To see the other types of publications on this topic, follow the link: MOLECULAR DYNAMCS.
Dissertations / Theses on the topic 'MOLECULAR DYNAMCS'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'MOLECULAR DYNAMCS.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
GABAS, FABIO. "IMPLEMENTATION OF SEMICLASSICAL THEORIES FOR SPECTROSCOPY." Doctoral thesis, Università degli Studi di Milano, 2019. http://hdl.handle.net/2434/612132.
Full textAbstract:
Vibrational spectroscopy is a fundamental tool for detecting and understanding the structure of molecular systems. Alongside the experimental measures, theoretical methods have been always employed to interpret and understand vibrational spectra.
The semiclassical approach has demonstrated its reliability in the field, especially by means of the recent “Multiple Coherent” and “Divide and Conquer” formulations.
In this PhD thesis the implementation and application of these modern techniques to a variety of molecular systems are presented, ranging from isolated medium size molecules to complex supramolecular systems, up to more than one hundred degrees of freedom.
In particular the vibrational features of glycine, deoxyguanosine, a small dipeptide and glycine-based supramolecular systems are illustrated and discussed.
A final Section is dedicated to the possibility to employ the Amber94 classical molecular force field, for computationally cheaper semiclassical calculations.
This work demonstrates and highlights the validity and accuracy of semiclassical methods as theoretical spectroscopicy tools by successfully detecting quantum effects in medium size systems, whereas other formulations fail.
2
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.
Full textAbstract:
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 systems of mesogens, using molecular dynamics simulations and isotropic initial conditions. We study the relationship between molecular bend angle and phase behavior for molecules constructed from 11 potentials. We find that the phase behaviour splits into two regions, above and below a critical bend angle. Molecules wider than this angle exhibit isotropic, uniaxial nematic and smectic A phases. Narrower molecules show no uniaxially aligned phases, and instead have a clustered phase with short-range ordering and no global alignment director. Increasing system size improves the smectic layering in the wider molecules, but does not affect the global alignment of the narrower molecules. Our model is extended to include the effect of the arm length of the molecule by changing the number of potentials from which the mesogens are constructed. As the molecule is reduced in size, the critical bend angle is seen to move slowly towards more linear molecules, reducing the size of the parameter space in which uniaxial nematic alignment is possible. At 5 beads, all mesophases are seen to disappear and systems remain isotropic. We also study the behaviour of binary mixtures of bent-core molecules, both of differing arm lengths and of differing bend angles. For arm length mixtures, molecules are seen to remain mixed in the isotropic and nematic phases, and phase separate on transition to a smectic phase. In addition, uniaxial nematic phases are induced in systems that have no nematic phase of their own in isolation. For mixtures of different bend angles, systems remain fully mixed in the smectic phases for differences of up to 10 degrees, and beyond this the two components begin to separate at the nematic–smectic transition.
3
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.
Full textAbstract:
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 automotive engine parts. The interactions between additive molecules are first determined using density-functional theory calculations. The interactions are then validated against available experimental data, and incorporated in to large-scale molecular-dynamics (MD) simulations, which are used to explore the structure and frictional properties of lubricated surfaces. The surfaces considered are alumina and iron oxide. The lubricating oils are squalane and hexadecane, which are representative of automotive lubricants, and the additive molecules are stearic acid, oleic acid and various oleamides. MD simulations are performed over wide ranges of the relevant physical conditions, namely pressure, temperature, and shear rate. The additives adsorb on to the surfaces and provide a physical connection between the surfaces and the lubricating liquid. The structures of adsorbed films are analysed in microscopic detail using functions of atomic positions and molecular geometry. Several important trends are identified, linking molecular isomerism and architecture with the structure and stability of the adsorbed film. In addition, the simulation results are used to gain insight on recent experimental measurements of film structure. The friction coefficients in various situations are computed and analysed with reference to the structures of the adsorbed films. The synthesis of these data and observed trends yields new insights on the intimate link between the molecular properties of lubricants, and the macroscopic frictional properties of macroscopic lubricated engine parts.
4
Baker, Joseph Lee. "Steered Molecular Dynamics Simulations of Biological Molecules." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/205416.
Full textAbstract:
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, filamentous proteins constructed from a subunit (pilin) found to emanate from the surface of pathogenic bacteria. They can withstand large forces (~100 pN), and are implicated in infection. SMD simulations are performed to study the response of the filament to an applied force. Our simulations reveal that stability of the pilus likely results from hydrophobic contacts between pilin domains buried within the filament core. Along the filament surface, gaps are formed between pilin globular head domains. These gaps reveal an amino acid sequence that was also observed to become exposed in the experimentally stretched filament. We propose two other regions initially hidden in the native filament that might become exposed upon stretching.The multidrug resistance transporter EmrD, found in the inner membrane of Escherichia coli is also the target of our studies. EmrD removes harmful drugs from the bacterial cell. We use MD to explore equilibrium dynamics of the protein, and MD/SMD to study drug interactions and transport along its central cavity. Motions supporting a previously proposed lateral diffusion pathway for substrate from the cytoplasmic membrane leaflet into the central cavity were observed. Additionally, interactions of a few specific residues with CCCP have been identified.Finally, we describe network analysis as an approach for analyzing conformational sampling by MD simulations. We demonstrate for several model systems that networks can be used to visualize both the dominant conformational substates of a trajectory and the connectivity between them. Specifically, we compare the results of various clustering algorithms to the network layouts and show how information from both methods can be combined.
5
Wildman, Jack. "Molecular dynamics simulations of conjugated semiconducting molecules." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3261.
Full textAbstract:
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 calculations. In doing so, we illustrate the role of increasing conjugated backbone and alkyl side-chain length on inter-monomer dihedral angle potentials and atomic partial charge distributions. The scheme we develop forms a minimal route to conjugated force-field parameterisation without substantial loss of accuracy. We then present a validation of our force-field parameterisation scheme based on self-consistent measures, such as dihedral angle distributions, and experimental measures, such as persistence lengths, obtained from MD simulations. We have subsequently utilised MD simulations to investigate the interplay of solvent and increasing side-chain lengths, the emergence of conjugation breaks, and the wormlike chain nature of conjugated oligomers. By utilising MD simulation geometries as input for quantum chemical calculations, we have investigated the role of conformational disorder on absorption spectral broadening and the formation of localised excitations. We conclude that conformational broadening is effectively independent of backbone length due to a reduction in the effect of individual dihedral angles with increasing length and also show that excitation localisation occurs as a result of large dihedral angles and molecular asymmetry.
