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1
Illa, Tuset Sílvia. "Molecular modelling of quatsome nanovesicles." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667197.
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This thesis is devoted to the theoretical and computational study at atomistic and molecular scales of the properties of novel organic nanoparticles called “Quatsomes” (vesicles made by mixing CTAB cationic surfactant and cholesterol) as well as the interactions of Quatsomes with different types of fluorescent molecules. The methodology employed is computational molecular modelling. It includes modelling of the interactions between molecules at different scales and resolutions (DFT electronic structure calculations, atomistic molecular mechanics force fields and coarse-grain molecular mechanics force fields) and molecular dynamics simulations at atomistic and coarse-grain molecular resolutions. Most of the results have observable consequences that have been confirmed experimentally.
The thesis is divided into an Introduction to the topic (with a brief explanation of the main experimental results and the main theoretical concepts), a chapter describing in detail the methods to be employed in the thesis, four chapters containing new results and a chapter with conclusions and perspectives.
The results of the thesis are presented in two parts. The first part (Chapters 3 and 4) contains the results concerning the simulations and calculations of structure and properties of the Quatsome vesicle from atomistic and coarse-grain molecular simulations. The second part (Chapters 5 and 6) contains the simulation study of the interaction of Quatsome vesicles with different types of dyes. The atomistic simulation results presented in Chapter 3 provide a detailed characterization of the properties of the Quatsome bilayer. The molecular organization of the components across the bilayer (positioning, orientation and diffusion of the component molecules) was studied as well as mechanical properties such as bending modulus and area expansion modulus. The effect of temperature and added salt was also analyzed. Remarkably, it was found that the orientation of the molecules has a spontaneous symmetry breaking between the two leaflets of the bilayer and states with different orientations coexist, a theoretical prediction that has been tested experimentally. In Chapter 4 two coarse-grain Martini-type parametrizations of a force field for CTAB surfactant (one for explicit solvent and one for implicit solvent simulations) was developed and successfully tested against atomistic simulations. The model was further employed to perform simulations of full Quatsome vesicles. These simulations revealed that the Quatsome vesicle is made of planar faces linked by curved defects, a kind of vesicle organization never found before. These predictions were confirmed by experimental Cryo-TEM images. Chapters 5 and 6 start by developing (from DFT) CHARMM compatible atomistic force fields for simulation of different dyes (fluorescein in Chapter 4 and DiD and DiI in Chapter 5). These force fields were employed in molecular dynamics simulations of the interactions of these dyes with Quatsomes. The results demonstrate that despite the hydrophilic fluorescein dye interacts strongly with Quatsome (via electrostatic interactions), the adsorption of the dye competes with the more favorable formation of soluble molecular clusters. Hence, a more suitable approach is to employ hydrophobic dyes such as DiI and DiD. The simulations reported in the thesis show that these dyes are integrated in the bilayer without deforming or altering the Quatsome and without aggregating inside the Quatsome bilayer, thus providing suitable alternatives for developing fluorescent vesicles.
The conclusions and perspectives section shows that the thesis not only present many new results but also has many possible future perspectives in different directions: vesicles with resonant energy transfer, conceptual aspects regarding the spontaneous self-assembly of vesicles, possibility of replacing the components by other different bilayer components. All these options have been initially explored and all of them are very promising.
2
Stansfield, Phillip James. "Molecular modelling of potassium channels." Thesis, University of Leicester, 2007. http://hdl.handle.net/2381/29963.
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This study uses the structural coordinates of the determined K+ channels to create comparative models of three diverse members of this family, with the aim of enabling a better understanding of the function of these channels. The K+ channel of primary interest is the hERG K+ channel. The pharmacology of this channel is of considerable interest as serendipitous block of K+ conduction pore may result in cardiac arrest. A set of known antagonists have been docked into novel comparative models of hERG to propose how these drugs interact with the channel. The models have also been subjected to molecular dynamics simulations to investigate the drug binding in more detail and to gain a structural understanding of two critical biophysical properties of this channel: activation and inactivation. Additionally, ancillary domains of the channel have been modelled to provide a tool for interpreting detailed structure-function relationships for the hERG channel. The second channel investigated is the TASK-1 channel. Comparative models of this channel have been created to evaluate mutations that alter selectivity and pH sensitivity. The final K+ channel studied is the Kir2.1 channel. A fundamental property of this channel is its block by polyamines, which prevents the efflux of K+. Comparative models have been created, with a series of polyamine analogues docked into the membrane and cytoplasmic pore regions of this channel. Overall, this study has illuminated the structural basis of several biophysical properties that are intrinsic to normal K+ channel function.
3
Breed, Jason. "Molecular modelling of ion channels." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308690.
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Peng, B. "Molecular modelling of petroleum processes." Thesis, University of Manchester, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515182.
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Park, N. "Modelling shocks using molecular dynamics." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/5826.
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The study of shocks in solid, crystalline metals has been ongoing since the early works of Rankine and Hugoniot in the latter half of the 19th century. However, the understanding of the behaviour of such materials under these extreme conditions remains an area of active research because of the paucity with which models can predict experimental observations. The modern era has seen a huge increase in the ability to solve many of the problems of this area of study by numerical, rather thatn analytic, means. One of these tools has been the use of computers to provide a numerical solution to the many–body problem posed by consideration of the medium as being composed of interacting atoms. The issue, then, has been transferred from one of dealing with many particles (which remains a problem for some aspects) to one of being able to develop a model which correctly describes the atomic interactions. However, it has been found that approximately correct models provide sufficient fidelity to enable qualitative studies to be undertaken. The study undertaken here has used this advantage to consider the behaviour of metallic materials under weak shock conditions. A comparison with some previous studies is given, which shows that, in order to avoid certain behaviours not observed experimentally, the simulation must contain thermal motion equivalent to at least room temperature. This thermal motion, and its resultant misalignment of the atoms, prevents spurious transfer of uni-directional momentum into rebounding translational supersonic waves. Further examination of the initial generation of dislocations indicates differences in the behaviour of not only the three high symmetry directions, but in the way that shear stress is relieved initially in low symmetry crystals as well. This behaviour gives some indication as to how the elastic precursor, commonly observed in weak shock experiments, decays from the level predicted by the Rankine–Hugoniot conservation relations to the much lower level observed experimentally. However, a very large discrepancy exists between the amplitude of the elastic wave observed in these simulations and that of experiments. It is shown that the existence of defects within the crystal can account for at least some of this discrepancy. However, computational limitations not only prevent the creation of realistic sample sizes, but also prevent the simulation of realistic defect densities and microstructures. This computational limtation, then, means that it is not currently possible to recreate the low Hugoniot elastic limits observed experimentally. The inability of atomistic simulations to recreate experimental data notwithstanding, useful analysis of shock behaviour is demonstrated. This fortuity is used to examine the behaviour of bicrystals under shock loading. It is shown that the difference in shock speed, together with the difference in response of the two crystal orientations leads to an interaction which modifies the behaviour from that observed in single crystal simulations. Further use is made of the ability of modern simulation methods to recreate salient features of dynamic processes to examine the behaviour of metallic substrates under high–speed impact from nanometer sized particles. Here the plasticity of the substrate is shown to be vital to ensuring that the simulation results are faithful to experiment, and hence to space science work. In order to capture this behavioour correctly, issues of substrate size and boundary behaviour are seen to be key.
