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1
Wang, Yin 1951. "Influences of membrane biophysical properties on the Metarhodopsin I to Metarhodopsin II transition in visual excitation." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282520.
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Current biophysical studies of membrane proteins are centered on the relation of their structures to key biological functions of membranes in terms of lipid-protein interactions. The conformational transition of rhodopsin from Metarhodopsin I to Metarhodopsin II (Meta I-Meta II) is the triggering event for the visual process. Meta II is the activated form of the visual receptor and binds a signal transducing G protein (transducin), followed by two amplification stages which lead to generation of a visual nerve impulse. Herein, flash photolysis and surface plasmon resonance (SPR) spectroscopy techniques have been used to monitor the Meta I-Meta II transition of rhodopsin in various membrane recombinants. The flash photolysis experiments clearly show a substantial shift to the left of the Meta I-Meta II equilibrium for rhodopsin in egg phosphatidylcholine recombinant membranes. Investigation of the influences on rhodopsin function by non-lamellar forming lipids reveals a characteristic relationship between the Gibbs free energy change for the Meta I-Meta II equilibrium of rhodopsin and the intrinsic curvature of the lipid bilayer. Complementary SPR studies suggest a protrusion of the protein at the activated Meta II state which may be associated with exposure of recognition sites for the signal transducing G protein on the cytoplasmic surface of rhodopsin. All the experimental results obtained here are consistent with the hypothesis of a new flexible surface biomembrane model. The Meta II state is favored by a negative spontaneous curvature of the bilayer, corresponding to an imbalance of the lateral forces within the polar head groups and acyl chains. The mean curvature of membrane bilayer in the Meta II state reflects the small spontaneous curvature of the lipid bilayer in the vicinity of protein. Relief of the lipid curvature frustration in the Meta II state energetically couples the lipids to the photoexcitation of rhodopsin. Consideration of the various energetic contributions suggests the bilayer curvature free energy provides a reservoir of work in the modulation of rhodopsin function in the visual process. These studies that biophysical properties of the liquid-crystalline lipid bilayer are important in relation to protein function and may be relevant to the biomedical investigations of visual dysfunction.
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McCarthy, William James 1964. "An ab initio study of low-frequency, large-amplitude molecular vibrations." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/290692.
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The ab initio treatments of molecular vibrational motion often invoke only the harmonic oscillator approximation. For vibrational modes whose amplitudes access anharmonic regions of the potential energy surface, the harmonic oscillator approximation fails. Low-frequency large-amplitude vibrations, in particular, can access anharmonic regions in addition to other minima of the potential energy surface. Ab initio harmonic frequencies are often scaled to lower values by empirical factors which presumably account for anharmonicity effects as well as an incomplete basis set and account of electron correlation. However, the scaling of those ab initio harmonic frequencies corresponding to low-frequency large-amplitude vibrations results in theoretical values that are still typically several times larger than the experimental values. It is demonstrated in this dissertation that transforming the nuclear motion Hamiltonian to internal coordinates facilitates construction of ab initio potential energy curves, or surfaces, pertaining to low-frequency large-amplitude molecular vibrational modes. The use of internal coordinates complicates the expression of the kinetic energy in the Hamiltonian, and makes it difficult to obtain. Six different methods for determining the kinetic energy expression in internal coordinates are presented and reviewed. The computational implementation of these six methods was performed to allow their critique. Several example calculations of the presented methodology are given. The solution for the vibrational expectation values of the modes expressed by the developed Hamiltonian was also computationally implemented. The resultant theoretical transition frequencies of the molecular systems of 2-sulpholene and 2-aminopyrimidine are combined with experimental studies, and demonstrate the practical usefulness of the presented methodology.
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Choi, Jeong-Mo. "Multi-Scale Theoretical Investigations of Protein Interactions and Evolution." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493545.
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Evolution of biological systems requires players of multiple layers, from atoms and molecules to organisms and populations. Expression of a gene is operated by molecular machineries for transcription, translation, regulation, and maintenance, which work in concert to produce certain macroscopic and observable phenotypes. And when these phenotypes are exposed to selective pressures, more fit phenotypes (with their genes, molecular machineries, and interaction networks) survive in the population. While the relationship of a gene to its cellular consequences is not fully elucidated, it is known that molecular interactions are one of the key factors that determine the relationship.
In this dissertation, we introduce several theoretical tools to study protein interactions and evolution, and show their applications at various scales. The first tool is a coarse-grained scoring function that predicts binding free energy of a protein complex. The scoring function is a simple linear combination of exposed interface areas of different amino acids. In spite of the simplicity, it shows a reasonable predictive power, and predicts correct biochemistry qualitatively. The second is an analytical theory of a spin model on a simple graph, developed by using conventional statistical mechanics. We separated structural and energetic contributions to the free energy of the system, and also obtained a closed form of linear graph contributions. The closed form is applied to predict sequence space free energy of lattice proteins. Lastly, we introduce statistical methods to analyze cellular proteomes and transcriptomes. They can extract global responses of proteomes and transcriptomes to a perturbation, and also responses of specific gene groups. We applied the methods to E. coli and yeast systems to address questions on the genotype-phenotype relationship and evolution.Chemistry and Chemical Biology
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Chavan, Archana G. "Exploring the molecular architecture of proteins| Method developments in structure prediction and design." Thesis, University of the Pacific, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3609082.
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Proteins are molecular machines of life in the truest sense. Being the expressors of genotype, proteins have been a focus in structural biology. Since the first characterization and structure determination of protein molecule more than half a century ago1, our understanding of protein structure is improving only incrementally. While computational analysis and experimental techniques have helped scientist view the structural features of proteins, our concepts about protein folding remain at the level of simple hydrophobic interactions packing side-chain at the core of the protein. Furthermore, because the rate of genome sequencing is far more rapid than protein structure characterization, much more needs to be achieved in the field of structural biology. As a step in this direction, my dissertation research uses computational analysis and experimental techniques to elucidate the fine structural features of the tertiary packing in proteins. With these set of studies, the knowledge of the field of structural biology extends to the fine details of higher order protein structure.
