise; Empirical potential based Quasi-continuum Theory (EQT)

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

APA (6^th Edition):

Sanghi, T. (2016). Multiscale models for structure and dynamics of confined fluids. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/92711

Chicago Manual of Style (16^th Edition):

Sanghi, Tarun. “Multiscale models for structure and dynamics of confined fluids.” 2016. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/92711.

MLA Handbook (7^th Edition):

Sanghi, Tarun. “Multiscale models for structure and dynamics of confined fluids.” 2016. Web. 01 Mar 2021.

Vancouver:

Sanghi T. Multiscale models for structure and dynamics of confined fluids. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2016. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/92711.

Council of Science Editors:

Sanghi T. Multiscale models for structure and dynamics of confined fluids. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2016. Available from: http://hdl.handle.net/2142/92711

12. Gamini, Ramya Bhargavi. Molecular mechanisms of gating and selectivity in transport channels.

Degree: PhD, 0319, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/45293

► Transport channels and pores are of fundamental importance for translocation of molecules across the otherwise-impermeable biological membrane. As a conduit for the passage of material,… (more)

▼ Transport channels and pores are of fundamental importance for translocation of molecules across the otherwise-impermeable biological membrane. As a conduit for the passage of material, specific membrane channels must accomplish the task of selective transport of molecules, while preventing unnecessary loss of other cellular material. The nuclear pore complex (NPC), and the mechanosensitive channel of small conductance, MscS are the focus of the research presented in this thesis. NPCs are sole gateways for passage of material across the nuclear envelope of eukaryotic cells. Several unstructured proteins that are rich in phenylaline- glycine motifs (FG-nups) form the central transport channel. Small molecules passively diffuse through the channel but, larger molecules are selectively transported via transport factors (TFs), which apparently interact with the FG-repeats of the nups in the channel. To understand how nups are assembled in the interior of the NPC, assemblies of one kind of nup, starting from different initial states, are investigated. Results suggest nups form different structures in different regions of the central channel. While only molecules of size < 9nm can penetrate through, a limit known for passive diffusion, the resulting structure posed a selectivity barrier for larger molecules that can be penetrated only via TF interactions. Mechanosensitive (MS) channels, bacterial inner-membrane proteins, open and close in response to mechanical stimuli such as changes in membrane tension during osmotic stress. These channels act as safety valves preventing cell lysis upon hypoosmotic cell swelling: the channels open under membrane tension to release osmolytes along with water. MscS, consists, beside the transmembrane channel, of a large cytoplasmic domain (CD) that features a balloon-like, water filled chamber opening to the cytoplasm through seven side pores and a small distal pore. The CD is apparently a molecular sieve covering the channel, that optimizes loss of osmolytes during osmoadaptation. Diffusion theory and MD simulations are employed to explore the transport kinetics of Glu- and K+ as representative osmolytes. A role of a filter is suggested for the CD such that it balances passage of Glu- and K+ osmolytes, to yield a largely neutral efflux, thereby, reducing cell depolarization in the open state that also conserves to a large degree the essential metabolite Glu-. 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%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (committee member), Champaign%22%20%2Bcontributor%3A%28%22Grosman%2C%20Claudio%20F.%22%29&pagesize-30">Grosman, Claudio F. (committee member).

Subjects/Keywords: Transport Channels; Molecular Dynamics; nuclear pore complex; mechanosensitive channel of small conductance

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

APA (6^th Edition):

Gamini, R. B. (2013). Molecular mechanisms of gating and selectivity in transport channels. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/45293

Chicago Manual of Style (16^th Edition):

Gamini, Ramya Bhargavi. “Molecular mechanisms of gating and selectivity in transport channels.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/45293.

MLA Handbook (7^th Edition):

Gamini, Ramya Bhargavi. “Molecular mechanisms of gating and selectivity in transport channels.” 2013. Web. 01 Mar 2021.

Vancouver:

Gamini RB. Molecular mechanisms of gating and selectivity in transport channels. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/45293.

Council of Science Editors:

Gamini RB. Molecular mechanisms of gating and selectivity in transport channels. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/45293

13. Chandler, Danielle. Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7.

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

URL: http://hdl.handle.net/2142/29569

► This dissertation presents research on two different biological systems: (1) the light-harvesting proteins in the chromatophores of purple photosynthetic bacteria, and (2) the structure and… (more)