6
Hall, Benjamin A. "Methods for Multiscale Molecular Modelling." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504367.
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Christopher, David. "Molecular dynamics modelling of nanoindentation." Thesis, Loughborough University, 2002. https://dspace.lboro.ac.uk/2134/6924.
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This thesis presents an atomic-scale study of nanoindentation, with carbon materials and both bcc and fcc metals as test specimens. Classical molecular dynamics (MD) simulations using Newtonian mechanics and many-body potentials, are employed to investigate the elastic-plastic deformation behaviour of the work materials during nanometresized indentations. In a preliminary model, the indenter is represented solely by a non-deformable interface with pyramidal and axisymmetric geometries. An atomistic description of a blunted 90° pyramidal indenter is also used to study deformation of the tip, adhesive tip-substrate interactions and atom transfer, together with damage after adhesive rupture and mechanisms of tip-induced structural transformations and surface nanotopograpghy. To alleviate finite-size effects and to facilitate the simulation of over one million atoms, a parallel MD code using the MPI paradigm has also been developed to run on multiple processor machines. The work materials show a diverse range of deformation behaviour, ranging from purely elastic deformation with graphite, to appreciable plastic deformation with metals. Some qualitative comparisons are made to experiment, but available computer power constrains feasible indentation depths to an order of magnitude smaller than experiment, and over indentation times several orders of magnitude smaller. The simulations give a good description of nanoindentation and support many of the experimental features.
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Lumley, James Andrew. "Molecular modelling of biological activity." Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393752.
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Grant, Guy Hamilton. "Molecular modelling of silicon compounds." Thesis, University of Liverpool, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329403.
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Smith, Derek John. "Molecular modelling of antifreeze proteins." Thesis, University of York, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313768.
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Tyrrell, Graham Philip. "Modelling the myosin molecular motor." Thesis, University of York, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247144.
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Theodorou, Doros Nicolas. "Molecular modelling of polymeric glasses." Thesis, Massachusetts Institute of Technology, 1985. http://hdl.handle.net/1721.1/15293.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1985.<br>MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE.<br>Bibliography: leaves 193-199.<br>by Doros Nicolas Theodorou.<br>Ph.D.
13
Searle, Stephen M. J. "Molecular modelling of immunoglobulin folds." Thesis, University of Bath, 1997. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246005.
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Richardson, Kevin John. "Submillimetre molecular line observations and modelling of molecular clouds." Thesis, Queen Mary, University of London, 1985. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1705.
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Submillimetre molecular line observations of molecular clouds in our galaxy are presented, and the data analysed using various alternative cloud models. A critical review is given of the methods commonly used to interpret molecular line data, including both theoretical considerations and issues relating to calibration and comparability of results obtained with different telescopes. A detailed comparison is made between results predicted from large velocity gradient (LVG) models, including the generalisation to non-monotonic velocity flows, and those given by "microturbulent" clouds. An LVG model is employed in an investigation of conditions in the molecular outflows frequently found in star formation regions, for which observations in the CO J=3-2 rotational transition at 345 GHz are presented. These are combined with lower frequency data from the literature to derive various properties of the outflows for a sample of 13 sources. The most important result is that local H2 densities exist in the outflows which are higher, typically by an order of magnitude, than previously derived average values obtained using only lower frequency data. Observations are presented of the S255 and DR21 clouds in the transitions CO J=2-1, CO J=3-2, CS J=7-6, HCN J=4-3, HCO+ J=4-3 and -3- H13CO+ J=4-3 and are supplemented by continuum data at 350 s. n and (for DR21) at 20 pm. It is shown that, although some features of the data can be understood in terms of an LVG model, there is compelling evidence for fragmentation of the clouds on length scales much smaller than the cloud sizes. The data are used to constrain the local H2 densities and relative molecular abundances in the clumpy cloud cores, and compared with lower frequency results from the literature. The implications of these results for the star formation environment are discussed, and an assessment made of possible strategies for their further investigation.
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Pérez, Mirón Javier. "Molecular Modelling of Switchable[2]Rotaxanes." Doctoral thesis, Universitat Autònoma de Barcelona, 2008. http://hdl.handle.net/10803/3278.