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Wu, Yali 1974. "Numerical simulations of the effect of peripheral proteins on lipid bilayers." Thesis, McGill University, 1998. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=20980.
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We present numerical simulations of the effect of the peripheral proteins on physical properties of lipid bilayers. The ten-state Pink model, which is originally proposed to describe the main transition of pure saturated lipid bilayers, is extended in order to examine both one-component lipid bilayers and binary lipid bilayers containing peripheral proteins. The peripheral protein is introduced as a positively charged cylinder which covers seven lipid chains and the protein-lipid interaction is assumed to be mainly electrostatic.Metropolis Monte Carlo simulations are performed to describe the thermodynamic properties of the model including lipid-protein interaction in terms of order parameters and microconfigurations. The calculations are carried out for two minimal models where the protein concentration in the bilayer surface is either fixed or varies as the external conditions are changed. The basic phase behavior of lipid-protein systems are presented for each model. In both models, the lipid-protein interaction manifests itself by changes in the physical and thermodynamic properties of lipid bilayers and protein aggregation in the main transition region due to the forming of the gel-fluid phase coexistence.
Finally, a non-equilibrium model due to Sabra and Mouristen is modified to describe the non-equilibrium phenomena of lipid bilayers with peripheral proteins which has two internal states. The steady-state of the system and its comparison to the case of integral proteins are described. The thesis is concluded in the final chapter which contains a discussion of future work.
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Nevzorov, Alexander 1969. "Dynamical and equilibrium properties of membrane constituents and nucleic acids from deuterium NMR spectroscopy." Diss., The University of Arizona, 1998. http://hdl.handle.net/10150/282662.
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The chemically non-perturbing deuterium (²H) spin probe provides a unique tool for investigating equilibrium and dynamical properties of lipids, integral membrane proteins, and nucleic acids in relation to their biological activity. Analysis of ²H nuclear magnetic resonance (NMR) relaxation rates gives information about reorientation rates and mean-squared amplitudes; whereas simulation of the spectral lineshapes obtained within the biological temperature range yields bond angles and degree of ordering. In the first part of the dissertation, the frequency dependent ²H NMR spin-lattice relaxation rates (R₁(Z)) for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) vesicles has been analyzed in combination with the corresponding ¹³C R₁(Z) relaxation rates, which enabled one for the first time to unify the ²H and ¹³C relaxation data for lipids in terms of dynamical models for slow order fluctuations. However, none of the existing models is able to account simultaneously for the ²H R₁(Z) frequency dispersion and the orientation dependent ²H R₁(Z) and quadrupolar order (R1Q relaxation rates of DMPC. A new composite membrane deformation model is proposed which simultaneously describes both the frequency and orientation dependent data. Influence of cholesterol on lipid dynamics is also investigated by analyzing the orientational anisotropy of the ²H R₁(Z) and R₁(Q) relaxation rates for DMPC-d54:cholesterol (1/1). The composite membrane deformation model including variable residual coupling tensor predicts a significant variation in the degree of chain entanglement along the acyl chains as a result of lipid-cholesterol interaction, and a smaller contribution from collective motions indicating an increase in the bilayer rigidity versus pure lipid systems. The second part of the dissertation describes a general method for calculating ²H NMR lineshapes of uniaxially-oriented samples. Several intermediate transformations of the coupling tensor are introduced, describing the position of the bond with respect to the symmetry axis, the distribution of the symmetry axes, and the orientation of the specimen as a whole. Lineshapes are calculated using a Monte Carlo method which allows one to effectively treat complicated geometries. The closed-form expression is also derived. The method has been successfully applied to the ²H NMR spectra of bacteriorhodopsin, and helped to resolve previous controversies between the different interpretations of X-ray diffraction studies versus ²H NMR regarding the conformations of Na-DNA at low humidity.
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Lemon, Christopher Michael. "Donor-Acceptor Constructs for Optical Oxygen Sensing and Corroles: Photophysics, Electronic Structure, and Photochemistry." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493300.
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Metabolic tumor profiling illustrates the spatiotemporal distribution of key analytes to assess and quantify tumor growth, metabolism, and response to therapy. Since the tumor microenvironment is characterized by hypoxia, the ability to track and quantify changes in oxygen concentration as a function of disease progression or therapy is crucial to the advancement of targeted therapeutics. The ability to monitor these changes necessitates the development of non-invasive sensors that are small enough to penetrate into tumor tissue and monitor dynamic changes with high resolution in real time.
To address this challenge, this thesis details the design, synthesis, and characterization of optical oxygen sensors that combine a fluorescent semiconductor quantum dot (QD) with a Pd(II) porphyrin or Au(III) corrole as the oxygen-responsive phosphor. In these constructs, the QD donor serves as a photon antenna and transfers the absorbed energy to the appended porphyrin or corrole acceptor by Förster resonance energy transfer (FRET). The triplet state of the phosphor is quenched by molecular oxygen and is responsive over the biologically relevant 0–160 Torr O2 range. These donor–acceptor conjugates are prepared by self-assembly in organic solvents or micelle encapsulation in aqueous media. The Pd(II) porphyrin micelles were then used for in vivo imaging and oxygen sensing in murine models.
