Dissertations / Theses on the topic 'Interaction energy calculation'
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Almlöf, Martin. "Computational Methods for Calculation of Ligand-Receptor Binding Affinities Involving Protein and Nucleic Acid Complexes." Doctoral thesis, Uppsala University, Department of Cell and Molecular Biology, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7421.
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The ability to accurately predict binding free energies from computer simulations is an invaluable resource in understanding biochemical processes and drug action. Several methods based on microscopic molecular dynamics simulations exist, and in this thesis the validation, application, and development of the linear interaction energy (LIE) method is presented.
For a test case of several hydrophobic ligands binding to P450cam it is found that the LIE parameters do not change when simulations are performed with three different force fields. The nonpolar contribution to binding of these ligands is best reproduced with a constant offset and a previously determined scaling of the van der Waals interactions.
A new methodology for prediction of binding free energies of protein-protein complexes is investigated and found to give excellent agreement with experimental results. In order to reproduce the nonpolar contribution to binding, a different scaling of the van der Waals interactions is neccesary (compared to small ligand binding) and found to be, in part, due to an electrostatic preorganization effect not present when binding small ligands.
A new treatment of the electrostatic contribution to binding is also proposed. In this new scheme, the chemical makeup of the ligand determines the scaling of the electrostatic ligand interaction energies. These scaling factors are calibrated using the electrostatic contribution to hydration free energies and proposed to be applicable to ligand binding.
The issue of codon-anticodon recognition on the ribosome is adressed using LIE. The calculated binding free energies are in excellent agreement with experimental results, and further predict that the Leu2 anticodon stem loop is about 10 times more stable than the Ser stem loop in complex with a ribosome loaded with the Phe UUU codon. The simulations also support the previously suggested roles of A1492, A1493, and G530 in the codon-anticodon recognition process.
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Panel, Nicolas. "Étude computationnelle du domaine PDZ de Tiam1." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLX062/document.
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Les interactions protéine-protéine sont souvent contrôlées par de petits domaines protéiques qui régulent les chemins de signalisation au sein des cellules eucaryotes. Les domaines PDZ sont parmi les domaines les plus répandus et les plus étudiés. Ils reconnaissent spécifiquement les 4 à 10 acides aminés C-terminaux de leurs partenaires. Tiam1 est un facteur d'échange de GTP de la protéine Rac1 qui contrôle la migration et la prolifération cellulaire et dont le domaine PDZ lie les protéines Syndecan-1 (Sdc1), Caspr4 et Neurexine. Des petits peptides ou des molécules peptidomimétiques peuvent potentiellement inhiber ou moduler son activité et être utilisés à des fins thérapeutiques. Nous avons appliqué des approches de dessin computationnel de protéine (CPD) et de calcul d'énergie libre par simulations dynamique moléculaire (DM) pour comprendre et modifier sa spécificité. Le CPD utilise un modèle structural et une fonction d'énergie pour explorer l'espace des séquences et des structures et identifier des variants protéiques ou peptidiques stables et fonctionnels. Nous avons utilisé le programme de CPD Proteus, développé au laboratoire, pour redessiner entièrement le domaine PDZ de Tiam1. Les séquences générées sont similaires à celles des domaines PDZ naturels, avec des scores de similarité et de reconnaissance de pli comparables au programme Rosetta, un outil de CPD très utilisé. Des séquences contenant environ 60 positions mutées sur 90, ont été testées par simulations de DM et des mesures biophysiques. Quatre des cinq séquences testées expérimentalement (par nos collaborateurs) montrent un dépliement réversible autour de 50°C. Proteus a également déterminer correctement la spécificité de la liaison de quelques variants protéiques et peptidiques. Pour étudier plus finement la spécificité, nous avons paramétré un modèle d'énergie libre semi-empirique de Poisson-Boltzmann ayant la forme d'une énergie linéaire d'interaction, ou PB/LIE, appliqué à des conformations issues de simulations de DM en solvant explicite de complexes PDZ:peptide. Avec trois paramètres ajustables, le modèle reproduit correctement les affinités expérimentales de 41 variants, avec une erreur moyenne absolue de 0,4~kcal/mol, et donne des prédictions pour 10 nouveaux variants. Le modèle PB/LIE a ensuite comparé à la méthode non-empirique de calcul d'énergie libre par simulations alchimiques, qui n'a pas de paramètre ajustable et qui prédit correctement l'affinité de 12 complexes Tiam1:peptide. Ces outils et les résultats obtenus devraient nous permettre d'identifier des peptides inhibiteurs et auront d'importantes retombées pour l'ingénierie des interactions PDZ:peptideSmall protein domains often direct protein-protein interactions and regulate eukaryotic signalling pathways. PDZ domains are among the most widespread and best-studied. They specifically recognize the 4-10 C-terminal amino acids of target proteins. Tiam1 is a Rac GTP exchange factor that helps control cellmigration and proliferation and whose PDZ domain binds the proteins syndecan-1 (Sdc1), Caspr4, and Neurexin. Short peptides and peptidomimetics can potentially inhibit or modulate its action and act as bioreagents or therapeutics. We used computational protein design (CPD) and molecular dynamics (MD) free energy simulations to understand and engineer its peptide specificity. CPD uses a structural model and an energy function to explore the space of sequences and structures and identify stable and functional protein or peptide variants. We used our in-house Proteus CPD package to completely redesign the Tiam1 PDZ domain. The designed sequences were similar to natural PDZ domains, with similarity and fold recognition scores comarable to the widely-used Rosetta CPD package. Selected sequences, containing around 60 mutated positions out of 90, were tested by microsecond MD simulations and biophysical experiments. Four of five sequences tested experimentally (by our collaborators) displayed reversible unfolding around 50°C. Proteus also accurately scored the binding specificity of several protein and peptide variants. As a more refined model for specificity, we parameterized a semi-empirical free energy model of the Poisson-Boltzmann Linear Interaction Energy or PB/LIE form, which scores conformations extracted from explicit solvent MD simulations of PDZ:peptide complexes. With three adjustable parameters, the model accurately reproduced the experimental binding affinities of 41 variants, with a mean unsigned error of just 0.4 kcal/mol, andgave predictions for 10 new variants. The PB/LIE model was tested further by comparing to non-empirical, alchemical, MD free energy simulations, which have no adjustable parameters and were found to give chemical accuracy for 12 Tiam1:peptide complexes. The tools and insights obtained should help discover new tight binding peptides or peptidomimetics and have broad implications for engineering PDZ:peptide interactions
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Ramadugu, Sai Kumar. "Carbohydrate-protein interactions: structure, dynamics and free energy calculations." Diss., University of Iowa, 2013. https://ir.uiowa.edu/etd/1731.
