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1
Holzknecht, Christopher [Verfasser]. "Berechnungen zu fluiden Phasengrenzen mit Ansätzen für die freie Energie im Vergleich mit molekulardynamischen Simulationen / Christopher Holzknecht." Aachen : Shaker, 2006. http://d-nb.info/1166514056/34.
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Krien, Uwe [Verfasser]. "Erweiterung der Bewertungskriterien von regionalen Strom-Wärme-Modellen durch die Kopplung mit einem überregionalen Modell : Eine freie Python Toolbox / Uwe Krien." Düren : Shaker, 2020. http://d-nb.info/1225654041/34.
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Sheng, Shuhong. "Investigations into superhard nitride- and oxide-based nanocomposites by means of combined ab initio DFT and thermodynamic calculations." kostenfrei, 2010. https://mediatum2.ub.tum.de/node?id=822033.
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Piccini, GiovanniMaria. "Ab initio free energies of adsorption from anharmonic vibrations." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2015. http://dx.doi.org/10.18452/17239.
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Die Thermodynamik von Adsorptionsvorgängen wurde mittels quantenchemischer Methoden und der statistischen Thermodynamik untersucht. Eine neue rechentechnische Methode wird vorgestellt, die den Mangel an Genauigkeit vorhandener Methoden zur Untersuchung periodischer Systeme, wie z. B. der Dichte-Funktional-Theorie, behebt, und es ermöglicht thermodynamische Funktionen mit chemischer Genauigkeit zu bestimmen. Das im Rahmen dieser Arbeit entwickelte Protokoll besteht aus verschiedenen rechentechnischen Schritten, als da wären, eine Strukturoptimierung in Normalkoordinaten anstatt in kartesischen Koordinaten, eine numerische Berechnung der harmonischen Frequenzen durch Abtasten der Potentialenergieoberfläche entlang der Normalkoordinaten und anschließender anharmonischer Korrektur. Die Normalkoordinatenoptimierung garantiert eine korrekte Relaxation der Struktur mit ausschließlich reellen harmonischen Frequenzen. Die anharmonischen Korrekturen ermöglichen eine gute Beschreibung der Schwingungsstrukturen von Systemen die durch eine besonders Flache PES gekennzeichnet sind. Gleichzeitig, wird durch die Verwendung eines QM:QM-Hybridverfahrens zur Bestimmung des elektronischen Anteils der Adsorptionsenergie eine höhere Genauigkeit in der Bestimmung der Korrelationsenergie im Vergleich zu DFT garantiert. Der elektronische Anteil der Adsorptionsenergie, sowie der Schwingungsthermische Anteil werden abschließend kombiniert um einen genauen Wert der thermodynamischen Funktionen zu erhalten.The thermodynamic of adsorption is investigated from the vibrational point of view using quantum chemical methods via statistical mechanics. Due to the lack of accuracy of the present available methods for investigating periodic systems, such as plane-wave density functional theory (DFT), a novel computational strategy is presented to overcome these limitations and bring the estimate of the thermodynamic functions within chemical accuracy limits. The protocol presented in this work consists of different computational steps, namely a structure optimization using normal mode coordinates instead of Cartesians, a numerical harmonic frequency calculation via sampling of the potential energy surface along the normal mode coordinates and the inclusion of anharmonic correction to the latter. The normal mode coordinate optimization ensures a proper relaxation of the structure and a reliable set of real harmonic frequencies while the anharmonic corrections account for a proper description of the vibrational structure of a system characterized by a very flat potential energy surface. Parallel to these calculations the electronic part of the adsorption energy is corrected using a hybrid QM:QM scheme to account the electronic correlations effects more accurately than DFT. The hybrid electronic adsorption energy and the vibrational thermal contributions obtained using anharmonic corrections are finally combined to get accurate estimate of the adsorption thermodynamic functions.
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Richter, Wolfgang, and Joachim Seifert. "Zur Anordnung von freien Heizflächen in Gebäuden mit höherem Wärmeschutzniveau." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1200579061673-72892.
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Die immer schneller steigenden Energiepreise haben in der jüngsten Vergangenheit eine breite Diskussion über Energieeffizienz und alternative Erzeugungsverfahren ausgelöst. Von besonderer Bedeutung ist dies für den Gebäudesektor und die darin installierte Anlagentechnik, da in Deutschland ca. 30 % des Energieverbrauches hier anfallen. Eine Minderung dieses Verbrauches kann nur durch eine Vielzahl von Maßnahmen erreicht werden, die schon bei der Planung berücksichtigt werden müssen. Vor diesem Hintergrund wird in diesem Artikel die Anordnung von freien Heizflächen im Raum untersucht sowie energetische und wärmephysiologische Ergebnisse aufgezeigt. Die beschriebenen Analysen wurden für eine repräsentative Raumgeometrie vorgenommen, wodurch es möglich ist, die Aussagen auf eine Vielzahl von Räumen zu übertragenThe steady rise in energy prices has recently triggered a broad discussion on energy efficiency and alternative methods of generation. Since approximately 30 % of the total energy consumption is attributable to HVAC installations (Heating, Ventilation and Air Conditioning), this sector is acutely relevant for the building industry and for building services. Reduction of the building energy consumption can be achieved only by applying a wide range of measures across the whole process from planning to the realisation stage. Considering the aforementioned, the influence on thermal comfort and energy consumption of different radiator positions within a room is described in the following paper. The analysis was carried out for a representative room geometry, which allows the results to be applied to a broad spectrum of real room configurations
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Mohamed, Noor Asidah Binti. "The evaluation of protein-ligand binding free energies using advanced potential energy function." Thesis, University of Southampton, 2018. https://eprints.soton.ac.uk/428049/.
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Electronic polarisation is one of the components that plays an important role in many biomolecular systems. The effects of polarisation will act differently depending on the local environment of the system, such as in DNA, proteins and membranes. Traditionally, molecular mechanical force fields describe electrostatics as the interactions of fixed, atom-centred, point charges. Hence the past decade has seen many additions and improvements to existing force fields to better correlate dynamics with experimental observations. A better description of electrostatics by the inclusion of electronic polarisation is one such improvement. The AMOEBA polarisable force field is one of many possible models that is designed to be capable of capturing this effect. AMOEBA includes mutually polarising induced atomic dipoles at every atomic site, as well as a multipolar representation of fixed electrostatics. To investigate applications of AMOEBA and where its successes over existing fixed-charge methods may lie, we first evaluate features and performance of the AMOEBA polarisable force field in simple systems based on the evaluation of solvation free energies for small molecules in a range of common organic solvents. Here, we pointed out several challenges and limitations of AMOEBA in this study involving non-aqueous solvents. Then, we further our investigation on more complex systems including protein-ligand interactions. Initially, clear cases of failure in fixed-point-charge force fields were identified by exploring the sensitivity of the calculated free energies to parameter sets and simulation protocols of protein-ligand systems, focusing on binding free energy calculations of the cytochrome c peroxidase protein using the AMBER force field. Finally, we use these results to inform binding free energy calculations for testing of the AMOEBA force field. We discuss the implications of these results for better understanding and improving AMOEBA to aid its full implementation in other biological applications.
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Mayer, Jürgen. "Investigation of the biophysical basis for cell organelle morphology." Master's thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-26600.
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It is known that fission yeast Schizosaccharomyces pombe maintains its nuclear envelope during mitosis and it undergoes an interesting shape change during cell division - from a spherical via an ellipsoidal and a peanut-like to a dumb-bell shape. However, the biomechanical system behind this amazing transformation is still not understood. What we know is, that the shape must change due to forces acting on the membrane surrounding the nucleus and the microtubule based mitotic spindle is thought to play a key role. To estimate the locations and directions of the forces, the shape of the nucleus was recorded by confocal light microscopy. But such data is often inhomogeneously labeled with gaps in the boundary, making classical segmentation impractical. In order to accurately determine the shape we developed a global parametric shape description method, based on a Fourier coordinate expansion. The method implicitly assumes a closed and smooth surface. We will calculate the geometrical properties of the 2-dimensional shape and extend it to 3-dimensional properties, assuming rotational symmetry.