In the search for alternative phosphors for optical oxygen sensing, a variety of metallocorrole complexes were prepared. Although these derivatives were not phosphorescent, they have provided insight into the photophysics, electronic structure, and photochemistry of corroles, as described in the second half of this thesis. The photophysical properties of free-base, Au(III), Sb(III), and Sb(V) corroles were interrogated. The role of corrole as a non-innocent ligand was then explored for copper and silver complexes. Analysis of these compounds reveals that copper complexes are Cu(II) corrole radical cations, while the silver analogs are authentic Ag(III) complexes. Finally, the photochemistry of Sb(V) corroles was studied for both C–H activation of organic substrates and halogen evolution as a potential solar fuel. Together, these studies examine fundamental photophysics and electronic structure, as well as provide examples where these complexes may be used to mediate photochemical transformations.Chemistry and Chemical Biology
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Miao, Yinglong. "All-atom multiscale computational modeling of viral dynamics." [Bloomington, Ind.] : Indiana University, 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3380113.
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Thesis (Ph.D.)--Indiana University, Dept. of Chemistry, 2009.Title from PDF t.p. (viewed on Jul 19, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7590. Adviser: Peter J. Ortoleva.
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Fawzi, Nicolas Lux. "Contrasting disease and non-disease protein aggregation by molecular simulations." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3289317.
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Thesis (Ph. D.)--University of California, San Francisco with the University of California, Berkeley, 2007.Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7470. Adviser: Teresa Head-Gordon.
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Zou, Sirui. "The Mechanistic Basis of Dynein Microtubule Binding and Its Regulation." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226071.
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Eukaryotic cells use a diverse toolbox of cytoskeletal motors to transport and position cellular materials in space and time. Two microtubule-based motors—kinesin and dynein—transport organelles, RNA and protein cargos over long-distances. While multiple kinesin motors are used for long-distance plus- end-directed transport, a single type of dynein—cytoplasmic dynein 1— performs nearly all minus-end-directed tasks. Despite cytoplasmic dynein’s role in such diverse activities, many aspects of its molecular mechanism remain poorly understood. My thesis work uses a combination of cryo-electron microscope (EM) structural biology and single-molecule approaches to provide novel insights into the mechanistic basis of how dynein interacts with its microtubule track and how microtubule binding is regulated by the ubiquitous co-factor, Lis1.
First, we solved a 9.7A structure of dynein’s microtubule binding domain bound to microtubules. This structure allowed us to identify large conformational changes that occur in dynein’s microtubule-binding domain upon track binding. We hypothesize that these conformational changes allosterically regulate the ATP hydrolysis cycle in dynein’s motor domain, which is located over 25 nm from the site of microtubule binding. Molecular dynamics simulations, followed by single-molecule assays, allowed us to identify dynamic salt bridge switches in dynein, which can tune its affinity for the microtubule. The native dynein, which has been selected for submaximal processivity, might allow a broader dynamic range for regulation.
Second, we identified how dynein is regulated by its ubiquitous co-factor, Lis1. Our three-dimensional cryo-EM structures of the dynein-Lis1 complex showed dynein’s mechanical element, the linker, is in an altered position in the presence of Lis1. Fluorescence resonance energy transfer (FRET) and single- molecule studies indicated that Lis1 binding to dynein sterically blocks the dynein linker from reaching its normal docking site, which may interrupt dynein’s mechanochemical cycle and prevent its release from microtubules.
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Cuccia, Louis A. "Biophysical properties of dimeric phospholipids." Thesis, McGill University, 1996. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=42007.
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A series of unusual bipolar and bis-phospholipids (dimeric phospholipids) have been studied. The structure, conformation, morphology and biophysical properties of the resulting phospholipid aggregates were investigated.Deuterium magnetic resonance spectroscopy ($ sp2$H NMR) was used to study and characterize the conformation and acyl chain order in oriented bipolar lipid membranes. The $ sp2$H-NMR studies indicated a large and constant value for the order parameter (S$ rm sb{mol})$ for all positions along the bipolar lipid diacyl chain for mechanically oriented, magnetically oriented and unoriented samples. This indicates that the great majority ($>$90%) of the bipolar lipid exists in a highly ordered spanning conformation.
Dimeric phospholipid aggregate morphologies were studied using $ sp{31}$P NMR, small angle X-ray scattering, electron microscopy, differential scanning calorimetry, and the Langmuir film balance technique in order to study the relationship between lipid structure and aggregate morphology. Dimeric phospholipids favour a lamellar morphology. A number of lipid structure-dependent features have been observed including tri-lamellar structures, extended ripple phases and hexagonal phases.
Dimeric and non-hydrolyzable phospholipids were used to study the phenomenon of interfacial activation of extracellular phospholipase A$ sb2$ (EC. 3.1.1.4) (PLA$ sb2)$ in relation to lipid phase, substrate conformation and mobility. Kinetic results and product analyses are consistent with a situation where the spanning conformer of bipolar phospholipids is resistant to PLA$ sb2$-catalyzed hydrolysis but the hairpin conformer is readily hydrolyzed. Finally, an analysis of interfacial kinetics in non-hydrolyzable matrices indicated varying degrees of interfacial inhibition and hydrolysis product activation. This has not been explicitly recognized before and affects the choice of assay conditions for PLA$ sb2.$
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Dressen, Donald George. "An Investigation of the Interaction Between Graphene and Hydrated Ions." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493386.
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The ability of graphene and carbon nanotubes to generate an electric potential from flowing fluids has attracted much interest. The effect is thought to occur because certain ionic and molecular species bind to the surface of these materials more strongly than others. Although several physical models have been proposed, none has yet been rigorous enough to be confirmed by experiment. In this work, I describe an electromechanical device, i.e. a supercapacitive electrical energy generator (SCEEG) made with graphene electrodes, that generates electricity from oscillating droplets of electrolyte solutions and ionic liquids. I provide a theoretical model of how the graphene SCEEG (G-SCEEG) works that quantitatively agrees with experimental results. More importantly, the model allows one to characterize electrochemically-useful properties of the interaction between graphene and hydrated ions from the device’s experimentally measured output. The identity of the ions that preferentially adsorb to graphene as well as the effective surface density and effective binding energy of these ions can all be determined using the G-SCEEG. Additionally, both the capacitance per unit area and the surface potential of the graphene-solution interface can also be determined.
