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Dissertations / Theses on the topic 'Reactive force field molecular dynamics simulations'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Strickland, Christopher E. "Reactive molecular dynamics force field for simulating hydrogenated boron nitrogen compounds and interactions with silica surfaces." Online access for everyone, 2007. http://www.dissertations.wsu.edu/Thesis/Fall2007/C_Strickland_110907.pdf.

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2

Rimsza, Jessica M. "Reactions and Interfacial Behaviors of the Water–Amorphous Silica System from Classical and Ab Initio Molecular Dynamics Simulations." Thesis, University of North Texas, 2016. https://digital.library.unt.edu/ark:/67531/metadc849660/.

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Due to the wide application of silica based systems ranging from microelectronics to nuclear waste disposal, detailed knowledge of water-silica interactions plays an important role in understanding fundamental processes, such as glass corrosion and the long term reliability of devices. In this dissertation, atomistic computer simulation methods have been used to explore and identify the mechanisms of water-silica reactions and the detailed processes that control the properties of the water-silica interfaces due to their ability to provide atomic level details of the structure and reaction path

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3

Raymand, David. "Surface and Interface Studies of ZnO using Reactive Dynamics Simulation." Doctoral thesis, Uppsala universitet, Strukturkemi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-129304.

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About 90% of all chemicals are produced with the help of catalysts, substances with the ability to accelerate reactions without being consumed. Metal oxides play a prominent role in catalysis, since they are able to act reversibly in many chemical processes. Zink oxide (ZnO) is used to catalyse a number of industrially important reactions. For many of these reactions water is present as a reactant, product, or byproduct. The surface structure has a significant impact on the catalytic activity. However, currently, no experimental method simultaneously offers the spatial and temporal resolution

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4

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.

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5

Mohomed, Naleem Mohomed Nawavi. "Molecular dynamics simulations of aqueous ion solutions." Diss., Kansas State University, 2017. http://hdl.handle.net/2097/35458.

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Doctor of Philosophy<br>Department of Chemistry<br>Paul Edward Smith<br>The activity and function of many macromolecules in cellular environments are coupled with the binding of ions such as alkaline earth metal ions and poly oxo anions. These ions are involved in the regulation of important processes such as protein crystallization, nucleic acid and protein stability, enzyme activity, and many others. The exact mechanism of ion specificity is still elusive. In principle, computer simulations can be used to help provide a molecular level understanding of the dynamics of hydrated ions and their

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6

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.

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7

Edström, Filip. "Parametrization of Reactive Force Field using Metropolis Monte Carlo." Thesis, Umeå universitet, Institutionen för fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-161972.

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8

Andrews, Casey Tyler. "Coarse grained potential functions for proteins derived from all-atom explicit-solvent molecular dynamics simulations." Diss., University of Iowa, 2014. https://ir.uiowa.edu/etd/1949.

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The use of computational simulation to study the dynamics and interactions of macromolecules has become an important tool in the field of biochemistry. A common method to perform these simulations is to use all-atom explicit-solvent molecular dynamics (MD). However, due to the limitations in computational power currently available, this method is not practical for simulating large-scale biomolecular systems on long timescales. An alternative is to perform implicit-solvent Brownian dynamics (BD) simu

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9

Kang, Myungshim. "Molecular dynamics simulations and theory of intermolecular interactions in solutions." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/1282.

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10

Chia, Chung Lim. "Classical and ReaxFF molecular dynamics simulations of fuel additives at the solid-fluid interface." Thesis, University of Manchester, 2019. https://www.research.manchester.ac.uk/portal/en/theses/classical-and-reaxff-molecular-dynamics-simulations-of-fuel-additives-at-the-solidfluid-interface(a1a5cb5d-3283-4ebc-9ef1-b44aac16821b).html.

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In the automotive industry, a kind of fuel additives, known as surfactant, is used to protect metallic surfaces. Its efficiency strongly depends on factors such as temperature, solvent properties and the presence of other surfactants in the system. In this thesis, both classical and ReaxFF molecular dynamics (MD) simulations are used in studying the impacts of these factors on the adsorption of organic surfactants at the fluid-solid interface. Firstly, a classical MD simulation study of competitive adsorption is carried out on a multi-functional phenol and amine surfactant model with ethanol a

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11

Ivani, Iván. "Parmbsc1: Parameterization and Validation of a new State-of-the-art Force Field for DNA Simulations." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/402737.