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The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulation, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecular dynamics as well as the thermodynamic integration formalism, we have been able to study the role of water on the surface of homopolysaccharides as well as complex oligosachharides, we have been able to produce a prediction of the bound structure of triantennary oligosaccride on the asialoglycoprotein receptor, we have been able to estimate the free energy of binding of ManΑ1→2Man to the HIV-1 inactivating protein, Cyanovirin-N as well as the relative binding free energies of mutants of Cyanovirin-N to the same ligand.
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Chang, Zhongwen, Pär Olsson, Nils Sandberg, and Dmitry Terentyev. "Interaction Energy Calculations of Edge Dislocation with Point Defects in FCC Cu." KTH, Reaktorfysik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-122396.
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In order to improve the dislocation bias (DB) model of swelling under irradiation, a large scale of atomistic simulation of the interaction in face centered cubic (FCC) Cu model lattice between an edge dislocation (ED) and point defects such as a vacancy, a self-interstital atom (SIA) have been performed for various configurations. It is found dislocation core splits into partial cores after energy relaxation. Interactions with any SIA conficurations is one order of magnitute larger than with a vacancy. The reason that SIA creats a larger dilatation volumn than the vacancy is directly observed from calculation. Furthurmore, within the interaction range, an octahedron position rather than dumbbell in <100> direction is observed in the stable state after relaxation in interactions between a edge dislocation and a dumbbell SIA. Comparision of interaction energy in analytical and atomistic calculation shows that analytical one has a stronger interaction in vacancy-ED systems, suggesting that the bias factor (BF) from analytical calculation is larger than from atomistic calculation.QC 20130530
Generation IV reactor research and development (GENIUS)
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Reid, K. S. C. "Application of interactive force and energy calculations to enzyme-substrate docking." Thesis, Imperial College London, 1987. http://hdl.handle.net/10044/1/47803.
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Hermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.
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Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.
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Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.
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Nervall, Martin. "Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8338.
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Vazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.
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This work discusses applications of computational simulations to a wide variety of chemical systems, to investigate intermolecular interactions to develop force field parameters and gain new insights into chemical reactivity and structure stability. First, we cover the characterization of hydrogen-bonding interactions in pyrazine tetracarboxamide complexes employing quantum topological analyses. Second we describe the use of quantum mechanical energy decomposition analysis (EDA) and non-covalent interactions (NCIs) analysis to investigate hydrogen-bonding and intermolecular interactions in a series of representative 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([bmim][Tf2N]) ion pairs extracted from classical equilibrium and non-equilibrium molecular dynamics simulations. Thirdly, we describe the use of multipolar/polarizable AMOEBA force field to study the extraction of benzene from a gasoline model employing 1,3-dimethylimidazolium tetrafluorobrorate, [DMIM][BF4], and ethylmethylimidazolium tetrafluorobrorate, [EMIM][BF4]. Fourthly, we cover the recent improvements and new capabilities of the QM/MM code "LICHEM". Finally, we describe the use of polarizable ab initio QM/MM calculations and study the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4], and ground state destabilization in uracil DNA glycosylase (UDG).
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Chaudhari, Mrunalkumar. "First Principles Calculations of the Site Substitution Behavior in Gamma Prime Phase in Nickel Based Superalloys." Thesis, University of North Texas, 2012. https://digital.library.unt.edu/ark:/67531/metadc149571/.