6
Panesar, Kuldeep Singh. "Quantum molecular dynamics of guest molecules in supramolecular complexes." Thesis, University of Nottingham, 2009. http://eprints.nottingham.ac.uk/10741/.
Full textAbstract:
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 inequivalent methyl-group environments have been identified and characterised in p-tert-butylcalix[4]arene(1:1)toluene, p-tert-butylcalix[4]arene(1:1)gamma-picoline and p-isopropylcalix[4]arene(2:1)p-xylene. In many of the calixarene complexes the proton spin-lattice relaxation has been observed to be strongly dependent on the thermal history of the sample. Temperature-dependent measurements of proton T1 in samples of p-tert-butylcalix[4]arene(1:1)toluene with partially deuterated guest molecules reveal a systematic reduction in T1 at low temperatures with increased degree of deuteration. Calixarene and fullerene host-guest complexes have been identified as having a potential application in cryogenic MAS-NMR as cryorelaxor complexes, capable of being attached to a large biomolecule and encouraging proton spin-lattice relaxation. The suitability of the calixarene complexes for use in this capacity has been investigated by measuring the temperature-dependence of proton T1 at low temperatures. The quantised rotational and translational motion of dihydrogen confined within an open-cage fullerene—namely, aza-thio-open-cage-fullerene (ATOCF)—has been revealed by inelastic neutron scattering (INS) measurements. The splitting of excited rotational and translational states, due to the low symmetry of the ellipsoidal fullerene cavity, has been directly measured. Assignment of the peaks observed in the INS spectrum has been aided by analysis of the Q-dependence of excitation bands. The thermodynamics of ortho- and parahydryogen have been investigated via temperature dependence measurements. INS measurements have allowed the anistropic rotational potential experienced by the H2 rotor to be determined.
7
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.
Full text
8
Chen, Jen Hui. "Molecular Dynamics and Interactions in Liquids." Thesis, North Texas State University, 1985. https://digital.library.unt.edu/ark:/67531/metadc331452/.
Full textAbstract:
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 vibrational dephasing time of [C-D(H) stretch] is twice as long in CD2Cl2 as in CH-^C^, and the relaxation time of (C-Cl stretch) is greater in CI^C^ than in CD2CI2. Isotropic relaxation times for all three stretching vibrations are significantly shorter in C^BrCl than in CI^C^ or CI^B^. Application of the Kubo model revealed that derived modulation times are close to equal for equivalent vibrations in the various dihalomethanes. Thus, the more efficient relaxation of the A^ modes in CE^BrCl can be attributed almost entirely to the broader mean squared frequency perturbation of the vibrations in this molecule.
9
Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.
Full text
10
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.
Full textAbstract:
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 mixed lamellar/nonlamellar lipid membranes tend to adopt the ubiquitous bilayer structure, the presence of nonlamellar lipids is known to have profound effects on key membrane properties, such as internal distributions of stress and elastic properties. This dissertation examines permeation through lamellar and nonlamellar lipid membranes by utilising atomistic molecular dynamics simulations in conjunction with two di erent methods, the z-constraint and the z-restraint, in order to obtain transfer free energy profiles, diffusion profiles and permeation coefficients. An assessment of these methods is performed in search for the optimal, with the goal to create an automated, accurate and robust permeation study framework. Part of the dissertation involves the creation of the corresponding software. Furthermore, this work examines the effect of changing the lamellar vs. nonlamellar lipid composition on the passive permeation mechanism of a series of 13 small molecules and drugs. These nonlamellar lipids are known to affect the lateral pressure distribution inside the membranes. This work investigates the hypothesis that the differences in lateral pressure should increase the resistance to permeation. The results indicate that, upon addition of nonlamellar lipids, permeation is hindered for small molecules but is facilitated for the largest. All results are in agreement with previous experimental and computational studies. This work represents an advancement towards the development of more realistic in silico permeability assays, which may have a substantial future impact in the area of rational drug design.
11
Gatchell, Michael. "Molecular Hole Punching : Impulse Driven Reactions in Molecules and Molecular Clusters." Doctoral thesis, Stockholms universitet, Fysikum, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-129523.
Full textAbstract:
When molecules are excited by photons or energetic particles, they will cool through the emission of photons, electrons, or by fragmenting. Such processes are often thermal as they occur after the excitation energy has been redistributed across all degrees-of-freedom in the system. Collisions with atoms or ions may also lead to ultrafast fragmentation in Rutherford-like scattering processes, where one or several atoms can literally be knocked out of the molecule by the incoming projectile before the energy can be completely redistributed. The resulting fragmentation pathways can in such knockout processes be very different from those in thermal processes. This thesis covers extensive studies of collisions between ions/atoms and isolated Polycyclic Aromatic Hydrocarbon (PAH) molecules, isolated fullerene molecules, or clusters of these. The high stabilities and distinct fragmentation channels make these types of molecules excellent test cases for characterizing knockout-driven fragmentation and the reactions that these processes can lead to. I will present experimental measurements for a wide range of energies and compare them with my own molecular dynamics simulations and quantum chemical calculations. In this thesis, I present an in-depth study of the role of knockout in the energetic processing of molecules and clusters. The competition between knockout and thermally driven fragmentation is discussed in detail. Knockout-driven fragmentation is shown to result in exotic fragments that are far more reactive than the intact parent molecules or fragments from thermal processes. When such reactive species are formed within molecular clusters efficient molecular growth can take place on sub-picosecond timescales. The cluster environments are crucial here because they protect the newly formed molecules by absorbing excess energy. This is a possible pathway for the growth of large PAHs, fullerenes, and similar carbonaceous complexes found in, for instance, the interstellar medium.At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 1: Submitted.
12
Åkesson, Patrik. "Molecular Dynamics of the Adsorption of Organic Molecules on Organic Substrates." Thesis, Linköpings universitet, Institutionen för fysik, kemi och biologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-103688.