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En aquesta tesi s'ha desenvolupat i utilitzat una potent estrategia computacional per a l'estudi, tant estructural, dinàmic i energètic, de nous [2]rotaxanes que van ser sintetizats i caracteritzats experimentalment pel grup de recerca col·laborador del Prof. Donald Fitzmaurice de la University College Dublin, a Irlanda. Com a etapa preliminar, es van estudiar uns pseudorotaxans formats per les mateixes estacions que presentaven els nous [2]rotaxans. Es va modelitzar el comportament dels pseudorotaxans en diferents dissolvents (CH3CN i CH3OH) i amb la presència de dos tipus de contraions (PF6- i Br-). <br/>Es va voler aprofundir en el coneixement de les interaccions entre el macrocicle i les estacions. En aquesta direcció, es van determinar les energies de complexació dels complexes estació-macrocicle i també la variació energètica davant la posició del macrocicle respecte l'eix del pseudorotaxà. Els results obtinguts computacionalment van ser comparats amb els resultats obtinguts en estudis experimentals en dissolució (RMN, espectroscòpia d'absorció òptica, voltametria cíclica). <br/>Posteriorment, es va examinar el moviment traslacional del macrocicle degut a la reducció de les estacions del [2]rotaxà realitzant simulations de Perturbació d'Energia Lliure. Existeix una important contribució metodològica present en el desenvolupament de les parametritzacions per a modelitzar amb AMBER els ions PF6- i Br- i les estacions utilitzades en aquesta tesi. També s'han detectat deficiències en el mòdul RESP durant la comprovació del seu funcionament.<br/>Els [2]rotaxans estudiats són interessants ja que presenten força aplicacions pràctiques en el futur. Un dels grups bloquejador del [2]rotaxà es pot quedar unit a la superfície d'un elèctrode o alguna nanopartícula semiconductora. Així doncs, com a resultat de la col·laboració de tots dos grups es pot concloure que s'ha generat informació útil que pot ajudar a realitzar un millor disseny de [2]rotaxans i supermolècules relacionades que tinguin la capacitat de funcionar com a interrupturs bi-estables i puguin ésser utilitzats en la contrucció de futurs sistemes electrònics, en particular, com a dispositius bi-estables d'emmagatzematge d'informació.<br>En esta tesis se ha desarrollado y utilizado una potente estrategia computacional para el estudio, tanto estructural, dinámico como energético, de nuevos [2]rotaxanos que fueron sintetizados y caracterizados experimentalmente por el grupo de investigación colaborador del profesor Donald Fitzmaurice de la University College Dublin, en Irlanda. Como etapa preliminar, se estudiaron unos pseudorotaxanos formados por las mismas estaciones que presentaban los nuevos [2]rotaxanos. Se modelizó el comportamiento de pseudorotaxanos en diferentes disolventes (CH3CN y CH3OH) y con la presencia de dos tipos de contraiones (PF6- y Br-). <br/>Se quería profundizar en el conocimiento de las interacciones entre el macrociclo y las estaciones. En esta dirección, se determinaron las energías de complejación de los complejos estación-macrociclo y también la variación energética según la posición del macrociclo respecto el eje del pseudorotaxano. Los resultados obtenidos computacionalmente fueron comparados con los resultados obtenidos en estudios experimentales en disolución (RMN, espectroscopía de absorción óptica, voltametría cíclica). <br/>Posteriormente, se examinó el movimiento traslacional del macrociclo debido a la reducción de las estaciones del [2]rotaxano realizando simulaciones de Perturbación de Energía Libre. Existe una importante contribución metodológica presente en el desarrollo de las parametrizaciones para modelizar en AMBER los iones PF6- y Br- y las estaciones utilizadas en esta tesis. También se han detectado deficiencias en el módulo RESP durante la comprobación de su funcionamento.<br/>Los [2]rotaxanos estudiados son interesantes ya que presentan numerosas aplicaciones prácticas en el futuro. Uno de los bloqueadores del [2]rotaxano se puede unir a la superficie de un electrodo o a alguna nanopartícula semiconductora. Por tanto, como resultado de la colaboración de ambos grupos se puede concluir que se ha generado información útil que puede ayudar a realizar un mejor diseño de [2]rotaxanos y supermoléculas relacionadas que tengan la capacidad de funcionar como interruptores bi-estables y puedan ser utilizados en la construcción de futuros sistemas electrónicos, en particular, como dispositivos bi-estables de almacenamiento de información.<br>Powerful computational strategy is outlined and tested for studying the structure, dynamics and the energetics of novel modified [2]rotaxanes which were synthesized and experimentally characterized by a collaborative group of Prof. Donald Fitzmaurice from the University College Dublin, Ireland. As a first necessary step, [2]pseudorotaxanes had been examined that contain in the axles the same bipyridinyl stations of the [2]rotaxanes. The behavior of the pseudorotaxanes in two different solvents, acetonitrile and methanol is modeled at the presence of two types of counterions, PF6- and Br-. <br/>In this way an insight is gained into the interactions between the crown ether ring and the stations. Complexation energies for the viologen-crown complexes were determined, as well as the energy profiles for the movement of the crown macroring along the axle of the pseudorotaxane. The computed data for the [2]rotaxanes are compared with results from solution studies (NMR, optical absorption spectroscopy, cyclic voltametry). <br/>In addition, the shuttling of the ring in the [2]rotaxane induced by stepwise reduction of the viologen stations is examined by FEP simulations. An important methodological contribution presents the development of parameterizations for the modeling with AMBER of the hexafluorophosphate and the bromine anions and the viologens. Some deficiencies of RESP have been also noticed when testing its performance. <br/>The [2]rotaxanes studied present an interesting case with probable future practical applications. Namely, one of the bulky stoppers of the [2]rotaxane can be used to attach the rotaxane to the surface of an electrode or semiconductor nanoparticle. Thus the joint efforts of the two groups could be expected to produce useful information that can help in the rational design of [2]rotaxanes and related supermolecules capable of functioning as bi-stable switches for use in the next generation electronics, in particular as bistable devices for information storage.
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Fange, David. "Modelling Approaches to Molecular Systems Biology." Doctoral thesis, Uppsala universitet, Molekylärbiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132864.
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Implementation and analysis of mathematical models can serve as a powerful tool in understanding how intracellular processes in bacteria affect the bacterial phenotype. In this thesis I have implemented and analysed models of a number of different parts of the bacterium E. coli in order to understand these types of connections. I have also developed new tools for analysis of stochastic reaction-diffusion models. Resistance mutations in the E. coli ribosomes make the bacteria less susceptible to treatment with the antibiotic drug erythromycin compared to bacteria carrying wildtype ribosomes. The effect is dependent on efficient drug efflux pumps. In the absence of pumps for erythromycin, there is no difference in growth between wildtype and drug target resistant bacteria. I present a model explaining this unexpected phenotype, and also give the conditions for its occurrence. Stochastic fluctuations in gene expression in bacteria, such as E. coli, result in stochastic fluctuations in biosynthesis pathways. I have characterised the effect of stochastic fluctuations in the parallel biosynthesis pathways of amino acids. I show how the average protein synthesis rate decreases with an increasing number of fluctuating amino acid production pathways. I further show how the cell can remedy this problem by using sensitive feedback control of transcription, and by optimising its expression levels of amino acid biosynthetic enzymes. The pole-to-pole oscillations of the Min-proteins in E. coli are required for accurate mid-cell division. The phenotype of the Min-oscillations is altered in three different mutants: filamentous cells, round cells and cells with changed membrane lipid composition. I have shown that the wildtype and mutant phenotypes can be explained using a stochastic reaction-diffusion model. In E. coli, the transcription elongation rate on the ribosmal RNA operon increases with increasing transcription initiation rate. In addition, the polymerase density varies along the ribosomal RNA operons. I present a DNA sequence dependent model that explains the transcription elongation rate speed-up, and also the density variation along the ribosomal operons. Both phenomena are explained by the RNA polymerase backtracking on the DNA.<br>Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 715
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Smith, Michael J. "Molecular modelling of MHC/peptide complexes." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297304.
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Docherty, Robert. "Modelling the morphology of molecular crystals." Thesis, University of Strathclyde, 1989. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=21215.