▼ This dissertation presents research on two different biological systems: (1) the light-harvesting proteins in the chromatophores of purple photosynthetic bacteria, and (2) the structure and function of the Hepatitis C viroporin p7. Purple photosynthetic bacteria form membranous pseudo-organelles called chromatophores which house the photosynthetic machinery. These chromatophore structures are formed out of the cytoplasmic membrane into various species-dependent shapes, such as spheres or flat lamellar folds. AFM images show that chromatophores are densely populated by the light harvesting complexes LH1 and LH2. LH1 is always found surrounding the reaction center, forming LH1-RC core complexes, which may be elliptically-shaped monomers or S-shaped dimers depending on the species of bacteria. LH2 is a small ring-shaped complex which is produced to expand the light-harvesting capacity of the chromatophore. In addition to their role in photosynthesis, the LH2 and LH1-RC proteins may also influence the overall structure of the chromatophore organelle. Molecular dynamics simulations were employed to explore the effects of LH2s and monomeric LH1-RC complexes on the shape of the surrounding membrane. It will be demonstrated that small aggregates of LH2 complexes can induce membrane curvature, but that mixtures of LH2 and LH1-RC monomers cannot. Several factors that influence the degree of curvature are identified, and the implications of these findings on chromatophore organization and morphology are discussed. Hepatitis C virus (HCV) currently affects about 2% of the world's population, is a major source of cirrhosis and cancer of the liver, and is very difficult to treat. HCV is both prolific in virion production and fast mutating, making it highly resistant to drug therapies. Therefore, the identification of novel drug targets is highly desirable. The HCV genome encodes ten different proteins, one of which is a small transmembrane protein called p7, which oligomerizes to form ion-conducting pores. The presence of functional p7 has been shown to be critical for the late stages of the viral lifecycle, making it a potential drug target. This dissertation explores several possibilities for the structure of the p7 oligomer, finding that p7 displays a preference for hexameric or heptameric arrangements in molecular dynamics simulations, but that tetramers and pentamers are also stable in simulation. These results suggest that p7 displays some plasticity in terms of its oligomerization, and that multiple oligomerization states could co-exist, though only some would form functional channels. Further investigations in to the hexameric model identified specific residues which may be involved in channel gating. Finally, the hexameric model was fitted into a 3-dimensional cryo-electron microscopy density map of a hexameric p7; simulations of that structure in DHPC and POPC lipids illustrated the flexibility of p7 in adapting to different lipid environments. 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 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: photosynthetic bacteria; chromatophore; light-harvesting complexes; LH2; membrane curvature; Hepatitis C; Hepatitis C virus (HCV); viroporin; p7

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APA (6^th Edition):

Chandler, D. (2012). Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29569

Chicago Manual of Style (16^th Edition):

Chandler, Danielle. “Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/29569.

MLA Handbook (7^th Edition):

Chandler, Danielle. “Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7.” 2012. Web. 01 Mar 2021.

Vancouver:

Chandler D. Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/29569.

Council of Science Editors:

Chandler D. Computational investigations into two biological processes: membrane reshaping by light-harvesting proteins in the chromatophores of purple bacteria, and oligomerization and pore formation by the Hepatitis C viroporin p7. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29569

14. Chan, Kwok Yan. Structural analyses of the ribosome by hybrid approach.

Degree: PhD, 0240, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/50422

► The ribosome is the molecular machine which reads and translates genetic information into proteins in all living cells. Lack of an atomic-resolution structure of the… (more)

▼ The ribosome is the molecular machine which reads and translates genetic information into proteins in all living cells. Lack of an atomic-resolution structure of the ribosome in its actual functional states prevents our understanding of the ribosome. A hybrid approach overcomes the challenge by combining experimental data from X-ray crystallography and cryo-electron microscopy with computing, permitting one to resolve atomic-level structures of intermediates of the functional ribosome and, thereby, to advance our understanding of ribosome function and the underlying physical mechanisms. In this thesis works we further developed an existing hybrid approach, namely the molecular dynamics flexible fitting (MDFF) method, and apply it to the ribosome. We improved MDFF in two regards, first by incorporating structural symmetry information into the fitting protocol and second by the use of a so-called implicit solvent model. In pursuit of the needed methodological development we participated in the Cryo-EM Modeling Challenge 2010, competing with the MDFF method against other hybrid methods. Two aspects of ribosomal functions were investigated. First we studied bacterial resistance to the antibiotic tetracycline, a study that involved a detail investigation of processes in the ribosome. Second we employed MDFF and molecular dynamics simulations to characterize the dynamics of a ribosome-bound chaperone, called trigger factor. 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%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (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%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member), Champaign%22%20%2Bcontributor%3A%28%22Peng%2C%20Jen-Chieh%22%29&pagesize-30">Peng, Jen-Chieh (committee member).

Subjects/Keywords: ribosome; molecular dynamics flexible fitting; cryo-electron microscopy; Tet(O); tetracycline; trigger factor; chaperone

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APA (6^th Edition):

Chan, K. Y. (2014). Structural analyses of the ribosome by hybrid approach. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/50422

Chicago Manual of Style (16^th Edition):

Chan, Kwok Yan. “Structural analyses of the ribosome by hybrid approach.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/50422.

MLA Handbook (7^th Edition):

Chan, Kwok Yan. “Structural analyses of the ribosome by hybrid approach.” 2014. Web. 01 Mar 2021.

Vancouver:

Chan KY. Structural analyses of the ribosome by hybrid approach. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/50422.

Council of Science Editors:

Chan KY. Structural analyses of the ribosome by hybrid approach. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/50422

15. Hsin, Ya-chieh. Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity.

Degree: PhD, 0240, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/16835

► In this article, three biological inquiries on cellular functions investigated through a combination of theoretical and computational methods are discussed: the morphology of the biological… (more)