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Classical force fields are the core of classical simulations, particularly of molecular dynamics (MD), a technique that is changing our view on the structure, flexibility and function of biological macromolecules. Originated from the pioneering work of Lifson’s group in the sixties, force fields have been in continuous evolution, improving in each generation the accuracy in the representation of proteins and nucleic acid. Force field development is tightly connected to the refinement of simulation procedures and to the extension of simulation time scales. Thus, as simulation time passed the

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12

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.

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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 pert

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13

Bhatta, Ram S. "Dynamics of Coupled Large Amplitude Motions from Small Non-Rigid Molecules to Conjugated Polymers." University of Akron / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=akron1353339449.

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14

Miller, Mark Stephen. "Use of osmotic coefficient measurements to validate and to correct the interaction thermodynamics of amino acids in molecular dynamics simulations." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6476.

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Molecular dynamics simulations are an increasingly valuable tool to biochemical researchers: advances in computational power have expanded the range of biomolecules that can be simulated, and parameters describing these interactions are increasingly accurate. Despite substantial progress in force field parameterization, recent simulations of protein molecules using state-of-the-art, fixed-charge force fields revealed that the interactions among and within protein molecules can be too favorable, resulting in unrealistic aggregation or structural collapse of the proteins being simulated. To unde

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15

Kapustin, Yaroslav A. "Forcefield-Based Simulations of Bulk Structure of Mo-V-(Te, Nb)-O M1 Phase Catalysts for Selective Propane Ammoxidation to Acrylonitrile." University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1296848202.

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16

Tran, Thanh Thuy. "Lattice model for amyloid peptides : OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides." Thesis, Sorbonne Paris Cité, 2016. http://www.theses.fr/2016USPCC187/document.

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La maladie d’Alzheimer touche plus de 40 millions de personnes dans le monde et résulte de l’agrégation du peptide beta-amyloïde de 40/42 résidus. En dépit de nombreuses études expérimentales et théoriques, le mécanisme de formation des fibres et des plaques n’est pas élucidé, et les structures des espèces les plus toxiques restent à déterminer. Dans cette thèse, je me suis intéressée à deux aspects. (1) La détermination du noyau de nucléation (N*) de deux fragments (Aβ)16-22 et (Aβ)37-42. Mon approche consiste à déterminer les paramètres OPEP du dimère (Aβ)16-22 en comparant des simulations M

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17

Villa, Francesco. "Computer simulations to engineer PDZ-peptide recognition." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLX076/document.

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Les interactions protéine-protéine (IPPs) médient la signalisation cellulaire. Leur ingénierie peut fournir des informations et conduire au développement de molécules thérapeutiques. Les domaines PDZ sont des médiateurs importants de IPPs. Elles lient les 4--10 résidus C-terminaux de protéines cibles. Elles lient aussi les peptides correspondants, qui peuvent servir de systèmes modèles ou d'inhibiteurs. Nous avons développé deux approches computationnelles et les avons appliquées au domaine PDZ de la protéine Tiam1, un facteur d'échange pour la protéine Rac, impliqué dans la protrusion neurona

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18

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.

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19

Pacaud, Fabien. "Étude des propriétés physicochimiques de verres borosilicatés et de borosilicates de lanthane par dynamique moléculaire à partir d’un champ de force polarisable." Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066504/document.

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Dans le cadre de la vitrification de déchets nucléaires, la connaissance et la maîtrise des propriétés structurales et dynamiques des verres incluant les radioéléments sont importantes (dans le liquide et le solide). Elles influencent notamment la qualité du colis de verre, la durée de vie du procédé de vitrification et la quantité de produits de fission qu’il est possible d’introduire. Des simulations de dynamique moléculaire ont été réalisées afin d’analyser l’influence de la composition des matrices vitreuses sur les propriétés structurales et dynamiques. Le verre nucléaire industriel R7T7

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20

Konduri, Suchitra. "Computational investigations of molecular transport processes in nanotubular and nanocomposite materials." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/28281.

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Thesis (M. S.)--Chemical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Nair, Sankar; Committee Member: Koros, William; Committee Member: Ludovice, Peter; Committee Member: Meredith, Carson; Committee Member: Thio, Yonathan; Committee Member: Zhou, Min.

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21

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.

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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

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22

Lorenz, Erik E. "Atomistische Modellierung und Simulation des Filmwachstums bei Gasphasenabscheidungen." Master's thesis, Universitätsbibliothek Chemnitz, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-159520.

