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Papchenko, O. "Free energy." Thesis, Сумський державний університет, 2013. http://essuir.sumdu.edu.ua/handle/123456789/33782.
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At school we were thought that if we include bulb in electrical circuit our battery will be discharging. The energy of battery will be spent to the lighting of bulb, however this theory gives us not correct imagination. This explanation implies that battery has some amount of energy and spend it on the bulb. Interesting but at the same time teacher shows us correct model of these process. Pay you attention that amperage in all circuit is the same. So the question is how much energy our bulb is spending during its work? The answer is zero. The energy is not spent it just converted from one form to another. So why battery cannot just maintain the work of bulb forever?
When you are citing the document, use the following link http://essuir.sumdu.edu.ua/handle/123456789/33782
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Cave-Ayland, Christopher. "Quantum free energy techniques." Thesis, University of Southampton, 2014. https://eprints.soton.ac.uk/375028/.
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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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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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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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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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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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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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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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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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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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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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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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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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Setiadi, Jeffry. "Free Energy Molecular Dynamics Simulations of Glutamate Transporters." Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/20932.
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Molecular dynamics (MD) is a powerful computational tool that paves the way to understand the dynamics and function of life at the molecular level. MD coupled with advanced free energy calculations, and in-silico methods can reveal the underlying mechanism of a physical process that cannot be probed with experimental techniques. The primary investigation in this thesis is to use MD with free energy calculations to explain and elucidate the protein-ligand interactions in glutamate transporters. Glutamate is the major excitatory neurotransmitter in the nervous system and understanding such mechanism may reveal the causes of many pathological conditions linked to glutamate transporters. Here, this thesis presents the results three anomalies observed previously from both experimental and computational studies. First, the instability of a sodium ion bound to the Na2 site observed in simulations is caused by the undercharging of the sulphur atom of the methionine residue in the NMDGT motif. Second, the binding of aspartate to GltPh requires two sodium ions bound in an intermediate state rather than the observed sites revealed from crystallography. Third, the escape of the last sodium ion in the inward-facing conformation shows structural changes in the protein in agreement with experimental observations. An estimate of the escape time from the Na3 site to the bulk indicates this as a slow process in GltPh but is not the rate-limiting step in the transport cycle. As secondary projects, the K+ permeation in gramicidin A (gA) embedded in different lipid membranes and ion solvation in a water droplet is investigated. The potential of mean force (PMF) profile reveals a larger barrier for gA embedded in POPC than in NODS lipid membranes due to the stronger dipole moment of the phosphorus atom. Finally, using spherical boundary condition (SBC) without a buffer zone in the liquid-vacuum interface can give the correct ion-solvation free energy provided a larger system is used.
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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.
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Michel, Julien. "The use of free energy simulations as scoring functions." Thesis, University of Southampton, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.494715.
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Aldeghi, Matteo. "Free energy calculations in drug design : application to bromodomains." Thesis, University of Oxford, 2016. https://ora.ox.ac.uk/objects/uuid:d36a729c-4385-408d-9a21-92dfa339cf3c.
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Computer simulations of biomolecules have been improving at a pace that is faster than Moore's law for microprocessors in the last few decades. Thanks to advances in theory, hardware, and algorithms it is increasingly possible to study biological processes at relevant spatial and temporal resolutions, and to exploit simulation for quantitative predictions. One area that can potentially benefit greatly from such computational predictions is that of drug discovery. Since the inception of the concept of rational drug design, the prediction of how tightly an organic molecule binds to a macromolecular partner has been one of the chief objectives of computational chemistry. Computers already play a fundamental support role during the drug discovery process, and today many novel approaches that aim at studying the details of drug binding and predicting binding affinity are being actively investigated. In this thesis, I report a series of studies that aim to evaluate the potential utility of free energy calculations based on molecular simulations for drug design. In particular, I focus on the prediction of small-molecule binding affinities to the epigenetic target of bromodomains. Bromodomains are small protein modules that have been found in 46 human proteins involved in gene regulation. Given their role in various diseases, in particular cancer and inflammation, a number of bromodomain inhibitors are currently being investigated both in the laboratory and the clinic. Here, it is shown how thorough calculations based on explicit-solvent simulations and all-atom force fields can accurately reproduce binding free energies for this protein family. Rigorous free energy calculations are also compared to more approximate methods based on the post-processing of the simulation trajectories in implicit solvent. Finally, a recently proposed method for the estimation of water binding free energy is employed to study water displaceability from bromodomain binding pockets.
