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1
Legha, Prem, University of Western Sydney, of Science Technology and Environment College, and of Science Food and Horticulture School. "Molecular structure and odor mixture perception." THESIS_CSTE_SFH_Legha_P.xml, 2004. http://handle.uws.edu.au:8081/1959.7/549.
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The sense of smell is a primal sense for humans as well as animals.In everyday life the smells encountered are composed of dozens, even hundreds of odors; few arise from a single odorant. Enormous numbers of odors occur due to the vast variation in the concentration, size and structure of odorant molecules that makes olfaction differ from simpler visual or auditory dimensions. Accordingly, little is known about the ways in which changes in molecular structure and concentration of individual odorants change odor quality. Also, currently not much is understood about synergism/antagonism, how one odorant masks or suppresses another in mixtures and there is no method for predicting which odor will be suppressed. The two main objectives of this thesis were to determine whether a part of a molecular structure rather than the whole structure plays a key role in odor quality and whether a key part of a molecule can be used to choose antagonists for that odorant. For this study three classes of musks and two potential antagonists were used. The results of the study are discussed in some detail. It is concluded that future studies of the importance of molecular structure in mixture interactions require substantially more information on the relation between structure and odor quality to allow systematic studies to be developed. In summary the two hypotheses investigated were not supported by the results. Importantly, however, they do support the view that it is likely that odor quality is dependent on the whole structure of an odorant not a single feature.<br>Master of Science (Hons)
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Legha, Prem. "Molecular structure and odor mixture perception." Thesis, View thesis, 2004. http://handle.uws.edu.au:8081/1959.7/549.
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The sense of smell is a primal sense for humans as well as animals.In everyday life the smells encountered are composed of dozens, even hundreds of odors; few arise from a single odorant. Enormous numbers of odors occur due to the vast variation in the concentration, size and structure of odorant molecules that makes olfaction differ from simpler visual or auditory dimensions. Accordingly, little is known about the ways in which changes in molecular structure and concentration of individual odorants change odor quality. Also, currently not much is understood about synergism/antagonism, how one odorant masks or suppresses another in mixtures and there is no method for predicting which odor will be suppressed. The two main objectives of this thesis were to determine whether a part of a molecular structure rather than the whole structure plays a key role in odor quality and whether a key part of a molecule can be used to choose antagonists for that odorant. For this study three classes of musks and two potential antagonists were used. The results of the study are discussed in some detail. It is concluded that future studies of the importance of molecular structure in mixture interactions require substantially more information on the relation between structure and odor quality to allow systematic studies to be developed. In summary the two hypotheses investigated were not supported by the results. Importantly, however, they do support the view that it is likely that odor quality is dependent on the whole structure of an odorant not a single feature.
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Legha, Prem. "Molecular structure and odor mixture perception." View thesis, 2004. http://library.uws.edu.au/adt-NUWS/public/adt-NUWS20040723.142239/index.html.
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Thesis (M.Sc. (Hons)) -- University of Western Sydney, 2004.<br>"This thesis was submitted in fulfilment of the requirements for the degree of Master of Science (Hons) in the Centre for Advanced Food Research, University of Western Sydney, June 2004" Includes bibliography.
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Austin, Nick Donnelly. "Tools for Computer-Aided Molecular and Mixture Design." Research Showcase @ CMU, 2017. http://repository.cmu.edu/dissertations/894.
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This thesis explores mathematical optimization techniques to address the computeraided molecular and mixture design problems (CAMD/CAMxD). In particular, we leverage the power of mixed-integer linear programs (MILPs) to quickly and efficiently design over the massive chemical search space. These MILPs, when coupled with state-ofthe- art derivative-free optimization (DFO) methods, make for an efficient optimization strategy when designing mixtures of molecules or when considering a single molecule design problem that involves difficult thermodynamics or process models. In the first chapter, we provide a very general overview of the field of CAMD as addressed from the perspective of mathematical optimization. We discuss many relevant quantitative structure-property relationships (QSPRs) and provide constraints typically used in CAMD/CAMxD optimization problems. The second chapter introduces our DFO-based molecular/mixture design algorithm and describes how this approach enables a much greater molecular diversity to be considered in the search space as compared to traditional methods. Additionally, this chapter looks at a few case studies relevant to crystallization solvents and provides a detailed comparison of 27 different DFO algorithms for solving these problems. The third chapter introduces COSMO-RS/-SAC as alternatives to UNIFAC as the method used to capture mixture thermodynamics for a variety of CAMD/CAMxD problems. To fully incorporate COSMO-RS/-SAC into CAMD, we introduce group contribution (GC) methods for estimating a few necessary parameters for COSMO-based methods. We demonstrate the utility of COSMO-RS/-SAC in a few case studies for which UNIFAC-like methods are insufficient. In the fourth chapter, we investigate reaction solvent design using COSMO-based methods. COSMO-RS is particularly suitable for these problems as they allow for modeling of many relevant species in chemical reactions (transition states, charges, etc.) directly at the quantum level. This information can be immediately passed to the CAMD problem. We investigate a number of solvent design problems for a few difficult reactions. We summarize the work and provide a few future directions in the final chapter. Overall, this thesis serves to push the field of CAMD forward by introducing new methods to more efficiently explore the massive chemical search space and to enable a few new classes of problems which were previously untenable.
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Izadi, Homa. "A novel pseudo-azeotrope mosquito repellent mixture." Thesis, University of Pretoria, 2016. http://hdl.handle.net/2263/81873.
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Repellents play a key role in preventing mosquito-borne diseases such as malaria by reducing
human-vector contact. The general mechanism of action relies on providing a repelling vapour
around the applied area on the skin. Thus, the proper evaporation rate and consistency of the
composition of the released vapour are factors determining the performance of repellent
formulations. The formulation should evaporate fast enough to provide a sufficient level of
repellence during its life time. However, if evaporation proceeds too fast, then it will be
depleted rapidly so that activity is lost within a short period of time, which makes the repellent
inefficient.
Several controlled-release approaches have been developed to improve both the protection time
and level. However, these techniques have inherent drawbacks from the industrial point of
view. Moreover, these techniques mostly focus only on reducing the release rate, while the
consistency of the vapour composition has not been addressed.
In the present study, a novel approach towards controlling the evaporation behaviour of
repellents is proposed. It is based on engineering the molecular interactions in order to design
negative pseudo-azeotrope formulations. Negative pseudo-azeotrope mixtures are less volatile
than the pure parent components and they do not undergo separation during evaporation. The feasibility of the idea was investigated by studying the molecular structure of generally
available repellents. Among known molecular interactions, hydrogen bonding has the most
likely impact on the formation of azeotropes and in particular pseudo-azeotropes. Thus,
established repellents were classified based on their chemical structures and their capability to
take part in hydrogen bonding. Next, a simple spectroscopic method for anticipating pseudoazeotropes
formation was developed. Binary compositions of nonanoic acid and ethyl
butylacetylaminopropionate (IR3535) showed a potential for forming pseudo-azeotrope
mixtures. Hence R3535 and nonanoic acid were selected as model compounds to test the
hypothesis.
An experimental technique to confirm pseudo-azeotrope formation and to locate the
composition of the probable pseudo-azeotrope point was required. To this end, an oven test
was designed. The temporal mass loss, under an isothermal program, of a series of evaporating
mixtures was measured. Simultaneously, the Fourier transform infrared (FTIR) spectra of the
liquid remaining was recorded. Inverse analysis techniques were used to determine the
composition of remaining liquid mixtures from the recorded FTIR spectra. The oven tests
revealed that, as vaporisation progressed, the composition of the liquid remaining and the
emitted vapour converged to a fixed IR3535 content of ca. 75 mol%. Mixtures close to this
composition also featured the lowest volatility. Oven test also showed that the composition of
the liquid mixtures diverged from the fixed IR3535 content of ca. 10 mol%. Mixtures close to
this composition featured the highest volatility. These observations showed that IR3535 and
nonanoic acid forms two pseudo-azeotrope compositions, i.e. a negative pseudo-azeotrope at
an IR3535 content of ca. 75 mol%, and a positive pseudo-azeotrope at IR3535 content of ca.
10 mol%.
Thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) were applied
to check these results. TGA confirmed that the negative pseudo-azeotrope mixture is less
volatile while the positive pseudo-azeotrope is more volatile than the parent compounds. The
DSC results revealed that in comparison with the pure compounds, negative pseudo-azeotrope
had a lower boiling point onset while the positive pseudo-azeotrope had a higher boiling point.
Although negative pseudo-azeotrope repellent formulations have the desired lower constant
release rate, their repellent activity needed to be tested. This is due to the fact that mixing the ingredients to formulate a negative pseudo-azeotrope results in interactions among the
components. As a consequence, the inherent repellence effect of the compounds might have
been impaired in the mixture.
The modified arm-in-cage test was used to test the repellence of the controlled-release repellent
formulation i.e. the negative pseudo-azeotrope of the IR3535 + nonanoic acid system. Results
showed that the mixture featured improved performance with respect to both repellence
efficacy and persistence. Moreover, the negative pseudo-azeotrope also exhibited a knock
down effect, even resulting in mortality of most of the test mosquitoes.
