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Laming, Gregory John. "Density functional theory for molecules." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336907.
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Jenny, Nicolas [Verfasser]. "Synthesis of New Functional Molecules for Molecular Electronics / Nicolas Jenny." München : Verlag Dr. Hut, 2012. http://d-nb.info/1026652278/34.
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Olaoye, Olufemi Opeyemi. "Density functional calculation of simple molecules." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/20345.
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Thesis (MSc)--Stellenbosch University, 2012.AFRIKAANSE OPSOMMING: Berekeninge met Density Functional Theory (DFT) is ’n nuttige tegniek om die dinamika van molekules op potensiële energievlakke te verstaan. Beginnende met ’n prototipe molekuul formaldimien, wat die kern vorm van die groter fotochromiese molekuul dithizonatophenyl kwik (DPM), word die modellering van die molekuul meer ingewikkeld tot laasgenoemde bestudeer kan word asook sy fotochromiese afgeleides wat vervanging van elektronryk en elektronarm radikale by orto, meta en para posisies van die phenyl ringe insluit. DFT berekeninge word met spektra van Absorpsiespektroskopie met UV en sigbare lig asook tyd opgeloste spektra, verkry dmv femtosekondespektroskopie, vergelyk. In pol^ere aprotiese, pol^ere protiese en nie-pol^ere oplosmiddels, isomeriseer die molekuul om die C=N dubbelbinding. Daar kan tussen die twee isomere onderskei word deur dat die een in oplossing in sy grondtoestand blou en die ander een oranje voorkom. Die isomerisering is’n fotogeinduseerde proses. Die optimering van die molekul^ere struktuur, absorpsiespektra, oplosmiddel-afhanklikheid, en potensiële energievlak metings van die molekuul word bestudeer. Die sterk/swak wisselwerking wat in pol^ere protiese/aprotiese oplosmiddels verskyn word geopenbaar deur die hoe/lae absorpsie van die sekond^ere bande van die molekules. Daar is gevind dat die absorpsiespektra van DPM bathochromies in oplosmiddels met hoë diëlektriese konstantes is. Vir die potensiële energievlak berekeninge van die grondtoestand word rigiede en ontspanne metodes gebruik waar laasgenoemde met gebroke simmetrie berekeninge verkry word. Van alle metodes wat vir berekeninge gebruik was, gee die B3LYP/CEP-31G metode die beste benadering aan eksperimentele data. Alle berekeninge word gedoen met twee bekende sagteware pakkette; Amsterdam Density Functional (ADF) en Gaussian, wat op twee verskillende DFT metodes gebaseer is.
ENGLISH ABSTRACT: Density functional theory is a useful computational tool in the understanding of molecular dynamics on potential energy surfaces. Starting with a prototype molecule formaldimine, the photochromic molecule dithizonatophenylmercury II (DPM) and a set of its photochromic derivatives, (involving substitutions of electron donating and electron withdrawing substituents at ortho, meta and para positions of the dithizonato phenyl rings), are studied through density functional calculation in comparison with steady state absorption spectra obtained from UV-Visible and femto second spectroscopy experiments. In polar aprotic, polar protic and non-polar solvents these molecules isomerise around C=N double bond chromophore, from orange electronic ground states to blue electronic ground states upon photo-excitation. We investigate the structural optimisations, the absorption spectra, the solvent dependence and the potential energy surface (PES) of these molecules. The strong (weak) interactions exhibited by the polar protic (aprotic) solvents used are revealed through high (low) absorbance in the secondary bands of these molecules. The absorption spectra of DPM are found to be bathochromic in solvents with high dielectric constants. For the ground state PES calculation we make use of rigid and relaxed methods, and the latter is obtained through broken symmetry calculation. Of all the methods used in calculation, B3LYP/CEP-31G method gives the best approximation to the experimental data. All calculations are done using the two renown software, Amsterdam Density Functional (ADF) and Gaussian, availing their different density functional methods.
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Pace, Giuseppina. "Self-assembly of functional molecules at surfaces." Université Louis Pasteur (Strasbourg) (1971-2008), 2007. https://publication-theses.unistra.fr/public/theses_doctorat/2007/PACE_Giuseppina_2007.pdf.
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Les nanotechnologies tendent à générer et exploiter de nouvelles structures ayant une taille caractéristique allant de 1 à 100 nanomètres, ceci dans le but de fabriquer des matériaux fonctionnels ainsi que des composants électroniques. Durant les dernières décennies, un effort a été particulièrement dévolu à la création et l’étude de composants électroniques de taille extrêmement réduite utilisant des molécules individuelles en tant que composants électroactifs, ce domaine de recherche s’appelle l’électronique moléculaire. Ce travail de thèse s’inscrit dans ce contexte scientifique et est plus particulièrement focalisé sur la caractérisation physico-chimique à l’échelle du nanomètre des propriétés de commutation de molécules modèles pour, à terme, les implémenter au sein de composants moléculaire. Au long de ce travail, nous nous sommes appliqué à étudier les conditions requises pour qu’une molécule chimisorbée au sein d’une monocouche auto-assemblée (ou SAM pour Self Assembled Monolayer) puisse se comporter comme un interrupteur. Un interrupteur moléculaire peut-être défini comme une molécule ayant la capacité de changer son état de manière contrôlée, ceci résultant d’un stimuli externe physique ou chimique comme par exemple la lumière, un changement de pH, la coordination réversible d’ions ou l’application d’un potentiel. Un des principaux challenges de l’électronique moléculaire est de préserver les caractéristiques commutatrices de ces molécules lorsqu’elles sont adsorbées sur des substrats solides. Nous avons donc focalisé notre attention sur des interrupteurs moléculaires pouvant s’ancrer sur des substrats solides tout en formant des auto-arrangements bidimensionnels. Les monocouches d’organothiols auto-assemblées sur des surfaces cristallines d’or se sont avérées être de bons candidats puisqu’elles sont connues pour leur grande stabilité sous environnement inerte, ainsi que pour leur grande reproductibilité et leur ordre à grande distance (jusqu’à quelques centaines de nanomètres). De plus, au vue de leurs propriétés physico-chimiques contrôlées, les monocouches d’organothiols représentent de bons éléments pour le développement de « biosensors » ou plus généralement de l’électronique moléculaire[. . . ]This work is aimed at establishing a correlation between molecule-substrate and molecule-molecule interactions in view of the future implementation of nano-electronic devices based on unctional molecules. In particular, we studied the self-assembly behaviour of organic thiols functionalized molecules holding potential to act as switches on solid substrates. We focused on the isomerization of azobenzene based Self-Assembled Monolayers (SAMs) on gold substrates. A fine tuning of interchain interactions within the SAM made it possible to obtain high yield of isomerization. We also devised a new method to isolate individual functional molecules in a host SAM. In the final chapter we present our studies on the self-assembly properties of grid-like supramolecular architectures. Sub-molecularly resolved Scanning Tunneling Microscopy studies offered direct insights into structural and dynamic properties of the monolayers
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Pace, Giuseppina Samori Paolo. "Self-assembly of functional molecules at surfaces." Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/885/01/PACE_Giuseppina_2007.pdf.