Using a mechanical model for the lipid bilayer and the so called Helfrich-Canham free energy we want to calculate the minimum energy shape while respecting system-specific constraints to the surface and the enclosed volume. Comparing it with the observed shape leads to the forces. This provides the needed research tools to study forces based on images.
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Mayer, Jürgen. "Investigation of the biophysical basis for cell organelle morphology." Master's thesis, Max-Planck-Institut für Molekulare Zellbiologie und Genetik, 2008. https://tud.qucosa.de/id/qucosa%3A25225.
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It is known that fission yeast Schizosaccharomyces pombe maintains its nuclear envelope during mitosis and it undergoes an interesting shape change during cell division - from a spherical via an ellipsoidal and a peanut-like to a dumb-bell shape. However, the biomechanical system behind this amazing transformation is still not understood. What we know is, that the shape must change due to forces acting on the membrane surrounding the nucleus and the microtubule based mitotic spindle is thought to play a key role. To estimate the locations and directions of the forces, the shape of the nucleus was recorded by confocal light microscopy. But such data is often inhomogeneously labeled with gaps in the boundary, making classical segmentation impractical. In order to accurately determine the shape we developed a global parametric shape description method, based on a Fourier coordinate expansion. The method implicitly assumes a closed and smooth surface. We will calculate the geometrical properties of the 2-dimensional shape and extend it to 3-dimensional properties, assuming rotational symmetry.
Using a mechanical model for the lipid bilayer and the so called Helfrich-Canham free energy we want to calculate the minimum energy shape while respecting system-specific constraints to the surface and the enclosed volume. Comparing it with the observed shape leads to the forces. This provides the needed research tools to study forces based on images.
9
Cave-Ayland, Christopher. "Quantum free energy techniques." Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/375028/.
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Donnini, S. (Serena). "Computing free energies of protein-ligand association." Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514285745.
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Abstract
Spontaneous changes in protein systems, such as the binding of a ligand to an enzyme or receptor, are characterized by a decrease of free energy. Despite the recent developments in computing power and methodology, it remains challenging to accurately estimate free energy changes. Major issues are still concerned with the accuracy of the underlying model to describe the protein system and how well the calculation in fact emulates the behaviour of the system.
This thesis is largely concerned with the quality of current free energy calculation methods as applied to protein-ligand systems. Several methodologies were employed to calculate Gibbs standard free energies of binding for a collection of protein-ligand complexes, for which experimental affinities were available. Calculations were performed using system description with different levels of accuracy and included a continuum approach, which considers the protein and the ligand at the atomic level but includes solvent as a polarizable continuum, and an all-atom approach that relies on molecular dynamics simulations.
In most such applications, the effects of ionic strength are neglected. However, the severity of this approximation, in particular when calculating free energies of charged ligands, is not very clear. The issue of incorporating ionic strength in free energy calculations by means of explicit ions was investigated in greater detail and considerable attention was given to the affinities of charged peptides in the presence of explicit counter-ions. A second common approximation is concerned with the description of ligands that exhibit multiple protonation states. Because most of current methods do not model changes in the acid dissociation constants of titrating groups upon binding, protonation equilibria of such ligands are not taken into account in free energy calculations. The implications of this approximation when predicting affinities were analysed.
Finally, when calculating free energies of binding, a correct description of the interactions between the protein and the ligand is of fundamental importance. However, active sites of enzymes, where strained conformations may hold a functional role, are not always accurately modelled by molecular mechanics force fields. The case of a strained planar proline in the active site of triosephosphate isomerase was investigated using an hybrid quantum mechanics/molecular mechanics method, which implies a higher level of accuracy.
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Kurusu, Tamaki. "Computer simulation of free energies to predict cis/trans equilibria of prolyl peptides and solvation free energies of phenylalanyl peptides." Thesis, Virginia Tech, 1996. http://hdl.handle.net/10919/45091.
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Two computer simulation studies were performed; one to help understand the
structure-function relationships of prolyl peptides (Part I) and the other to help predict more
efficient pharmaceutical drug delivery by molecular modification of small peptides (Part II).
In Part I, the free energy perturbation (FEP) method, using AMBER, was utilized to calculate the Gibbs free energy difference between cis and trans conformers of Ace-Tyr-Pro- NMe and Ace-Asn-Pro-NMe, from which the ratio of cis to trans conformers was obtained. Our simulation generated much lower %cis for both peptides as compared with experimental values and possible problems in our computational schemes are presented. However, our results were encouraging in that they predicted preference of trans conformers for both peptides and higher %cis for Ace-Tyr-Pro-NMe, compared to Ace-Asn-Pro-NMe, which agrees with experimental results.
Part II applied semi empirical (AMS0L) and microscopic simulation (POLARIS) methods to obtain the solvation free energies of a series of phenylalanyl peptides with various degrees of methylation on their backbone nitrogens. It was clearly predicted that as a peptide length increased, so solvation free energy decreased, indicating less favorable permeability through the cell membrane system, in agreement with data in the literature. AMSOL also showed that solvation free energy change upon methylation was variable depending on the position of the substituted backbone nitrogen, which disagrees with the literature. However, non-systematic solvation free energy change of small amines upon methylation was successfully predicted by AMSOL, in good accord with experimental data.
Master of Science
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Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies." Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.
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Accurate prediction of binding free energies of protein-ligand system has long been a focus area for theoretical and computational studies; with important implications in fields like pharmaceuticals, enzyme-redesign, etc. The aim of this project was to develop such a predictive model for calculating binding free energies of protein-ligand systems based on the LIE-SASA methods. Many models have been successfully fit to experimental data, but a general predictive model, not reliant on experimental values, would make LIE-SASA a more powerful and widely applicable method. The model was developed such that There is no significant increase in computational time No increase in complexity of system setup No increase in the number of empirical parameters. The method was tested on a small number of protein-ligand systems, selected with certain constraints. This was our training set, from which we obtain the complete expression for binding free energy. Expectedly, there was good agreement with experimental values for the training set On applying our model to a similar sized validation set, with the same selection constraints as for the training set, we achieved even better agreement with experimental results, with lower standard errors. Finally, the model was tested by applying it to a set of systems without such selection constraints, and again found good agreement with experimental values. In terms of accuracy, the model was comparable to a system specific empirical fit that was performed on this set. These encouraging results could be an indicator of generality.
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Witzler, Lucas Torres. "Metodologia para reconstrução de séries históricas de vento e geração eólica visando a análise da complementariedade energética no Sistema Interligado Nacional." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/3/3143/tde-31122015-105629/.
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Nos últimos leilões de energia promovidos pelo Governo projetos eólicos foram protagonistas, sendo a fonte com maior número de projetos cadastrados e vencedores. Nessa perspectiva, que de fato tem fomentado o interesse, tanto por empreendedores como por agentes do setor elétrico, pelo entendimento dos fatores de risco que podem influenciar o retorno financeiro dos investidores que encontraram nesta fonte uma alternativa interessante para diversificar seu portfólio de projetos. Diante desta oportunidade, este trabalho tem como objetivo desenvolver uma metodologia para reconstrução de séries históricas de geração eólica possibilitando estudos energéticos de complementariedade entre fontes. Esta dissertação possibilitou a avaliação da complementariedade energética entre os recursos eólicos e hídricos. Por meio da análise da correlação entre séries de geração de energia eólica e hídrica, foi possível identificar o benefício energético existente na formação de um portfólio hidro-eólico. A complementariedade entre a energia eólica e hidráulica possibilita que geradores que possuam portfolio com ambas as fontes compartilhem a exposição dos riscos relacionados à sazonalidade dos ventos, beneficiando diretamente o mercado consumidor com diminuição dos custos na geração.In recent energy auctions, held by the government wind projects were protagonists, being the source with the highest number of registered and winning projects. From this perspective, which in fact has stimulated interest, both as investors by electrical sector agents, by understanding the risk factors that may influence the financial returns to investors who have found this an interesting alternative source to diversify its project portfolio. Considering this opportunity, this work aims to develop a methodology for reconstruction historical series of wind generation enabling studies of complementarity between energy sources. This work has enabled an evaluation of complementarity between wind and hydro generation. By analyzing, the correlation between wind and hydro series was possible to identify the energetic benefit in a composition of a hydro-wind portfolio. The complementarity between wind and hydropower enables generators in the same portfolio share risks related to exposure due to seasonality of winds, directly benefiting the market with lower generations costs, driven by increased competition resulting from the participation of wind power in all segments of marketing.