The presence of two pseudo-azeotrope points at different composition in the IR3535 +
nonanoic acid system is a rare occurrence, analogous to double azeotropy. Thus, molecular
simulation techniques were used to explore the nature of system and the interactions
responsible for this unique behaviour. Gibbs-Monte Carlo simulation results suggest that
variations in the sizes of the molecular clusters present in the liquid at various compositions
might be responsible. They revealed that IR3535 and nonanoic acid in neat form are both highly
structured liquids. The break-down in the structure of IR3535 at high concentrations of the acid
may be the origin of increased evaporation rate and formation of the positive pseudo-azeotrope.
On the other hand, negative pseudo-azeotrope may be resulted from formation of bulkier
clusters at the ration of 3:1 (IR3535: nonanoic acid).<br>Thesis (PhD (Chemical Technology))--University of Pretoria, 2016.<br>English<br>PhD (Chemical Technology)<br>Unrestricted
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Adrien, Berthault. "Molecular simulation of mixtures in lipid bilayers." Doctoral thesis, Universitat Rovira i Virgili, 2018. http://hdl.handle.net/10803/664727.
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L'objectiu principal d'aquesta tesi doctoral és estendre un mètode ràpid i fiable (camp simple de mitjana cadena) per estudiar barreges en equilibri i en particular mescles de lípids i petits col·loides inserits en membranes lipídiques, capaços de considerar la presència de components addicionals i unir models de simulació molecular i teories elàstiques per membranes anfifíliques. Per aconseguir aquest objectiu, proposem parametritzar els paràmetres amb el mètode de camp de mitjana cadena simple per reproduir les característiques de les bicapes de lípids DMPC en equilibri comparant amb resultats de simulació publicats prèviament i dades experimentals. La tesi presenta el treball realitzat per assolir els objectius específics d'aquesta tesi doctoral: dades moleculars fiables completament parametritzats capaços de reproduir el comportament de les membranes lipídiques amb un únic tipus de component, l'estudi de les seves propietats d'equilibri interactuant amb molècules addicionals i els seus efectes en la línia de tensió per al cas específic de la creació de porus i un enfocament dinàmic per a l'estudi de la dinàmica de les membranes fetes de diverses cadenes anfifíliques, en particular en presència de porus<br>El objetivo principal de esta tesis doctoral es extender un método rápido y confiable (campo simple de media cadena) para estudiar mezclas en equilibrio y en particular mezclas de lípidos y pequeños coloides insertados en membranas lipídicas, capaces de considerar la presencia de componentes adicionales y unir modelos de simulación molecular y teorías elásticas para membranas anfifílicas. Para lograr este objetivo, proponemos parametrizar los parámetros con el método de campo de media cadena simple para reproducir las características de las bicapas de lípidos DMPC en equilibrio comparando con resultados de simulación publicados previamente y datos experimentales. La tesis presenta el trabajo realizado para alcanzar los objetivos específicos de esta tesis doctoral: datos moleculares fiables completamente parametrizados capaces de reproducir el comportamiento de las membranas lipídicas con un único tipo de componente, el estudio de sus propiedades de equilibrio interactuando con moléculas adicionales y sus efectos en la línea de tensión para el caso específico de la creación de poros y un enfoque dinámico para el estudio de la dinámica de las membranas hechas de varias cadenas anfifílicas, en particular en presencia de poros<br>The main goal of this Doctoral thesis is to extend a fast and reliable method (Single Chain Mean Field) to study mixtures at equilibrium and in particular mixtures of lipids and small colloids inserted into lipid membranes, able to consider the presence of additional components and bridge molecular simulation models and elastic theories for amphiphilic membranes. In order to achieve this objective, we proposed to parametrise the parameters for the Single Chain Mean Field method to reproduce the features of DMPC lipid bilayers at equilibrium involving comparisons with previously published simulation results and experimental data. The thesis reports the work performed to achieve the specific objectives of this doctoral thesis: reliable fully parametrised molecular details able to reproduce the behaviour of lipid membranes made of a single type of component, the study of their equilibrium properties interacting with additional molecules and their effects on the line tension for the specific case of the pore creation and a dynamical approach to study the dynamics of membranes made of various amphiphilic chains, in particular in the presence of pores.
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Sans, Amanda Dzintra. "TRANSFERABLE STEP-POTENTIALS FOR HALOGENATED HYDROCARBONS AND MIXTURE PREDICTIONS FROM SPEADMD." University of Akron / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=akron1161032534.
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Hill, Christopher Julian. "Molecular and phenotypic stress responses of Daphnia magna to selected pesticides and a binary pesticide mixture." Thesis, University of Reading, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529956.
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lehman, joshua h. "Optimizing Gas Mixture Composition for the RTPC Detector for BONuS 12 at Jefferson Lab." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/5810.
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The main objective of this thesis is to perform a study of and optimize the most direct and practical gas mixture composition inside the Radial Time Projection Chamber for the Barely-Offshell Nucleon Structure (BONuS 12) detector for use in the CLAS 12 detector in Experimental Hall B at Thomas Jefferson National Accelerator Facility (JLab). The optimization of these conditions will enhance the performance and resolution of the detector. The original BONuS 6 experiment utilized a gas composition of 80 % He and 20% Dimethyl Ether (DME). With the extensive 12 GeV energy upgrade constructed at JLab and the new BONuS 12 detector established , it is imperative that the gas composition utilized, is best suited to facilitate the experimental needs and demands. BONuS 12 is an experiment designed to measure the momentum of recoiling spectator protons down to 70 MeV/c. This technique will extract the structure function Fn 2 at large x from 0.1 up to 0.8 over a significant range in Q2 and W from the nucleon mass, with a beam energy of 11 GeV, enabling us to essentially select free neutrons.
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DI, NATALE Marilena Vita. "Impacts of weathered microplastics on bioavailability of pollutants in Paracentrotus lividus and Danio rerio: molecular and ecotoxicological approaches." Doctoral thesis, Università degli Studi di Palermo, 2022. https://hdl.handle.net/10447/560342.
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Plastic materials provide countless applications in every sector of human life, from food and health preservation to textiles and electronics industry (Cole et al., 2011;Thompson et al., 2009) which is resulting in huge amount of plastic waste. Recently, it was estimated that plastics account for the 80-90% of the whole marine litter (Derraik, 2002) and over 5 trillion microscopic plastic fragments are floating on the surface of the World Oceans (Eriksen et al., 2014).
The predominant form of marine plastic litter is called “Microplastics (MPs)", terminology by Thompson et al. 2004, used to indicate small plastic fragments, fibers and granules of microscopic size (1 μm to 5 mm in diameter). Being small in size, they are likely to be ingested and accumulate by different classes of organisms (Wright et al., 2013), even can be consumed by algae and bacteria (Mattsson et al., 2015; Bouwmeester et al., 2015). Their presence, therefore, can represent a growing threat to ecosystems and to organisms for which it can represent a hazard (Galloway and Lewis, 2016).
MPs are known to interact with a variety of chemicals in the environment through many sorption mechanisms (Yu et al., 2019). Owing to their ability to sorb xenobiotic chemicals, MPs are regarded as vectors of hazardous contaminants to aquatic organisms (Torres et al., 2021). The study of the interactions and the sorption mechanisms occurring between the sorbent (microplastic polymer) and sorbate (chemical contaminant) are important to improve our understanding of MP-mediated contaminant transfer as well as the impact of MPs on the marine environment, especially considering MPs from natural environment. MPs in natural environments undergo weathering processes due to physico-chemical interactions with environmental stress, including with biota. Over time, these stressors may lead to a progressive degradation of plastic polymers and affect their sorption capacity as well as their behavior in aquatic environments. In this context, it is key to know the bioavailable fraction able to determine a potential ecotoxicity in organisms, and to investigate the role of MPs in transferring bioavailable hazardous chemicals to aquatic biota. A multidisciplinary approach to evaluate the influence of the different factors altering plastic surface as well as to investigate the interactions behind the complex mixtures between toxicants and MPs should be considered. The aim of this chapter is to review the main MPs properties focusing particular reference on the sorption mechanisms of MPs, the factors that influence those mechanisms, the sorption behavior of a wide range of chemical contaminants and toxicity associated to combined exposures to MPs and pollutants. An overview of studies that allow relating toxicity to the sorption to MPs and help understand its importance for the bioavailability of chemical compounds is included. A pilot study carried out to evaluate the sorption, over time, of different metals and BDE-47 on a pristine model MP is described. Finally, the objectives of this thesis are presented.
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Travascio, Francesco. "Modeling Molecular Transport and Binding Interactions in Intervertebral Disc." Scholarly Repository, 2009. http://scholarlyrepository.miami.edu/oa_dissertations/322.