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Gasphasenabscheidungen werden zur Produktion dünner Schichten in der Mikro- und Nanoelektronik benutzt, um eine präzise Kontrolle der Schichtdicke im Sub-Nanometer-Bereich zu erreichen. Elektronische Eigenschaften der Schichten werden dabei von strukturellen Eigenschaften determiniert, deren Bestimmung mit hohem experimentellem Aufwand verbunden ist. Die vorliegende Arbeit erweitert ein hochparalleles Modell zur atomistischen Simulation des Wachstums und der Struktur von Dünnschichten, welches Molekulardynamik (MD) und Kinetic Monte Carlo-Methoden (KMC) kombiniert, um die Beschreibung beliebig

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23

Thakore, Vaibhav. "Nonlinear dynamic modeling, simulation and characterization of the mesoscale neuron-electrode interface." Doctoral diss., University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5529.

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Extracellular neuroelectronic interfacing has important applications in the fields of neural prosthetics, biological computation and whole-cell biosensing for drug screening and toxin detection. While the field of neuroelectronic interfacing holds great promise, the recording of high-fidelity signals from extracellular devices has long suffered from the problem of low signal-to-noise ratios and changes in signal shapes due to the presence of highly dispersive dielectric medium in the neuron-microelectrode cleft. This has made it difficult to correlate the extracellularly recorded signals with

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24

Lorenz, Erik E. "Atomistische Modellierung und Simulation des Filmwachstums bei Gasphasenabscheidungen." Master's thesis, Fraunhofer ENAS, 2014. https://monarch.qucosa.de/id/qucosa%3A20181.

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Gasphasenabscheidungen werden zur Produktion dünner Schichten in der Mikro- und Nanoelektronik benutzt, um eine präzise Kontrolle der Schichtdicke im Sub-Nanometer-Bereich zu erreichen. Elektronische Eigenschaften der Schichten werden dabei von strukturellen Eigenschaften determiniert, deren Bestimmung mit hohem experimentellem Aufwand verbunden ist. Die vorliegende Arbeit erweitert ein hochparalleles Modell zur atomistischen Simulation des Wachstums und der Struktur von Dünnschichten, welches Molekulardynamik (MD) und Kinetic Monte Carlo-Methoden (KMC) kombiniert, um die Beschreibung beliebig

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25

Olivieri, Lilian. "Recherche et caractérisation par dynamique moléculaire d'états intermédiaires pour la complexation entre la protéine FKBP12 et des ligands de haute affinité." Thesis, La Réunion, 2012. http://www.theses.fr/2012LARE0011/document.

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FKBP12 est une protéine ubiquitaire, principalement cytosolique, qui est au carrefour de plusieurs voies signalétiques. Son abondance naturelle dans les tissus nerveux peut être reliée à son implication dans les maladies neurodégénératives telles que les maladies d'Alzheimer et de Parkinson ainsi que dans les neuropathies périphériques et diabétiques ou dans des blessures des cordons spinaux. De nombreuses études ont montré que des molécules exogènes (ligands) venant se fixer sur cette protéine permettent la régénération d'un grand nombre de connexions neuronales endommagées. Une difficulté pr

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26

Heinze, Georg. "Untersuchung von Oxidationsprozessen an Siliziumnanodrähten mittels Molekulardynamik." Bachelor's thesis, Universitätsbibliothek Chemnitz, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-231999.

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Siliziumnanodrähte (SiNWs) bieten eine aussichtsreiche Grundlage zur Entwicklung neuartiger nanoelektronischer Bauelemente, wie Feldeffekttransistoren oder Sensoren. Dabei ist insbesondere die Oxidation der Drähte interessant, weil diese weitreichenden Einfluss auf die elektronischen Eigenschaften der Bauelemente hat, die aus den SiNWs gefertigt werden. Die Größe der untersuchten Strukturen erfordert eine atomistische Analyse des Oxidationsprozesses. In der vorliegenden Arbeit wird der bisher wenig verstandene Beginn der Oxidation dünner Drähte molekulardynamisch simuliert, wobei als Potential

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27

Heinze, Georg. "Molekulardynamische Simulation der Oxidation dünner Siliziumnanodrähte: Einfluss von Draht- und Prozessparametern auf die Struktur." 2018. https://monarch.qucosa.de/id/qucosa%3A32834.