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Amon, Lynn. "Methods for calculating the free energy of atomic clusters /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/8595.
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Oliveira, Ederlon Ribeiro de. "Maintenance Energy Requirements of Free Ranging Goats and Sheep." DigitalCommons@USU, 1987. https://digitalcommons.usu.edu/etd/4555.
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Measurements of energy expenditures for domestic animals are used as a basis to determine the total energy requirements for maintenance and for production. Most studies on energy metabolism have been conducted under controlled, confinement conditions, and the results extrapolated to free - ranging animals. Such approaches do not always represent the real energy costs of free existence in the range or pasture environment.
This study compared energy expenditures of sheep and goats under free-grazing conditions and assessed the accuracy of the carbon dioxide entry rate technique (CERT) as compared to the oxygen consumption method. In addition, 24-hour activity budgets were used to construct energy budgets for both animal species. These estimates were compared to CERT measurements. Dietary organic matter, crude protein, gross energy, digestible protein, and digestible energy intakes, as well as the apparent digestibility coefficients for crude protein and gross energy were compared for both species in one of the grazing trials.
The validation of CERT yielded the linear regression equation: Y = 0.878 + 5.333 ER where Y energy expenditure in Kcal·min-1, and ER is the C02 entry rate in grams of C02 carbon·min-1. The coefficient of determination (r2) was 0.979, and the residual standard deviation of ± 0.12 Kcal·min-1. Daily energy expenditure of goats was higher (P<.OS) than that of sheep in all grazing experiments. The overall means were 127.1 and 88.4 Kcal·Bw-.75.d-1 for goats and sheep, respectively.
High ambient temperatures during one of the grazing trials apparently caused heat stress to the grazing animals. Both species responded to this situation by using behavioral adaptations and avoidance mechanisms.
The energy budget method over-estimated energy expenditures of sheep by 9 percent, and grossly underestimated the energy expenditures of goats by 39 percent.
The nutritive value of the diets selected by both species was similar . However, goats had higher (P< .OS) organic matter, crude protein, gross energy, digestible protein and digestible energy intakes. The apparent crude protein digestibility coefficient for goats was 20 percent higher (P<.OS) than that for sheep. On the other hand, gross energy digestibility coefficients were similar for both species. Goats appeared to have an edge in meeting their dietary protein requirements under free- ranging conditions.
CERT can predict energy expenditures within ± 8 percent of the mean. It is a feasible technique for assessing energy expenditures of small ruminants under range conditions. The energy budget method was not reliable for estimating energy costs in small ruminants, especially goats.
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Maiani, Andrea. "Minimum Free Energy Paths of Vortices Nucleation in Superconductors." Thesis, KTH, Fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-263049.
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Ramadugu, Sai Kumar. "Carbohydrate-protein interactions: structure, dynamics and free energy calculations." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/1731.
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The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulation, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of ManΑ1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand.
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Taylor, Zoe Rebecca. "Improving the efficiency of computation of free energy differences." Thesis, Curtin University, 2011. http://hdl.handle.net/20.500.11937/2424.