Although this work focuses on a SCEEG device whose electrodes are made from graphene, the electrodes can, in principle, be made from any conductive material, e.g. metals, such as gold, and semiconductors, such as indium-tin-oxide. All SCEEGs described in this thesis, however, work by exchanging charge between two supercapacitors, i.e. capacitors that spontaneously form at the interface between an electrode and an electrolyte solution (or ionic liquid) as a result of ionic adsorption. Charge exchange occurs not by charging and discharging these interfacial capacitors but instead by increasing and decreasing their capacitance. This is accomplished mechanically as a moving droplet wets and dewets the electrodes. The changing interfacial capacitance acts as a source of current; the flow of current through the device’s internal impedance creates an electric potential; and, when connected to an external load, the SCEEG is then capable of generating electric power.
I show that a G-SCEEG can generate a peak power of up to 7 μW from the oscillatory motion of two 20 μL droplets of 6.0 M HCl. I demonstrate that the device can be successfully modeled as a source of alternating current that is in parallel with a time-varying internal impedance. Using this model and the G-SCEEG’s output, I determine that the chloride anions in 6.0 M HCl adsorb to graphene with the greatest effective surface density (5.6 x 10^12 ions/cm^2) and induce in it the largest charge density (900 nC/cm^2) of all the solutions I studied. These chloride anions adsorb to graphene with an effective binding energy of 350 meV, in turn producing an electric potential of 690 mV at the graphene-solution interface. I also find that the density and the sign of the surface charge induced in graphene are dependent on the ionic species present in each solution, the concentration and pH of the solution, and the presence of multi-layers in the graphene electrodes with the solution’s pH providing the greatest effect.
Finally, I describe in this dissertation the study of the Raman spectral properties of suspended mono- and multi-layer graphene membranes and the use of graphene and graphite to electrostatically trap DNA from an aqueous solution. I conclude by explaining the unique methods I developed during the course of this work including the synthesis of large-grain graphene using chemical vapor deposition (CVD) and the transfer of large areas of CVD-grown graphene to hydrophobic substrates.Biophysics
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Nichols, Alexander J. "Optical Molecular Sensing in Complex Biological Environments." Thesis, Harvard University, 2014. http://nrs.harvard.edu/urn-3:HUL.InstRepos:14226087.
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Although techniques in molecular imaging have advanced considerably over the past several decades, there remain numerous categories of biological molecular targets that are refractory to straightforward imaging. Among these is molecular oxygen, which is vital to a host of physiological as well as pathological processes, as well as the amorphous pigment pheomelanin, which may play a formerly unappreciated role in melanoma carcinogenesis.
This thesis describes two related bodies of work that advance techniques in oxygen and pheomelanin imaging, respectively. First, inspired by a desire to understand how hypoxia affects cancer chemotherapy on a cellular level, we designed and synthesized a novel oxygen-sensitive, dendritic nanoconstruct that is capable of spontaneously penetrating through hundreds of microns of multiple cellular layers. After demonstrating our nanoconjugate's oxygen sensitivity using time-domain phosphorescence lifetime measurements, we demonstrate that it retains its oxygen sensitivity in a 3D spheroid in vitro model of ovarian cancer through the use of a custom-made, near infrared-optimized confocal phosphorescence imaging system. Drawing from this approach, we then describe the fabrication and calibration of a separate oxygen-sensing bandage platform for use in wound-healing applications, and demonstrate its use in ex vivo and in vivo animal systems.
The second body of work describes the use of non-linear four-wave mixing techniques to facilitate straightforward imaging of the molecular pigment pheomelanin. Recent findings suggest that pheomelanin may play a previously unappreciated role in melanoma carcinogenesis, even in the complete absence of an ultraviolet light insult. However, due to its pale color, pheomelanin is difficult to visualize against a skin background, making its study challenging. After constructing a femtosecond-pulsed coherent anti-Stokes Raman scatter (CARS) microscopy imaging system, we use imaging and spectroscopy to provide proof-of-concept that pheomelanin can be imaged through a combination of CARS microscopy and electronically-enhanced four-wave mixing. We then use our non-linear imaging system to specifically observe pheomelanin in isolated "redhead" mouse melanocytes, and show through an siRNA gene knock-down strategy that our system can be used to observe changes in pheomelanin signal upon modification of biological pathways known to affect pheomelanin synthesis.
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Kistler, Kurt Andrew. "Using Quantum Mechanics to Investigate the Photophysical Properties of the DNA and RNA Bases and their Fluorescent Analogs." Diss., Temple University Libraries, 2010. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/73855.
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ChemistryPh.D.
