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1
Porwal, Vishal Kumar. "Theoretical Tools to Study Solvation in Liquid and Nanoconfined Phases." Electronic Thesis or Diss., Université de Lorraine, 2022. http://www.theses.fr/2022LORR0239.
Abstract:
Le confinement à l’échelle moléculaire est l’un des domaines les plus fascinants et les plus complexes en constante évolution. Une fois rationalisées, les conséquences du confinement sur la structure moléculaire et électronique des chromophores peuvent être utilisées pour affiner leurs propriétés optiques et ainsi les exploiter dans le développement de nouvelles technologies. En chimie des matériaux, démêler la nature complexe des phases nanoconfinées peut guider dans la synthèse de nouveaux composés aux propriétés polyvalentes. Ce projet est consacré au développement de stratégies computationnelles ad hoc pour parvenir à une interprétation moléculaire de l’impact de l’environnement sur les propriétés conformationnelles, vibrationnelles et optiques de molécules organiques. En collaboration avec un groupe expérimental, nous avons analysé le comportement d’anions organiques confinés dans des matériaux argileux. En nous focalisant sur l’évolution des bandes carboxylates avec l’augmentation de l’hydratation, nous avons caractérisé les changements des modes de liaison de l’anion avec la surface en utilisant des simulations de dynamique moléculaire classique. La deuxième partie du projet, réalisée avec des collaborateurs italiens, est basée sur une approche intégrée multi-niveaux pour obtenir un champ de force sophistiqué du 2,2’-bipyridine-3,3’-diol. Cette molécule subit un transfert de proton intramoléculaire à l’état excité, et les données expérimentales indiquent une sensibilité de ses propriétés à un environnement nanoconfiné. Notre étude de la surface d’énergie potentielle et du spectre d’absorption dans l’eau par une approche séquentielle classique-quantique a apporté des progrès significatifs sur la caractérisation des équilibres tautomères et sur leur effet sur les propriétés optiques du chromophoreConfinement on a molecular scale is one of the most fascinating and complexfields in continuous progress. Once rationalized, the consequences of confinement on themolecular and electronic structure of chromophores can be used to fine-tune their optical properties and thus exploit them in the development of photochemical technologies. In material chemistry, untangling the complex nature of nanoconfined phases can help provide essential knowledge to fine-tune the synthesis of new compounds with versatile properties. This project is devoted to the development of ad hoc computational strategies to achieve a molecular interpretation of the impact of the environment on the conformational, vibrational, and optical properties of organic molecules. In collaboration with an experimental group, we analyzed the behavior of organic anions confined in the interlayer of clay like materials. Focusing on the evolution of the carboxylate bands with increasing hydration, we characterized the changes in the binding modes of the anion by using classical molecular dynamics simulations. The second part of the project, carried out with Italian collaborators, is based on an integrated multilevel approach providing a sophisticated force field for 2,2’-bipyridine-3,3’-diol. This molecule undergoes excited state intramolecular proton transfer, and experimental data point to a fine sensitivity of its properties to a nanoconfined environment. Our study of the potential energy surface and the absorption spectrum in water using a sequential classical-quantum mechanical approach brought significant progress in the characterization of the tautomeric equilibria and their effect on the optical properties of the chromophore
2
Razavi, Seyed Mostafa. "CROSS-PLATFORM FORCE FIELD DEVELOPMENT BASED ON FORCE-SMOOTHED POTENTIAL MODELS." University of Akron / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=akron1590770530909963.
3
DURHAM, PHILIP R. "Force Field Development for Calbindin D9k." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1218547540.
4
Zollars, Eric Stafford Pierce Niles A. "Force field development in protein design /." Diss., Pasadena, Calif. : Caltech, 2006. http://resolver.caltech.edu/CaltechETD:etd-06052006-155305.
5
Li, Xinbi. "Developing and Validating a Complete Second-order Polarizable Force Field for Proteins." Digital WPI, 2015. https://digitalcommons.wpi.edu/etd-dissertations/196.
Abstract:
One of the central tasks for biomolecular modeling is to develop accurate and computationally cheap methods. In this dissertation, we present the development of a brand new polarizable force field—Polarizable Simulations with Second order Interaction Model (POSSIM) involving electrostatic polarization. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. POSSIM force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters have been employed in further development of the POSSIM fast polarizable force field for proteins. The POSSIM framework has been expanded to include a complete polarizable force field for proteins. Most of the parameter fitting was done to high-level quantum mechanical data. Conformational geometries and energies for dipeptides have been reproduced within average errors of ca. 0.5 kcal/mol for energies of the conformers (for the electrostatically neutral residues) and 9.7º for key dihedral angles. We have also validated this force field by simulating an elastin-like polypeptide GVG(VPGVG)3 in aqueous solution. Elastin-like peptides with the (VPGVG)n motif are known to exhibit anomalous behavior of their radius of gyration that increases when temperature is lowered (the so called inverse temperature transition). We have simulated the system with the OPLS-AA and POSSIM force fields and demonstrated that our newly developed polarizable POSSIM parameters permit to capture the experimentally observed decrease of the radius of gyration with increasing temperature, while the fixed-charges OPLS-AA ones do not. Furthermore, our fitting of the force field parameters for the peptides and proteins has been streamlined compared with the previous generation of the complete polarizable force field and relied more on transferability of parameters for non-bonded interactions (including the electrostatic component). The resulting deviations from the quantum mechanical data are similar to those achieved with the previous generation, thus the technique is robust and the parameters are transferable. At the same time, the number of parameters used in this work was noticeably smaller than that of the previous generation of our complete polarizable force field for proteins, thus the transferability of this set can be expected to be greater and the danger of force field fitting artifacts is lower. Therefore, we believe that this force field can be successfully applied in a wide variety of applications to proteins and protein-ligand complexes.
6
SA, QINA. "Developing the Polarizable Force Field: Focus on Amino Acid Residues." Digital WPI, 2011. https://digitalcommons.wpi.edu/etd-theses/1010.
Abstract:
"Polarizable force field has been successfully used in molecular modeling for years, especially in biological and protein simulations. In this research thesis, development of a new polarizable force field ―POSSIM (POlarizable Simulations with Second order Interaction Model) involving electrostatic polarization is described and parameters for several protein residues were produced. In this research thesis, the POSSIM force field was extended to the side chains of the following residues: lysine, glutamic acid, prontonated hisidine, phenylalanine and tryptophan. This work involved producing parameters for methyl ammonium, acetate ion, imidazolium cation, benzene and pyrrole molecules. The parameters fitting procedure starts from the molecular complex with dipolar electrostatic probes of a many-body system to produce polarizabilities, compute the energies, then charges and Lennard-Jones parameters are produced by fitting to gas-phase dimerization calculations, followed by the torsional parameters fitting and end up with the pure liquid simulations. In all the cases, three-body energies, dimerization energies and distances agree well to the accurate quantum mechanical results. The final parameters obtained assured the error of less than 2% in the heat of vaporization and average volume results compared with the available experimental data. Unlike the quantum mechanical calculations, the polarizable force field computations require a relatively small amount of computational resources. Moreover, compared to fixed-charges empirical force fields, polarizable force fields are much more accurate in a number of energy calculations. In the following chapters, the results obtained with this particular polarizable force field are discussed."
7
Isegawa, Miho. "Development of polarizable force field with charge response kernel." 京都大学 (Kyoto University), 2009. http://hdl.handle.net/2433/126573.
8
Jiao, Yuanfang. "The development of accurate force fields for protein simulation." Diss., Kansas State University, 2012. http://hdl.handle.net/2097/13946.
Abstract:
Doctor of PhilosophyDepartment of Chemistry
Paul E. Smith
Computer simulations have provided a wealth of information concerning a wide range of systems. The precision of computer simulation results depends on the degree of sampling (time scales) achieved, while the accuracy of the results (given sufficient sampling) depends on the quality of force field used. A force field provides a description of the energy for a system of interest. Recently, we have been developing a Kirkwood Buff (KB) force field for molecular dynamics simulations of biological systems. This force field is based on the KB Theory of solutions, emphasizing the accurate description of intermolecular interactions, and reasonably reproducing a range of other physical properties from experiment. In this approach simulation results in terms of KB integrals can be directly compared with experimental data through a KB analysis of the solution properties. The approach therefore provides a simple and clear method to test the capability of a force field. Here we firstly studied a series of alcohol-water mixtures in an attempt to validate the transferability and additivity of the force field. A general fluctuation theory was applied to investigate the properties of these systems, and to compare with computer simulation results. The possible effects of cosolvents on peptides and proteins were then investigated using N-methylacetamide as model for the peptide backbone and urea as cosolvent. A possible explanation for the urea denaturation of protein structure was provided using a thermodynamics point of view involving transfer free energies and preferential interactions obtained from the KB integrals. Finally, potentials for protein backbone and sidechain torsions were developed by fitting to quantum mechanical calculations and NMR data. Simulations of a variety of peptides and proteins in aqueous solutions were then performed to demonstrate the overall reliability of the force field.
9
Morley, S. David. "The development of the COSMIC force field for biomolecular applications." Thesis, University of Nottingham, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335404.