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Fernandez, Marcelo Richter. "Contratação ótima para comercialização de energia elétrica." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/258867.
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Orientadores: Christiano Lyra Filho, Leontina Maria Viana Graziadio PintoDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação
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Resumo: Este trabalho propõe o desenvolvimento de metodologia para a operação de um portfólio de contratos de compra e venda de energia elétrica no ambiente de contratação livre utilizando conceitos de otimização, em especial de programação linear, matemática financeira e estatística, além de considerar também as regras de comercialização de energia do setor elétrico brasileiro. Isso permite que comercializadores maximizem seus resultados financeiros pela alocação ótima de seus contratos de compra e venda de energia. Além disso, permite a simulação de cenários alternativos de consumo, variações de preços de curto prazo e opções de contrato. A partir dessas informações, os agentes de comercialização de energia elétrica podem realizar comparações entre as várias alternativas de operações no mercado de energia; podem também comparar essas ações com outras propostas de investimentos. Estudos de casos ilustram a aplicação da metodologia a cenários reais do sistema elétrico brasileiro. A análise desses resultados permite avaliar benefícios alcançados e sugere possibilidades de desdobramentos
Abstract: This work proposes the development of a new approach for the operation of electric energy contracts in the Brazilian free market. It uses concepts of linear optimization, financial mathematics, statistics and considers the Brazilian free market regulation. The methodology allows traders to maximize their profits by using the optimal allocation for each energy contract. It also allows traders to simulate trading with different scenarios of energy consumption by the customers, spot market prices, future market prices and long term contracts. Results allow investors to compare energy trading options with other alternatives for investments. Case studies illustrate the application of the proposed methodology to real world scenarios; benefits are also evaluated
Mestrado
Mestre em Engenharia Elétrica
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Ribeiro, Erika Barbosa. "Desafios para expansão do mercado de fontes incentivadas: uma análise de atratividade do ponto de vista do consumidor especial." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/3/3143/tde-20072009-151157/.
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Este trabalho tem como objetivo analisar a atratividade da contratação de energia proveniente de fontes incentivadas PCHs, Biomassa, Eólica e Solar - no mercado livre, para empresas do setor comercial com conjunto de unidades consumidoras que atendam às exigências da Resolução ANEEL nº 247/2006. Esta resolução representa um marco importante para a comercialização de energia incentivada, permitindo que unidades consumidoras que possuem o mesmo CNPJ ou estão localizadas em áreas contíguas contratem essa energia, desde que o somatório das demandas do agrupamento de unidades totalize, no mínimo, 500 kW. É apresentado ao longo deste trabalho o processo de gestão de contratos de energia no ambiente livre, focando nas alterações resultantes da nova regulamentação para consumidores especiais. A atratividade da contratação de energia incentivada é analisada através de uma simulação de custos nos ambientes livre e cativo, para 20 unidades consumidoras. É realizado um comparativo do perfil de consumo destas unidades para identificar diferenças entre as que apresentam viabilidade econômica para contratação de energia incentivada e as demais, também foram considerados na simulação diferentes cenários de preços e o impacto do investimento no Sistema de Medição e Faturamento.This work aims at analyzing the attractiveness of renewable energy sources contracting SHPs, Biomass, Aeolic and Solar in the free market for commercial enterprises whose consumption units are in accordance with ANEELs Resolution n° 247/2006. This resolution represents an important landmark in the commercialization of renewable energy for it allows the consumer units with the same CNPJ or located in adjacent areas to contract this kind of energy, only if the sum of the units demands amount to at least 500 kW. The process of energy contracts management in free contracting ambience is presented in this research, which also focuses on the modifications that result from the new regulation for special consumers. The attractiveness of renewable energy contracting is analyzed through a simulation of costs in free contracting ambiences and in ambiences arranged to 20 consumer units. Comparison with these units consuming profile was made in order to identify differences between the units that have economic feasibility for renewable energy contracting and the other ones. In the simulation, different price scenarios and the investments impact on the Measurement System for Billing were also taken into account.
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Essex, Jonathan Wynne. "Free-energy calculations in molecular biology." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314884.
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Yildirim, Ismail. "Surface Free Energy Characterization of Powders." Diss., Virginia Tech, 2001. http://hdl.handle.net/10919/27525.
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Microcalorimetric measurements and contact angle measurements were conducted to study the surface chemistry of powdered minerals. The contact angle measurements were conducted on both flat and powdered talc samples, and the results were used to determine the surface free energy components using Van Oss-Chaudhury-Good (OCG) equation. It was found that the surface hydrophobicity of talc increases with decreasing particle size. At the same time, both the Lifshitz-van der Waals (gSLW) and the Lewis acid-base (gSAB) components (and, hence, the total surface free energy (gS)) decrease with decreasing particle size. The increase in the surface hydrophobicity and the decrease in surface free energy (gS) can be attributed to preferential breakage of the mineral along the basal plane, resulting in the exposure of more basal plane surfaces to the aqueous phase.
Heats of immersion measurements were conducted using a flow microcalorimeter on a number of powdered talc samples. The results were then used to calculate the contact angles using a rigorous thermodynamic relation. The measured heat of immersion values in water and calculated contact angles showed that the surface hydrophobicity of talc samples increase with decreasing particle size, which agrees with the direct contact angle measurements. A relationship between advancing water contact angle qa, and the heat of immersion (-DHi) and surface free energies was established. It was found that the value of -DHi decrease as qa increases.
The microcalorimetric and direct contact angle measurements showed that acid-base interactions play a crucial role in the interaction between talc and liquid. Using the Van Oss-Chaudhury-Goodâ s surface free energy components model, various talc powders were characterized in terms of their acidic and basic properties. It was found that the magnitude of the Lewis electron donor, gS-, and the Lewis electron acceptor, gS+, components of surface free energy is directly related to the particle size. The gS- of talc surface increased with decreasing particle size, while the gS+ slightly decreased. It was also found that the Lewis electron-donor component on talc surface is much higher than the Lewis electron-acceptor component, suggesting that the basal surface of talc is basic.
The heats of adsorption of butanol on various talc samples from n-heptane solution were also determined using a flow microcalorimeter. The heats of adsorption values were used to estimate % hydrophilicity and hydrophobicity and the areal ratios of the various talc samples. In addition, contact angle and heat of butanol adsorption measurements were conducted on a run-of-mine talc sample that has been ground to two different particle size fractions, i.e., d50=12.5 mm and d50=3.0 mm, respectively. The results were used to estimate the surface free energy components at the basal and edge surfaces of talc. It was found that the total surface free energy (gS) at the basal plane surface of talc is much lower than the total surface free energy at the edge surface. The results suggest also that the basal surface of talc is monopolar basic, while the edge surface is monopolar acidic. The results explain why the basicity of talc surface increases with decreasing particle size as shown in the contact angle and microcalorimetric measurements.
Furthermore, the effects of the surface free energies of solids during separation from each other by flotation and selective flocculation were studied. In the present work, a kaolin clay sample from east Georgia was used for the beneficiation tests. First, the crude kaolin was subjected to flotation and selective flocculation experiments to remove discoloring impurities (i.e., anatase (TiO2) and iron oxides) and produce high-brightness clay with GE brightness higher than 90%. The results showed that a clay product with +90% brightness could be obtained with recoveries (or yields) higher than 80% using selective flocculation technique. It was also found that a proper control of surface hydrophobicity of anatase is crucially important for a successful flotation and selective flocculation process. Heats of immersion, heats of adsorption and contact angle measurements were conducted on pure anatase surface to determine the changes in the surface free energies as a function of the surfactant dosage (e.g. hydroxamate) used for the surface treatment. The results showed that the magnitude of the contact angle and, hence, the surface free energy and its components on anatase surface varies significantly with the amount of surfactant used for the surface treatment.Ph. D.