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Computer programs have been written which allow morphological calculations based on a knowledge of internal crystal structure to he carried out. Details of the programs are presented along with the guidelines developed for their use. The programs were used to compare and contrast the current methods employed for relating crystal shape to structure and to confront specific problems in that field. Calculations on a range of compounds show that the morphologies derived from the simple Donnay-Harker (DHI) model give almost as good a fit to the observed form as the more sophisticated attachment energy (AE) calculations except when strong bonding directions were present. In the first study of its type all the methods currently favoured in the literature including the Ising and PBC approaches as well as DH and AE models were applied to benzophenone. All the models gave the same theoretical morphology. One problem remaining in the field of relating crystal structure and morphology is that of polar morphology. None of the current methods can account for a polar morphology. Surface, bulk, isolated molecule charge distributions were used in a modification of the classical attachment energy model to account for urea exhibiting a polar morphology when growth from the vapour phase. For the disruptive type of tailor made additives an improvement in the current methodology is proposed with the calculation of an additional parameter. This additional parameter accounts for the morphology with an additive present and gives good agreement with the test case of benzamide crystals grown with benzoic acid as an additive. The additive approach also allowed the effects of toluene solvent on the crystal habit of benzophenone to be considered By treating toluene as a tailor made additive it was possible from calculations to identify the likely sites of toluene incorporation and the subsequent effect on crystal growth. The results from the calculation were consistent with experiment.
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Hussain, Abrar. "Molecular modelling of protein-ligand interactions." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.587840.
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In this thesis we discuss the role played by computational methods in drug discovery and present studies chiefly using molecular simulation methodologies to characterise the binding of compounds that may serve as leads for antitumour agents against two separate proteins. We report flexible docking and QSAR studies on aplyronine A, and its analogues, a potent inhibitor of the actin protein system. Our findings delineate the mechanism by which the compounds bind to an actin monomer and highlight key features of the compounds that are fundamental for actin- depolymerisation, which instigates the necessary cytotoxic response. We show that the docking energy scores for the compounds are highly correlated with experimental depolymerisation data. The results are relevant for the design of a putative set of analogues and the development of efficacious actin-targeting cancer drugs. In a second study, we focus on the ETS domain of the Elk-l transcription factor, which is key to the protein's stability and a potential target for therapeutic compounds. The work presented identifies peptide binders of the ETS domain that may be used to inform the design of peptidomimetic compounds. Using MD simulations we show the domain undergoes conformational reorganisation at the α Iβ 1 loop. By taking frames from the MD trajectory of the loop region, we conducted virtual screening experiments for libraries of all possible di- and tri-peptides against each frame. The di- peptides showed no particular preference towards the binding site. However, several tri-peptides made specific interactions with key residues involved in Elk-l dimerisation. Further, we performed peptide-bound dynamics and relative binding free energy simulations to assess the stability of each complex, and to rank more accurately the best binding peptides identified from the docking calculations. We proposed a series of peptide binders for synthesis and experimental binding studies. The thesis ends with a brief discussion on some of the limitations to, and recent advancements in the field of computational modelling, particularly in the realm of atomistic simulations for computer-aided drug discovery.
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Todde, Guido. "Exploring Protein Functions by Molecular Modelling." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-114401.
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Proteins are one of the most important families of biological macromolecules. Proteins can assume many different structures. This makes them perfect to serve a wide range of functions in all organisms. In the last decades, molecular modeling has become an important and powerful tool in the investigation of biological systems. Adopting different computational methods many protein functions and structure related problems can be explored. This thesis focuses on three different protein issues. The structural changes induced by high temperature on a large enzyme were investigated simulating the denaturation of glucose oxidase. Molecular dynamics (MD) simulations at different high temperatures were performed. The transition state of the denaturation process was found and the relative ensemble of structures characterized. Different protein properties were analyzed and found in agreement with experimental and theoretical data. Moreover the breaking points of the protein were localized and point mutations on the protein sequence were suggested. Antifreeze proteins (AFP) allow different organisms to survive in subzero environments. These proteins lower the freezing point of physiological fluids. MD simulations of the snow flea AFP (sfAFP) in water have shown partial instability of the protein structure. When attached to different ice planes at the ice/water interface, the sfAFP induces local ice melting. AFPs are divided into two categories: hyperactive and moderately active depending on their antifreeze power. The water diffusion profile of ice/water systems containing one protein from each family were compared. The ice/water interface width was found to be broadened to different extent by the two proteins, while a control protein (ubiquitin) did not affect the interface thickness. Hemoglobin is the oxygen carrier in all vertebrates. Mutation along the protein sequence can alter the protein functionality and its capability of binding molecular oxygen. Density Functional Theory methods were applied in the calculation of the oxygen binding energy of the wild type hemoglobin and four other variants. Evaluations on the electronic structures and on the binding energies of the different hemoglobin variants suggest that perhaps none of the mutated hemoglibins efficiently bind oxygen.<br><p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>
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Betts, Tyrone. "Molecular modelling of calcium modulated proteins." Thesis, University of Newcastle Upon Tyne, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308880.
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Fey, Natalie. "Molecular modelling of ferrocenes and arylphosphines." Thesis, Keele University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368982.
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Gong, Luwen. "Molecular characterisation and modelling of hydroprocesses." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/molecular-characterisation-and-modelling-of-hydroprocesses(a2514b5b-93e0-41d2-abbb-6c515774e188).html.
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Petroleum is a valuable natural resource, and it is therefore of great significance to exploit the maximum economic potentials of the hydrocarbon molecules. Under current circumstances, marginal profit of the refining industry is highly affected by heavier and sourer crude oils, stricter environmental regulations, more stringent product specifications and higher market demands of lighter products, all of which emphasize the importance of secondary processes such as hydrotreating and hydrocracking. The lumping methods for process modelling are no longer applicable as they fail to predict properties and compositions of products, which are strictly restricted by specifications. They cannot provide detailed strategies of process control, schedule and optimisation either. Therefore, molecular management, which aims to fulfill the value of every single molecule, is the key for the refining industry to have a sustainable future. In this work, the molecular type homologous series (MTHS) matrix has been adapted and improved for molecular characterisation of petroleum fractions. The pseudo-component based MTHS matrix is extended to heavy fractions up to 800K and homologous series for hydrocarbons with heteroatoms are incorporated in the improved MTHS matrix. Molecular structure-property correlations are developed to estimate properties of sulphur compounds, which enhances the applicability and feasibility of this new MTHS matrix. In terms of the transformation method, the volume average boiling point (VABP) concept is introduced to consider both the distribution of molecules in one homologous series and the interactions between different homologous series. The proposed MTHS is applied to predicting cetane number of a light cycle oil stream, and has discovered the influence of the composition of hydrocarbon types on the cetane number in specified temperature cuts. Furthermore, the MTHS methodology is applied in the molecular modelling of diesel hydrotreating and hydrocracking. For diesel hydrotreater, a molecular modelling of three-phase reactor is developed, and the effects of various operation conditions on both the performance of the reactors and the changes of different compounds are investigated. According to the analysis of sulphur compounds concentration profile through the reactors and distribution of the molecules in the MTHS, a new two-parallel reactor process model is proposed in terms of ultra low sulphur diesel (ULSD) production, which benefits from not only lower capital and operating costs, but also flexible control to maintain high throughput and profits. A rigorous molecular modelling of hydrocracker is developed based on the MTHS characterisation of feedstock and product. Individual reaction kinetics in the complex reaction network is estimated by the quantitative structure/reactivity correlations (QSRC). The model is capable of predicting gas and liquid products properties, yields, distribution of naphtha, jet fuel, diesel fuel and residue in the liquid fraction as well as compositions of different types of hydrocarbon in specified temperature ranges with high accuracy.