Full textAbstract:
A great interest has been shown for self-assembled organic nano-structures that can be used in a variety of optoelectronic applications, from element detection to home electronics. It is known from experimental research that sexiphenyl (6P) grown on muscovite mica substrate form uniaxially self-assembled nanofibers which together with sexithiophene (6T) deposited on top gives the possibility to tune their polarized emission. A key to continue develop and explore the full potential of this technique is to understand the mechanisms behind the growth. This thesis investigate the initial growth of 6P and 6T on a 6PProject P25154-N20 "Hetero-epitaxy of organic-organic nanofibers"
13
Blackshaw, Kenneth Jacob. "Investigating the Molecular Choreography of Atmospherically Relevant Molecules: A Dynamics Study." W&M ScholarWorks, 2019. https://scholarworks.wm.edu/etd/1563899032.
Full textAbstract:
Investigating and understanding the chemistry of the atmosphere has historically been an important research topic. This importance has only strengthened in the recent decades as technological advancements have drastically increased anthropogenic emissions of hydrocarbons and nitroaromatic compounds. Indeed, we are in an era of unprecedented change of the chemical composition of the troposphere and never before has an in-depth understanding of atmospheric chemical properties been more sought-after. This study seeks to fill that need by probing the molecular dynamics of atmospherically relevant molecules through the use of velocity map imaging (VMI). In particular, we utilize VMI to study the photolysis dynamics of brown carbon (BrC) chromophores and nitrosothiol compounds, as well as the collisional quenching dynamics of nitric oxide (NO) and molecular oxygen (O2). BrCs represent an important category of carbon-based aerosols that have, until recently, been considered spectroscopically similar to black carbon aerosols. It is now known that, due to nitroaromatic chromophores, BrCs absorb increasingly well from the visible region to the ultra-violet (UV) region. This study has shown that the probed nitroaromatic chromophores, nitrobenzene, ortho-nitrophenol, and nitroresorcinol, all yield nonstatistical energy partitioning. This deviation from statistical expectations is largely attributed to long-range dipole-dipole forces that inhibit the partitioning of energy to internal energy levels. Nitrosothiols are secondary aerosols that play a large role in the nucleation of aerosols as well as the formation of acid rain. Ion images of NO photofragments from 355 nm photolysis are largely anisotropic. The angular dependence of these images can be correlated to the dynamical signatures of dissociation process. Not only is NO and O2 collisional quenching a common occurrence in the atmosphere, it is also documented to take place during laser induced florescence experiments making data acquisition from such experiments difficult. Through the use of VMI combined with a dual channel pulse valve, the NO (X2Π) nonreactive collision product is probed. Analysis of state-resolved ion images indicates O2 (c1Σu-) is the preferred coproduct of this nonreactive collision. Additionally, product state distributions indicate a Λ-doublet propensity for NO (X2Π) rotational states. Physical properties, such as those determined in this study, are imperative for the formation of accurate climate models. Therefore, molecular dynamics studies are required to actively combat atmospheric hazards like air pollution and global climate change.
14
Mitsari, Efstratia. "Guest-molecule dynamics and conductivity effects in carbon-based molecular solids." Doctoral thesis, Universitat Politècnica de Catalunya, 2016. http://hdl.handle.net/10803/397721.
Full textAbstract:
Disordered systems are abundant in everyday life and so their study is of importance from a scientific and a technological point of view. The most common non-crystalline solid phases are structural glasses (e.g. window glass), in which both translational and orientational degrees of freedom are disordered. While at low temperature (in the glass state) the disorder is static, at higher temperature a viscous state is reached, where the disorder is dynamic (as in a liquid). Other systems exist, namely molecular solids, which display different types of disorder (either static or dynamic depending on temperature) due to the larger variety of microscopic degrees of freedom compared to atomic solids(ch. 1). For instance, molecular solids display phases in which the molecules' average centers of mass occupy lattice positions while their orientations are disordered (orientationally disordered phases). Such phases are usually formed by small molecules or molecules with a globular shape like the carbon-only fullerene molecule (C60). Molecular solids display low electrical conductivities due to localization of valence electrons on single molecules, so that electron hopping is the main charge transport mechanism. The type of disorder, and whether it is static or dynamic, are both factors that have an important impact on the conductivity. This thesis is an experimental study of the dynamic disorder and conduction properties of molecular solids, focusing in particular on hydrated molecular materials and on fullerene systems. The experimental technique of choice, which allows studying simultaneously molecular dynamics and electrical conductivity, is broadband dielectric spectroscopy (ch. 2 and 3). Studying water inside organic systems is of great importance in several contexts, ranging from the study of food texture and the stability of biotechnology products and pharmaceuticals to the investigation of macromolecular function in biochemical systems for which hydration water plays a preeminent role. Fullerene solids are relatively simple systems to study the impact of water and in general of heterogeneous species inside an organic matrix. Hydrophilic or hygroscopic fullerene derivatives can be obtained by functionalization with oxygen or hydroxyl groups, as in the case of the fullerenol molecule (ch. 5). We show in this thesis that water molecules not only display interesting orientational dynamics, but they also contribute to the enhancement of the conductivity due to proton hopping through surface hydration layers. These phenomena are not specific to functionalized fullerenes (ch. 5) but also to other organic materials, as we show for the case of an organic dye of the rhodamine family (ch. 4). As for the dynamics of the fullerene molecules themselves, it is well known that the solid phase of pure C60 exhibits order-disorder orientational transition. We show that a derivative of C60 functionalized with oxygen-containing groups also displays several orientational transitions,reminescent of that of solid C60 (ch. 6). Finally, we analyze the structural and dynamic orientational disorder in a co-crystal of C60 with a small ethane derivative (C60:(1,1,2)-trichloroethane (ch. 7). We are able to observe two distinct orientational dynamics of the ethane molecules. To the best of our knowledge, ours is the first-ever report of the relaxation dynamics of guest molecules intercalated inside C60. Considering the very