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Oda, Katsunari. "Synthetic studies on silicon-containing functional molecules." 京都大学 (Kyoto University), 2007. http://hdl.handle.net/2433/136238.
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Katzer, Frank. "Molecular genetic and functional analyses of surface molecules of Theileria annulata sporozoites." Thesis, University of York, 1995. http://etheses.whiterose.ac.uk/9778/.
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Sahai, Erik Anand. "Functional analysis of RhoA and its effector molecules." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.300839.
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Campitiello, Marilena <1983>. "Synthesis of Self-Assembling Molecules for Functional Materials." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amsdottorato.unibo.it/8165/1/Marilena%20Campitiello_Tesi.pdf.
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The research carried out during these three years was developed as part of the MolArNet Project, supported by the European Commission, which aims at giving a first demonstration of molecular Quantum-dot Cellular Automata (QCA) elementary devices as a feasible approach to unconventional computation. Here we describe the design and synthesis of novel alkyl substituted guanosine-ferrocene derivatives, and their self-assembly at the solid/liquid interface on highly oriented pyrolitic graphite (HOPG). Supramolecular self-assembly of these derivatives has been accomplished in solutions by NMR and CD spectroscopy and on surface by STM and AFM techniques.
We have shown that supramolecular structures formed by ferrocene-exposing guanosines in solutions and at surfaces can be tuned by introducing sterically demanding substituents, ranging from G-ribbons to G4 cation-free architectures. This self-assembly is governed by the formation of H-bonds between guanosines that dictates the spatial localization of ferrocenes, ultimately forming 1D conjugated arrays that may be employed as prototypes of supramolecular nanowires.
In this thesis we also explored the possibility of using porphyrin derivatives carrying ferrocene residues directly connected to the porphin core, as alternative approach to QCA implementation. Preliminary electrochemical studies using cyclic voltammetry show that porphyrins can be used as a two/four dots cells.
During the period at the University of Maryland, in the Prof. Jeffery Davis’ research group, I worked on the synthesis and characterization of specific dyes, containing azobenzene groups, in order to insert them in the guanosine hydrogels. These dyes are capable, in principle, to change their conformation in a reversible way, through an external light stimulus. Thus, it could be possible to obtain photoresponsive hydrophilic gels, able to break and reform themselves in a controlled manner.
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Gatchell, Michael. "Molecular Hole Punching : Impulse Driven Reactions in Molecules and Molecular Clusters." Doctoral thesis, Stockholms universitet, Fysikum, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-129523.
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When molecules are excited by photons or energetic particles, they will cool through the emission of photons, electrons, or by fragmenting. Such processes are often thermal as they occur after the excitation energy has been redistributed across all degrees-of-freedom in the system. Collisions with atoms or ions may also lead to ultrafast fragmentation in Rutherford-like scattering processes, where one or several atoms can literally be knocked out of the molecule by the incoming projectile before the energy can be completely redistributed. The resulting fragmentation pathways can in such knockout processes be very different from those in thermal processes. This thesis covers extensive studies of collisions between ions/atoms and isolated Polycyclic Aromatic Hydrocarbon (PAH) molecules, isolated fullerene molecules, or clusters of these. The high stabilities and distinct fragmentation channels make these types of molecules excellent test cases for characterizing knockout-driven fragmentation and the reactions that these processes can lead to. I will present experimental measurements for a wide range of energies and compare them with my own molecular dynamics simulations and quantum chemical calculations. In this thesis, I present an in-depth study of the role of knockout in the energetic processing of molecules and clusters. The competition between knockout and thermally driven fragmentation is discussed in detail. Knockout-driven fragmentation is shown to result in exotic fragments that are far more reactive than the intact parent molecules or fragments from thermal processes. When such reactive species are formed within molecular clusters efficient molecular growth can take place on sub-picosecond timescales. The cluster environments are crucial here because they protect the newly formed molecules by absorbing excess energy. This is a possible pathway for the growth of large PAHs, fullerenes, and similar carbonaceous complexes found in, for instance, the interstellar medium.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Submitted.
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Ornatska, Maryna. "Shell design of functional hyperbranched molecules for surface assembly." [Ames, Iowa : Iowa State University], 2006.
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Main, Alison. "Structural and functional studies of fibronectin type III molecules." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359449.
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Ingamells, Victoria Elizabeth. "Exchange-correlation potentials for molecules in density functional theory." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627101.
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Van, Poll Maaike Laetitia. "Functionalisation of PDMS via self-assembly of functional molecules." Thesis, University of Cambridge, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.611734.
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Zurek, Eva D. "Density functional theory (DFT) studies of solids and molecules." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-27968.
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Furness, J. W. "Extending density-functional theory to molecules in magnetic fields." Thesis, University of Nottingham, 2017. http://eprints.nottingham.ac.uk/39336/.