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Teo, Chuan-Tze. "Conformation and reactivity in molecular modelling." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615977.
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Martin, Andrew R. "Molecular modelling of antibody combining sites." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257962.
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Antibodies are capable of high specificity interactions with a virtually infinite range of substrates (antigens). This property has lead to a number of scientific and medical applications. The extreme variability is essentially confined to 6 hypervariable loops or 'CDRs' which constitute the antigen combining site. To make intelligent modifications to antibody affinity and specificity, by methods such as site directed mutagenesis, requires an understanding of the relationship between primary sequence and three dimensional structure of the combining site. A new 'combined algorithm' which makes use of both knowledge-based and ab initio (conformational search) modelling approaches is presented. It is routinely and reliably able to predict the conformation of all six CDRs and requires no arbitrary decisions by the user. All known protein structures are searched for loops of conformation similar to known antibody structures. These are positioned onto the conserved framework and the loops are processed into a form suitable for conformational search using the program CONGEN (Bruccoleri and Karplus, Macromolecules 18(1985),2767--2773). The midsection of each loop is deleted and reconstructed by conformational search. The conformations generated are screened using a solvent-modified potential and, from the low energy conformations, a final choice is made on the basis of structurally determining residues. The method presented provides a route by which to model modifications to known antibody structures or to model complete antibody combining sites - either in combination with other less computer intensive methods, or alone. The procedure has been tested by the individual modelling of the 6 CDR's of two antibodies, in the presence of the crystal structure of the other 5 loops. In addition, it has been applied to modelling CDR's which are difficult to model by other methods and to the construction of a complete antibody combining site. In all cases the algorithm performed very well.
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Pedersen, Jan T. "Molecular modelling of antibody combining sites." Thesis, University of Bath, 1993. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332966.
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Whitelegg, Nicholas R. J. "Molecular modelling of antibody combining sites." Thesis, University of Bath, 1998. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.300880.
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Soprani, Lorenzo <1994>. "Molecular modelling of organic functional materials." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2022. http://amsdottorato.unibo.it/10361/1/PhD_Thesis_Soprani.pdf.
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The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials.
In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules.
Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description.
This thesis presents an approach that combines QM calculations with a classical Molecular Dynamics (MD) approach by means of accurate QM-derived force fields.
It is based on a careful selection of the most relevant molecular degrees of freedom, whose potential energy surface is calculated at QM level and reproduced by the analytic functions of the force field, as well as by an accurate tuning of the approximations introduced in the model of the process to be simulated.
This is made possible by some tools developed purposely, that allow to obtain and test the FF parameters through comparison with the QM frequencies and normal modes.
These tools were applied in the modelling of three processes: the npi* photoisomerisation of azobenzene, where the FF description was extended to the excited state too and the non-adiabatic events were treated stochastically with Tully fewest switching algorithm; the charge separation in donors-acceptors bulk heterojunction organic solar cells, where a tight-binding Hamiltonian was carefully parametrised and solved by means of a code, also written specifically; the effect of the protonation state on the photoisomerisation quantum yield of the aryl-azoimidazolium unit of the axle molecule of a rotaxane molecular shuttle.
In each case, the QM-based MD models that were specifically developed gave noteworthy information about the investigated phenomena, proving to be a fundamental key for a deeper comprehension of several experimental evidences.
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Kalweit, Marco. "Molecular modelling of meso- and nanoscale dynamics." Thesis, Cranfield University, 2008. http://hdl.handle.net/1826/2637.
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Molecular modelling of meso- and nanoscale dynamics is concerned with length and time
scales that are in the transition zone from molecular to continuum models. Molecular
simulation methods, in particular molecular dynamics (MD), only allow the simulation of
relatively small nanoscale systems. Continuum methods, such as computational fluid dynamics
(CFD), are applicable at macroscopic scales but cease to be valid for nanoscales.
This thesis is focused on hybrid MD-CFD methods with geometrical decomposition that
seek to bridge the gap between molecular and continuum modelling.
The hybrid solution interface (HSI) establishes the coupling between the molecular and
the continuum domain. In this work, different realisation approaches for the HSI, flux and
state coupling, are discussed and compared. A detailed investigation on MD flux boundary
conditions, the most crucial part of a flux based HSI, is carried out. Different schemes
for the imposition of mass, momentum and energy fluxes through convective and viscous
transport are presented: direct and indirect flux imposition for convective fluxes; the imposition
of momentum fluxes through reflective walls, external forces and the reverse velocity
scheme; and imposition of energy fluxes through external forces and an energy transfer
scheme. Different combinations of these schemes are compared for standard flow situations.
The momentum and energy transfer by an external force creates a relaxation zone at
the MD boundary. The characteristics of this zone is investigated in detail and a theoretical
model for the density profile has been derived. The reverse velocity scheme has been created
as part of this work to avoid the problems encountered when using the external force
for the momentum transfer. It is shown that indirect convective flux imposition in conjunction
with the reverse velocity scheme gives the best results for the standard flow situations.
The scheme is also tested for liquid flow past Carbon nanotubes.
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Doughty, Stephen William. "Molecular modelling of voltage-gated calcium channels." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362014.
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Leeke, Caleb. "Environmental fate prediction using molecular modelling techniques." Thesis, Northumbria University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367406.
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Jiranusornkul, Supat. "Molecular modelling studies of DNA damage recognition." Thesis, University of Nottingham, 2008. http://eprints.nottingham.ac.uk/11303/.
