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1
Dean, Delphine Marguerite Denise 1978. "Molecular electromechanics : modeling electrostatic forces between GAG molecules." Thesis, Massachusetts Institute of Technology, 2001. http://hdl.handle.net/1721.1/86649.
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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2001.Includes bibliographical references (p. 81-83).
by Delphine Marguerite Denise Dean.
M.Eng.and S.B.
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Eckel, Rainer. "Single molecules and nanocrystals: molecular recognition forces and optomechanical switching." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=978888227.
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Bermingham, Charlotte R. "Measurement of pico/femto-Newton scale forces using the lateral molecular force microscope." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715803.
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Wells, B. H. "Studies in intramolecular forces." Thesis, University of Oxford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.355824.
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Gellert, P. R. "Spectroscopic and theoretical studies of intermolecular forces." Thesis, University of Oxford, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.234945.
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Jones, Andrew. "Quantum drude oscillators for accurate many-body intermolecular forces." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/4878.
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One of the important early applications of Quantum Mechanics was to explain the Van-der-Waal’s 1/R6 potential that is observed experimentally between two neutral species, such as noble gas atoms, in terms of correlated uncertainty between interacting dipoles, an effect that does not occur in the classical limit [London-Eisenschitz,1930]. When many-body correlations and higher-multipole interactions are taken into account they yield additional many-body and higher-multipole dispersion terms. Dispersion energies are closely related to electrostatic interactions and polarisation [Hirschfelder-Curtiss-Bird,1954]. Hydrogen bonding, the dominant force in water, is an example of an electrostatic effect, which is also strongly modified by polarisation effects. The behaviour of ions is also strongly influenced by polarisation. Where hydrogen bonding is disrupted, dispersion tends to act as a more constant cohesive force. It is the only attractive force that exists between hydrophobes, for example. Thus all three are important for understanding the detailed behaviour of water, and effects that happen in water, such as the solvation of ions, hydrophobic de-wetting, and thus biological nano-structures. Current molecular simulation methods rarely go beyond pair-wise potentials, and so lose the rich detail of many-body polarisation and dispersion that would permit a force field to be transferable between different environments. Empirical force-fields fitted in the gas phase, which is dominated by two-body interactions, generally do not perform well in the condensed (many-body) phases. The leading omitted dispersion term is the Axilrod-Teller-Muto 3-body potential, which does not feature in standard biophysical force-fields. Polarization is also usually ommitted, but it is sometimes included in next-generation force-fields following seminal work by Cochran [1971]. In practice, many-body forces are approximated using two-body potentials fitted to reflect bulk behaviour, but these are not transferable because they do not reproduce detailed behaviour well, resulting in spurious results near inhomogeneities, such as solvated hydrophobes and ions, surfaces and interfaces. The Quantum Drude Oscillator model (QDO) unifies many-body, multipole polarisation and dispersion, intrinsically treating them on an equal footing, potentially leading to simpler, more accurate, and more transferable force fields when it is applied in molecular simulations. The Drude Oscillator is simply a model atom wherein a single pseudoelectron is bound harmonically to a single pseudonucleus, that interacts via damped coulomb interactions [Drude,1900]. Path Integral [Feynman-Hibbs,1965] Molecular Dynamics (PIMD) can, in principle, provide an exact treatment for moving molecules at finite temperature on the Born- Oppenheimer surface due to their pseudo-electrons. PIMD can be applied to large systems, as it scales like N log(N), with multiplicative prefactor P that can be effectively parallelized away on modern supercomputers. There are other ways to treat dispersion, but all are computationally intensive and cannot be applied to large systems. These include, for example, Density Functional Theory provides an existence proof that a functional exists to include dispersion, but we dont know the functional. We outline the existing methods, and then present new density matrices to improve the discretisation of the path integral. Diffusion Monte Carlo (DMC), first proposed by Fermi, allows the fast computation of high-accuracy energies for static nuclear configurations, making it a useful method for model development, such as fitting repulsion potentials, but there is no straightforward way to generate forces. We derived new methods and trial wavefunctions for DMC, allowing the computation of energies for much larger systems to high accuracy. A Quantum Drude model of Xenon, fit in the gas-phase, was simulated in the condensed-phase using both DMC and PIMD. The new DMC methods allowed for calculation of the bulk modulus and lattice constant of FCC-solid Xenon. Both were in excellent agreement with experiment even though this model was fitted in the gasphase, demonstrating the power of Quantum Drudes to build transferable models by capturing many-body effects. We also used the Xenon model to test the new PIMD methods. Finally, we present the outline of a new QDO model of water, including QDO parameters fitted to the polarisabilities and dispersion coefficients of water.
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Jayachandran, Christina [Verfasser]. "Molecular DNA Sensors to Measure Distribution of Cytoskeletal Forces / Christina Jayachandran." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://d-nb.info/1217062807/34.
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Ganti, Raman S. "Microscopic forces and flows due to temperature gradients." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/274324.
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Nano-scale fluid flow is unlike transport on the macro-scale. Pressure gradients typically dominate effects on a large scale while thermal gradients contribute negligibly to the motion of fluid. The situation entirely reverses on the nano-scale. At a microscopic level, flows induced by thermal gradients are caused by forces that act on atoms or molecules near an interface. These thermo-osmotic forces cannot, at present, be derived analytically or measured experimentally. Clearly, it would be useful to calculate these forces via molecular simulations, but direct approaches fail because in the steady-state, the average force per particle vanishes, as the thermo-osmotic force is balanced by a gradient in shear stress. In our journey to indirectly calculate the osmotic force, we met another unknown in the field of molecular theory at interfaces: the microscopic pressure tensor. The latter is an open problem since the microscopic pressure near an interface is not uniquely defined. Using local thermodynamics theories, we relate the thermo-osmotic force to the gradient of the microscopic pressure tensor. Yet, because the pressure is not uniquely defined, we arrive at multiple answers for the thermo-osmotic force, where at most one can be correct. To resolve the latter puzzle, we develop a direct, non-equilibrium simulation protocol to measure the thermo-osmotic force, whereby a thermal gradient is imposed and the osmotic force is measured by eliminating the shear force. Surprisingly, we find that the osmotic force cannot be derived from the gradient of well-known microscopic pressure expressions. We, therefore, derive a thermodynamic expression that gets close. In this work, we report the first, direct calculation of the thermo-osmotic force while simultaneously showing that standard microscopic pressure expressions fail to predict pressure gradients.
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Zhang, Ying. "Dynamic spatio-temporal interaction of morphogens, forces and growth in embryonic morphogenesis." [Bloomington, Ind.] : Indiana University, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3297105.
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Thesis (Ph.D.)--Indiana University, Dept. of Physics, 2007.Title from dissertation home page (viewed Sept. 29, 2008). Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0881. Adviser: James A. Glazier.
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Marla, Krishna Tej. "Molecular thermodynamics of nanoscale colloid-polymer mixures: chemical potentials and interaction forces." Available online, Georgia Institute of Technology, 2004, 2004. http://etd.gatech.edu/theses/available/etd-08102004-105655/.
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Thesis (Ph. D.)--Chemical Engineering, Georgia Institute of Technology, 2006.Dr. J. Carson Meredith, Committee Chair ; Dr. Charles A. Eckert, Committee Member ; Dr. Clifford L. Henderson, Committee Member ; Dr. Rigoberto Hernandez, Committee Member ; Dr. Peter J. Ludovice, Committee Member. Vita. Includes bibliographical references.
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Marla, Krishna Tej. "Molecular Thermodynamics of Nanoscale Colloid-Polymer Mixtures: Chemical Potentials and Interaction Forces." Diss., Georgia Institute of Technology, 2004. http://hdl.handle.net/1853/7604.
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Nanoscale colloidal particles display fascinating electronic, optical and reinforcement properties as a consequence of their dimensions. Stable dispersions of nanoscale colloids find applications in drug delivery, biodiagnostics, photonic and electronic devices, and polymer nanocomposites. Most nanoparticles are unstable in dispersions and polymeric surfactants are added generally to improve dispersability and control self-assembly. However, the effect of polymeric modifiers on nanocolloid properties is poorly understood and design of modifiers is guided usually by empirical approaches. Monte Carlo simulations are used to gain a fundamental molecular-level understanding of the effect of modifiers properties on the thermodynamics and interaction forces of nanoscale colloidal particles. A novel method based on the expanded ensemble Monte Carlo technique has been developed for calculation of the chemical potential of colloidal particles in colloid-polymer mixtures (CPM). Using this method, the effect of molecular parameters like colloid diameter, polymer chain length, colloid-polymer interaction strength, and colloid and polymer concentrations, on the colloid chemical potential is investigated for both hard-sphere and attractive Lennard-Jones CPM. The presence of short-chain polymeric modifiers reduces the colloid chemical potential in attractive as well as athermal systems. In attractive CPM, there is a strong correlation between polymer adsorption and colloid chemical potential, as both show a similar dependence on the polymer molecular weight. Based on the simulation results, simple scaling relationships are proposed that capture the functional dependence of the thermodynamic properties on the molecular parameters. The polymer-induced interaction forces between the nanoparticles have been calculated as a function of the above parameters for freely-adsorbing and end-grafted homopolymer modifiers. The polymer-induced force profiles are used to identify design criteria for effective modifiers. Adsorbing modifiers give rise to attractive interactions between the nanoparticles over the whole parameter range explored in this study. Grafted surface modifiers lead to attraction or repulsion based on the polymer chain length and grafting density. The polymer-induced attraction in both adsorbing and grafted modifiers is attributed primarily to polymer intersegmental interactions and bridging. The location of the thermodynamic minimum corresponding to the equilibrium particle spacing in nanoparticle-polymer mixtures can be controlled by tuning the modifier properties.
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Thote, Amol Janardan Gupta Ram B. "Molecular bonding in product engineering." Auburn, Ala., 2005. http://hdl.handle.net/10415/1275.
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Augustus, Adebayo Samuel. "Attractive steric interactions." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.391708.
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Gensler, Manuel. "Binding forces in metallo-supramolecular coordination compounds." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2017. http://dx.doi.org/10.18452/17728.
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Multivalente Wechselwirkungen sind in diversen biomolekularen und supramolekularen Systemen anzutreffen. Gewöhnlich werden sie durch ihre thermische Stabilität charakterisiert. Doch auch das mechanische Reißverhalten ist relevant: Ein System mit großer Reißlänge (Verformbarkeit) weist zwar eine geringere Reißkraft auf, kann aber besser auf äußere Einflüsse ohne Bindungsbruch reagieren. Daher besteht ein zunehmendes Interesse an Modellen zur Vorhersage der mechanischen Stabilität multivalenter Wechselwirkungen. Einzelmolekül-Kraftspektroskopie (SMFS) ist eine nützliche Methode, um den Reißprozess nichtkovalenter Wechselwirkungen zu studieren. Im Rahmen dieser Dissertation wurden mono- und bivalenten Pyridine, komplexiert und verbunden durch Cu(II) und Zn(II), entworfen und untersucht. Die drei bivalenten Pyridine wiesen unterschiedlich flexible Rückgratstrukturen auf (flexibel, teilflexibel, steif). Überraschenderweise wurde ein anderer Trend für die Verformbarkeiten gemessen (flexibel > steif > teilflexibel). Durch Vergleich von experimentellen Daten mit ab-initio Berechnungen konnten komplexe Reißmechanismen vorgeschlagen werden: Das Lösungsmittel war entscheidend und führte zu wasserverbrückten Zwischenprodukten, was die Verformbarkeit aller Systeme stark erhöhte. Im bivalente System mit teilflexiblem Rückgrat, koordiniert durch Cu(II), rissen beide Bindungen gleichzeitig bei vergleichsweise großen Kräften. Die beiden anderen Systeme mit Cu(II) wurden in zweistufigen Prozessen voneinander getrennt, was kleinere Reißkräfte zur Folge hatte. Insbesondere das flexible System war zwar thermisch stabiler, brach aber leichter als das monovalente System. Damit wurde zum ersten Mal der große Einfluss des Rückgrats, bei sonst gleicher Art von Wechselwirkung, auf die mechanische Stabilität bivalenter Wechselwirkungen gezeigt. Außerdem ist das entwickelte Modellsystem sehr nützlich für weiterführende Untersuchungen in biologisch relevanten wässrigen Lösungsmitteln.Multivalent interactions are ubiquitous in biomolecular and supramolecular systems. They are commonly characterized by their thermal stability in terms of average bond lifetime or equilibration constant. However, also mechanical stabilities are relevant: A system with high rupture length (malleability) has a lower rupture force, but can more easily adopt to external constraints without rupture. Thus it is of ever-increasing interest to find appropriate models that allow predictions on the mechanical stability of multivalent interactions. Single-molecule force spectroscopy (SMFS) is a powerful tool to study the rupture process of non-covalent interactions. In the present thesis, a comprehensive study on the mechanical stability of bivalent pyridine coordination compounds with the metal ions Cu(II) and Zn(II) was performed. Surprisingly, three different backbone flexibilities (high, intermediate, low) did not correlate with the measured malleabilities (high > low > intermediate). Instead, comparison between experimental results and ab-initio calculations revealed more complex underlying rupture mechanisms: Due to the aqueous environment, hydrogen bound complexes were formed and important intermediate structures that strongly increased malleabilities. Both interactions of the intermediately flexible bivalent system with Cu(II) broke simultaneous, yielding comparatively large rupture forces. The bivalent interactions of high and low backbone flexibility with Cu(II) broke stepwise at smaller forces. Although being thermally more stable, the highly flexible system even broke at lower forces than the monovalent system. Thereby it was shown for the first time, that rupture forces of similar systems can be tuned over a broad range, just by changing the connecting backbone structure. Furthermore, the developed approach is a rich toolkit to study further the balanced interplay between rupture force and malleability in biologically relevant aqueous solvents.