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The density-functional theory (DFT) of Hohenberg and Kohn [1] has become the Swiss army knife of the quantum chemist, able to tackle nearly all electronic structure problems with impressive accuracy and efficiency, and it is common to see DFT calculations reported alongside experimental observations in the wider chemical literature. Some systems remain problematic for DFT however and, as DFT was constructed to simulate the systems commonly encountered in the chemistry lab, magnetic fields and the electron currents they induce are completely absent from the theory. Instead, DFT must be generalised for use in a magnetic field by including these currents directly, becoming current-density-functional theory (CDFT) [2]. By making this generalisation it is hoped that the practical utility of standard DFT can be leveraged to investigate molecules in both weak and strong magnetic fields. Whilst the study of molecular systems in strong magnetic fields is clearly of astrochemical and academic interest [3–7], it is reasonable to ask what place such calculations have with regards to laboratory problems, and what the eventual goal of CDFT is. To answer this one should look, for example, to the laboratory field semi-conductor systems that have been shown to be good analogues of molecules in strong fields [8,9]. Empirical studies of such systems show that a proper description of the magnetic effects is likely to be essential for their accurate simulation and, with the large size of these systems, the low cost correlated description of CDFT is likely to be instrumental in understanding their electronic structure. The theoretical framework for CDFT has long been established, only very recently however has a computer code, London, been available to actually perform self-consistent molecular CDFT calculations in strong magnetic fields [10, 11]. As a result of this absence, the functionals and approximations that comprise CDFT remain relatively untested. This thesis aims to utilise the London code to address this absence, first establishing the accuracy of existing CDFT functionals before developing the ideas to investigate the effect of a strong magnetic field on various aspects of electronic structure. The thesis begins by establishing the necessary theoretical foundations of DFT in Chapter 1 and its extension to CDFT in Chapter 2. The accuracy of a number of CDFT functionals is tested in Chapter 3 for predicting both the weak field magnetic phenomena encountered on earth, and the more exotic physics found in strong fields. The course of this study reveals a modified implementation of the meta-generalised gradient approximation (mGGA) class of functionals to be particularly well suited to strong field CDFT, providing a promising route to high accuracy descriptions of strong field phenomena. Using the modified mGGA functionals, Chapter 4 makes use of the interpretive powers of CDFT and the Kohn–Sham orbitals in order to develop a qualitative understanding of strong field electronic structure, and the origins of a new bonding mechanism, termed perpendicular paramagnetic bonding. This exploration of strong field phenomena provides a rationalisation for the the successes of the mGGA functionals, highlighting the importance of self-interaction error in strong magnetic fields. The presence of a strong magnetic field has a complicated effect on the excited electronic states, with important consequences for molecular structure in a field. The maximum overlap method (MOM) of Gilbert et al. [12] is employed in Chapter 5 in the context of strong field Hartree–Fock theory to facilitate the study of excited states in magnetic fields. The MOM method is shown to give an excellent agreement with high accuracy calculations and paves the way for a MOM-CDFT program capable of giving an accurate, correlated description of excited states in a field. The rest of the thesis moves away from directly dealing with the complications of a magnetic field, and instead considers the optimised effective potential (OEP) method in DFT as a means to fully orbital dependent functionals. This investigation is made with an eye to the future extension of CDFT to incorporate the OEP method, enabling the use of orbital dependent functionals in the CDFT description of molecules in magnetic fields. Such functionals are expected to be an effective route to higher accuracy calculations, as the currents induced by the magnetic field are inherently orbital dependent quantities themselves. The core framework of magnetic field free OEP is explored in Chapter 6 and a previously unrecognised connection between the recently proposed variational principle of Gidopolous [13] and the Lieb functional [14] is established. The optimised effective potential problem is notoriously ill behaved in a finite basis representation and the problem of regularising its equations to give physical potentials remains unsolved, despite considerable effort. Previous regularisation schemes are severely limited by their requirement for a user defined regularisation strength parameter, with no a priori guide towards the correct choice. This requirement prevents the OEP method from being used as a black box method and restricts the basis set combinations that can be considered. Chapter 7 addresses the absence of a satisfactory regularisation solution by first thoroughly studying the general ill-posed problem and the classical techniques employed in its regularisation. From this base, a fully automatic regularisation scheme is constructed to automatically tune regularisation strength from measures that are internal to the OEP. In doing so, an optimal regularisation is applied throughout the calculation, removing the need for a manually set parameter. The automatic scheme is then augmented with information from the potential basis set and shown to produce a physically meaningful potential from a single OEP calculation, regardless of the basis sets chosen. Finally, Chapter 8 summarises the work and discusses future directions for the continued development of the field.
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Chai, Jeng-Da. "Orbital-free density functional theory of atoms, molecules, and solids." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/3125.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2005.Thesis research directed by: Chemical Physics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Guo, Yufei. "The local-density-functional theory : application to atoms and molecules." Thesis, McGill University, 1990. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=74535.
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The generalized local-spin-density functional (G-LSD) theory is proposed which avoids (a) the physical restriction used in the generalized exchange local-spin-density functional (GX-LSD) theory; (b) the homogeneous electron-density approximation in the Hartree-Fock-Slater (HFS) theory and in the Gaspar-Kohn-Sham (GKS) theory; and (c) the time-consuming step to search the optimal exchange parameter for each atom or ion in the X$ alpha$ and $ Xi$a theories. Theoretically, the G-LSD theory is more rigorous than the GX-LSD, HFS, GKS, and $ Xi$a theories. Numerically, the statistical total energies for atoms are better in the G-LSD theory than in the GKS theory.Ionization potentials and electron affinities of atoms, the stability of singly and doubly charged negative ions, and the electronegativities, and hardnesses of the fractional charged atoms with Z $<$ 37 are calculated by the SIC-GX-LSD theory with the GWB Fermi-hole parameters and electron-correlation correction.
The self-interaction correction (SIC) is introduced into the multiple-Scattering X$ alpha$ (MS-X$ alpha$) method and used to calculate some molecules and molecular anions. The results show that the ionization potentials from the negative of the one-electron eigenvalues are as good as those obtained in the transition state calculation and in very good agreement with experiment.
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Khanzada, Umme Kulsum. "Functional studies of cell adhesion molecules, neuroplastins 65 and 55." Thesis, Royal Holloway, University of London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269631.
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Gantenbein, Markus [Verfasser]. "Small Organic Molecules: Building Blocks of Functional Materials / Markus Gantenbein." München : Verlag Dr. Hut, 2015. http://d-nb.info/1074063554/34.
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Cragg-Hine, Ian. "Early main group metal complexes of multi-functional organic molecules." Thesis, University of Cambridge, 1995. https://www.repository.cam.ac.uk/handle/1810/271932.
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Tonogaki, Keisuke. "Synthesis of olefin-based functional organic molecules using organoboron platforms." 京都大学 (Kyoto University), 2006. http://hdl.handle.net/2433/144036.
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Kyoto University (京都大学)0048
新制・課程博士
博士(工学)
甲第12352号
工博第2681号
新制||工||1379(附属図書館)
24188
UT51-2006-J344
京都大学大学院工学研究科合成・生物化学専攻
(主査)教授 吉田 潤一, 教授 村上 正浩, 教授 杉野目 道紀
学位規則第4条第1項該当
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McQuaker, Stephen. "Functional molecules to test the free radical theory of ageing." Thesis, University of Glasgow, 2013. http://theses.gla.ac.uk/4211/.
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Oxidative stress at a cellular level resulting from reactive oxygen species (ROS) has been implicated as a key factor in the ageing process and the development of age-related diseases. Mitochondria are the primary source of endogenously generated ROS through the leakage of electrons from the respiratory chain to molecular oxygen. Therefore there is a lot of interest in investigating ROS production and their biological impacts on both a cellular level and whole organism level. A mitochondria-targeted hydrogen peroxide (H2O2) probe (MitoB) i and a mitochondria-targeted nitric oxide (•NO) probe (MitoDA) iii have been prepared to allow the detection and quantification of mitochondrial concentrations of these species in vitro and in vivo. These utilise the selective reactivity of boronic acids with H2O2 and 1,2-dianilines with the combination of •NO and oxygen respectively to afford specific reaction products. These conversions are readily detectable by ESI-MS and quantified using deuterated internal standards. The mitochondrial membrane potential (ΔΨm) is directly linked to levels of ROS production, with an elevated ΔΨm resulting in increased ROS production. Mitochondrial membrane potential moderators that release uncoupling molecules from caged precursors selectively in the presence of H2O2 were developed. Two untargeted analogues, DNP-SUM v and FCCP-SUM viii were prepared to release 2,4-dinitrophenoxyl anions (DNP–, vi) or carbonyl cyanide-p-trifluoromethoxyphenylhydrazonyl anions (FCCP–, ix) respectively and their pseudo-first order kinetics assessed. Two mitochondria-targeted analogues, MitoDNP-SUM(1) x and MitoDNP-SUM(2) xi designed to release DNP– vi inside the mitochondrial matrix were prepared. Their abilities to lower the ΔΨm and therefore the ROS producing capabilities in isolated rat skeletal muscle mitochondria in response to endogenously generated H2O2 were assessed. Work was also conducted towards the development of mitochondria-targeted photo-activatable probes that could potentially release small functional bioactive compounds from caged precursors inside individual mitochondria upon selective irradiation.