▼ In this article, three biological inquiries on cellular functions investigated through a combination of theoretical and computational methods are discussed: the morphology of the biological membrane, assembly of a multi-protein complex, and the molecular origin of elasticity in muscle protein. In the photosynthetic purple bacterium Rhodobacter (Rba.) sphaeroides, light is absorbed by membrane-bound light-harvesting proteins LH1 and LH2. LH1 directly surrounds the reaction center (RC) and, together with PufX, forms a dimeric (RC-LH1-PufX)2 protein complex known as the photosynthetic core complex. In LH2-de???cient Rba . sphaeroides mutants, core complex dimers aggregate into tubular vesicles with a radius of ???25-55 nm, making core complex dimer one of the few integral membrane proteins known to actively induce membrane curvature. A three-dimensional electron microscopy density map showed that the Rba . sphaeroides core complex dimer exhibits a prominent bend at its dimerizing interface. To investigate the curvature properties of this highly bent protein, molecular dynamics simulations were employed to ???t an all-atom structural model of the core complex dimer within the electron microscopy density map. The simulations reveal how the dimer produces a membrane with high local curvature, the curvature matching the size of the tubular vesicles containing only core complex dimers. To understand the molecular basis of the bent geometry of the Rba . sphaeroides core complex dimer, the PufX protein was subject to further investigation. To date, no high resolution structure is available for the entire Rba. sphaeroides core complex dimer. In particular, the location of PufX within the core complex dimer is debated. Placement of PufX has direct implication on the dimerizing mechanism and the self-assembly process of the Rba. sphaeroides core complex dimer. We have constructed and tested via molecular dynamics a model of PufX dimer based on the Glycophorin A (GlyA) dimer. The PufX dimer model was shown to be structurally stable both in its monomeric and dimeric states, and the residues participating in PufX helix-helix interactions in the dimeric state were identi???ed. The dimerized PufX helices display a stable GlyA-like crossing angle, which, during the self-assembly process, possibly results in the highly bent and V-shaped structure of core complex dimer responsible for inducing local membrane curvature in the photosynthetic membrane. Titin is a mechanical protein that protects muscle from overstretching by producing a restoring force when a muscle ???ber is extended beyond its normal length. Force spectroscopy studies have shown that titin exhibits several regimes of elasticity. Disordered segments bring about a soft, entropic spring-type elasticity; secondary structures of titins immunoglobulin-like (Ig-) and ???bronectin type III-like (FN-III) domains provide a sti??? elasticity. We demonstrated that titin exhibits a third type of elasticity due to tertiary structure and involving domain-domain… 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%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member), Champaign%22%20%2Bcontributor%3A%28%22Hubler%2C%20Alfred%20W.%22%29&pagesize-30">Hubler, Alfred W. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member).

Subjects/Keywords: molecular dynamics; steered molecular dynamics; photosynthesis; membrane curvature; protein-induced membrane curvature; molecular modeling; protein complex assembly; muscle elasticity; titin; mechanical protein; elastic protein

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APA (6^th Edition):

Hsin, Y. (2010). Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/16835

Chicago Manual of Style (16^th Edition):

Hsin, Ya-chieh. “Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/16835.

MLA Handbook (7^th Edition):

Hsin, Ya-chieh. “Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity.” 2010. Web. 01 Mar 2021.

Vancouver:

Hsin Y. Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/16835.

Council of Science Editors:

Hsin Y. Computational investigations of cellular functions: Three cases on membrane morphogenesis, organization and assembly of a multi-protein complex, and the molecular origin of muscle elasticity. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/16835

16. Liu, Yanxin. Computational investigations of protein dynamics and its implications for biological functions.

Degree: PhD, 0240, 2013, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/45294

► Computer simulation is a powerful approach to study protein dynamics and functions. We employed molecular dynamics (MD) simulations to investigate large conformational changes in proteins,… (more)

▼ Computer simulation is a powerful approach to study protein dynamics and functions. We employed molecular dynamics (MD) simulations to investigate large conformational changes in proteins, including folding, dimerization, and unfolding, and how these conformational changes help the proteins perform their biological functions. We first study protein folding, a process by which a protein acquires its functional structure and is related to many neurodegenerative diseases. A fast-folding five-helix bundle λ-repressor fragment is chosen as a model system. A length of 80 amino acid residues puts it on the large end among all known microsecond folders and its size poses a computational challenge for MD studies. We simulate the folding of a novel λ-repressor fast-folding mutant λ*HG) in explicit solvent using an all-atom description. By means of a recently developed tempering method, we observe reversible folding and unfolding of λ-repressor in a 10-μs trajectory. The folding kinetics is also investigated through a set of MD simulations run at different temperatures that together cover more than 125 μs. The protein is seen to fold into a native-like topology at intermediate temperature and a slow-folding pathway is identified. For two other lambda-repressor mutants, λ*YG and λ*YA, we study pressure effect on the protein dynamics. A short refolding time of 2 μs was reported for λ*YG in pressure-jump experiments. To investigate this pressure-jump induced fast folding behavior, MD simulations of more than 35 μs are carried out on the λ*YG mutant. High-pressure denatured states are found to contain a significant amount of helical structure. Upon pressure drop, the protein refolds into the native state in 20 μs. The simulations confirm the existence of pressure-jump induced fast folding pathway for λ*YG. We also perform over 50 μs pressure-jump simulations on λ*YA with four different force fields. Two of the force fields yield compact non-native states with misplaced α-helix content within a few microseconds of the pressure drop. We conclude that the pressure-denatured state of λ*YA contains mainly residual helix and little β-sheet; following a fast pressure-drop, at least some λ*YA forms misplaced helical structure within microseconds. We hypothesize that non-native helix at helix-turn interfaces traps the protein in compact non-native conformations. These traps delay the folding of at least some of the protein population to the native state, reflected as the millisecond slow folding phase in pressure jump experiments. Based on the simulations, we predict specific mutations at the helix-turn interfaces that should speed up refolding from the pressure-denatured state. In addition to being a spontaneous process, protein folding can also be modulated through external factors, such as flow, light, or mechanical force. Flow-induced shear has been identified as a regulatory driving force in blood clotting. Shear induces β-hairpin folding of the glycoprotein Ibα β-switch which increases affinity for binding to the von… 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%22Dahmen%2C%20Karin%20A.%22%29&pagesize-30">Dahmen, Karin A. (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%22Gruebele%2C%20Martin%22%29&pagesize-30">Gruebele, Martin (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 simulation; protein folding; enhanced sampling; lambda-repressor; glycoprotein; flow-induced protein folding; myosin VI; motor protein

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APA (6^th Edition):

Liu, Y. (2013). Computational investigations of protein dynamics and its implications for biological functions. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/45294

Chicago Manual of Style (16^th Edition):

Liu, Yanxin. “Computational investigations of protein dynamics and its implications for biological functions.” 2013. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/45294.