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Cheng, Mao-Sen. "Molecular beam electric resonance spectroscopy of CO-SO₂ and Kr-SO₂ complexes /." view abstract or download file of text, 2000. http://wwwlib.umi.com/cr/uoregon/fullcit?p9998027.
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Thesis (Ph. D.)--University of Oregon, 2000.Typescript. Includes vita and abstract. Includes bibliographical references (leaves 110-113). Also available for download via the World Wide Web; free to University of Oregon users.
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Aviat, Félix. "Development of High Performance Molecular Dynamics : Fast Evaluation of Polarization Forces The truncated conjugate gradient (TCG), a non-iterative/fixed-cost strategy for computing polarization in molecular dynamics: Fast evaluation of analytical forces Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations." Thesis, Sorbonne université, 2019. http://www.theses.fr/2019SORUS498.
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La dynamique moléculaire classique est un outil précieux pour explorer le monde de l’infiniment petit, notamment lorsque l’on parle de systèmes biologiques (protéines). Ces simulations sont basées sur des modèles plus ou moins avancés, où la prise en compte des électrons n’est pas évidente. La polarisabilité permet la prise en compte de la mobilité des nuages électronique tout en conservant un cadre classique. Elle peut-être décrite par des dipôles induits, dont le calcul demande la résolution d’un schéma auto-cohérent (SCF), coûteux en terme de temps de calcul et source d’instabilité. Dans cette thèse, nous proposons un nouvel algorithme permettant un traitement plus rapide et plus stable des dipôles induits, basé sur la troncature du Gradient Conjugué. La précision, la versatilité, l’efficacité du Gradient Conjugué Tronqué (TCG) sont évalués sur plusieurs système. Son application à des calculs plus sensibles d’énergie libre est également testée. Le TCG est enfin utilisé afin de mettre au point de nouveaux intégrateurs de dynamique moléculaire permettant d’importantes accélérations. On démontre finalement que TCG est un outil polyvalent, adaptable, efficace, qui permet une accélération considérable des dynamiques polarisables longuesClassical molecular dynamics is a precious tools to explore the infinitely small world, e.g. when considering biological systems (such as proteins). These simulations are based on physical models of various precision and complexity, where taking electrons into account is not easy. Polarizability allows one to take into account the mobility of the electronic density, while keeping the classical description framework. It can be described using induced dipoles, whose computation is done through a Self-Consistent procedure, which is costly in terms of computational time and can also cause instability. In this thesis, we introduce a new algorithm allowing a faster and more stable treatment of the induced dipoles, based on the truncation of the Conjugate Gradient. Accuracy, versatility, efficiency of the so-called Truncated Conjugate Gradient (TCG) are evaluated on various systems. Its applicability to free energy calculations is also tested. TCG is finally used in order to derive new molecular dynamics integrators allowing for considerable accelerations. To sum this up, TCG proves to be a polyvalent, adaptable, efficient tool, which allows for substantial acceleration of long polarizable dynamics
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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.
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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.
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Kim, Sung-Soo. "Surface forces apparatus (SFA) studies on n-octadecyltriethoxysilane self-assembled monolayers on untreated and plasma-treated mica." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/289739.
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Prehydrolyzed n-octadecyltriethoxysilane (OTE) molecules were self-assembled as a monolayer on both untreated and argon/water vapor plasma-treated mica. The properties and stability of these monolayers have been qualitatively and quantitatively investigated with a surface forces apparatus (SFA) under various environmental conditions The interaction force between the OTE monolayers immersed in water showed that plasma treatment reduced the range of the steep short-range repulsion and motivated the water vapor studies. The humidity tests revealed a substantial monolayer swelling in the untreated case at 95% RH or higher but there was no swelling in the plasma treated case. Furthermore, adhesive force measurements as a function of variations in environmental conditions such as temperature, relative humidity, contact time, and high stress showed that the plasma treated OTE monolayer appears to be more stable than the untreated monolayer in high humidities. In dry conditions both rnonolayers are molecularly smooth, well ordered and highly compact as well as mechanically robust and tenacious. Finally, the thickness compressibility studies in both dry and humid conditions suggested that the OTE phase state for both the plasma treated and untreated cases is pseudo-crystalline. Further, these studies suggested that the monolayer on both plasma treated and untreated mica does not fully cover the entire surface and likely exists as two very discrete phase states composed of large crystalline polymerized OTE domains and somewhat hydrophilic gaseous regions. The results from several different SFA experiments strongly indicates the OTE-SAM is covalently attached at least partially to the plasma treated mica while the monolayer weakly physisorbs to the untreated mica surface. Accordingly, due to the covalent connection, the OTE-SAM on plasma treated mica is more stable particularly in highly humid or even completely wet environments although it is thought the monolayer does not fully cover the mica surface.
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Law, Timothy R. "An algorithm for computing short-range forces in molecular dynamics simulations with non-uniform particle densities." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/111980/.
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We develop the projection sorting algorithm, used to compute pairwise short-range interaction forces between particles in molecular dynamics simulations. We contrast this algorithm to the state of the art and discuss situations where it may be particularly effective. We then explore the efficient implementation of the projection sorting algorithm in both on-node (shared memory parallel) and off-node (distributed memory parallel) environments. We provide AVX, AVX2, KNC and AVX-512 intrinsic implementations of the force calculation kernel. We use the modern multi- and many-core architectures: Intell Haswell, Broadwell Knights Corner (KNC) and Knights Landing (KNL), as representative slice of modern High Performance Computing (HPC) installations. In the course of implementation we use our algorithm as a means of optimising a contemporary biophysical molecular dynamics simulation of chromosome condensation. We compare state-of-the-art Molecular Dynamics (MD) algorithms and projection sorting, and experimentally demonstrate the performance gains possible with our algorithm. These experiments are carried out in single- and multi-node configurations. We observe speedups of up to 5x when comparing our algorithm to the state of the art, and up to 10x when compared to the original unoptimised simulation. These optimisations have directly affected the ability of domain scientists to carry out their work.
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Shinto, Hiroyui. "Interfacial Microstructures and Interaction Forces between Colloidal Particles in Simple and complex Fluids-Molecular Dynamics Simulation-." Kyoto University, 1999. http://hdl.handle.net/2433/77943.
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Vedam, Venkata S. "Stability of carbon dioxide and methane hydrates in water in presence of small driving forces using MD simulations." Morgantown, W. Va. : [West Virginia University Libraries], 2009. http://hdl.handle.net/10450/10794.
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Thesis (M.S.)--West Virginia University, 2009.Title from document title page. Document formatted into pages; contains viii, 93 p. : ill. (some col.), col. map. Includes abstract. Includes bibliographical references.
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Narth, Christophe. "Développement de champs de forces polarisables : vers la dynamique moléculaire SIBFA." Thesis, Paris 6, 2015. http://www.theses.fr/2015PA066739/document.
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Le but de cette thèse est une revisite du potentiel SIBFA. Ceci inclut un travail et une réflexion sur la méthodologie de cette approche avec une implémentation proposant une utilisation plus large. De plus, une nouvelle calibration de champ de forces raffiné est permise aujourd’hui. En effet, la décomposition d’énergie intermoléculaire SAPT donne accès à toutes les composantes avec rigueur. La reproduction des résultats ab-initio par un potentiel analytique laisse entrevoir des applications prometteuses. Au-delà du coup de calcul considérablement réduit par rapport aux méthodes de chimie quantique, son intégration dans un code de dynamique moléculaire ouvre les portes à de nombreuses études encore plus prometteuses hors de portée de la chimie quantique. Enfin l’optimisation de ce code, avec une parallélisation bien étudiée, en feront un outil majeur de la biochimie. Dans une première partie, nous introduirons les notions et principes essentiels à la dynamique moléculaire. Un premier chapitre exposera la mécanique classique utilisé dans les programmes les plus distribués et utilisés. Un second chapitre introduira les méthodes permettant un meilleur traitement des interactions non-covalentes essentielles dans les études de complexes ligand-récepteur. Une seconde partie abordera de manière plus concrète la stratégie d’implémentation de SIBFA dans Tinker. Celle-ci s’organisera autour de trois chapitres, traitant chaque composante énergétique intermoléculaire. L’objectif de cette thèse est de proposer un socle solide autour du traitement des interactions non covalentes dans le cadre des champs de forces polarisables de dernières générations et de présenter le modèle d’eau hybride AMOEBA/SIBFAThe purpose of this thesis is to revisit the potential of SIBFA (Sum of Interactions Between Fragments Ab initio computed) [...]
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Bindis, Michael P. "Students' misconceptions about intermolecular forces as investigated through paper chromatography experiments and the Molecular Attractions Concept Inventory." Miami University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=miami1379167186.
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Gonzalez, Gutierrez Cristina. "Mechanical forces in the binding of single domain antibodies developed for therapeutics : from molecular to cellular response." Thesis, Aix-Marseille, 2018. http://www.theses.fr/2018AIXM0492/document.
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Les anticorps thérapeutiques sont couramment utilisés pour le traitement contre le cancer. Ils sont sélectionnées par leur affinité avec leur antigène mesuré normalement dans un environnent à trois dimensions (3D). Cependant, de fois les interactions anticorps-antigène ont lieu à l’interface entre deux cellules (i.e. 2D). Nous faisons l’hypothèse que les contraintes physiques à cette l’interface telles que la force et le mouvement relatif des molécules confinées aux surfaces modulent les propriétés de la liaison anticorps-antigène. Notre but est d’explorer les liens entre la mécanique de la liaison et la réponse cellulaire. Pour quantifier la cinétique 2D et la mécanique de ces interactions, nous avons effectué des mesures en utilisant la chambre à flux laminaire des deux anticorps à domaine unique (sdAbs) ciblant le récepteur CD16 exprimé dans la cellule Natural Killer (NK) et cinq sdAbs ciblant le marqueur tumoral HER-2 exprimé dans certains cancers. Nos résultats montrent des liaisons glissantes, idéales et pour la première fois, une liaison accrocheuse dans des interactions anticorps-antigène. Des expériences d’adhésion cellulaire montrent une corrélation entre la résistance à la force de la liaison accrocheuse et une meilleure adhésion des NK. Des sdAbs ont été sélectionnés pour constituer des anticorps bi-specifiques (bsAbs) capables de recruter des NK contre des cellules cancéreuses HER-2+. Ces bsAbs induisent une cytotoxicité supérieur a celle de l’anticorps de référence. Leur efficacité est modulée par la mécanique du coté antiCD16 du bsAbs en fonction de la nature de la cellule cancéreuse, suggérant un rôle de la force pour les faibles densités de HER-2Therapeutic antibodies have become a major treatment in cancer due in part to their ability to recruit immune cells onto tumours. They are selected on the basis of their affinity for their antigen in a three dimensions (3D) environment. However, in some major modes of action, antibodies do bind the antigen at the interface between immune cells and target cells. We hypothesize that the physical constraints of cell-cell interface (i.e. 2D), including force and relative motion of molecules confined at surfaces, modulate the antigen-antibody binding. Specifically, we aim at exploring the links between bond mechanics and cellular response. To quantify 2D kinetics and mechanics, we perform measurements using the laminar flow chamber of two Single Domains Antibodies (sdAbs) against the surface receptor CD16 expressed in Natural Killer (NK) cells and five sdAbs against the tumoral marker HER-2 expressed in some breast cancers. Our results show three different bond dissociation behaviour under force; slip, ideal and for the first time, a catch bond. Cell adhesion experiments over sdAb antiCD16 coated surfaces reveal a correlation between antibody resistance to force and a larger spreading of NK cells. Based on their force behaviour, some sdAbs were selected to be fused forming bi-specific antibodies (bsAbs) able to recruit NK cells toward HER-2+ cancer cells. All new bsAbs display a better efficacy in cytotoxicity than the reference therapeutic antibody. We show that their efficacy is modulated by the mechanical behaviour of the antiCD16 side, depending on the nature of the target cell line, which may hint to an effect of force dependence in the limit of low antigen coverage
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Jun, Janice. "THE OFFENSE-DEFENSE BALANCE IN IMMUNITY." Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1467997330.