10
Sharma, Ity. "Developing and validating Fuzzy-Border continuum solvation model with POlarizable Simulations Second order Interaction Model (POSSIM) force field for proteins." Digital WPI, 2015. https://digitalcommons.wpi.edu/etd-dissertations/393.
Abstract:
"The accurate, fast and low cost computational tools are indispensable for studying the structure and dynamics of biological macromolecules in aqueous solution. The goal of this thesis is development and validation of continuum Fuzzy-Border (FB) solvation model to work with the Polarizable Simulations Second-order Interaction Model (POSSIM) force field for proteins developed by Professor G A Kaminski. The implicit FB model has advantages over the popularly used Poisson Boltzmann (PB) solvation model. The FB continuum model attenuates the noise and convergence issues commonly present in numerical treatments of the PB model by employing fixed position cubic grid to compute interactions. It also uses either second or first-order approximation for the solvent polarization which is similar to the second-order explicit polarization applied in POSSIM force field. The FB model was first developed and parameterized with nonpolarizable OPLS-AA force field for small molecules which are not only important in themselves but also building blocks of proteins and peptide side chains. The hydration parameters are fitted to reproduce the experimental or quantum mechanical hydration energies of the molecules with the overall average unsigned error of ca. 0.076kcal/mol. It was further validated by computing the absolute pKa values of 11 substituted phenols with the average unsigned error of 0.41pH units in comparison with the quantum mechanical error of 0.38pH units for this set of molecules. There was a good transferability of hydration parameters and the results were produced only with fitting of the specific atoms to the hydration energy and pKa targets. This clearly demonstrates the numerical and physical basis of the model is good enough and with proper fitting can reproduce the acidity constants for other systems as well. After the successful development of FB model with the fixed charges OPLS-AA force field, it was expanded to permit simulations with Polarizable Simulations Second-order Interaction Model (POSSIM) force field. The hydration parameters of the small molecules representing analogues of protein side chains were fitted to their solvation energies at 298.15K with an average error of ca.0.136kcal/mol. Second, the resulting parameters were used to reproduce the pKa values of the reference systems and the carboxylic (Asp7, Glu10, Glu19, Asp27 and Glu43) and basic residues (Lys13, Lys29, Lys34, His52 and Lys55) of the turkey ovomucoid third domain (OMTKY3) protein. The overall average unsigned error in the pKa values of the acid residues was found to be 0.37pH units and the basic residues was 0.38 pH units compared to 0.58pH units and 0.72 pH units calculated previously using polarizable force field (PFF) and Poisson Boltzmann formalism (PBF) continuum solvation model. These results are produced with fitting of specific atoms of the reference systems and carboxylic and basic residues of the OMTKY3 protein. Since FB model has produced improved pKa shifts of carboxylic residues and basic protein residues in OMTKY3 protein compared to PBF/PFF, it suggests the methodology of first-order FB continuum solvation model works well in such calculations. In this study the importance of explicit treatment of the electrostatic polarization in calculating pKa of both acid and basic protein residues is also emphasized. Moreover, the presented results demonstrate not only the consistently good degree of accuracy of protein pKa calculations with the second-degree POSSIM approximation of the polarizable calculations and the first-order approximation used in the Fuzzy-Border model for the continuum solvation energy, but also a high degree of transferability of both the POSSIM and continuum solvent Fuzzy Border parameters. Therefore, the FB model of solvation combined with the POSSIM force field can be successfully applied to study the protein and protein-ligand systems in water. "
11
Awati, Rohan Vivek. "Development of accurate computational methods for simulations of adsorption and diffusion in zeolites." Diss., Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54945.
Abstract:
The overall objective of this thesis has been to develop accurate computational methods for the diffusion and adsorption of small gases in zeolites. Firstly, the effect of the zeolite framework flexiblity on the single component and binary diffusion of various gases were discussed. Results indicate that for tight fitting molecules the rigid framework approximation can produce order(s) of magnitude difference in diffusivities as compared to the simulations performed with a fully flexible framework. We proposed two simple methods in which the flexible structure of a zeolite is approximated as a set of discrete rigid snapshots. Both methods are orders of magnitude more efficient than the simulations with the fully flexible structure. Secondly, we use a combined classical and quantum chemistry based approach to systematically develop the force fields based on DFT calculations for interactions of simple molecules like CH4, N2, linear alkanes, and linear alkenes in zeolites. We used a higher level of theory known as the DFT/CC method to correct DFT energies that were used in the periodic DFT calculations to develop force fields. Our results show that DFT-derived force fields give good predictions of macroscopic properties like adsorption isotherms in zeolites. The force fields are transferrable across zeolites and hence can be further used to screen materials for different storage and separation applications.
12
Sarsam, Joanne. "Development and application of atomistic force fields for ionic materials." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/12253.
Abstract:
In the field of molecular dynamics (MD), the time evolution of a set of interacting atoms is determined by integrating their equations of motion using Newton’s Second Law. By using efficient potentials that capture the essential physics of a material, the properties of systems containing tens of thousands of atoms can be accurately modelled. This thesis describes three substantial developments in the science and simulation of ionic materials. In the opening chapters, we provide an introduction to the field of atomistic simulation, covering the theory and methods used in both classical molecular dynamics and density-functional theory (DFT). The use of DFT calculations in the parametrisation of force fields for molecular dynamics is described, and we discuss how the software used for MD and potential parametrisation has been radically overhauled and made more efficient and user friendly during the course of this work. We then study aluminium oxide, and develop a new potential which is faster and simpler than the current state of the art alumina potentials. The new potential is tested and found to accurately describe a range of physical properties. The potential is then applied to the study of intrinsic defects in alumina. Finally, we attempt to improve our description of heterogeneous ionic materials by developing and implementing a coupled charge-equilibration and polarisable ion model applicable to non-molecular systems. A review of the existing literature on the subject is made, before we describe the mathematical and physical reasoning behind our new implementation. Our method is found to be numerically accurate, and is subsequently applied to the study of defects and surfaces in magnesium oxide.
13
Williamson, Ricky Lawrence. "Near-field optical and shear force microscopy : instrument development, theoretical background and applications." Thesis, University of Bristol, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.296690.
14
Mick, Jason Richard. "Force field development with GOMC, a fast new Monte Carlo molecular simulation code." Thesis, Wayne State University, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10105010.
Abstract:
In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.
15
Ugarte, La Torre Diego Renato. "Force field development for performing coarse-grained molecular dynamics simulations of biological membranes." Doctoral thesis, Kyoto University, 2021. http://hdl.handle.net/2433/265177.
16
Shah, Premal S. Rees Douglas C. "Advances in force field development and sequence optimization methods for computational protein design /." Diss., Pasadena, Calif. : California Institute of Technology, 2005. http://resolver.caltech.edu/CaltechETD:etd-04042005-142719.
17
Del, Frate Gianluca. "Development, validation and application of accurate molecular force fields for complex soft matter systems." Doctoral thesis, Scuola Normale Superiore, 2018. http://hdl.handle.net/11384/85815.
18
Lee, Michael V. "Development of chemomechanical functionalization and nanografting on silicon surfaces /." Diss., CLICK HERE for online access, 2007. http://contentdm.lib.byu.edu/ETD/image/etd2023.pdf.
19
Winger, Moritz Christoph Ludwig. "Classical molecular dynamics simulations at different levels of resolution : force field development and applications /." Zürich : ETH, 2008. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=18076.
20
Hempel, Sascha [Verfasser]. "Force Field Development for Activity Coefficient Calculations in Aqueous Amino Acid Solutions / Sascha Hempel." München : Verlag Dr. Hut, 2015. http://d-nb.info/1069020559/34.
21
Verma, Abhinav. "Development and application of a free energy force field for all atom protein folding." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/987646559/34.
22
McAliley, James Hodges. "Development of improved torsional potentials in classical force field descriptions of poly (lactic acid)." Connect to this title online, 2009. http://etd.lib.clemson.edu/documents/1252938067/.
Abstract:
Thesis (Ph.D.) -- Clemson University, 2009.Contains additional supplemental file. Title from first page of PDF file. Document formatted into pages; contains xxxv, 339 p. ; also includes graphics (chiefly col.).
23
Verma, Abhinav [Verfasser]. "Development and application of a free energy force field for all atom protein folding / Abhinav Verma." Karlsruhe : Forschungszentrum Karlsruhe, 2007. http://d-nb.info/987646559/34.
24
Musanur, Abrar Siraj. "Development of an empirical force field and molecular dynamics simulation of N,N'-dialkylimidazolium ionic liquids." Thesis, Stellenbosch : Stellenbosch University, 2004. http://hdl.handle.net/10019.1/53737.
Abstract:
Thesis (MSc)--Stellenbosch University, 2004ENGLISH ABSTRACT: In an ongoing study an empirical force field that can correctly model N,N'- dialkylimidazolium halide ionic liquids, the Imidazolium Ionic Liquid Force Field - IILFF, was developed based on experimental data obtained from the Cambridge Structural Database (CSD) and data calculated using Gaussian98. Different conformations of the isolated cations were optimised at the Hartree-Fock level using the 6-31G(d) basis set. Structural, vibrational and partial atomic charge data of the lowest energy conformation of each cation were taken as observables during optimisation of the force field parameters. Initial parameters of the IILFF were taken from existing force fields and were optimised using the above mentioned data. The IILFF was used to minimise isolated cations as well as crystals. These results were successfully tested against isolated cations minimised using Gaussian98 and the experimental crystals. Finally, the melting process of the 1,3-dimethylimidazolium chloride crystal was studied using an NPT ensemble starting from an ordered crystal cell and increasing the simulation temperature beyond the experimental melting temperature. The IILFF was then used to calculate the potential energy of the system.