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Amalraj, S. F. "Structure and properties of conducting polymers modified with functional molecules." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2008. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/2628.
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Cao, Jie. "Assessment of density functional methods for computing structures and energies of organic and bioorganic molecules." Thesis, University of St Andrews, 2011. http://hdl.handle.net/10023/2589.
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The work in this thesis mainly focuses on the assessment of density functional methods for computing structures and energies of organic and bioorganic molecules. Previous studies found dramatic conformational and stability changes from B3LYP to MP2 geometry optimization for some Tyr-Gly conformers. Possible reasons could be large intramolecular basis set superposition errors (BSSEs) in the MP2 calculations and the lack of dispersion in the B3LYP calculations. The fragmentation method and three kinds of rotation methods were used to investigate intramolecular BSSE. It is concluded that the rotation method cannot be used to correct intramolecular BSSE along a rotation profile. Another methodology is to employ modern density functionals. We focused on M06-L with the Tyr-Gly conformer ‘book6’. Potential energy profiles were determined by computing the energy for geometries optimized at various fixed values of a distance that controls the degree of foldedness of the structure. M06-L manifested itself as a very promising method to investigate the potential energy surface of small peptides containing aromatic residues. To predict Tyr-Gly structures, 108 potential conformers were created with a Fortran program. The geometry optimizations were done using M06-L/6-31G(d) and M05-2X/6-31+G(d). Two schemes were employed and the most stable conformers were compared to the 20 stable conformers found by B3LYP. Both schemes found 10 conformers similar to one of the B3LYP stable conformers, as well as several newly found conformers. The study of a missing B3LYP stable conformer showed that the possible reason of missing conformers may be the lack in dispersion in B3LYP theory. To study the hydration effect, we studied the conformations of neutral and zwitterionic 3-fluoro-γ-aminobutyric acid (3F-GABA) in solution using different solvation models, mainly the explicit water molecule models. Zwitterionic forms of 3F-GABA are preferred in solution. M06-2X performs better in calculating transition energy profiles than MP2.
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Carpenito, Carmine. "Expression and functional analysis of murine intercellular adhesion molecule 1 (ICAM-1)." Thesis, University of British Columbia, 1990. http://hdl.handle.net/2429/28939.
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Cell adhesion molecules enhance Interactions between adjacent cells In order to mediate a large variety of functions of the Immune system. An antibody against the murine lymphocyte surface antigen MALA-2 has previously been shown to Inhibit mixed lymphocyte response. A λgt10 cDNA library from NS-1 cells was screened and a cDNA clone, K3-1.1, was previously isolated. It had significant homology to the human ICAM-1 gene. This thesis covers the isolation of a second cDNA clone, K4-1.1, and its comparison to K3-1.1 In terms of expression, function and distribution.
The two clones are identical in sequence with the exception of the 5’ ends. Expression of these two clones was examined using a transient expression system of COS cell transfection. Cell surface expression of the K3-1.1 clone could not be detected by FACS analysis. Even when the 5' untranslated region of the K3-1.1 clone (which has 10 potential translation start sites) was removed, protein could not be detected at the cell surface, intracellularly, or extracellularly. However, K4-1.1 expression was detected at the cell surface. Northern blot analysis reveals that there are two distinct messages which are likely to be represented by the two clones. When the northern blot was probed with the 5' end of the K3-1.1 clone, only one of the messages was detected. This together with the result of Southern blot analysis suggests that the two messages are likely the result of alternate splicing.
In order to examine the interactions of the murine ICAM-1 with the surface of other cells, an expression system which would produce large amounts of a secreted soluble form was established. The soluble protein was purified from the supernatant of transfected cells by an antibody-affinity column and used in preliminary binding assays.Medicine, Faculty of
Medical Genetics, Department of
Graduate
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Cotí, Karla Karina. "I. Hydrodynamics--focusing microreactor II. Mechanically interlocked molecules for functional materials /." Diss., Restricted to subscribing institutions, 2010. http://proquest.umi.com/pqdweb?did=2026899211&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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Bronner, Christopher [Verfasser]. "Photoinduced and Thermal Reactions of Functional Molecules at Surfaces / Christopher Bronner." Berlin : Freie Universität Berlin, 2014. http://d-nb.info/1053653751/34.
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Li, Jing [Verfasser], and Thomas [Akademischer Betreuer] Drewello. "Modern Mass Spectrometry of Functional Molecules / Jing Li. Gutachter: Thomas Drewello." Erlangen : Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 2013. http://d-nb.info/1054164355/34.
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Cunningham, Beth. "Density functional studies of sulfur-nitrogen and period 2 fluoride molecules." Thesis, University of Hull, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421982.
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Bradbury, Peta. "Structural homology and functional similarity: Cas family proteins, NEDD9 and p130Cas are functionally distinct focal adhesion molecules." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/15865.
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The majority of work to date pertaining to the Cas family proteins has focused on specifically on p130Cas. Thus, given the strong sequence and structural homologies shared between NEDD9 and p130Cas, similar roles have been attributed to NEDD9. This project focused on the regulatory roles of Src kinase and FAK in determining the molecular exchange of NEDD9 at focal adhesions. The direct interaction of FAK and NEDD9 recruited NEDD9 to focal adhesions, while confocal FRAP analysis revealed Src kinase phosphorylation of NEDD9 stabilised NEDD9 at focal adhesions and regulated cell migration, a result that is in stark contrast to that described for p130Cas. The importance of the structurally homologous C-terminal Focal Adhesion Targeting (FAT) domains of NEDD9, p130Cas and FAK in regulating focal adhesion mechanotransduction and mechanosensing were also studied. Using overlap-extension PCR, FAT domain exchanged constructs were generated and subjected to numerous microscopy based assays. Distinct, rigidity-specific functional roles for each FAT domain were subsequently identified. The p130Cas FAT domain was identified as a novel rigidity-dependent mechanosensor, while the NEDD9 and FAK FAT domains were found to be functionally analogous. Taken together, these findings contribute to the understanding of the molecular mechanisms that underpin focal adhesion biology and cell migration, and importantly highlight the functional differences of structurally homologous proteins.