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Nickel based superalloys have superior high temperature mechanical strength, corrosion and creep resistance in harsh environments and found applications in the hot sections as turbine blades and turbine discs in jet engines and gas generator turbines in the aerospace and energy industries. The efficiency of these turbine engines depends on the turbine inlet temperature, which is determined by the high temperature strength and behavior of these superalloys. The microstructure of nickel based superalloys usually contains coherently precipitated gamma prime (?) Ni3Al phase within the random solid solution of the gamma () matrix, with the ? phase being the strengthening phase of the superalloys. How the alloying elements partition into the and ? phases and especially in the site occupancy behaviors in the strengthening ? phases play a critical role in their high temperature mechanical behaviors. The goal of this dissertation is to study the site substitution behavior of the major alloying elements including Cr, Co and Ti through first principles based calculations. Site substitution energies have been calculated using the anti-site formation, the standard defect formation formalism, and the vacancy formation based formalism. Elements such as Cr and Ti were found to show strong preference for Al sublattice, whereas Co was found to have a compositionally dependent site preference. In addition, the interaction energies between Cr-Cr, Co-Co, Ti-Ti and Cr-Co atoms have also been determined. Along with the charge transfer, chemical bonding and alloy chemistry associated with the substitutions has been investigated by examining the charge density distributions and electronic density of states to explain the chemical nature of the site substitution. Results show that Cr and Co atoms prefer to be close by on either Al sublattice or on a Ni-Al mixed lattice, suggesting a potential tendency of Cr and Co segregation in the ? phase.
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Lemkul, Justin Alan. "Molecular Modeling of the Amyloid β-Peptide: Understanding the Mechanism of Alzheimer's Disease and the Potential for Therapeutic Intervention." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77318.
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Alzheimer's disease is the leading cause of senile dementia in the elderly, and as life expectancy increases across the globe, incidence of the disease is continually increasing. Current estimates place the number of cases at 25-30 million worldwide, with more than 5.4 million of these occurring in the United States. While the exact cause of the disease remains a mystery, it has become clear that the amyloid β-peptide (Aβ) is central to disease pathogenesis. The aggregation and deposition of this peptide in the brain is known to give rise to the hallmark lesions associated with Alzheimer's disease, but its exact mechanism of toxicity remains largely uncharacterized.
Molecular dynamics (MD) simulations have achieved great success in exploring molecular events with atomic resolution, predicting and explaining phenomena that are otherwise obscured from even the most sensitive experimental techniques. Due to the difficulty of obtaining high-quality structural data of Aβ and its toxic assemblies, MD simulations can be an especially useful tool in understanding the progression of Alzheimer's disease on a molecular level.
The work contained herein describes the interactions of Aβ monomers and oligomers with lipid bilayers to understand the mechanism by which Aβ exerts its toxicity. Also explored is the mechanism by which flavonoid antioxidants may prevent Aβ self-association and destabilize toxic aggregates, providing insight into the chemical features that give rise to this therapeutic effect.Ph. D.
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Stevenson, Paul. "Nuclear structure calculations using many-body perturbation theory with a separable interaction." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312333.
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Okazaki, S., N. Yoshii, and K. Fujimoto. "Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations." AIP Publishing, 2012. http://hdl.handle.net/2237/20840.
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Vorvolakos, Angelos. "Artificial neural network methods in high energy physics and their application to the identification of quark and gluon jets in electroproton collisions." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314217.
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Calabrò, Gaetano. "Accelerating molecular simulations : implication for rational drug design." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/16439.
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The development and approval of new drugs is an expensive process. The total cost for the approval of a new compound is on average 1.0 - 1.2 billion dollars and the entire process lasts about 12 - 15 years. The main difficulties are related to poor pharmacokinetics, lack of efficacy and unwanted side effects. These problems have naturally led to the question if new and alternative methodologies can be developed to find reliable and low cost alternatives to existing practices. Nowadays, computer-assisted tools are used to support the decision process along the early stages of the drug discovery path leading from the identification of a suitable biomolecular target to the design/optimization of drug-like molecules. This process includes assessments about target druggability, screening of molecular libraries and the optimization of lead compounds where new drug-like molecules able to bind with sufficiently affinity and specificity to a disease-involved protein are designed. Existing computational methods used by the pharmaceutical industry are usually focused on the screening of library compounds such as docking, chemoinformatics and other ligand-based methods to predict and improve binding affinities, but their reliable application requires improvements in accuracy. New quantitative methods based on molecular simulations of drug binding to a protein could greatly improve prospects for the reliable in-silico design of new potent drug candidates. A common parameter used by medicinal chemists to quantify the affinity between candidate ligands and a target protein is represented by the free energy of binding. However, despite the increased amount of structural information, predicting binding free energy is still a challenge and this technique has found limited use beyond academia. A major reason for limited adoption in the industry is that reliable computer models of drug binding to a protein must reproduce the change in molecular conformations of the drug and protein upon complex formation and this includes the correct modelling of weak non-covalent interactions such as hydrogen bonds, burials of hydrophobic surface areas, Van der Waals interactions, fixations of molecular degrees of freedom solvation/desolvation of polar groups and different entropy contributions related to the solvent and protein interactions. For several classes of proteins these phenomena are not easy to model and often require extremely computationally intensive simulations. The main goal of the thesis was to explore efficient ways of computing binding affinities by using molecular simulations. With this aim, novel software to compute relative binding free energies has been developed. The implementation is based on alchemical transformations and it extended a preexisted piece of software Sire, a molecular modeling framework, by using the OpenMM APIs to run fast molecular dynamics simulations on the latest GPGPU technology. This new piece of software has equipped the scientific community with a flexible and fast tool, not only to predict relative binding affinities, but also a starting point to develop new sampling methods for instance hybrid molecular dynamics and Monte Carlo. The implementation has been validated on the prediction of relative hydration free energy of small molecules, showing good agreement with experimental data. In addition, non-additive effects to binding affinities in series of congeneric Thrombin inhibitors were investigated. Although excellent agreement between predicted and experimental relative binding affinities was achieved, it was not possible to accurately predict the non-additivity levels in most of the examined inhibitors, thus suggesting that improved force fields are required to further advance the state-of-the art of the field.