AFRIKAANSE OPSOMMING: In 'n voortgaande studie om 'n empiriese kragveld te bou wat N,N' -dialkielimidasoliumhalied ioniese vloeistowwe korrek kan modelleer is die Imidasolium Ioniese Vloeistof Kragveld (nVK) ontwikkel. Die kragveld is ontwikkel gebasseer op eksperimentele data verkry uit die Cambridge Strukturele Databasis (CSD) asook uit data vanaf Gaussian98 berekeninge. Verskillende konformasies van die geïsoleerde katione is geoptimiseer deur middel van Hartree Fock 6-31G(d) berekeninge. Strukturele data, asook vibrasies en gedeeltelike atoom ladings van die laagste energie konformasie van elke katioon is gebruik as waarneembare veranderlikes vir die bepaling van die optimale kragveld parameters. Beginwaardes vir die nVK is geneem uit bestaande kragvelde en geoptimiseer met behulp van bogenoemde data. Die IIVK is gebruik om geïsoleerde katione asook kristalle te minimiseer. Die resultate is suksesvol getoets teen geïsoleerde katione wat met behulp van Gaussian98 geminimiseer is en eksperimenteel bepaalde kristalle. Laastens is die smeltproses van die 1,3-dimetielimidasolium chloried kristal bestudeer met behulp van 'n NPT ensemble. Daar is begin by 'n geordende kristal en die simulasie temperatuur is verhoog tot meer as die eksperimentele smeltpunt. Die IIVK is dan gebruik om die potensiële energie van die sisteem te bepaal.
25
Shang, Guangyi. "Development of a shear force scanning near-field optical microscope for biological applications: imaging ans spectroscopy." Reims, 2004. http://www.theses.fr/2004REIMS005.
Abstract:
Un microscope à champ proche optique basé sur un nouveau senseur de force fonctionnant dans le mode cisaillement a été développé. Il peut être combiné à un microspectrofluorimètre confocal laser pour des applications biologiques et utilisé dans différents modes de fonctionnement. Le mécanisme de détection des forces de cisaillement a été expérimentalement étudié. Il s'avère que l'origine principale de ce mécanisme est le contact intermittent de la sonde avec la surface de l'échantillon qui permet de contrôler la distance pointe-surface. Les paramètres expérimentaux concernant l'imagerie ainsi que les artefacts dus à la géométrie de la sonde sont discutés. Des images en champ proche optique d'un réseau de silicium dans le mode réflexion ainsi que la spectroscopie de structures électroluminescentes dans le mode collection ont été respectivement obtenues. Comme étude préliminaire pour des applications biologiques, la distribution de P-glycoprotéines dans la membrane plasmatique de petites cellules cancéreuses de langue humaine a été étudiée avec une résolution inférieure à la limite de résolution due à la diffraction. Cette distribution n'est pas homogène et se présente sous forme de petits amas. De plus, des spectres de fluorescence ont été obtenus sur des cellules cancéreuses du poumon humain colorées avec la sonde fluorescente JC-1. Des variations dans le spectre de fluorescence ont été mises en évidence avec une résolution verticale de l'ordre de 100 nm. Ces résultats suggèrent que notre système est un outil d'investigation prometteur pour des applications biologiques, capable de fournir des informations dignes d'intérêt permettant de mieux comprendre certains problèmes biologiquesBased on a new force sensor, a shear force scanning near-field optical microscope (ShF-SNOM), that can be operated in the different modes and combined with a confocal laser microspectrofluorometer (CLMF) for biological applications, has been developed. Shear force mechanism was experimentally studied and the knocking mechanism is the main origin responsible for shear force distance control in our system. Experimental parameters concerning the shear force imaging and artifacts due to probe geometric effects are discussed. Shear force and near-field imaging of a silicon grating in the reflection mode, imaging and spectroscopy of electroluminescent structures in the collection mode are demonstrated respectively. As a preliminary study for biological applications, the distribution of P-glycoprotein (P-gp) in the plasma membrane of human small cell lung cancer cells were investigated with sub-diffraction limit resolution. The distribution of P-gp in the cell membrane was found to be not homogenous and cluster formation of P-gp in the membrane was observed. In addition, fluorescence spectra were recorded in a single living cell of human breast adenocarcinoma cells stained with the fluorescent dye JC-1. The variations in fluorescence spectra were measured with vertical resolution of about 100 nm. These results suggest that our system would be a promising tool for biological applications and provide valuable information for understanding some biological problems
26
Kraska, Jenna M., Ann Marie Swisher, Michael W. Ramsey, C. Nelson, William A. Sands, G. Gregory Haff, H. Hasegawa, Jeff McBride, Margaret E. Stone, and Michael H. Stone. "Relationship of Peak Isometric Strength to Rate of Force Development Among Collegiate Track and Field Athletes." Digital Commons @ East Tennessee State University, 2008. https://dc.etsu.edu/etsu-works/4096.
Abstract:
Explosive strength, a function of rate of force development (RFD), is a primary determinant for the amount of peak force that can be produced in critical sport performance time periods ( e.g. foot contact time). Evidence indicates that maximum strength and RFD are correlated. However, the characteristics of this relationship are not well established among athletes. This study examined the relationship of peak isometric force (IPF) and RFD from a mid-thigh pull, among male and female track and field athletes. Athletes were 12 sprinters (S), 10 jumpers (JP) and 12 cross-country runners (XC). Force-time curve analysis was conducted for each (2 trials) isometric pull and averaged for analyses. IPF and RFD from 0 - 200 ms were determined from appropriate curves. IPFs were normalized using an allometric (IPFa) scaling equation: absolute force/ (body mass (kg)0.67). ICCs were previously shown to be > 0.9. Relationships were established with Pearson's r; statistical differences with a Bonferroni adjusted t-Test. IPF, IPFa and RFD were greater in males than females for S and JP but not for XC. IPF, IPFa and RFD were greater for S and JP compared to XC. Similar relationships of IPF to RFD were noted among groups S(r = 0.85), JP (r = 0.87), XC (r = 0.88). Among males, n = 19, the relationship ofIPF to RFD was r = 0.89 and was somewhat higher compared to females, n = 15, (r = 0.78). Overall (n = 34) relationship between IPF and RFD was r = 0.90. These data indicate a strong relationship between maximum strength and "explosiveness" that is independent.
27
Naseem-Khan, Sehr. "Development of a polarizable ab initio force field : From separability of intermolecular interactions to condensed phase properties." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS564.
Abstract:
Grâce aux récents progrès de l’informatique, il devient alors possible d’utiliser des champs de forces polarisables sophistiqués tel que SIBFA. En effet, le potentiel intermoléculaire SIBFA et ses gradients sont désormais implémentés dans le code Tinker-HP. La calibration initiale de SIBFA est basée sur la méthode RVS, une méthode de décomposition de l’énergie seulement accessible au niveau Hartree-Fock. Ainsi, les objectifs de ce travail sont double : i) choisir une nouvelle méthode référence de décomposition de l’énergie afin d’obtenir les paramètres de SIBFA au niveau corrélé ; ii) réaliser des simulations de dynamiques moléculaires. La première partie de cette thèse est dédiée à l’étude ab initio de la séparabilité de l’interaction intermoléculaire prédit par les méthodes de décomposition de l’énergie dites variationnelles et perturbationnelles. Nous avons fait des améliorations de l’énergie d’induction au sein de la méthode SAPT(DFT) et nous avons proposé une nouvelle définition du transfert de charge. La seconde partie de cette thèse est dédiée au développement du potentiel polarisable de l’eau de SIBFA, et à notre stratégie pour calculer les propriétés en phase condensée. L’étude ab initio de la séparabilité de l’énergie totale intermoléculaire SAPT(DFT) a mené à une séparabilité totale des contributions du potentiel SIBFA au niveau post Hatree-Fock. Cette thèse marque un réel progrès pour le potentiel SIBFA qui finalise son approche bottom-up : à partir de calculs ab initio en phase gaz vers des simulations de dynamiques moléculaires et des prédictions précises des propriétés en phase condenséeThanks to the recent progresses of computer sciences de-multiplying the available computational resources, the possibility of using sophisticated polarizable force fields such as SIBFA becomes a reality. Indeed, the SIBFA intermolecular potential and its gradients are now implemented in the Tinker-HP package. The original calibration of SIBFA was based on the RVS method, an energy decomposition analysis only available at the Hartree–Fock level of theory. Therefore, the goals of this work are double : i) choosing a new energy decomposition analysis reference scheme in order to upgrade the SIBFA parameters at the correlated level of theory ; ii) performing molecular dynamics. The first part of this thesis is dedicated to the study of the separability of the ab initio intermolecular interaction energy predicted by both variational and perturbational Energy Decomposition Analysis methods. We have made improvements for the induction energy term within the SAPT(DFT) method, and we have proposed a new charge transfer definition. The second part of this thesis is dedicated to the development of the SIBFA polarizable water model and to our definition of a strategy to compute condensed phase properties. The ab initio study of the separability of the total SAPT(DFT) intermolecular interaction energy has led the SIBFA potential to achieve both full separability of its components and high accuracy at the post Hartree-Fock level. This thesis marks a turning-point for the SIBFA potential, finalizing its global bottom-up strategy going from gas phase ab initio computations towards molecular dynamics simulations and accurate condensed phase properties predictions
28
Razavi, Seyed Mostafa. "OPTIMIZATION OF A TRANSFERABLE SHIFTED FORCE FIELD FOR INTERFACES AND INHOMOGENEOUS FLUIDS USING THERMODYNAMIC INTEGRATION." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1481881698375321.
