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Dissertations / Theses on the topic 'Molecular dynamics simulations (MD)'

Author: Grafiati

Published: 4 June 2025

Last updated: 15 July 2025

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1

Sharma, Arjun. "Molecular Dynamics Simulations of Stimuli-Responsive Polymers." ScholarWorks@UNO, 2016. http://scholarworks.uno.edu/td/2275.

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Polymers that undergo dramatic changes in structural conformations in response to numerous stimuli such as temperature, pH, electric and magnetic fields, light inten- sity, biological molecules, and solvent polarity, are known as stimuli-responsive or ”smart” polymers. There is a broad range of very promising applications of these materials in catalysis, environmental remediation, sensors or actuator systems, and as delivery systems of therapeutic agents. Researchers have been trying to mimic smart polymers based on properties of polymers found in nature such as proteins, carbohydrates and nuc

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2

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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3

Guinto, Ferdiemar Cardenas Jr. "Investigating Secondary Structure Features of YAP1 Protein Fragments Using Molecular Dynamics (MD) and Steered Molecular Dynamics (SMD) Simulations." Scholarly Commons, 2017. https://scholarlycommons.pacific.edu/uop_etds/2973.

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Molecular dynamics (MD) is a powerful tool that can be applied to protein folding and protein structure. MD allows for the calculation of movement, and final position, of atoms in a biomolecule. These movements can be used to investigate the pathways that allow proteins to fold into energetically favorable structures. While MD is very useful, it still has its limitations. Most notable, computing power and time are of constant concern. Protein structure is inherently important due to the direct link between the structure of a protein and its function. One of the four levels of protein stru

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4

Hedman, Fredrik. "Algorithms for Molecular Dynamics Simulations." Doctoral thesis, Stockholm University, Department of Physical, Inorganic and Structural Chemistry, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1008.

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<p>Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel MD simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed. </p><p>A method for performing <i>ab initio </i>MD is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored.</p><p>

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5

Svensson, Pamela H. W. "Molecular Dynamics Simulations of CsCl in Water." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-382908.

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Salt is a common substance of which the structure has been investigated in this study. Molecular dynamics simulations has been performed of a solution of Caesium Chloride in water for four different concentrations. Radial distribution functions show a change in the structure of oxygen-oxygen with increasing concentration, especially for the second solvent shell. Contributions of the ions increases the separation between the water molecules and a long range peak of approximately 0.9 nm appears for higher concentrations. The results can be compared with experimental results performed at Swedish

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6

Babbi, Matteo. "Studying the alignment of 5-cyanobiphenyl on a polydimethylsiloxane surface through Molecular Dynamics simulations." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2018. http://amslaurea.unibo.it/16675/.

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For 40 years, at the University of Bologna, a group of researchers coordinated by professor Claudio Zannoni has been studying liquid crystals by employing computational techniques. They have developed effective models of these interesting, and still far from being completely understood, systems. They were able to reproduce with simulations important features of some liquid crystal molecules, such as transition temperature. Then they focused their attention on the interactions that these molecules have with different kinds of surface, and how these interactions affect the alignment of liquid cr

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7

Gu, Yina. "Protein Dynamics, Loop Motions and Protein-Protein Interactions CombiningNuclear Magnetic Resonance (NMR) Spectroscopy with Molecular Dynamics (MD)Simulations." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1480416947335008.

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8

Kokou, Leopold Lambert Yaovi. "Molecular Dynamics Simulations of the Structures of Europium Containing Silicate and Cerium Containing Aluminophosphate Glasses." Thesis, University of North Texas, 2012. https://digital.library.unt.edu/ark:/67531/metadc149624/.

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Rare earth ion doped glasses find applications in optical and photonic devices such as optical windows, laser, and optical amplifiers, and as model systems for immobilization of nuclear waste. Macroscopic properties of these materials, such as luminescence efficiency and phase stability, depend strongly on the atomic structure of these glasses. In this thesis, I have studied the atomic level structure of rare earth doped silicate and aluminophosphate glasses by using molecular dynamics simulations. Extensive comparisons with experimental diffraction and NMR data were made to validate the struc

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9

Vedam, Venkata S. "Stability of carbon dioxide and methane hydrates in water in presence of small driving forces using MD simulations." Morgantown, W. Va. : [West Virginia University Libraries], 2009. http://hdl.handle.net/10450/10794.