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Raghoonanan, Venisha. "Molecular characterization and in vitro functional analysis of putative immunoprotective molecules in the soft tick, Ornithodoros savignyi." Diss., University of Pretoria, 2010. http://hdl.handle.net/2263/29182.
Full textAbstract:
Since ticks are classified as hematophagous ectoparasites, the primary feeding event involves a bloodmeal on a vertebrate host. Such activities facilitate the ingestion of microorganisms which may be detrimental to the survival of a tick. It is observed, however, that ticks are able to survive such invasion by microorganisms and in several cases, facilitate the transmission of pathogens, while themselves remaining unaffected. This phenomenon is attributed to the innate immune system of ticks. The focus of this project is on stimulus-induced immunoreactive peptides known as antimicrobial peptides. In chapter 2, an attempt was made to identify a homolog of the anti Gram-positive and bacteriostatic peptide microplusin, in the salivary glands of the argasid tick Ornithodoros savignyi. It was reported previously that tissue and life stage specific expression of this transcript occurs in the fat body of adult, fully fed, female Rhipicephalus (Boophilus) microplus ticks. The positive control used for this study was unsuccessful due to the incorrect tissue and life stage of R. (B.) microplus ticks. No significant homolog was identified due to the possible existence of stringent regulation of expression as well as differences in the induction stimuli between argasid and ixodid ticks. Lysozyme catalyzes the cleavage of the β-1,4 glycosidic bond between N-acetyl muramic acid and N-acetyl glucosamine of the peptidoglycan layer of bacterial cell walls affording the molecule antibacterial activity. In argasid ticks, lysozyme was observed to be induced by feeding. In chapter 3, an attempt was made to elucidate the O. savignyi homolog of the O. moubata lysozyme molecule. The partial sequence obtained revealed the presence of a lysozyme homolog in O. savignyi. The tissue expression profile revealed constitutive expression in the midgut and ovaries and induction of transcription in the hemolymph upon feeding. In salivary glands, upregulation was observed following ingestion of Gram-positive bacteria. In chapter 4, the tissue expression profile of O. savignyi defensin was investigated. It was found that transcription is induced following the ingestion of Gram-positive bacteria, while in the hemolymph upregulation was observed upon feeding. Furthermore, chapter 4 saw the attempts made at the RNAi mediated silencing of the lysozyme and defensin transcripts. Silencing, analysed by real time PCR, was not efficient as no statistically significant silencing was observed. Observation of the phenotype revealed mortality. However, statistical analysis of silencing revealed that the mortality observed was not due to silencing, but non-specific and possibly the result of injury during injection. Overall, the abovementioned experiments revealed the tissue specificity of expression of ixodid microplusin and that a more strategic approach is required for the elucidation of the argasid homolog. The partial O. savignyi lysozyme sequence was elucidated together with the tissue expression profile of this molecule and O. savignyi defensin. The RNAi experiments require optimization for future studies.Dissertation (MSc)--University of Pretoria, 2010.
Biochemistry
unrestricted
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Tekin, Emine Deniz. "Investigation Of Biologically Important Small Molecules: Quantum Chemical And Molecular Dynamics Calculations." Phd thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612343/index.pdf.
Full textAbstract:
In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electronic properties of these molecules were found. These theoretical studies could clarify the role of these molecules on human health before they are commercially developed and used. In addition, unfolding dynamics of small peptide sequences (DDATKTFT and its variants) in immunoglobulin G-binding protein G was investigated. Protein folding and unfolding is one of the most important unsolved problems in molecular biology. Because of the large number of atoms involved in protein folding, it is a massive computational problem. The hope is that, one could understand this mechanism with the help of molecular dynamics simulation on small peptides. One of our findings is that the location of the hydrogen bonds is important for the stability of the peptide.
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Lim, I.-Im Stephanie. "Molecularly mediated assembly of nanoparticles towards functional nanostructures." Diss., Online access via UMI:, 2008.
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Stremlau, Stephan [Verfasser]. "High Resolution Vibrational Spectroscopy of Functional Organic Molecules at Surfaces / Stephan Stremlau." Berlin : Freie Universität Berlin, 2015. http://d-nb.info/1075493617/34.
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Bhamrah, Harley Jasvir Kaur. "A UV assisted methodology for functional oxide film formation from small molecules." Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/40387.
Full textAbstract:
The development of organic electronics has progressed rapidly due to the demand for lower cost, large scale fabrication of devices using inexpensive materials with flexible substrates. The field has seen the discovery of many suitable organic substitutes for traditional electronic component materials, in particular, by polymers and small molecules. One class of materials, metal oxides, have yet to find organic alternatives capable of performing to standards required. In this thesis, a non-toxic, room temperature method for functional oxide film formation from small molecules frequently employed as active layers in devices is explored to fully determine the mechanism by which the metal oxide is formed. Comparison of precursors, ZnPc (zinc phthalocyanine) and ZnTPP (zinc tetraphenylporphyrin), with contrasting morphology when deposited as thin films demonstrates the importance of the oxygen-assisted mechanism and its relation to grain boundaries. It is demonstrated that efficiency of oxide formation may be improved by choice of a crystalline precursor. Heterostructures of ZnPc and PTCDA (3,4,9,10-perylenetetracarboxylic dianhydride), an archetypal organic semiconductor, are used as a model to determine the effect of the UV process for oxide production on underlying organic layers. We show that approximately half the precursor film reacts before the underlying layer is affected. The structures also reveal no effect of molecular orientation on the rate of oxide formation and templated films of ZnPc on PTCDA are correctly indexed for the first time. The use of PTCDA also confirms that inclusion of an oxygen-containing molecule can be employed as a method to increase the rate of film degradation. Finally, nanosphere lithography of ZnPc films is combined with the UV assisted process to form regular arrays of hollow triangular nanostructures or pillars with the aim of creating structures suitable for photonic use.
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Ortiz, Ruben Santamaria. "Density functional theory of kinetic and exchange energies of atoms and molecules." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276885.
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Candel, Busquets Inmaculada. "Functional silica materials for controlled release, sensing and elimination of target molecules." Doctoral thesis, Universitat Politècnica de València, 2014. http://hdl.handle.net/10251/39101.
Full textAbstract:
La presente tesis doctoral titulada “Materiales de sílice funcionales para la
liberación controlada, detección y eliminación de moléculas de interés” se centra
en el diseño y desarrollo de materiales híbridos orgánico-inorgánicos mediante la
aplicación de los conceptos de Química Supramolecular. Durante el desarrollo de
la presente tesis doctoral se han preparado y caracterizado diferentes materiales
de base silícea para distintas aplicaciones.