broad variety of (partially) disordered structures that can be obtained in binary systems containing fullerene molecules, these solids may represent model systems to investigate the impact of disorder and of the interaction geometry on the molecular dynamics of heterogeneous systems. The results of this thesis represent a first step in the direction of extending the current experimental knowledge of disordered solid phases to more complex systems of relevance in organic organic chemistry and biology, or with possible commercial applications.Los sistemas desordenados son muy comunes en nuestra vida cotidiana y su estudio tiene por tanto un impacto importante. Las fases sólidas más comunes son los vidrios estructurales (e.g. los vidrios típicos) en los que tanto los grados de libertad de orientación como de translación están desordenados. A bajas temperaturas (estado vítreo) el desorden es estático, mientras que a temperaturas más altas se alcanza un estado fluido viscoso, donde el desorden es dinámico (como en un líquido). Existen también otros sistemas sólidos, formados por moléculas, que pueden presentar diferentes tipos de desorden (estático o dinámico) debido a la gran variedad de los grados de libertad moleculares en comparación con los sólidos formados exclusivamente por átomos (ch.1). Así existen sólidos moleculares que presentan fases en los que las moléculas tienen movimientos de reorientación manteniendo invariables sus centros de masa (fases orientacionalmente desordenadas). Estas fases pueden estar formadas por moléculas pequeñas o por moléculas con forma globular, como la molécula de fulereno (C60). La baja conductividad eléctrica de los sólidos moleculares es debida a la localización de los electrones de valencia en cada molécula individual, de modo que el mecanismo principal de transporte de carga es el salto (''hopping'') de los electrones entre las moléculas. El tipo de desorden, y si el desorden es estático o dinámico, son factores que tienen un impacto importante en la conductividad del material. Esta tesis es un estudio experimental del desorden dinámico y de las propiedades de conducción en los sólidos moleculares, y está especialmente dirigida al estudio en materiales moleculares hidratados y en sistemas con fulereno. La técnica de caracterización que permite un estudio de la dinámica molecular y de la conductividad eléctrica de manera simultánea es la espectroscopia dieléctrica (ch. 2 y 3). La tesis presta también una especial atención al estudio de la influencia del agua en sistemas orgánicos moleculares, debido a la importancia en muchas aplicaciones, desde la textura de los alimentos, o la estabilidad de productos biotecnológicos, hasta la investigación de la función macromolecular en sistemas bioquímicos, en los que el agua de hidratación tiene un papel fundamental. Los sólidos de fulereno son sistemas sencillos para estudiar el impacto de especies moleculares heterogéneas en el interior de una matriz orgánica. Tanto los derivados higroscópicos como hidrofóbicos del fulereno se pueden obtener por funcionalización con grupos de oxígeno, como en el caso de la molécula de fullerenol (ch. 5). Esta tesis demuestra que las moléculas de agua tienen una dinámica orientacional muy variada y, además, que su presencia contribuye a la conductividad debido a los saltos de los protones a través de los diferentes niveles de hidratación de la superficie. Estos fenómenos se detectan también en otros materiales orgánicos, como es el caso de un colorante orgánico de la familia de la rodamina (ch. 4). En cuanto a la propia dinámica de las moléculas del fulereno, es conocido que la fase sólida de C60 tiene una transición orientacional orden-desorden. De forma paralela, se demuestra la existencia de transiciones similares en un derivado de C60 (oxC60, ch.5). Por último, se estudia también el desorden orientacional, estructural y dinámico, en un cristal mixto formado por C60 y 1,1,2-tricloroetano (ch.7).). En este sistema se observan dinámicas orientacionales asociadas a las conformaciones moleculares del tricloroetano, representando así un estudio sobre la dinámica de moléculas huéspedes intercaladas estructuralmente en una matriz de C60. Los resultados de esta tesis representan un primer paso para profundizar en el conocimiento de sólidos con fases desordenadas y para el progreso en sistemas más complicados y relevantes en el campo de la química y de la biología orgánica, o con posibles aplicaciones comerciales.
15
Tekin, Emine Deniz. "Investigation Of Biologically Important Small Molecules: Quantum Chemical And Molecular Dynamics Calculations." Phd thesis, METU, 2010. http://etd.lib.metu.edu.tr/upload/12612343/index.pdf.
Full textAbstract:
In this thesis, six small molecules (S-allylcysteine, S-allyl mercaptocysteine, allicin, methyl propyl disulfide, allyl methyl sulfide and dipropylsulfide) that are found in garlic and onion, and are known to be beneficial for human health were studied using molecular mechanics, semi-empirical methods, ab-initio (Restricted Hartree Fock), and density functional theory. Using the same methods, a synthetic pyrethroid pesticide molecule, called cyfluthrin, was also studied. Structural, vibrational and electronic properties of these molecules were found. These theoretical studies could clarify the role of these molecules on human health before they are commercially developed and used. In addition, unfolding dynamics of small peptide sequences (DDATKTFT and its variants) in immunoglobulin G-binding protein G was investigated. Protein folding and unfolding is one of the most important unsolved problems in molecular biology. Because of the large number of atoms involved in protein folding, it is a massive computational problem. The hope is that, one could understand this mechanism with the help of molecular dynamics simulation on small peptides. One of our findings is that the location of the hydrogen bonds is important for the stability of the peptide.
16
Stafford, Adam Paul. "The dynamics and molecular flexibility of liquid crystal molecules and their moieties." Thesis, University of Bristol, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.266883.
Full text
17
Batchelor, Colin. "Molecular Rydberg dynamics." Thesis, University of Oxford, 2003. http://ora.ox.ac.uk/objects/uuid:46b5699b-1dcf-4860-8d76-09fc487a09d4.
Full textAbstract:
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, 4669-4675) and the as-yet unpublished work of Glab on the photoelectron branching ratios of the nd and nf Rydberg lines of the water molecule. The effect of resonances between electronic and rotational motion in Rydberg molecules is investigated using multichannel quantum defect theory with special reference to the time-resolved wave packet experiments of Smith et al. (R. A. L. Smith, J. R. R. Verlet, E. D. Boleat, V. G. Stavros and H. H. Fielding, Faraday Discuss., 2000, 115, 63-70).
18
O'Mahony, John. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.277879.
Full text
19
Docker, M. P. "Molecular photodissociation dynamics." Thesis, University of Nottingham, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.378987.
Full text
20
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.