MLA Handbook (7^th Edition):

Liu, Yanxin. “Computational investigations of protein dynamics and its implications for biological functions.” 2013. Web. 01 Mar 2021.

Vancouver:

Liu Y. Computational investigations of protein dynamics and its implications for biological functions. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2013. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/45294.

Council of Science Editors:

Liu Y. Computational investigations of protein dynamics and its implications for biological functions. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2013. Available from: http://hdl.handle.net/2142/45294

17. Tanner, David. Lengthening the timescale reach of molecular dynamics.

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

URL: http://hdl.handle.net/2142/31144

► Molecular dynamics (MD) is a computational method employed for studying the dynamics of nanoscale biological systems on nanosecond to microsecond timescales. Using MD, researchers can… (more)

Subjects/Keywords: molecular dynamics; implicit solvent; Graphics Processing Units (GPU); High Performance Computing (HPC); flagellum; protein translocation

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APA (6^th Edition):

Tanner, D. (2012). Lengthening the timescale reach of molecular dynamics. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/31144

Chicago Manual of Style (16^th Edition):

Tanner, David. “Lengthening the timescale reach of molecular dynamics.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/31144.

MLA Handbook (7^th Edition):

Tanner, David. “Lengthening the timescale reach of molecular dynamics.” 2012. Web. 01 Mar 2021.

Vancouver:

Tanner D. Lengthening the timescale reach of molecular dynamics. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/31144.

Council of Science Editors:

Tanner D. Lengthening the timescale reach of molecular dynamics. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/31144

18. 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 01, 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. 01 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 01]. 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

19. Nieuwkoop, Andrew. Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR.

Degree: PhD, 0335, 2012, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/29544

► Solid state NMR (SSNMR) is a structure determination technique uniquely suited to study protein aggregates and fibrils. Unlike solution NMR or X-ray crystallography, SSNMR can… (more)

Subjects/Keywords: Solid-state NMR; protein structure determination; fibrils; GB1; alpha synuclein; Parkinson’s disease; TEDOR; proton detection; nuclear magnetic resonance (NMR)

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APA (6^th Edition):

Nieuwkoop, A. (2012). Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/29544

Chicago Manual of Style (16^th Edition):

Nieuwkoop, Andrew. “Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR.” 2012. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/29544.

MLA Handbook (7^th Edition):

Nieuwkoop, Andrew. “Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR.” 2012. Web. 01 Mar 2021.

Vancouver:

Nieuwkoop A. Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2012. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/29544.

Council of Science Editors:

Nieuwkoop A. Structure determination of proteins and protein aggregates by magic-angle spinning solid-state NMR. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2012. Available from: http://hdl.handle.net/2142/29544

20. Mears, Patrick. Illuminating the relationship between flagellar activity and bacterial swimming.

Degree: PhD, 0240, 2014, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/49486

► Bacterial swimming and chemotaxis serves as a model system for understanding information processing in living organisms. My thesis project was focused on studying the swimming… (more)

▼ Bacterial swimming and chemotaxis serves as a model system for understanding information processing in living organisms. My thesis project was focused on studying the swimming behavior of Escherchia coli bacterial cells. These cells swim by rotating helical filaments called flagella. An individual cell can have anywhere from 1 to 10 flagella. In a process called chemotaxis, cells modulate the rotational direction of their flagella to modify their swimming behavior and move towards more favorable environments. The primary goal of this thesis was to determine how the number of flagella on a cell affects its swimming behavior. I designed and constructed a unique instrument, combining optical tweezers and high-speed fluorescence imaging. This instrument allowed me to simultaneously measure the activity of the individual flagella on a cell, while also monitoring the swimming behavior of the cell. These results provided a large amount of data regarding the relationship between flagella number, CW bias and tumble bias. In particular, I discovered that the tumble bias of a swimming cell is robust against variations in flagellar number. Cells with 2 flagella and cells with as many as 8 flagella have the same average tumble bias. Many other results regarding this system are presented throughout this thesis. The goals and organization of the thesis are summarized in Chapter 1. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Chemla%2C%20Yann%20R.%22%29&pagesize-30">Chemla, Yann R. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Kuhlman%2C%20Thomas%20E.%22%29&pagesize-30">Kuhlman, Thomas E. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Chemla%2C%20Yann%20R.%22%29&pagesize-30">Chemla, Yann R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Dahmen%2C%20Karin%20A.%22%29&pagesize-30">Dahmen, Karin A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member).

Subjects/Keywords: Escherichia coli; biophysics; optical tweezers; chemotaxis; fluoresence imaging; systems biology

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APA (6^th Edition):

Mears, P. (2014). Illuminating the relationship between flagellar activity and bacterial swimming. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/49486

Chicago Manual of Style (16^th Edition):

Mears, Patrick. “Illuminating the relationship between flagellar activity and bacterial swimming.” 2014. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/49486.

