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Dissertations / Theses on the topic 'Molecular dynamics'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Sargant, Robert John. "Molecular dynamics simulations of elongated molecules." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-elongated-molecules(35c31c02-aa1f-4c87-bab9-db81d813974b).html.

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The existence of a thermotropic biaxial nematic liquid crystal phase has been a topic of great interest for almost half a century. Of the various mesogenic shapes suggested as being able to form this phase, theory has suggested that the V-shaped or "bent-core" molecule is one of the most promising candidates. In this thesis we use a simple mesogenic model of a bent-core molecule, constructed from a number of repulsive Weeks-Chandler-Andersen potentials that are assembled into a rigid V shape. Using this model we explore the spontaneous phase behaviour that occurs in a wide array of different s

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2

Baker, Joseph Lee. "Steered Molecular Dynamics Simulations of Biological Molecules." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205416.

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Molecular dynamics (MD) simulation, which employs an empirical potential energy function to describe the interactions between the atoms in a system, is used to investigate atomistic motions of proteins. However, the timescale of many biological processes exceeds the reach of standard MD due to computational limitations. To circumvent these limitations, steered molecular dynamics (SMD), which applies external forces to the simulated system, can be used.Dynamical properties of the gonococcal type IV pilus (GC-T4P) from the bacteria Neisseria gonorrhoeae are first considered. T4 pili are long, fi

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3

Wildman, Jack. "Molecular dynamics simulations of conjugated semiconducting molecules." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3261.

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In this thesis, we present a study of conformational disorder in conjugated molecules focussed primarily on molecular dynamics (MD) simulation methods. Along with quantum chemical approaches, we develop and utilise MD simulation methods to study the conformational dynamics of polyfluorenes and polythiophenes and the role of conformational disorder on the optical absorption behaviour observed in these molecules. We first report a classical force-field parameterisation scheme for conjugated molecules which defines a density functional theory method of accuracy comparable to high-order ab-initio

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4

Batchelor, Colin. "Molecular Rydberg dynamics." Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:46b5699b-1dcf-4860-8d76-09fc487a09d4.

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A simple theory relating the dynamics of electrons to the long-range properties of the molecular ionic core is developed for asymmetric top molecules in general and water in particular. It is combined with the molecular version of multichannel quantum defect theory developed by Fano and Jungen and applied to the resonance-enhanced multiphoton ionization spectra of Child and Glab (M. S. Child and W. G. Glab, J. Chem. Phys., 2001, 112, 3754-3765), the mass-analysed threshold ionization spectra of Dickinson et al. (H. Dickinson, S. R. Mackenzie and T. P. Softley, Phys. Chem. Chem. Phys., 2000, 2,

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5

O'Mahony, John. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.277879.

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6

Docker, M. P. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378987.

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7

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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8

Lin, Jr-Hung. "Nonatomistic molecular dynamics /." Aachen : Shaker, 2008. http://d-nb.info/991265556/04.

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9

Doig, Michael. "Molecular dynamics simulations of surface-active molecules under dynamic conditions found in engines." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/17968.

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Lubricants oils play an important role in a wide range of industrial and mechanical processes, where they are used to reduce both the friction and wear between interacting moving surfaces. The current understanding of lubrication is mainly based on empirical evidence, obtained from experiment. In this work, computer simulations are used to gain insight into the microscopic processes that lead to the modification of friction and wear by additive molecules adsorbed on sheared surfaces lubricated by thin liquid films. The specific area of application under consideration is the lubrication of auto

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10

Chen, Jen Hui. "Molecular Dynamics and Interactions in Liquids." Thesis, North Texas State University, 1985. https://digital.library.unt.edu/ark:/67531/metadc331452/.

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Various modern spectroscopies have been utilized with considerable success in recent years to probe the dynamics of vibrational and reorientational relaxation of molecules in condensed phases. We have studied the temperature dependence of the polarized and depolarized Raman spectra of various modes in the following dihalomethanes: dibromomethane, dichloromethane, dichloromethane-d2, and bromochloromethane. Among other observed trends, we have found the following: Vibrational dephasing times calculated from the bend) and (C-Br stretch) lineshapes are of the same magnitude in CI^B^. The vibratio

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11

Siavosh-Haghighi, Ali. "Topics in molecular dynamics." free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3164542.