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Reid, Suazette N. "Synthetic stratergies [sic] towards a diureidocalix[4]arene." Thesis, Georgia Institute of Technology, 2004. http://hdl.handle.net/1853/4961.
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Self-organization is a common occurrence among molecules in nature and questions of how and why these molecules interact and come together by intermolecular forces has been under investigation by those interested in molecular recognition. Synthetic molecules able to mimic nature have become important in the area of supramolecular chemistry. Calixarenes are a group of molecules that is being investigated for their ability to self-assemble into dimeric capsules. Such capsules can be very useful for catalysis, molecular recognition and for encapsulation. The synthetic stratergies involved in the synthesis of a diureidocalix[4]arene is presented. In this case the taget molecule is a tetrapropylcalix[4]arene substituted on the upper rim with two urea groups separated by a hydrocarbon chain will be synthesized. This molecule can then be used to investigate its dimerization properties.
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Li, Zhujie. "“Water-in-salt” electrolyte for supercapacitors : a molecular dynamics study." Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS482.
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Les électrolytes de type "water-in-salt" sont composés d'un sel dissous en très grande quantité dans de l'eau, au point que celle-ci devient minoritaire. Parmi ceux-ci les mélanges employant le bis(trifluoromethane) sulfonimide de lithium (LiTFSI) en tant que sels sont très prometteurs pour des applications de stockage électrochimique de l'énergie. Cependant les propriétés des liquides et des interfaces qu'ils forment ne sont pas encore bien connues. Au cours de cette thèse, nous avons réalisé des simulations de dynamique moléculaire de water-in-salts à base de LiTFSI sur une large gamme de concentration. Sa validité est fortement conditionnée par le champ de forces utilisé pour représenter les interactions entre les atomes, c'est pourquoi dans un premier temps nous avons testé une série de champs de forces issus de la littérature. Celui permettant de reproduire au mieux des mesures de viscosité et de coefficients d'auto-diffusion a alors été retenu. Nous avons ainsi pu déterminer la variation de la coordinence des ions lithium vis-à-vis des molécules d'eau et des ions TFSI avec la concentration. Nous avons pu observer que pour les systèmes les plus concentrés, une déshydratation partielle des ions lithium a lieu, ce qui impacte fortement la viscosité du milieu. Nous avons ensuite simulé des interfaces entre ces liquides et des électrodes de carbone à différents potentiels, ce qui nous a permis de déterminer la capacité de stockage. Nous avons observé une forte dissymétrie entre les électrodes positives et négatives, qui sont attribuées à la différence de taille très marquée entre les cations et les anions“Water-in-salt” solvents are a new class of electrolytes with very promising electrochemical properties for energy storage applications. The purpose of this work is to understand the microscopic mechanisms of these superconcentrated electrolytes at play. We use atomistic molecular dynamics to simulate systems of water in LiTFSI at various salt concentrations. On the basis of comparisons of simulated and measured dynamic properties, i.e. the viscosity, diffusion coefficient and conductivity, we systematic test and develop the force fields used for the ions. As a consequence, an optimized force field is proposed, which enables the accurate modeling of such systems. The structural properties are systematically investigated on various aspects for the salt at a superconcentrated state, which shed new light on the connections between ions and water molecules. Apart from these simulations of the bulk electrolytes, we also study the water-in-salt electrolyte at interfaces, in which the capacitive performance of this electrolyte in supercapacitors are explored. The differential capacitance displays a number of nontrivial features accompanying a series of peaks in the potential region from 0 to 3 V. The study of structural evolutions of the interfacial electrolytes shows that many structural changes occur in the layer of adsorbed liquid when the potential of the electrode is changed, which are at the origin of those observed peaks in the differential capacitance
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Lemke, Sandra Beatrice [Verfasser], and Reinhard [Akademischer Betreuer] Fässler. "Analysis of molecular forces transmitted by Talin during muscle development in vivo / Sandra Beatrice Lemke ; Betreuer: Reinhard Fässler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2019. http://d-nb.info/1188564293/34.
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Li, Zhenwei. "On-the-fly machine learning of quantum mechanical forces and its potential applications for large scale molecular dynamics." Thesis, King's College London (University of London), 2014. http://kclpure.kcl.ac.uk/portal/en/theses/onthefly-machine-learning-of-quantum-mechanical-forces-and-its-potential-applications-for-large-scale-molecular-dynamics(2a2f33a6-fa0c-44e3-8689-f4cf3f1c9198).html.
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Material simulation using molecular dynamics (MD) at the quantum mechanical (QM) accuracy level has gained great interest in the community. However, the bottleneck arising from the O(N3) scaling of QM calculation has enormously limited its investigation scope. As an approach to address this issue, in this thesis, I proposed a machine-learning (ML) MD scheme based on Bayesian inference from CPU-intensive QM force database. In this scheme, QM calculations are only performed when necessary and used to augment the ML database for more challenging prediction case. The scheme is generally transferable to new chemical situations and database completeness is never required. To achieve the maximal ML eciency, I use a symmetrically reduced internal-vector representation for the atomic congurations. Signicant speed-up factor is achieved under controllable accuracy tolerance in the MD simulation on test case of Silicon at dierent temperatures. As the database grows in conguration space, the extrapolative capability systematically increases and QM calculations are nally not needed for simple chemical processes. In the on-the-y ML force calculation scheme, sorting/selecting out the closest data congurations is used to enhance the overall eciency to scale as O(N). The potential application of this methodology for large-scale simulation (e.g. fracture, amorphous, defect), where chemical accuracy and computational eciency are required at the same time, can be anticipated. In the context of fracture simulations, a typical multi-scale system, interesting events happen near the crack tips beyond the description of classical potentials. The simulation results by machine-learning potential derived from a xed database with no enforced QM accuracy inspire a theoretical model which is further used to investigate the atomic bond breaking process during fracture propagation as well as its relation with the initialised vibration modes, crack speed, and bonding structure.
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Marcelli, Gianluca, and g. marcelli@imperial ac uk. "The role of three-body interactions on the equilibrium and non-equilibrium properties of fluids from molecular simulation." Swinburne University of Technology. Centre for Molecular Simulation, 2001. http://adt.lib.swin.edu.au./public/adt-VSWT20060112.082425.
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The aim of this work is to use molecular simulation to investigate the role of
three-body interatomic potentials in noble gas systems for two distinct
phenomena: phase equilibria and shear flow. In particular we studied the
vapour-liquid coexisting phase for pure systems (argon, krypton and xenon) and
for an argon-krypton mixture, utilizing the technique called Monte Carlo Gibbs
ensemble. We also studied the dependence of the shear viscosity, pressure and
energy with the strain rate in planar Couette flow, using a non-equilibrium
molecular simulation (NEMD) technique.
The results we present in this work demonstrate that three-body interactions
play an important role in the overall interatomic interactions of noble gases. This
is demonstrated by the good agreement between our simulation results and the
experimental data for both equilibrium and non-equilibrium systems.
The good results for vapour-liquid coexisting phases encourage performing
further computer simulations with realistic potentials. This may improve the
prediction of quantities like critical temperature and density, in particular of
substances for which these properties are difficult to obtain from experiment.
We have demonstrated that use of accurate two- and three-body potentials for
shearing liquid argon and xenon displays significant departure from the
expected strain rate dependencies of the pressure, energy and shear viscosity.
For the first time, the pressure is convincingly observed to vary linearly with an
apparent analytic y2 dependence, in contrast to the predicted y3/2 dependence
of mode -coupling theory. Our best extrapolation of the zero -shear viscosity for
argon gives excellent agreement (within 1%) with the known experimental data.
To the best of our knowledge, this the first time that such accuracy has been
achieved with NEMD simulations. This encourages performing simulations with
accurate potentials for transport properties.
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Wu, Xiaojing. "Contribution to the Development of Advanced Approaches for Electron and Molecular Dynamics Simulations in Extended Biomolecules." Thesis, Université Paris-Saclay (ComUE), 2018. http://www.theses.fr/2018SACLS252/document.
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Cette thèse porte sur deux projets visant au développement de nouvelles approches pour simuler les dynamiques moléculaire et électronique avec application à des biomolécules étendues. Dans la première partie nous cherchons à améliorer significativement la précision des simulations des propriétés rédox des protéines. Dans ce contexte, l'objectif est de recourir à de champ de force reposant sur une description multipolaire des interactions électrostatiques (AMOEBA) pour estimer les potentiels redox d'hémoprotéines. Nous avons dérivé des paramètres pour AMOEBA afin de décrire précisément les interactions électrostatiques avec l'hème. Une amélioration très encourageante est obtenue par rapport aux champs de forces standard. Le second projet vise à développer de nouvelles méthodes pour étudier la dynamique des électrons dans des biomolécules à l'échelle attoseconde en incluant les effets d'environnement. Nous avons conçu un couplage original entre la théorie de la fonctionnelle de la densité dépendant du temps (RT-TDDFT) et un modèle de mécanique moléculaire polarisable (MMpol). Une implémentation efficace et robuste de cette méthode a été réalisée dans le logiciel deMon2k. L'utilisation de techniques d'ajustements de densités électroniques auxiliaires permet de réduire drastiquement le coût de calcul des propagations RT-TDDFT/MMpol. La méthode est appliquée à l'analyse de la dissipation d'énergie dans l'environnement d'un peptide excité par un impulsion laserThis thesis involves two projects devoted to the development of advanced approaches for simulating molecular and electron dynamics in extended biomolecules. The first project aims at significantly improving the accuracy of redox potentials of proteins by numerical simulations. A sophisticated force field relying on a multipolar description of electrostartic interactions (AMOEBA) is used to perform molecular dynamics simulations onheme proteins. We derived parameters for AMOEBA to accurately describe electrostatic interactions with hemein both ferrous and ferric states. Very encouraging improvements are obtained compared to the standard force fields. The second project aims at developing original approaches for simulating ultrafast electron dynamics in biomolecules in contact to polarizable environments. We devised acombination of Real-time Time-Dependent Density Functional Theory (RT-TDDFT) and polarizable Molecular Mechanics (MMpol). An efficient and robust implementation of this method has been realized in deMon2k software. Density fitting techniques allow to reduce the computational cost of RT-TDDFT/MMpol propagations. The methodology is applied to understand the mechanisms of energy dissipation of a peptide excited by a laser pulse
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Gonzalez, Claramonte Laura. "Novel sensors technologies applied to force spectroscopy in molecular biology." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/285406.