29
Konrad, Manuel [Verfasser], and W. [Akademischer Betreuer] Wenzel. "Development and application of force fields for molecular simulations / Manuel Konrad ; Betreuer: W. Wenzel." Karlsruhe : KIT-Bibliothek, 2021. http://d-nb.info/1238147887/34.
30
Waibel, Christian [Verfasser], and Joachim [Akademischer Betreuer] Groß. "Development of a polarizable transferable force field for vapor-liquid equilibria calculations / Christian Waibel ; Betreuer: Joachim Groß." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2019. http://d-nb.info/1199397695/34.
31
Gee, Moon Bae. "Computer simulation and theory of amino acid interactions in solution." Diss., Manhattan, Kan. : Kansas State University, 2010. http://hdl.handle.net/2097/4272.
32
Webb, Benjamin M. "Development of polarizable force fields and hybrid QM/MM methods for the study of reaction mechanisms." Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:5bf68dc6-0d39-464e-b145-16e255b043c4.
Abstract:
Computational chemists have successfully simulated many systems by applying the principles of quantum mechanics, while approximate molecular mechanical models have seen great utility in problems of biochemical interest. In recent years, a number of methods have been developed to combine the advantages of both techniques. In this study the so-called QM/MM method is developed and applied to the determination of the free energy of a simple Menshutkin SN2 chemical reaction. This is an extremely demanding process, well beyond the computational capacity of an average workstation, and thus a Beowulf-class Linux cluster is constructed to perform the calculations, and tested for a variety of computational chemistry applications. A number of methods for improving the QM/MM approach are considered in this work. The Fluctuating Charge, or FlucQ, polarizable molecular mechanics force field is implemented in a flexible manner within the CHARMM package and tested for a variety of systems, including the SN2 test case. Several drawbacks of the original method are addressed and overcome. Both molecular dynamics and Monte Carlo techniques are used within the QM/MM framework to investigate the SN2 reaction, and the two methods are compared. Techniques are developed and tested to increase the efficiency of QM/MC calculations to the point where they become competitive with QM/MD. Extremely expensive QM treatments are shown to be required to obtain accurate energies for the Menshutkin reaction. A method is developed and tested, and compared with the traditional ONIOM technique, for dramatically reducing the computational time required to use these treatments for QM/MC simulations, paving the way for fully ab initio high basis set QM/MM simulation.
33
Wu, Xiaojing. "Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS252/document.
Abstract:
Cette thèse porte sur deux projets visant au développement de nouvelles approches pour simuler les dynamiques moléculaire et électronique avec application à des biomolécules étendues. Dans la première partie nous cherchons à améliorer significativement la précision des simulations des propriétés rédox des protéines. Dans ce contexte, l'objectif est de recourir à de champ de force reposant sur une description multipolaire des interactions électrostatiques (AMOEBA) pour estimer les potentiels redox d'hémoprotéines. Nous avons dérivé des paramètres pour AMOEBA afin de décrire précisément les interactions électrostatiques avec l'hème. Une amélioration très encourageante est obtenue par rapport aux champs de forces standard. Le second projet vise à développer de nouvelles méthodes pour étudier la dynamique des électrons dans des biomolécules à l'échelle attoseconde en incluant les effets d'environnement. Nous avons conçu un couplage original entre la théorie de la fonctionnelle de la densité dépendant du temps (RT-TDDFT) et un modèle de mécanique moléculaire polarisable (MMpol). Une implémentation efficace et robuste de cette méthode a été réalisée dans le logiciel deMon2k. L'utilisation de techniques d'ajustements de densités électroniques auxiliaires permet de réduire drastiquement le coût de calcul des propagations RT-TDDFT/MMpol. La méthode est appliquée à l'analyse de la dissipation d'énergie dans l'environnement d'un peptide excité par un impulsion laserThis thesis involves two projects devoted to the development of advanced approaches for simulating molecular and electron dynamics in extended biomolecules. The first project aims at significantly improving the accuracy of redox potentials of proteins by numerical simulations. A sophisticated force field relying on a multipolar description of electrostartic interactions (AMOEBA) is used to perform molecular dynamics simulations onheme proteins. We derived parameters for AMOEBA to accurately describe electrostatic interactions with hemein both ferrous and ferric states. Very encouraging improvements are obtained compared to the standard force fields. The second project aims at developing original approaches for simulating ultrafast electron dynamics in biomolecules in contact to polarizable environments. We devised acombination of Real-time Time-Dependent Density Functional Theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol). An efficient and robust implementation of this method has been realized in deMon2k software. Density fitting techniques allow to reduce the computational cost of RT-TDDFT/MMpol propagations. The methodology is applied to understand the mechanisms of energy dissipation of a peptide excited by a laser pulse
34
Mngadi, Vela. "Development of a force field with condensed phase consistent charges for N,N' - dialkylimidazolium room temperature ionic liquids." Master's thesis, University of Cape Town, 2015. http://hdl.handle.net/11427/20001.
Abstract:
Most force field models for Room temperature ionic liquids cannot properly elucidate statics and dynamics. It is in this context that we set to assess the most efficient way to model RTILs while maintaining the integrity of the liquids statics and dynamics. The development approach begins with the investigation of the effects that the linear scaling of partial atomic charges on nonpolarisable force fields from a reference potential has on the structure and dynamics of the room temperature ionic liquids (RTILs) 1-butyl-3-methylimidazolium tetraflouroborate [C4MIM][BF4] and 1-butyl-3-methylimidazolium hexaflourophosphate [C4MIM][PF6]. The results show that the three-dimensional structure of the liquid is changed ever so slighter by the linear scaling of atomic charges. While dynamic properties such as viscosity and self-diffusion coefficients were majorly affected by charge scaling. Self-diffusion coefficients that span a range of four orders of magnitude between the original model and the scaled model where the ionic charge was ±0.6 e. Viscosity estimates calculated using the Green-Kubo and the Einstein relationships revealed that the linear scaling of atomic charges results in increased mobility of the simulated liquid. Implicit inclusion of polarisation effects was investigated, Here a new charge scheme development using Quantum mechanics/Molecular mechanics (QM/MM) methods in CHARMM 35 interfaced with GAMESS-UK was propose. The atomic charges were derived from liquid phase calculations using an iterative procedure. This was carried out for individual ions and cation-anion pairs, for the analysis of charge transfer, within the liquid environment. The results obtained gave predictions of density, liquid structure and self-diffusion coefficients that were in excellent agreement with experimental data available. This method is preferable over the commonly used charge scaling methodology which is deem as an unphysical approach for the simulation of [C4MIM][BF4] and [C4MIM][PF6]. A polarisable force field based on the Drude oscillator model is presented. The model proves to be most effective for the simulation of RTILs. The force field accurately reproduced experimental results for the physicochemical properties reviewed.
35
Govind, Rajan Ananth. "Atomistic modeling and simulations of 2D materials : chemical vapor deposition, nanoporous defects, force-field development, wetting, and friction." Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/121706.
Abstract:
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2019
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
Two-dimensional (2D) materials, such as, graphene, transition metal dichalcogenides (TMDs) (e.g., molybdenum disulfide (MoS₂)), and hexagonal boron nitride (hBN), have recently received considerable attention, due to their layer-number-dependent optoelectronic, mechanical, and barrier properties. However, physical understanding of the controlled synthesis and interfacial behavior of 2D materials is still lacking. In this thesis: First, I construct a generalized mechanistic model for the growth of TMD monolayers using chemical vapor deposition (CVD). Combining kinetic Monte Carlo (KMC) simulations and a chemical engineering transport model, I am able to predict the experimentally-observed shape and size evolution of the MoS₂ morphology inside a CVD reactor. Second, I address the challenge of solving the Isomer Cataloging Problem (ICP) for lattice nanopores in 2D materials.
Combining electronic structure density functional theory (DFT) calculations, KMC simulations, and chemical graph theory, I generate a catalog of unique, most-probable isomers of 2D lattice nanopores, demonstrating remarkable agreement with experimental microscopy data for nanopores in graphene and hBN. Third, I study the photoluminescent properties of nanoporous defects in hBN by combining my solution to the ICP with extensive hybrid DFT calculations of electronic bandgaps. Doing so, I map the experimentally-observed emission energies to one or more defect shapes in hBN, thereby demonstrating structure-property relationships for defects in hBN, with implications for single-photon emission from hBN devices. Fourth, using molecular dynamics (MD) simulations, I show that electrostatic interactions play a negligible role in determining the contact angle and the friction coefficient of water on the MoS₂ basal plane.