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Koh, Meng hock. "Fission-barriers and energy spectra of odd-mass actinide nuclei in self-consistent mean-field calculations." Thesis, Bordeaux, 2015. http://www.theses.fr/2015BORD0208/document.
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Alors qu’il existe de nombreux calculs microscopiques de barrières de fission pour des noyaux composés pair-pairs, il n’y a cependant que relativement peu de tels calculs pour des noyaux de masse impaire. Ceci est dû aux complications induites par la brisure de la symétric de reversement du sens du temps au niveau du champ moyen qui est engendrée par la présence d’un nucleon non apparié. Pour éviter cette difficulté, des calculs existants pour des noyaux de masse impaire ont tout simplement négligé ces effets de brisure de la symétrie de reversement du sens du temps.Dans ce travail, on se donne pour but d’améliorer la description des barrières de fission, aussi bien que des propriétés spectroscopiques du niveau fondamental et de l’état isomérique de fission,pour quelques isotopes de masse impaire dans la région des actinides en prenant en compte de tels effets. Ceci a été réalisé dans le cadre du formalisme de Skyrme–Hartree–Fock plus BCS avec blocking en adaptant ce formalisme à la brisure de la symétrie considérée. L’interaction résiduelle d’appariement a été approchée par une force de séniorité dont les paramètres ont été ajustés pour reproduire les différences de masse pair-impair de quelques noyaux de la région des actinides.Les énergies des têtes de bande rotationnelle de basse énergie ont été calculées dans le cadre du modèle unifié de Bohr-Mottelson pour quatre noyaux bien déformés (235U, 239Pu, 237Np, 241Am)produisant un bon accord qualitatif avec les données pour les noyaux impairs en neutrons. L’accord significativement moins bon obtenu pour les noyaux impairs en protons pourrait résulter de l’usage de l’approximation de Slater pour l’interaction d’échange de Coulomb. Les énergies de déformation de deux noyaux impairs en neutrons (235U, 239Pu) ont été calculées pour quelques configurations de particule individuelle, jusqu’après la barrières de fission externe. La symétrie axiale a été imposée tandis que la brisure de la symétrie droite-gauche (ou de parité intrinsèque) a été permise dans la région de la seconde barrière. Les hauteurs des barrières de fission pour ces noyaux impairs dépendent significativement des configurations de particule individuelle. Un accord qualitatif avec les données disponibles pour les hauteurs de barrières des noyaux impairs considérés et leurs voisins pair-pairs a été généralement obtenuWhile there have been numerous microscopic calculations on fission barriers of even-even compoundnuclei, there are however, relatively few such work dedicated to odd-mass nuclei. This is dueto the complications posed by the breaking of the time-reversal symmetry at the mean-field leveldue to the presence of an unpaired nucleon. In order to circumvent this difficulty, previous fission barriercalculations of odd-mass nuclei have been performed by neglecting the effect of time-reversalsymmetry breaking. This work aims to improve on the description of fission barriers as well asthe spectroscopic properties of ground and fission-isomeric state, of some odd-mass actinide nucleiby taking the effect of time-reversal symmetry breaking into account. This has been perfomedwithin a Skyrme-Hartree-Fock-plus-BCS framework with blocking, where the BCS formalism hasbeen adapted to accomodate this symmetry breaking. The Skyrme nucleon-nucleon effective forcehas been used with various sets of parameters (SIII, SkM*, SLy5*). The residual pairing interactionhas been approximated by seniority forces whose neutron and proton parameters have beenfitted to reproduce the odd-even mass differences of some actinide nuclei. The low-lying rotationalband-head energies evaluated within the Bohr-Mottelson unified model have been determined forfour well-deformed odd-nuclei (235U, 239Pu, 237Np, 241Am) yielding a good qualitative agreementto the data for odd-neutron nuclei. The agreement was significantly less good for the odd-protonnuclei, possibly due to the use of the Slater approximation for the exchange Coulomb interaction.The deformation energies of two odd-neutron nuclei (235U and 239Pu) have been calculated forsome single-particle configurations up to a point beyond the outer fission-barrier. Axial symmetrynuclear shape has been assumed while a breaking of the left-right (or intrinsic parity) symmetryhas been allowed around the outer fission-barrier. The fission-barrier heights of such odd-neutronnuclei depend significantly on the particle configurations. A special attention has been paid tothe very important rotational correction to deformation energies. In particular, the correction ofthe moment of inertia calculated from the usual Belyaev expression was considered. Overall, aqualitative agreement with available data on fission-barrier heights for the considered odd-neutronnuclei and their even neighbours has been obtained
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Kedziora, Gary S. "The graphical unitary group approach to configuration interaction calculations: an application to the dipole moment and potential energy surface of the water molecule /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487857546386283.