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Low back pain represents a significant concern in the United States, with 70% of individuals experiencing symptoms at some point in their lifetime. Although the specific cause of low back pain remains unclear, symptoms have been strongly associated with degeneration of the intervertebral disc. Insufficient nutritional supply to the disc is believed to be a major mechanism for tissue degeneration. Understanding nutrients' transport in intervertebral disc is crucial to elucidate the mechanisms of disc degeneration, and to develop strategies for tissue repair (in vivo), and tissue engineering (in vitro). Transport in intervertebral disc is complex and involves a series of electromechanical, chemical and biological coupled events. Despite of the large amount of studies performed in the past, transport phenomena in the disc are still poorly understood. This is partly due to the limited number of available experimental techniques for investigating transport properties, and the paucity of theoretical or numerical methods for systematically predicting the mechanisms of solute transport in intervertebral disc. In this dissertation, a theoretical and experimental approach was taken in order to investigate the mechanisms of solute transport and binding interactions in intervertebral disc. New imaging techniques were developed for the experimental determination of diffusive and binding parameters in biological tissues. The techniques are based on the principle of fluorescence recovery after photobleaching, and allow the determination of the anisotropic diffusion tensor, and the rates of binding and unbinding of a solute to the extracellular matrix of a biological tissue. When applied to the characterization of transport properties of intervertebral disc, these methods allowed the establishment of a relationship between solute anisotropic and inhomogeneous diffusivity and the unique morphology of human lumbar annulus fibrosus. A mixture theory for charged hydrated soft tissues was presented as a framework for theoretical investigations on solute transport and binding interactions in cartilaginous tissues. Based on this theoretical framework and on experimental observations, a finite element model was developed to predict solute diffusive-convective-reactive transport in cartilaginous tissues. The numerical model was applied to simulate the effect of mechanical loading on solute transport and binding interactions in cartilage explants and intervertebral disc.
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Guo, Xiang Yang [Verfasser], Daniel [Gutachter] Sebastiani, and Bettina G. [Gutachter] Keller. "Molecular dynamics simulations of molecules under confined geometry : from binary mixture to perfluorinated polyphile ; [kumulative Dissertation] / Xiang Yang Guo ; Gutachter: Daniel Sebastiani, Bettina G. Keller." Halle (Saale) : Universitäts- und Landesbibliothek Sachsen-Anhalt, 2020. http://d-nb.info/1227301758/34.
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Cheung, Hiu-yee Zelda, and 張曉宜. "Neuroprotection by a mixture of herbal extracts following axotomy: its effect on the molecular mechanisms ofaxotomized retinal ganglion cell death." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2002. http://hub.hku.hk/bib/B31242984.
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Cheung, Hiu-yee Zelda. "Neuroprotection by a mixture of herbal extracts following axotomy : its effect on the molecular mechanisms of axotomized retinal ganglion cell death /." Hong Kong : University of Hong Kong, 2002. http://sunzi.lib.hku.hk/hkuto/record.jsp?B25205444.
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Cai, Laizhong. "Evidence for molecular activated recombination of He single ions from particle balance measurements in helium and hydrogen mixture plasmas in PISCES A." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p3320080.
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Thesis (Ph. D.)--University of California, San Diego, 2008.<br>Title from first page of PDF file (viewed September 11, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 138-143).
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Griebel, Matthew Alexander. "Viscoelastic Anisotropic Finite Element Mixture Model of Articular Cartilage using Viscoelastic Collagen Fibers and Validation with Stress Relaxation Data." DigitalCommons@CalPoly, 2012. https://digitalcommons.calpoly.edu/theses/743.
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Experimental results show that collagen fibers exhibit stress relaxation under tension and a highly anisotropic distribution. To further develop the earlier model of Stender [1], the collagen constituent was updated to reflect its intrinsic viscoelasticity and anisotropic distribution, and integrated with an existing mixture model with glycosaminoglycans and ground substance matrix. A two-term Prony series expansion of the quasi-linear viscoelastic model was chosen to model the viscoelastic properties of the collagen fibers. Material parameters were determined by using the simplex method to minimize the sum of squared errors between model results and experimental stress relaxation data of tissue in tension. Collagen elastic fiber modulus was calculated by fitting to the equilibrium data and viscoelastic parameters were determined by fitting to the relaxation curve. Results of newborn (~1-3 week old) untreated bovine articular cartilage explants from the patellar femoral groove as well as explants cultured in transforming growth factor-β1 (TGF-β1), from both the superficial (~0-0.5 mm from the articular surface) and middle (~0.5-1.0 mm from the articular surface) layers were compared to examine the effects of TGF- β1. TGF-β1 has been shown to maintain or even enhance mechanical properties of articular cartilage in compression and tension [2, 3] and this study continues with the hope that it may be used to improve tissue engineering of mature cartilage to better survive implantation in vivo for the successful repair of articular cartilage defects. Results show that TGF-β1 has a maturational effect on collagen, causing the tissue to become stiffer through an increase in elastic collagen fiber modulus and less viscous through shorter relaxation time and less stress relaxation (tissue retained a higher percentage of residual stress). The results of this study further advance the understanding of the effects of location and treatment with TGF-β1.
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DI, LEO SIMONE. "SELECTIVE ASSEMBLY, PHASE TRANSITIONS AND MOLECULAR KINETICS OF DNA OLIGOMERS." Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/923222.
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In the last few years it has been shown that the spontaneous self-assembly process of short DNA and RNA duplexes into liquid crystal ordering is a likely potential route that led to the formation of first nucleic acids able to support biological activities. In particular, it has been experimentally demonstrated that liquid crystal domains behave as suitable micro-reactors to trigger polymerization between the stacked and not initially chemically linked short nucleic acids. Even paired mononucleotides at high enough concentration exhibit liquid crystal ordering, unveiling the crucial role of Watson-Crick selectivity and stacking attractive interactions among base pairs. In such a possible prebiotic context, DNA sequences with both random nucleobases sequence and length are likely to be formed. Surprisingly, it has been shown that even random DNA sequence of fixed length can support liquid crystal ordering at high concentration.
The aim of this PhD thesis is to extend the knowledge of DNA liquid crystals self-assembly in the following four directions.
First, I explored the selectivity of interaction in nucleic acids solutions of random-sequence DNA oligomers of different length L. The combination of experimental results and a suitable developed theoretical model revealed a not negligible percentage of perfect duplexes.
Second, I investigated the process that leads to the onset of the nematic liquid crystal phase in aqueous solutions of DNA duplexes. The combination of static light scattering experiments and computer simulations made possible the study of both aggregation and local ordering of DNA duplexes in the isotropic phase, where no positional order is developed, and in proximity of the isotropic-nematic phase boundary. This study gives an insight of the role on the development of local orientational order among DNA duplexes both far and in proximity of the isotropic-nematic phase boundary.
Third, I studied the diffusion of short DNA duplexes with attractive and repulsive interactions in the isotropic phase as a function of temperature. I found that the temperature dependence of diffusion coefficients reflects via an Arrhenius law the interduplex attractive interactions, whereas diffusion of repulsive duplexes is partially well described in terms of repulsive hard spheres.
Fourth, I investigated phase diagrams of mixtures of DNA single strands and duplexes with various polycations that show liquid-liquid phase separations. This phenomena leads to the onset of a concentrated but still liquid phase of polyelectrolytes, called coacervate, in a bulk phase where polyelectrolytes are diluted. The most surprising result I found, it is the insurgence of liquid crystals in coacervates with 12 nucleobases long random DNA oligomers and polylysine at different ionic strengths.
I believe that this PhD thesis adds important pieces to the self-assembly of nucleic acids puzzle, and in particular it shows how randomness of nucleic acids is not an impasse to both hybridization of defectless duplexes and liquid crystal ordering.
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Westerlund, Annie M. "Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles." Licentiate thesis, KTH, Biofysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-234888.
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Ca2+ and calmodulin play important roles in many physiologically crucial pathways. The conformational landscape of calmodulin is intriguing. Conformational changes allow for binding target-proteins, while binding Ca2+ yields population shifts within the landscape. Thus, target-proteins become Ca2+-sensitive upon calmodulin binding. Calmodulin regulates more than 300 target-proteins, and mutations are linked to lethal disorders. The mechanisms underlying Ca2+ and target-protein binding are complex and pose interesting questions. Such questions are typically addressed with experiments which fail to provide simultaneous molecular and dynamics insights. In this thesis, questions on binding mechanisms are probed with molecular dynamics simulations together with tailored unsupervised learning and data analysis. In Paper 1, a free energy landscape estimator based on Gaussian mixture models with cross-validation was developed and used to evaluate the efficiency of regular molecular dynamics compared to temperature-enhanced molecular dynamics. This comparison revealed interesting properties of the free energy landscapes, highlighting different behaviors of the Ca2+-bound and unbound calmodulin conformational ensembles. In Paper 2, spectral clustering was used to shed light on Ca2+ and target protein binding. With these tools, it was possible to characterize differences in target-protein binding depending on Ca2+-state as well as N-terminal or C-terminal lobe binding. This work invites data-driven analysis into the field of biomolecule molecular dynamics, provides further insight into calmodulin’s Ca2+ and targetprotein binding, and serves as a stepping-stone towards a complete understanding of calmodulin’s Ca2+-dependent conformational ensembles.<br><p>QC 20180912</p>
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Vašíčková, Kamila. "Interakce tenzidů se směsí hyaluronanů o různé molekulové hmotnosti." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2012. http://www.nusl.cz/ntk/nusl-216904.