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Thesis (M.S.)--West Virginia University, 2009.<br>Title from document title page. Document formatted into pages; contains viii, 93 p. : ill. (some col.), col. map. Includes abstract. Includes bibliographical references.

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10

Åman, Ken. "Water Relaxation Processes as Seen by NMR Spectroscopy Using MD and BD Simulations." Doctoral thesis, Umeå University, Chemistry, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-394.

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<p>This thesis describes water proton and deuterium relaxation processes, as seen by Nuclear Magnetic Resonance (NMR) spectroscopy, using Brownian Dynamics (BD) or Molecular Dynamics (MD) simulations. The MD simulations reveal new detailed information about the dynamics and order of water molecules outside of a lipid bilayer. This is very important information in order to fully understand deuterium NMR measurements in lipid bilayer systems, which require an advanced analysis, because of the complicated water motion (such as tumbling and self-diffusion). The BD simulation methods are combined w

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11

Fu, Xuebing. "How trehalose protects DNA in the dry state: a molecular dynamics simulation." Texas A&M University, 2008. http://hdl.handle.net/1969.1/86002.

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Molecular dynamics simulations were conducted on a system consisting of a decamer DNA solvated by trehalose and water (molecular ratio= 1:2), to mimic a relatively dry state for the DNA molecule. Simulations were performed at two different temperatures, 300 K and 450 K. The B-form DNA structure was shown to be stable at both temperatures. The analysis of hydrogen bonds between trehalose/water and DNA revealed that trehalose and backbone DNA formed the largest number of hydrogen bonds and thus constituted the major effect of structural protection for DNA. The number of hydrogen bonds formed by

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12

Xie, Yinghong. "MD simulations of bio-nano-system : controllable translocation and selective separation of single-stranded DNAs through a polarized CNT membrane /." Click to view the E-thesis via HKUTO, 2007. http://sunzi.lib.hku.hk/HKUTO/record/B39559026.

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13

謝迎洪 and Yinghong Xie. "MD simulations of bio-nano-system: controllable translocation and selective separation of single-stranded DNAs through a polarized CNT membrane." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2007. http://hub.hku.hk/bib/B39559026.

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14

Bos�ko, Jaroslaw Tomasz, and jbosko@unimelb edu au. "Molecular simulation of dendrimers under shear." Swinburne University of Technology. Centre for Molecular Simulation, 2005. http://adt.lib.swin.edu.au./public/adt-VSWT20050804.141034.

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In this work flow properties of dendrimers are studied with the aid of molecular simulations. For the first time the results of the nonequilibrium molecular dynamics simulations of the dendrimers in the melt are reported. Molecules are modelled at the coarse-grained level using the bead-spring model. The objective of this research is to analyse the influence of the molecular topology in the macroscopic flow behaviour of the melts. Systems of dendrimers of generations 1 to 4 undergoing planar shear are compared to the melts composed of linear chain polymers. The internal structure and shap

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15

Kammler, Marvin. "MD simulations of atomic hydrogen scattering from zero band-gap materials." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0003-C17A-A.

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16

Cuchillo, Rémi Jean-Michel José. "Discovering and exploiting hidden pockets at protein interfaces." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/10521.

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The number of three-dimensional structures of potential protein targets available in several platforms such as the Protein Data Bank is subjected to a constant increase over the last decades. This observation should be an additional motivation to use structure-based methodologies in drug discovery. In the recent years, different success stories of Structure Based Drug Design approach have been reported. However, it has also been shown that a lack of druggability is one of the major causes of failure in the development of a new compound. The concept of druggability can be used to describe prote

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Davydova, Alexandra. "MD simulation of H2 plasma/graphene interaction for innovative etching processes development." Thesis, Grenoble, 2014. http://www.theses.fr/2014GRENT054.

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Graphène est un matériau bidimensionnel unique physique, chimique et les propriétés mécaniques. Il pourrait être prometteur pour de nouvelles applications, mais le contrôle nm échelle de traitement de graphène défis la technologie actuelle, en particulier dans le traitement du plasma, empêchant ainsi le développement de la technologie à base de graphène à l'échelle industrielle<br>Graphene is a two-dimensional material with unique physical, chemical and mechanical properties. It could be promising for novel applications, but the nm-scale control of graphene processing challenges current techno

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18

Okyay, Çağla. "Experimental study and molecular dynamics (MD) modeling of a nucleic acid in nano-confinement." Electronic Thesis or Diss., université Paris-Saclay, 2024. https://www.biblio.univ-evry.fr/theses/2024/2024UPASF063.pdf.