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Bhowmick, Somnath. "Theory on lower bound energy and quantum chemical study of the interaction between lithium clusters and fluorine/fluoride." Thesis, Aix-Marseille, 2015. http://www.theses.fr/2015AIXM4394.
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En chimie quantique, le principe variationnel est largement utilisé pour calculer la limite supérieure de l'énergie exacte d'un système atomique ou moléculaire. Des méthodes pour calculer la valeur limite inférieure de l'énergie existent mais sont bien moins connues. Une méthode précise pour calculer une telle limite inférieure permettrait de fournir une barre d'erreur théorique pour toute méthode de chimie quantique. Nous avons appliqué des méthodes de type variance pour calculer différentes énergies limites inférieures de l'atome d'hydrogène en utilisant des fonctions de base gaussiennes. L'énergie limite supérieure se trouve être toujours plus précise que ces différentes limites inférieures, i.e. plus proche de l'énergie exacte. L'importance de points singuliers sur l'évaluation de valeurs moyennes d'opérateurs quantiques a également été soulignée.Nous avons étudié les réactions d'adsorption d'un atome de fluor et d'un ion fluorure sur de petits agrégats de lithium Li$_n$ (n=2-15), à l'aide de méthodes de chimie quantique précises. Pour le plus petit système, nous avons montré que la formation de complexes stables Li$_2$F et Li$_2$F$^-$ se produit par un transfert d'électrons sans barrière et à longue portée, de Li$_2$ vers F pour le système neutre et l'inverse pour le système anionique. De telles réactions pourraient être rapides à très basse température. De plus, les complexes formés présentent des caractéristiques uniques de "longue liaison". Pour les systèmes plus gros Li$_n$F/Li$_n$F$^-$ ($n\geqslant4$), nous avons montré que les énergies d'adsorption peuvent être aussi grandes que 6~eV selon le site d'adsorption et que plus d'un état électronique est impliqué dans le processus d'adsorption. Les complexes formés présentent des propriétés intéressantes de "super alcalins" et pourraient servir d'unités de base dans la synthèse de composés à transfert de charge avec des propriétés ajustablesIn quantum chemistry, the variational principle is widely used to calculate an upper bound to the true energy of an atomic or molecular system. Methods for calculating the lower bound value to the energy exist but are much less known. An accurate method to calculate such a lower bound would allow to provide a theoretical error bar for any quantum chemistry method. We have applied variance-like methods to calculate different lower bound energies of a hydrogen atom using Gaussian basis functions. The upper bound energy is found to be always more accurate than the lower bound energies, i.e. closer to the exact energy. The importance of singular points on mean value evaluation of quantum operators has also been brought to attention.The adsorption reactions of atomic fluorine (F) and fluoride (F$^-$) on small lithium clusters Li$_n$ (n=2-15) have been investigated using accurate quantum chemistry ab initio methods. For the smallest system, we have shown that the formation of the stable Li$_2$F and Li$_2$F$^-$ complexes proceeds via a barrierless long-range electron transfer, from the Li$_2$ to F for the neutral and conversely from F$^-$ to Li$_2$ for the anionic system. Such reactions could be fast at very low temperature. Furthermore, the formed complexes show unique long bond characteristics. For the bigger Li$_n$F/Li$_n$F$^-$ systems ($n\geqslant 4$), we have shown that the adsorption energies can be as large as 6~eV depending on the adsorption site and that more than one electronic state is implied in the adsorption process. The formed complexes show interesting "superalkali" properties and could serve as building blocks in the synthesis of charge-transfer compounds with tunable properties
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Takacs, Zoltan. "Chloromethane Complexation by Cryptophanes : Host-Guest Chemistry Investigated by NMR and Quantum Chemical Calculations." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-81472.
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Host–guest complexes are widely investigated because of their importance in many industrial applications. The investigation of their physico–chemical properties helps understanding the inclusion phenomenon. The hosts investigated in this work are cryptophane molecules possessing a hydrophobic cavity. They can encapsulate small organic guests such as halo–methanes (CH2Cl2, CHCl3). The encapsulation process was investigated from both the guest and the host point of view. With the help of Nuclear Magnetic Resonance (NMR), the kinetics of complex formation was determined. The information was further used to obtain the activation energies of the processes. Having done this on five different cryptophanes, it is possible to relate the energies to structural differences between the hosts. Via the dipolar interaction between the guest’s and host’s protons, one can get information on the orientation of the guest inside the cavity. Moreover, the dynamics of the guest can be further investigated by its relaxation properties. This revealed restricted motion of the guest inside the host cavity. Not only the nature of the guest plays an important role. The host is also changing its properties upon encapsulation. All the cryptophanes investigated here can exchange rapidly between many conformers. These conformers have different–sized cavities. Quantum chemical optimization of the structure of the conformers makes volume estimation possible. Not only the cavity volumes, but also the quantum-chemically obtained energies and the calculated chemical shifts of the carbon–13 atoms can be helpful to follow the changes of the host upon complex formation. The host cannot be considered as a rigid entity. Analysis of variable temperature proton and carbon-13 spectra shows that the encapsulation can be considered as a mixture of conformational selection and induced fit. The structures of the formed complexes are further investigated by means of two-dimensional nuclear Overhauser spectroscopy (NOESY). The complex formation, its kinetics and thermodynamics are found to be a complicated function of structure elements of the host, the cavity size and the guest size and properties.At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 4: Accepted. Paper 5: Manuscript.