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The behavior of the system consisted by mixture of two different molecular weight hyaluronates and surfactant was investigated. Mixtures were 17 kDa hyaluronate with 1,46 MDa, 73 kDa with 1,46 MDa, 300 kDa with 1,46 MDa, 806 kDa with 1,46 MDa and 1800 kDa with 1,46 MDa. These compounds were always mixed in the weight ratios 70:30, 50:50 and 30:70. As the surfactant cetrimonium bromide and TWEEN 20 were used. Interactions were studied in aqueous solution with different ionic strength. Sudan red was used as hydrophobic dye. In all experimental series with cetrimonium bromide was observed phenomenon of discontinuous separated phases, described as pearls. Samples containing pearls were tested on stability, were dried and rehydrated back, as were also heated in solution. Subsequently, the particle size was measured in the remaining sample after pearls were filtrated. Mixtures of hyaluronate were characterized by measuring the viscosity using rheology microrheology. It was found that these compounds are heterogeneous and each sample point is not the same viscosity.
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Smortsova, Yevheniia. "Dye sensitized solar cells efficiency improvement : optimization of the electrolyte using ionic liquids/molecular solvents mixture and study of the photodynamic properties of organic indolinic derivative dyes." Thesis, Lille 1, 2018. http://www.theses.fr/2018LIL1R061/document.
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Parmi les énergies renouvelables, l’énergie solaire est la plus puissante. L’élément clé des DSSCs est le photosensibiliseur, par lequel la génération de photocourant est possible. L’autre élément important est l’électrolyte. Les liquides ioniques (Ils) sont utilisés en tant qu’électrolytes dans les DSSCs du fait de leurs propriétés chimiques: pression de vapeur basse, haute résistance thermique et chimique, polarité et phase modulables, etc. L’objectif de cette thèse est de comprendre les processus photophysiques dans les colorants dérivés d’indolines dans les solvants moléculaires (MS) et les mélanges IL/MS. L’influence du solvant sur les propriétés spectroscopiques de D131, D102, D149 and D205 est d’abord étudiée par spectroscopie stationnaire d’absorption et de fluorescence. Ensuite, la spectroscopie résolue en temps est employée pour étudier leur photophysique et sa dépendance au solvant. Ces expériences ont permis de démontrer l’influence des paramètres d'aptitude de donneur de liaison hydrogène et d'accepteur de liaison hydrogène des solvants. Le rôle majeur de la dynamique de solvatation dans la dynamique des états excités de ces colorants a été montré. Ce phénomène a été suivi dans les mélanges IL/MS en utilisant une sonde fluorescente classique, C153, et des techniques de fluorescence résolues en temps et de dynamique moléculaire. Les réponses de solvatation multi-régimes de ces mélanges sont dirigées par le renforcement de la liaison hydrogène entre la sonde et les composants des mélanges. Les résultats de cette these apportent beaucoup à la compréhension des processus photophysiques fondamentaux régissant les sensibiliseurs et les électrolytes dans les DSSCs<br>Among all the renewable energy sources, solar energy is the most powerful source far ahead wind or geothermal energies. The first key component of DSSCs is the photosensitizer. It is through this component that the most important steps of photocurrent generation are possible. On the other hand, ionic liquids (ILs) have been proposed as electrolyte for DSSCs due to their peculiar properties: low vapor pressure, high thermal and chemical robustness, tunability of polarity and phase behaviour etc. The objective of this thesis was to get an understanding of the photophysics in the indoline derivated dyes in molecular solvents (MS) and in the IL/MS mixtures. Firstly, the solvent dependence of the spectroscopic properties of D131, D102, D149 and D205 was studied by the steady-state UV-Vis absorption and fluorescence spectroscopy. Then, time-resolved spectroscopy was used to elucidate their photophysics and its solvent dependence. These experiments helped to discern the influence of the hydrogen bond donor and acceptor abilities of the solvent. The solvation dynamics was shown to play a major role in the excited state dynamics of these dyes. This process in IL/MS mixtures was elucidated using the classic fluorescent probe C153 by the means of time-resolved spectroscopy and MD simulations. The complex multi-regime solvation response in these systems was shown to be shaped by the strengthening of the hydrogen bonding between the probe and the mixture components. The results of this thesis work contribute to the fundamental understanding of the photodynamics of the sensitizer and the response of the electrolyte used in the DSSCs
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Seehamart, Kompichit. "Investigation of the diffusion mechanisms of several hydrocarbons in the Metal-Organic-Framework Zn(tbip)." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-68125.
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Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. The reasons for this influence are investigated with the aid of probability density plots, free energy landscapes and barriers, along with a determination of the structural changes accompanying increasing c. It is found that for flexible lattices, the tighter, more constrained parts of the channels become wider at higher c; this allows more molecules to diffuse in the central region of the channels.
The investigations for Zn(tbip) have been extended to three equimolar mixtures of ethane/ethane, CO2/ethane and CO2/methanol. The simulations take into account the lattice flexibility. The diffusional characteristics are discussed in relation to molecule properties and lattice geometry. The results show that Zn(tbip) may be a useful material for separating methane/ethane and CO2/ethane mixtures at low concentrations, and CO2/methanol mixtures at high concentrations.
The temperature and concentration dependence of the self-diffusivity of propane diffusion in Zn(tbip) have been investigated as well by performing normal MD and hyper-MD with bias potential simulations. The obtained temperature dependence of the self-diffusivities is analyzed using an Arrhenius relationship, yielding the activation energy to be 9.53 kJ/mol and the pre-exponential factor to be 4.48×10-9 m2s-1. Using this hyper-MD method, interesting mechanisms of the propane molecules able to pass each other and exchange their sites in the channels can be observed. Because of mutual hindrance of propane molecules, the propane self-diffusivities decrease with increasing concentration.
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Olsson, Gustaf D. "Fundamental Studies of Molecular Interactions in Complete Prepolymerization Mixtures of Molecularly Imprinted Polymers." Thesis, University of Kalmar, School of Pure and Applied Natural Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:hik:diva-2366.
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<p>In the present work, molecular dynamics simulations were used to evaluate the molecular interactions in prepolymerization mixtures, as occurring during production of molecularly imprinted polymers. The systems simulated were produced based on earlier studies for reference of results. Four systems were simulated in order to investigate the effect on molecular interactions based upon the choice of porogen (acetonitrile or chloroform) and proton transfers. The systems consisted of phenylalanine anilide as template, methacrylic acid as functional monomer, ethylene glycol dimethacrylate as crosslinker and 2,2’-azobis-(2-methylpropionitrile) as radical initiator, with either acetonitrile or chloroform as porogen. Trajectories from the simulations were evaluated through radial distribution function analysis, grid density analysis and hydrogen bond analysis to investigate molecular interactions and complex formations in the simulated complete prepolymerization mixtures. Focus was on functional monomer-template, crosslinker-template and template-template complex formations. The results showed that the porogen influences molecular interactions in complete prepolymerization mixtures. Formation of higher order complexes was confirmed in all of the systems involving all of the investigated molecular species in the prepolymerization mixtures. The results could also confirm the presence of previously observed complexes between functional monomer and template (2:1 and 1:1 stoichiometry) and the prevalence of template dimerization, as well as a high involvement of crosslinker in complex formation.</p>
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Pillai, Mahesh R. "The Effect of a 2,2',4,4'-Tetrachlorobiphenyl (PCB 47) and 3,3',4,4'-Tetrachlorobiphenyl (PCB 77) Mixture on Enzymes Involved in the Synthesis of Catecholamines in the Rat Adrenal Gland." Bowling Green, Ohio : Bowling Green State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=bgsu1214235690.
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Zhao, Yue. "Etude de l'orientation dans les melanges compatibles de polymeres a base de poly(methyl methacrylate)." Paris 6, 1987. http://www.theses.fr/1987PA066673.
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Les travaux ont porte sur l'oriention et la relaxation de chaine du polymethacrylate de methyle et des melanges avec des polymeres compatibles lors de l'etirage au-dessus de la temperature de transition vitreuse
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Winters, Ian Douglas. "The rheological and structural properties of blends of polyethylene with paraffin wax." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45833.
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This research addresses and illuminates a little understood region of miscible polymer mixtures and demonstrates a new means of separating wax from such blends. The method, termed Deformation Induced Phase Segregation potentially eliminates need of toxic processing solvents for wax removal or recovery in these types of blends.
Previous theories of polymer combinations address them exclusively as solutions or as blends, two independent classes having very different behaviors. This study provides bridge connecting these two classes by identifying crossover points between them and the behaviors exhibited therein. The blends of this form were found to be semi-miscible, forming a homogenous phase in the melt but a two-phase system in the solid, with the rheological behavior influenced by the polymer's molecular weight and architecture. It also demonstrates practical promise of this regime by introducing a mechanical compression process to separate the wax phase from such a type of blend. This process potentially permits production of ultra-high molecular weight polyethylene (UHMwPE) films and fibers by melt processing, thereby obviating need of otherwise essential but expensive and environmentally unfriendly toxic solvents.