MLA Handbook (7^th Edition):

Mears, Patrick. “Illuminating the relationship between flagellar activity and bacterial swimming.” 2014. Web. 01 Mar 2021.

Vancouver:

Mears P. Illuminating the relationship between flagellar activity and bacterial swimming. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2014. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/49486.

Council of Science Editors:

Mears P. Illuminating the relationship between flagellar activity and bacterial swimming. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2014. Available from: http://hdl.handle.net/2142/49486

21. Sathe, Chaitanya. Computational study of graphene nanopore sensor for DNA sensing.

Degree: PhD, 1200, 2015, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/72941

► Inexpensive and fast methods to sequence the genome of individuals using nanopore technology can lead to tremendous advancement in the eld of modern medicine. The… (more)

▼ Inexpensive and fast methods to sequence the genome of individuals using nanopore technology can lead to tremendous advancement in the eld of modern medicine. The thickness of the membranes employed in nanopore-based sensors presents a fundamental limitation to the physical dimension, of the translocating DNA molecule, that can be resolved. Typical solid-state membranes are too thick and usually fail to recognize single nucleotides on a DNA strand. Graphene is a sub-nanometer membrane, comprising of carbon atoms arranged in a honeycomb lattice, with remarkable electronic and mechanical properties. The thickness of a graphene membrane (3 A) is comparable to the vertical stacking distance between base pairs in the DNA (3.5 A) making graphene an ideal candidate for DNA sequencing. Resolving at the atomic level electric eld-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics (MD) simulations, in principle, can achieve such resolution and are employed to investigate the e ects of applied voltage, DNA conformation and sequence as well as pore charge on the translocation characteristics of DNA. In addition, graphene is electrically active and transverse electronic currents along the graphene membrane can complement ionic current measurements, and potentially extend the molecular sensing capability of graphene-based nanopores. We have combined the self-consistent Poisson-Boltzmann formal- ism with Non-Equilibrium Green's Function (NEGF) technique along with charge densities of DNA arising from MD simulations to show detection of rotational and positional conformation of a double-stranded DNA (dsDNA), inside the nanopore, via sheet currents in graphene nanoribbons. Furthermore, we show the ability of such transverse electronic currents to detect conformational transition, arising due to forced extension, of the dsDNA molecule from helical to zipper form, and also detect ssDNA translocation at single base pair resolution. Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Leburton%2C%20Jean-Pierre%22%29&pagesize-30">Leburton, Jean-Pierre (advisor), Champaign%22%20%2Bcontributor%3A%28%22Leburton%2C%20Jean-Pierre%22%29&pagesize-30">Leburton, Jean-Pierre (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%22Lyding%2C%20Joseph%20W.%22%29&pagesize-30">Lyding, Joseph W. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Bashir%2C%20Rashid%22%29&pagesize-30">Bashir, Rashid (committee member).

Subjects/Keywords: Nanopore; DNA Sequencing; Molecular Dynamics; Graphene; Electron Transport

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APA (6^th Edition):

Sathe, C. (2015). Computational study of graphene nanopore sensor for DNA sensing. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/72941

Chicago Manual of Style (16^th Edition):

Sathe, Chaitanya. “Computational study of graphene nanopore sensor for DNA sensing.” 2015. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/72941.

MLA Handbook (7^th Edition):

Sathe, Chaitanya. “Computational study of graphene nanopore sensor for DNA sensing.” 2015. Web. 01 Mar 2021.

Vancouver:

Sathe C. Computational study of graphene nanopore sensor for DNA sensing. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2015. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/72941.

Council of Science Editors:

Sathe C. Computational study of graphene nanopore sensor for DNA sensing. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2015. Available from: http://hdl.handle.net/2142/72941

University of Illinois – Urbana-Champaign

22. Miao, Lingling. Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations.

Degree: PhD, 0240, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/14747

► As the only pathways connecting the cell???s nucleus and cytoplasm, nuclear pore complexes (NPCs) enable and control the import and export between cell???s cytoplasm and… (more)

▼ As the only pathways connecting the cell???s nucleus and cytoplasm, nuclear pore complexes (NPCs) enable and control the import and export between cell???s cytoplasm and nucleoplasm. The NPC allows small molecules (<40 KDa) to diffuse freely into and out of the nucleus, while excluding large molecules, which are only allowed to pass when bound to transport receptors. Anchored on the inner surface of the NPC central pore are many intrinsically unstructured FG-nups, proteins that contain phenylalanine-glycine repeating sequences (FG-repeats) separated by hydrophilic linker regions. Because of the unstructured nature of FG-nups, no imaging method has been able to capture the collective conformation of these proteins in detail. However, their collective behavior inside the NPC central pore is important to understand the NPC???s selective transport. In this thesis, molecular dynamics has been used to model and study a representative volume of the FG-nup-filled central pore. One FG-nup was divided into 25 segments, each containing 100 amino acids. The 25 segments were then tethered onto a planar surface to mimic the anchoring of FG-nups onto the central pore surface, forming a 5 ?? 5 array. Separation between tethering points was adjusted to render a similar FG-repeat density as that of the NPC. Computational simulations of the array suggested a dynamic brush-like structure, inside which the FG-nup segments form different bundles. Many FG-repeats were observed on the bundle surface without binding to another FG-repeat, offering a favorable environment for transport receptors, proteins that bind to FG-repeats as shown by both experiment and simulation. Further simulations confirmed that the brush-like structure is able to distinguish between transport receptors and inert proteins at its entrance. During the 200 ns simulations, transport receptor NTF2 gradually entered the brush while the inert protein barely did. Although both NTF2 and the inert protein were found to have many FG-repeats bound to them, binding events lasted only for short durations for the inert protein. The brush-like structure proposed and studied here shows great promise in functioning as the selective barrier of the NPC. 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%22Tajkhorshid%2C%20Emad%22%29&pagesize-30">Tajkhorshid, Emad (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%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member), Champaign%22%20%2Bcontributor%3A%28%22Stack%2C%20John%20D.%22%29&pagesize-30">Stack, John D. (committee member).

