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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 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.
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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, 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.
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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 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.
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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, 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).
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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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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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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 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.
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Lin, Jr-Hung. "Nonatomistic molecular dynamics /." Aachen : Shaker, 2008. http://d-nb.info/991265556/04.
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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 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.
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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 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.
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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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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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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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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 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.
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Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.
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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 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.
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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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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 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.
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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 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.
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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 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.
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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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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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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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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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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>Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared. </p><p>Next, a method for treating electrostatic interactions in MD simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform---ENUF for short. The method scales as <i>N log N</i>, where <i>N </i>is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs.</p><p>Finally, an outlook is given and some directions for further developments are suggested.</p>
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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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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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Huhges, Samantha Jayne. "Molecular dynamics simulations of LysU." Thesis, Imperial College London, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269701.
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Elcock, Adrian Hamilton. "Molecular dynamics simulations of DNA." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.239313.
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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 many–body problem posed by consideration of the medium as being composed of interacting atoms. The issue, then, has been transferred from one of dealing with many particles (which remains a problem for some aspects) to one of being able to develop a model which correctly describes the atomic interactions. However, it has been found that approximately correct models provide sufficient fidelity to enable qualitative studies to be undertaken. The study undertaken here has used this advantage to consider the behaviour of metallic materials under weak shock conditions. A comparison with some previous studies is given, which shows that, in order to avoid certain behaviours not observed experimentally, the simulation must contain thermal motion equivalent to at least room temperature. This thermal motion, and its resultant misalignment of the atoms, prevents spurious transfer of uni-directional momentum into rebounding translational supersonic waves. Further examination of the initial generation of dislocations indicates differences in the behaviour of not only the three high symmetry directions, but in the way that shear stress is relieved initially in low symmetry crystals as well. This behaviour gives some indication as to how the elastic precursor, commonly observed in weak shock experiments, decays from the level predicted by the Rankine–Hugoniot conservation relations to the much lower level observed experimentally. However, a very large discrepancy exists between the amplitude of the elastic wave observed in these simulations and that of experiments. It is shown that the existence of defects within the crystal can account for at least some of this discrepancy. However, computational limitations not only prevent the creation of realistic sample sizes, but also prevent the simulation of realistic defect densities and microstructures. This computational limtation, then, means that it is not currently possible to recreate the low Hugoniot elastic limits observed experimentally. The inability of atomistic simulations to recreate experimental data notwithstanding, useful analysis of shock behaviour is demonstrated. This fortuity is used to examine the behaviour of bicrystals under shock loading. It is shown that the difference in shock speed, together with the difference in response of the two crystal orientations leads to an interaction which modifies the behaviour from that observed in single crystal simulations. Further use is made of the ability of modern simulation methods to recreate salient features of dynamic processes to examine the behaviour of metallic substrates under high–speed impact from nanometer sized particles. Here the plasticity of the substrate is shown to be vital to ensuring that the simulation results are faithful to experiment, and hence to space science work. In order to capture this behavioour correctly, issues of substrate size and boundary behaviour are seen to be key.
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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, adhesive tip-substrate interactions and atom transfer, together with damage after adhesive rupture and mechanisms of tip-induced structural transformations and surface nanotopograpghy. To alleviate finite-size effects and to facilitate the simulation of over one million atoms, a parallel MD code using the MPI paradigm has also been developed to run on multiple processor machines. The work materials show a diverse range of deformation behaviour, ranging from purely elastic deformation with graphite, to appreciable plastic deformation with metals. Some qualitative comparisons are made to experiment, but available computer power constrains feasible indentation depths to an order of magnitude smaller than experiment, and over indentation times several orders of magnitude smaller. The simulations give a good description of nanoindentation and support many of the experimental features.
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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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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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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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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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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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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 several fundamental organometallic reactions. Chapter 1 provides a brief overview of key molecular dynamics details. Chapters 2-4 provide details on for three classic organometallic reactions involving alkane C-H bonds. These Chapters are from previously published works (J. Am. Chem. Soc. 2018, 140, 11039; Organometallics 2019, 38, 2280; Organometallics, 2021, 40, 1454). Chapter 5 provides details about progress toward performing quasiclassical molecular dynamics simulations of organometallic reactions in explicit organic solvent.