La primera parte de la tesis se centra en el desarrollo de materiales de base silícea
capaces de variar su comportamiento fluorescente en función de la presencia o
ausencia de un cierto analito en el medio. Estos materiales emplean como soporte
nanopartículas de sílice que se funcionalizan superficialmente con dos unidades
diferentes, una coordinante y una indicadora (un fluoróforo). La interacción del
analito de interés (en nuestro caso aniones) con la unidad coordinante modificará
las propiedades emisivas del fluoróforo. Así, se han preparado dos materiales en
los cuales el grupo fluorescente es rodamina mientras que el grupo coordinante
es un imidazolato o una sal de guanidinio respectivamente. Una vez
caracterizados ambos materiales se estudió su comportamiento frente a
diferentes especies aniónicas a diferentes concentraciones resultando selectivos a
la presencia de benzoato (el material funcionalizado con imidazolatos),
dihidrógeno fosfato e hidrógeno sulfato (el material funcionalizado con sales de
guanidinio).
El tercer capítulo de la tesis se centra en la aplicación de materiales híbridos
orgánico-inorgánicos para la detección y eliminación de especies altamente
tóxicas como son los agentes neurotóxicos. Estos son compuestos
organofosforados capaces de causar graves lesiones en el sistema nervioso
central. En una primera aproximación se emplea el concepto de puerta molecular
para la detección de agentes neurotóxicos. Para ello, se utiliza como soporte
inorgánico un material mesoporoso de sílice (MCM-41) cuyos poros se cargan con
un colorante que actúa de indicador mientras que la superficie externa del mismo se funcionaliza con una molécula capaz de reaccionar con dichos agentes
neurotóxicos. Dicha molécula es capaz de interaccionar entre sí (mediante enlaces
de hidrógeno) formando una red que mantiene bloqueada la salida de los poros.
En presencia de DCP (dietilclorofosfato, un simulante de agente neurotóxico), y
después de que este reaccione con dicha molécula, se produce una reorganización
espacial que permite la liberación del colorante. De este modo, la presencia de los
agentes neurotóxicos está señalizada mediante un cambio de color. En una
segunda aproximación se aborda el uso de soportes inorgánicos de tipo MCM-41
como materiales para la eliminación de agentes neurotóxicos. Para ello se
modificaron químicamente las superficies de estos materiales silíceos mediante
tratamiento con distintas bases. Como consecuencia de este tratamiento básico
los silanoles de la superficie se desprotonan dando lugar a los correspondientes
silanolatos (nucleófilos fuertes). Estos silanolatos son capaces de reaccionar con
los agentes neurotóxicos descomponiéndolos y favoreciendo su eliminación de un
medio contaminado.
Por último, se estudia la aplicación de materiales híbridos orgánico-inorgánicos
funcionalizados con puertas moleculares en aplicaciones de liberación controlada,
concretamente, en liberación controlada intracelular de fármacos de interés. El
material híbrido consta de un soporte de sílice mesoporosa cuyos poros se cargan
con un compuesto citotóxico (camptotecina) y su superficie externa se
funcionaliza con una gluconamida. La presencia de una monocapa densa de
gluconamidas por el exterior del material inhibe la liberación del compuesto
citotóxico. Al añadir enzimas con capacidad para hidrolizar enlaces amida
(amidasa y pronasa) se produce la liberación de la camptotecina. El correcto
funcionamiento del material se comprobó in vitro e in vivo (en células HeLa).Candel Busquets, I. (2014). Functional silica materials for controlled release, sensing and elimination of target molecules [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/39101
TESIS
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Ho, Chian Sing. "Inquiry of Lipid Membranes Interacting with Functional Peptides and Polyphenol Drug Molecules." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6255.
Full textAbstract:
Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those membrane additives modulate the phase behavior of free-standing GUVs, as well as the miscibility transition temperature (Tm). We find that M2TM increases Tm and causes vesicle budding; polyglutamine aggregates disrupt lipid membranes; and the three polyphenol compounds exert disparate effects on GUV Tm.
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Wei, Daniel S. "Modeling of complex molecules adsorbed on copper surfaces." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53084.
Full textAbstract:
There has been growing demands towards the efficient production of enantiopure compounds through either asymmetric synthesis or separation from racemic mixtures. Recent studies have examined numerous different methods that may address this challenge. One of these methods involved the interaction of chiral molecules on achiral metal surfaces such as copper to create chiral templates while another method utilizes the interaction of chiral molecules on intrinsically chiral surfaces. Earlier studies using nonhybrid Density Functional Theory (DFT) functional has provided some insights into the geometric structures and relative energies of some of these interactions, but it failed to achieve quantitative agreement with experimental studies. Using dispersion corrected DFT functionals, this thesis present a study of chemisorbed dense adlayers of glycine and alanine on Cu(110) and Cu(3,1,17), physisorbed R-3-methycyclohexanone (R-3MCHO) on Cu(100), Cu(110), Cu(111), Cu(221), and Cu(643)R, and the hydrogenation of formaldehyde and methoxide on Zn or Zr heteroatoms promoted Cu surfaces.
In the dense glycine and alanine adlayer study, we have resolved a disagreement between experimental observation made on LEED, STM, and XPD, and we showed that heterochiral and homochiral glycine adlayer coexist on Cu(110). Our model failed to show the minute enantiospecificity for dense alanine adlayer on Cu(3,1,17) which indicated a numeric limitation for computational modeling of surface adsorption. In the physisorbed system, the dispersion corrected methods calculated adsorption energies were in better quantitative agreement with the experimentally observed values than the nonhybrid functionals, but it also created a significant overestimation of total adsorption energies. On the other hand, our model had indicated a previously unexpected adsorbate-induced surface reconstruction on Cu(110). This is promising news in term of computational modeling's capability in examining surface-adsorbate interaction on an atomic scale. As for the hydrogenation of formaldehyde and methoxide on copper surfaces, the model showed that the increased binding strength between the reaction intermediates and the heteroatom promoted copper surfaces to be the primary contributor of the increased reaction rates. Furthermore, our model had also indicated that while clustered heteroatoms are relatively rare, a significant portion of reaction takes place near these clustered structures. It is our hope that the results and techniques presented in this thesis can be used to better understand and predict the interaction of more complex surface-adsorbate interactions.
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Luukkonen, Sohvi. "Hydration of drug-like molecules with molecular density functional theory and the hybrid-4th-dimension Monte Carlo approach." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASF030.