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Poudel, Pramod Prasad. "NOVEL AROMATIC ION–PAIRS: SYNERGY BETWEEN ELECTROSTATICS AND Π-FACE AROMATIC INTERACTIONS." UKnowledge, 2012. http://uknowledge.uky.edu/chemistry_etds/4.
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This dissertation focuses on the design and study of charged aromatic molecules where weak π-π interactions synergize with electrostatic interactions to enhance the overall interaction between aromatic moieties. Each chapter investigates some aspect of this hypothetical synergy between electrostatics and π-face aromatic cohesion.
The first chapter unveiled the importance of electrostatics in the intramolecular stacking of flexible aromatic molecular templates 1-2Br and 2a. While our previous studies found dicationic molecular template 1-2Br to have intramolecular π-stacking between electron poor pyridinium and electron rich xylylene moieties, no such stacking interaction was observed in the neutral analog 2a.
Chapter two systematically explored the stacking pattern of electron poor aromatics in the form of oxygen- and / or nitrogen- substituted triangulenium cations, [1(NR)3]+ and [1(O)3(OH)3]+. As indicated in the chemical literature, triazatriangulenium cations [1(NR)3]+ with N- ethyl (and longer alkyl chains) chains were found to pack as face-to-face dimers. This study found the formation of columnar, face-to-face, n-meric association between aromatic cations in the structures with decreased steric interactions of the side chains in the stacking planes ([1(NMe)3]+ and [1(O)3(OH)3]+). Similar iso-structural triangulene based aromatic anions, (2)- and (3)2- didn’t indicate any facial interactions in the solid states.
The possible synergy between unit charge electrostatics and π-face aromatic interactions was explored in aromatic ion pairs 1•2 of triangulene based aromatic cations and aromatic anions. This charge-assisted π-π stacking seems to be the novel way of getting strong π-system interactions where the strongest non-covalent force and the weakest non-covalent force: ionic bonding and π-stacking respectively synergize together. The π-π interaction between ionic aromatics in the solid state was investigated by means of single crystal x-ray diffraction and powder x-ray diffraction (PXRD). The interaction in the solution state was examined by UV-Vis spectroscopy, electrospray ionization mass spectroscopy (ESI-MS) and electrochemical studies. Studies found that optimal synergy was possible only in the ion pairs with no steric interactions of alkyl (or aryl) side chains in the stacking planes (1(O)3•2 & 1(NMe)3•2) and the interaction was found to be comparable with the strongest radical-assisted π-stacking described in the chemical literature.
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Jämbeck, Joakim P. M. "Computer Simulations of Heterogenous Biomembranes." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101297.
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Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated. A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems. A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs. In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted. The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.
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Daggag, Dalia. "Computational Study on Binding of Naturally Occurring Aromatic and Cyclic Amino Acids with Graphene." DigitalCommons@Robert W. Woodruff Library, Atlanta University Center, 2019. http://digitalcommons.auctr.edu/cauetds/203.
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The knowledge on the conformations of amino acids is essential to understand the biochemical behaviors and physical properties of proteins. Comprehensive computational study is focused to understand the conformational landscape of three aromatic amino acids (AAAs): tryptophan, tyrosine, and phenylalanine. Three different density functionals (B3LYP, M06-2X and wB97X-D) were used with two basis sets of 6-31G(d) and 6-31+G(d,p) for geometry optimizations of the conformers of AAAs followed by the vibrational frequencies. The goal was to identify the right choice of density functional theory (DFT) level for conformational analysis of amino acids by comparing the computational data against the available experimental results. Calculated infrared (IR) frequency values indicated that wB97X-D/6-31+G(d,p) level is less favorable than other DFT levels in case of O-H and N-H stretching frequencies for the conformers of AAAs. The C=O stretching frequencies at different computational levels were in good agreement with the experimental results.
Interactions of AAAs (tryptophan, tyrosine, and phenylalanine) and two cyclic amino acids (histidine and proline) individually with two finite-sized graphene sheets (C62H20 and C186H36) were explored using M06-2X/6-31G(d) level. Computational investigations of the binding of amino acids with graphene provide knowledge for designing of new graphene-based biological/biocompatible materials. Selected conformers for each amino acid with different orientations on the surface of graphene were examined. The purpose of computational study on graphene-amino acids interactions was to identify the preferred conformer of amino acid to bind on graphene as well as to find the influence of amino acid binding on the band gap of graphene. Different conformers of AAAs generally prefer parallel orientation through π-π interactions to bind with graphene. However, bent orientation is more preferred over parallel to bind on the surface of graphene in case of conformer having relative energy approximately equal to 5 kcal/mol for all three AAAs. Histidine generally exhibits higher binding affinity than proline to form complex with graphene. The binding energies in the aqueous medium were slightly lower than those obtained in the gas phase with some exceptions. The adsorption of amino acids did not affect the band gap of graphene.
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Buch, Mundó Ignasi 1984. "Investigation of protein-ligand interactions using high-throughput all-atom molecular dynamics simulations." Doctoral thesis, Universitat Pompeu Fabra, 2012. http://hdl.handle.net/10803/101407.