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12

Castelow, D. A. "Molecular dynamics of rods." Thesis, University of Cambridge, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303841.

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13

Summerfield, Dean. "Studies of molecular dynamics." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318460.

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14

Craig, Ian R. "Ring polymer molecular dynamics." Thesis, University of Oxford, 2006. http://ora.ox.ac.uk/objects/uuid:f3c37800-6fc7-4d8b-b135-94d94a7cf4e1.

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This thesis presents the ring polymer molecular dynamics (RPMD) approximation to the Kubo-transformed time correlation function and shows how it may be used as the basis of an approximate quantum-mechanical method for determining the dynamical properties of condensed-phase molecular systems. The performance of the RPMD method is initially investigated by calculating the position (q<sup>ˆ</sup>), and position-cubed (q<sup>ˆ3</sup>), autocorrelation functions of a series of onedimensional potential wells of varying anharmonicity. It is then applied to the evaluation of the incoherent dynamic str

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15

Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.

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16

Edmunds, David. "Coarse-grained molecular dynamics." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/25112.

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In this work, we investigate the application of coarse-graining (CG) methods to molecular dynamics (MD) simulations. These methods provide access to length and time scales previously inaccessible to traditional materials simulation techniques. However, care must be taken when applying any coarse-graining strategy to ensure that we preserve the material properties of the system we are interested in. We discuss common CG strategies, including their strengths, weaknesses and ease of application. The theory of coarse-graining is discussed within the framework of statistical mechanics, together wit

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17

Simon, Jean-Marc, Ole-Erich Haas, Signe Kjelstrup, and Ramstad Astrid Lund. "Dynamical behaviour of H 2 molecules on graphite surface: a molecular dynamics study." Diffusion fundamentals 6 (2007) 37, S. 1-2, 2007. https://ul.qucosa.de/id/qucosa%3A14214.

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18

Sanz-Navarro, Carlos F. "Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics." Thesis, Loughborough University, 2002. https://dspace.lboro.ac.uk/2134/6814.

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The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact p

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19

Panesar, Kuldeep Singh. "Quantum molecular dynamics of guest molecules in supramolecular complexes." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10741/.

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The quantum motion of guest molecules has been studied in a variety of calixarene host-guest complexes, and in a endohedral fullerene complex. The guest molecules of the calixarene complexes studied each comprise weakly hindered methyl groups, which undergo rotation via quantum tunnelling, even at cryogenic temperatures. The rotational motion of the guest methyl-groups has been studied by making temperature and frequency-dependent measurements of proton T1, using field-cycling NMR, thus revealing the spectral density functions of the magnetic dipole-dipole interaction. Crystallographically ine

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20

Jensen, C. H. "Molecular dynamics and complexity analysis of molecular systems." Thesis, University of Cambridge, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.605591.

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In this thesis, Complexity Analysis, which is defined as the use of Markov models and Computational Mechanics, is applied to Molecular Dynamics simulations of peptides. To achieve this, the trajectories from the Molecular Dynamics simulations are clustered into conformational states and by investigating the time series of these states, statistical models are constructed. A basic property of a Markov model is that the probability distribution of the subsequent states depends only on the current state and not the history. This has previously been used to develop a method for testing the model wh

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21

Yimer, Yeneneh Yalew. "Molecular Ordering, Structure and Dynamics of Conjugated Polymers at Interfaces: Multiscale Molecular Dynamics Simulations." University of Akron / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=akron1416796729.

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22

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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23

Gräfe, Stefanie. "Laser-control of molecular dynamics." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=976127016.

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24

Vilfan, Andrej. "Collective dynamics of molecular motors." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=959980024.

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25

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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26

Bekker, Hendrik. "Molecular dynamics simulation methods revised." [Groningen] : [Groningen] : Rijksuniversiteit Groningen ; [University Library Groningen] [Host], 1996. http://irs.ub.rug.nl/ppn/14860532X.