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Bass, Alexander. "Molecular dynamics simulations of sonoluminescence." Diss., Restricted to subscribing institutions, 2009. http://proquest.umi.com/pqdweb?did=1790349561&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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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 extrêmes requièrent la simulation de systèmes toujours plus grands avec une physique de plus en plus complexe. L’adaptation des codes de DM aux architectures exaflopiques est donc un enjeu essentiel.Cette thèse propose la conception et l’implémentation d’une plateforme dédiée à la simulation de très grands systèmes de DM sur les futurs supercalculateurs. Notre architecture s’organise autour de trois niveaux de parallélisme: décomposition de domaine avec MPI, du multithreading massif sur chaque domaine et un système de vectorisation explicite. Nous avons également inclus une capacité d’équilibrage dynamique de charge de calcul. La conception orienté objet a été particulièrement étudiée afin de préserver un niveau de programmation utilisable par des physiciens sans altérer les performances.Les premiers résultats montrent d’excellentes performances séquentielles, ainsi qu’une accélération quasi-linéaire sur plusieurs dizaines de milliers de cœurs. En production, nous constatons une accélération jusqu’à un facteur 30 par rapport au code utilisé actuellement par les chercheurs du CEA<br>In the exascale race, supercomputer architectures are evolving towards massively multicore nodes with hierarchical memory structures and equipped with larger vectorization registers. These trends tend to make MPI-only applications less effective, and now require programmers to explicitly manage low-level elements to get decent performance.In the context of Molecular Dynamics (MD) applied to condensed matter physics, the need for a better understanding of materials behaviour under extreme conditions involves simulations of ever larger systems, on tens of thousands of cores. This will put molecular dynamics codes among software that are very likely to meet serious difficulties when it comes to fully exploit the performance of next generation processors.This thesis proposes the design and implementation of a high-performance, flexible and scalable framework dedicated to the simulation of large scale MD systems on future supercomputers. We managed to separate numerical modules from different expressions of parallelism, allowing developers not to care about optimizations and still obtain high levels of performance. Our architecture is organized in three levels of parallelism: domain decomposition using MPI, thread parallelization within each domain, and explicit vectorization. We also included a dynamic load balancing capability in order to equally share the workload among domains.Results on simple tests show excellent sequential performance and a quasi linear speedup on several thousands of cores on various architectures. When applied to production simulations, we report an acceleration up to a factor 30 compared to the code previously used by CEA’s researchers
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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 efficienze impareggiabili sfruttando la fissione del singoletto. Quest’ultimo è un processo di moltiplicazione eccitonica in cui, per una certa classe di materiali, un eccitone di singoletto si separa in due eccitoni di tripletto, si raddoppiando potenzialmente i portatori di carica. È necessario ancora molto lavoro per beneficiare pienamente della fissione del singoletto nel fotovoltaico; in particolare, è richiesto un maggior grado di controllo sul trasporto e sui meccanismi di dissociazione degli eccitoni alle interfaccie etero-organiche per poter estrarre efficacemente gli eccitoni di tripletto. Allo scopo di comprendere più a fondo tali processi, nella camera ANCHOR-SUNDYN della linea di luce ALOISA ad Elettra abbiamo sviluppato un apparato sperimentale per misure di spettroscopia ai raggi X risolte in tempo, in cui le dinamiche eccitoniche nei film organici possono essere caratterizzate usando spettroscopie di fotoemissione e di assorbimento di raggi X con una risoluzione di 100ps. Qui, possiamo combinare le misure risolte in tempo con spettroscopie a raggi X e UV tradizionali, per una più dettagliata analisi dei campioni.
Abbiamo applicato questo approccio ad interfacce donore/accettore, sistemi prototipo per i dispositivi fotovoltaici organici; abbiamo studiato gli stati eccitati di tripletto nel pentacene mediante misure di assorbimento di raggi X risolte in tempo, con cui è stato individuato un picco legato all’eccitazione con una vita media di 0.3±0.2 ns sotto alla risonanza del LUMO, che abbiamo associato alle molecole nello stato di tripletto. Nella scala dei picosecondi, misure svolte al laser ad elettroni liberi FLASH rivelano una risposta dei fotoelettroni che riteniamo legata alla dissociazione dell’eccitone di tripletto all’interfaccia con lo strato di C60 sottostante. Abbiamo osservato un effetto analogo anche in spettri di fotoemissione pompa-sonda su interfacce di tetracene / ftalocianina di rame. Su questo sistema, abbiamo variato la lunghezza d’onda del fotone di pompa per eccitare selettivamente i due materiali, ed abbiamo esaminato il diverso comportamento degli eccitoni fotogenerati; la presenza di un campo elettrico transiente nella scala dei microsecondi suggerisce che gli eccitoni di tripletto sono coinvolti nel trasferimento di carica che avviene dal tetracene alla ftalocianina di rame, in accordo con studi precedenti. I risultati qui presentati dimostrano che le spettroscopie a raggi X risolte in tempo possono fornire informazioni valide per la caratterizzazione delle dinamiche eccitoniche in interfacce etero-organiche.<br>In recent years, the need for a more sustainable economic development contributed to the increasing interest in renewable energy sources. With encouraging trends on power conversion efficiencies and manufacturing costs, photovoltaics is expected to be the workhorse for the production of green energy in the future. Silicon is currently the dominant photovoltaic technology but, in the past decade, novel solutions based on organic semiconductors became attractive for their potential of overcoming the Shockley-Queisser limit and offering unmatched efficiencies by exploiting singlet fission. The latter is an exciton multiplication process in which, for a certain class of materials, a singlet exciton splits into two triplet excitons, thus potentially doubling the charge carriers. Significant work is still necessary to fully benefit of singlet fission in photovoltaics; in particular, a higher degree of control over exciton transport and dissociation mechanisms at hetero-organic interfaces is required for efficiently harvesting triplet excitons. To the aim of better understanding such processes, at the ANCHOR-SUNDYN endstation of the ALOISA beamline at Elettra we developed an experimental setup for time-resolved X-ray spectroscopies, in which the exciton dynamics in organic films can be characterized by X-ray photoemission and absorption spectroscopies with a 100 ps resolution. Here, we can combine time-resolved measurements with standard X-ray and UV spectroscopies for a more detailed analysis of the samples.