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Force plays an essential role in all fields of biology. Measurement of these forces with high precision provides information about the structure, dynamics, intra and intermolecular interactions, and the mechanical properties of the biomolecules and, in general, about molecular basis of diverse biological phenomena. Different techniques have been developed to address this task, particularly at the single molecule level. The main objective accomplished in this work of thesis is the development of sensors technologies applied to force spectroscopy measurements and the demonstration of its possibilities in real molecular studies. Scanning probe microscopy (SPM) is a fast growing technology that has been the source for the development of an immense variety of applications to investigate materials and molecules at nanoscale. As another technology, SPM is constantly improving through different advances in instrumentation level and the emergence of new applications. From the analysis of the main limitations of quartz tuning fork (QTF) based nanosensors on one side and the conventional force spectroscopy with cantilever tips on the other side, the main considerations have been determined for the technological developments on force microscopy applications.
One of the main limitations of tuning fork probes is that they are usually custom-made because no commercial probes suitable for a wide range of experiments are available. The custom-made devices show considerable variation in dynamic response, poor lateral resolution and the characterization of the sensors remains unclear for force quantification. A new controller is developed to ensure the same dynamic response of different sensors in order to maintain the conditions in which the measurements are conducted. Also, a new method to improve lateral resolution of the QTF probes when working in liquid is proposed in this thesis based on attaching a standard AFM tip to the end of the fiber probe which has been previously sharpened. A method to calculate the spring constant of the QTF based sensors from easily measurable parameters is presented in this thesis. The method is based on a finite element analysis (FEA) model which includes the electrical part and can be used to calculate the spring constant of a QTF accurately for quantitative measurements. Results obtained in real biological experiments are promising and show the possibilities of the shear force microscopy improvements developed in this work of thesis. In a first experiment, a self-assembled monolayer (SAM) of micropatterned antibodies was imaged with three different techniques and in a second experiment, a molecular interaction analysis was done between biotin- streptavidin complex and results are compared with those obtained with AFM tip.
The main problem for comparing steered molecular dynamics (SMD) simulation results with experimental data is that SMD simulations were restricted to nanosecond timescales (due to the high computational demand of all-atomistic simulations). A high-speed force spectroscopy methodology has been developed to achieve rates comparable to SMD simulations. The validation of the technique is performed with titin unfolding measurements allowing the direct comparison of experimental and simulated forces.La fuerza juega un papel esencial en todos los campos de la biología. Las fuerzas experimentadas y generadas por las biomoléculas son múltiples en la naturaleza y pueden ir desde los subpiconewtons hasta varios nanonewtons. La medida de estas fuerzas con alta precisión proporciona información acerca de la estructura, la dinámica, las interacciones intra e intermoleculares y las propiedades mecánicas de las biomoléculas. Se han desarrollado diferentes técnicas para hacer frente a esta tarea, en particular a nivel de moléculas individuales. El principal objetivo en este trabajo de tesis ha sido el desarrollo de tecnologías de sensores aplicadas a la espectroscopia de fuerzas y la demostración de sus posibilidades en estudios moleculares reales. La microscopía de sonda de barrido (SPM) es una tecnología de rápido crecimiento que ha sido la fuente para el desarrollo de una inmensa variedad de aplicaciones para investigar materiales y moléculas a la nanoescala. A partir del análisis de las principales limitaciones de los nanosensores basados en tuning fork (TF) por un lado y la espectroscopia de fuerzas convencional con puntas de AFM por otro lado, se han determinado las principales consideraciones para los desarrollos tecnológicos. Una vez que la tecnología se ha desarrollado, se han llevado a cabo diferentes experimentos biológicos con el objetivo de demostrar las posibilidades de las tecnologías desarrolladas en aplicaciones reales: (i) Diferentes técnicas de imagen de biomoléculas se han comparado con sensores TF. La muestra estudiada ha sido una monocapa auto-ensamblada (SAM) de anticuerpos microestructurada. (ii) Se han realizado medidas cuantitativas de interacción molecular entre el sistema biotina- estreptavidina midiendo las energías de adhesión a diferentes velocidades de tracción y los resultados se han comparado con los obtenidos con medidas de AFM. (iii) Medidas de desplegamiento de la proteína titina se han realizado con la nueva técnica desarrollada de espectroscopia de fuerzas a velocidades alcanzadas por simulación (~4 milímetros por segundo) pudiendo comparar los resultados experimentales con simulaciones.
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Bradshaw, David S. "Quantum electrodynamical analysis of nonlinear optical effects deriving from the laser irradiation of molecular systems : resonance energy transfer and optomechanical forces." Thesis, University of East Anglia, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.426673.
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Leask, Peter John. "Probing nuclear molecular analogue states in carbon, boron and beryllium isotopes." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.369340.
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Thaunay, Florian. "Développement de champs de forces polarisables et applications à la spectroscopie vibrationnelle." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLX037/document.
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La spectroscopie de dissociation par absorption de photons infrarouges (IRPD) permet d’obtenir les signatures vibrationnelles d’espèces chargées en phase gazeuse, telles que de petits peptides ou des ions hydratés dans des agrégats d’eau. L’attribution des modes de vibration pour établir une relation entre le spectre expérimental et une structure moléculaire est une tâche délicate et nécessite le recours à la modélisation moléculaire.Ce manuscrit présente un ensemble d’outils théoriques pour le calcul et l’attribution de spectres vibrationnels, basée principalement sur la dynamique moléculaire classique et le champ de forces polarisable AMOEBA, ainsi que son application à des ions gazeux de tailles diverses. Les ions hydratés dans des agrégats d’eau M(H2O)n (n allant de 6 à 100) sont caractérisés par une dynamique importante, et leur spectre expérimental ne peut pas être décrit par une seule structure. La signature des peptides évolue avec la température et les effets d’anharmonicité dynamique. Ils peuvent également être le siège de mécanismes de transfert de proton, présentant une signature vibrationnelle très caractéristique.La surface d’énergie potentielle de ces systèmes est explorée par la dynamique moléculaire classique en trajectoires individuelles ou avec échange de répliques, afin d’engendrer des structures énergétiquement stables. Pour les plus petits systèmes, les méthodes quantiques DFT et post-HF sont utilisées pour confirmer les structures de plus basse énergie, calculer leurs spectres IR statiques et proposer des attributions des modes de vibration. Pour les plus systèmes de plus grandes tailles, c’est-à-dire les ions dans des gouttes d’eau de plusieurs dizaines de molécules, la simulation des spectres IR à température finie est basée sur la transformée de Fourier de la fonction d’autocorrélation du moment dipolaire (DACF), calculée pour une trajectoire de dynamique moléculaire classique. Cette méthode n’offrant pas d’accès direct aux modes normaux de vibration, nous avons implémenté une méthode d’attribution dynamique, basée sur la Driven Molecular Dynamics (DMD) et couplée au DACF. La combinaison AMOEBA/DACF/DMD a été utilisée pour reproduire et attribuer le spectre du dipeptide Ace-Phe-Ala-NH2, et ceux d’ions hydratés dans des agrégats d’eau.Enfin, la signature vibrationnelle d’un transfert de proton ne peut être décrite, ni par des méthodes statiques quantiques, ni par la dynamique classique. Sa modélisation a nécessité le développement d’un modèle Empirical Valence Bond (EVB) à deux états, couplé au champ de forces polarisable AMOEBA. Le modèle EVB a été implémenté dans la suite logicielle Tinker. Il permet de reproduire le comportement dynamique du transfert de proton au sein de petits peptides et de diacides déprotonés, ainsi que la signature spectroscopique observée expérimentalement.Une partie importante des applications de ces développements concerne des ions simples hydratés dans des nano-gouttelettes, et en particulier l’ion sulfate de grande importance environnementale. Nous avons pu reproduire de façon satisfaisante, pour la première fois, les spectres d’agrégats contenant jusqu’à 100 molécules d’eau. Le principal contributeur à cette spectroscopie expérimentale est l’équipe d’E. Williams à l’université de Californie à Berkeley. Nous avons établi avec eux une collaboration pour compléter ce travail en modélisant les spectres IR d’ions sulfates hydratés [SO4(H2O)n=9-36]2-, dont ils ont obtenu les signatures expérimentalesSpectroscopy dissociation by absorption of infrared photons (IRPD) provides vibrational signatures of charged species in the gas phase, such as small peptides or hydrated ions in water clusters. The vibrational normal modes assignment to establish a relationship between the experimental spectrum and molecular structure is a delicate task and requires the use of molecular modeling.This manuscript presents a set of theoretical tools for calculation and assignment of vibrational spectra, based mainly on classical molecular dynamics and polarizable AMOEBA force field, and its application to gaseous ions of various sizes. Hydrated ions in water clusters M(H2O)n (n in 6-100 range) are characterized by a dynamic behavior, and their experimental spectrum can not be described by a single structure. The signature of peptides changes with temperature and dynamic anharmonicity effects. They can also be the site of proton transfer mechanisms, with a very characteristic vibrational signature.The potential energy surface of these systems is explored by classical molecular dynamics in individual trajectories or replica exchange to generate energetically stable structures. For smaller systems, quantum methods, as DFT and post-HF, are used to confirm the lowest energy structures, calculate their static IR and propose normal modes assignments. For larger systems, i.e ions in water drops of several tens of molecules, the simulation of IR spectra at finite temperature is based on the Fourier transform of the autocorrelation function of the dipole moment (DACF), calculated during a classical molecular dynamics trajectory. As this method does not allow direct access to the vibrational normal modes, we implemented a method of dynamic assigments, based on the Driven Molecular Dynamics (DMD) and coupled to the DACF. The combination AMOEBA /DACF / DMD was used to reproduce and assign the spectrum of the dipeptide Ace-Phe-Ala-NH2, and those of hydrated ions in water clusters.Finally, the vibrational signature of a proton transfer can not be described by quantum static methods or by classical dynamics. Its modeling required the development of a two states Empirical Valence Bond Model (EVB), coupled with AMOEBA polarizable force field. The two states EVB model was implemented in the software TINKER. It can reproduce the dynamic behavior of proton transfer in small peptides and deprotonated acids, as well as the spectroscopic signatures observed experimentally.An important part of the applications of these developments relates simple hydrated ions in nano-droplets, and in particular the sulfate ion of great environmental importance. We were able to reproduce satisfactorily, for the first time, the spectra of clusters containing up to 100 water molecules. The main contributor to this experimental spectroscopy is the team of E. Williams from the University of California of Berkeley. We have established cooperation with them to complete this work by modeling the IR spectra of hydrated sulfates ions [SO4(H2O) n=9-36]2-, for which they obtained experimental signatures
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Jackson, George. "Phase separation in solutions of large spherical particles." Thesis, University of Oxford, 1986. http://ora.ox.ac.uk/objects/uuid:9db7de2e-b365-4433-8e14-746efb32c070.
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The effect of large size ratios of solute to solvent on the critical properties and phase behaviour of binary mixtures of spherical particles is investigated using an "augmented van der Waals" equation of state. The equation used is essentially a van der Waals equation with an improved hard sphere repulsive term. Molecular dynamics and constant-pressure Monte Carlo simulations of binary mixtures of hard spheres with different diameter ratios and mole fractions are undertaken to check the adequacy of the hard sphere equation. Good agreement is found, even for systems with large differences in size. Furthermore, many of the hard sphere mixtures exhibited a transition from a fluid to a solid phase at high densities. Phase boundaries are calculated for model mixtures comprising spheres of different sizes between which there are long-ranged attractive forces. Particular attention is paid to the case in which the ratio of sizes is infinite. The systems show a wide variety of behaviour that includes liquid-liquid and gas-gas immiscibility, and the formation of negative azeotropes. Calculations investigating the effect of different attractive interactions between the small and large spheres show that as the magnitude of this interaction is increased, liquid-liquid immiscibility becomes the dominant feature of the phase diagram at moderate temperatures. The extent of liquid-liquid coexistence is greatest at large size differences. These model systems are shown to reproduce some of the behaviour of aqueous solutions of surfactants if it is assumed that the large spheres are models of the micelles and the small spheres models of the solvent molecules. The properties of binary lattice mixtures of bifunctional molecules whose ends are chosen to mimic surfactant and solvent molecules are also briefly investigated, to determine the effect of the asymmetric surfactant molecule on the phase separation. Closed-loops emerge in the phase diagrams as the surfactant character of one of the species is increased.
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Jonasson, Gabriella. "Étude théorique de l’extinction de fluorescence des protéines fluorescentes : champ de forces, mécanisme moléculaire et modèle cinétique." Thesis, Paris 11, 2012. http://www.theses.fr/2012PA112121/document.