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Siliziumnanodrähte (SiNWs) bieten aufgrund ihrer exzellenten elektrostatischen Kontrollierbarkeit eine gute Grundlage für die Entwicklung neuartiger Bauelemente, wie rekonfigurierbarer Feldeffekttransistoren (RFETs). Da SiNWs durch die Oxidation gezielt verzerrt werden können und diese Verzerrung die Bandstruktur des Siliziums verändert, bietet der Oxidationsprozess eine Möglichkeit, die Leitungseigenschaften der RFETs zu modulieren und eine symmetrische Transfercharakteristik zu erhalten. Die Untersuchung von SiNWs mit Durchmessern im einstelligen Nanometerbereich bedarf eines atomistischen A

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28

Matthes, Dirk. "Spontaneous aggregation of fibril-forming peptides studied by Molecular Dynamics simulations." Doctoral thesis, 2011. http://hdl.handle.net/11858/00-1735-0000-000D-F04B-3.

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29

Pecheanu, Rodica. "Molecular Dynamics Simulations of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine and 5-(4-butyloxyphenyl)-2-octyloxypyrimidine Liquid Crystal Phases." Thesis, 2009. http://hdl.handle.net/1974/5295.

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Molecular dynamics simulations of the liquid crystal phases of 2-(4-butyloxyphenyl)-5-octyloxypyrimidine (2PhP) and 5-(4-butyloxyphenyl)-2-octyloxy-pyrimidine (5PhP) are the focus of this thesis. The 2PhP and 5PhP mesogens display different liquid crystalline phase sequences, despite having very similar molecular structures. Specifically, both mesogens consist of aromatic phenyl and pyrimidine cores in between two flexible alkoxy tails, but they differ in the preferred core conformation. A multi-site coarse-grained model, in which the aromatic rings are represented by soft quadrupolar ellips

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30

Loccisano, Anne Elizabeth. "Molecular dynamics simulation studies of DNA and proteins force field parameter development for small ligands and convergence analysis for simulations of biomolecules /." 2007. http://etd1.library.duq.edu/theses/available/etd-12032007-105817/unrestricted/LoccisanoDissertation.pdf.

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Thesis (Ph.D.)--Duquesne University, 2007.<br>Title from document title page. Abstract included in electronic submission form. Includes bibliographical references (p. 32-55; 109-116; 185-191; 290-299; 330-332).

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31

Mahajan, Chetan Vasant. "Atomistic and molecular simulations of novel acid-base blend membranes for direct methanol fuel cells." 2013. http://hdl.handle.net/2152/23030.

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One of the main challenges to transform highly useful Direct Methanol Fuel Cells (DMFC) into a commercially viable technology has been to develop a low cost polymer electrolyte membrane (PEM) with high proton conductivity, high stability and low methanol crossover under operating conditions desirably including high temperatures. Nafion, the widely used PEM, fails to meet all of these criteria simultaneously. Recently developed acid-base polymer blend membranes constitute a promising class of PEMs alternative to Nafion on above criteria. Even though some of these membranes produce better perfor

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32

Lenahan, Frances D., Thomas M. Koller, Tobias Klein, and Andreas P. Fröba. "Improvement of a transferable force field for the prediction of self-diffusivity, viscosity, surface tension, and density of long-chained linear and branched alkanes and alcohols up to 573 K by molecular dynamics simulations." 2019. https://ul.qucosa.de/id/qucosa%3A72428.

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33

BARVÍKOVÁ, Hana. "Studium interakcí organické hmoty a jejích složek pomocí molekulární dynamiky." Master's thesis, 2014. http://www.nusl.cz/ntk/nusl-173115.

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Humic acids and humates are principal components of humic substances major organic constituents of soil, peat, coal and water around the world. I was involved in research into molecular dynamics simulations of interactions of quartz surfaces with aqueous solutions of ions and small organic molecules representing basic building blocks of larger biomolecules and functional groups of organic matter. We studied interactions of molecules with surfaces for a set of surface charge densities corresponding to the experimentally or environmentally relevant ranges of pH values employing molecular mechani

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34

Heinze, Georg. "Untersuchung von Oxidationsprozessen an Siliziumnanodrähten mittels Molekulardynamik." Bachelor's thesis, 2017. https://monarch.qucosa.de/id/qucosa%3A20849.

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Siliziumnanodrähte (SiNWs) bieten eine aussichtsreiche Grundlage zur Entwicklung neuartiger nanoelektronischer Bauelemente, wie Feldeffekttransistoren oder Sensoren. Dabei ist insbesondere die Oxidation der Drähte interessant, weil diese weitreichenden Einfluss auf die elektronischen Eigenschaften der Bauelemente hat, die aus den SiNWs gefertigt werden. Die Größe der untersuchten Strukturen erfordert eine atomistische Analyse des Oxidationsprozesses. In der vorliegenden Arbeit wird der bisher wenig verstandene Beginn der Oxidation dünner Drähte molekulardynamisch simuliert, wobei als Potential

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