We apply this approach to donor/acceptor interfaces, the prototypical architectures of organic photovoltaic devices; we investigate triplet excited states in pentacene by means of time-resolved X-ray absorption, which displays a pump-induced feature with a 0.3±0.2 ns lifetime below the LUMO resonance, that we associated to molecules in the triplet state. On the picosecond time scale, measurements performed at the FLASH free-electron laser reveal a photoelectron response that we deem related to the triplet exciton dissociation at the interface with the underlying C60 film. A similar effect is also observed in pump-probe photoemission spectra of tetracene / copper phthalocyanine interfaces. On this second system, we tuned the pump wavelength to selectively excite the two materials and examined the different behavior of the photogenerated excitons; the presence of a transient field in the microsecond time scale suggests that triplet excitons are involved in the charge transfer that occurs from tetracene to copper phthalocyanine, in agreement with previous studies. The results presented here demonstrate that time-resolved X-ray spectroscopies can provide valuable information for the characterization of exciton dynamics in hetero-organic interfaces.
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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 dynamics plays a crucial role, not only ionic vibrations, but also oxygen diffusion.</p><p>In this thesis, the structure and dynamics of several ionic crystalline compounds and their surfaces have been studied by means of Molecular dynamics (MD) simulations and Lattice dynamics (LD) calculations. The main focus lies on CeO<sub>2-x</sub>, but also CeO<sub>2</sub>, MgO and CaF<sub>2</sub> have been investigated.</p><p>The presence of oxygen vacancies in ceria is found to lead to significant distortions of the oxygen framework around the defect (but not of the cerium framework). As a consequence, a new O-O distance emerges, as well as a significantly broadened Ce-O distance distribution.</p><p>The presence of oxygen vacancies in ceria also leads to increased dynamics. The oxygen self-diffusion in reduced ceria was calculated from MD simulations in the temperature range 800-2000 K, and was found to follow an Arrhenius behaviour with a vacancy mechanism along the crystallographic <100> directions only.</p><p>The cation and anion vibrational surface dynamics were investigated for MgO (001) using DFT-LD and for CaF<sub>2</sub> (111) in a combined LEED and MD study. Specific surface modes were found for MgO and increased surface dynamics was found both experimentally and theoretically for CaF<sub>2</sub>, which is isostructural with CeO<sub>2</sub>.</p><p>Many methodological aspects of modeling dynamics in ionic solids are also covered in this thesis. In many cases, the representation of the model system (slab thickness, simulation box-size and the choice of ensemble) was found to have a significant influence on the results.</p>
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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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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 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.
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Edman, Lars. "Single molecule dynamics /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4025-8/.
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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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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 assistance in this regard mainly through molecular simulations. But atomistically simulations of large functional motions make computations, currently, unaffordable. The problem is that large-scale motions are rooted in the very fast elemental ones; so, in order to observe a biological-functional conformational change we have to keep track of all the elemental motions occurring. The gap in the time scale of both extremes of motions is devastating: fast motions are over 1015 times faster than functional ones.
In this Thesis, I present our contribution to extend the simulation time range, in an effort towards more predictive computational models. We explored alternative methods to retrieve molecular motions from the underlying physical forces governing proteins. The method used is named Discrete Molecular Dynamics and represents by itself a significant improvement in computational efficiency. In order to go further, we lower the resolution of protein models to a coarse-grained representation both in terms of number of particles and interaction functions. We benefited from several existing algorithms to simplify calculations keeping the models as much accurate as possible. Putting all this methodological innovations together, we developed models to follow conformational transitions of proteins, from local re-arrangements to motions changing drastically the protein structure. Also, we applied novel computational approaches to account for protein flexibility upon recognizing and binding other interacting proteins.