I show that other planes (e.g., the zigzag plane) are polar with respect to interactions with water, thereby illustrating the role of edge effects in MoS₂. Fifth, I combine lattice dynamics calculations with DFT-based MD simulations to develop a force field for hBN for use in mechanical and interfacial applications. The force field predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy, and demonstrates remarkable agreement with the interlayer and water-hBN binding energies predicted by advanced ab initio calculations. Finally, using MD simulations, I study the wetting and frictional properties of hBN by three different liquids of varying degrees of polarity. I infer that electrostatic interactions affect the frictional properties of various liquids in contact with hBN to different extents, and propose the mean-squared total lateral force as a physical metric to rationalize this observation.
This finding implies that liquids with lower wettability can exhibit higher friction on hBN surfaces. In conclusion, the theoretical and simulation methods developed and applied in this thesis should inform the synthesis of 2D materials, and their use in various applications, such as, optoelectronic devices, mechanical composites, and membranes for gas separation and water desalination.
by Ananth Govind Rajan.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Chemical Engineering
36
Zhang, Hao. "Model development and stability analysis for a turbocharger rotor system under multi-field coupled forces." Thesis, University of Huddersfield, 2012. http://eprints.hud.ac.uk/id/eprint/15019/.
Abstract:
Automotive turbochargers have been widely applied in vehicles in order to increase the power output of internal combustion engines by increasing the air to fuel ratio entering the piston cylinders. Turbochargers use the exhaust flow to spin a turbine at speeds of up to 140,000 r/min. Under such extreme working conditions, even a weak vibration can lead to the bearing failure and the whole turbocharger destroyed. In order to guarantee a safe operation, it is necessary to carry out a theoretical research on the dynamics performance of turbochargers. Therefore, the primary objective of this research is to develop a dynamics model for the turbocharger rotor system under multi-field coupled forces and then to study the dynamic characteristics and the stability of its rotor system according to the simulation and experimental results. A turbocharger is a special kind of rotating machinery because of the following aspects: Firstly, the turbocharger rotor system is supported by floating ring bearings. The impact of nonlinear multi-field coupled forces must be considered. Secondly, the turbocharger rotor system is a multi-span rotor bearing system that makes the modeling and simulation more complicated. Thirdly, the working speed range of the turbocharger covers multiple orders of critical speeds. This flexible rotor system cannot be studied using the conventional theory of rigid rotors. In this thesis, the lubrication system of a turbocharger is initially investigated. The analytical expressions of the hydrodynamic pressure distribution in the floating ring bearing are derived using the infinitely long bearing theory, taking into account the oil inlet pressure and the cavitation area. The influences of external loads and oil inlet pressure on the oil flow rate into the inner clearance are analytically investigated, while considering the effect of the rotation of the ring. A finite element model is then developed for the turbocharger rotor system. In this model, the excitation forces considered include rotor imbalance, hydrodynamic forces, lubricant feed pressure and the dead weight. The dimensionless form of Capone hydrodynamic force model is extended into the floating ring bearing. Following model development, modal analysis is carried out on both a free rotor system and a turbocharger rotor system. The effects of the structural parameters and working conditions, such as the rotor imbalance, lubricant viscosity, bearing clearances and lubricant feed pressure, on the stability of the turbocharger rotor system are studied. A turbocharger test rig is then designed and developed to monitor the turbocharger shaft motion. The experimental data agree well with the simulation results from the theoretical model. The primary contribution of the current research can be categorized into the following aspects: Firstly, the analytical expressions of the hydrodynamic pressure distribution have been solved. The equilibrium positions of the journal and ring have been deduced under different external loads and lubricant feed pressure. The relationship between the oil flow rate and the rotational velocity of the shaft has been obtained. Secondly, Capone hydrodynamic force model is introduced and extended to simulate the dynamic performance of the floating ring bearing. The analytical expression of the hydrodynamic forces of double oil films have been derived based on the dimensionless form of the Reynolds Equations. Thirdly, the motion of the turbocharger shaft is simulated within a speed range of 0 to 8,000 rad/s. The influences of structural parameters and working conditions on the stability of the turbocharger rotor system are clearly understood. It should be noted that the developed model still needs to be validated when turbocharger is operated at a relatively high speed, although it agrees well with experimental results within the speed range of 0 to 2,000 rad/s.
37
Aktosun, Erdem. "Identification of hydrodynamic forces developed by flapping fins in a watercraft propulsion flow field." ScholarWorks@UNO, 2014. http://scholarworks.uno.edu/td/1900.
Abstract:
In this work, the data analysis of oscillating flapping fins is conducted for mathematical model. Data points of heave and surge force obtained by the CFD (Computational Fluid Dynamics) for different geometrical kinds of flapping fins. The fin undergoes a combination of vertical and angular oscillatory motion, while travelling at constant forward speed. The surge thrust and heave lift are generated by the combined motion of the flapping fins, especially due to the carrier vehicle’s heave and pitch motion will be investigated to acquire system identification with CFD data available while the fin pitching motion is selected as a function of fin vertical motion and it is imposed by an external mechanism. The data series applied to model unsteady lifting flow around the system will be employed to develop an optimization algorithm to establish an approximation transfer function model for heave force and obtain a predicting black box system with nonlinear theory for surge force with fin motion control synthesis.
38
Kraska, Jenna M., Ann M. Kinser, Corey B. Whitted, Jon Keller, Michael W. Ramsey, G. Gregory Haff, William A. Sands, Margaret E. Stone, and Michael H. Stone. "Relationship of Isometric Peak Force and Rate of Force Development to Coaches Rank, Agility, and Agility Endurance Charactristics Among Female American Collegiate Football (Soccer) Players." Digital Commons @ East Tennessee State University, 2007. https://dc.etsu.edu/etsu-works/4097.
39
Kulkarni, Ambarish R. "Multiscale modeling of nanoporous materials for adsorptive separations." Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53053.
Abstract:
The detrimental effects of rising CO₂ levels on the global climate have made carbon abatement technologies one of the most widely researched areas of recent times. In this thesis, we first present a techno-economic analysis of a novel approach to directly capture CO₂ from air (Air Capture) using highly selective adsorbents. Our process modeling calculations suggest that the monetary cost of Air Capture can be reduced significantly by identifying adsorbents that have high capacities and optimum heats of adsorption. The search for the best performing material is not limited to Air Capture, but is generally applicable for any adsorption-based separation. Recently, a new class of nanoporous materials, Metal-Organic Frameworks (MOFs), have been widely studied using both experimental and computational techniques. In this thesis, we use a combined quantum chemistry and classical simulations approach to predict macroscopic properties of MOFs. Specifically, we describe a systematic procedure for developing classical force fields that accurately represent hydrocarbon interactions with the MIL-series of MOFs using Density Functional Theory (DFT) calculations. We show that this force field development technique is easily extended for screening a large number of complex open metal site MOFs for various olefin/paraffin separations. Finally, we demonstrate the capability of DFT for predicting MOF topologies by studying the effect of ligand functionalization during CuBTC synthesis. This thesis highlights the versatility and opportunities of using multiscale modeling approach that combines process modeling, classical simulations and quantum chemistry calculations to study nanoporous materials for adsorptive separations.
40
Painter, Keith B., G. Gregory Haff, Michael W. Ramsey, Jeff McBride, N. Travis Triplett, William A. Sands, Hugh S. Lamont, Margaret E. Stone, and Michael H. Stone. "Strength Gains: Block Vs DUP Weight-Training among Track and Field Athletes." Digital Commons @ East Tennessee State University, 2012. https://dc.etsu.edu/etsu-works/4132.
Abstract:
Recently, the comparison of “periodized” strength training methods has been a focus of both exercise and sport science. Daily undulating periodization (DUP), using daily alterations in repetitions, has been developed and touted as a superior method of training, while block forms of programming for periodization have been questioned. Therefore, the purpose of this study is to compare block to DUP in Division I track and field athletes. Thirty-one athletes were assigned to either a 10-wk block or DUP training group in which sex, year, and event were matched. Over the course of the study, there were 4 testing sessions, which were used to evaluate a variety of strength characteristics. Although performance trends favored the block group for strength and rate of force development, no statistically significant differences were found between the 2 training groups. However, statistically different (P ≤ .05) values were found for estimated volume of work (volume load) and the amount of improvement per volume load between block and DUP groups. Based on calculated training efficiency scores, these data indicate that a block training model is more efficient than a DUP model in producing strength gains.
41
Keller, Michel. "Development of a multi-scale approach using chemical kinetics and reactive force field molecular dynamics to model soot formation and oxidation." Thesis, Institut polytechnique de Paris, 2019. http://www.theses.fr/2019IPPAE005.