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Vieira, Mariano George Sousa. "Chemical study of two Xylopia species and resolution of natural products by matrix assisted diffusion ordered spectroscopy (MAD)." Universidade Federal do CearÃ, 2014. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=13132.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel Superior<br>Conselho Nacional de Desenvolvimento CientÃfico e TecnolÃgico<br>Xylopia nitida and Xylopia sericea are commonly known as âembira-brancaâ and âpimenta do sertÃoâ, respectively, belonging to Annonaceae family. The chromatographic analysis of X. nitida roots allowed isolation of a trachlyobane diterpene, ent-trachlyoban-18,19-diol and its acetylated product, ent-18,19-diacetoxy-trachylobane, a kaurene diterpene, ent-kaur-16-en-18,19-diol, two aporphinic alkaloids, 5,6,6a,7-tetrahydro-1-methoxy-(6aS)-4H-benzo[de][1,3]benzodioxolo[5,6-g]quinoline e xylopine, and a glucoside, named 1-O-ethyl-β-D-glucopiranose. Also using chromatographic analysis of X. sericea fruits were obtained a kaurane diterpene, kauran-16β-ol and a diterpenes mixture, ent-kaur-16-en-19-oic acid and beyer-15-19-oic acid. The structures of these compounds were elucidated by spectroscopic studies (IR, MS and NMR). In the second part of this work, has been showed the diffusion-ordered spectroscopy (DOSY) as a powerful tool in natural product mixture analysis. The assignment of NMR signals to specific components in a mixture is a challenging task. DOSY has provided important progress in this area, allowing the signals originating from individual components of different molecular sizes to be distinguished. However, when the sizes of the compounds are similar and/or the spectra are overlapped, signal assignment can easily become intractable. The use of a co-solute in a matrix-assisted DOSY (MAD) experiment can be a useful solution, improving diffusional (and sometimes spectral) resolution by exploiting selective binding to the matrix. The challenge is to apply MAD to molecules with high structural similarity, for example in natural product mixtures. Various surfactants, including SDS, AOT and CTAB have previously been shown to be effective in MAD analysis. Here we present an important addition, the Brij family of nonionic surfactants. We demonstrate the use of Brij micelles and other systems in mixed solvents with a variety of mixtures relevant to natural products.<br>Xylopia nitida e X. sericea, conhecidas popularmente como embira-branca e pimenta do sertÃo, respectivamente, sÃo espÃcies pertencentes à famÃlia Annonaceae. A anÃlise cromatogrÃfica dos extratos hexÃnico e etanÃlico das raÃzes de X. nitida possibilitou o isolamento de um diterpeno de esqueleto traquilobano, ent-traquiloban-18,19-diol e seu derivado acetilado, ent-18,19-diacetÃxi-traquilobano, um diterpeno de esqueleto caureno, ent-caur-16-en-18,19-diol, dois alcalÃides aporfÃnicos, 5,6,6a,7-tetraidro-1-metoxi-(6aS)-4H-benzo[de][1,3]benzodioxolo[5,6-g]quinolina e xylopina e um glicosÃdeo, 1-O-etil-β-D-glicopiranose, todos de carÃter inÃdito na literatura, exceto os dois Ãltimos. AtravÃs da anÃlise cromatogrÃfica do extrato hexÃnico dos frutos de X. sericea foi possÃvel obter um diterpeno de esqueleto caurano denominado cauran-16β-ol e uma mistura de diterpenos, Ãcido ent-caur-16-en-19-Ãico e Ãcido beier-15-en-19-Ãico. O isolamento dos constituintes quÃmicos presentes nos extratos da raiz e frutos de X. nitida e X. sericea, respectivamente, foi realizada por mÃtodos cromatogrÃficos convencionais e a determinaÃÃo estrutural das substÃncias isoladas foi realizada a partir de mÃtodos espectromÃtricos como: IV, EM, RMN 1H, 13C e DEPT 135 incluindo tÃcnicas bidimensionais como, COSY, HSQC e HMBC. A primeira parte deste trabalho relata o estudo quÃmico das raÃzes de X. nitida e dos frutos de X. sericea. A espectroscopia ordenada por difusÃo ou DOSY (Diffusion Ordered Spectroscopy) provà um meio para uma âseparaÃÃo virtualâ de compostos, atravÃs de um mapa bidimensional onde em um eixo temos o deslocamento quÃmico e em outro observamos o coeficiente de difusÃo (D) das molÃculas na mistura. A separaÃÃo de sinais somente à possÃvel quando espÃcies difundem a diferentes velocidades. Na quÃmica de produtos naturais, frequentemente nos deparamos com misturas de compostos quimicamente semelhantes e de tamanhos muito similares, o que torna limitado o experimento DOSY tradicional. Entretanto, o coeficiente de difusÃo das substÃncias pode ser modificado pela adiÃÃo de co-solutos e/ou co-solventes, surgindo a partir daà a espectroscopia ordenada por difusÃo assistida por matriz (matrix-assisted DOSY ou MAD). VÃrios surfactantes, incluindo SDS, AOT e CTAB tÃm se mostrado efetivos em anÃlises por MAD. Neste trabalho, experimentos MAD foram realizados com algumas misturas de produtos naturais com similaridades estruturais utilizando o Ãcido perfluoro-octanÃico (PFOA), polivinilpirrolidona (PVP) e os surfactantes Brij 78 e 98, que por sua vez, ainda nÃo haviam sido utilizados para esse propÃsito. NÃs tambÃm demonstramos a formaÃÃo de micelas de Brij 78 e 98 em misturas dos solventes DMSO-d6 e D2O.
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Dixit, Sanhita. "Molecular models of hydration in methanol-water mixtures." Thesis, University of Edinburgh, 2002. http://hdl.handle.net/1842/10880.
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The work presented in this thesis addresses the issue of hydration of a simple amphiphile-like molecule; methanol. High-resolution Raman spectroscopy is used to study methanol-water mixtures over the whole concentration range. A highly non-linear dependence of the carbon-oxygen and carbon-hydrogen stretching frequencies with composition is observed. The data suggest the first global picture of the progressive hydration of methanol: water first breaks up the molecular chains which exist in pure methanol, and then completely hydrates the hydroxyl groups before solvating in hydrophobic methyl groups. In order to corroborate this proposed picture, neutron diffraction experiments using hydrogen/deuterium substitution were performed on a concentrated methanol in water mixture (70 mole% methanol : 30 mole% water) and a dilute methanol in water mixture (5 mole% methanol : 95 mole% water). The diffraction data were modelled using the Empirical Potential Structural Refinement technique. In the concentrated mixture, although there is insufficient water for the classical hydrophobic mechanism to operate, the structural effects observed are consistent with those that might be expected in a hydrophobically driven system. An unexpected reduction is found in the methyl-methyl contact distance compared to pure methanol, which corresponds to an overall compressive effect apparently driven by hydrogen bonding of the added water to the alcohol hydroxyl groups. Surprisingly, the water structure is largely preserved in this mixture. The results obtained provide unambiguous evidence for the preferential interaction of the methanol hydroxyl group with water and suggest that hydrogen bonding interactions between water and polar groups of amphiphilic molecules may be more important than previously thought.
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Bemrose, Richard Antony. "A molecular dynamics study of liquid crystal mixtures." Thesis, Sheffield Hallam University, 1999. http://shura.shu.ac.uk/19339/.
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Results are presented from molecular dynamics simulations of binary liquid crystal mixtures using a generalisation of a well established Gay-Berne intermolecular potential. The simulations are undertaken in both the microcanonical (NVE) and the isoenthalpic-isobaric (NPH) ensembles. Firstly a 50:50 mixed system is simulated in the NVE ensemble containing generalised Gay-Berne (GGB) rod-like molecules with length to breadth axial ratios of 3.5:1 (molecules A) and 3:1 (molecules B). The molecules in this system differs only slightly from the well-characterised Gay-Berne (GB) potential with length to breadth ratio of 3:1. It is shown that the system exhibits isotropic (/), nematic (N) and smectic-B (SmB) phases with both the I-N and N-SmB phase boundaries not clearly defined. Competition between two density waves parallel to the director of the same wavelength but different phase lead to a pre-smectic ordering preceding the N-SmB phase transition. The longer molecules are shown to have a consistently higher order parameter the difference being greatest in the nematic phase and decrease with lowering temperature. Although a degree of local ordering is shown within each smectic layer the smectic phase is fully commensurate. Secondly, phase behaviour diagrams are presented from a series of constant-NPH simulations over a range of pressures and concentrations. The binary mixtures exhibit a rich phase behaviour, displaying isotropic, nematic, smectic-A (SmA), induced smectic-A and smectic-B phases depending on the choice of pressure and concentration. It is shown that the temperature range over which the nematic phase is stable can be extended greater than either homogeneous system by elevating the system pressure and/or by choice of concentration, agreeing with experimental results. The mixture exhibits a stable SmA island at a mole fraction of xa = 0.50 depending on the choice of pressure and a narrow induced SmA phase at xa = 0.25.
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García, Ramírez Marcela. "MMélanges cellulose-polyamide 66 : morphologie des phases, miscibilité et mobilité moléculaire." Université Joseph Fourier (Grenoble), 1994. http://www.theses.fr/1994GRE10060.