In a second stage, we investigated the echo of protein flexibility and dynamics printed out in the sequence of the protein. We observed over the history of the sequence that instead of one single native structure, proteins were tuned to have several conformations. We exploited this flexibility signature in the sequence to predict protein motions and eventually alternative protein conformations. Finally, we use our efficient tools to move protein dynamics analysis to the proteome scale. We searched for all proteins having two known conformations, a symptom of a conformational transition, and then, we used those conformations to follow the motion from one state to the other. We analyzed and structured all that dynamical information of proteins and connected our results to the most detailed simulation methods available to dissect the fine details of proteins dynamical behavior when required.<br>Secuencia, estructura y dinámica forman un trío un insoslayable en el funcionamiento de las proteínas. El proceso evolutivo codificó la dinámica en la estructura de las proteínas, que a su vez, está codificada en la secuencia. Descifrar los mecanismos que rigen el movimiento de las proteínas requiere la fusión de experimentos y modelos teóricos. Los modelos teóricos proporcionan asistencia necesaria a través de simulaciones moleculares, pero su costo computacional es tan elevado que puede impedir el estudio. El problema radica en que los movimientos biológicamente interesantes son la consecuencia de un cúmulo de movimientos de alta frecuencia, que es necesario seguir para comprender los movimientos funcionales. La brecha entre ambos tiempos asciende a un impresionante ratio de 1015.
En esta Tesis, presento métodos para aumentar la eficacia de los cálculos moleculares con el objetivo de acortar la diferencia entre el tiempo de lo que es simulable a lo que es biológicamente interesante. El método utilizado es Discrete Molecular Dynarnics y representa por sí mismo una mejora significativa en la eficiencia computacional. En resumen, hemos desarrollado modelos para seguir transiciones conformacionales de proteínas, desde movimientos locales hasta otros que cambian radicalmente la forma de la proteína. Dichos métodos fueron aplicados tanto a transiciones conformacionales como a interacciones proteína-proteína. En una segunda etapa, buscamos la imprenta en la secuencia del patrón de flexibilidad de la proteína, con el objetivo de predecir los cambios de conformación. Finalmente, utilizando los métodos desarrollados hemos concluido un análisis a gran escala sobre la dinámica de las proteínas, simulando todas las transiciones cuyos dos extremos fueron determinados experimentalmente. Los resultados de dichas simulaciones fueron integrados con los métodos de simulación más fiables disponibles, para aumentar en nivel de detalle cuando sea necesario.
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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 a range of complex geometries at the nano-scale. Comparison for validation is with full-scale MD simulations here, but the computational cost of the enhanced CFD is negligible in comparison with the MD. It is shown that this enhanced CFD can predict unsteady nano-scale ows in non-trivial geometries. A converging-diverging nano-scale channel is modelled where the fl uid fl ow is driven by a time-varying body force. The time-dependent mass fl ow rate predicted by the enhanced CFD agrees well with a MD simulation of the same configuration. Conventional CFD predictions of the same case are wholly inadequate. It is demonstrated that accurate predictions can be obtained in geometries that are more complex than the planar MD pre-simulation geometry that provides the nano-scale fl uid properties. The robustness of the enhanced CFD is tested by application to water fl ow along a (15,15) carbon nanotube (CNT) and it is found that useful fl ow information can be obtained. The enhnaced CFD model is applied as a design optimisation tool on a bifurcating two-dimensional channel, with the target of maximising mass fl ow rate for a fixed total volume and applied pressure. At macro scales the optimised geometry agrees well with Murray's law for optimal branching of vascular networks; however, at the nano-scale, the optimum result deviates from Murray's law, and a corrected equation is presented. However, it is found that as the mass flow rate increases through the channel high pressure losses occur at the junction of the network. These high pressure losses also have an impact on the optimal design of a network.
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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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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 models, to study the dissolution process in water under sink conditions, because of their contrasting solubility in water. The dissolution rate in different water models was examined and it was found that they differ considerably. However, the overall mechanism for the dissolution process remains the same. Dissolution was found to be an activated process with the detachment of molecules from the crystal being the rate limiting step. Crystals with different shapes (cubic and cylindrical) were used to study the effect of shape on the dissolution process.
The dissolution process for urea was found to occur in three steps, an initial rapid stage, where the molecules at the edges and corners go into the solution, a long intermediate stage with a nearly constant dissolution rate, and a final stage where the crystals lose their crystalline structure and dissolve completely. The fixed rate law stage was found to be described by a simple rate law derived from classical models.
It was found that there is an additional step in the dissolution process for aspirin, occurring between the initial rapid stage and the fixed rate law stage, during which the crystal attains a solution annealed shape. The fixed rate law stage was again found to be described by a simple rate law.
The results obtained are in agreement with an earlier dissolution study of NaCl crystals, thus it appears that the classical rate laws can be used to describe the dissolution of a variety of complex molecular and ionic crystals.<br>Science, Faculty of<br>Chemistry, Department of<br>Graduate
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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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