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There has been a recent focus on investigating the properties of semi-conductors at the nanoscale as it is well known that the band-gap of semi-conducting materials is altered due to quantum confinement effects. The potential to fine-tune a material's properties based solely on particle size has raised significant interest both in experimental and computational studies. Zinc sulfide is one of the most studied metal sulfide semi-conductor minerals, due to its potential technological applications.Computational studies of the structural and thermodynamic properties of zinc sulfide nanoparticles and bulk structures have been performed throughout this work. A variety of computational methods have been employed, including molecular dynamics, lattice dynamics, first principles calculations, and free energy techniques, such as metadynamics and free energy perturbation. The thermodynamic stability of zinc sulfide nanoparticles as a function of size and shape has been studied. Investigation of the phase space of these systems required the use of enhanced sampling methods. The metadynamics method was specifically utilised to explore as many structures as possible in combination with extensive simulations. The use of first principles methods for these exploratory simulations was found to be prohibitively expensive, and so force field methods were primarily utilised. Throughout this investigation several force fields were used to compare and contrast their accuracy, while first principles calculations were performed, where possible, to assist in the interpretation and validation of the results.In the present study, two different collective variables, the trace of the inertia tensor and the Steinhardt bond order parameters, have been implemented and their performance in metadynamics compared. The trace of the inertia tensor was found to be useful for exploring clusters of small sizes, while the Q4 Steinhardt parameter, which describes the crystalline order of a solid, is more applicable to larger clusters. Both of these metadynamics studies resulted in clusters displaying zeolite structural motifs, including the zeolite framework `BCT'. This led us to investigate more thoroughly the stability of different zinc sulfide zeolite analogues, thereby highlighting the strengths and weaknesses of all the force fields employed. Many force fields are found to be unable to accurately represent the order of stability for bulk polymorphs.First principles calculations also highlighted that the BCT phase is less stable than either of the bulk polymorphs of zinc sulfide, in contrast to the order of stability obtained by force fields lacking a torsional term, both from literature and the rigid ion model developed during the current study. The larger nanoparticles cleaved from wurtzite exhibited internal strain upon relaxation. A new hypothetical zeolite framework was constructed from the distorted core of these clusters, and was found to possess structural similarities with the `APC' framework. The APC framework is composed of double crankshaft-chains with ”ABCABC…” stacking, while the hypothetical framework identified is formed by the same composite building unit with `ABAB: : : ' type stacking. For all the force fields used the new hypothetical framework was lower in energy than the APC framework, but higher in energy than sphalerite, wurtzite or the BCT phase.Free energy differences between small ZnS clusters in vacuum were calculated using the path variable technique, and also using static methods within the quasi-harmonic approximation. Similar values were obtained using both of these methods, validating the path collective variables used with metadynamics as an effective means of obtaining free energy differences for clusters in vacuum.In addition to clusters in vacuum, a number of studies of ZnS clusters in water were also performed. Both force field and first principles studies were employed to validate the ZnS-water interactions used for the binding energies of water to small clusters. As a further validation, the free energies of solvation of Zn2+ and S2?? in aqueous solution were calculated. The free energy of solvation for the sulfide anion was found to be close to the experimental value, while the parameters for Zn2+-water were found to require substantial modification as the solvation free energy was in error by 500 kJ/mol. While newly derived ZnS-water parameters may prove to be superior for describing ZnS clusters in bulk water, a repetition of the binding energy calculations for individual water molecules bound to ZnS clusters gave energies 2-3 times greater than those obtained via first principles methods and using the five other force fields investigated. These results highlight the issues present when attempting to transfer a model fitted in a certain way to a different application. In particular, the many-body and polarisation effects present when modelling water need to be considered when parameterising ZnS-water interactions.
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Dhavale, V. M. "Low-platinum and platinum-free electrocatalysts for energy applications." Thesis(Ph.D.), CSIR-National Chemical Laboratory, Pune, 2015. http://dspace.ncl.res.in:8080/xmlui/handle/20.500.12252/1994.
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Rocklin, Gabriel Jacob. "Predicting charged protein-ligand binding affinities using free energy calculations." Thesis, University of California, San Francisco, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3587895.
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Predicting protein-ligand binding free energy from physical principles is a grand challenge in biophysics, with particular importance for drug discovery. Free energy calculations compute binding affinities by using classical mechanics to model the protein and ligand at atomic resolution, and using statistical mechanics to analyze simulations of these models. The binding affinities computed from these simulations are fully rigorous and thermodynamically correct for the model (with adequate sampling), and will agree with experimentally measured binding affinities if the model is accurate. Because free energy calculations capture the full statistical complexity of binding for flexible molecules at ambient temperature, they offer the greatest potential for quantitative accuracy of any physical method for predicting binding.