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27

Williams, Stewart. "Spectroscopic investigation of molecular dynamics /." Thesis, Connect to this title online; UW restricted, 1989. http://hdl.handle.net/1773/8655.

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28

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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29

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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30

Park, N. "Modelling shocks using molecular dynamics." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/5826.

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The study of shocks in solid, crystalline metals has been ongoing since the early works of Rankine and Hugoniot in the latter half of the 19th century. However, the understanding of the behaviour of such materials under these extreme conditions remains an area of active research because of the paucity with which models can predict experimental observations. The modern era has seen a huge increase in the ability to solve many of the problems of this area of study by numerical, rather thatn analytic, means. One of these tools has been the use of computers to provide a numerical solution to the m

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31

Christopher, David. "Molecular dynamics modelling of nanoindentation." Thesis, Loughborough University, 2002. https://dspace.lboro.ac.uk/2134/6924.

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This thesis presents an atomic-scale study of nanoindentation, with carbon materials and both bcc and fcc metals as test specimens. Classical molecular dynamics (MD) simulations using Newtonian mechanics and many-body potentials, are employed to investigate the elastic-plastic deformation behaviour of the work materials during nanometresized indentations. In a preliminary model, the indenter is represented solely by a non-deformable interface with pyramidal and axisymmetric geometries. An atomistic description of a blunted 90° pyramidal indenter is also used to study deformation of the tip, ad

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32

Sutcliffe, Julia H. "Quantum studies of molecular dynamics." Thesis, University of Nottingham, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282566.

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33

Bell, Andrew John. "Spectroscopic investigations of molecular dynamics." Thesis, University of Southampton, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.280858.

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34

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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35

Van, Heusden Carolina Monica. "Distributed polarizabilities for molecular dynamics." Thesis, University of Cambridge, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627513.

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36

Lane, Ian Michael. "Ultrafast molecular dynamics at surfaces." Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612786.

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37

Carlsen, Ryan Wayne. "Molecular Dynamics of Organometallic Systems." BYU ScholarsArchive, 2021. https://scholarsarchive.byu.edu/etd/9230.

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Metal-mediated organometallic reactions are critical for both catalytic and synthetic chemistry. Density functional theory (DFT) potential-energy calculations are routinely used with a transition-state theory type of approach to understand and predict the reaction mechanisms of organometallic reactions. However, these calculations do not include atomic momentum and thus ignore dynamic effects. Molecular dynamics is a powerful tool for elucidating mechanistic details of chemical reactions. In this dissertation, quasiclassical molecular dynamics studies reveal key mechanistic details about sever

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38

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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39

Cieren, Emmanuel. "Molecular Dynamics for Exascale Supercomputers." Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0174/document.

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Dans la course vers l’exascale, les architectures des supercalculateurs évoluent vers des nœuds massivement multicœurs, sur lesquels les accès mémoire sont non-uniformes et les registres de vectorisation toujours plus grands. Ces évolutions entraînent une baisse de l’efficacité des applications homogènes (MPI simple), et imposent aux développeurs l’utilisation de fonctionnalités de bas-niveau afin d’obtenir de bonnes performances.Dans le contexte de la dynamique moléculaire (DM) appliqué à la physique de la matière condensée, les études du comportement des matériaux dans des conditions extrême

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40

COSTANTINI, ROBERTO. "Exciton Dynamics in Molecular Heterojunctions." Doctoral thesis, Università degli Studi di Trieste, 2020. http://hdl.handle.net/11368/2967981.

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Negli ultimi anni, la necessità di uno sviluppo economico più sostenibile ha contribuito ad aumentare l’interesse verso le fonti di energia rinnovabili. Con tendenze incoraggianti nell’efficienza di conversione e nei costi di produzione, si prevede che il fotovoltaico avrà un ruolo cruciale per la produzione di energia verde in futuro. Il silicio è attualmente la tecnologia dominante nel fotovoltaico ma, nel passato decennio, soluzioni innovative basate sui semiconduttori organici sono diventate interessanti per la possibilità di oltrepassare il limite di Shockley-Queisser e di offrire efficie

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41

Gotte, Anders. "Dynamics in Ceria and Related Materials from Molecular Dynamics and Lattice Dynamics." Doctoral thesis, Uppsala University, Department of Materials Chemistry, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7374.