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Les protéines fluorescentes, comme la GFP (green fluorescent protein), sont des protéines naturellement fluorescentes qui sont utilisées pour leur rôle de marqueur, permettant de localiser des protéines dans les cellules et d'en suivre les déplacements. De nombreuses études expérimentales et théoriques ont été menées ces dix dernières années sur les protéines fluorescentes. De là, se forge une compréhension essentiellement qualitative du rôle de la protéine vis-à-vis de l’obtention ou non d’une émission radiative : il apparaît que la protéine permet la fluorescence en bloquant les processus qui la désactivent ; ces processus de désactivation sont très rapides et efficaces (à l'échelle de la picoseconde) dans le cas du chromophore seul, et ils sont bien identifiés comme étant des torsions autour des liaisons intercycles (tau et phi). Dans la protéine, la sensibilité des temps de vie de fluorescence à des mutations proches ou non du chromophore, à des modifications de pH ou de température laisse supposer un contrôle de la dynamique du chromophore par différents paramètres, sans qu’ils soient pour autant identifiés et mis en relation.Une étude de la dynamique de la protéine permettrait de faire la lumière sur les mécanismes responsables de ces phénomènes photophysiques pour lesquels une analyse structurale ne suffit pas. Cependant l'étude de la dynamique est limitée par la taille du système (>30 000 atomes), par l'échelle de temps des phénomènes photophysiques considérés (dizaine de nanosecondes) et par le fait que les deux torsions tau et phi sont fortement couplées dans l'état excité du chromophore. Ces trois facteurs excluent les méthodes de dynamique existantes aujourd'hui ; dynamique quantique (AIMD), dynamique mixte classique-quantique (QM/MD) et dynamique moléculaire classique (MD).Nous avons surmonté le problème par la modélisation de la surface d’énergie potentielle de torsion du chromophore à l’état excité basée sur des calculs quantiques de haute précision, par une interpolation des valeurs obtenues par une expression analytique appropriée en fonction des angles de torsion tau et phi et avec une précision suffisante pour reproduire des barrières de l’ordre de la kcal/mol, et enfin, par l’implémentation de cette expression analytique dans le programme parallèle AMBER. Une deuxième difficulté théorique concerne la simulation et l’analyse statistique d’événements peu fréquents à l’échelle de la nanoseconde, et dont on ne connait pas le chemin de réaction, ici les déformations de la protéine et du chromophore conduisant aux géométries favorables à la conversion interne. Grâce à ces développements et aux simulations qu'ils ont permises, nous avons réalisé la première modélisation de la désactivation non-radiative par conversion interne à l’échelle de la nanoseconde dans trois protéines fluorescentes différentes. L’analyse des dynamiques moléculaires classiques nous donne une évaluation quantitative des temps de vie de l’extinction de fluorescence, en accord avec les données expérimentales. Par ailleurs elle nous a permis d'identifier les mouvements moléculaires concertés de la protéine et du chromophore conduisant à cette extinction. De ces résultats, émerge une représentation plus complète du mécanisme qui libère la torsion du chromophore ou qui la déclenche : il peut venir d’un mouvement spécifique de la protéine, qui se produit à l’échelle de la nanoseconde, ou bien de plusieurs mouvements spécifiques, plus fréquents (rupture de liaisons hydrogène, rotation de chaînes latérales, dynamique d'agrégats d’eau), mais qui coïncident seulement à l’échelle de la nanoseconde. Ces mouvements spécifiques n’ont pas un coût énergétique important mais la nécessité de leur coïncidence crée un délai de l’ordre de quelques nanosecondes alors que dans le vide la torsion se produit en quelques picosecondes. Dans le cas des protéines étudiées, on a identifié en grande partie les mécanismes et les acides aminés qui sont impliquésFluorescent proteins, like GFP (green fluorescent protein), are efficient sensors for a variety of physical-chemical properties and they are extensively used as markers in living cells imaging. These proteins have been widely studied both experimentally and theoretically the last decade. The comprehension of the protein's role in the regulation of the radiative emission is today essentially qualitative: it appears that the protein enables the fluorescence by blocking the processes that deactivates it; the deactivating processes are very quick and efficient (on the picosecond time scale) when the chromophore is isolated, and they are identified as being the torsions around the central bonds of the chromophore (tau and phi). The fluorescence lifetimes of a protein is very sensitive to mutations in the vicinity of the chromophore, to modifications in pH or in temperature. This seems to indicate a control of the dynamics of the chromophore by different parameters, that are not necessarily identified.A study of the dynamics of the protein would allow a deeper understanding of the mechanisms that are responsible for the fluorescence quenching. From a theoretical point of view, one is faced with three difficulties in this type of study: the size of the system (>30 000 atoms including a water box), the required time scale (tens of nanoseconds) and the fact that the torsions tau and phi are strongly coupled in the excited state of the chromophore. We must thus rule out the already existing dynamics methods: quantum dynamics (AIMD), mixed classical-quantum dynamics (QM/MD) and classical molecular dynamics (MD).We have overcome this problem by modeling the torsional potential energy surface of the chromophore in the first excited state trough high precision quantum calculations, by interpolating the energy values with an analytical fitting expression depending on the torsions tau and phi and with a precision high enough to reproduce barriers of the order of 1 kcal/mol, and lastly, by implementing this fitting expression in a parallelized version of the MD program AMBER. Another theoretical difficulty concerns the simulation and the statistical analysis of rare events on the nanosecond time scale without knowing the reaction path in advance, i.e. the deformations of the protein and of the chromophore leading to geometries where the internal conversion is favored. As a result of these developments and of the simulations they have enabled, we have been able to model, for the first time, the non-radiative deactivation by internal conversion at the nanosecond time scale in three different fluorescent proteins. The analysis of the classical molecular dynamics gives us a quantitative evaluation of the lifetime of the fluorescence extinction, in agreement with experimental results. In addition, it has allowed us to identify the concerted molecular movements between the protein and the chromophore leading to this extinction. A more complete representation of the mechanism that liberates or provokes the chromophore torsion emerges from these results: it could be a specific movement of the protein, that occurs on the nanosecond timescale, or several specific movements that occur more frequently (breakage of a hydrogen bond, rotation of side chains, dynamics of a water cluster), but that coincide only on the nanosecond time scale. These specific movements do not have a high energy cost but the need for them to coincide creates a delay of several nanoseconds compared to the chromophore torsion in vacuo which occurs after a few picoseconds. In the proteins we have studied (GFP, YFP and Padron), we have identified the principle components of the mechanisms and the amino acids that are implicated in this chromophore-protein interplay
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Funke, Jonas Jörg Verfasser], Hendrik [Akademischer Betreuer] [Gutachter] [Dietz, Matthias [Gutachter] Rief, and Reinhard [Gutachter] Fässler. "Nanoscale instruments for the positioning of molecules, for the measurement of molecular forces, and for the quantification of conformational equilibria / Jonas Jörg Funke ; Gutachter: Matthias Rief, Hendrik Dietz, Reinhard Fässler ; Betreuer: Hendrik Dietz." München : Universitätsbibliothek der TU München, 2017. http://d-nb.info/1137010509/34.
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Petet, Thomas J. Jr. "Characterization of Poly(dimethylsiloxane) Blends and Fabrication of Soft Micropillar Arrays for Force Detection." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4649.
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Diseases involving fibrosis cause tens of thousands of deaths per year in the US alone. These diseases are characterized by a large amount of extracellular matrix, causing stiff abnormal tissues that may not function correctly. To take steps towards curing these diseases, a fundamental understanding of how cells interact with their substrate and how mechanical forces alter signaling pathways is vital. Studying the mechanobiology of cells and the interaction between a cell and its extracellular matrix can help explain the mechanisms behind stem cell differentiation, cell migration, and metastasis. Due to the correlation between force, extracellular matrix assembly, and substrate stiffness, it is vital to make in vitro models that more accurately simulate biological stiffness as well as measure the amount of force and extracellular matrix assembly. To accomplish this, blends of two types of poly(dimethylsiloxane) (PDMS) were made and the material properties of these polymer blends were characterized. A field of 5µm or 7µm microscopic pillars (referred to as posts) with a diameter of 2.2µm were fabricated from these blends. Each combination of PDMS blend and post height were calibrated and the stiffness was recorded. Additionally, polymer attachment experiments were run to ensure cells survived and had a normal phenotype on the different blends of PDMS when compared to pure PDMS. Finally, cells were placed onto a field of posts and their forces were calculated using the new stiffness found for each blend of post. Varying the PDMS material stiffness using blends allow posts to be much more physiologically relevant and help to create more accurate in vitro models while still allowing easy and accurate force measurement. More biologically relevant in vitro models can help us acquire more accurate results when testing new drugs or examining new signaling pathways.
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Louisfrema, Wilfired. "Caractérisation des oxydes nanoporeux contenant des ions lourds en milieu aqueux." Thesis, Paris Sciences et Lettres (ComUE), 2016. http://www.theses.fr/2016PSLEE055/document.
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Les aluminosilicates poreux cristallins tels que les zéolithes cationiques de type faujasite sont largement étudiés en raison de leurs propriétés d’adsorption, d’échange ionique et de catalyse, ce qui leurs valent d’être engagées dans de nombreuses applications industrielles, qui font intervenir de plus en plus de cations multivalents (détergents/ adoucissants, craquage catalytique, décontamination,...). Ces différentes applications industrielles ont en commun les propriétés d’adsorption, résultant d’une part de la taille de leurs pores du même ordre de grandeur que les espèces introduites, et d’autre part de leur composition chimique qui conduit à des charges de charpente, à l’origine de sites de forte interaction ou de répulsion localisés. Dans ces applications, les zéolithes sont hydratées. L’eau est associée aux processus mis en jeu et influence ainsi les autres propriétés du matériau. La modélisation moléculaire est un outil de choix pour prédire et comprendre les propriétés microscopiques du matériau hydraté, qui sont difficilement accessibles expérimentalement. Ce travail de modélisation porte plus précisément sur le comportement des cations multivalents dans les matériaux zéolithiques hydratés, en collaboration avec des expérimentateurs. Notre étude sur une zéolithe faujasite Y a permis tout d’abord de clarifier la migration des cations sodium au cours de la déshydratation, et de prédire la localisation cationique dans le matériau hydraté en présence d’ions bivalents. De plus, nous avons montré qu’il était possible de rationaliser conjointement la migration des cations et les déformations structurales dans la faujasite au cours de l’adsorption d’eau. À cet effet, nous avons développé une méthode d’analyse pour la localisation cationique. La bonne performance d’un champ de force polarisable démontrée au cours de ce travail ouvre la voie à l’étude de la dynamique globale du système, en permettant le suivi de la migration cationique simultanément à la déformation de la charpente. A plus long terme, cette approche pourra être étendue à d’autres ions multivalents d’intérêt (terres rares, éléments f, ...)Porous crystalline aluminosilicates such as cationic zeolites, are widely studied because of their adsorption, ion exchange and catalytic properties, which explain their use in many industrial applications. Examples of the latter, which involve in particular multivalent cations, include detergents/softeners, catalytic cracking, or decontamination. Such industrial applications of zeolites all exploit their adsorption properties, which vary as a function of the pore size, comparable to the adsorbing molecules, or chemical composition, which results in charges within the framework, and in turn strong binding or repulsive sites. Importantly, in such applications zeolites are hydrated. Water is involved in the microscopic processes and thus influences all properties of the material. Molecular modeling is a weapon of choice to predict and understand the microscopic properties of the hydrated material, which are difficult to access experimentally. More precisely, the present modeling work deals with the behavior of multivalent cations in hydrated zeolites, in collaboration with experimentalists. Our study on zeolite Y faujasite first allowed us to clarify the migration of sodium cations upon dehydration and to predict the cation localisation in the hydrated material in the presence of divalent cations. Furthermore, we rationalized the coupled migration of cations and deformation of the framework upon water adsorption. To this end, we have developed a new method for the analysis of cation localization. The good performance of a polarizable force field demonstrated here paves the way for the study of the dynamics of the whole system, following in particular the simultaneous migration of cations and deformation of the framework. Such an approach could be later extended to other multivalent ions of industrial interest (rare Earths, f-block elements, ...)