Here, I (& coauthors) present several studies relating to using free energy calculations to predict protein-ligand binding affinities for charged compounds. First, we introduce the Separated Topologies method, an approach for using free energy calculations to predict relative binding affinities of unrelated ligands. This method is useful for studying charged compounds because charged compounds are very difficult to study using absolute binding calculations, increasing the importance of relative binding calculations. Second, we use free energy calculations to predict absolute binding affinities for charged molecules to a simplified protein binding site, which is specially designed for studying charged interactions. These predictions are compared to new experimental affinity measurements and new high-resolution structures of the protein-ligand complexes. We find that all affinities are predicted to be too strong, and that this error is directly correlated with the polarity of each ligand. By uniformly weakening the strength of electrostatic interactions, we are more successful at predicting binding affinity. Third, we design and validate an analytical correction scheme to correct binding free energy calculations of ions for artifacts caused by the periodic boundary conditions employed in simulations. Fourth, we examine the sensitivity of binding affinities from free energy calculations to the force field parameters used in the simulations. This provides insight into the strength of electrostatic interactions in protein simulations, complementing our previous work comparing simulation results to experiments. Finally, we discuss potential future directions of this work.
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Smith, Graham. "The measurement of free energy by Monte Carlo computer simulation." Thesis, University of Edinburgh, 1996. http://hdl.handle.net/1842/6466.
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One of the most important problems in statistical mechanics is the measurement of free energies, these being the quantities that determine the direction of chemical reactions and--the concern of this thesis--the location of phase transitions. While Monte Carlo (MC) computer simulation is a well-established and invaluable aid in statistical mechanical calculations, it is well known that, in its most commonly-practised form (where samples are generated from the Boltzmann distribution), it fails if applied directly to the free energy problem. This failure occurs because the measurement of free energies requires a much more extensive exploration of the system's configuration space than do most statistical mechanical calculations: configurations which have a very low Boltzmann probability make a substantial contribution to the free energy, and the important regions of configuration space may be separated by potential barriers. We begin the thesis with an introduction, and then give a review of the very substantial literature that the problem of the MC measurement of free energy has produced, explaining and classifying the various different approaches that have been adopted. We then proceed to present the results of our own investigations. First, we investigate methods in which the configurations of the system are sampled from a distribution other than the Boltzmann distribution, concentrating in particular on a recently developed technique known as the multicanonical ensemble. The principal difficulty in using the multicanonical ensemble is the difficulty of constructing it: implicit in it is at least partial knowledge of the very free energy that we are trying to measure, and so to produce it requires an iterative process. Therefore we study this iterative process, using Bayesian inference to extend the usual method of MC data analysis, and introducing a new MC method in which inferences are made based not on the macrostates visited by the simulation but on the transitions made between them. We present a detailed comparison between the multicanonical ensemble and the traditional method of free energy measurement, thermodynamic integration, and use the former to make a high-accuracy investigation of the critical magnetisation distribution of the 2d Ising model from the scaling region all the way to saturation. We also make some comments on the possibility of going beyond the multicanonical ensemble to `optimal' MC sampling. Second, we investigate an isostructural solid-solid phase transition in a system consisting of hard spheres with a square-well attractive potential. Recent work, which we have confirmed, suggests that this transition exists when the range of the attraction is very small (width of attractive potential/ hard core diameter ~ 0.01). First we study this system using a method of free energy measurement in which the square-well potential is smoothly transformed into that of the Einstein solid. This enables a direct comparison of a multicanonical-like method with thermodynamic integration. Then we perform extensive simulations using a different, purely multicanonical approach, which enables the direct connection of the two coexisting phases. It is found that the measurement of transition probabilities is again advantageous for the generation of the multicanonical ensemble, and can even be used to produce the final estimators. Some of the work presented in this thesis has been published or accepted for publication: the references are G. R. Smith & A. D. Bruce, A Study of the Multicanonical Monte Carlo Method, J. Phys. A. 28, 6623 (1995). [reference details doi:10.1088/0305-4470/28/23/015] G. R. Smith & A. D. Bruce, Multicanonical Monte Carlo Study of a Structural Phase Transition, to be published in Europhys. Lett. [reference details Europhys. Lett. 34, 91 (1996) doi:10.1209/epl/i1996-00421-1] G. R. Smith & A. D. Bruce, Multicanonical Monte Carlo Study of Solid-Solid Phase Coexistence in a Model Colloid, to be published in Phys. Rev. E [reference details Phys. Rev. E 53, 6530–6543 (1996) doi:10.1103/PhysRevE.53.6530].