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La technologie des nanopores s'est imposée comme un outil puissant pour étudier le transport biomoléculaire, en particulier pour la translocation et le dézippage des molécules d'ADN. Les études expérimentales ont montré la capacité des nanopores de l'α-hémolysine (αHL) à distinguer différentes séquences et orientations d'ADN. Cependant, les résultats expérimentaux fournissent principalement des informations sur le courant bloqué et le temps de translocation, laissant les détails au niveau moléculaire du processus de dézippage inexplorés. Bien que les simulations de dynamique moléculaire tout-a

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19

Gebus, Adrien. "From lipid-mediated molecular interactions to a synergistic antimicrobial activity : a study of PGLa and magainin 2 amphipathic peptides using NMR spectroscopy and in silico molecular dynamics simulations." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAF017.

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PGLa et magainin 2 sont deux peptides amphiphiles, avec une activité antimicrobienne synergique. Nous avons étudié la structure et la dynamique de ces peptides, ainsi que leurs interactions avec les membranes. Par spectroscopie RMN en phase solide et liquide nous avons obtenu des informations sur la structure de PGLa dans un environnement hydrophobe.Un modèle 3D de PGLa en micelles a été construit, et différentes populations de PGLa en bicouche lipidique on été identifiées. Des simulations de MD ont permis d'étudier l'interaction de PGLa et magainin 2 entre eux et avec avec la membrane. Nous e

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Cascio, Michele. "Coupled Molecular Dynamics and Finite Element Methods for the simulation of interacting particles and fields." Doctoral thesis, Università di Catania, 2019. http://hdl.handle.net/10761/4120.

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The dynamical simulation of many particle systems is currently a widespread technique in many fields: e.g. nuclear and atomic physics, computational material science, computational chemistry, molecular biology and pharmacology. Under the locution Molecular Dynamics (MD) we can regroup a variety of approaches and numerical codes, whereas the commonalities are: 1) the atomistic (or nuclear) resolution (i.e. particles are atoms or nucleons), 2) the force derivation, starting from the systems configuration, through semi-classical (also called semi-empirical) or quantum mechanics based theoretic

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21

Gutheim, Sabina. "Characterization of Alcohol Modulation of a Pentameric Ligand-gated Ion Channel with Electrophysiology and Molecular Dynamics Simulations." Thesis, KTH, Tillämpad fysik, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-296530.

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Pentameric ligand-gated ion channels (pLGICs) are membrane receptors that play a crucial role in every living organism. The pLGIC protein structure forms a pore through the membrane of a cell that can let specific ions pass through, upon activation by endogenous agonists. pLGICs are allosterically modulated by ligands binding at allosteric sites, that either stabilize a certain conformation or change the binding affinity of the endogenous agonist. However, much remains unknown about the exact way in which these modulators bind to and affect pLGICs. An increased understanding could help in the

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22

Stelzl, Lukas Sebastian. "Studying marcomolecular transitions by NMR and computer simulations." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6e4bbe06-fc58-471b-a932-d940fe78b9a5.

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Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shield

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23

Turelli, Michele. "Combined MD/DFT protocol for the simulation of molecular materials for organic solar cells." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/294003.

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In much of the literature about organic photovoltaics, the topic is framed within the current landscape of energy production and the research on these materials is cited as a possible solution to the energy crisis looming ahead. Despite being the most frequent, this is by no means the only perspective that can be offered. Indeed, the same research may also be set within the larger perspective offered by the field of functional materials. These materials are usually exploited for their particular responses to electrical, magnetic and chemical stimuli and are at the basis of many technologies fu

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Turelli, Michele. "Combined MD/DFT protocol for the simulation of molecular materials for organic solar cells." Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/294003.

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In much of the literature about organic photovoltaics, the topic is framed within the current landscape of energy production and the research on these materials is cited as a possible solution to the energy crisis looming ahead. Despite being the most frequent, this is by no means the only perspective that can be offered. Indeed, the same research may also be set within the larger perspective offered by the field of functional materials. These materials are usually exploited for their particular responses to electrical, magnetic and chemical stimuli and are at the basis of many technologies fu

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25

Lexelius, Rebecka. "Formation of Monolayered Phospholipids using Molecular Dynamics." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-356370.