Subjects/Keywords: Nuclear pore complex; NPC selective transport; FG-nups; FG-repeats; Transport receptors; Molecular dynamics; MD simulations

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

APA (6^th Edition):

Miao, L. (2010). Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/14747

Chicago Manual of Style (16^th Edition):

Miao, Lingling. “Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/14747.

MLA Handbook (7^th Edition):

Miao, Lingling. “Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations.” 2010. Web. 01 Mar 2021.

Vancouver:

Miao L. Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/14747.

Council of Science Editors:

Miao L. Selective transport of the nuclear pore complex studied through all-atom and coarse-grained molecular dynamics simulations. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/14747

University of Illinois – Urbana-Champaign

23. Cruz, Eduardo. Transport properties of synthetic nanopores.

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

URL: http://hdl.handle.net/2142/15530

► In recent years, advances in nanotechnology have allowed researchers to manufacture pores in synthetic membranes with subnanometer precision, so-called synthetic nanopores. Immersed in aqueous solution,… (more)

▼ In recent years, advances in nanotechnology have allowed researchers to manufacture pores in synthetic membranes with subnanometer precision, so-called synthetic nanopores. Immersed in aqueous solution, these nanopores can be deployed to study the translocation of charged molecules and ions, a process of main importance in biology. However, researchers run into problems to build and control such small devices. Surface properties, thermal fluctuations and the discreteness of matter dominate at the nanoscale, producing phenomena not observed in the microscale. Indeed, little is known about the molecular level dynamics inside nanopores or the mechanism by which molecules and ions interact with nanopore walls. Molecular dynamics simulations can provide detailed atomistic images involving nanopores and physiological solutions. The work presented in this thesis uses molecular dynamics simulations to study synthetic nanopores made with two different materials: silica and polyethylene terephthalate. For simulated silica nanopores, the lack of suitable force fields to represent the interactions of the silica with other molecules in solution is a mayor problem. To address this problem, a novel silica force field was developed, which accurately reproduces the hydrophobicity of realistic amorphous silica surfaces. Such force field was employed to study the ionic conduction through silica nanopores. The simulations revealed that the atomic topography of the silica nanopore plays a major role in ionic conduction, producing phenomena such as ionic rectification. For polymeric polyethylene terephthalate nanopores, this thesis presents a protocol to assemble atomic models of polymeric bulk materials, which are then used to sculpt polymer nanopore models that reproduce the key features of experimental devices, namely a conical geometry and a negative surface charge density. The polymeric nanopore models were used to study on a novel phenomenon reported in nanopores, so called nanoprecipitation oscillations. The simulations unveiled the atomic detail mechanism of the nanoprecipitation phenomenon. 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%22Aksimentiev%2C%20Aleksei%22%29&pagesize-30">Aksimentiev, Aleksei (committee member), Champaign%22%20%2Bcontributor%3A%28%22Aluru%2C%20Narayana%20R.%22%29&pagesize-30">Aluru, Narayana R. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Timp%2C%20Gregory%20L.%22%29&pagesize-30">Timp, Gregory L. (committee member).

Subjects/Keywords: synthetic nanopore; molecular dynamics simulations; ionic rectification; nanoprecipitation; water contact angle; amorphous silica; polyethylene terephthalate

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

APA (6^th Edition):

Cruz, E. (2010). Transport properties of synthetic nanopores. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/15530

Chicago Manual of Style (16^th Edition):

Cruz, Eduardo. “Transport properties of synthetic nanopores.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/15530.

MLA Handbook (7^th Edition):

Cruz, Eduardo. “Transport properties of synthetic nanopores.” 2010. Web. 01 Mar 2021.

Vancouver:

Cruz E. Transport properties of synthetic nanopores. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/15530.

Council of Science Editors:

Cruz E. Transport properties of synthetic nanopores. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/15530

University of Illinois – Urbana-Champaign

24. 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 01, 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. 01 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 01]. 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

University of Illinois – Urbana-Champaign

25. Yung, Man Hong. Physical challenges of quantum computation.

Degree: PhD, 0240, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/14565

► This is a study of several physical challenges for building a quantum computer, a hypothetical device which is capable of accomplishing tasks unachievable by the… (more)

Subjects/Keywords: quantum computation; quantum information; decoherence; quantum state transfer; error correlation; adiabatic quantum computing; quantum simulation

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

APA (6^th Edition):

Yung, M. H. (2010). Physical challenges of quantum computation. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/14565

Chicago Manual of Style (16^th Edition):

Yung, Man Hong. “Physical challenges of quantum computation.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/14565.

MLA Handbook (7^th Edition):

Yung, Man Hong. “Physical challenges of quantum computation.” 2010. Web. 01 Mar 2021.

Vancouver:

Yung MH. Physical challenges of quantum computation. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/14565.