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Peterson, Robert E. "Shielding requirements for an energy-recovery LINAC Free Electron Laser." Monterey, California. Naval Postgraduate School, 2011. http://hdl.handle.net/10945/10671.
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Many Free Electron Lasers (FELs) utilize high current, high energy electron beams. Inevitably, a small fraction of the electrons in the beam will exist outside the core beam; these electrons are referred to as beam halo. The halo electrons will travel down an FEL's transport system with the core electrons; any portion of those halo electrons that intercept transport system components can generate radiation that is harmful to the operating personnel. The amount of shielding that is required to keep personnel safe from radiation exposure is evaluated as a function of the lost halo current. Using the modeling software FLUKA, an analysis is presented describing the amount of necessary shielding for a given shielding material.
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Woods, Christopher J. "The development of free energy methods for protein-ligand complexes." Thesis, University of Southampton, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396741.
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Rebane, Aleksander. "Exploring Free Energy Landscapes of SNARE Assembly Using Optical Tweezers." Thesis, Yale University, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10957335.
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Scientists have long sought to understand the working principles of protein machinery. A decisive step towards this goal has been the development of the Gibbs free energy landscape of protein folding. However, measurement of energy landscapes has remained challenging, particularly when folding occurs over one or more intermediates. An important example is soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex assembly, in which the energetics and kinetics of multiple assembly steps are coupled to distinct stages of vesicle maturation and membrane fusion in synaptic exocytosis. As a result, a quantitative test of this fundamental biophysical mechanism remains outstanding. In recent years it has become possible to measure energy landscapes of proteins in the presence of force using a single-molecule manipulation technique called optical tweezers (OT). However, derivation of energy landscapes in the absence of force from OT data has remained difficult. Here, we present a comprehensive OT data analysis method that uses information from high-resolution protein structures to derive a simplified energy landscape of protein folding at zero force by model fitting of the experimental measurements. We apply our method to derive the energetics, kinetics, and intermediate conformations of SNARE assembly for the wild-type complex and a number of mutants with known phenotypes. We characterize how the steps in SNARE assembly function in the respective stages of synaptic exocytosis and provide quantitative verification of the coupling mechanism. Finally, we investigate the mechanism by which two SNARE mutations cause severe neurological disease. In sum, our work provides a complete methodology to measure energy landscapes to reveal the underlying mechanisms of protein function.
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Morozov, Alexandre V. "Free energy functions in protein structural stability and folding kinetics /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/9690.
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Suzuki, Yohichi. "Free energy landscape of dipolar system : statistical and dynamical analysis." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/136910.
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Mossa, Alessandro. "Analytic Properties of the Free Energy: the Tricritical Ising Model." Doctoral thesis, SISSA, 2004. http://hdl.handle.net/20.500.11767/3983.
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Dalla, Sega Marco <1990>. "Molecular Dynamics Simulations and Free Energy Calculations of HemQ Proteins." Master's Degree Thesis, Università Ca' Foscari Venezia, 2016. http://hdl.handle.net/10579/8964.
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HemQ proteins are a novel discovered class of proteins that play an important role in the heme biosynthetic pathway in Firmicutes and Actinobacteria. HemQ catalyzes two consecutive oxidative decarboxylations of coproheme molecule, cleaving off two propionate groups to yield heme b, following a reaction that is not yet known. The coproheme demonstrates a high binding affinity toward HemQ, with an extremely fast binding rate, whereas heme b is bound less tightly. This suggests a possible reaction mechanism, where the coproheme released by the HemH enzyme is immediately bound by HemQ, which then catalyzes the decarboxylation of propionates in position 2 (p2) and 4 (p4) of the porphyrin ring to form the respective vinyl groups. The heme b molecule thus formed is then released due to its lower binding affinity, probably caused by the decreased non-bonded interactions with the protein after the two propionates have been cleaved off. However the reaction mechanism is poorly understood. Molecular dynamics simulations and free energy calculations are used to better understand the dynamics of this protein and the reaction it catalyzes. Typical analysis are performed to study the structural behavior of this protein, while free energy calculations are conducted using two different approaches: the thermodynamic integration (TI) and the Linear Interaction Energy (LIE) method.
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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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White, E. "Respiration chamber-free measurement of oxygen consumption in sheep." Thesis, University of Reading, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.372674.