The ability of the nucleic acids to absorb ultraviolet light and remain relatively photostable is a property upon which life depends. The nucleobases, which are the primary chromophores, when irradiated display rapid radiationless decay back to the ground state, in general faster than is needed for photoreaction. Fluorescent analogs of these bases have structures similar to the nucleic acid bases, but display much longer excited state lifetimes. Theoretical investigations using quantum mechanical methods can provide insight into the precise mechanisms of these decay processes, and to the molecular specifics that contribute to them. The results of multi-reference configuration interaction (MRCI) ab initio investigations into these mechanisms are presented, with emphasis on cytosine and its fluorescent analog 5-methyl-2-pyrimidinone (5M2P). A comprehensive picture of the potential energy surfaces of these two bases is given, including stationary points and conical intersections, where radiationless transitions are promoted, between up to three state surfaces, as well as pathways connecting these points for each base. Cytosine is shown to have two different energetically accessible radiationless decay channels. The fluorescence of 5M2P is also demonstrated theoretically, with mechanism proposed. The potential energy surfaces of the two bases have many close similarities, with the different photophysical properties being attributed to subtle energetic differences between the two bases. Nonadiabatic coupling and the geometric phase effect are analyzed in detail near conical intersections in cytosine, including in a region close to a three-state conical intersection. A substituent effect study on the 2-pyrimidinone ring system shows that the presence, position and orientation of the amino group in cytosine is central to its photophysical properties, particularly its high absorption energy, and can be explained with a simple Frontier Molecular Orbital model. The effects of water solvent on the excitation energies of cytosine and uracil are theoretically investigated using two multi-reference ab initio methods, a quantum mechanical molecular mechanics method using MRCI (MRCI-QM/MM), and the fragment molecular orbital multiconfiguration self-consistent field method (FMO-MCSCF). The solvatochromic shifts calculated from both methods agree well with other more expensive methods and experimental data. The effects of water on the photophysical pathways of cytosine is also investigated using MRCI-QM/MM, including considerations of solvent reorganization. Results show that the overall effect of water on the decay mechanisms is small, with neither decay channel being significantly blocked or favored.
Temple University--Theses
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Kang, Myungshim. "Molecular dynamics simulations and theory of intermolecular interactions in solutions." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1282.
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Cisek, Katryna. "Rational Optimization of Small Molecules for Alzheimer’s Disease Premortem Diagnosis." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338325484.
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Fu, Josephine K. Y. "Functional characterization of the teleost multiple tissue (tmt) opsin family and their role in light detection." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:39bc18bb-16cb-4549-94cd-5f872daafe7e.
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In addition to a central circadian clock in the suprachiasmatic nucleus (SCN), zebrafish (Danio rerio) have local clock systems in their peripheral tissues. These peripheral tissues express a complement of clock genes that can be synchronized with the 24 h light/dark cycle and thus may be entrained by light. To date, teleost multiple tissue (tmt) opsin identified from Fugu rubripes and Danio rerio is the only opsin that has been proposed as a candidate to mediate this cellular photoentrainment (Moutsaki et al., 2003). Here we report the discovery of a multigene family of tmt opsins found not only in the teleost fishes, but in vertebrates,including amphibians, birds, reptiles, and some mammals. Phylogenetic analysis demonstrated that this gene family consists of three main classes, tmtI, tmtII and tmtIII, with each duplicating further to give two paralogues in the zebrafish genome. Their predicted amino acid sequences contain most of the characteristic features for the function of a photopigment opsin, as well as seven transmembrane segments indicative of a G protein coupled receptor (GPCR) superfamily. Significantly, reverse transcription polymerase chain reaction (RT-PCR) reveals that the tmt opsin genes in zebrafish are both temporally and spatially regulated. To investigate if these tmt photopigments mediate light-activated currents in cells, each opsin was expressed in vitro and the responses characterised by calcium imaging, whole-cell patch clamp electrophysiology, UV-Vis spectrophotometric analysis, and bioluminescence reporter assay. Collectively, these data suggest that some of the opsin photoproteins signal via Gi-type G protein pathway. Interestingly, the spectral analysis obtained shows that most tmt opsins tested are UV-sensitive when reconstituted in vitro with 11-cis and all-trans retinal, indicating an intrinsic bistable dynamics. Using site directed mutagenesis on one of the tmt opsins, tmt10, the potential spectral tuning sites involved in UV detection were tested. As part of this study, tmt opsin cDNAs were isolated from three populations of Mexican tetra (Astyanax mexicanus): surface, Pachon and Steinhardt. This allowed for a direct comparison between the tmt opsins present in the dark adapted species (cavefish) versus those of the light adapted species (zebrafish). It is hoped that the findings from this project will contribute to our understanding of non-visual light detection in fish and the evolution of their non-image forming photoreception.
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Aggrawal, Manali. "Study of DNA damage on DNA G-quadruplexes and biophysical evaluation of the effects of modified bases (lesions) on their conformation and stability." Scholarly Commons, 2014. https://scholarlycommons.pacific.edu/uop_etds/134.
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Exposure of DNA to reactive oxygen species (ROS) results in the modified nucleobases (lesions) as well as strand scissions under physiological conditions. Due to its lowest oxidation potential (1.29 eV), guanine is the most easily oxidisable nucleobase. Furthermore, it has been observed that the 5'-guanine in G-tracts (e.g. GGG) has even lower oxidation potential (1.00 V vs. NHE). One of the representative G-rich examples is telomeres that consist of repeating units of 5'-d [TTAGGG]-3' found at the ends of chromosomes. Telomeres play an important role in biological functions, serving as guardians of genome stability; however, their G-rich nature implies that they can be readily oxidized. So how does nature protect these biologically important regions from oxidation? We believe the formation of a secondary structure known as G-Quadruplex in telomeric regions can partly serve as a protective role. In the first part of this work, we investigated DNA G-Quadruplex damage under various oxidation conditions and compare the damage results with single-stranded telomeric sequences. Damage to G-Quadruplex is generally less than single strands and is condition dependent. Guanines are the primary damage sites, but damage of adenine and thymine is also possible. Based on our studies, telomeric DNA can be readily oxidized to produce DNA lesions. How do DNA lesions affect the conformation and the stability of telomeric G-Quadruplex DNA? In the second part, we sought to address this question using various biophysical methods. Several native (OxodG, OxodA, and abasic site) and non-native (8-NH 2 -dA and 8-Br-dA) lesions were tested. UV thermal denaturation and circular dichroism revealed that the conformation and the stability of G-Quadruplex DNA are dependent on the location and the type of lesion in the sequence. G-Quadruplex DNA containing OxodG maintains its conformation with a decreased stability. Abasic site in the TTA loop affects the conformation of G-Quadruplex DNA but shows little effect on its stability. An unexpected stabilization of telomeric G-Quadruplex DNA was observed when deoxyadenosine (dA) in the loops was replaced with its native oxidized form OxodA. This is the first example of native DNA lesion that increases the stability of G-Quadruplex DNA. Like OxodA lesion, 8-NH 2 -dA (a non native DNA lesion) increases the stability of G-Quadruplex DNA while 8-Br-dA only affects the stability in KCl but has no significant effect in NaCl. In addition, studies of the effect of OxodA lesion on the human telomerase activity using TRAP assay will be discussed.