Full textAbstract:
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 molecular simulations field, their limitations, and their development. Chapter 2 concentrates on the description of methods used in this work to perform molecular dynamics simulations of cucurbit[6]uril in aqueous and salt solutions as well as metal-isopropanol interface. This is followed by Chapter 3 that outlines main areas in our life where these systems can be used. The development of instruments is as important as the scientific part of molecular simulations like methods and algorithms. Parallelization procedure of the atomistic molecular dynamics program YASP for shared-memory computer architectures is described in Chapter 4. Parallelization was restricted to the most CPU-time consuming parts: neighbour-list construction, calculation of non-bonded, angle and dihedral forces, and constraints. Most of the sequential FORTRAN code was kept; parallel constructs were inserted as compiler directives using the OpenMP standard. Only in the case of the neighbour list the data structure had to be changed. The parallel code achieves a useful speed-up over the sequential version for systems of several thousand atoms and above. On an IBM Regatta p690+, the throughput increases with the number of processors up to a maximum of 12-16 processors depending on characteristics of the simulated systems. On dual-processor Xeon systems, the speed-up is about 1.7. Certainly, these results will be of interest to other scientific groups in academia and industry that would like to improve their own simulation codes. In order to develop a molecular receptor or choose from already existing ones that fits certain needs one must have quite good knowledge of non-covalent host-guest interactions. One also wants to have control over the capture/release process via environment of the receptor (pH, salt concentration, etc.). Chapter 5 is devoted to molecular dynamics simulations preformed to study the microscopic structure and dynamics of cations bound to cucurbit[6]uril (CB[6]) in water and in aqueous solutions of sodium, potassium, and calcium chloride. The molarities are 0.183M for the salts, and 0.0184M for CB[6]. The cations bind only to CB[6] carbonyl oxygens. They are never found inside the CB[6] cavity. Complexes with Na+ and K+ mostly involve one cation, whereas with Ca2+ single- and double-cation complexes are formed in similar proportions. The binding dynamics strongly depends on the type of cation. A smaller size or higher charge increases the residence time of a cation at a given carbonyl oxygen. The diffusion dynamics also corresponds to the binding strength of cations: the stronger binding the slower diffusion and reorientation dynamics. When bound to CB[6], sodium and potassium cations jump mainly between nearest or second-nearest neighbours. Calcium shows no hopping dynamics. It is coordinated predominantly by one CB[6] oxygen. A few water molecules (zero to four) can occupy the CB[6] cavity, which is delimited by the CB[6] oxygen faces. Their residence time is hardly influenced by sodium and potassium ions. In the case of calcium the residence time of the inner water increases notably. A simple structural model for the cations acting as “lids” over the CB[6] portal cannot, however, be confirmed. The slowing of the water exchange by the ions is a consequence of the generally slower dynamics in their presence and of their stable solvation shells. The study of binding behaviour of simple hydrophobic (Lennard-Jones) particles by CB[6] showed that these particles do not bind. A simple test showed that the size of hydrophobic particles in this case is important for a stable encapsulation. Another challenging field of research is the metal-organic interfaces. Particularly, transition metals are more difficult as they form chemical bonds, though sometimes very weak, with a large number of organic compounds. In Chapter 6 a molecular dynamics model and its parameterization procedure are devised and used to study adsorption of isopropanol on platinum(111) (Pt(111)) surface in unsaturated and oversaturated coverages regimes. Static and dynamic properties of the interface between Pt(111) and liquid isopropanol are also investigated. The magnitude of the adsorption energy at unsaturated level increases at higher coverages. At the oversaturated coverage (multilayer adsorption) the adsorption energy reduces, which coincides with findings by Panja et al. in their temperature-programmed desorption experiment (ref. 25). The density analysis showed a strong packing of molecules at the interface followed by a depletion layer and then by an oscillating density profile up to 3 nm. The distribution of individual atom types showed that the first adsorbed layer forms a hydrophobic methyl “brush”. This “brush” then determines the distributions further from the surface. In the second layer methyl and methine groups are closer to the surface and are followed by the hydroxyl groups; the third layer has exactly the inverted distribution. The alternating pattern extends up to about 2 nm from the surface. The orientational structure of molecules as a function of distance of molecules is determined by the atoms distribution and surprisingly does not depend on the electrostatic or chemical interactions of isopropanol with the metal surface. However, possible formation of hydrogen bonds in the first layer is notably influenced by these interactions. The surface-adsorbate interactions influence mobility of isopropanol molecules only in the first layer. Mobility in the higher layers is independent of these interactions. Finally, Chapter 7 summarizes main conclusions of the studies presented in this thesis and outlines perspectives of the future research.
21
Lin, Jr-Hung. "Nonatomistic molecular dynamics /." Aachen : Shaker, 2008. http://d-nb.info/991265556/04.
Full text
22
Epiphaniou, Nicholas. "Modelling of Dynamic Friction Across Solid Material Interfaces Using Molecular Dynamics Techniques." Thesis, Cranfield University, 2009. http://hdl.handle.net/1826/4458.
Full textAbstract:
The topic of this PhD is to investigate materials interfaces under the application of com-pressive forces and dynamic friction. Friction studies are important in applications for high-speed machining and ballistic penetration modelling, two areas where it is important to understand the behaviour of rapidly moving interfaces. Gaining insight into the velocity dependence of the effective tangential force, and its time-evolution, under various external loads is also of particular interest. It is important to understand on an atomic and/or molec-ular level the fundamentals of tribological processes. Some of the processes investigated in this thesis include plastic deformation due to high compression, the response of materials when sliding occurs in terms of temperature variation across the interface and its relation-ship with atomic diffusion. Moreover, the materials dependence on operating conditions of temperature, loading and dynamic friction are factors that ultimately determine the design of tribological systems.
In the last few years it has been shown that materials properties depend on the size, as smaller specimens are relatively stronger than larger ones. This thesis is aiming to em-ploy state of the art numerical and theoretical methods, which are vital to give a significant insight and understanding of the fundamental issues concerning dynamic friction of tribo-logical processes at the atomic scale. The mechanical behaviour is investigated in detail to reveal an accurate theoretical description of the frictional force at metallic surfaces. Special consideration is taken into account for the mechanism that causes dissipation in the form of heat. The strong deformation when materials undergo dynamic friction causes energy to dissipate away from the interface at a high rate.
Additionally, investigation of the plastic deformation and its variation under conditions prevalent at high speed sliding is carried out. Knowledge of the yield point under these conditions is important to obtain accurate constitutive models for the shear stresses. In-vestigating how the material strength varies under sliding friction and obtaining accurate evaluation of the stresses involved has proved difficult and time consuming. This is primar¬ily attributed to the fact that experiments are difficult to conduct and expensive facilities are required. This thesis focuses on aspects of this complex process with the aid of molecular dynamic simulations.
23
Olsson, Gustaf D. "Fundamental Studies of Molecular Interactions in Complete Prepolymerization Mixtures of Molecularly Imprinted Polymers." Thesis, University of Kalmar, School of Pure and Applied Natural Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:hik:diva-2366.