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Arsenovic, Paul. "Development and Validation of a Novel Resonant Energy Transfer (FRET) Biosensor to Measure Tensile Forces at the LINC Complex in Live Cells." VCU Scholars Compass, 2017. https://scholarscompass.vcu.edu/etd/5116.
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There is a large body of evidence supporting the theory that cell physiology largely depends on the mechanical properties of its surroundings or micro-environment. More recently studies have shown that changes to intra-cellular mechanical properties can also have a meaningful impact on cell function and in some cases lead to the progression of ailments or disease. For example, small changes to the protein sequence of a structural nuclear envelope protein called lamin-A is known to cause a variety of neurological and musculoskeletal diseases referred to as laminopathies. Currently, there is little incite into how these mutations lead to disease progression due in part to an inability to measure protein-specific mechanical changes and how these alterations may relate to disruptions in intra-cellular signaling or function. \par To improve upon the ability to measure mechanical properties inside living cells, a previously validated, genetically-encoded resonant energy transfer (FRET)-force biosensor was modified to localize to the nuclear envelope. This biosensor integrated into the nuclear envelope protein Nesprin-2G and senses small deformations that are resolved by indirect measurements of spectroscopic fluctuations in the fluorescent emission of the sensor. To accurately measure these changes, a new spectral-imaging technique named SensorFRET was developed which can resolve small changes in the FRET sensor under varying levels of fluorescent intensity and with known absolute precision. Using SensorFRET, the Nesprin-2G biosensor (Nesprin-TS) reported changes in actomyosin contractility, nuclear shape, and nuclear deformation. Using Nesprin-TS, fibroblasts derived from patients with Hutchinson-Gilford progeria syndrome (HGPS) reported less force on Nesprin-2G molecules relative to healthy fibroblasts on average.\par To demonstrate how intra-cellular forces on the nucleus may impact normal cell physiology, bone-marrow derived mesenchymal stem cells (MSCs) were genetically modified such that the cytoskeleton was decoupled from the nucleus by saturating KASH binding proteins with a non-functional truncated protein called DN-KASH. MSCs treated with DN-KASH preferentially differentiated into osteocytes (bone cells) at a higher rate than MSCs exposed to osteogenic growth factors. This osteogenic preference after DN-KASH treatment was independent of the cell substrate topology and did not significantly alter integrin expression. However, this tendency to differentiate into osteocytes was dependent on substrate stiffness. Overall, the data imply that an intra-cellular force-dependent mechanism connected to the cell nucleus strongly influences MSC differentiation.
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Sesé, i. Castel Gemma. "Simulació per dinàmica de Langevin generalitzada en sistemes de partícules interactives." Doctoral thesis, Universitat de Barcelona, 1990. http://hdl.handle.net/10803/1795.
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L'anàlisi des del punt de vista dinàmic d'un sistema format per un conjunt de partícules que interactuen entre sí pot realitzar-se mitjançant diferents mètodes de simulació (Allen et al., 1987). D'entre tots ells, el més conegut és el mètode de la Dinàmica Molecular (DM), que es basa en la resolució numèrica de les equacions clàssiques que regeixen el moviment de cadascuna de les partícules que constitueixen un sistema. En moltes ocasions això pot ultrapassar les possibilitats de càlcul de què es disposa, la qual cosa ens impulsa a centrar el nostre interès en l'estudi d'una part del sistema. És per aquesta raó que ha augmentat darrerament l'interès despertat pels mètodes estocàstics de simulació, que simplifiquen considerablement l'anàlisi d'un sistema, ja que permeten estudiar-ne únicament una part sense efectuar una consideració explícita de la resta, i que poden esdevenir en alguns casos alternatives a l'ús de la DM.Els mètodes estocàstics es basen en la resolució de les Equacions de Langevin. Si en un sistema tenim dos tipus de partícules, als quals corresponen dues escales de temps molt diferenciades, la dinàmica de les partícules més lentes podrà descriure's satisfactòriament per Equacions de Langevin sense memòria. Les partícules simulades són partícules Brownianes i les simulacions així obtingudes seran de Dinàmica Browniana. Els sistemes de partícules col·loïdals en dissolució són especialment adequats per aquest tipus de tractament. Ara bé, si les partícules en les quals se centra el nostre interès no poden considerar-se Brownianes, caldrà que el seu moviment es calculi mitjançant la resolució d'equacions de Langevin Generalitzades (ELG). Aquest mètode de simulació s'anomena Dinàmica de Langevin Generalitzada (DLG), que està especialment indicat pels casos en què les partícules omeses tenen similars característiques, pel que fa a llur massa i tamany, a les que simularem d'una forma explícita. Per exemple, els sistemes formats per electròlits en dissolució haurien de ser simulats per DLG. Fins i tot en el domini de les macromolècules, si aquestes volen tractar-se àtom a àtom, pot ser necessària la consideració d'aquest mètode.
Aquest treball s'ha centrat en l'estudi de la DLG. S'hi ha considerat que cada partícula evoluciona segons una Equació de Langevin Generlitzada (ELG) (Ciccotti et al., 1981). En aquesta equació la part del sistema que s'omet a la simulació es té en compte mitjançant una força de fricció que depèn d'una funció memòria i una força estocàstica. L'equació inclou també la força causada per la interacció amb les altres partícules explícitament considerades, i que també ha de veure's afectada per la resta del sistema.
Donat que l'ELG és una equació de caràcter fenomenològic, resulta interessant efectuar un test d'aquest mètode de simulació, ja iniciat en anteriors treballs. En aquesta tesi s'ha incidit especialment en l'anàlisi de les propietats temporals i espai-temporals. L'estudi s'ha efectuat sobre sistemes simples, com per exemple els constituïts per àtoms de Kriptó o d'Argó, ja que requereixen potencials de curt abast i, per tant, simulacions relativament poc costoses.
Per tal que les partícules simulades presentin un comportament el més semblant possible al que tindrien en el sistema total, cal escollir amb certa cura les diferents funcions que apareixen al segon membre de l'ELG. Per a això, s'ha de tenir en compte que les interaccions entre les partícules es realitzen en un "medi" no considerat explícitament, però que les influencia. És per això que aquestes interaccions es calcularan a partir d'un potencial de força mitjana que anomenarem efectiu (Guàrdia et al., 1987) i que depèn de la concentració de partícules de solut. També en dependrà la funció memòria, present a l'ELG. En aquest treball hem proposat un mètode per a calcular aquestes funcions, que anomenarem funcions memòria efectives (Padró et al, 1998).
En l'obtenció dels potencials de força mitjana i de les funcions memòria efectives hem partit, respectivament, de la funció de distribució radial (g(r)) i de la funció d'autocorrelació de velocitats (C(t)) corresponents a les partícules simulades. Hem calculat aquestes funcions a partir dels resultats de les simulacions dels sistemes complets realitzades per DM. Hem comprovat que, almenys per a sistemes simples, aquestes funcions existeixen i permeten una correcta reproducció tant de l'estructura com de la dinàmica dels sistemes estudiats. Per a això hem analitzat funcions de correlació que es refereixen al comportament de cada partícula i són la g(r), la C(t), i també la funció desplaçament quadràtic mitjà i el coeficient d'autodifusió (Hansen et al., 1986).
Paral·lelament, aquest estudi ens ha portat a analitzar les equacions de Langevin, tot avaluant les forces estocàstiques que hi apareixen. En aquestes equacions, la força total que actua sobre una partícula se separa en dues parts: un terme de fricció i un terme estocàstic. Aquesta separació és purament teòrica, cosa que provoca que les forces estocàstiques no siguin mesurables experimentalment, i que només puguin caracteritzar-se mitjançant la simulació, que en aquesta ocasió serà utilitzada com a eina per a l'anàlisi de la validesa d'hipòtesis i propietats teòriques.
Aquestes forces estocàstiques s'han calculat en simulacions de DM, i s'ha comprovat que satisfan totes les propietats que els són característiques des d'un punt de vista teòric (Sesé et al., 1990). Donat que les funcions memòria efectives s'utilitzen en aquests càlculs, els resultats obtinguts constitueixen una prova més de la bondat d'aquestes funcions.
D'altra banda, la distribució estadística que segueixen les forces estocàstiques presenta algunes diferències quantitatives respecte a una distribució Gaussiana. Ara bé, tot i que en les nostres simulacions per DLG es parteix d'una distribució d'aquest tipus no s'ha detecta cap problema que pugi associar-se a la no Gaussianitat d'aquestes forces.
També s'ha calculat la funció d'autocorrelació de les forces estocàstiques sobre una partícula de massa infinita i s'ha comparat amb la mateixa funció corresponent a la partícula en moviment. S'ha comprovat que aquestes funcions presenten algunes diferències i que, tot i que per ions en aigua aquestes diferències són gairebé negligibles, cal anar en compte a l'hora d'extendre la hipòtesis de la seva igualtat a tot tipus de sistemes.
I, finalment, coneguts els potencials de força mitjana i les funcions memòria efectives, hem realitzat un test més ampli de la DLG. Ja que aquesta tècnica es presenta en tant que mètode simplificador de la DM, el test consistirà en comparar els resultats obtinguts per ambdós mètodes, de manera que les evolucions obtingudes per DM es consideraran exactes. S'ha comprovat que els resultats de la DLG per altres funcions de correlació microscòpiques, com les funcions de Van Hove, estan en concordància amb els obtinguts per DM. Ara bé, s'ha constatat l'existència de serioses discrepàncies en les funcions de correlació creuades de velocitats corresponents a partícules diferents. Això és natural ja que es tracta d'una propietat col·lectiva que depèn en gran mesura dels efectes dels fluxes de dissolvent induïts per les mateixes partícules de solut, és a dir, de les interaccions hidrodinàmiques, negligides en els simulacions realitzades per DLG.
BIBLIOGRAFIA:
ALLEN M.P. and TILDESLEY D.J., 1987, Computer simulation of liquids. Claredon Press-Oxford
CICCOTTI G. and RYCKAERT J.P., 1981, J. Stat. Phys. 26, 73.
GUÀRDIA E., GÓMEZ-ESTÉVEZ J.L. and PADRÓ J.A., 1987, J.Chem.Phys. 86, 6438.
HANSEN J.P. and MC DONALD I.R., 1986, Theory of simple liquids. Academic Press.
PADRÓ J.A., GUÀRDIA E. and SESÉ G., 1988, Molec. Phys. 63, 355.
SESÉ G., GUÀRDIA E. and PADRÓ J.A., 1990, J. Stat. Phys. 60, 501.
Generalized Langevin Dynamics (GLD) is a stochastic simulation method that allows to perform the study of subsystems made up of non-Brownian particles (solute), i.e., whose masses and sizes are similar to the ones of the particles of the rest (solvent). The method requires the numerical resolution of a Generalized Langevin Equation (GLE) for every solute particle. The suitability of the GLD method for a realistic description of a system of interacting particles in solution is discussed. Our study has been focused on the dynamical properties of the solute in dense liquid mixtures. To begin with this study, a procedure for obtaining effective memory functions which include the average effects of the indirect solute-solvent-solute interactions is proposed. Using those effective memory functions, the random and frictional forces on the atoms of the solute, which include the effect of their collisions with the solvent, are calculated from Molecular Dynamics (MD) simulations.
Moreover, the validity of the usual assumptions on the statistical properties of the random forces is carefully analysed. MD simulations of realistic dense liquids have been used to characterize the random forces which appear when the GLD is used for the description of the atomic motions. Our results show that the distribution of frequencies of the random forces ressembles the ordinarily assumed Gaussian distribution, but some discrepancies appear when quantitative analyses are performed. In addition, the properties of such forces, generated from MD simulations using the GLE, are the ones ordinarily required for the random ones.
Finally, the GLD method has been tested against the MD simulation of the complete system. It has been proved that computer simulations based on the GLE and assuming a Gaussian distribution for the random forces permit quite good reproductions of the analysed structural and dynamical properties of the solute (radial distribution functions, velocity autocorrelation functions, diffusion coefficients, Van Hove functions .), provided that effective mean force potentials and effective memory functions are used. As the hydrodynamic interactions have been neglected in our study, the disagreements for the collective properties are important.