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Ignace, Richard. "Long-Wavelength, Free–Free Spectral Energy Distributions from Porous Stellar Winds." Digital Commons @ East Tennessee State University, 2016. https://dc.etsu.edu/etsu-works/2685.
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The influence of macroclumps for free–free spectral energy distributions (SEDs) of ionized winds is considered. The goal is to emphasize distinctions between microclumping and macroclumping effects. Microclumping can alter SED slopes and flux levels if the volume filling factor of the clumps varies with radius; however, the modifications are independent of the clump geometry. To what extent does macroclumping alter SED slopes and flux levels? In addressing the question, two specific types of macroclump geometries are explored: shell fragments (pancake-shaped) and spherical clumps. Analytic and semi-analytic results are derived in the limiting case that clumps never obscure one another. Numerical calculations based on a porosity formalism is used when clumps do overlap. Under the assumptions of a constant expansion, isothermal, and fixed ionization wind, the fragment model leads to results that are essentially identical to the microclumping result. Mass-loss rate determinations are not affected by porosity effects for shell fragments. By contrast, spherical clumps can lead to a reduction in long-wavelength fluxes, but the reductions are only significant for extreme volume filling factors.
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Wall, Ian. "New simulation methods for the prediction of binding free energies." Thesis, University of Southampton, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313217.
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Lobato, Emilio Marcus de Castro. "Determination of Surface Free Energies and Aspect Ratio of Talc." Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/35743.
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Microcalorimetric measurements and contact angle measurements were conducted to assess the surface chemistry of the mineral talc. The contact angles were performed on both flat and powdered samples and the results were used to determine the surface free energy components and parameters (SFEC) using the acid-base theory for solids, according to the van Oss-Chaudhury-Good approach. It was found that the surface hydrophobicity of talc increases with decreasing particle size up to a limit after which hydrophilicity (polarity) increases. The increase in hydrophobicity was attributed to the increase of the delamination of the lamellar talc particles. Delamination is a comminution mechanism that preferentially exposes talc's hydrophobic basal planes, while fracture is another mechanism that breaks the lamellae, rupturing covalent bonds thus exposing more hydrophilic edge surfaces. The decrease in hydrophobicity, beyond a given particle size, could be related to the prevail of fracture over delamination during grinding which generated more hydrophilic edge surfaces.
The flow microcalorymetry combined with thin layer wicking allowed the separate estimation of the SFEC at the basal plane and edge surfaces of talc. The results suggested that the basal surface of talc is monopolar basic, while the edge surface is monopolar acidic, which are in agreement with the crystal structure of the mineral.
The combination of two particle size distribution techniques, which are based on different physical principles, permitted the quantitative determination of the aspect ratio of highly anisometric particles, such as talc. The same trend obtained using flow microcalorimetry was observed for the evolution of the aspect ratio as a function of particle fineness, i.e. the fracture prevails over delamination after achieving a maximum aspect ratio value of about 35. The agreement between two distinct methods was considered rather encouraging.
Master of Science
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McGinnis, Roger D. "Free Electron Laser development for directed energy." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2000. http://handle.dtic.mil/100.2/ADA387898.
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Dissertation (Ph.D. in Physics) Naval Postgraduate School, Dec. 2000.Dissertation advisor, Colson, William B. "December 2000." Includes bibliographical references (p. 131-133). Also available in print.
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Liu, Yang, and 刘洋. "Free energy simulations of important biochemical processes." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/196036.
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Free energy simulations have been widely employed to compute the thermodynamic properties of many important biochemical processes. In the first part of this dissertation, two important biochemical processes, protonation/deprotonation of acid in solution and solvation of small organic molecules, are investigated using free energy simulations.
Accurate computation of the pKa value of a compound in solution is important and challenging. To efficiently simulate the free energy change associated with the protonation/deprotonation processes in solution, a new method of mixing Hamiltonian, implemented as an approach using a fractional protonin the hybrid quantum mechanics/molecular mechanics (QM/MM) scheme, is developed. This method is a combination of a large class of λ-coupled free-energy simulation methods and the linear combination of atomic potential approach. Theoretical and technical details of this method, along with the calculation results of the pKa value of methanol and methanethiol molecules in aqueous solution, are discussed. The simulation results show satisfactory agreement with experimental data.
Though the QM/MM method is one of the most useful methods in the modeling of biochemical processes, little attention has been paid to the accuracy of QM/MM methods as an integrated unit. Therefore, the solvation free energies of a set of small organic molecules are simulated as an assessment of ab initio QM/MM methods. It shows that the solvation free energy from QM/MM simulations can vary over a broad range depending on the level of QM theory / basis sets employed. Diffuse functions tend to over-stabilize the solute molecules in aqueous solution. The deviations pose a pressing challenge to the future development of new generation of MM force fields and QM/MM methods if consistency with QM methods becomes a natural requirement.
In the second part of the dissertation, the dynamic and energetic properties of two molten globule (MG) protein molecules, α-lactalbumin(α-LA) and monomeric chorismate mutase (mCM) are investigated using molecular dynamics simulations. The exploring of the molecular mechanism of protein folding is a never-settled battle while the properties of MG states and their roles in protein folding become an important question. The MGs show increased side chain flexibility while maintain comparable side-chain coupling compared to the native state, which partially explains the preserving of native-like overall conformation. The enhanced sampling method, temperature-accelerated molecular dynamics (TAMD), is used for the study of the hydrophobic interactions inside both biomolecules. The results suggest that these hydrophobic cores could overcome energy barriers and repack into new conformation states with even lower energies.
The repacking of the hydrophobic cores in MGs might be served as a criterion for recognizing the MGs in large class of biomolecules.published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy
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Tyka, Michael. "Absolute free energy calculations for biomolecular systems." Thesis, University of Bristol, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439666.
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Rogers, David M. "Using Bayes' theorem for free energy calculations." Cincinnati, Ohio : University of Cincinnati, 2009. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1251832030.
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Thesis (Ph. D.)--University of Cincinnati, 2009.Advisor: Thomas L. Beck. Title from electronic thesis title page (viewed Jan. 21, 2010). Keywords: Bayes; probability; statistical mechanics; free energy. Includes abstract. Includes bibliographical references.
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Schopf, Patrick. "Development and application of free energy methods." Thesis, University of Southampton, 2013. https://eprints.soton.ac.uk/366938/.
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The development of free energy simulation protocols for calculating relative binding free energies of ligands is presented in this thesis. To this end, the protein Dihydroorotate Dehydrogenase (DHODH), complexed to a highly congeneric series of compounds that show ambiguities in their binding modes, was studied in detail. To estimate the systematic error in force fields, relative free energies of hydration have been calculated using Replica-exchange Thermodynamic Integration (RETI) for sets of force field parameters and atomic partial charges in a classical molecular mechanics environment as well as a novel hybrid molecular mechanics/quantum mechanics model. The results demonstrated that all force fields and methods employed yield similar estimates of the relative free energies, while GAFF and OPLS-AA in conjunction with AM1BCC and AM1CM1A charges, respectively, performed best. To balance accuracy and ease of generating parameters, GAFF in conjunction with AM1BCC charges was selected to be the most valuable for describing the inhibitors in DHODH. To rigorously assess the thermodynamic end states for the ligands, crystal hydrates present in the binding site of DHODH have been investigated using the Just-Add-Water-molecules (JAWS) algorithm, Grand-canonical Monte Carlo (GCMC) simulations and the double-decoupling approach (DDM). These findings clearly suggested a change in hydration networks for both the inhibitors and their different binding modes, while all three approaches essentially yield identical results. This allowed us to construct free energy cycles using the single and dual topology approach in order to calculate the free energies of binding of the ligands as well as the stability of their binding modes. The results obtained were precise within the error of the methods, but not accurate, and allowed to complement the crystallographic findings.