Council of Science Editors:

Yung MH. Physical challenges of quantum computation. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/14565

University of Illinois – Urbana-Champaign

26. Rajan, Aruna. Analysis of Molecular Dynamics Simulations of Protein Folding.

Degree: PhD, 0240, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/14582

► Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics… (more)

▼ Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over which many small proteins fold, all atom MD simulations of protein folding are now becoming popular. To distill features of such large folding trajectories, we must develop methods that can both compress trajectory data to enable visualization, and that can yield themselves to further analysis, such as the finding of collective coordinates and reduction of the dynamics. Conventionally, clustering has been the most popular MD trajectory analysis technique, followed by principal component analysis (PCA). Simple clustering used in MD trajectory analysis suffers from various serious drawbacks, namely, (i) it is not data driven, (ii) it is unstable to noise and change in cutoff parameters, and (iii) since it does not take into account interrelationships amongst data points, the separation of data into clusters can often be artificial. Usually, partitions generated by clustering techniques are validated visually, but such validation is not possible for MD trajectories of protein folding, as the underlying structural transitions are not well understood. Rigorous cluster validation techniques may be adapted, but it is more crucial to reduce the dimensions in which MD trajectories reside, while still preserving their salient features. PCA has often been used for dimension reduction and while it is computationally inexpensive, being a linear method, it does not achieve good data compression. In this thesis, I propose a different method, a nonmetric multidimensional scaling (nMDS) technique, which achieves superior data compression by virtue of being nonlinear, and also provides a clear insight into the structural processes underlying MD trajectories. I illustrate the capabilities of nMDS by analyzing three complete villin headpiece folding and six norleucine mutant (NLE) folding trajectories simulated by Freddolino and Schulten [1]. Using these trajectories, I make comparisons between nMDS, PCA and clustering to demonstrate the superiority of nMDS. The three villin headpiece trajectories showed great structural heterogeneity. Apart from a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane formed by helices 2 and 3 was observed towards the end of the folding process in all trajectories, when nearly all native contacts had been formed. However, the transition occurred through a different series of steps in all trajectories, indicating that it may not be a common transition in villin folding. The trajectories showed competition between local structure formation/hydrophobic… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Oono%2C%20Yoshitsugu%22%29&pagesize-30">Oono, Yoshitsugu (advisor), Champaign%22%20%2Bcontributor%3A%28%22Chemla%2C%20Yann%20R.%22%29&pagesize-30">Chemla, Yann R. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Oono%2C%20Yoshitsugu%22%29&pagesize-30">Oono, Yoshitsugu (committee member), 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%22Vishveshwara%2C%20Smitha%22%29&pagesize-30">Vishveshwara, Smitha (committee member).

Subjects/Keywords: protein folding; molecular dynamics simulations; non-metric multidimensional scaling; principal component analysis; clustering; villin headpiece; norleucine mutant

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

APA (6^th Edition):

Rajan, A. (2010). Analysis of Molecular Dynamics Simulations of Protein Folding. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/14582

Chicago Manual of Style (16^th Edition):

Rajan, Aruna. “Analysis of Molecular Dynamics Simulations of Protein Folding.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/14582.

MLA Handbook (7^th Edition):

Rajan, Aruna. “Analysis of Molecular Dynamics Simulations of Protein Folding.” 2010. Web. 01 Mar 2021.

Vancouver:

Rajan A. Analysis of Molecular Dynamics Simulations of Protein Folding. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/14582.

Council of Science Editors:

Rajan A. Analysis of Molecular Dynamics Simulations of Protein Folding. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/14582

University of Illinois – Urbana-Champaign

27. Eargle, John. Simulation and visualization of dynamics in RNA-protein complexes in translation.

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

URL: http://hdl.handle.net/2142/15521

► Translation, the process of reading genetic information and synthesizing the corresponding proteins, is universal and found throughout the three domains of life. The flow of… (more)

▼ Translation, the process of reading genetic information and synthesizing the corresponding proteins, is universal and found throughout the three domains of life. The flow of information in translation involves a series of distinct but highly conserved RNA??protein complexes with the ribosome being the largest ribonucleoprotein complex in the cell. As the molecular instantiation of the genetic code, tRNA plays a central role in the translational machinery where it interacts with several proteins and other RNAs during the course of protein synthesis. We use molecular dynamics (MD) simulations informed by evolutionary analysis to investigate the dynamics of several RNA??protein complexes involved in translation. Many analysis methods and tools were developed during the course of this study. We present the evolutionary analysis environment MultiSeq, dynamical network analysis and visualization, and a protocol for the preparation of RNA??protein MD simulations. For several Class I aminoacyl-tRNA synthetases (aaRSs), the rate determining step in aminoacylation is the dissociation of the charged tRNA from the enzyme. Through molecular modeling, internal pKa calculations, and MD simulations, distinct, mechanistically relevant post-transfer states with the charged tRNA (Glu-tRNA(Glu)) bound to glutamyl-tRNA synthetase are considered. The behavior of these nonequilibrium states is characterized as a function of time using dynamical network analysis, local energetics, and changes in free energies to estimate transitions that occur during the release of the tRNA. Dynamical network analysis reveals that there are a large number of suboptimal paths through the protein??RNA complex that can be used for communication between the identity elements on the tRNAs and the catalytic site in the aaRS??tRNA complexes. Residues and nucleotides in the majority of pathways bridging communities, local substructures that are highly intraconnected but loosely interconnected, are evolutionarily conserved and are predicted to be important for allosteric signaling. The same monomers are also found in a majority of the suboptimal paths. Modifying these residues or nucleotides has a large effect on the communication pathways in the protein??RNA complex consistent with kinetic data. The highly conserved general base Glu41 is proposed to be a part of a proton relay system for destabilizing the bound charging amino acid following aminoacylation. Addition of elongation factor Tu (EF-Tu) to the aaRS??tRNA complex stimulates the dissociation of the tRNA core and acceptor stem. We use MD simulations to investigate the dynamics of the EF-Tu??GTP??aa-tRNA(Cys) complex and the roles played by Mg2+ ions and modified nucleosides on the free energy of RNA??protein binding. Combined energetic and evolutionary analyses identify the coevolution of residues in EF-Tu and aa-tRNAs at the binding interface. Highly conserved EF-Tu residues are responsible for both attracting aa-tRNAs as well as providing nearby nonbonded repulsive energies which help fine-tune… Advisors/Committee Members: Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (advisor), Champaign%22%20%2Bcontributor%3A%28%22Luthey-Schulten%2C%20Zaida%20A.%22%29&pagesize-30">Luthey-Schulten, Zaida A. (Committee Chair), Champaign%22%20%2Bcontributor%3A%28%22Ha%2C%20Taekjip%22%29&pagesize-30">Ha, Taekjip (committee member), Champaign%22%20%2Bcontributor%3A%28%22Martinis%2C%20Susan%20A.%22%29&pagesize-30">Martinis, Susan A. (committee member), Champaign%22%20%2Bcontributor%3A%28%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (committee member).