Full textAbstract:
In the present work, molecular dynamics simulations were used to evaluate the molecular interactions in prepolymerization mixtures, as occurring during production of molecularly imprinted polymers. The systems simulated were produced based on earlier studies for reference of results. Four systems were simulated in order to investigate the effect on molecular interactions based upon the choice of porogen (acetonitrile or chloroform) and proton transfers. The systems consisted of phenylalanine anilide as template, methacrylic acid as functional monomer, ethylene glycol dimethacrylate as crosslinker and 2,2’-azobis-(2-methylpropionitrile) as radical initiator, with either acetonitrile or chloroform as porogen. Trajectories from the simulations were evaluated through radial distribution function analysis, grid density analysis and hydrogen bond analysis to investigate molecular interactions and complex formations in the simulated complete prepolymerization mixtures. Focus was on functional monomer-template, crosslinker-template and template-template complex formations. The results showed that the porogen influences molecular interactions in complete prepolymerization mixtures. Formation of higher order complexes was confirmed in all of the systems involving all of the investigated molecular species in the prepolymerization mixtures. The results could also confirm the presence of previously observed complexes between functional monomer and template (2:1 and 1:1 stoichiometry) and the prevalence of template dimerization, as well as a high involvement of crosslinker in complex formation.
24
Wu, Tao. "Structure-function analysis of vascular tethering molecules using atomic force microscope." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/31844.
Full textAbstract:
Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2009.Committee Chair: Zhu, Cheng; Committee Member: Barry, Bridgette; Committee Member: Boyan, Barbara; Committee Member: McEver, Rodger; Committee Member: McIntire, Larry. Part of the SMARTech Electronic Thesis and Dissertation Collection.
25
Swann, Andrew Thomas. "Characterization of polymer-supported homogeneous catalysts by molecular modeling." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26702.
Full textAbstract:
Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2009.Committee Chair: Ludovice, Pete; Committee Member: Grover, Martha; Committee Member: Jones, Christopher; Committee Member: Realff, Matthew; Committee Member: Sherrill, David. Part of the SMARTech Electronic Thesis and Dissertation Collection.
26
Dong, Guangjiong. "Dynamics of molecules in pulsed optical lattices and its application to molecular optics." Thesis, Heriot-Watt University, 2003. http://hdl.handle.net/10399/428.
Full text
27
Haas, Ole-Erich, Jean-Marc Simon, and Signe Kjelstrup. "Adsorption-desorption kinetics of H 2 molecules on graphite: a molecular dynamics study." Diffusion fundamentals 11 (2009) 29, S. 1-2, 2009. https://ul.qucosa.de/id/qucosa%3A13978.
Full text
28
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.
Full text
29
Rogers, Christopher Reed. "A Comprehensive Integration and Analysis of Dynamic Load Balancing Architectures within Molecular Dynamics." DigitalCommons@USU, 2009. https://digitalcommons.usu.edu/etd/412.
Full textAbstract:
The world of nano-science is an ever-changing field. Molecular Dynamics (MD) is a computational suite of tools that is useful for analyzing and predicting behaviors of substances on the molecular level. The nature of MD is such that only a few types of computations are repeated thousands or sometimes millions of times over. Even a small increase speedup or efficiency of an MD simulator can compound itself over the life of the simulation and have a positive and observable effect. This thesis is the end result of an attempted speedup of the MD problem. Two types of MD architectures are developed: a dynamic architecture that is able to change along with the computational demands of the system, and a static architecture that is configured in terms of processing elements to be best suited to a variety of computational demands. The efficiency, throughput, area, and speed of the dynamic and static architectures are presented, highlighting the improvement that the dynamic architecture presents in its ability to provide load balancing.
30
Munz, Marton. "Computational studies of protein dynamics and dynamic similarity." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:2fb76765-3e43-409b-aad3-b5202f4668b3.
Full textAbstract:
At the time of writing this thesis, the complete genomes of more than 180 organisms have been sequenced and more than 80000 biological macromolecular structures are available in the Protein Data Bank (PDB). While the number of sequenced genomes and solved three-dimensional structures are rapidly increasing, the functional annotation of protein sequences and structures is a much slower process, mostly because the experimental de-termination of protein function is expensive and time-consuming. A major class of in silico methods used for protein function prediction aim to transfer annotations between proteins based on sequence or structural similarities. These approaches rely on the assumption that homologous proteins of similar primary sequences and three-dimensional structures also have similar functions. While in most cases this assumption appears to be valid, an increasing number of examples show that proteins of highly similar sequences and/or structures can have different biochemical functions. Thus the relationship between the divergence of protein sequence, structure and function is more complex than previously anticipated. On the other hand, there is mounting evidence suggesting that minor changes of the sequences and structures of proteins can cause large differences in their conformational dynamics. As the intrinsic fluctuations of many proteins are key to their biochemical functions, the fact that very similar (almost identical) sequences or structures can have entirely different dynamics might be important for understanding the link between sequence, structure and function. In other words, the dynamic similarity of proteins could often serve as a better indicator of functional similarity than the similarity of their sequences or structures alone. Currently, little is known about how proteins are distributed in the 'dynamics space' and how protein motions depend on structure and sequence. These problems are relevant in the field of protein design, studying protein evolution and to better understand the functional differences of proteins. To address these questions, one needs a precise definition of dynamic similarity, which is not trivial given the complexity of protein motions. This thesis is intended to explore the possibilities of describing the similarity of proteins in the 'dynamics space'. To this end, novel methods of characterizing and comparing protein motions based on molecular dynamics simulation data were introduced. The generally applicable approach was tested on the family of PDZ domains; these small protein-protein interaction domains play key roles in many signalling pathways. The methodology was successfully used to characterize the dynamic dissimilarities of PDZ domains and helped to explain differences of their functional properties (e.g. binding promiscuity) also relevant for drug design studies. The software tools developed to implement the analysis are also introduced in the thesis. Finally, a network analysis study is presented to reveal dynamics-mediated intramolecular signalling pathways in an allosteric PDZ domain.
31
Oguz, Cihan. "Control-oriented modeling of discrete configuration molecular scale processes applications in polymer synthesis and thin film growth /." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/19867.
Full textAbstract:
Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2008.Committee Chair: Gallivan, Martha A.; Committee Member: Hess, Dennis; Committee Member: Lee, Jay H.; Committee Member: Li, Mo; Committee Member: Ludovice, Pete.