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Weigt, Jürgen. "Die Förderung der Stromerzeugung aus erneuerbaren Energien in der Europäischen Union Probleme und Herausforderungen im Spannungsfeld zwischen Binnenmarkt und Umweltschutz." Frankfurt, M. Berlin Bern Bruxelles New York, NY Oxford Wien Lang, 2009. http://d-nb.info/994906196/04.
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Leite, Rodolfo Paula 1991. "O modelo de Uhlenbeck-Ford e cálculos de energia livre de sistemas na fase fluida." [s.n.], 2015. http://repositorio.unicamp.br/jspui/handle/REPOSIP/276946.
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Orientador: Maurice de KoningDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
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Resumo: Neste trabalho, apresentamos um estudo a respeito do modelo de Uhlenbeck-Ford como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, utilizando metodos de simulacao molecular. Este sistema artificial, que e caracterizado por um potencial puramente repulsivo e que diverge rapidamente, foi originalmente proposto como um modelo para o estudo teorico de gases imperfeitos. Este modelo foi motivado pelo fato de que todas as integrais de muitos corpos, envolvidas no calculo dos coeficientes viriais, podem ser facilmente calculadas analiticamente. Entretanto apenas oito coeficientes eram conhecidos. Dois novos coeficientes (..10 e ..11) foram determinados para o modelo neste trabalho, alem de uma expressao essencialmente exata para a equacao de estado e energia livre de Helmholtz em funcao de um parametro adimensional. Este nos permitira reunir todas as informacoes a respeito da energia livre do sistema em uma unica expressao, independentemente da escolha de parametros do potencial. Por fim, exploraremos a aplicabilidade deste modelo como um sistema de referencia para calculos de energia livre de sistemas na fase fluida, usando tecnicas de simulacao molecular a partir de processos fora de equilibrio. Nossos resultados para o fluido de Lennard-Jones e para o silicio liquido, descrito pelo potencial de Stillinger-Weber, demonstraram que o modelo de Uhlenbeck-Ford servira como um sistema de referencia para o calculo de energia livre de sistemas na fase fluida
Abstract: In this work, we present a study of the Uhlenbeck-Ford model as a reference system for freeenergy calculations of fluid-phase systems by molecular simulation methods. This artificial system, which is characterized by a rapidly-decaying purely repulsive potential, was originally proposed as a model for the theoretical study of imperfect gases, enabled by the fact that all the many-center integrals involved in the virial coefficients can be easily computed analytically. Although only eight coefficients were known. Two new coefficients (..10 e ..11) were determined for the model in this work, in addition to an essentially accurate expression to the equation of state and Helmholtz free-energy as a function of a dimensionless parameter. This will allow us to gather all information regarding the system of free-energy in a single expression, regardless of the choice of potential parameters. In the end, we explore the applicability of this model as a reference system for free-energy calculations of fluid-phase systems, using non equilibrium process with molecular simulation techniques. Our results for thevLennard-Jones fluid and liquid silicon, described by Stillinger-Weber potential, demonstrate that the Uhlenbeck-Ford model can be used as a reference system for free-energy calculations of fluid-phase systems
Mestrado
Física
Mestre em Física
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Shi, Yuanyuan. "Materials and molecules for pollution free clean energy." Doctoral thesis, Universitat Rovira i Virgili, 2018. http://hdl.handle.net/10803/664725.
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La combustió dels combustibles fòssils ha causat problemes mediambientals i energètics a nivell mundial, la qual cosa influeix en la salut i les activitats humanes. Amb la motivació de contribuir per resoldre aquests problemes, hem realitzat una sèrie de recerques per explorar materials i molècules per a la generació d'energia lliure de contaminació, com és l'energia solar convertida en hidrogen que proposa aquesta tesi. Hem analitzat estadísticament les partícules contaminants en l'aire, partícules de PM2.5, les quals indiquen que els agregats de sutge rics en carboni mostren una adhesividad i agregació molt altes. Més del 50% de les partícules PM2.5 interactuen fortament amb el substrat generant una capa molt prima (<10 nm) la qual és molt estable (fins i tot sota estrès mecànic) i que està composta de metalls alcalins, hidrogen i grups CH. Després de l'estudi sobre partícules contaminants en l'aire, ens hem centrat en l'estudi de dispositius de divisió d'aigua mitjançant radiació solar per explorar la generació d'hidrogen a gran escala. En aquesta tesi, ens hem centrat principalment en la recerca de materials i molècules per a divisors de molècules d'aigua fotoelectroquímics (PEC) i fotovoltaic-electrolítics (PV-EC). Els nostres resultats mostren que en els dispositius PEC, poden dipositar-se en la superfície dels foto-ànodes de silici pel·lícules primes metàl·liques de coure i níquel, podent formar CuO i NiOX respectivament. Tots dos materials actuen com a catalitzadors molt actius per a la reacció d'oxidació d'aigua i alhora com una capa protectora de la corrosió per a superfície de silici. D'altra banda, els dispositius PV-EC, pels quals hem utilitzat un ànode basat en molècules catalizadoras de Ruteni, s'ha integrat amb cèl·lules solars d'unió triple. Aquests dispositius han aconseguit una eficiència màxima de conversió energia solar-hidrogen del 21,2% a pH neutre i just per sota de la il·luminació solar sense cap polarització externa. Aquests resultats contribueixen a la generació d'hidrogen per conversió solar a gran escala.La combustión de los combustibles fósiles ha causado problemas medioambientales y energéticos a nivel mundial, lo que influye en la salud y las actividades humanas. Con la motivación de contribuir para resolver estos problemas, hemos realizado una serie de investigaciones para explorar materiales y moléculas para la generación de energía libre de contaminación, como es la energía solar convertida en hidrógeno que propone esta tesis. Hemos analizado estadísticamente las partículas contaminantes en el aire, partículas de PM2.5, las cuales indican que los agregados de hollín ricos en carbono muestran una adhesividad y agregación muy altas. Más del 50% de las partículas PM2.5 interactúan fuertemente con el sustrato a través de una capa muy delgada (<10 nm) de trazas oscura la cual es muy estable incluso bajo estrés mecánico y está compuesta de metales alcalinos, hidrógeno y grupos CH. Después del estudio sobre partículas contaminantes en el aire, nos hemos centrado en el estudio de dispositivos de división de agua mediante radiación solar para explorar la generación de hidrógeno a gran escala. En esta tesis, nos hemos centrado principalmente en la investigación de materiales y moléculas para divisores de moléculas de agua fotoelectroquímicos (PEC) y fotovoltaico-electrolíticos (PV-EC). Nuestros resultados muestran que en los dispositivos PEC, pueden depositarse en la superficie de los foto-ánodos de silicio películas delgadas metálicas de cobre y níquel, pudiendo formar CuO y NiOX respectivamente. Ambos materiales actúan como catalizadores muy activos para la reacción de oxidación de agua y a la vez como una capa protectora de la corrosión para superficie de silicio. Por otro lado, los dispositivos PV-EC, para los que se usó un ánodo basado en moléculas catalizadoras de Rutenio, se ha integrado con células solares de unión triple comerciales. Estos dispositivos han logrado una eficiencia máxima de conversión energía solar-hidrógeno del 21,2% a pH neutro y justo por debajo de la iluminación solar sin ninguna polarización externa. Estos resultados allanan el camino para la generación de hidrógeno por conversión solar a gran escala.