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How DNA repair proteins search and recognise the rare sites of damage from the massive numbers of normal DNA remains poorly understood. FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine) is one of the most prevalent guanine derived lesions involving opening of the imidazole ring. It is typically repaired by formamidopyrimidine-DNA glycosylase (Fpg) as an initial step in base excision repair; if not repaired, the lesion generates a G: C -+ T: A transversion. Unfortunately, studies on the recognition of FapydG have been hindered by difficulties to synthesise and incorporate the FapydG residue into a DNA duplex. Crystal structures of Fpg-DNA complexes have demonstrated three common recognition events: the protein specifically binding to the extrahelical lesion, bending DNA centred on the damaged base, and flipping the damage into the pocket. Thus, molecular modelling and dynamics simulation have been used to gather dynamical information of those recognition events for damaged and undamaged DNA. The simulations were initially performed when FapydG or G occurs in several dodecamer B-DNA sequences in aqueous solution, then inside the lesion-recognition pocket of Fpg, and during the flipping pathway from the helical stack to an extrahelical position. The influence of the damage on DNA stability and flexibility was first investigated. Energetic analysis revealed that damage to DNA does appear to destabilise the duplex. DNA curvature analysis and a novel combined method of the principal component analysis (PCA) and the Mahalanobis distance (DM) indicated that damaged DNA can adopt the observed protein-bound conformation with lower energetic penalties than its normal counterpart. Results of these studies have provided the validation of DNA bending enhancement by the FapydG lesion. It also suggested that intrinsic DNA bending could be a principal element of how the repair protein locates the lesion from vast expanse of normal bases. Considering the specific recognition of FapydG by Fpg, the aF-/39 loop of the Fpg enzyme may function as a gatekeeping to accommodate the lesion while denying the normal base. Remarkably fluctuating movement of the flipped G residue and the aF-ß9 loop is due to the formation of the non-specific Fpg/G complex with a lower binding energy by 8.4 kcal/mol compared to the specific Fpg/FapydG complex. Free-energy profiles for both damaged and undamaged base flipping were generated from the umbrella sampling simulations and the Weight Histogram Analysis Method (WHAM). An energy barrier for flipping the damage out from the helix is 2.7 kcal/mol higher than its equivalent G and the lesion is highly stabilised inside the pocket. In contrast, G flipping seems to be rapidly rotated out and into the duplex without the formation of a specific complex. These studies could unravel a potentially comprehensive process of the repair protein to find and recognise the lesion through the slow kinetic pathway in which the more deformable damaged DNA is initially located by the protein; the protein subsequently compresses the duplex into an appropriate angle and direction to form a specific protein-DNA complex prior to being flipped and repaired.
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Beevers, Andrew James. "Molecular modelling of self assembled peptide nanostructures." Thesis, University of Leeds, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275634.
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Hadjigeorgiou, Christina. "Molecular modelling studies on bidentate iron chelators." Thesis, King's College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298845.
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Qiu, Song. "Molecular communication systems : design, modelling and experimentation." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/95162/.
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Molecular Communications (MC) is an increasingly attractive technique to enable the communication and networking of devices in environments where traditional communication techniques may not be suitable. MC has been used to convey information in both human society and in animal populations and been studied on both the microscale and the macroscale. On the basis of these studies, this thesis focuses on characterising MC channel models under different environments and examining the impact these models have on the communication performance. The thesis begins by reviewing the latest developments in MC including communication paradigm, channel models, modulation schemes and forward error correction codes. It then provides the comprehensive research methods used during the PhD, including the construction of complex propagation environments and molecular communication equipments, and explains the procedures of the experimentation. The thesis then goes on to analyse the channel model for static environment. A novel capture probability expression of a finite sized receiver and the performance metrics of bit error rate, throughput and round-trip-time are derived. Experimentally, the additive noise in the channel response was found to conform to a Nakagami distribution. Afterwards, the thesis characterises two dynamic channel models, namely, the fading distribution due to temperature fluctuations, which is validated by numerical simulations, and the mobile channel where both transmitter and receiver are in mobility and in order to combat transposition errors, positional-distance codes are applied. Furthermore, the energy model of the bacteria based mobile relay channel is proposed to demonstrate a superior energy efficiency. Finally, the thesis goes on to propose a potential application of MC to locate a hidden entity with an unknown location in a vast underwater search space. Two molecular messaging methods for location discovery are proposed: a chemical encoding messaging method, and a Rosenbrock gradient ascent algorithm. The two chemical methods are found to offer attractive performance trade-offs in complexity and robustness. To conclude, the potential future work on MC channel modelling is identified in complex geometric environments.
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Uzoh, O. G. "Modelling molecular flexibility for crystal structure prediction." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1460832/.
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In the crystal packing of molecules wherein a single bond links aromatic groups, a change in the torsion angle can optimise close packing of the molecule. The improved intermolecular interactions, Uinter, outweigh the conformational energy penalty, ΔEintra, to give a more stable lattice energy, Elatt = Uinter + ΔEintra. This thesis uses this lattice energy model hierarchically in a new Crystal Structure Prediction (CSP) algorithm, CrystalPredictor version 1.6, which varies the low-barrier torsion angles at the start of generating hypothetical crystal structures. The crystal structure of 1-benzyl-1H-tetrazole was successfully predicted in an informal ‘blind test’ when given the chemical diagram and the number of molecules in the asymmetric unit cell. Then, the concept of whether specific molecular fragments favour polymorphism (i.e. polymorphophore) was investigated by analysing the crystal energy landscapes of the monomorphic fenamic acid and the polymorphic derivative tolfenamic acid. The CSP results show that the polymorphophore promotes but does not guarantee polymorphism and that the substituents on the polymorphophore fragment decide the relative energies of the crystal structures. Molecular Dynamics (MD) cannot use this lattice energy model because many ab initio calculations of ΔEintra on a single molecule are expensive. However, the examination of the physical origin of the torsional barrier in fenamates aided the derivation of an analytical model fo ΔEintra. This thesis develops codes for fitting analytical intramolecular force fields to ab initio conformational profiles of fenamates. An intramolecular exp-6 atom-atom term (for the non-bonded repulsion-dispersion contributions) plus a cosine term (that represents the changes to the Molecular Orbitals) accurately model the ab initio conformational energy surfaces of fenamic and tolfenamic acids. This thesis provides a first step in extending ΔEintra data generated from CSP studies to help MD on condensed phases of pharmaceutical-like organic molecules.
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Mitchell, Felicity. "Modelling protein flexibility using molecular simulation methods." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525167.
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Sun, Jianjun. "Molecular modelling and integration analysis of hydroprocessors." Thesis, University of Manchester, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.706487.
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Jokiaho, Olli-Pekka. "Spectral modelling of molecular nitrogen in Aurora." Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/161195/.