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Investigation of protein-ligand interactions has been a long-standing application for molecular dynamics (MD) simulations given its importance to drug design. However, relevant timescales for biomolecular motions are orders of magnitude longer than the commonly accessed simulation times. Adequate sampling of biomolecular phase-space has therefore been a major challenge in computational modeling that has limited its applicability. The primary objective for this thesis has been the brute-force simulation of costly protein-ligand binding modeling experiments on a large computing infrastructure. We have built and developed GPUGRID: a peta-scale distributed computing infrastructure for high-throughput MD simulations. We have used GPUGRID for the calculation of protein-ligand binding free energies as well as for the reconstruction of binding processes through unguided ligand binding simulations. The promising results presented herein, may have set the grounds for future applications of high-throughput MD simulations to drug discovery programs.
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Delandar, Arash Hosseinzadeh. "Modeling defect structure evolution in spent nuclear fuel container materials." Doctoral thesis, KTH, Materialteknologi, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-206175.
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Materials intended for disposal of spent nuclear fuel require a particular combination of physical and chemical properties. The driving forces and mechanisms underlying the material’s behavior must be scientifically understood in order to enable modeling at the relevant time- and length-scales. The processes that determine the mechanical behavior of copper canisters and iron inserts, as well as the evolution of their mechanical properties, are strongly dependent on the properties of various defects in the bulk copper and iron alloys. The first part of the present thesis deals with precipitation in the cast iron insert. A nodular cast iron insert will be used as the inner container of the spent nuclear fuel. Precipitation is investigated by computing effective interaction energies for point defect pairs (solute–solute and vacancy–solute) in bcc iron using first-principles calculations. The main considered impurities in the iron matrix include 3sp (Si, P, S) and 3d (Cr, Mn, Ni, Cu) solute elements. By computing interaction energies possibility of formation of different second phase particles such as late blooming phases (LBPs) in the cast iron insert is evaluated. The second part is devoted to the fundamentals of dislocations and their role in plastic deformation of metals. Deformation of single-crystal copper under high strain rates is simulated by employing dislocation dynamics (DD) method to examine the effect of strain rate on mechanical properties as well as dislocation microstructure development. Creep deformation of copper canister at low temperatures is studied. The copper canister will be used in the long-term storage of spent nuclear fuel as the outer shell of the waste package to provide corrosion protection. A glide rate is derived based on the assumption that at low temperatures it is controlled by the climb rate of jogs on the dislocations. Using DD simulation creep deformation of copper at low temperatures is modeled by taking glide but not climb into account. Moreover, effective stresses acting on dislocations are computed using the data extracted from DD simulations.QC 20170428
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Roux, Raphaël. "Étude probabiliste de systèmes de particules en interaction : applications à la simulation moléculaire." Phd thesis, Université Paris-Est, 2010. http://tel.archives-ouvertes.fr/tel-00597479.
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Ce travail présente quelques résultats sur les systèmes de particules en interaction pour l'interprétation probabiliste des équations aux dérivées partielles, avec des applications à des questions de dynamique moléculaire et de chimie quantique. On présente notamment une méthode particulaire permettant d'analyser le processus de la force biaisante adaptative, utilisé en dynamique moléculaire pour le calcul de différences d'énergies libres. On étudie également la sensibilité de dynamiques stochastiques par rapport à un paramètre, en vue du calcul des forces dans l'approximation de Born-Oppenheimer pour rechercher l'état quantique fondamental de molécules. Enfin, on présente un schéma numérique basé sur un système de particules pour résoudre des lois de conservation scalaires, avec un terme de diffusion anormale se traduisant par une dynamique de sauts sur les particules
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Remmert, Sarah M. "Reduced dimensionality quantum dynamics of chemical reactions." Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:7f96405f-105c-4ca3-9b8a-06f77d84606a.
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In this thesis a reduced dimensionality quantum scattering model is applied to the study of polyatomic reactions of type X + CH4 <--> XH + CH3. Two dimensional quantum scattering of the symmetric hydrogen exchange reaction CH3+CH4 <--> CH4+CH3 is performed on an 18-parameter double-Morse analytical function derived from ab initio calculations at the CCSD(T)/cc-pVTZ//MP2/cc-pVTZ level of theory. Spectator mode motion is approximately treated via inclusion of curvilinear or rectilinear projected zero-point energies in the potential surface. The close-coupled equations are solved using R-matrix propagation. The state-to-state probabilities and integral and differential cross sections show the reaction to be primarily vibrationally adiabatic and backwards scattered. Quantum properties such as heavy-light-heavy oscillating reactivity and resonance features significantly influence the reaction dynamics. Deuterium substitution at the primary site is the dominant kinetic isotope effect. Thermal rate constants are in excellent agreement with experiment. The method is also applied to the study of electronically nonadiabatic transitions in the CH3 + HCl <--> CH4 + Cl(2PJ) reaction. Electrovibrational basis sets are used to construct the close-coupled equations, which are solved via Rmatrix propagation using a system of three potential energy surfaces coupled by spin-orbit interaction. Ground and excited electronic surfaces are developed using a 29-parameter double-Morse function with ab initio data at the CCSD(T)/ccpV( Q+d)Z-dk//MP2/cc-pV(T+d)Z-dk level of theory, and with basis set extrapolated data, both corrected via curvilinear projected spectator zero-point energies. Coupling surfaces are developed by fitting MCSCF/cc-pV(T+d)Z-dk ab initio spin orbit constants to 8-parameter functions. Scattering calculations are performed for the ground adiabatic and coupled surface models, and reaction probabilities, thermal rate constants and integral and differential cross sections are presented. Thermal rate constants on the basis set extrapolated surface are in excellent agreement with experiment. Characterisation of electronically nonadiabatic nonreactive and reactive transitions indicate the close correlation between vibrational excitation and nonadiabatic transition. A model for comparing the nonadiabatic cross section branching ratio to experiment is discussed.