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Cette etude porte sur la mise en uvre et la caracterisation de melanges a base de cellulose et polyamide 66. Ces materiaux ont ete prepares par le procede de dissolution-coagulation en utilisant comme solvant commun, un melange de n-oxyde de n-methyl morpholine et de phenol. La caracterisation des materiaux a ete realisee a l'aide de differentes techniques telles que la microscopie electronique a balayage, la diffraction des rayons x, la calorimetrie differentielle a balayage, la resonance magnetique nucleaire a haute resolution et la spectrometrie mecanique-dynamique. Les melanges cellulose/polyamide 66 forment principalement un systeme heterogene. La separation de phases se produit lors du melange des deux solutions de cellulose et de polyamide. Elle s'accompagne de la cristallisation du polyamide. Cependant, une miscibilite partielle entre ces polymeres a ete mise en evidence. Elle se traduit par une diminution de l'enthalpie de fusion du polyamide et par une augmentation de la temperature de transition vitreuse de sa phase amorphe. La spectrometrie mecanique a ete utilisee pour mesurer la mobilite moleculaire dans la phase amorphe riche en polyamide, en tenant compte des effets de couplage mecanique entre les phases. Les resultats ont ete confrontes a une analyse theorique de cette mobilite developpee pour les polymeres amorphes. Cette miscibilite est une consequence de la presence de liaisons hydrogene entre la cellulose et le polyamide 66. Il en resulte une bonne compatibilite entre les polymeres, conduisant a de bonnes proprietes mecaniques en traction
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Berryman, P. J. "Molecular dynamics simulations of ethanol and ethanol-water mixtures." Thesis, University of Surrey, 2006. http://epubs.surrey.ac.uk/804937/.
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Binder, Kurt, Subir K. Das, Michael E. Fisher, Jürgen Horbach, and Jan V. Sengers. "Interdiffusion in critical binary mixtures by molecular dynamics simulation." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-193274.
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A simulation study of the static and dynamic critical behavior of a symmetric binary Lennard-Jones mixture is briefly reviewed. Using a combination of semi-grand-canonical Monte Carlo (SGMC) and molecular dynamics (MD) methods near the critical temperature of liquid-liquid unmixing, the correlation length and “susceptibility” related to the critical concentration fluctuations are estimated, as well as the self- and interdiffusion coefficients. While the self-diffusion coefficient does not show a detectable critical anomaly, the interdiffusion coefficient is found to vanish when one approaches the critical temperature at fixed critical concentration. It is shown that in the corresponding Onsager coefficient both a divergent singular part and a nonsingular background term need to be taken into account. With appropriate finite-size scaling analysis (the particle numbers studied for the dynamics lie only in the range from N = 400 to 6400), the critical behavior of the interdiffusion coefficient is found to be compatible both with the theoretically predicted behavior and with corresponding experimental evidence.
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Binder, Kurt, Subir K. Das, Michael E. Fisher, Jürgen Horbach, and Jan V. Sengers. "Interdiffusion in critical binary mixtures by molecular dynamics simulation." Diffusion fundamentals 6 (2007) 10, S. 1-12, 2007. https://ul.qucosa.de/id/qucosa%3A14184.
Full textAbstract:
A simulation study of the static and dynamic critical behavior of a symmetric binary Lennard-Jones mixture is briefly reviewed. Using a combination of semi-grand-canonical Monte Carlo (SGMC) and molecular dynamics (MD) methods near the critical temperature of liquid-liquid unmixing, the correlation length and “susceptibility” related to the critical concentration fluctuations are estimated, as well as the self- and interdiffusion coefficients. While the self-diffusion coefficient does not show a detectable critical anomaly, the interdiffusion coefficient is found to vanish when one approaches the critical temperature at fixed critical concentration. It is shown that in the corresponding Onsager coefficient both a divergent singular part and a nonsingular background term need to be taken into account. With appropriate finite-size scaling analysis (the particle numbers studied for the dynamics lie only in the range from N = 400 to 6400), the critical behavior of the interdiffusion coefficient is found to be compatible both with the theoretically predicted behavior and with corresponding experimental evidence.
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Voigt, Arne-Christian. "Heteronuclear Molecules from a Quantum Degenerate Fermi-Fermi Mixture." Diss., lmu, 2009. http://nbn-resolving.de/urn:nbn:de:bvb:19-106171.
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Olsen, Michele Lynn. "Experiments with Feshbach molecules in a Bose-Fermi mixture." Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3337140.
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Fu, Guopeng. "Molecular Complexation and Phase Diagrams of Urea/Polyethylene Glycol Mixtures." University of Akron / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=akron1366631616.
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Ahmadi, Aphrodite. "Hydrodynamics and rheology of mixtures of biopolymers and molecular motors." Related electronic resource: Current Research at SU : database of SU dissertations, recent titles available full text, 2008. http://wwwlib.umi.com/cr/syr/main.
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Chen, Feng. "Molecular dynamics simulations of solution mixtures and solution/vapor interfaces." Diss., Manhattan, Kan. : Kansas State University, 2010. http://hdl.handle.net/2097/2421.
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Vaz, Graça Raquel Veiga. "Experimental measurement and molecular dynamics simulation of diffusivities in supercritical mixtures." Doctoral thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/14917.
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Doutoramento em Engenharia Química<br>This work focuses diffusivities due to their importance in the design and
simulation of rate-controlled processes. Three approaches are followed:
phenomenological modeling through the development of predictive
macroscopic models, molecular dynamics simulations, and experimental
measurement by the chromatographic peak broadening technique.
Self-diffusion coefficients of model and real fluids were firstly studied using
entropy based scaling laws. Rosenfeld, Dzugutov and Bretonnet expressions
were tested using a large database previously compiled, involving 1727 data
points. It was shown that they fail in the entire range of density and
temperature, and that diffusivity depends not only on residual entropy but also
on the size/geometry of the molecule (through a chain size parameter). For
these reasons, a new universal correlation using artificial neural networks was
proposed, which relates self-diffusivities with residual entropy and chain size
parameter. It is valid for both model and real fluids, whether spherical or
asymmetrical, polar or non-polar (global AARD = 9.13%). Moreover, a simple
analytical expression was devised for spherical systems, and provides only
4.61% of error based uniquely on residual entropy.
Three modified hydrodynamic expressions were proposed to accurately
estimate tracer diffusivities (D12) in supercritical carbon dioxide (SC-CO2),
based on the Wilke-Chang, Scheibel and Lusis-Ratcliff equations. They relate
D12 with the ratio between temperature and solvent viscosity (T/η1), and solute
molar volume at normal boiling point (Vbp), as in the original models. The
introduction of two universal constants reduce the average errors from [11.70–
23.16]% to [8.26–8.51]% for a large database of 150 systems and 4484 data
points over wide ranges of temperature and pressure.
In an attempt to adopt more reliable solute properties, four improved Stokes-
Einstein based models were devised by modifying Wilke-Chang, Scheibel,
Lusis-Ratcliff, and Tyn-Calus equations, where Vbp values were substituted by
critical volumes. They achieve similar results to the previous approach (AARD
= 7.86-8.56%) for an equivalent database. Further statistics confirmed the good
and sturdy nature of these models to accurately predict tracer diffusivities in
SC-CO2 for any kind of solute.
Another predictive model was developed for supercritical systems, combining
two terms – background plus singular – to accurately estimate diffusivities not
only far but also near the critical point, where asymptotic behavior is observed.
The model achieves an average error of 6.20% for a large database,
performing equally well for polar and non-polar solutes, and in the whole
pressure-temperature plane, while expressions from literature deliver 11.62-
75.17% errors.
Molecular dynamics simulations were performed to study the diffusivities of
propanone, butanone, 2-pentanone and 3-pentanone in SC-CO2. They were
computed using Einstein formula, and their dependence on temperature,
pressure (or density), and molecular size was analyzed. A local structural
analysis was further accomplished by calculating some radial distribution
functions and coordination numbers to disclose and interpret the local
environment of CO2 around each group composing ketone molecules.
An experimental setup to measure diffusion coefficients by chromatographic
peak broadening technique was designed, assembled and tested. Tracer
diffusivities of α-pinene in SC-CO2 were determined at 313.15, 323.15 and
333.15 K, and pressures from 175 to 275 bar. The dependency of D12 upon
temperature, pressure, solvent density, and hydrodynamic behavior has been
examined in detail. Finally, the experimental data were modeled using
equations developed in this work and good results were obtained (AARD = 2.48 – 3.56%); well-known expressions from the literature were also considered.<br>Neste trabalho estudaram-se coeficientes de difusão devido à sua importância
no projeto e simulação de processos conduzidos por cinética. Foram seguidas
três abordagens: modelação fenomenológica através do desenvolvimento de
modelos macroscópicos preditivos, simulações de dinâmica molecular e
medição experimental pela técnica cromatográfica de abertura de pico.