Full textAbstract:
Le développement d’un médicament prend en moyenne plus de 10 ans pour un coût de 1 Mrd de dollars. Pour accélérer le processus et diminuer le coût, on utilise des méthodes in-silico lors de l’étape de découverte qui consiste à cribler ~10⁵ molécules de type médicament pour proposer quelques candidats à l’étape préclinique. Le critère majeur est l’affinité entre la molécule potentielle et la cible biologique. L’interaction se passant dans notre corps: cette affinité doit être prédite dans l’eau et le médicament doit être soluble dans l’eau pour avoir accès à la cible. Globalement, les effets de solvatation ont un rôle important dans la conception de médicaments. Numériquement, pour un champ de force donné, la solvatation peut être étudiée par des méthodes de simulation exactes mais coûteuses, par des modèles de continuum rapides mais qui ignorent la nature moléculaire du solvant, enfin par des théories des liquides approximatives mais capables de garder l’information moléculaire du solvant tout en diminuant le temps de calcul. L’objectif de cette thèse étant la prédiction des énergies libres d’hydratation (ELH) de molécules de type médicament par des méthodes qui soient les plus précises et plus rapides possibles, elle se concentre sur deux approches originales: Le Monte-Carlo hybride à 4ème dimension, une nouvelle méthode pour calculer les ELH selon le principe de Jarzynski à partir simulations courtes hors-équilibre pendant lesquelles on introduit ou retire le soluté doucement depuis le solvant avec un paramètre de couplage dépendant du temps. Nous montrons que cette approche est capable de prédire les ELH de molécules de type pharmaceutique 4-6 fois plus rapidement que l’approche classique de perturbation de l’énergie libre. La théorie de la fonctionnelle de densité moléculaire, une approche de théorie des liquides qui permet l’étude des propriétés de solvatation de n’importe quelle soluté rigide. Dans son état actuel, dans l’approximation hyper-netted-chain couplée à une correction de pression, nous montrons qu’elle est capable de prédire les ELH des mêmes molécules avec une précision de respectivement 0.5 ou 1.0 kcal/mol par rapport aux simulations ou aux données expérimentales, avec une accélération de calcul de l’ordre de 10³-10⁴ par rapport aux simulations. H4D-MC est considéré ici comme une source de références pour développer plus avant la MDFT, elle-même une méthode suffisamment rapide pour être envisagée dans un processus de criblage haut-débitThe development of a drug takes on average over 10 yr. for a cost of 1B dollars. To speed up the process, and reduce its cost, in-silico methods are used at the drug discovery stage. It consists of screening ~10⁵ drug-like molecules to propose few candidates to the pre-clinical stages. The main criterion is the affinity between the potential drug molecule and biological target. As the interaction happens the body, these affinities need to be predicted in water and the molecule needs to be water-soluble to access the receptor. Overall, solvation properties play an important role in drug design. Numerically, for a given force-field, solvation can be studied either with exact but time-consuming simulation methods, fast continuum models that lose the molecular nature of the solvent, or approximate liquid state theories that keep the solvent molecular information while speeding-up the computation. In this thesis, we focus on the prediction of the hydration free energies (HFE) of drug-like molecules with methods that are as fast and precise as possible, and we concentrate on two original approaches: Hybrid-4th-dimension Monte Carlo, a novel method that computes the HFEs according to the Jarzynski principle from short non-equilibrium simulations in which the solute is inserted or removed from the solvent with a time-depending coupling parameter. This approach is shown to predict the HFEs of drug-like molecules 4-6 times faster than the classical free energy perturbation approach. Molecular density functional theory, a liquid-state-theory approach that allows the study of the equilibrium solvation properties of any rigid solute. In its current level, the hyper netted-chain approximation coupled with a pressure correction, it is shown to predict the HFEs of drug-like molecules within 0.5 and 1.0 kcal/mol of simulations and experimental data, respectively, for an average computational speed-up 10³-10⁴ with respect to simulations. H4D-MC is considered here as a source of reference data for MDFT developments. MDFT is itself fast enough to be foreseen in a high-throughput screening pipeline
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Mondal, Biswajit. "Novel pd-catalyzed carbon-carbon and carbon-heteroatom cross coupling reactions towards the synthesis of diverse functional molecules." Thesis, University of North Bengal, 2021. http://ir.nbu.ac.in/handle/123456789/4373.
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Rolf, Bettina. "Functional analysis of the cell adhesion molecules L1, CHL1 and NCAM in vivo." [S.l. : s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=965755711.
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Abdullah, Gadija. "Functional analysis of miRNA regulated genes in prostate cancer as potential diagnostic molecules." University of the Western Cape, 2016. http://hdl.handle.net/11394/5648.
Full textAbstract:
>Magister Scientiae - MScProstate Cancer is the leading cause of cancer-related death in males in the Western world. It is a common biological disease originating from the reproductive system of the male namely, the prostate gland, usually in older patients (over the age of 50) and with a family history of this disease. The disease shows clinical aggressiveness due to genetic alterations of gene expression in prostate epithelial cells. Prostate cancer is currently diagnosed by biopsy and prostate cancer screening via the Prostate-Specific Antigen (PSA) blood test. Early detection is critical and although PSA was discovered to aid in the diagnoses of this cancer at its early stages, it has a disadvantage due to its low specificity thus causing unnecessary biopsies of healthy individuals and overtreatment of patients. Although various studies and efforts have been made to identify the ideal biomarker for prostate cancer and many even being applied to clinical use, it is still challenging and has not replaced the best-known biomarker PSA. PSA test has minimal invasive characteristics, at relatively low cost together with high sensitivity but low specificity. Biomarker discovery is a challenging process and a good biomarker has to be sensitive, specific and its test highly standardized and reproducible as well as identify risk for or diagnose a disease, assess disease severity or progression, predict prognosis or guide treatment. Computational biology plays a significant role in the discovery of new biomarkers, the analyses of disease states and the validation of potential biomarkers. Bioinformatic approaches are effective for the detection of potential micro ribonucleic acid (miRNA) in cancer. Altered miRNA expression may serve as a biomarker for cancer diagnosis and treatment. Small non-protein coding RNA, miRNA are small regulatory RNA molecules that modulate the expression of their target genes. miRNAs influence numerous cancer-relevant processes such as proliferation, cell cycle control, apoptosis, differentiation, migration and metabolism. Discovery and existence of extracellular miRNAs that circulate in the blood of cancer patients has raised the possibility that miRNAs may serve as novel diagnostic markers. Since a single miRNA is said to be able to target several mRNAs, aberrant miRNA expression is capable of disrupting the expression of several mRNAs and proteins. Biomarker discovery for prostate cancer of mRNA and miRNA expression are strongly needed to enable more accurate detection of prostate cancer, improve prediction of tumour aggressiveness and facilitate diagnosis. The aim of this project was to focus on functional analyses of genes and their protein products regulated by previously identified miRNA in prostate cancer using bioinformatics as a tool. Most proteins function in collaboration with other proteins and therefore this study further aims to identify these protein-protein interactions and the biological relevance of these interactions as it relates to Prostate cancer. Various computational databases were used such as STRING, DAVID and GeneHub-GEPIS for functional analyses of these miRNA regulated genes. The main focus was on the 21 genes regulated by several miRNAs identified in a previous study. Results from this study identified six genes; ERP44, GP1BA, IFNG, SEPT2, TNFRSF13C and TNFSF4, as possible diagnostic biomarkers for prostate cancer. These results are promising, since the targeted biomarkers would be easily detectable in bodily fluids with the Gene Ontology (GO) analysis of these gene products showing enrichment for cell surface expression. The six genes identified in silico were associated to transcription factors (TFs) to confirm regulatory control of these TFs in cancer promoting processes and more specifically prostate cancer. The CREB, E2F, Nkx3-1 and p53 TFs were discovered to be linked to the genes IFNG, GP1BA, SEPT2 and TNFRSF13C respectively. The expression of these TFs show strong association with cancer and cancer related pathways specifically prostate cancer and thus demonstrates that these genes can be assessed as possible biomarkers for prostate cancer. The prognostic and predictive values of the candidate genes were evaluated to assess their relationship to prognosis of this disease by means of several in silico prognostic databases. The results revealed expression differences for the majority of the candidate genes were not significantly sufficient to be distinguished as strong prognostic biomarkers in several prostate cancer populations. Although one marker, GP1BA was supported as having prognostic value for prostate cancer based on it's statistical pvalue in one of the prostate cancer patient datasets used. Another candidate gene SEPT2 showed promise as it has some prognostic value in the early stages of the disease. Although the results yielded, based on the in silico analysis, were not the discovery of an ideal diagnostic marker based on the set criteria in this study, further analysis using a molecular approach qRT-PCR can be considered for a detailed followup study on selected candidate genes to evaluate their roles in disease initiation and progression of prostate cancer using cell lines as well as patient samples.