Abstract:
La présente étude décrit la mise au point d'une approche multi-échelles pour la modélisation des processus pendant la formation et l'oxydation précoce de la suie. Pour ce faire, des calculs cinétiques détaillés et macroscopiques en phase gazeuse sont utilisés, à l'aide de Chemkin, pour modéliser la combustion dans un réacteur fermé hétérogène dans des conditions diverses. Afin d'étudier l'impact de la température, du mélange de carburant et du rapport d'équivalence, une gamme de ces trois paramètres a été analysée. A partir des résultats des calculs de cinétique de réaction, des molécules pertinentes pour la formation de suie, appelées précurseurs de suie, ont été extraites et selon certains critères introduits dans des boîtes de simulation pour modéliser la formation de liaisons entre les molécules de précurseurs de suie par modélisation de la dynamique moléculaire du champ de force réactif. Afin d'obtenir la meilleure description de ces processus, trois champs de forces réactives sont évalués et comparés aux calculs ab initio. L'effet des paramètres de simulation utilisés dans l'approche de modélisation moléculaire du champ de force réactive, comme la température et le pas de temps, sur la précision des calculs est étudié et analysé pour confirmer les conditions optimales de modélisation. Les impacts de la température, du mélange de combustible et du rapport d'équivalence des calculs de Chemkin se traduisent par les compositions des précurseurs de suie et l'influence des différentes compositions a été étudiée sur le taux et la structure des molécules nouvellement formées. Les structures qui en résultent se comparent bien aux résultats expérimentaux précédemment rapportés. En outre, le taux de formation de liaison entre les précurseurs de suie est en corrélation linéaire avec la température à laquelle les précurseurs de suie sont produits, tandis que le combustible et le rapport d'équivalence n'ont pas d'incidence directe sur le taux de réaction. Les structures de croissance générées sont regroupées : 1) hydrocarbures polycycliques directement liés, 2) aliphatiquement liés et 3) hydrocarbures polycycliques péricondensés. On constate que la quantité de molecules aliphatiquement liés augmente avec la quantité de contenu aliphatique du mélange de carburant. De plus, un schéma de réaction est présenté montrant les voies de réaction les plus représentatives pour former des structures de croissance dans chaque classe de grumeaux et leur interconversion éventuelle. L'impact des différences structurelles dans les structures générées par la formation de liaisons entre les précurseurs de suie, sur leur cinétique d'oxydation est testé. Pour ces quatre oxydants différents, ce sont des radicaux oxygène, des radicaux hydroxyle, des radicaux hydroperoxyle et des radicaux méthoxy, qui sont introduits et les réactions modélisées. On constate que deux des oxydants introduits se décomposent et interagissent largement et ne réagissent donc pas avec les structures de suie naissantes formées. Pour les deux autres oxydants, la cinétique des réactions d'oxydation avec les structures de suie naissantes est étudiée. On peut montrer que la cinétique est différente pour les espèces qui possèdent une chaîne latérale aliphatique par rapport à celles qui n'en possèdent pas. Enfin, les énergies d'activation des réactions d'oxydation sont estimées, en traçant la constante de vitesse sur la température inverse. Les énergies d'activation trouvées se comparent bien aux expériences et autres études de modélisation de la littérature. Le présent travail - qui applique une approche combinée de calculs cinétiques macroscopiques en phase gazeuse et de simulations de champ de force atomique réactive - offre une bonne alternative pour obtenir des différences structurelles de suie naissante pour une large gamme de conditions thermodynamiques et des mécanismes de réaction détaillés pour les processus de formation et d'oxydation des suiesIn the present study bond formation reactions between soot precursors and their role in the soot inception process is investigated. The soot precursors were generated in macroscopic detailed gas-phase kinetic calculations and according to certain criteria introduced in simulation boxes to model bond formation between soot precursor molecules with reactive force field molecular dynam-ics modeling. The impacts of temperature, fuel mixture and equivalence ratio have been investigated on the rate and structure of the newly formed molecules. The resulting structures compare well to previously reported experimental results. Furthermore, the bond formation rate between PAH is found to be linearly correlated with the temperature at which the PAH precursors are generated, while fuel and equivalence ratio do not have a direct impact on the reaction rate. The generated growth structures are lumped in: 1) directly linked, 2) aliphatically linked and 3) pericondensed polycyclic hydrocarbons. It is found that the amount of aliphatically linked PAH increases with the amount of aliphatic content of fuel mixture. Finally, a reaction scheme is presented displaying the most representative reaction pathways to form growth structures in each lumping class and their eventual intercon-version. The present work – that applies a combined approach of macroscopic gas-phase kinetic calculations and atomistic reactive force field simulations – offers a good alternative to obtain structural differences of nascent soot for a broad range of thermodynamic conditions and detailed reaction mechanisms for soot inception process
42
Jämbeck, Joakim P. M. "Computer Simulations of Heterogenous Biomembranes." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101297.
Abstract:
Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated. A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems. A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs. In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted. The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.
43
Swisher, Anna Meisinger. "Anthropometric, Strength, and Power Determinants of Throwing Performance in Collegiate Throwers." Digital Commons @ East Tennessee State University, 2009. https://dc.etsu.edu/etd/1866.
Abstract:
The purpose of this study was to identify the anthropometric, strength, and power characteristics that best predict throwing performance. Seventeen male D-I throwers (age = 19.1 ± 1.2 y; body mass = 115.1 ± 15.3 kg; height = 1.85 ± 0.06 m) were assessed for maximum strength and power. A five variable linear regression (r = 0.94, r2 = 0.88, F(5,11) = 15.89, p < 0.001, SEE = 0.68) explained 88% of the variation in shot put (SP) performance. A five variable linear regression (r = 0.91, r2 = 0.83, F(5,11) = 10.509, p = 0.001, SEE = 1.18) explained 83% of the variation in weight throw (WT) performance. Both SP and WT correlated strongly with measures of explosive strength and power (r = 0.48-0.78). Best predictors of performance were static vertical jumps and 7.26 kilogram overhead shot throw; better throwers possess greater maximum strength and power.
44
Lobanova, Olga. "Development of coarse-grained force fields from a molecular based equation of state for thermodynamic and structural properties of complex fluids." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/26139.
Abstract:
In spite of the vast array of modelling techniques and force fields available, the study of the phase behaviour, structure, microstructure, and dynamics of mixtures remains a challenging task. A systematic coarse-graining (CG) methodology is employed in this thesis involving the parameterisation of force fields using a top-down approach, by effectively describing a large number of target macroscopic thermodynamic states with a rigorous molecular-based equation of state. A recent incarnation of the Statistical Associating Fluid Theory (SAFT-gamma) is used. The underlying force field is based on the Mie intermolecular potential, which is a generalised form of the Lennard-Jones potential with a variable and versatile form of the repulsive and attractive interactions. The coarse-grained force fields developed in this manner are used directly in Molecular Dynamics simulations in order to explore the dynamical, structural, and interfacial properties, which can not be directly accessed by the equation of state (unless a suitable treatment of the inhomogenous properties of the system is made). The goal of any coarse-graining procedure is to derive simple, but accurate, robust, and transferable force fields. By aiming for the simplicity, the coarse-grained models developed in our work are typically based on the three-to-one mapping, i.e., one bead containing approximately three heavy atoms, or one-to-one mapping for the small spherical molecules, with the polar, directional, and long-ranged interactions between the beads treated implicitly using the effective spherically-symmetric Mie potentials. The SAFT-gamma Mie coarse-graining methodology is exemplified for a number of fluid systems of different complexities, including pure component systems, such as: the homologous series of n-alkanes, n-perfluoroalkanes, semifluorinated alkanes, ethers and water; binary and ternary mixtures, comprising the carbon dioxide, n-alkanes, and water; and finally the aqueous mixtures of alkyl polyoxyethylene glycol non-ionic surfactants. An accurate representation of the vapour-liquid properties with both, the equation of state and molecular simulation, is obtained for the molecules of different size and chemical nature. Describing the properties of water is, however, a much more difficult task. The CG model suffers from issues associated with the transferability and representability of the various properties for different thermodynamic conditions, as a consequence of the aggressive averaging of the strongly directional and polar forces into an effective spherically symmetrical potential. It has been shown that an isotropic single-site CG model based on a spherically symmetrical potential cannot capture all of the thermodynamic properties of water simultaneously (the issue of representability). Two different CG models of water are proposed: the first is designed to accurately reproduce the saturation liquid density and vapour pressure, and the second to capture the saturation liquid density and surface tension with high precision. Both models benefit from an accurate parameterisation of temperature dependence following the target properties over the entire temperature range of the fluid. An additional model is developed based on the two-to-one mapping, enabling more efficient large scale simulations in, for example, biomolecular systems. The models of the binary mixtures are developed by using the corresponding pure component models with an additional adjustable parameter to account for the unlike interactions; the latter are obtained by considering appropriate properties of the mixtures such as the fluid-phase equilibria or the thermodynamic properties of mixing. The unlike interactions are shown to be transferable for a quantitative description of the phase behaviour over a wide range of conditions and for the systems of related components. We are able to obtain an accurate prediction of the azeotropic point, critical loci, tree phase line, global density, and the shape of phase envelopes for studied mixtures. The quality of predictions is found comparable to the results from the atomistic models and other equations of state. The aqueous mixtures of alkyl polyoxyethylene glycol non-ionic surfactants are a key final goal of the research presented in this thesis. The CG models of the surfactants are developed within the SAFT-gamma group-contribution framework, where each functional group is derived from an accurate representation of the corresponding chemical moiety. By capturing a delicate interplay of the repulsive and attractive intermolecular interactions and obtaining the right balance between energetic and entropic effects, the various phase morphologies at ambient conditions can be reproduced in agreement with the experimental findings over the entire concentration range. The force fields developed in the current work allow for a prediction of key structural and interfacial properties. The Molecular Dynamics simulations reveal the spontaneous formation of micelles at low surfactant concentrations and a self-assembly into a bilayer at high surfactant concentrations. The aggregation numbers, the critical micelle concentration, area per molecule, the surface excess properties, and bilayer thickness are found in very good agreement with experimental data. This is very encouraging considering that only macroscopic thermophysical properties are used to develop the underlying force fields that describe the fine interactions between the molecules in the system. Despite the simplicity, coarse-grained force fields are shown to be robust and transferable; they can be applied to predict the properties which were not used in the original parameterisation procedure, with an accuracy comparable to the more sophisticated and computationally demanding models.