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A custom made five panel filter mosaic window was designed, installed and operated with the HiTIES (High Throughput Imaging Echelle Spectrograph) at the Nordlysstasjonen in Svalbard, Norway (78.2025N and 15.829E). The filter provides images of the resonant scattered spectra of N+ 2 1N (0,1), (1,2), (2,3) bands and a neutral N2 2P (0,3) band. Ab initio models were created for describing the populations of vibrational and rotational energy levels in both excited and ionised N2 molecules in the ionosphere. In the rotational profiles the species are treated to be in thermal equilibrium, whereas the vibrational levels assume a non-thermal steady state time independent model. Rotational temperatures were evaluated for different auroral forms for the N+ 2 (0,2) band from the magnetic zenith and along the meridian slit in HiTIES data from winter. A clear trend in neutral temperature is found, with higher values for times of lower energy precipitation. The relationship between resonant scattering of solar photons via N+ 2 and direct emission from electron impact on N2 was evaluated qualitatively and quantitatively with HiTIES data from January-March 2007. A relationship was found that clearly indicates the emission profiles are a function of primary electron energy and solar shadow height when auroral arcs are partially sunlit during events of electron precipitation.
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Marques, Igor Oliveira. "Molecular modelling of transmembranar transporters for chloride." Master's thesis, Universidade de Aveiro, 2011. http://hdl.handle.net/10773/7403.
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Mestrado em Biomedicina Farmacêutica<br>Ion transport across cell membranes is crucial for the maintenance of cellular and
organic homeostasis. When the ions transport is impaired, several disorders may arise,
such as channelopathies. Over the last decade, potential synthetic substitutes for the
impaired ion channels have been developed, with the ability to mimetic their functions. In
this context, tripodal synthetic molecules incorporating thiourea binding groups were
experimentally investigated as anion receptors and transmembranar transporters. The
obtained results demonstrated the ability of these carrier molecules to mediate the
chloride diffusion across POPC lipid vesicles. Inspired by these hints, computational
studies with two molecules of this receptors’ set were undertaken in solution and in
phospholipid membrane, using molecular mechanics calculations and molecular
dynamics simulations, with the GAFF force field. This thesis reports and analyses the
results obtained.
The solution studies carried out in dimethyl sulfoxide/water solution show that the anion
associations are stabilised by multiple N-H•••Cl- hydrogen bonds. In contrast, when
solvated in water, the receptors promptly released the anion. The observed behaviours
suggest the potential use of these carriers as membrane transporters.
Before the evaluation of the chloride associations’ behaviour in the membrane model,
the water model and phospholipid atomic charges to be utilized along with GAFF,
describing the phospholipid bilayer, were investigated. The best set of parameters found
is composed of SPC/E water model and unconstrained RESP atomic charges.
The two chloride associations were placed in an overhydrated membrane model in two
alternative starting positions: inside of the bilayer and in the water phase. Generally, the
migration of the receptors to the water/lipid interface was observed. Moreover, in the first
scenario, the chloride release occurs when the carrier reaches the interface, while in the
second one, the chloride release happens in the water phase, before the receptors’
internalization. In most cases, the receptors have nested themselves near the lipid head
groups, exerting little effect on the studied biophysical membrane parameters.<br>O transporte de iões através da membrana celular é crucial para a manutenção da
homeostasia celular e orgânica. Quando o transporte de iões está afectado, várias
patologias podem surgir, tais como canalopatias. Durante a última década surgiram
vários potenciais substitutos de origem sintética para os canais iónicos afectados, com
a capacidade de mimetizarem as suas funções. Neste contexto, receptores sintéticos
trípodes, incorporando grupos de reconhecimento tioureia, foram investigados
experimentalmente como receptores de aniões e transportadores transmembranares.
Os resultados obtidos demonstraram a capacidade destes carregadores para mediarem
a difusão de cloreto através de vesículas lipídicas de POPC. Com base nestes indícios,
realizaram-se estudos computacionais com duas moléculas desta série de receptores,
em solução e numa membrana fosfolípidica, utilizando cálculos de mecânica molecular
e simulações de dinâmica molecular, com recurso ao campo de forças GAFF. Nesta
tese são apresentados e analisados os resultados obtidos.
Os estudos efectuados em solução de dimetilsulfóxido/água mostram que as
associações com cloreto são estabilizadas por múltiplas ligações de hidrogénio
N-H•••Cl-. Por oposição, quando solvatados em água, os receptores perdem
imediatamente o anião. Os comportamentos observados sugerem a utilização potencial
destas moléculas como transportadores membranares.
Antes da avaliação do comportamento das associações com cloreto no modelo de
membrana, investigou-se o modelo de água e as cargas atómicas dos fosfolípidos,
utilizados conjuntamente com o GAFF na descrição da bicamada fosfolípidica.
Determinou-se que o melhor conjunto de parâmetros consiste no modelo de água
SPC/E e cargas atómicas RESP não constrangidas.
As duas associações com cloreto foram colocadas em duas posições iniciais
alternativas num modelo de membrana super-hidratado: dentro da bicamada e na fase
aquosa. Genericamente, observou-se a migração de ambos os receptores para a
interface água/lípido. Adicionalmente, no primeiro cenário, a libertação do cloreto ocorre
com a chegada receptores à interface, enquanto que, no segundo cenário, o cloreto é
libertado na fase aquosa antes da internalização dos receptores. Na maioria dos casos,
os receptores aninharam-se perto das cabeças dos fosfolípidos, afectando ligeiramente
alguns dos parâmetros biofísicos da membrana.
41
Liu, Luyi. "Molecular characterisation and modelling for refining processes." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/molecular-characterisation-and-modelling-for-refining-processes(2844bcd8-070c-4f91-ba83-1deb7f1600a7).html.