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<p>In discussions of heterogeneous catalysis and other surface-related phenomena, the dynamical properties of the catalytic material are often neglected, even at elevated temperatures. An example is the three-way catalyst (TWC), used for treatment of exhaust gases from combustion engines operating at several hundred degrees Celsius. In the TWC, reduced ceria (CeO<sub>2-x</sub>) is one of the key components, where it functions as an oxygen buffer, storing and releasing oxygen to provide optimal conditions for the catalytic conversion of the pollutants. In this process it is evident that dynamic

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42

Mizuno, Hideyuki. "Molecular Dynamics Simulation Studies of Dynamical Properties of Supercooled Liquids." 京都大学 (Kyoto University), 2012. http://hdl.handle.net/2433/157540.

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43

Palaiokostas-Avramidis, Michail. "Molecular dynamics simulations of small molecule permeation through lipid membranes." Thesis, Queen Mary, University of London, 2017. http://qmro.qmul.ac.uk/xmlui/handle/123456789/31859.

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Passive permeation through biological membranes is an important mechanism for transporting molecules and regulating the cellular content. Studying and understanding passive permeation is also extremely relevant to many industrial applications, including drug design and nanotechnology. In vivo membranes typically consist of mixtures of lamellar and nonlamellar lipids. Lamellar lipids are characterised by their tendency to form lamellar bilayer phases, which are predominant in biology. Nonlamellar lipids, when isolated, instead form non-bilayer structures such as inverse hexagonal phases. While

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44

Edman, Lars. "Single molecule dynamics /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4025-8/.

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45

Seo, Youngmi. "Structure and Dynamic Properties of Interfacially Modified Block Copolymers from Molecular Dynamics Simulations." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1492628195548591.

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46

Sfriso, Pedro. "Biological applications of discrete molecular dynamics." Doctoral thesis, Universitat de Barcelona, 2016. http://hdl.handle.net/10803/397796.

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Sequence, structure and dynamics are an indivisible tandem to understand protein function. Luckily, evolution imposed a hierarchical rational between that facilitates the analysis: dynamics are encoded in the structure, which in turn, is encoded in the sequence. Decipher the mechanisms governing protein function requires contributions from diverse fields, particularly to follow molecular motions. There are technological limitations to monitor local, elemental, protein movements, since they are too fast to be followed by current experimental set-ups. Theoretical models provide necessary assista

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47

Holland, David M. "Nano-scale computational fluid dynamics with molecular dynamics pre-simulations." Thesis, University of Warwick, 2015. http://wrap.warwick.ac.uk/72851/.

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A procedure for using Molecular Dynamics (MD) simulations to provide essential fl uid and interface properties for subsequent use in Computational Fluid Dynamics (CFD) calculations of nano-scale fluid fl ows is presented. The MD presimulations enable an equation of state, constitutive relations, and boundary conditions to be obtained for any given fl uid/solid combination, in a form that can be conveniently implemented within an otherwise conventional Navier-Stokes solver. The results presented demonstrate that these enhanced CFD simulations are capable of providing good fl ow field results in

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48

Lockwood, Daren M. "Molecular dynamics investigations of protein volumetric properties and electronic dynamics /." Digital version accessible at:, 2000. http://wwwlib.umi.com/cr/utexas/main.

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49

Anand, Abhinav. "A molecular dynamics investigation of the dissolution of molecular solids." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/63029.

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The dissolution of molecular solids is an important process, which has been studied for over a century. However, a lot of work is still needed for a detailed understanding of the molecular mechanism of dissolution, because of the complex nature of many molecular solids, and the large time scales required for simulation studies. In this thesis we study the dissolution of molecular solids, to examine if classical models (which assume that the rate is proportional to an active surface area) can be used to describe the dissolution profile of these solids. Urea and aspirin molecules are used as

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50

Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.

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