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The very fundamental properties of biological membranes can be understood by studying their formation. This sets a good foundation for research related to how the membranes interact with organic molecules and ions; something of great value in the quest of explaining transport phenomena through cell membranes. It is furthermore of growing interest within the pharmacological research and contributes to the apprehension of life at the molecular level. In this thesis Molecular Dynamics has been used to simulate how evenly distributed phospholipids solvated in water leads to the formation of monola

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Wang, Guangyu. "An MD-SPH Coupled Method for the Simulation of Reactive Energetic Materials." University of Cincinnati / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1491559185266293.

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Zhang, Wei. "Computer simulation of secondary structure of biological and synthetic macromolecules." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/29729.

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Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009.<br>Committee Chair: Ludovice, Pete; Committee Member: Chen, Rachel; Committee Member: Harvey, Steve; Committee Member: Sambanis, Athanassios; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.

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Bekele, Selemon. "Structural and Dynamical Properties of Water and Polymers at Surfaces and Interfaces: A Molecular Dynamics Investigation." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron1530040420616781.

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Jaeger, Tamara D. "Insights into Physical Aging of Thermally-Quenched and Solvent-Cast Polymers from Molecular Dynamics Simulation." University of Akron / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=akron1597238400716617.

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30

Fritz, Susanne. "MD-Simulationen zur Adsorption von Additiven aus wässriger Lösung auf Calciumsulfat-Flächen." Doctoral thesis, Technische Universitaet Bergakademie Freiberg Universitaetsbibliothek "Georgius Agricola", 2015. http://nbn-resolving.de/urn:nbn:de:bsz:105-qucosa-173886.

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Die Adsorption von Additiven an den Oberflächen eines Kristallisates wird als eine hauptsächliche Ursache für die Beeinflussung von Kristallwachstum und Morphologie angesehen und spielt bei vielen Kristallisationsprozessen eine entscheidende Rolle. Gerade für die Calciumsulfate, die im Millionen-Tonnen-Maßstab jährlich in Deutschland verarbeitet werden, stellt der Additiv-Einsatz einen Hauptkostenfaktor dar, während gleichzeitig die Additivwirkung mechanistisch nicht ausreichend gut verstanden und damit derzeit nicht vorhersagbar ist. Zur Erlangung eines besseren Verständnisses wurden mit Hil

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31

Pezzotti, Simone. "DFT-MD simulations and theoretical SFG spectroscopy to characterize H-Bonded networks at aqueous interfaces : from hydrophobic to hydrophilic environments Structural definition of the BIL and DL: a new universal methodology to rationalize non-linear χ(2)(ω) SFG signals at charged interfaces, including χ(3)(ω) contributions What the Diffuse Layer (DL) Reveals in Non-Linear SFG Spectroscopy 2D H-Bond Network as the Topmost Skin to the Air-Water Interface Combining ab-initio and classical molecular dynamics simulations to unravel the structure of the 2D-HB-network at the air-water interface 2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations Spectroscopic BIL-SFG Invariance Hides the Chaotropic Effect of Protons at the Air-Water Interface Molecular hydrophobicity at a macroscopically hydrophilic surface Graph theory for automatic structural recognition in molecular dynamics simulations DFT-MD of the (110)-Co3O4 cobalt oxide semiconductor in contact with liquid water, preliminary chemical and physical insights into the electrochemical environment". Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLE008.

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Améliorer notre connaissance de la structure de l'eau dans l'environnement spécial offert par une interface est essentiel pour la compréhension de nombreux phénomènes naturels et applications technologiques. Pour révéler cette structure interfaciale de l'eau, des techniques capables de fournir des informations microscopiques, de manière sélective, pour cette couche interfaciale (BIL) sont nécessaires. Dans le présent travail de thèse, nous avons donc étudié les interfaces aqueuses au niveau moléculaire, en couplant la modélisation théorique à partir de simulations DFT-MD avec les spectroscopie

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WANG, ZHENG. "HIERARCHICAL APPROACH TO PREDICTING TRANSPORT PROPERTIES OF A GRAMICIDIN ION CHANNEL WITHIN A LIPID BILAYER." University of Cincinnati / OhioLINK, 2003. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1069794237.