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Swisher, Ann Marie, Jenna M. Kraska, Michael W. Ramsey, Keith B. Painter, C. Gooden, Andrew S. Layne, William A. Sands, et al. "The Relationship of Peak Isometric Strength to Peak Aerobic Power and 3000 M Performance in Cross-country Runners." Digital Commons @ East Tennessee State University, 2008. https://dc.etsu.edu/etsu-works/4095.
Abstract:
Certain variables: peak aerobic power (PAP), running economy, and lactate threshold, act as limiting factors for endurance running. However, all of the mechanisms underlying high-level endurance running are not completely clear. Alterations in maximum and explosive strength P27 have been shown to effect positive changes in endurance performance, likely by altering P28 running economy. If strength related factors affect running economy, then this should be evident in the running performance of long-distance runners and perhaps PAP. The purpose of this study was to examine the relationships between peak isometric strength (IPF), explosive strength (rate of force development, RFD), PAP and 3 k performance (3KT) among 5 female and 7 male (n = 12) X-country runners. Force-time curve analysis was conducted for each (2 trials) isometric pull and averaged for analyses. IPF and RFD from 0 - 200 ms were determined from appropriate curves. IPFs were normalized using an allometric (IPFa) scaling equation: absolute force/ (body mass (kg)0.67). ICCs were previously shown to be > 0.9. Relationships were established with Pearson's r; statistical differences with at-Test (p < 0.05). !PF, IPFa and RFD were not different between sexes. PAP was statistically greater in males. Correlations were: PAP vs 3KT (r = -0.92); !PF vs PAP (r = 0.58), 3KT (r = -0.66); IPFa vs PAP (r = 0.45), 3KT (r = 0.45). RFD vs PAP (r = 0.58), 3KT (r = -0.65). Results indicate that strength characteristics correlate moderately to strongly with PAP and 3KT. Data suggests that strong.
46
Ansorg, Kay [Verfasser], and Bernd [Gutachter] Engels. "Development of Accurate Physically Grounded Force Fields for Intermolecular Cation-$\pi$ Interactions based on SAPT Energy Decomposition Analysis and Computational Investigation of Covalent Irreversible Vinyl Sulfone-based Protease Inhibitors / Kay Ansorg. Gutachter: Bernd Engels." Würzburg : Universität Würzburg, 2016. http://d-nb.info/111204101X/34.
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Parot, Jeremie. "Développement méthodologique du fractionnement par couplage flux / force (AF4) et spectroscopie optique pour l'étude de la matière organique dissoute aquatique : application aux estuaires de Seine et de Gironde." Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0363/document.
Abstract:
La matière organique dissoute (MOD) est constituée d’un mélange hétérogène et complexe de molécules. Elle intervient dans de nombreux processus physiques, biologiques et chimiques dans les milieux aquatiques, et notamment dans les grands cycles biogéochimiques ou le transport et la biodisponibilité des contaminants.Ainsi un des enjeux actuels de nombreux domaines de recherche (chimie, écologie, océanographie) est de mieux comprendre et caractériser la MOD dans l’environnement. Dans ce contexte-là, l’objectif de ces travaux a été le développement d’une méthodologie analytique pour l’analyse et la séparation, en fonction de la taille, par fractionnement par couplage flux-force avec flux asymétrique (AF4) de la MOD. Le développement a principalement porté sur la phase mobile, le flux croisé, le temps de focus et l’utilisation d’étalons organiques proches de la MOD, permettant de calculer sa masse moléculaire moyenne.Cette méthode optimisée, couplée à un détecteur UV/Vis, équipée d’une membrane de 1kDa, d’un espaceur de 490μm et d’une phase mobile de 5mM en tampon phosphate a permis l’étude de la dynamique de la MOD.L’application de cette méthode couplée aux techniques de spectroscopie optique (absorbance et fluorescence) a permis l’étude de la MOD dans les estuaires de Seine et de Gironde mettant en avant les effets de la marée et des saisons sur la taille et le type de MOD.De plus, différentes approches statistiques ont été développées afin de mieux appréhender les multiples variables (analytiques ou environnementales) et notamment les modèles de régression linéaire ou les cartes auto-organisatrices de KohonenDissolved organic matter (DOM) is a heterogeneous and complex mixture of molecules. It is involved in many physical, biological and chemical processes in aquatic ecosystems, especially in the major biogeochemical cycles or transport and bioavailability of contaminants.Thus one of the current issues in many areas of research (chemistry, ecology, oceanography) is to better understand and characterize DOM in the environment. In this context, the aim of this work was the development of an analytical methodology for DOM analysis and separation, depending on its size, by asymmetrical flow field-flow fractionation (AF4). The development focused on the mobile phase, the cross-flow, the focus time and the use of organic macromolecules standards close to DOM, in order to calculate its molecular weight.This optimized method, coupled with a UV/Vis detector, equipped with a 1kDa membrane, a 490μm spacer and a mobile phase of 5 mM phosphate buffer allowed us to study the MOD dynamics in estuarine environments.The application of this method coupled to optical spectroscopy techniques (absorbance and fluorescence) permitted the study of MOD in the Seine and Gironde estuaries and to highlight the tidal and the seasonal effects on the size and type of DOM.Furthermore, different statistical approaches have been developed to better understand the multiple variables (analytical or environmental), especially linear regression models or self-organizing maps (Kohonen)
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Drechsel, Nils Jan Daniel 1980. "Development of a multiscale protocol for the study of energetics of protein dymanics." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/125071.
Abstract:
Multiscale Molecular Dynamics is a popular trend in the field of computational chemistry and physics. Coarse-grained force-fields have been around for years, and used independently, but used cooperatively with all-atom force-fields combines their advantages and cancels their disadvantages. This seems to be the case, however, only when they are both compatible. In this thesis, a Multiscale Molecular Dynamics Protocol is introduced, based on earlier work by Benjamin Messer, Z. Fan, Arieh Warshel, and in other parts by Christopher Fennel and Ken Dill. The protocol consists of the following tool-set:
• A parametrization machinery that created a new coarse-grained force-field named AmberCG.
• A multiscale thermodynamic cycle utilized within a free energy perturbation context to cooperatively use the best of coarse-grained and all-atom force-fields.
• A collective variable that performs a linearization of the phase space to improve separation of product and reactant states.
• A new algorithm to calculate functional quantities on spheres bounded by complicated solvent accessible surface areas - which as a special case calculates the amount of solvent accessible surface area.
• A novel algorithm based on simple one dimensional Depth-Buffers, to identify atoms which actively form the boundary of the solvent accessible surface areas.
Executing the protocol involves the following steps:
1. Construction of a coarse-grained force-field, based on an all-atom force-field. This involves setting up coarse-grained potentials and optimization of their parameters against selected reference structures and conformations.