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Jin, Dongliang. "Thermodynamique et cinétique de la formation de l'hydrate de méthane confiné dans un milieu nanoporeux : théorie et simulation moléculaire." Thesis, Université Grenoble Alpes (ComUE), 2018. http://www.theses.fr/2018GREAY076/document.
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L'hydrate de méthane est un cristal non-stœchiométrique dans lequel les molécules d'eau forment des cages liées par liaison hydrogène qui piégent des molécules de méthane. Des ressources abondantes en hydrate de méthane peuvent être trouvées sur Terre, en particulier dans les roches poreuses minérales (par exemple, l'argile, le permafrost, les fonds marins, etc.). Pour cette raison, la compréhension de la thermodynamique et de la cinétique de formation de l'hydrate de méthane confiné dans des milieux poreux suscite beaucoup d'attention. Dans cette thèse, nous combinons la modélisation moléculaire et des approches théoriques pour déterminer la thermodynamique et la cinétique de formation de l'hydrate de méthane confiné dans des milieux poreux. Tout d'abord, l'état de l'art en matière de thermodynamique et de cinétique de formation de l'hydrate de méthane est présenté. Deuxièmement, différentes stratégies de simulation moléculaire, y compris des calculs d'énergie libre utilisant l'approche de la molécule d'Einstein, la méthode de coexistence directe et la technique textit{hyperparallel tempering}, sont utilisées pour évaluer la stabilité de l'hydrate de méthane à différentes températures et pressions. Troisièmement, parmi ces stratégies, la méthode de coexistence directe est choisie pour déterminer le déplacement du point de fusion lors du confinement dans des pores, $Delta T_m = T_m^{pore} - T_m^{bulk} $ où $ T_m^{pore}$ et $T_m^{bulk}$ sont les températures de fusion d'hydrate de méthane non confiné et confiné. Nous avons constaté que le confinement diminue la température de fusion, $T_m^{pore} < T_m^{bulk} $. Le changement de température de fusion en utilisant la méthode de la coexistence directe est cohérent avec l'équation de Gibbs-Thompson qui prédit que le décalage de la température de fusion dépend linéairement de l'inverse de la taille des pores, $Delta T_m/T_m^{bulk} sim k_{GT}/ D_p$. La validité quantitative de cette équation thermodynamique classique pour décrire de tels effets de confinement et de surface est également abordée. Les tensions de surface des interfaces hydrate-substrat et eau-substrat sont déterminées à l'aide de la dynamique moléculaire pour valider quantitativement l'équation de Gibbs-Thompson. Des simulations de dynamique moléculaire sont également effectuées pour déterminer les propriétés thermodynamiques importantes de l'hydrate de méthane non confiné et confiné: (a) conductivité thermique $lambda$ en utilisant le formalisme de Green-Kubo et la fonction d'autocorrélation du flux thermique; (b) expansion thermique $alpha_P$ et compressibilité isotherme $kappa_T$. Enfin, des conclusions et perspectives pour des travaux futurs sont présentéesMethane hydrate is a non-stoichiometric crystal in which water molecules form hydrogen-bonded cages that entrap methane molecules. Abundant methane hydrate resources can be found on Earth, especially trapped in mineral porous rocks (e.g., clay, permafrost, seafloor, etc.). For this reason, understanding the thermodynamics and formation kinetics of methane hydrate confined in porous media is receiving a great deal of attention. In this thesis, we combine computer modeling and theoretical approaches to determine the thermodynamics and formation kinetics of methane hydrate confined in porous media. First, the state-of-the-art on the thermodynamics and formation kinetics of methane hydrate is presented. Second, different molecular simulation strategies, including free energy calculations using the Einstein molecule approach, the direct coexistence method, and the hyperparallel tempering technique, are used to assess the phase stability of bulk methane hydrate at various temperatures and pressures. Third, among these strategies, the direct coexistence method is chosen to determine the shift in melting point upon confinement in pores, $Delta T_m = T_{m}^{pore} - T_{m}^{bulk}$ where $T_m^{pore}$ and $T_m^{bulk}$ are the melting temperatures of bulk and confined methane hydrate. We found that confinement decreases the melting temperature, $T_m^{pore}
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Pietilä, Lars-Olof. "Molecular mechanics and force field studies of weakly coupled conjugated molecules and molecular crystals." Hki : Finnish Society of Sciences and Letters : Academic Bookstore [distr.], 1988. http://catalog.hathitrust.org/api/volumes/oclc/57854229.html.
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Cisek, Katryna. "Rational Optimization of Small Molecules for Alzheimer’s Disease Premortem Diagnosis." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1338325484.
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El, maangar Asmae. "L’extraction raisonnée de métaux stratégiques par des hydrotropes." Thesis, Université de Montpellier (2022-….), 2022. http://www.theses.fr/2022UMONS004.
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L’extraction liquide-liquide (LL) est la technologie principale de séparation employée dans les procédés hydrométallurgiques pour le recyclage des métaux stratégiques nécessaires à l’économie circulaire. La mise en œuvre industrielle du recyclage repose sur le contrôle du transfert d’espèces entre une solution concentrée d’électrolytes contenant les cations métalliques à extraire sélectivement et une solution de tensioactif lipophile associé à un solvant non miscible à l’eau et des « modificateurs de phase ». Une limitation des procédés d’extraction LL tel qu’utilisés actuellement est la formation de la 3ème phase. De plus, ils induisent un lourd impact environnemental en raison de l’utilisation de volumes élevés de réactifs et l’emploi intensif de solvants organiques non respectueux de l’environnement. Une des stratégies pour répondre à ces problématiques est d’utiliser des systèmes à base d’hydrotropes.Les hydrotropes sont une famille de molécules utilisés pour des applications en biochimie analytique, pharmaceutique et en cosmétique. Ces molécules n’ont jamais été étudiées dans le cadre du recyclage des métaux. Cette thèse est consacrée à la compréhension et la mise en œuvre d’hydrotropes pour l’extraction des métaux, ainsi qu’à l’identification des forces motrices mises en jeu.Ce travail décrit via la démarche « iénaïque », associant les approches supramoléculaire et colloïdale, ce qui se passe lorsque l’on remplace respectivement le diluant, le modificateur de phase et même l’extractant par des hydrotropes. Deux types d’hydrotropes sont étudiés : des hydrotropes qui sont des tensioactifs neutres courts et des hydrotropes électrolytes comme le salicylate de sodium. Dans chaque cas, la détermination des diagrammes de phases et de la nanostructuration des phases sont des préalables nécessaires à la compréhension des forces moléculaires à l’origine des transferts mesurés. L’utilisation des techniques de fluorescence de rayons X, de diffusion de rayons X et des neutrons, de tensiométrie interfaciale ainsi que de calorimétrie ont été déterminantes pour la compréhension des mécanismes sous-jacents à l’extraction hydrotropique.Au prix d’une augmentation de complexité des schémas procédés liés à la solubilité de l’hydrotrope dans les phases aqueuses, nous démontrons que l’emploi d’hydrotropes à la place du diluant ou même à la place de l’extractant, compris par la décomposition « iénaïque », amènent à un gain d’un ordre de grandeur en intensification de procédé et/ou en volume d’effluents produits, ouvrant la voie à l’extraction « raisonnée » des métaux en vue de leur recyclage depuis la mine urbaineLiquid-liquid extraction (LLE) is the main separation technology used in hydrometallurgical processes for the recycling of strategic metals needed for a circular economy. The industrial implementation of recycling relies on the control of the transfer of species between a concentrated solution of electrolytes containing the metal cations to be selectively extracted and a solution of lipophilic surfactant associated with a water-immiscible solvent and “phase modifiers”. A limitation of LLE processes as currently used is the formation of the 3rd phase. In addition, they induce a heavy environmental impact due to the use of high volumes of reagents and the intensive use of non-environmentally friendly organic solvents. One possible strategy to overcome these problems is by using hydrotrope-based systems.Hydrotropes are a family of molecules used for applications in analytical biochemistry, pharmaceuticals and cosmetics. These molecules have never been studied in the context of metal recycling. This thesis is devoted to the understanding and implementation of hydrotropes for metal extraction, as well as to the identification of the driving forces involved.This work uses the “ienaics” approach to measure and understand what happens when the diluent, the phase modifier and even the extractant are replaced by hydrotropes, respectively. Two types of hydrotropes are studied: hydrotropes that are short neutral surfactants and electrolyte hydrotropes such as sodium salicylate. In each case, the determination of the phase diagrams and the nanostructuration of the phases are necessary prerequisites to understand the molecular forces at the origin of the measured transfers. The use of X-ray fluorescence, X-ray and neutron scattering, interfacial tensiometry and calorimetry techniques have been decisive for the understanding of the mechanisms underlying hydrotropic extraction.At the cost of an increase in complexity of the process schemes related to the solubility of the hydrotrope in the aqueous phases, we demonstrate that the use of hydrotropes instead of the diluent or even instead of the extractant, understood by the “ienaics” decomposition, leads to a gain of an order of magnitude in process intensification and/or in volume of effluents produced, opening the way to the “reasoned” extraction of the metals for their recycling from the urban mine
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Hinaux, Hélène. "Evolution du développement de l’œil chez le poisson cavernicole aveugle Astyanax mexicanus." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA11T023/document.