32
Siavosh-Haghighi, Ali. "Topics in molecular dynamics." free to MU campus, to others for purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3164542.
Full text
33
Castelow, D. A. "Molecular dynamics of rods." Thesis, University of Cambridge, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303841.
Full text
34
Summerfield, Dean. "Studies of molecular dynamics." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318460.
Full text
35
Craig, Ian R. "Ring polymer molecular dynamics." Thesis, University of Oxford, 2006. http://ora.ox.ac.uk/objects/uuid:f3c37800-6fc7-4d8b-b135-94d94a7cf4e1.
Full textAbstract:
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 (qˆ), and position-cubed (qˆ3), autocorrelation functions of a series of onedimensional potential wells of varying anharmonicity. It is then applied to the evaluation of the incoherent dynamic structure factors of liquid para-hydrogen at 14 K. Finally, the RPMD method is used to determine canonical rate coefficients for two onedimensional models of bimolecular chemical reactions and a multidimensional model of a solution-phase proton transfer reaction. For each application, the accuracy of the RPMD method is established by comparison with exact quantum-mechanical results and/or with experiment. Throughout this work, an emphasis is placed upon identifying the situations in which the RPMD approximation breaks down. It is found that the RPMD method is capable of providing an accurate approximation to the time correlation functions of a variety of condensed-phase molecular systems. Situations for which it is inaccurate include correlation functions which correlate highly nonlinear operators and those involving significant quantum interference effects in the real-time dynamics.
36
Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.
Full text
37
Edmunds, David. "Coarse-grained molecular dynamics." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/25112.
Full textAbstract:
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 with an analytic derivation of the CG partition function for a harmonic potential. We then apply this theory to a simple system of two interacting dimers, obtaining expressions for the CG free and internal energy. This example serves as a motivation for how to coarse-grain more realistic systems numerically. We introduce five different approaches to generating a CG potential, which we have termed the rigid and relaxed approximation, the constrained pair approach, the unconstrained box approach and the entropic approach. We apply each of these techniques to a system of C60 molecules, comparing our results against reference fully atomistic MD simulations of the same system. We find that the constrained pair approach provides an optimal balance between ease of generation and accuracy when compared to the reference model.
38
Zhang, Junfang. "Computer simulation of nanorheology for inhomogenous fluids." Australasian Digital Thesis Program, 2005. http://adt.lib.swin.edu.au/public/adt-VSWT20050620.095154.
Full textAbstract:
Thesis (PhD) - Swinburne University of Technology, School of Information Technology, Centre for Molecular Simulation - 2005.A thesis submitted in fulfilment of requirements for the degree of Doctor of Philosophy, Centre for Molecular Simulation, School of Information Technology, Swinburne University of Technology - 2005. Typescript. Bibliography: p. 164-170.
39
Waller, Mark Paul. "Experimental and theoretical studies of the electron distribution in weak molecular interactions." Thesis, The University of Sydney, 2006. https://hdl.handle.net/2123/28058.
Full textAbstract:
This thesis has contributed to understanding of weak molecular interactions via a study of
the experimental and theoretical electron density (ED). Single crystal neutron and X-ray
diffraction experiments have enabled experimental quantification of a range of weak interand
intramolecular interactions in a series of biologically important molecules.
Complementary high level quantum chemical calculations have also been carried out on all
systems, and the results have been critically compared with the experimental data, often
using ‘Atoms-in-Molecules’ quantum theory.
This thesis presents a new method for the analysis of X-ray diffraction experiments within a
molecular orbital framework. This method enables quantum operators to be applied to an
experimentally-derived density matrix. In Chapter 2 the method is developed, validated and
applied to scattering data for two molecular crystals.
Chapter 3 reports a careful analysis of hybrid density functional methods for the modelling
of aromatic n-rt stacking interactions. This was achieved Via critical comparison with some
powerful ab initio methods, and exhaustive validation was performed on both chemically
and biologically interesting aromatic awn stacked complexes. A useful linear correlation is
developed for representing the interaction energy of rc-stacked systems using electron
density critical point data.
Chapter 4 presents two experimental electron density studies using the tried-and-tested
multipole model for two molecular crystals containing O—H...O and O—N...O hydrogen
bonds: (Z)-N-methyl-C-phenylnitrone and 9-ethynly-9-fluorenol.
A separate study of cholesterol derivatives in Chapter 5 presents calculated gas—phase
electrostatic moments was used to interpret experimental data on the same molecules
embedded in lipid membranes.
In Chapter 6, halogen-halogen interactions are investigated in an experimental electron
density study of two perfluorinated isomorphs. The same intermolecular interactions are also
analysed using second order perturbation theory.
In Appendix 7.2 the experimental electron density study of two isomeric complexes of
ternary Co(III) with aromatic amino acids is presented. The interaction energy of the 313-317
and N-H...:t intramolecular interactions is estimated. The combined experimental and
theoretical study has provided valuable insight into atomic transferability using the
multipole model.
40
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.
Full textAbstract:
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 process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper- NID is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this.
41
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.
Full textAbstract:
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 which is based on calculating and comparing eigenvalues for Markov models constructed at different time steps. Here, the method is applied to a simulation of the four residue peptide VPAL and it is found that the Markov model is accurate at a minimum time step of 100ps. The determination of the time step using this test is, however, subjective, so I have developed a method which is based on Computational Mechanics to determine the minimum time step at which the dynamics are Markovian. An important part of the application of a Markov model is the clustering of the Molecular Dynamics simulation into conformational states. The effect of varying the clustering of the simulation is investigated by calculating the mean first passage times between conformational states as the cluster boundaries are varied. It is found that the mean first passage times are sensitive to specific clustering, and to reduce the model sensitivity to variations in clustering, it is especially important to exclude sparsely populated states from the model. Finally, it is demonstrated that the folding time of a slow folding protein can be very sensitive to changes in the Markov model transition matrix. This implies that folding times calculated using Molecular Dynamics cannot meaningfully be compared to folding times obtained from experiments.
42
Fischer, Michael, Jan Handt, and Rüdiger Schmidt. "Nonadiabatic quantum molecular dynamics with hopping. III. Photoinduced excitation and relaxation of organic molecules." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-151805.