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Menon, Sindhu. "Biophysical studies of pathogen recognition by C-type lectins /." 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3363035.
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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009.Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3528. Adviser: Deborah E. Leckband. Includes bibliographical references (leaves 143-160) Available on microfilm from Pro Quest Information and Learning.
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Ludtke, Steven Jay. "Structural studies of membrane lytic peptides: A comparison of magainin and melittin." Thesis, 1996. http://hdl.handle.net/1911/16992.
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Magainin and melittin are 2 members of a class of small amphipathic helical peptides which act as potent antibiotics or toxins. It has been shown that the peptides in this class interact directly with the lipid bilayer rather than with protein targets within the membrane. Using oriented circular dichroism, lamellar x-ray diffraction and small angle in-plane neutron scattering we have determined the structures formed by these peptides on association with the bilayer. We have found that magainin forms 'wormhole' channels in the lipid bilayer and melittin solubilizes the membrane by the formation of peptide bounded discoid micelles. This is compared with our earlier results for alamethicin which forms channels using the barrel-stave model. The discovery that three ostensibly similar peptides form completely different structures is quite surprising, and emphasizes how much work remains to be done in this field. Hopefully the methods used and the motifs identified in this thesis will provide a good basis for continuing studies of similar peptides.
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Harroun, Thad Alan. "Hydrophobic matching and membrane mediated interactions in lipid bilayers." Thesis, 2000. http://hdl.handle.net/1911/19502.
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Hydrophobic matching, in which transmembrane proteins cause the surrounding lipid bilayer to adjust its thickness to match the hydrophobic surface of the protein, is a commonly accepted idea in biophysics, but one that until now has not been experimentally tested. One important consequence is that protein interactions will be mediated by the energy cost of deforming the membrane from its protein free state. With X-ray scattering techniques we tested these ideas with the peptide gramicidin embedded in DLPC and DMPC bilayers. Gramicidin pushes the different membranes to a common thickness as expected from hydrophobic matching. Concurrently, gramicidin-gramicidin nearest neighbor distance decreases with increasing mismatch, which confirms that the strain in the lipid bilayer gives rise to an attractive potential between the proteins.
We have taken a continuum theory approach to the analysis of the experimental results. This approach treats the energetics of membrane-protein interactions as a function of the material properties of the membrane such as bending rigidity and compressibility. Using numerical methods and a novel simulation technique, we have successfully demonstrated the theoretical relationship between membrane thickness change and protein correlation. By quantitatively reproducing our experimental results, we have shown that the theory of membrane deformation is sufficient to explain the phenomena of hydrophobic matching.
We also include a study on the peptide melittin as an example of the type of protein-lipid system we want to understand better. We answer the question of the orientation of the peptide when making membrane pores.
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Pogorelov, Taras Vladimirovich. "Application and development of molecular dynamics methods to examine the energy landscapes of protein folding and transient protein-protein complexes /." 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3223693.
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Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006.Source: Dissertation Abstracts International, Volume: 67-07, Section: B, page: 3822. Adviser: Zaida Luthey-Schulten. Includes bibliographical references (leaves 92-106). Available on microfilm from Pro Quest Information and Learning.
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Park, Hyokeun. "Single-molecule fluorescence studies of ReAsH and myosin VI /." 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3250307.
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Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006.Source: Dissertation Abstracts International, Volume: 68-02, Section: B, page: 0998. Adviser: Paul R. Selvin. Includes bibliographical references (leaves 110-118). Available on microfilm from Pro Quest Information and Learning.
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Punwong, Chutintorn. "Direct QM/MM simulations of the excited state dynamics of Retinal Protonated Schiff Base in isolation and in complex environments /." 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3363060.
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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009.Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3367. Adviser: Todd J. Martinez. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.
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Kim, Seung Joong. "Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation /." 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337825.
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Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2008.Source: Dissertation Abstracts International, Volume: 69-11, Section: B, page: 6636. Adviser: Taekjip Ha. Includes bibliographical references (leaves 241-254). Available on microfilm from Pro Quest Information and Learning.
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Li, Ying. "Multidimensional solid-state NMR studies of membrane proteins /." 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3314838.
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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008.Source: Dissertation Abstracts International, Volume: 69-05, Section: B, page: 2850. Adviser: Chad M. Rienstra. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.
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"Enhanced sampling method for free energy calculation and large scale conformational change." Thesis, 2009. http://hdl.handle.net/1911/61757.
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A method of directly computing the partition function (or the corresponding free energy) and accelerating configurational sampling is developed. In an expanded ensemble, the method can quickly sample a broad distribution and yield accurate results for the partition function. The method is shown to be efficient and accurate in studying thermodynamic properties, searching low-energy configurations of difficult molecular systems and counting solutions of puzzles.
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Hudock, Hanneli. "Dynamics of UV-excited uracil, thymine, and cytosine /." 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337798.
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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2008.Source: Dissertation Abstracts International, Volume: 69-11, Section: B, page: 6821. Adviser: Todd J. Martinez. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.
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"Illuminating biomolecular interactions with localized surface plasmon resonance." Thesis, 2010. http://hdl.handle.net/1911/62203.