Subjects/Keywords: translation; elongation factor Tu; tRNA; aminoacyl-tRNA synthetase

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

APA (6^th Edition):

Eargle, J. (2010). Simulation and visualization of dynamics in RNA-protein complexes in translation. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/15521

Chicago Manual of Style (16^th Edition):

Eargle, John. “Simulation and visualization of dynamics in RNA-protein complexes in translation.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/15521.

MLA Handbook (7^th Edition):

Eargle, John. “Simulation and visualization of dynamics in RNA-protein complexes in translation.” 2010. Web. 01 Mar 2021.

Vancouver:

Eargle J. Simulation and visualization of dynamics in RNA-protein complexes in translation. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/15521.

Council of Science Editors:

Eargle J. Simulation and visualization of dynamics in RNA-protein complexes in translation. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/15521

University of Illinois – Urbana-Champaign

28. Comer, Jeffrey R. Nanopore technology for DNA sequencing.

Degree: PhD, 0240, 2010, University of Illinois – Urbana-Champaign

URL: http://hdl.handle.net/2142/16812

► The pursuit of inexpensive DNA sequencing lies at the interface between nanotechnology and biotechnology???where silicon nanopores, nanoscale electrodes, and self-assembled molecular structures are as common… (more)

▼ The pursuit of inexpensive DNA sequencing lies at the interface between nanotechnology and biotechnology???where silicon nanopores, nanoscale electrodes, and self-assembled molecular structures are as common as restriction enzymes, ???uorescence detection, and genetic engineering. The motivation for this pursuit stems from the promise that personalized genomic information can make health care safer, faster, and more effective. Beyond the realm of human health, inexpensive sequencing is poised to have lasting impacts for the whole of biology. However, the integration of nanotechnology with biotechnology raises many difficult and interesting questions. Computer simulations can assist in answering these questions by providing a means to ???see??? nanoscale events that cannot be imaged by any experimental method. In the development of nanopore devices for DNA sequencing, computation has played a key role in revealing how DNA behaves in the high electric ???eld and con???ned geometry of a nanopore. In this dissertation, I describe my contribution to computational work for the development of nanopore-based sequencing technology. In simulations which have been corroborated by experiments, I have found that DNA adopts qualitatively different conformations in nanopores of different sizes and that nanopores of the appropriate geometry can be used to trap DNA and control its conformation. By developing a method that can provide millisecond-long current simulations with atomic resolution, I have determined conditions under which the sequence of this trapped DNA can be discriminated by ion current measurements. 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%22Chemla%2C%20Yann%20R.%22%29&pagesize-30">Chemla, Yann R. (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%22Schulten%2C%20Klaus%20J.%22%29&pagesize-30">Schulten, Klaus J. (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; sequencing; DNA sequencing; nanopore; nanopore sequencing; bionanotechnology; computer simulations; force spectroscopy; nucleic acids; transmembrane transport; Brownian dynamics

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

APA (6^th Edition):

Comer, J. R. (2010). Nanopore technology for DNA sequencing. (Doctoral Dissertation). University of Illinois – Urbana-Champaign. Retrieved from http://hdl.handle.net/2142/16812

Chicago Manual of Style (16^th Edition):

Comer, Jeffrey R. “Nanopore technology for DNA sequencing.” 2010. Doctoral Dissertation, University of Illinois – Urbana-Champaign. Accessed March 01, 2021. http://hdl.handle.net/2142/16812.

MLA Handbook (7^th Edition):

Comer, Jeffrey R. “Nanopore technology for DNA sequencing.” 2010. Web. 01 Mar 2021.

Vancouver:

Comer JR. Nanopore technology for DNA sequencing. [Internet] [Doctoral dissertation]. University of Illinois – Urbana-Champaign; 2010. [cited 2021 Mar 01]. Available from: http://hdl.handle.net/2142/16812.

Council of Science Editors:

Comer JR. Nanopore technology for DNA sequencing. [Doctoral Dissertation]. University of Illinois – Urbana-Champaign; 2010. Available from: http://hdl.handle.net/2142/16812

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