Full textAbstract:
Photoinduced excitation and relaxation of organic molecules (C2H4 and CH2NH+2) are investigated by means of nonadiabatic quantum molecular dynamics with hopping (NA-QMD-H), developed recently [Fischer, Handt, and Schmidt, paper I of this series, Phys. Rev. A 90, 012525 (2014)]. This method is first applied to molecules assumed to be initially ad hoc excited to an electronic surface. Special attention is drawn to elaborate the role of electron-nuclear correlations, i.e., of quantum effects in the nuclear dynamics. It is found that they are essential for a realistic description of the long-time behavior of the electronic relaxation process, but only of minor importance to portray the short-time scenario of the nuclear dynamics. Migration of a hydrogen atom, however, is identified as a quantum effect in the nuclear motion. Results obtained with explicit inclusion of an fs-laser field are presented as well. It is shown that the laser-induced excitation process generally leads to qualitatively different gross features of the relaxation dynamics, as compared to the field-free case. Nevertheless, the nuclear wave packet contains all subtleties of the cis-trans isomerization mechanism as observed without a laser field.
43
Freitas, Rodrigo Moura 1989. "Molecular simulation = methods and applications = Simulações moleculares : métodos e aplicações." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/278440.
Full textAbstract:
Orientador: Maurice de KoningDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
Made available in DSpace on 2018-08-23T00:50:21Z (GMT). No. of bitstreams: 1 Freitas_RodrigoMoura_M.pdf: 11496259 bytes, checksum: 41c29f22d80da01064cf7a3b9681b05f (MD5) Previous issue date: 2013
Resumo: Devido aos avanços conceptuais e técnicos feitos em física computacional e ciência dos materiais computacional nos estamos aptos a resolver problemas que eram inacessíveis a alguns anos atrás. Nessa dissertação estudamos a evolução de alguma destas técnicas, apresentando a teoria e técnicas de simulação computacional para estudar transições de fase de primeira ordem com ênfase nas técnicas mais avançadas de calculo de energia livre (Reversible Scaling) e métodos de simulação de eventos raros (Forward Flux Sampling) usando a técnica de simulação atomística da Dinâmica Molecular. A evolução e melhora da e ciência destas técnicas e apresentada junto com aplicações a sistemas simples que permitem solução exata e também ao caso mais complexo da transição de fase Martenstica. Também apresentamos a aplicação de métodos numéricos no estudo do modelo de Pauling para o gelo. Nos desenvolvemos e implementamos um novo algoritmo para a criação e ciente de estruturas de gelo desordenadas. Este algoritmo de geração de cristais de gelo nos permitiu criar células de gelo Ih de tamanhos que não eram possíveis antes. Usando este algoritmo abordamos o problema de efeitos de tamanho finito não estudados anteriormente
Abstract: Due to the conceptual and technical advances being made in computational physics and computational materials science we have been able to tackle problems that were inaccessible a few years ago. In this dissertation we study the evolution of some of these techniques, presenting the theory and simulation methods to study _rst order phase transitions with emphasis on state-of-the-art free-energy calculation (Reversible Scaling) and rare event (Forward Flux Sampling) methods using the atomistic simulation technique of Molecular Dynamics. The evolution and efficiency improvement of these techniques is presented together with applications to simple systems that allow exact solution as well as the more the complex case of Martensitic phase transitions. We also present the application of numerical methods to study Pauling\'s model of ice. We have developed and implemented a new algorithm for efficient generation of disordered ice structures. This ice generator algorithm allows us to create ice Ih cells of sizes not reported before. Using this algorithm we address finite size effects not studied before
Mestrado
Física
Mestre em Física
44
Huang, Pengyu. "Multiscale Modelling of Dynamic Contact Angles for CO2-Water-Silica Systems." Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/20937.
Full textAbstract:
The capillary and dynamic wetting behaviour in porous media is crucial in many engineering problems which are highly related to the multiphase interactions between fluids and solids. This thesis will focus on the behaviour of dynamic contact angle of the supercritical CO2/water flow in the silica slit as a function of the contact line velocity at both the nanoscale and microscale, which can help us gain an in-depth understanding of the dynamic processes in CO2 geosequestration in saline aquifers. Our molecular dynamics (MD) simulations calculate the contact angle quantitatively at different velocities at the nanoscale and also validate the molecular kinetic theory through the detailed analysis of the equilibrium jump distance and frequency of the water and CO2 molecules at the solid surfaces. While the MD simulations provide the results of dynamic contact angle at the nanoscale, which can be suitable for the nanopores of the low permeability rock, the dynamic contact angle behaviour at the microscale is also important and investigated in this thesis. This work also develops a coarse-grained molecular dynamic (CGMD) framework to model the liquid-vapour-solid interactions at the microscale. The newly developed CGMD framework has been applied and extended to the study of the dynamic contact angle for the CO2-water-silica system at the microscale. The microscale CGMD simulation of CO2-water-silica system shows that there is an increase in the CO2 contact angle as the increase of the contact line velocity at three different pressures. The dynamic contact angles under a water pressure of 18.9 MPa seem to be slightly larger than those under the water pressures of 9.41 MPa and 14.3 MPa. Moreover, the comparison between the MD and CGMD results suggests that there could be a pore size effect on the dynamic contact angle for the studied CO2-water-silica system.
45
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.
Full text
46
Henritzi, Patrick [Verfasser], Michael [Akademischer Betreuer] Vogel, and Bernd [Akademischer Betreuer] Stühn. "A Molecular Dynamics Simulation Study of Dynamic Processes in Molecular Glass-Forming Liquids / Patrick Henritzi. Betreuer: Michael Vogel ; Bernd Stühn." Darmstadt : Universitäts- und Landesbibliothek Darmstadt, 2014. http://nbn-resolving.de/urn:nbn:de:tuda-tuprints-40253.
Full text
47
Henritzi, Patrick Verfasser], Michael [Akademischer Betreuer] [Vogel, and Bernd [Akademischer Betreuer] Stühn. "A Molecular Dynamics Simulation Study of Dynamic Processes in Molecular Glass-Forming Liquids / Patrick Henritzi. Betreuer: Michael Vogel ; Bernd Stühn." Darmstadt : Universitäts- und Landesbibliothek Darmstadt, 2014. http://d-nb.info/1110901534/34.
Full text
48
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.
Full text
49
Gräfe, Stefanie. "Laser-control of molecular dynamics." [S.l. : s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=976127016.
Full text
50
Vilfan, Andrej. "Collective dynamics of molecular motors." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=959980024.
Full text