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Le poisson Astyanax mexicanus présente, au sein de la même espèce, plusieurs populations de poissons de rivières (SF) et de poissons de grottes aveugles (CF). Chez les poisons cavernicoles aveugles, les yeux se développent presque normalement pendant l’embryogenèse. Mais 24 heures après la fécondation (hpf), quand l’embryon éclot, le cristallin entre en apoptose, ce qui déclenche la dégénérescence progressive de l’œil entier. Mon projet de thèse visait à comprendre le mécanisme conduisant à l’apoptose du cristallin, jusqu’alors totalement incompris, en partant du postulat selon lequel le défaut devait avoir lieu pendant les stades précoces du développement du cristallin. Le cristallin se développe à partir d’une placode, un épaississement de l’ectoderme au stade neurula. Toutes les placodes, qui donnent naissance à des organes des sens de la tête, sont issues du champ panplacodal, situé à la bordure de la plaque neurale antérieure à 10 hpf. Nous avons comparé la régionalisation de ce champ chez les deux morphes, par hybridations in situ de gènes marqueurs des différentes placodes. Chez le CF, le territoire présomptif du cristallin est réduit à 10 hpf, et le cristallin est plus petit à tous les stades étudiés. D’autre part, la placode olfactive est étendue, et donne naissance à un épithélium olfactif plus large chez le CF. Les modifications de taille de ces deux placodes pourraient être le résultat évolutif d’un « trade-off » entre ces deux composantes sensorielles. La régionalisation modifiée du champ panplacodal chez le CF est due au moins partiellement à des différences spatiales et temporelles d’expression des molécules de signalisation Shh, Fgf, et peut-être Bmp4.Nous avons pensé que la petite taille du cristallin pouvait être la cause directe de son entrée en apoptose, par un défaut d’effet de communauté. Nous avons réalisé une ablation laser partielle des cellules précurseurs du cristallin à 12-14 hpf chez l’embryon SF, mimant ainsi la taille du cristallin CF. L’apoptose dans le petit cristallin des larves SF à 60 hpf n’a pas été augmentée, ce qui montre que la petite taille n’est pas suffisante pour induire l’apoptose.L’apoptose du cristallin pourrait aussi provenir de défauts de morphogenèse ou d’un problème de lignage cellulaire. Nous utilisons donc l’imagerie biphoton in vivo sur des embryons SF et CF, de 10 à 24 hpf, préalablement injectés au stade une cellule avec des ARNm de H2B-mCherry et Ras-GFP pour marquer les noyaux et les membranes. Les premiers résultats sur les poissons de surface montrent que nous pouvons suivre à rebours les cellules du cristallin de la fin du film jusqu’au champ panplacodal, et étudier la morphogenèse et les divisions.La différenciation du cristallin est également affectée chez le CF : au moins 5 cristallines, qui sont des protéines structurales du cristallin, ne sont pas exprimées correctement chez le CF, d’après des hybridations in situ et des qPCR. Cependant, le rôle fonctionnel de deux de ces modifications d’expression a été testé, et individuellement, elles n’expliquent pas le phénotype apoptotique. Nous émettons l’hypothèse qu’une combinaison de défauts d’expression de plusieurs cristallines serait à l’origine de l’apoptose du cristallin CF. Enfin, et plus largement, les forces évolutives qui ont conduit à la perte de l’œil chez Astyanax mexicanus ne sont pas encore comprises. Par une étude d’évolution moléculaire à l’échelle du transcriptome nous avons identifié des mutations fixées entre SF et CF, et avons pu mettre en évidence une accumulation de mutations dans des « gènes d’yeux » chez les CF. Cela suggère un relâchement de la pression de sélection sur ces gènes, peut-être devenus inutiles dans l’obscurité. De même, les séquences des cristallines de CF paraissent accumuler des mutations fixées à un taux élevé vu leur bas niveau de polymorphismeThe fish Astyanax mexicanus presents, within the same species, several populations of river-dwelling surface fish (SF) and blind cave-living fish (CF). In blind cavefish, the eyes first develop almost normally during embryogenesis. But 24 hours after fertilization (hpf), when the embryo hatches, the lens enters apoptosis, which triggers the progressive degeneration of the entire eye. My thesis project aimed at understanding the mechanism leading to lens apoptosis, which was so far unknown. We reasoned that the defect(s) should take place during the early stages of lens development. The lens develops from a placode, a thickening of the ectoderm at the neurula stage. All placodes, giving rise to sense organs of the head, originate from the “panplacodal” field, located at the border of the anterior neural plate at 10 hpf. We compared the patterning of the panplacodal field in the 2 morphs, using in situ hybridizations for placodal marker genes. In CF, the lens placode territory is reduced at 10 hpf, and the lens is smaller at all stages examined. Conversely, the olfactory placode is enlarged, and gives rise to a bigger olfactory epithelium in CF. The modifications in size of these two placodes could result evolutionarily from a trade-off between these two sensory components. Developmentally, the modified patterning of the panplacodal field in CF is at least partly due to the spatial and temporal differences in the expression of Shh and Fgf (and perhaps Bmp4) signaling molecules.We hypothesized that the small size of the lens could be the direct cause of its apoptosis, through a lack of community effect. We performed partial laser ablation of lens precursor cells at 12-14hpf in surface fish (thereby mimicking the CF lens size). Apoptosis in the resulting small lens of SF larvae at 60hpf was not enhanced, showing that small size is not sufficient to induce apoptosis. Lens apoptosis could also result from morphogenesis defects or from a problem in cell lineage. We are performing two-photon live imaging, from 10 to 24 hpf, of SF and CF embryos previously injected at the one cell stage with H2B-mCherry and Ras-GFP mRNAs to label nuclei and membranes. First results on surface fish show that we can back-track lens cells to the panplacodal field, and follow morphogenesis and divisions. Lens differentiation is also affected in cavefish: at least 5 crystallins, which are lens structural components, are not expressed correctly in CF, based on in situ hybridization and qPCR data. However the functional role of two of these expression modifications / losses was tested and, individually, they don’t seem to explain the apoptosis phenotype. We propose that a combination of several crystallins expression defects would explain CF lens apoptosis.Finally, and more globally, evolutionary forces that led to eye loss in Astyanax mexicanus are not yet understood. Through a transcriptome-wide molecular evolution approach, we identified fixed mutations in transcripts between SF and CF, and we could show an accumulation of mutations in “eye genes” in CF. This suggests that the selection is relaxed on these genes, that have maybe become useless in the dark. Similarly, CF crystallin sequences seem to accumulate fixed mutations at a high rate, considering their low polymorphism level
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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.
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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.
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Ramraj, Anitha. "Computational modelling of intermolecular interactions in bio, organic and nano molecules." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/computational-modelling-of-intermolecular-interactions-in-bio-organic-and-nano-molecules(7a41f3cd-1847-4ccf-8853-5fd8be2a2c15).html.
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We have investigated the noncovalent interactions in carbohydrate-aromatic interactions which are pivotal to the recognition of carbohydrates in proteins. We have employed quantum mechanical methods to study carbohydrate-aromatic complexes. Due to the importance of dispersion contribution to the interaction energy, we mainly use density functional theory augmented with an empirical correction for the dispersion interactions (DFT-D). We have validated this method with a limited number of high level ab initio calculations. We have also analysed the vibrational and NMR chemical shift characteristics using the DFT-D method. We have mainly studied the complexes involving β-glucose with 3-methylindole and p-hydroxytoluene, which are analogues of tryptophan and tyrosine, respectively. We find that the contribution for interaction energy mainly comes from CH/π and OH/π interactions. We find that the interaction energy of complexes involving CH/π and OH/π interactions is reflected in the associated blue and red shifts of vibrational spectrum. We also find that the interactions involving 3-methylindole are somewhat greater than those for p-hydroxytoluene. The C-H blueshifts are also in parallel with the predicted NMR proton shift. We have also tested different density functionals including both standard density functionals and newly developed M0x functionals and MP2 method for studying carbohydrate-aromatic complexes. The DFT-D method and M06 functionals of the M0x family are found to perform better, while B3LYP and BLYP functionals perform poorly. We find that the inclusion of a dispersion term to BLYP is found to perform better. The dispersion energy dominates over the interaction energy of carbohydrate-aromatic complexes. From the DFT-D calculations, we found that the complexes would be unstable without the contribution from dispersive energy. We have also studied the importance of noncovalent interactions in functionalization of nanotubes by nucleic acid bases and aromatic amino acids by using semi-empirical methods with dispersion term such asPM3-D and PM3-D*. We find that the both semi-empirical schemes give reasonable interaction energies with respect to DFT-D interaction energies. We have also used PM3-D method to study the adsorption of organic pollutants on graphene sheet and on nanotubes. We found that the semi-empirical schemes, which are faster and cheaper, are suitable to study these larger molecules involving noncovalent interactions and can be used as an alternative to DFT-D method. We have also studied the importance of dispersion interaction and the effect of steric hindrance in aggregation of functionalized anthracenes and pentacenes. We have also employed molecular dynamics simulation methods to study the aggregation of anthracene molecules in toluene solution.
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Iftner, Christophe. "Modélisation de complexes et agrégats moléculaires en matrice cryogénique." Thesis, Toulouse 3, 2015. http://www.theses.fr/2015TOU30160/document.
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Cette thèse présente le développement et les applications d'un formalisme hybride quantique-classique pour décrire la structure électronique d'un système actif avec un environnement cryogénique (agrégat ou matrice d'atomes de gaz rare). La description quantique de la structure électronique du système actif est faite dans le cadre d'une approximation de type Liaisons Fortes de la Théorie de la Fonctionnelle de la Densité, avec charges atomiques autocohérentes (SCC-DFTB). L'environnement de gaz rare est décrit par des potentiels classiques atome-atome (FF). L'interaction entre le sytème actif et les atomes de l'environnement cryogénique est représentée par des opérateurs matriciels locaux anisotropes électron-atome, ainsi que par des contributions de polarisation et de dispersion. La détermination des opérateurs et des paramètres d'interaction est extraite de calculs ab initio post Hartree-Fock (CCSD-T) sur les paires atome actif/atome d'argon. Les applications concernent les interactions entre hydrocarbures, agrégats d'eau isolés ou complexes hydrocarbures/eau avec des agrégats et ou des matrices d'argon. Le modèle est validé sur de petits systèmes (molécule C6H6 , molécule H2O) en interaction avec des atomes et agrégats d'argon. Nous avons ainsi déterminé les données structurales et énergétiques pour les agrégats (C6H6)Arn (n < 55) qui ont été comparées à des données ab initio (DFT, CCSD-T) pour les plus petits agrégats, ou à des calculs de champ de force publiés dans la littérature pour les agrégats de plus grande taille. Le modèle permet également un traitement unifié de différentes situations électroniques permettant ainsi la détermination de l'évolution des potentiels d'ionisation du système actif en fonction de la taille n de l'agrégat solvatant. Le modèle DFTB/FF a ensuite été appliqué à des molécules et nano-agrégats d'eau (H2O)n (n=2-6) insérés dans des matrices d'argon, représentées par des sous-ensembles finis du réseau cristallin cubique faces centrées. Des données structurales et énergétiques ont été obtenues. Des études de dynamique moléculaire ont permis la détermination de spectres infrarouges (IR) à température finie. La comparaison des spectres IR théoriques caractérisant une molécule d'eau en matrice avec les données expérimentales nous a permis de valider l'approche DFTB/FF. Le cas de l'hexamère (H2O)6, plus petit agrégat présentant une structure tri-dimensionnelle et caractérisé par plusieurs isomères stables, a été étudié de façon exhaustive : l'effet de la matrice sur les structures de certains de ces isomères a été mis en évidence, ainsi que des effets différentiels sur leur stabilités respectives. Une influence sur les positions des bandes IR des agrégats a également été montrée. Les résultats obtenus permettent une interprétation satisfaisante des données expérimentales existantes pour les plus petits agrégats. L'assignation des spectres expérimentaux de l'hexamère demeure incertaine. Enfin, des résultats préliminaires sur les structures, l'énergétique et les spectres IR à température finie ont été obtenus pour des complexes d'Hydrocarbures Aromatiques Polycycliques avec l'eau (HAP-H2O) en matrices d'argon. L'ensemble des données obtenues pour ces complexes est discuté en relation avec les résultats expérimentaux en environnement cryogénique obtenus dans l'équipe de Joëlle Mascetti de l'Institut des Sciences Moléculaires de l'Université Bordeaux I, dans le cadre d'une collaboration ANR (ANR PARCS no 13-BS08-0005). Ce travail a bénéficié d'une allocation de thèse co-financée par l'Institut de Physique du CNRS et le Conseil Régional de la région Midi-PyrénéesThis thesis presents the development and applications of an hybrid quantum-classical formalism in order to describe the electronic structure of an active system in a cryogenic environment (cluster or rare gas matrix). The quantum description of the electronical structure of the active system is based on a a tight-binding approximation of the density functional theory, with self-consistency regarding the charges (SCC-DFTB). The rare gaz environment is described via classical atom-atom potential (FF). The interaction between the active system and the atoms of the cryogenic environment is represented by local anisotropic matricial electron-atom operators, as well as by polarisation and dispersion contributions. Operators and interaction parameters are extracted from post Hartree-Fock \textit{ab initio} calculations (CCSD-T) of active atom/argon atom pairs. The applications involve hydrocarbons, isolated water clusters or hydrocarbon/water complexes in interaction with argon clusters or matrices. The model has been validated on small systems (C6H6 molecule, H2O molecule) in interaction with argon atoms and clusters. We have been able to determine structural and energetic data for (C6H6)Arn (n < 55) clusters which are benchmarked against ab initio results (DFT,CCSD-T) for the smaller sizes, or with respect to FF calculations, available in the literature, for larger sized clusters. The model enables to treat various electronic situations, allows in particular to determine the evolution of the ionization potentials of the active system as a function of the inert cluster size. The SCC-DFTB/FF model has then been applied to water molecules and water nano-clusters (H2O)n (n=2-6) embedded in argon matrices, represented by finite size cristal pieces of the face centered cubic lattice. Structural and energetical data have been obtained. Molecular dynamics studies have enabled the determination of finite temperature infrared (IR) spectra. Comparison between the theoretical and experimental spectra of the water monomer embedded in the matrix validates the SCC-DFTB/FF approach. The case of the water hexamer (H2O)6, the smallest cluster presenting a three-dimensional structure and caracterized by several low-energy isomers, has been investigated exhaustively : the effect of the matrix on the structures of some isomers has been shown as well as differential effects on their respective stabilities. An influence on IR lines positions has also been highlighted. Our theoretical study allows for a satisfactory interpretation of the experimental data for the smallest clusters (n<4). The assignment of the experimental spectra of the hexamer remains in discussion. Finally, preliminary results on structures, energetics and finite temperature IR spectra have been obtained for Polycyclic Aromatic Hydrocarbons (PAH) /water complexes. The results for the complexes are discussed in relation with experimental data obtained in the team of Joëlle Mascetti at the Institute of Molecular Sciences (University of Bordeaux I), in the context of an ANR collaborative project (ANR PARCS no 13-BS08-0005). The thesis has been co-financed by the CNRS Institute of Physics and Conseil Regional of Region Midi-Pyrénées