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André, Tomas. "Benchmarking Physical Properties of Water Models." Thesis, Uppsala universitet, Molekyl- och kondenserade materiens fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-388336.

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Water is a fundamental part of life as we know it, and by that also a fundamental for biology, chemistry, and parts of physics. Understanding how water behaves and interacts is key in many fields of all these three branches of science. Numerical simulation using molecular dynamics can aid in building insight in the behavior and interactions of water. In this thesis molecular dynamics is used to simulate common rigid 3 point water models to see how well they replicate certain physical and chemical properties as functions of temperature. This is done with molecular dynamics program GROMACS which

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Lorenz, Erik. "Entwicklung und Verifikation eines kombinierten Kinetic Monte Carlo / Molekulardynamik Modells zur Simulation von Schichtabscheidungen." Bachelor's thesis, Universitätsbibliothek Chemnitz, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-106314.

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Atomlagenabscheidung (ALD, Atomic Layer Deposition) ist als präzise Technik zur Abscheidung dünner Schichten bekannt. Mittels wechselweisen Einleitens von Precursorgasen in einen Reaktor erzeugt der Prozess auch auf strukturierten Substraten gleichmäßige dünne Schichten. Durch die selbstsättigende Natur der zu Grunde liegenden Reaktionen sind sowohl die Wachstumsrate als auch die Zusammensetzung wohldefiniert, weshalb sich Atomlagenabscheidung beispielsweise zur Herstellung nanoskopischer Bauelemente im Bereich der Mikroelektronik eignet. Obwohl Aluminiumoxid vermehrt Aufmerksamkeit für seine

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Seehamart, Kompichit. "Investigation of the diffusion mechanisms of several hydrocarbons in the Metal-Organic-Framework Zn(tbip)." Doctoral thesis, Universitätsbibliothek Leipzig, 2011. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-68125.

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Most of the computer simulations of molecules in Metal-Organic Frameworks (MOFs) to be found in the literature are done with rigid framework. But, Molecular Dynamics (MD) simulations of the self-diffusivity, Ds, of ethane within the one-dimensional 4.5 Å channels of the MOF type Zn(tbip)(H2 tbip = 5-tert-butyl isophthalic acid) presented in this work have shown not only quantitative, but also qualitative, differences in the Ds values for fixed and flexible lattices. Particularly, the dependence of Ds upon the concentration of molecules, c, is strongly influenced by the lattice flexibility. Th

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Creazzo, Fabrizio. "Oxygen evolution reaction at cobalt oxides/water interfaces : heterogeneous electrocatalysis by DFT-MD simulations & metadynamics Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts Ionic Diffusion and Proton Transfer in Aqueous Solutions under an Electric Field: State-of-The-Art Ionic diffusion and proton transfer of MgCl2 and CaCl2 aqueous solutions: an ab initio study under electric field DFT-MD of the (110)-Co 3 O 4 cobalt oxide semiconductor in contact with liquid water, preliminary chemical and physical insights into the electrochemical environment Enhanced conductivity of water at the electrified air–water interface: a DFT-MD characterization Ions tune interfacial water structure and modulate hydrophobic interactions at silica surfaces." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASE012.

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Dans cette thèse, des simulations DFT-MD couplées à des techniques inno-vantes de métadynamique, sont appliquées pour acquérir une compréhensionglobale des interfaces aqueuses d'oxyde de cobalt Co3O4 et CoO(OH) dansla catalyse de la réaction d'évolution de l'oxygène (OER), et ainsi éventuellement aider à la conception de nouveaux catalyseurs basés sur des matériaux non précieux, un domaine clé de la recherche scientifique et technologique, particulièrement important pour l'économie de l'hydrogène, pour les technologies vertes dans une période de temps avec une demande toujours plus croissantee

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Li, Hongfei. "Density functional simulations of defect behavior in oxides for applications in MOSFET and resistive memory." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274924.