Os coeficientes de autodifusão foram primeiramente focados, analisando-se
leis de redução baseadas na entropia residual. As expressões de Rosenfeld,
Dzugutov e Bretonnet foram testadas usando uma extensa base de dados
compilada previamente, envolvendo 1727 pontos. Mostrou-se que estas
equações falham em toda a gama de densidade e temperatura, e que a
difusividade depende não só da entropia residual mas também do
tamanho/geometria da molécula (através de um parâmetro que caracteriza o
tamanho da cadeia). Por estas razões propôs-se uma correlação universal
baseada em redes neuronais, que relaciona os coeficientes de autodifusão
com a entropia residual e o parâmetro de tamanho da molécula. Esta é válida
para fluidos modelo e reais, quer sejam moléculas esféricas ou não esféricas,
polares ou apolares (AARD global = 9.13%). Para além disso, uma expressão
analítica simples foi desenvolvida para sistemas esféricos, baseada apenas na
entropia residual, dando origem um erro médio de 4.61%,
Três expressões hidrodinâmicas modificadas foram propostas para estimar
com exatidão difusividades binárias a diluição infinita (D12) em dióxido de
carbono supercrítico (SC-CO2), baseadas nas equações de Wilke-Chang,
Scheibel e Lusis-Ratcliff. Estas relacionam D12 com a razão entre a
temperatura e a viscosidade do solvente (T/η1), e com o volume molar do
soluto à temperatura normal de ebulição (Vbp), tal como o fazem os modelos
originais. A introdução de duas constantes universais reduziu os erros médios
de [11.70–23.16]% para [8.26–8.51]%, calculados para uma extensa base de
dados de 150 sistemas e 4484 pontos experimentais, varrendo gamas largas
de pressão e temperatura.
Com o objetivo de se utilizar propriedades de soluto mais plausíveis, foram
propostos quatro modelos baseados na relação de Stokes-Einstein,
modificando as equações de Wilke-Chang, Scheibel, Lusis-Ratcliff e Tyn-
Calus, onde os valores de Vbp foram substituídos por volumes críticos. Estas
fornecem resultados similares aos da abordagem anterior (AARD = 7.86-
8.56%) para uma base de dados equivalente. O cálculo de outras grandezas
estatísticas permitiu confirmar a solidez destes modelos para prever
difusividades binárias de quaisquer solutos em SC-CO2.
Foi proposto outro modelo preditivo para sistemas supercríticos, combinando
dois termos – regular e singular – para estimar corretamente difusividades não
apenas longe mas também junto ao ponto crítico, onde se sabe existir um
comportamento assimptótico de D12. O modelo fornece um erro médio de
6.20% para toda a base de dados, com bom desempenho para solutos polares
e não polares em toda a gama pressão-temperatura, enquanto as expressões
da literatura atingem erros de 11.62-75.17%.
Foram efetuadas simulações de dinâmica molecular para estudar as
difusividades de propanona, butanona, 2-pentanona e 3-pentanona em SCCO2.
Estas foram calculadas usando a relação de Einstein, e as suas
dependências com a temperatura, pressão (ou densidade) e tamanho
molecular foram analisadas. Foi ainda conduzida uma análise estrutural local
dos sistemas através do cálculo de funções distribuição radial e números de
coordenação, para discriminar e interpretar o ambiente local do CO2 em torno
de cada grupo que compõe as moléculas de cetona.
Foi concebida, instalada e testada uma instalação experimental para medir
coeficientes de difusão pelo método cromatográfico de abertura de pico. Foram
determinadas difusividades de α-pineno a diluição infinita em SC-CO2 a
313.15, 323.15 e 333.15 K, e pressões entre 175 e 275 bar. Examinou-se em
pormenor a dependência de D12 com a temperatura, pressão e densidade do
solvente, e o seu comportamento hidrodinâmico. Por fim, os valores
experimentais foram modelados usando equações desenvolvidas neste
trabalho e obtiveram bons resultados (AARD = 2.48 – 3.56%); foram também
consideradas expressões bem conhecidas da literatura.
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Schnabel, Thorsten. "Molecular modeling and simulation of hydrogen bonding pure fluids and mixtures." Berlin Logos-Verl, 2008. http://d-nb.info/990567303/04.
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Haughney, Michael Francis. "A molecular dynamics study of selected polar liquids and their aqueous mixtures." Thesis, University of Cambridge, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.254062.
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Marla, Krishna Tej. "Molecular Thermodynamics of Nanoscale Colloid-Polymer Mixtures: Chemical Potentials and Interaction Forces." Diss., Georgia Institute of Technology, 2004. http://hdl.handle.net/1853/7604.
Full textAbstract:
Nanoscale colloidal particles display fascinating electronic, optical and reinforcement properties as a consequence of their dimensions. Stable dispersions of nanoscale colloids find applications in drug delivery, biodiagnostics, photonic and electronic devices, and polymer nanocomposites. Most nanoparticles are unstable in dispersions and polymeric surfactants are added generally to improve dispersability and control self-assembly. However, the effect of polymeric modifiers on nanocolloid properties is poorly understood and design of modifiers is guided usually by empirical approaches. Monte Carlo simulations are used to gain a fundamental molecular-level understanding of the effect of modifiers properties on the thermodynamics and interaction forces of nanoscale colloidal particles. A novel method based on the expanded ensemble Monte Carlo technique has been developed for calculation of the chemical potential of colloidal particles in colloid-polymer mixtures (CPM). Using this method, the effect of molecular parameters like colloid diameter, polymer chain length, colloid-polymer interaction strength, and colloid and polymer concentrations, on the colloid chemical potential is investigated for both hard-sphere and attractive Lennard-Jones CPM. The presence of short-chain polymeric modifiers reduces the colloid chemical potential in attractive as well as athermal systems. In attractive CPM, there is a strong correlation between polymer adsorption and colloid chemical potential, as both show a similar dependence on the polymer molecular weight. Based on the simulation results, simple scaling relationships are proposed that capture the functional dependence of the thermodynamic properties on the molecular parameters. The polymer-induced interaction forces between the nanoparticles have been calculated as a function of the above parameters for freely-adsorbing and end-grafted homopolymer modifiers. The polymer-induced force profiles are used to identify design criteria for effective modifiers. Adsorbing modifiers give rise to attractive interactions between the nanoparticles over the whole parameter range explored in this study. Grafted surface modifiers lead to attraction or repulsion based on the polymer chain length and grafting density. The polymer-induced attraction in both adsorbing and grafted modifiers is attributed primarily to polymer intersegmental interactions and bridging. The location of the thermodynamic minimum corresponding to the equilibrium particle spacing in nanoparticle-polymer mixtures can be controlled by tuning the modifier properties.
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Leroy, Frederic H. R., Allan D. Mackie, Pere Miró, Carles Bo, and Avalos Josep Bonet. "A molecular dynamics study of the diffusion coefficients in watertertbutyl alcohol mixtures." Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-194585.
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Jorge, Miguel Angelo da Silva. "Molecular simulation of the adsorption of water/organic mixtures on activated carbon." Thesis, University of Edinburgh, 2003. http://hdl.handle.net/1842/12321.
Full textAbstract:
The adsorption of mixtures of polar and non-polar species is influenced by both the structure and the surface chemistry of the adsorbent. Several molecular simulation techniques have been employed to study the effect of these factors on the extent and mechanism of adsorption of water and light hydrocarbons. In particular, the effect of pore size as well as the concentration, distribution and type of polar surface groups have been examined in a detailed and systematic way. It is shown in this thesis that the presence of polar sites on the surface of the carbon enhances the affinity of the adsorbent towards water. However, in most situations of practical interest, the most important variable was seen to be the concentration of polar sites, with their distribution and type playing only a minor part. This fundamental study formed a basis for the development of a model for activated carbon that can be used in an industrial context. The model for activated carbon includes a representation of the structure of the adsorbent using a distribution of slit-shaped pores, and of the surface chemistry, using a distribution of polar sites. The adsorption in single pores was calculated by grand canonical Monte Carlo simulation. The pore size distribution was obtained from an analysis of pure-ethane adsorption isotherms, while the polar site distribution was calculated by analysing pure-water adsorption. The performance of the model was assessed by comparing the simulated results for binary water/ethane adsorption with experimental adsorption data on a commercial activated carbon. The sensitivity of the predictions to changes in the surface chemistry of the model was examined. The model proposed here was seen to perform much better than the more widely used classical methods, opening good prospects for its use in industrial applications.
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Goetz, Jon Michael. "A study of molecular order and motion in nematic liquid crystal mixtures." W&M ScholarWorks, 1993. https://scholarworks.wm.edu/etd/1539623842.