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Komo, Adelaide. "Towards clean energy options : a study of energy use patterns in Zamdela (Sasolburg, Free State Province)." Diss., University of Pretoria, 2013. http://hdl.handle.net/2263/79262.
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In future, increasing attention will be paid worldwide to clean and sustainable energy household practices. More research is needed in South Africa to improve policy regarding patterns of domestic energy use, particularly in urban „townships‟ and rural areas. The predominantly quantitative studies conducted in South African townships in the 1980s emphasise the complexity of household energy use patterns and the difficulty of understanding these patterns by means of a simple theory.
This study therefore focuses on domestic energy use patterns in the Zamdela Township of Sasolburg in the Free State Province of South Africa. It addresses the community‟s main reasons for particular energy choices, including gender and power relations, together with the role of households‟ income profile in energy consumption and acquisition patterns. The field research methods included face-to-face interviews, participant observation and group discussions to obtain data on usage patterns, cultural practices, survival strategies, technical knowledge, source of income and the social interaction related to domestic energy use in the township. Above all, the role of human factors in energy acquisition and consumption (with special reference to the local authority‟s policy and the national energy policy) are considered.
Findings show that dirty energy sources are the predominant domestic energy sources used in the township. Factors that influence energy choices among township inhabitants are mainly gender relations, the income and composition of households, intra-household relations, education, vandalism, corruption, theft, fraud and harassment.
The study concludes that a laissez aller or laissez faire attitude among municipal officials hampers service delivery, and recommends that a policy of prosecuting perpetrators (such as corrupt officials) who stall development and service delivery be developed and implemented. The study also concludes that the extreme levels of energy poverty of large masses of people in the township cannot be improved without empowering women. Thus women‟s education should be targeted for effective township development. Because access to energy will probably remain a greater priority than environmental degradation for years to come, technologies that promote low smoke energy use techniques and practices should be promoted and supported.Dissertation (MSSc)--University of Pretoria, 2013.
Antropology and Archaelogy Community Development
MSSc
Unrestricted
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Williams, Robert E. "Naval electric weapons : the electromagnetic railgun and free electron laser /." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2004. http://library.nps.navy.mil/uhtbin/hyperion/04Jun%5FWilliams.pdf.
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Critchley, Andrew Duncan James. "Structure of free radicals." Thesis, University of Newcastle Upon Tyne, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.327188.
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Martínez, Monge Álvaro. "Free energy and information-content measurements in thermodynamic and molecular ensembles." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667026.
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Single-molecule experiments have emerged as a powerful tool that allow researchers to investigate the physical behavior of individual molecules with unprecedented resolution. The feasibility exerting forces at the piconewton scale (10^-12 N) and measuring nanometric displacements in the sub-millisecond scale, offer a widespread range of exciting possibilities. The major part of this thesis is devoted to address fundamental topics of statistical physics using single-molecule experiments. In particular, in the first part of the thesis, we aimed to study one of the eldest questions in statistical mechanics: the issue of ensemble inequivalence. By performing single- molecule experiments on a well-known molecule (the CD4 DNA hairpin), we have been able of exploring two conjugate ensembles: the fixed-extension and the force-fixed ensemble. Both ensembles are conjugate with respect to energy since the product force times extension equals has energy dimensions. We carried out experiments in the fixed-force ensemble using both optical tweezers and magnetic tweezers, and in the fixed-extension using optical tweezers. We have found that these two conjugate ensembles are not equivalent at the level of thermodynamics nor in kinetics. Moreover, we showed that the often-neglected boundary terms in the definition of the thermodynamic work are essential to the validity of the fluctuation theorem. The second part of this thesis is also merely theoretical. Recent single-molecule assays confirmed the connection between information theory and statistical physics. Single- molecule experiments have turned out to be the perfect playground to explore the thermodynamic implications of having —or lacking— information. It is worthwhile to mention the experimental realization of the Szilard engine and the experimental verification of Landauer’s limit. With the current existing results, the information-to- energy connection is well established. We have been able to experimentally demonstrate, for the first time, the reversed implication. We have been able to quantify the information-content of neutral molecular ensembles by means of thermodynamic measurements. That is, we experimentally demonstrated the energy- to-information conversion. Our works are built on what we call ensemble force spectroscopy, a systematic procedure capable of obtaining a robust characterization of molecular ensembles in the best tradition of statistical physics, by measuring few tens of molecules. In the final part of the thesis we aimed to measure the specific binding energy of a metallic ion to the tertiary structure of a three-way RNA junction belonging