The combustion of the fossil fuels has caused the global environment and energy problems, which influences human health and activities. With the motivation to make our contributions to solving these problems, we have performed a series of investigations to explore materials and molecules for pollution free clean energy, which is solar energy converted hydrogen in this thesis. We have statistically analyzed the airborne pollutant particles, PM2.5 particles, which indicates that the carbon-rich fluffy soot aggregates always show very high adhesiveness and aggregation. And more than 50% PM2.5 particles strongly interact with the substrate through a ultra-thin (< 10 nm) dark trace layer, which is very stable even under mechanical stress and it is consisted of alkali metals, hydrogen and CH groups. After the study about airborne pollutant particles, we have moved to the study of solar-driven water splitting devices for exploring the large-scale generation of hydrogen. In this thesis, we have mainly focused on the investigation of the materials and molecules for photoelectrochemical (PEC) and photovoltaic-electrolysis (PV-EC) water splitting devices. Our results show that in the PEC water splitting devices, copper and nickel metallic thin films can be deposited on the surface of silicon photoanodes, which can form CuO and NiOX respectively and then serve as very active catalysts for water oxidation reaction and a protecting layer for silicon surface from corrosion. And in PV-EC water splitting devices, the ruthenium molecular catalysts based anode has been used for the electrolyzer, which has been integrated with commercially available triple junction solar cells. This integrated PV-EC device achieves the highest solar-to-hydrogen efficiency of 21.2 % at neutral pH and just under solar illumination without any external bias. These results pave the way for the generation of large-scale solar converted hydrogen.
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Reinhardt, Martin [Verfasser]. "Variational Approaches to Free Energy Calculations / Martin Reinhardt." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2021. http://d-nb.info/1225556139/34.
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Acharya, Arjun R. "Free energy differences : representations, estimators, and sampling strategies." Thesis, University of Edinburgh, 2004. http://hdl.handle.net/1842/602.
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In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the choice of estimator, and the choice of sampling strategy. In addition we discuss how the classical framework may be extended to take into account quantum effects. Key words: Phase Mapping, Phase Switch, Lattice Switch, Simulated Tempering, Multi-stage, Weighted Histogram Analysis Method, Fast Growth, Jarzynski method, Umbrella, Multicanonical, Path Integral Monte Carlo, Path Sampling, Multihamiltonian, fluctuation theorem.
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Shaw, Katherine E. "Testing QM/MM Methods Using Free Energy Simulations." Thesis, University of Bristol, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525442.
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Chudyk, Ewa Iwona. "Calculating free energy profiles for enzyme catalysed reactions." Thesis, University of Bristol, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.633252.
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Hydrolysis of biologically active compounds by enzymes is one of the most important processes in living organisms. This thesis describes the use of molecular dynamics (MD) simulations and free energy calculations to investigate two types of enzymes that catalyse hydrolysis reactions: fatty acid amide hydrolase, a target for antidepressant drugs, and class A B-lactamases, responsible for emerging antibiotic resistance in bacteria. Fatty acid amide hydrolase (FAAH) is an enzyme that deactivates neurotransmitters involved in inducing sleep, anxiety, inflammatory and pain states. To investigate catalysis in FAAH, an empirical valence bond approach was used to study the first step of acylation with oleamide. Results from this approach were compared with previous quantum mechanics/molecular mechanics (QM/MM) potential energy simulations and with experimental data. Further analysis of the FAAH active site indicated residues important for catalysis, which may provide insight for inhibitor design.
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Martin, Garcia Ignacio. "Sludge free and energy neutral treatment of sewage." Thesis, Cranfield University, 2010. http://dspace.lib.cranfield.ac.uk/handle/1826/6530.
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Anaerobic biological processes have been recognized as the most suitable pathway towards sustainable wastewater treatment due to the lower energy required and the lower amounts of biosolids generated when compared to conventional aerobic technologies. The difficulties experienced with the implementation of anaerobic reactors for the treatment of low strength wastewater at low temperatures are related to the deterioration of treatment capacity and effluent quality due to inefficient removal of colloidal matter and biomass washout. Membrane technology can overcome the limitation of anaerobic bioreactors since they retain not only solids but also colloidal and high molecular weight organics. This thesis explores the potential of anaerobic membrane bioreactors as core technology for mainstream wastewater treatment. The impacts of seed sludge, temperatures and bioreactors configuration on treatment efficiency and membrane performance as well as nutrient removal using ion exchange resins are investigated. Cont/d.
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Hedkvist, Olle. "Finding the Free Energy Proles of Protein Transitions." Thesis, KTH, Teoretisk fysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-174847.
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Vasileiadis, Manolis. "Calculation of the free energy of crystalline solids." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/12638.
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The prediction of the packing of molecules into crystalline phases is a key step in understanding the properties of solids. Of particular interest is the phenomenon of polymorphism, which refers to the ability of one compound to form crystals with different structures, which have identical chemical properties, but whose physical properties may vary tremendously. Consequently the control of the polymorphic behavior of a compound is of scientific interest and also of immense industrial importance. Over the last decades there has been growing interest in the development of crystal structure prediction algorithms as a complement and guide to experimental screenings for polymorphs. The majority of existing crystal structure prediction methodologies is based on the minimization of the static lattice energy. Building on recent advances, such approaches have proved increasingly successful in identifying experimentally observed crystals of organic compounds. However, they do not always predict satisfactorily the relative stability among the many predicted structures they generate. This can partly be attributed to the fact that temperature effects are not accounted for in static calculations. Furthermore, existing approaches are not applicable to enantiotropic crystals, in which relative stability is a function of temperature. In this thesis, a method for the calculation of the free energy of crystals is developed with the aim to address these issues. To ensure reliable predictions, it is essential to adopt highly accurate molecular models and to carry out an exhaustive search for putative structures. In view of these requirements, the harmonic approximation in lattice dynamics offers a good balance between accuracy and efficiency. In the models adopted, the intra-molecular interactions are calculated using quantum mechanical techniques; the electrostatic inter-molecular interactions are modeled using an ab-initio derived multipole expansion; a semi-empirical potential is used for the repulsion/dispersion interactions. Rapidly convergent expressions for the calculation of the conditionally and poorly convergent series that arise in the electrostatic model are derived based on the Ewald summation method. Using the proposed approach, the phonon frequencies of argon are predicted successfully using a simple model. With a more detailed model, the effects of temperature on the predicted lattice energy landscapes of imidazole and tetracyanoethylene are investigated. The experimental structure of imidazole is Abstract | ii correctly predicted to be the most stable structure up to the melting point. The phase transition that has been reported between the two known polymorphs of tetracyanoethylene is also observed computationally. Furthermore, the predicted phonon frequencies of the monoclinic form of tetracyanoethylene are in good agreement with experimental data. The potential to extend the approach to predict the effect of temperature on crystal structure by minimizing the free energy is also investigated in the case of argon, with very encouraging results.
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Westacott, Robin E. "Direct free energy calculations applied to clathrate hydrates." Thesis, University of Reading, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.283787.
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Othmer, Jonathan Andrew Pierce Niles A. Pierce Niles A. "Algorithms for mapping nucleic acid free energy landscapes /." Diss., Pasadena, Calif. : Caltech, 2009. http://resolver.caltech.edu/CaltechETD:etd-12312008-153810.
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Strümpfer, Johan. "Computing free energy hypersurfaces for anisotropic intermolecular associations." Master's thesis, University of Cape Town, 2009. http://hdl.handle.net/11427/6290.
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Includes abstract.Includes bibliographical references.
Adaptive reaction coordinate force biaisng methods have been previously used for calculating the free energy of conformation and chemical reactions amongst others. Here a generalized method is described that is able to produce free energies in multiple dimension, descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method. To illustrate it a multidemensional intermolecular orientational free energy surface is calculated, and it is demonstrated how to invesrigate complex systems such as protein conformation and liquids.
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Bridgwater, Sally. "Accurate free energy methods for model organic solids." Thesis, University of Warwick, 2014. http://wrap.warwick.ac.uk/66466/.