Full textAbstract:
Materials which flow like fluids, but possess anisotropic properties like molecular crystals, are called 'liquid crystals'. Studies of liquid crystals contribute to our understanding of how molecular orientation influences macroscopic properties. This thesis presents experimental and theoretical investigations of molecular order and dynamics in nematic liquid crystal systems. First, deuterium nuclear magnetic resonance is used to determine the degree of orientational order of both components of a liquid crystal mixture simultaneously. The temperature dependence of the four order parameters is interpreted using a newly developed mean field theory of nematic binary mixtures composed of biaxial molecules. Next, mean field theory is applied to predict the phase behavior of arbitrarily shaped nematogens. For single component liquid crystals, the four order parameters needed to quantify orientational order of biaxial molecules in a biaxial nematic phase are calculated as a function of temperature for both rod-like and plate-like liquid crystals. For binary mixtures, temperature-concentration phase diagrams for a variety of molecular shapes are calculated. These theoretical predictions suggest that binary mixtures of highly asymmetric molecules with opposite shape anisotrophies may display stable biaxial nematic phases. Last, deuterium nuclear magnetic spin relaxation rates are measured as a function of temperature to investigate the molecular motion of a liquid crystal and a liquid crystal binary mixture. These experimental results are interpreted using an anisotropic viscosity model of molecular reorientation. The temperature dependence of the correlation times for the molecular motions is examined and discussed. It is demonstrated that mixing probe molecules into a liquid crystal has a profound effect on the molecular motion of the liquid crystal.
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Yan, Zoe Z. (Zoe Ziyue). "From strongly-interacting Bose-Fermi mixtures to ultracold molecules." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/130219.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, May, 2020<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (pages 193-213).<br>This thesis describes experiments on ultracold quantum gases. First, I discuss quantum simulation involving mixtures of bosonic and fermionic atoms. Second, I present work on creating and controlling ultracold dipolar molecules of ²³Na⁴⁰K. The rich phase diagram of Bose-Fermi mixtures was studied with our system of bosonic ²³Na and fermionic ⁴⁰K atoms. When the fermions were immersed as a minority species within a Bose-Einstein condensate, the system realized the canonical Bose polaron quasiparticle, which is an important paradigm in condensed matter physics. We investigated the strongly-coupled Bose polaron as it approached the quantum critical regime of the Bose-Fermi mixture. Using radiofrequency spectroscopy, we probed the binding energy and decay rate as a function of temperature.<br>In particular, the decay rate was found to scale linearly with temperature near the Planckian rate k[subscript B]T/h⁻ in the unitarity-limited regime, a hallmark of quantum critical behavior. Bose-Fermi mixtures host a complex spectrum of collective excitations, which can shed light on their properties such as collisional relaxation rates, equilibrium equations of state, and kinetic coefficients. We probed the low-lying collective modes of a Bose-Fermi mixture across different interaction strengths and temperatures. The spin-polarized fermions were observed to transition from ballistic to hydrodynamic flow induced by interactions with the bosonic excitations. Our measurements establish Bose-Fermi mixtures as a fruitful arena to understand hydrodynamics of fermions, with important connections to electron hydrodynamics in strongly-correlated 2D materials. The second part of this thesis describes the creation and manipulation of ultracold molecules in their ground state.<br>Molecules have more tunable degrees of freedom compared to atoms, paving the way for studies of quantum state-controlled chemistry, quantum information, and exotic phases of matter. We created loosely-bound Feshbach molecules from ultracold atoms, then transferred those molecules to their absolute electronic, vibrational, rotational, and hyperfine ground state by stimulated Raman adiabatic passage. The rotational level structure, sample lifetimes, and coherence properties were studied, culminating in a demonstration of second-scale nuclear spin coherence times in an ensemble of NaK. Controlling the intermolecular interactions - which can be tunable, anisotropic, and long range - is an outstanding challenge for our field. We induced strong dipolar interactions via the technique of microwave dressing, an alternative to using static electric fields to polarize the molecules.<br>The origin of these dipolar collisions was the resonant alignment of the approaching molecules' dipoles along their intermolecular axis, resulting in strong attraction. Our observations were explained by a conceptually simple two-state picture based on the Condon approximation.<br>by Zoe Z. Yan.<br>Ph. D.<br>Ph.D. Massachusetts Institute of Technology, Department of Physics
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Höft, Hans [Verfasser]. "Characteristics of pulsed operated dielectric barrier discharges in molecular gas mixtures / Hans Höft." Greifswald : Universitätsbibliothek Greifswald, 2015. http://d-nb.info/1072434830/34.
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Sirikitputtisak, Tule. "Molecular simulation study of noble gas + n-decane binary mixtures at reservoir conditions." Thesis, University of Manchester, 2014. https://www.research.manchester.ac.uk/portal/en/theses/molecular-simulation-study-of-noble-gas--ndecane-binary-mixtures-are-reservoir-conditions(6ff06bf5-5bd4-4429-8c42-3ca96b4347c4).html.
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Carbon capture and sequestration are considered to be a temporary fix to the climate change global crisis. Following the noble gas tracers injection field experiment at Salt Creek in the state of Wyoming, USA, these tracers may be used to characterise the reservoir as a potential geological sequestration site for carbon dioxide. This study aims to investigate various thermodynamics properties of the five noble gases (Xe, Kr, Ar, Ne, and He) in n-decane at reservoir conditions (340 K – 460 K and 10 MPa – 200 MPa). The study utilises the SKS force field to describe n-decane and both Gibbs Ensemble Monte Carlo and molecular dynamics simulations were used to investigate the solubility, diffusivity, and vapour-liquid equilibrium of the five binary mixtures. The size of the noble gases was found to be important in these nonpolar mixtures where typical interactions are weak and short-ranged. The enthalpies of solvation were calculated and found to be directly correlated to the size of the solute where the energy required for the formation of a cavity to accommodate the solute is compensated by the nature of the intermolecular interaction between solvent and solute. The mixture of Ar + n-decane is of interest particularly because the sigma value for Ar is very similar to that of the CH3 group, resulting in the overall non-mononicity of several thermodynamics properties. Additionally, maxima in enthalpies of solvation were observed in Xe and Kr in n-decane solution at 200 MPa. While these maxima were observed in two different species at similar conditions, they are accommodated by unusually high uncertainties - further investigation is required before definitive conclusions can be drawn. The results from the vapour-liquid equilibrium study of the five noble gas + n-decane binary mixtures were in good agreement with the Peng-Robinson equation of state predictions. What is more, the diffusion coefficient ratios amongst the five noble gases in n-decane were investigated in light of Stoke-Einstein’s relation and Enskog’s hard-sphere relation. Three different radii of solute-solvent interaction were investigated and the best fit was observed when R =radius of solute + radius of gyration of n-decane. Additionally, the diffusion coefficients were utilised in the reservoir simulation to investigate the role of diffusion within the reservoir.
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Yasuda, Shugo. "Studies on half-space problems for binary gas mixtures in molecular gas dynamics." 京都大学 (Kyoto University), 2005. http://hdl.handle.net/2433/144880.
Full textAbstract:
Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(工学)<br>甲第11523号<br>工博第2469号<br>新制||工||1334(附属図書館)<br>23166<br>UT51-2005-D273<br>京都大学大学院工学研究科航空宇宙工学専攻<br>(主査)教授 青木 一生, 教授 稲室 隆二, 教授 斧 髙一<br>学位規則第4条第1項該当
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Pallewela, Gayani Nadeera. "Theory and simulation of liquids and liquid mixtures." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/32495.
Full textAbstract:
Doctor of Philosophy<br>Department of Chemistry<br>Paul E. Smith<br>Kirkwood Buff (KB) theory is one of the most important theories of solutions. The theory can relate integrals over radial (pair) distribution functions (rdfs) in the grand canonical ensemble to common thermodynamic properties. An inversion of the KB theory has been proposed by Ben-Naim and this has led to the wide spread popularity of KB theory. The idea of the KB inversion procedure is to calculate KB integrals from available thermodynamic properties.
The KB theory can be used to validate the force field (ff) parameters used in molecular dynamics simulations. We have tested a series of small molecule ff parameters using KB theory that consists of both atom centered partial atomic charges and extra charge sites. The results indicate that using extra charge sites, derived from QM calculations, does not necessarily provide a more accurate representation of condensed phase properties. A further study aimed at an ongoing project of deriving new biomolecular ff parameters based on KB theory, has developed ff parameters for esters in order to represent the ester conjugation of the phospholipid molecule. The models were further tested against experimental properties.
Preferential solvation (PS) is an important concept of solution mixtures that can be described using KB theory. The difference between local composition and bulk composition in solution mixtures leads to the concept of PS. A generalized explanation based on local mole fractions was derived by Ben-Naim using KB theory. However, the original expressions have been modified over years. Here, we propose a new approach based on local volume fractions to explore PS in binary and ternary solution mixtures. Experimental and simulation data were used to examine different approaches to PS.
A relationship between the rdf and the triplet distribution function can be obtained using the Kirkwood Superposition Approximation (KSA). A combination of Fluctuation Solution Theory and experimental rdfs are used to examine the KSA at a series of state points for pure water. The accuracy of several other approximate relationships between the pair and triplet correlation functions was also investigated and are in good agreement for regions of the phase diagram where the compressibility is small.
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Leroy, Frederic H. R., Allan D. Mackie, Pere Miró, Carles Bo, and Avalos Josep Bonet. "A molecular dynamics study of the diffusion coefficients in watertertbutyl alcohol mixtures: A molecular dynamics study of the diffusion coefficients in watertertbutylalcohol mixtures: a comparison between All-Atoms and United-Atoms models." Diffusion fundamentals 3 (2005) 5, S. 1-2, 2005. https://ul.qucosa.de/id/qucosa%3A14293.
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