CSIR
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Ge, Xin [Verfasser]. "Scanning tunneling microscopy and spectroscopy of functional molecules on metal surfaces / Xin Ge." Kiel : Universitätsbibliothek Kiel, 2008. http://d-nb.info/1019755075/34.
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Gangopadhyay, Shruba. "Density Functional Theory Study of Molecules and Crystals Containing d and f Metals." Doctoral diss., University of Central Florida, 2011. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4897.
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Density Functional Theory (DFT) method is applied to study the crystal structure of transition metal and lanthanide oxides, as well as molecular magnetic complexes. DFT is a widely popular computational approach because it recasts a many-body problem of interacting electrons into an equivalent problem of non-interacting electrons, greatly reducing computational cost. We show that for certain structural properties like phase stability, lattice parameter and oxygen migration energetics pure DFT can give good agreement with experiments. But moving to more sensitive properties like spin state energetic certain modifications of standard DFT are needed. First we investigated mixed ionic-electronic conducting perovskite type oxides with a general formula ABO3 (where A =Ba, Sr, Ca and B = Co, Fe, Mn). These oxides often have high mobility of the oxygen vacancies and exhibit strong ionic conductivity. They are key materials that find use in several energy related applications, including solid oxide fuel cell (SOFC), sensors, oxygen separation membranes, and catalysts. Different cations and oxygen vacancies ordering are examined using plane wave pseudopotential density functional theory. We find that cations are completely disordered, whereas oxygen vacancies exhibit a strong trend for aggregation in L-shaped trimer and square tetramer structure. On the basis of our results, we suggest a new explanation for BSCF phase stability. Instead of linear vacancy ordering, which must take place before the phase transition into brownmillerite structure, the oxygen vacancies in BSCF prefer to form the finite clusters and preserve the disordered cubic structure. This structural feature could be found only in the first-principles simulations and cannot be explained by the effect of the ionic radii alone. In order to understand vacancy clustering and phase stability in oxygen-deficient barium strontium cobalt iron oxide (BSCF), we predict stability and activation energies for oxygen vacancy migration. Using symmetry constrained search and Nudged Elastic Band method, we characterize the transition states for an oxygen anion moving into a nearby oxygen vacancy site that is surrounded by different cations and find the activation energies to vary in the range 30-50 kJ/mol in good agreement with experimental data. Next we study spin alignments of single molecule magnets (SMM). SMMs are a class of polynuclear transition metal complexes, which characterized by a large spin ground state and considerable negative anisotropy. These properties lead to a barrier for the reversal of magnetization. For these reasons SMM are expected to be promising materials for molecular spintronics and quantum computing applications. To design SMM for quantum computation, we need to accurately predict their magnetic properties. The most important property is, Heisenberg exchange coupling constant (J). This constant appears in model Heisenberg Hamiltonian that can be written in general form as
H = −ΣJijSiSj
here Jij represents the coupling between the two magnetic centers i and j with the spin states Si and Sj. The positive J values indicate the ferromagnetic ground state and the negative ones indicate the antiferromagnetic ground state. We found pure DFT is not accurate enough to predict J values. We employ density functionals with a Hubbard U term that helps to counteract the unphysical delocalization of electrons due to errors in pure exchange-correlation functionals. Unlike most previous DFT+U studies, we calibrate U parameters for both metal and ligand
atoms using five binuclear manganese complexes as the benchmarks. We note delocalization of the spin density onto acetate ligands due to π-back bonding, inverting spin-polarization of the acetate oxygen atoms relative to that predicted from superexchange mechanism. This inversion may affect performance of the models assuming strict localization of the spins on magnetic centers for the complexes with bridging acetate ligands. Next, we apply DFT+U methodology for Mn12(mda) and Mn12(ada) complexes to calculate all six nearest neighbor Jij value. Our result shows both qualitative and quantitative agreement with experiments unlike other DFT studies. Using the optimized geometry of the ground spin state instead of less accurate experimental geometry was found to be crucial for this good agreement. The protocol tested in this study can be applied for the rational design of single-molecule magnets for molecular spintronics and quantum computing applications.
Finally we apply hybrid DFT methodology to calculate geometrical parameters for cerium oxides. We review the experimental and computational studies on the cerium oxide nanoparticles, as well as stoichiometric phases of bulk ceria. Electroneutral and nonpolar pentalayers are identified as building blocks of type A sesqioxide structure. The idealized structure of the nanoparticles is described as dioxide covered by a single pentalayer of sesquioxide, which explains the exceptional stability of subsurface vacancies in nanoceria. The density functional theory (DFT) predictions of the lattice parameters and bulk moduli for the Ce(IV) and Ce(III) oxides at the hybrid DFT level are also presented. The calculated values for both compounds agree with experiment and allow to predict changes in the lattice parameter with decreasing size of the nanoparticles. The results validate hybrid DFT as a promising method for future study the structure of oxygen vacancies and catalytic properties of ceria nanoparticles.ID: 029809473; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Thesis (Ph.D.)--University of Central Florida, 2011.; Includes bibliographical references (p. 117-128).
Ph.D.
Doctorate
Chemistry
Sciences
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Iaboni, Andrea. "An evolutionary and functional analysis of the extended B7 family of costimulatory molecules." Thesis, University of Oxford, 2002. http://ora.ox.ac.uk/objects/uuid:e769d4ab-81c9-4f92-918f-8ddfb718b596.
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Lynch, Mark Francis. "Chemical reactions of small molecules on metal surfaces : a density functional theory study." Thesis, Queen's University Belfast, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314017.
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Arkell, Ruth Maree. "Functional analysis of transforming growth factor-beta related molecules during early mouse development." Thesis, Open University, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.309864.
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