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The highly competitive market in the oil refining industry forces refiners look for more detailed information of both feedstocks and products to achieve the optimal economic performance. Due to stricter environmental legislations, the molecular level characterisation has been investigated by various researchers and shows promising advantages in modern refinery design and operation. Although various molecular characterisation methods have been developed, there is an unavoidable trade-off between keeping astronomical molecule details and practicality in industrial applications. In the meantime, many of these methodologies have different characteristics and different focuses according to a particular application purpose. Our aim is hence to tackle the problems of developing manageable and practical technical solutions for molecular characterisation of petroleum fractions for vary refinery processes. A pseudo-component based approach is developed within a modified MTHS (Molecular Type Homologous Series) matrix framework (Peng, 1999) to represent the molecular information of a particular refining stream. This proposed methodology incorporates both molecular type and pseudo-component information by the conjunction of homologous series and boiling points in the matrix framework. To increase the usability of this method, a 3-parameter gamma distribution function is introduced to describe the composition of each structural molecular type. Typical PIONA (paraffin, iso-paraffin, olefin, naphthene, aromatic) analysis, ratios between each homologous types and the percentage of particular carbon type are considered as well as the distillation curve and the density of a stream. More strict product specifications and environmental legislations make strong restriction to the benzene and aromatics content in gasoline products, which motivate refiners to understand, characterise and simulate gasoline catalytic reforming on molecular-level. In this work, kinetic and reactor model of naphtha catalytic reforming is developed based on the proposed MTHS method. The naphtha feedstock composition is represented by the MTHS matrix, and a kinetic network is constructed according to conversions among matrix elements. A process model proposed by Wu (2010) is employed for reforming modelling. The proposed model is then applied to a bench-scale semi-regenerative catalytic reforming unit, which contains 3 fixed-bed reactors, for validation. The influences of essential operating conditions, such as reactor inlet temperature, pressure and weight hourly space velocity (WHSV), on the product distribution and quality are explored. The developed characterisation is also applied in gasoline blending modelling. A molecular-level nonlinear gasoline blending model is developed based on proposed MTHS method with validation. Key properties such as Octane Numbers (ONs) and RVP are blended by molecular matrix elements, and the influence of molecular composition on bulk properties is obvious. A case of recipe optimisation is studied to show the applicability of the proposed method. The implementation of the developed MTHS method for catalytic reforming and gasoline blending demonstrates the compatibility when characterising different petroleum streams, and provides a common platform to simulate and optimise refining operations on the same molecular basis.
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Cosoli, Paolo. "Multi-scale molecular modelling for environmental systems." Doctoral thesis, Università degli studi di Padova, 2009. http://hdl.handle.net/11577/3426855.
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This thesis aims at exploring the potentialities of multiscale molecular simulation techniques for studying phenomena and processes of environmental interest. After a first description of the state of the art, relative to the molecular simulation techniques applications in the environmental engineering field, the thesis describes the most commonly employed molecular simulation techniques. The applications studied in this thesis are described in order to try to represent the
following representative areas of interest:
• Recycling and requalification of scrap materials
• Pollution removal
• Description and modelling of pollution phenomena
As a conclusion, we demonstrated how the adopted procedures for each area of interest in the environmental field can be implemented for more realistic (and complex) systems, or can be adapted for studies in similar contexts.<br>Le finalità del presente lavoro di tesi riguardano l’esplorazione delle potenzialità della simulazione molecolare multiscala nello studio di fenomeni e processi di interesse nel campo ambientale. Dopo una prima descrizione dello stato dell’arte relativo alle applicazioni delle tecniche di simulazione molecolare in campo ambientale, si descrivono le tecniche di simulazione più comunemente utilizzate. La tesi, nella sua parte applicativa, affronta quindi le seguenti tre macroaree, rappresentative di questo campo:
• Il riciclaggio e la riqualificazione dei materiali di scarto
• La rimozione di inquinanti
• La descrizione e la modellazione di fenomeni di inquinamento
In conclusione, si è dimostrato come le procedure adottate per ogni area di interesse in campo ambientale siano implementabili per sistemi via via più realistici (complessi) o adattabili a contesti simili.
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Gamblin, Richard James. "Molecular recognition mechanisms in DNA binding protein families, using molecular modelling techniques." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436398.
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Menche, Gerd. "Molecular modelling Untersuchungen zur Enantiomerentrennung in der HPLC." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=97430476X.
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Fransson, Linda. "Molecular modelling - understanding and prediction of enzyme selectivity." Licentiate thesis, KTH, School of Biotechnology (BIO), 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10532.
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<p>Molecular modelling strategies for evaluation of enzyme selectivity wereinvestigated with a focus on principles of how molecular interactionscould be evaluated to provide information about selectivity. Althoughmolecular modelling provides tools for evaluation of geometrical andenergy features of molecular systems, no general strategies for evaluationof enzyme selectivity exist. Geometrical analyses can be based uponinspection and reasoning about molecular interactions, which provide aneasily accessible way to gain information, but suffer from the risk of biasput in by the modeller. They can also be based on geometrical features ofmolecular interactions such as bond lengths and hydrogen-bond formation.Energy analyses are appealing for their modeller independenceand for the possibility to predict not only stereopreference, but also itsmagnitude.In this thesis, four examples of enantio- or regioselective serinehydrolase-catalysed reaction systems are presented together with developedmodelling protocols for explanation, prediction or enhancement ofselectivity. Geometrical as well as energy-based methodology were used,and provided an understanding of the structural basis of enzymeselectivity. In total, the protocols were successful in making qualitative explanationsand predictions of stereoselectivity, although quantitative determinationswere not achieved.</p>
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Hall, Katherine Frances. "Hybrid computational methods for modelling molecular excited states." Thesis, Imperial College London, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501445.
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Swift, Simone. "Molecular modelling of the complex polysaccharide heparan sulphate." Thesis, University of Huddersfield, 2011. http://eprints.hud.ac.uk/id/eprint/10739/.
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Heparan Sulphate plays an important role in many life processes and so an understanding of its role as a universal co-receptor is of great importance. Traditionally oligosaccharides derived from the related molecule heparin have been at the forefront of molecular drug design, due to its similarity in structure and function. To obtain a more complex and detailed picture of the role of HS in structural biology further complex work must be undertaken on HS. Here in this study a number of HS derived octasaccharides have been purified. Alongside this is work carried on HS derived decasaccharides, of which all have undergone extensive molecular modelling simulations. The role of the Iduronates in the HS structure, at monosaccharide level has indicated a major role for these structures in biological activity. Further work has indicated the level of sulphation is also a requirement which in turn influences conformational behaviour. Up until now this has only really been studied at the monosaccharide level and so this study has generated a number of different HS models which can confirm the importance of iduronate conformation in biological activity. Not only that but it has also been identified that certain torsional geometries within the glycosidic bonds between monosaccharides also has a major influence on conformation. Local deviations in the molecular modelling data suggest there is a slight difference between active and inactive oligosaccharides with the ability to bind and activate the HS:FGF2:FGFR IIIc complex. The implications of these and other structural insights are discussed with the implication heavily towards a combination of both torsional geometry and iduronate conformation in biological activity. To further aid our understanding HS dp10 oligosaccharides were docked into a FGF2 which was in a complex with a heparin hexasaccharide. Docking experiments were carried in order to attain structural information on the binding of these molecules. The Goodger oligosaccharides were docked into the X-ray crystal structure and were chosen specifically for their iduronate conformation or the torsional geometry.
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Adcock, Charlotte. "Molecular modelling and electrostatic properties of ion channels." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297941.
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Borg, Matthew Karl. "Hybrid molecular-continuum modelling of nano-scale flows." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=14367.
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Li, Yazhuo. "Crystallographic and molecular modelling studies of NQO2-complexes." Thesis, University of Nottingham, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537673.
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