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Noble metal nanoparticles exhibit localized surface plasmon resonance (LSPR), in which incident light causes a collective oscillation of a nanoparticle's free electrons. This phenomenon results in unique optical properties, including enhanced electric fields near the particle surface and an extinction peak at the resonant wavelength. The LSPR extinction peak's location is sensitive to the refractive index of the surrounding medium, especially in the volume closest to the particle surface. This makes plasmonic nanoparticles ideal for biosensing: their refractive index sensitivity can be used to transduce molecular binding signals. A method has been developed to use the optical extinction of films of gold nanorods to track antibody-antigen interactions in real time, resulting in a label-free kinetic immunoassay based on LSPR. Also, this method has been adapted to scattering spectra of single gold bipyramids. The single-particle approach has allowed the label-free detection of single biomolecules with kinetics information. These methods have future applications to both molecular biology and clinical assays.
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Matysiak, Silvina. "A multi-scale approach for macromolecular systems." Thesis, 2008. http://hdl.handle.net/1911/22185.
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Understanding biomolecular dynamics at different time and length scales is key to solving major problems in molecular biology and physical-chemistry. Because of the multiple scales that intrinsically coexist in biological macromolecules, the field has evolved through different paths, each focusing on different fixed resolutions. This thesis focuses on developing realistic models to describe complex biomolecular land-scapes at the mesoscale level, and a procedure to bridge different levels of molecular description for liquid water.
Toward this goal, we have proposed a realistic coarse-grained protein model and a technique to incorporate experimental data into the model to examine the long time-scale phenomenon of protein folding/misfolding. We have shown that simulations with this simplified protein representation can be used as a predictive tool for misfolding and aggregation of proteins.
Moreover, we have developed a coarse-grained model and an analytical theory to study another long time-scale phenomenon in biology: the translocation of DNA and RNA through nanopores. We have shown that our approach to the translocation process reproduces quantitatively, for the first time, all the experimentally observed trends and scaling behaviour, and provides insight into the different regimes present in the system.
Modeling explicit water is crucial for realistic biomolecular simulations, but is typically not computationally feasible. To overcome the computational impasse, we have proposed a coarse-grained water model that can reproduce remarkably well the behaviour of liquid water at physiological conditions, and a spatially adaptive procedure to change the molecular resolution of water on-the-fly from a coarse-grained to an all-atom representation. This adaptive multi-scale approach bridges the gap between the time and length scales accessible to simulations without losing atomistic detail on physically relevant regions.
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Hong, Liang. "Interactions and dynamics of soft materials /." 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3290460.
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Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2007.Source: Dissertation Abstracts International, Volume: 68-11, Section: B, page: 7596. Adviser: Steve Granick. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.
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"Polyelectrolyte properties of glycosaminoglycans as studied by laser light scattering." Tulane University, 1991.
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Dynamic and static light scattering measurements were made on high molecular weight, high purity hyaluronate from bacteria (BHA) and medium purity hyaluronate from cock's comb (CCHA), and proteoglycan monomers (PGM) from bovine nasal cartilage over a wide range of ionic strengths Cs, and solution concentrations Cp. BHA exhibited clear polyelectrolyte properties. Apparent persistence lengths within the wormlike chain model in the coil limit were estimated as a function of Cs. The total apparent persistence length varied from about 87A in the high Cs limit to nearly 400A at 1mM added NaCl. The apparent electrostatic persistence length varied approximately as Cs$\sp{-1/2}.$ Deviations from the theoretically predicted Cs$\sp{-1}$ dependence were investigated in terms of excluded volume effects. Dynamic light scattering yielded 'ordinary phase' diffusion coefficients whose dependence on Cp and Cs agreed reasonably well with hydrodynamic coupled mode theory in the linear limit. There was no evidence of an 'extraordinary phase' at low Cs for BHA. The overall results for medium purity CCHA are contrasted with those for BHA, the residual protein impurity $(\cong$0.7%) is thought to be source of the drastic difference in light scattering properties of the two hyaluronate. Clear peaks in the angular scattering intensity curve I(q), which moved towards higher scattering wave numbers q, as Cp$\sp{1/3}$ were found for PGM. This differs from Cp$\sp{1/2}$ dependence of scattering peaks found by neutron scattering from more concentrated polyelectrolyte solutions. There was evidence of simultaneous 'ordinary' and 'extraordinary' phases for PGM at low Cs. However, the 'extraordinary' phase was 'removable' by filtering. At higher Cs the PGM appear to behave as random non-free draining polyelectrolyte coils, with a near constant ratio of 0.67 between hydrodynamic radius and radius of gyration. The apparent persistence length varied as roughly Cs$\sp{-1/2}$ similar to various linear synthetic and biological polyelectrolytes. Electrostatic excluded volume theory accounted well for the dependence of A$\sb2$ on Cs. HA and oppositely charged polycations form large aggregates and a conformational change, from random coil to sphere, was found. PG-HA did form aggregate in the presence of link protein and no conformation change was observed. (Abstract shortened with permission of author.)acase@tulane.edu
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"Interaction of tunneling systems." Tulane University, 2007.