2. Parametrization of a solvation model which is compatible to the force-field.
3. Usage of the coarse-grained force-field to sample the conformational space of a reaction.
4. Correction of the coarse-grained results with an all-atom force-field.
5. Analysis of the results using appropriate collective coordinates.
6. Reiteration until accuracies are met.
Alternatively, instead of using the methods in the protocol, they
can be utilized stand-alone. They simplify calculations, thus provid-
ing speed-ups, while at the same time aiming to maintain or improve
accuracy. Of course, there is no free lunch, and often the methods will
include inaccuracies that exceed an acceptable threshold. However, the
multiscale protocol is meant to be seen as an iterative technique, in
which deficiency can be detected, and the protocol adjusted to restore
balance.Las simulaciones de dinámica molecular multiescala (Multiscale Molecular Dynamics) son una tendencia al alza en el sector de la Química y la Física computacionales. Los coarse-grained force-fields o campos de fuerza de grano grueso han existido desde hace años, utilizados de forma independiente, y también en cooperación con all-atom force-fields o campos de fuerza de todos los átomos dónde se combinan sus ventajas y cancelan sus desventajas. En este último caso sólo es cierto cuando los dos force-fields son compatibles. En esta tesis, introduzco un protocolo de Multiscale Molecular Dynamics basado en parte a trabajos anteriores de Benjamin Messer, Z. Fan, Arieh Warshel, y también en los de Christopher Fennell y Ken Dill. El protocolo consiste el siguiente conjunto de herramientas: 1. Un método de parametrización con cuál creé un nuevo coarse-grained force-field llamado AmberCG. 2. Un ciclo termodinámico multiescala utilizado en un contexto de perturbación de energía libre para usar cooperativamente el mejor de los coarse-grained force-fields y el de los all-atom force-fields. 3. Una variable colectiva que realiza una liberalización del espacio de fases para mejorar la separación de los estados de productos y reactivo. 4. Un nuevo algoritmo para calcular las cantidades funcionales en esferas limitadas por complicadas superficies accesibles al solvente - que como un caso especial calcula la cantidad de superficie accesible a solvente. 5. Un nuevo algoritmo basado en un buffer de profundidad, para identificar los átomos que forman activamente el límite de las superficies accesibles al solvente. La ejecución del protocolo implica los siguientes pasos: 1. Construcción de un coarse-grained force-field, basado en un all-atom force-field. Esto implica la creación de potenciales coarse-grained y la optimización de sus parámetros contra las estructuras de referencia seleccionados y sus conformaciones. 2. Parametrización de un modelo de solvatación compatible con el force-field. 3. Uso del coarse-grained force-field para muestrear el espacio con formacional de una reacción. 4. La corrección de los resultados coarse-grained con un all-atom force-field. 5. Análisis de los resultados utilizando coordenadas colectivas adecuadas. 6. Repetición hasta alcanzar las precisiones deseadas. Alternativamente, los métodos del protocolo pueden ser utilizados de forma independiente. Esto simplifica los cálculos y procura mantener, si no mejorar, la precisión. Sin embargo, todo tiene un coste y con frecuencia, los métodos incluirán inexactitudes que superarán el umbral aceptable. Aun y así, el protocolo multiescala es una técnica iterativa, en la que la deficiencia puede ser detectada, y el protocolo ajustado para restablecer el equilibrio.
49
Bhatti, Asif Iqbal. "Calculs ab-initio et simulations atomistiques des propriétés thermodynamiques et cinétiques de complexes de métaux de transition utilisés comme batteries." Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAI092/document.
Abstract:
Ce travail théorique vise à étudier, via les méthodes Premiers Principes, les propriétés des complexes de métaux de transitions, left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-} pour un usage en batterie. Pour cette étude ab-initio, les composés mono et bi-nucléaires ont été retenus. La pertinance de notre modélisation a été validée sur les composés mononucléaires. Nous nous sommes interessé au complexes de Fe, Ru et Cu pour lesquels une validation expérimentale était possible. Notre étude a principalement consisté à faire varier les degrés de liberté que nous possédons pour optimiser le voltage et la cinétique de chargement des batteries. Pour cela, nous avons fait varier le TM = Fe, Ru, et Cu, la nature des contre-ions Ci^{-}=PF_{6}^{-}, TFSI^{-} et ClO_{4}^{-} en interaction avec le polymère lors du processus de charge, ainsi que la longeur de la chaîne alkyl qui sépare les deux monomers dans le cas des composés binucléaires. Le composé à base de Fe avec une chaîne -left(CH_{2}right)_{n=6}- a été retenu comme le meilleur candidat pour une application batterie. Le composé à base Ru montre un comportement proche de celui du Fe, quant-au complexe de Cu, il présente des changements de géométrie locale sous chargement trop importants, le rendant peu apte à conduire à une cinétique efficace. Cette étude nous a permis de déterminer que l'approximation PBE était le meilleur choix possible pour modéliser nos complexes dans les conditions de fonctionnement en batterie (dans le champ créé par les contre-ions) et que l'approximation PBE0, généralement utilisée dans la littérature, ne pouvait rendre compte de la physico-chimie de nos composés dans de telles conditions.De surcroît, nous avons dévelopé pour le complexe de Fe, un potentiel atomistique de type “Champ de forces” de manière à pouvoir aborder les aspects dynamiques impliquant de plus grandes tailles de boîte de simulation. Ici, nous modélisons une structure 3D, totalement réticulée à partir de nos monomères à base de Fe. Nous nous sommes servi de la base de donnés DFT que nous avions généré (énergies, géométries, état de spin et fréquences vibrationnelles calculées) pour ajuster les paramètres entrant dans l'écriture du modèle. La construction de la géométrie initiale du polymère 3D a nécessité l'écriture d'un code de calcul visant à produire un arrangement complétement réticulé et à assigner les charges effectives issues des calculs DFT. Ce modèle nous a permis de déterminer les coefficients de diffusion des contre-ions pour les états totalement chargé et non-chargé. Un calcul plus ambitieux vise à déterminer les chemins de diffusion des contre-ions lors d'un processus de chargement en considérant un seul centre de degré d'oxydation 3+ au centre du polymère 3D, pour lequel les centres actifs possèdent un degré d'oxidation 2+. Les contre-ions assurent la neutralité globale.Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modelingAbstract Standard redox potentials for mono and bi-nuclear transition metal (TM) complexes left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-}, have been investigated using First Principles Calculation. Three metal centers are investigated: Fe, Ru, and Cu. Our modeling is validated on mono-nuclear compounds. This approach consists in determining the best small polymer (bi-nuclear) made out of these monomers for a battery application. For that, we varied the three available degrees of freedom i.e., the nature of the central TM atom (Fe, Ru, and Cu), counter-ions Ci=PF_{6}^{-}, TFSI^{-} and ClO_{4}^{-} in interaction with the polymer, and the alkyl chain -left(CH_{2}right)_{n}- of length n that connects both mono-nuclear in the bi-nuclear compound. The Iron compound with -left(CH_{2}right)_{n=6}- is found to be the best candidate. The left[Culeft(dmbpyright)_{2}right]^{n+}nCi^{-} complex shows too much structure deformation upon loading, making it less reliable for cathode material. Moreover, we studied two XC functional, PBE and PBE0 and found, for three complexes PBE approximation retains the ligand field picture whereas PBE0 functional induces an exaggerated and unexpected band dispersion by dissolving the ligand field picture expected for the octahedral environment of the TM in the studied complexes. These findings validate that hybrid functional for which it was designed to localize and cancel self-interaction error does not work for all system. More particularly, the PBE0 approximation fails to model the three complexes (Fe, Ru, and Cu) in functional conditions (in the field made by the counter-ions).Abstract Further, we have developed an atomistic potential relying on the Force Field scheme for the Iron complex in order to study the dynamical properties of this compound at larger simulation scale (3D reticulated polymerization made of our Fe complex monomers). We made an intensive use of our DFT data (energies, geometries, spin-state configurations and calculated vibrational properties) to develop the required parameters entering the model. Moreover, computational techniques (written python language) were developed specifically to create a 3D structure of transition metal complexes satisfying the condition to be fully reticulated. Bounding conditions had to be designed and a procedure aiming at fixing reliable and physical effective charges on each atom of the simulation cell (compatible with DFT results) were developed. Our first simulations have been attached to calculate the diffusion coefficients of the counter-ions in both the fully loaded and unloaded states. A more ambitious and realistic calculation aims at investigating the paths of the counter-ions when one single center starts to be loaded in an unloaded environment.Abstract Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modeling
50
Beckstein, Pascal. "Methodenentwicklung zur Simulation von Strömungen mit freier Oberfläche unter dem Einfluss elektromagnetischer Wechselfelder." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-232474.
Abstract:
Im Bereich der industriellen Metallurgie und Kristallzüchtung treten bei zahlreichen Anwendungen, wo magnetische Wechselfelder zur induktiven Beeinflussung von leitfähigen Werkstoffen eingesetzt werden, auch Strömungen mit freier Oberfläche auf. Das Anwendungsspektrum reicht dabei vom einfachen Aufschmelzen eines Metalls in einem offenen Tiegel bis hin zur vollständigen Levitation. Auch der sogenannte RGS-Prozess, ein substratbasiertes Kristallisationsverfahren zur Herstellung siliziumbasierter Dünnschichtmaterialien, ist dafür ein Beispiel. Um bei solchen Prozessen die Interaktion von Magnetfeld und Strömung zu untersuchen, ist die numerische Simulationen ein wertvolles Hilfsmittel. Für beliebige dreidimensionale Probleme werden entsprechende Berechnungen bisher durch eine externe Kopplung kommerzieller Programme realisiert, die für Magnetfeld und Strömung jeweils unterschiedliche numerische Techniken nutzen. Diese Vorgehensweise ist jedoch im Allgemeinen mit unnötigem Rechenaufwand verbunden. In dieser Arbeit wird ein neu entwickelter Methodenapparat auf Basis der FVM vorgestellt, mit welchem sich diese Art von Berechnungen effizient durchführen lassen. Mit der Implementierung dieser Methoden in foam-extend, einer erweiterten Version der quelloffenen Software OpenFOAM, ist daraus ein leistungsfähiges Werkzeug in Form einer freien Simulationsplattform entstanden, welches sich durch einen modularen Aufbau leicht erweitern lässt. Mit dieser Plattform wurden in foam-extend auch erstmalig dreidimensionale Induktionsprozesse im Frequenzraum gelöst.