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Defects in the functional oxides play an important role in electronic devices like metal oxide semiconductor field effect transistors (MOSFETs) and resistive random-access memories (ReRAMs). The continuous scaling of CMOS has brought the Si MOSFET to its physical technology limit and the replacement of Si channel with Ge channel is required. However, the performance of Ge MOSFETs suffers from Ge/oxide interface quality and reliability problems, which originates from the charge traps and defect states in the oxide or at the Ge/oxide interface. The sub-oxide layers composed of GeII states at the

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Lorenz, Erik. "Entwicklung und Verifikation eines kombinierten Kinetic Monte Carlo / Molekulardynamik Modells zur Simulation von Schichtabscheidungen." Bachelor's thesis, Fraunhofer Institut für elektronische Nanosysteme, 2012. https://monarch.qucosa.de/id/qucosa%3A18794.

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Atomlagenabscheidung (ALD, Atomic Layer Deposition) ist als präzise Technik zur Abscheidung dünner Schichten bekannt. Mittels wechselweisen Einleitens von Precursorgasen in einen Reaktor erzeugt der Prozess auch auf strukturierten Substraten gleichmäßige dünne Schichten. Durch die selbstsättigende Natur der zu Grunde liegenden Reaktionen sind sowohl die Wachstumsrate als auch die Zusammensetzung wohldefiniert, weshalb sich Atomlagenabscheidung beispielsweise zur Herstellung nanoskopischer Bauelemente im Bereich der Mikroelektronik eignet. Obwohl Aluminiumoxid vermehrt Aufmerksamkeit für seine

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39

Withrow, Travis P. "Computational Modeling of Atom Probe Tomography." The Ohio State University, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=osu1525763934302517.

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Vermeer, Louic Sebichniev. "NMR struture determination and MD simultations of membrane peptides and proteins : a peptide derived from H+-V-ATPase subunit alpha, and MscL." Toulouse 3, 2009. http://thesesups.ups-tlse.fr/492/.

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H+-V-ATPase est une protéine responsable de la translocation des protons. Les propriétés structurales d'un peptide dérivé de la sous-unité a de H+-V-ATPase, ont été étudiées. La structure dans des micelles de SDS a été déterminée par RMN. Il a été démontré par dichroisme circulaire que le peptide est structuré en feuillet beta dans l'octylglucoside à haut pH, tandis qu'il présente 60\% d'hélice alpha dans le SDS. Ces observations ont été expliquées par des simulations de dynamique moléculaire, qui ont démontré que le peptide est inseré dans la micelle de SDS à haut pH, alors qu'en présence d'o

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Tarmyshov, Konstantin B. "Molecular dynamics simulations." Phd thesis, [S.l.] : [s.n.], 2007. https://tuprints.ulb.tu-darmstadt.de/787/1/000_pdfsam_PhD_thesis_-_All_-_LinuxPS2PDF.ps.pdf.

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Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble via its development in time and space. Chapter 1 gives a short overview of techniques used today in mol

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Postma, Johannes Petrus Maria. "MD of H2O : a molecular dynamics study of water /." [S.l. : s.n.], 1985. http://bibpurl.oclc.org/web/32873.

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Pendrill, Robert. "Conformations of Flexible Oligosaccharides : Molecular Simulations and NMR spectroscopy." Doctoral thesis, Stockholms universitet, Institutionen för organisk kemi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-95480.

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The conformational preferences of several oligosaccharides are investigated herein using a combination of NMR spectroscopy and molecular dynamics (MD) simulations, focusing on the torsion angles associated with the glycosidic linkages. Strategies for obtaining usable J-HMBC spectra for carbons with an adjacent 13C label are described. By employing a selective pulse or a constant time modification, spectra free from interferences are obtained for site-specifically 13C labeled oligosaccharides. Intermolecular hydrogen bonding in sucrose is investigated using MD simulations performed at different

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Jelinek, Bohumir. "Molecular dynamics simulations of metals." Diss., Mississippi State : Mississippi State University, 2008. http://library.msstate.edu/etd/show.asp?etd=etd-11072008-130216.

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Huhges, Samantha Jayne. "Molecular dynamics simulations of LysU." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269701.

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Elcock, Adrian Hamilton. "Molecular dynamics simulations of DNA." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239313.

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Lundgren, Johan Mathias. "Molecular dynamics simulations of wetting." Thesis, University of Bristol, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397888.

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Bass, Alexander. "Molecular dynamics simulations of sonoluminescence." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1790349561&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.

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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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Koplin, Jessica. "Molecular dynamics simulations of RNA hairpins." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=977243346.

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