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Our work is dedicated to the investigation of the environmental effect on quantum tunneling of atoms in glasses when coupled with their nuclear magnetic moments and on positive charge transfer between base pairs of DNA in polar solvent We considered the effect of internal nuclear quadrupole interaction on quantum tunneling in complex multiatomic two-level systems and found two distinct regimes of strong and weak interactions. These regimes depend on the relationship between characteristic energy of the nuclear quadrupole interaction b* and bare tunneling coupling strength Delta0. When Delta0 > b* the internal interaction is negligible and tunneling remains coherent as determined by Delta 0. When Delta0 < b*, coherent tunneling breaks down and effective tunneling amplitude decreases by an exponentially small overlap factor eta* ≪ 1 between internal ground states of left and right wells of a tunneling system. This consequently affects the thermal and kinetic properties of tunneling systems at low temperatures T < b*. By the application of this theory, we can interpret the anomalous behavior of the resonant dielectric susceptibility in amorphous solids at low temperatures T < 5 mK, where nuclear quadrupole interaction breaks down coherent tunneling. We suggest conducting experiments with external magnetic fields to test our predictions and to clarify the internal structure of tunneling systems We also studied the tunneling of positive charge in DNA, which is another example of tunneling under conditions of strong interaction with the environment. The tight-binding Hamiltonian containing a quantum electron exchange integral and supplied by a classical linear interaction of the charge in DNA with water solvent polarization is taken to describe the experimental dynamics of the charge transfer reactions. Equilibrium constants of positive charge transfer between single, double guanine-cytosine (GC) and triple GC3 base pairs through the bridging adenine-thymine base pair were reproduced together with the corresponding differences in free energies. The effect of localization by the solvent polarization is shown to be much stronger than that of the quantum delocalization of the charge, which creates an asymmetric charge distribution in the ground state of the symmetric DNA base-pair sequencesacase@tulane.edu
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"Solvent and biomolecular interactions guiding assembly and recognition." Tulane University, 2010.
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Hydrophobic property of proteins drives it to form sub-nanometer organized structures such as alpha-helix, beta-strand. In biology this protein structural unit makes important class of functional macromolecules. Enzymatic activity, cellular signaling, ability to bind other molecules, and molecular transport are some of the important functions of protein assembly. Functional consequences of the physical interactions such as van der Waal's forces or electrostatic interaction, at play can be modulated by protein engineering techniques for applications in advanced biomaterial arenas. In addition, proteins folding to higher order structures in appropriate environment, and unfolding by removing those conditions underlie the importance of solvent interaction. Role of solvent activity is crucial and understanding of solvent interaction can be employed to commonly encountered chemical engineering problems as in evaluation of solute solubility This dissertation focuses on evaluation of solvation free energy of non-polar solute in organic solvent using molecular scaled particle theory. Molecular simulations of variety of organic solvents are performed and revised version of Reiss's scaled particle theory is utilized for predicting accurate solvation free energy. Next we investigate molecular mechanisms for specific recognition of organo-metallic ligand complexes by engineered antibodies. In addition, the technique to functionalize protein with polymer for structure stabilization has been scrutinized to elucidate the underlying mechanism. Molecular dynamic simulations were conducted on the hybrid protein-polymers and antibody systems, complementing and corroborating the experimental results observed In the first chapter organic solvent with varying topology such as linear alkanes, branched alkanes, cyclic alkanes and aromatic compound are simulated. The solvation free energy of cavity solute in solvent is determined by the probability of observing cavity of given size. This probability is systematically related to excess chemical potential using Reiss's scaled particle theory which treats multi-atomic molecule as a single spherical site. Reiss's revised version of scaled particle theory (MSPT) is presented recently which accurately evaluated the excluded volume of a multi-atomic molecule without resorting to single spherical site approximation. Systematic changes in the contact density for homologous aliphatic hydrocarbons observed from simulation are compared with MSPT. Accurate cavity solvation free energy for all the solvents is obtained from MSPT In the second chapter experimentally raised antibody 5B2 for specific binding of organo-metallic (or metal-ligand complex) - PbDTPA is modeled. The anionic organometallic ligand complex can bind to antibody pocket amino acids by variety of mechanisms such as hydrogen bonding, electrostatic interaction, or hydrophobic stacking. Efficient identification of these mechanisms aids in the timely response and optimization of novel biosensors. Simulations were performed for observation of binding between metal-ligand complex and antibody 5B2. The strong interaction of positively charged arginine, lysine and polar amino acids serine, tyrosine with oxygen sites on ligand-metal complex is responsible for efficient binding. Primary (cationic R95, K58 and polar S98, Y56) and secondary binding sites (cationic R50, polar Y97, Y33, S30c and non-polar W91) are identified from investigation of simulation results. Single site mutational simulations led to escape of the metal-ligand complex from antibody pocket, when binding sites were mutated to anionic or non-polar amino acids In the final chapter the simulation of protein 1CW and protein 1CW conjugated with poly(ethylene oxide) is performed to see enhancement of protein helical structure due to polymer presence to corroborate experimental results. This hybrid protein-polymer system possesses a more stable structure, compared to native protein systems, which makes it appealing for applications in peptide based drug therapies, hydrogel for tissue engineering, and controlled drug release. Quantification of individual amino acid interaction with ethylene oxide allowed us to generate hypothesis of helix-stabilization. Ethylene oxide preferentially interacts with cationic lysine and thereby stabilize hydrogen-bonding with neighboring amino acids. Side chain interference of cationic lysine with its neighbors is reduced as ethylene oxide acts as solvent to take away that interaction with a consequential increase in helicity. Polyalanine and lysine and arginine mutant polyalanine were conjugated with polymer and simulation results were quantified. Resultant enhanced helicity for cases of lysine and arginine mutants again proved role of destabilizing nature of cationic amino acids and subsequent solvent role of polymer in decreasing this destabilizing nature. We therefore conclude the interaction of lysine with ethylene oxide contributes to helix stability in original peptide 1CWacase@tulane.edu
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Absolon, Victor. "A comparison of biological and chemically induced leaching mechanisms of chalcopyrite." 2008. http://arrow.unisa.edu.au:8081/1959.8/48668.
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This dissertation reports a study of the dissolution mechanism which governs the leaching of Cu from chalcopyrite (CuFeS2) in acidic media at atmospheric pressure and examines the differences between chemical (abiotic), leaching and bioleaching. An array of solution, solid surface and bulk speciation studies were used to make a comprehensive study of the CuFeS2 leaching process(es).Thesis (PhD)--University of South Australia, 2008.