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We discuss existing free energy methods for use with investigation of solid-solid polymorphism. An alternative implementation for phase switch Monte Carlo is introduced which samples from two synchronised Markov chains exploring both polymorphs, using a set of generalised coordinates to transform between Markov chains. This is validated against the existing results for face-centred cubic (fcc) and hexagonal close-packed (hcp) hard sphere crystals. The extension to more complex crystals including flexibility and constraints is explored. This extension is applied to a hard sphere model of linear alkanes. A phase transition in density is accurately located between two polymorphs of n-butane with increasing density; this is suggested as a rigorous benchmark for free energy methods. We also demonstrate the importance of including anisotropic volume moves when simulating crystalline solids. Generalised coordinates for any fully flexible molecular system of soft particles are presented. These are used to investigate a coarse-grain model of cholesterol in regards to the polymorphic transition between two anhydrous cholesterol crystals. A phase transition in temperature is found and the limitations in the model are discussed.
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Pollard, Travis P. "Local Structure and Interfacial Potentials in Ion Solvation." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1491562324303743.
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Minami, Kazuhiko. "The free energies of six-vertex models and the n-equivalence relation." American Institite of Physics, 2008. http://hdl.handle.net/2237/12026.
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Oostenbrink, Chris [Verfasser]. "Free energies from biomolecular simulation: Force fields, methodology and applications / Chris Oostenbrink." Aachen : Shaker, 2005. http://d-nb.info/1181620961/34.
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Shamsudin, Khan Yasmin. "Computational methods for calculating binding free energies of ligands in COX-1." Licentiate thesis, Uppsala universitet, Beräknings- och systembiologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-226069.
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Tsang, Man Hong. "The calculation of solid-liquid interface free energies from biased atomistic simulations." Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/55870.
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The orientation dependence of the solid-liquid interface (SLI) free energy is an important parameter which determines orientation selection and the evolution of dendritic morphologies during the solidification of metallic melts. Atomistic simulations complemented with well-tempered metadynamics has been carried out to compute SLI free energies for the (100), (110) and (111) crystal interfaces of pure aluminium modelling using the empirical potential model of Mendelev and coworkers. The orientation dependence of the SLI free energy is known to be small, on the order of about 2%, and therefore great care was taken to quantify the accuracy of the metadynamics technique. It can be shown that significant reduction of the error can be achieved by averaging the free energy surfaces from many independent metadynamics runs. The supercell sizes considered in this work are sufficiently small to cause the observed melting temperature to deviate from the bulk melting temperature. Since the metadynamics method is susceptible to systematic errors caused by the latter temperature deviations, the interface-pinning method of locating melting points was used to locate the supercell-size dependent melting temperature and thereby eliminate this source of error. Sufficient accuracy has been achieved to resolve the finite-size contributions towards the estimated value of the SLI free energy caused by the finite dimensions of the supercells used; the values of SLI free energy obtained were found to depend strongly on both the supercell cross section and length. Attempts have been made to rationalise these finite-size effects based on the logarithmic scaling relations of Binder and Schmitz and coworkers. Estimates for the anisotropy ratio are obtained and compared with literature. Difficulties relating to the formation of twinned regions was encountered when applying the metadynamics technique to (111)-orientated supercells. The imposition of an appropriate restraining wall was found to inhibit the formation of these twins and thus allow the SLI free energy to be computed successfully. It is anticipated that the results of this study will provide an invaluable framework in any future attempt to estimate SLI free energies from small simulation cells which is a requirement perhaps necessitated by ab initio simulation.
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Sena, Hildo Costa de. "Efeitos da descarga corona em superfície de polipropileno em temperatura ambiente e acima." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/266860.
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Orientador: João Sinézio de Carvalho CamposDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química
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Resumo: Este trabalho avalia o efeito do tratamento por descarga corona em temperatura ambiente e acima para promover aumento da energia de superfície em filmes de polipropileno (PP). Submeteram-se amostras de polipropileno ao tratamento corona em sistema com geometria ponta-plano e utilizou-se de tensão de polarização dos eletrodos em 5kV . Avaliaram-se os efeitos do tratamento corona através de medidas de ângulo de contato pelo método da gota séssil, em função dos parâmetros: tempo de tratamento corona (2s a 90s), temperatura das amostras de polipropileno (25_C e 55_C) e distância entre os eletrodos (3mm e 5mm). Os resultados indicam influência significativa do tempo de tratamento corona e da distância intereletrodos. Ademais, o tratamento corona aumenta a energia de superfície dos filmes observada através da diminuição do valor do ângulo de contato entre amostra e gota d'água (inicialmente 88_ sem tratamento e 50_ após corona com 3mm de distância entre os eletrodos). Dentre os parâmetros e condições estudadas a temperatura não apresenta influência nos valores de ângulo de contato a fim de mudar a energia de superfície dos filmes. Em adição as medidas de ângulo de contato, medem-se propriedades físico-químicas da superfície do PP através da obtenção dos espectros dos filmes por espectrometria de infravermelho com transformações de Fourier (FT-IR) e de micrografias obtidas por microscopia eletrônica exploratória (MEV). A energia de superfície (antes e após tratamento corona) foi determinada utilizando-se os seguintes métodos: tensão superficial crítica (c), equação de estado (EE) e as aproximações de Owens/ Wendt (OW), Wu (Wu) e van Oss/ Chaudhury/ Good (VCG). A partir destes métodos encontra-se que: foram observadas diferenças entre os espectros de FT-IR obtidos nas diferentes condições de tratamento estudadas quando associadas a modificação por corona sob temperatura acima da ambiente (55_C _ 2_C). Alterações na topografia dos filmes de PP foram observadas após tratamento por descarga corona através da formação de grânulos, depressões, eriçamento e protuberâncias na superfície destes. Melhorias na energia livre superficial dos filmes de PP foram observadas após tratamento corona e variou aproximadamente de 36,9mN=m para 47,9mN=m em filmes sem tratamento superficial e após 10s de tratamento por descarga corona quando determinada através da aproximação de VCG, respectivamente
Abstract: The present study evaluates the effect of corona discharge treatment at room temperature and above in order to promote an increase of surface energy of polypropylene films. Polypropylene samples were subjected to corona treatment in tip-plane geometry system using bias voltage of 5kV between the electrodes. The effects of corona treatment were assessed by contact angle measurements using the sessile drop method, taking in account the following parameters: corona treatment time (2s to 90s), temperature of polypropylene samples (25_C and 55_C) and distance between the electrodes (3mm and 5mm). The results indicate significant influence of treatment time and the distance between the electrodes. Moreover, the corona treatment increases the surface energy of the films which was observed by decreasing the value of the contact angle between thesample and drop of water (initially 88_ without treatment and 50_ after corona with 3mm gap between the electrodes). Among the parameters and conditions studied, the temperature does not influence the values of contact angle in order to change the surface energy of the films. In addition the measures of contact angle, were carried out measures of physicochemical properties of the PP surface by obtaining the spectra of the films by infrared spectrometry with Fourier transformed (FT-IR) and micrographs obtained by scanning electron microscopy (SEM). The surface energy (before and after corona treatment) was determined using the following methods: critical surface tension (c), equation of state (EE) and approaches from Owens/ Wendt (OW), Wu (Wu) and van Oss/ Chaudhury/ Good (VCG). From these methods is turning out that: there were differences between the spectra obtained at different FT-IR treatment conditions studied when associate the corona modification at above room temperature (55_C _ 2_C). Changes in the topography of the films PP were observed after treatment by corona discharge due to formation of granules, depressions, bristling and bumps on their surface. Improvements in surface free energy of the PP films were observed after corona treatment, around from about 36,9mN=m in films without surface treatment up to 47,9mN=m after 10s of corona discharge when determined by VCG approach
Mestrado
Ciencia e Tecnologia de Materiais
Mestre em Engenharia Química
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Cunha, João Victor de Souza. "Aplicação de Monte Carlo para a geração de ensembles e análise termodinâmica da interação biomolecular." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/76/76132/tde-25112016-143220/.