to the central domain of the 16S ribosomal RNA (rRNA). From the physics perspective, to the best of our knowledge, first time we have been able to discern the free energy contribution due to the specific binding of magnesium ions to an RNA substrate by means of single-molecule assays. On the other hand, such molecule is able to form, besides its native conformation, a force-induced misfolded state. Despite this fact was already pointed out in previous single-molecule studies, there was a lack of knowledge regarding the molecular kinetics and the folding pathway. Aiming to fill this gap, we performed a thorough study of the three-helix RNA junction using dynamic force spectroscopy. As a result, we have characterized the full folding pathway of the molecule, including both the native and the misfolded structure. Furthermore, we have experimentally confirmed the fact that the presence of magnesium promotes the stabilization of the native structure and we have measured this contribution. We have found that magnesium is able to rescue the native structure from the misfolded structure via electrostatic interactions due to magnesium binding. This fact is biologically relevant, since we have been able to characterize the conditions in which a misfolded molecule is able to recover its native conformation.En esta tesis hemos abordado cuestiones fundamentales de la física estadística. En particular, hemos estudiado el problema de la equivalencia entre colectivos estadísticos, la conversión de energía a información y el estudio de las energías específicas de unión de iones metálicos a sustratos de RNA. Esta tesis doctoral se ha llevado a cabo empleando dos de los instrumentos de molécula individual más conocidos, las pinzas ópticas y las pinzas magnéticas. Ambas son técnicas que permiten la aplicación controlada de fuerzas mecánicas a los extremos de una molécula individual. El poder aplicar fuerzas a sistemas moleculares permite llevar a cabo una profunda caracterización de las propiedades físicas de los llamados sistemas pequeños. Las dimensiones de estos sistemas abarcan desde unos pocos nanómetros —una millonésima parte del metro— hasta varios cientos de nanómetros. Además, los sistemas pequeños están lejos del llamado límite termodinámico y están dominados por las fluctuaciones térmicas del entorno. Por lo tanto, debido a estas peculiaridades, el estudio de sistemas pequeños mediante los instrumentos de molécula individual permite impulsar y extender los horizontes de la física de no equilibrio.
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Gravoille, Pauline. "CASE STUDY OF ACTIVE FREE COOLING WITH THERMAL ENERGY STORAGE TECHNOLOGY." Thesis, KTH, Kraft- och värmeteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-77778.
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May 25, 2011, Reuters’ headline read: "New York State is prepared for summerelectricity demand". The NY operator forecasts for next summer a peak of 33GW, close to therecord ever reached. With soaring cooling demands, the electricity peak load represents a substantialconcern to the energy system. In the goal of peak shaving, research on alternative solutions based onThermal Energy Storage (TES), for both cooling and heating applications, has been largely performed.This thesis addresses thermal comfort applications with use of active free cooling through implementationof latent heat based TES. Active free cooling is based on the use of the freshness of a source, the outsideair for example, to cool down buildings. This work conceptualizes the implementation of TES basedcooling system with use of Phase Change Material in an in-house-built model. The principle of PhaseChange Material, or Latent Heat TES (LHTES), lies on latent energy which is the energy required for thematerial to change phase. In order to properly size this cooling system, a multi-objective optimization isadopted. This optimization, based on minimization of multi-objective functions, led to optimal designconfigurations. In parallel, the electrical consumption of the system and the volume uptake of the systemwere also considered. Through the obtained optimization studies, we identified non-linearinterdependency between the two objective functions: the cost of the system and the acceptable remainingcooling needs. By remaining cooling needs, we mean the cooling needs that the system cannot meet. As amatter of fact, sizing the system according to these cooling needs would imply a very high cost. It wasfound that for a certain amount of remaining cooling needs, the PCM-based cooling system reveals to bean interesting solution compared to conventional air conditioning in terms of electrical consumption andoverall system cost.Best Master Thesis Award, granted by French Academic Institute
Cold Thermal Energy Storage