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As interações moleculares, em especial as de caráter não-covalente, são processos-chave em vários aspectos da biologia celular e molecular, desde a comunicação entre as células ou da velocidade e especificidade das reações enzimáticas. Portanto, há a necessidade de estudar e criar métodos preditivos para calcular a afinidade entre moléculas nos processos de interação, os quais encontram uma gama de aplicações, incluindo a descoberta de novos fármacos. No geral, entre esses valores de afinidade, o mais importante é a energia livre de ligação, que normalmente é determinada por modos computacionalmente rápidos, porém sem uma forte base teórica, ou por cálculos muito complexos, utilizando dinâmica molecular, onde mesmo com um grande poder de determinação da afinidade, é muito custoso computacionalmente. O objetivo deste trabalho é avaliar um modelo menos custoso computacionalmente e que promova um aprofundamento na avaliação de resultados obtidos a partir de simulações de docking molecular. Para esta finalidade, o método de Monte Carlo é empregado para a amostragem de orientações e conformações do ligante do sítio ativo macromolecular. A avaliação desta metodologia demonstrou que é possível calcular grandezas entrópicas e entálpicas e analisar a capacidade interativa entre complexos proteína-ligante de forma satisfatória para o complexo lisozima do bacteriófago T4.The molecular interactions, especially the ones with a non-covalent nature, are key processes in general aspects of cellular and molecular biology, including cellular communication and velocity and specificity of enzymatic reactions. So, there is a strong need for studies and development of methods for the calculation of the affinity on interaction processes, since these have a wide range of applications like rational drug design. The free energy of binding is the most important measure among the affinity measurements. It can be calculated by quick computational means, but lacking on strong theoretical basis or by complex calculations using molecular dynamics, where one can compute accurate results but at the price of an increased computer power. The aim of this project is to evaluate a computationally inexpensive model which can improve the results from molecular docking simulations. For this end, the Monte Carlo method is implemented to sample different ligand configurations inside the macromolecular binding site. The evaluation of this methodology showed that is possible to calculate entropy and enthalpy, along analyzing the interactive capacity between receptor-ligands complexes in a satisfactory way for the bacteriophage T4.
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Almeida, Fernando Mattavo de. "Numerical simulation of the flow through an aqxial tidal-current turbine employing an elastic-free-surface approach." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/3/3135/tde-18092018-074509/.
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Together with the world economic growth is the increasing of energy generation demand. However, the upgrade of world power production capability could affect the environment negatively. Even the clean and renewable sources, such as hydroelectricity and wind powers have socio-economic and environmental disadvantages. For example, the required flooded area for a hydro power plant construction could devastate entire forests, and the installation of a wind farm power plant could affect migratory rotes of birds and generate high levels of noise. Hence, for the balancing of advantages and disadvantages of each power generation source, it is necessary to diversify, which requires investments in new power sources. In this context, the energy generation in the ocean is highlighted. The first point concerning the ocean energy is that there is no need of population removal from the installation area, such as the onshore based methods and the second point is that most of the population is concentrated in coastal areas. Therefore the production occurs near to the demand, decreasing the costs with energy distribution. The two main methodologies for harassing energy from oceans are based on gravity waves and in tides. And since the tidal cycles are governed mainly by the gravitational interaction between oceans, Moon and Sun, they are easily predictable, which increases the reliability of such systems. These works explores methodologies to analyse the power generation from a single axial tidal current turbine through a Steady State RANS methodology. Are discussed the effects of flow directionality, inlet velocity profile and turbulence levels and the results are compared with an experimental scheme. It is proposed an alternative methodology for free surface modelling in the CFD analysis. The usual methodology, VOF, it is based on a homogeneous, biphasic approach which requires an additional mesh refinement and is computationally expensive. This new methodology introduces an elastic wall approach in the free surface region in which the stiffness is calculated to provide the same restoring effect as gravity. In general, the results for open domain matched with the experimental results, validating the numerical model and the confined domain has shown a higher power and thrust coefficients if compared with the open domain, which is in accordance with the actuator disk theory approach. The elastic free surface presented convergence problems related to high Froude numbers and therefore to high deformations. However, a simulation with 10% of the original inlet velocity was performed, achieving reasonable results for both power and thrust coefficients evaluation.O crescimento econômico mundial e o aumento na demanda pela geração de energia andam juntos. No entanto, uma maior capacidade de produção de energia poderia afetar negativamente o meio ambiente. Mesmo as fontes limpas e renováveis, como a hidrelétrica e a eólica acarretam em impactos socioeconômicos e ambientais. Por exemplo, a construção de uma usina hidrelétrica demanda uma imensa área alagada que pode devastar florestas inteiras e a instalação de uma usina eólica pode afetar a migração de certas espécies de pássaros e produzir altos níveis de barulho. Portanto, para equilibrar as vantagens e desvantagens devidas a cada meio de produção de energia, é necessária a diversificação, que demanda de investimentos em novas fontes. Neste contexto, a geração de energia nos oceanos é destacada. O primeiro ponto a respeito desta fonte é de que não há a necessidade de remoção da população na área de instalação, tal como os métodos de geração dentro do continente. O segundo principal ponto é a respeito da distribuição de energia. A maior parte da população mundial vive em regiões costeiras, diminuindo, portanto, a distância entre a produção e demanda, reduzindo assim, seus custos. As duas principais metodologias para se explorar a energia proveniente dos oceanos são: Energia de Ondas e Energia de Marés. E considerando que os ciclos de mare são governados principalmente pela interação gravitacional entre os oceanos, lua e sol, eles são facilmente previsíveis, o que aumenta a confiabilidade dos sistemas de geração de energia baseados em marés. Este trabalho explora as metodologias para analisar a geração de energia a partir de uma única turbina axial de corrente de maré através de uma metodologia baseada nas equações de Navier-Stokes com a média de Reynolds, analisadas em regime permanente. São discutidos efeitos da direção do escoamento, perfil de velocidades na entrada e nos níveis de turbulência. Os resultados são comparados com experimentos. É proposta uma metodologia alternativa para a modelagem da superfície livre com CFD uma vez que a metodologia atual é baseada em um escoamento bifásico que demanda de um refinamento adicional da malha e é computacionalmente caro. A nova metodologia usa uma parede elástica na região da superfície livre com a rigidez ajustada para se obter o mesmo efeito de restauração que a gravidade. De maneira geral, os resultados para o domínio aberto se aproximaram dos resultados experimentais, validando o modelo numérico e além disso, o modelo considerando confinamento da turbine mostrou maiores valores para os coeficientes de potência e empuxo, estando portanto, de acordo com a teoria do disco atuador. O modelo com a superfície livre elástica apresentou problemas de convergência, relacionados com números de Froude elevados, uma vez que isto se relaciona com maiores deformações na região da superfície livre. Uma simulação com 10% da velocidade original foi realizada, obtendo-se resultados coerentes para ambos coeficientes de potência e empuxo.
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Minh, David. "Free energy reconstruction from irreversible single-molecule pulling experiments." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3258785.
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Thesis (Ph. D.)--University of California, San Diego, 2007.Title from first page of PDF file (viewed June 8, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 69-72).
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King, Paul M. "Application of free energy perturbation calculations to molecular biophysics." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257951.
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Handel, Richard James. "Calculating ice–water interfacial free energy by molecular simulation." Thesis, University of Leicester, 2009. http://hdl.handle.net/2381/8634.
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This study presents a calculation of the free energy of the ice–water interface using molecular simulation. The method used is an adaptation of the cleaving method, introduced by Broughton and Gilmer, and subsequently enhanced by Davidchack and Laird. The calculation is direct in the sense that an interface is formed during the simulation: isolated ice and water systems are transformed, via a sequence of reversible steps, into a single system of ice and water in contact. The method is essentially computational, that is, it does not correspond to any possible physical experiment, since non-physical potential energies are introduced (and subsequently removed) during the transformation process. The adaptation of the method to water presented significant challenges, notably the avoidance of hysteresis during the transformation, and the devising of an ‘external’ energy potential to control the position and orientation of water molecules. The results represent the first direct calculation by simulation of the solid–liquid interfacial free energy for a model of a molecular (as opposed to atomic) system.