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Zhang, Jiajing. "Insight into biomolecular structure, interaction and energetics from modeling and simulation." 2011. http://hdl.handle.net/2152/20672.
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A central goal of computational biophysics and biochemistry is to understand the behavior, interactions, and reactions of molecules, and to interpret and facilitate experimental design. The objective of this thesis research is to use the molecular modeling and simulation techniques to advance our understanding of principles in molecular structure properties, recognition and interaction at the atomic level. First, a physical molecular mechanics model is built to study the conformational properties of depsipeptide, which shows potential for engineered protein mimetics with controllable structure and function. We explore the possible kinase-substrate binding modes and the likelihood of an [alpha]-helix docking interaction within a kinase active site. Finally, efficient physical models based on a polarizable potential function are developed to describe the structural properties and calculate protein-ligand binding affinities accurately for both trypsin and matrix metalloproteinase.text
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Chen, Shih-Yuan, and 陳仕元. "Molecular Dynamics Study and Binding Free Energy Calculation on Recognition and Interaction Between Antibiotics and Oligonucleotides: (I) Mithramycin and DNA (II) Aminoglycosides and Ribosomal RNA A-Site." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/87189327231034454761.
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博士國立清華大學
分子醫學研究所
98
Molecular dynamics (MD) simulations allow detail analysis of structural dynamics of atomic–level phenomena such as binding recognition fundamental in Biology field. Binding interaction involved between (bio) –molecules can be evaluated by binding free energy calculation base on the law of thermodynamics. Conformational flexibility essential for investigating dynamic property can be estimated by calculating conformational entropy such as principal components analysis. Combination with these techniques can provide reasonable explanations for atomic–level phenomena that are difficult to explain on the basis of static models alone. Here we present the results of a series of conventional MD simulations on recognition and interaction between (I) a mithramycin dimer and a DNA duplex, (II) several aminoglycoside antibiotics and an oligonucleotide corresponding to rRNA A–site. Both kinds of antibiotics consist of a core structure where several sugar ring substitutions at different carbon positions. In part I of the study, we successfully built the dynamics model corresponding to the experimental structure and binding affinity, discussed the binding interaction, and found the cooperativity between this GC–specific DNA binding antibiotic and a decanucleotide duplex of two GC binding sites to be in an anticooperative manner. Following the MD protocol and modification of the force field parameters for this sugar–linked antibiotic, in part II of the study, we compared the binding recognition and hydration patterns between several aminoglycoside antibiotics and a RNA duplex corresponding to the aminoacyl–tRNA decoding site (A–site) of the 16S rRNA on the 30S subunit which is a crucial component of the bacterial translational machinery. We have built several dynamic models with reasonable binding free energies showing good linear correlation with the experimental data. The hydration sites around the U1406·U1495 pair in the A–site were analyzed to distinguish tightly bound water molecules from fast–exchanging ones which has been suggested to be useful for rational drug design. We found that the hydration sites with long residence time identified between ring III of two 4,6–disubstituted antibiotics (tobramycin and kanamycin A) and phosphate oxygen atoms of G1405/U1406 may be worthy of further exploration for rational design of this kind.
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Yang, Tianyi. "Free energy calculations of biopolymeric systems at cellular interface." 2009. http://hdl.handle.net/2152/7477.
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Cells interact with both tethered and motile ligands in their extra-cellular environment, which mediates, initiates and regulates a series of cellular functions, such as cell adhesion, migration, morphology, proliferation, apoptosis, bi-directional signal transduction, tissue homeostasis, wound healing among others. A fundamental understanding of the thermodynamics of receptor-mediated cell interaction is necessary not only from the aspect of physiology, but also for bioengineering applications, e.g. drug discovery, tissue engineering and biomaterial fabrication. Our models on free energy calculations of receptor mediated cell-matrix interactions supplement computational endeavors based on continuum mechanics. By incorporating conformational, entropic, solvation, steric effect, implicit and explicit interactions of receptors and extra-cellular ligand molecules, we can predict free energy, chemical equilibrium constant of binding, spatial and conformational distributions of biopolymers, adhesion force as functions of a set of key variables, e.g. surface coverage of receptor, interaction distance between cell and substrate, specific binding energy, implicit interaction strength, constraint in ligand’s conformation, size of motile nano-ligand, aggregation of receptors, sliding velocity relative to fluid. Our work has improved understanding of phenomena in cell-matrix interactions at both cellular and the molecular scales.text
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Xu, Fang. "Resonance-energy-transfer-based fluorescence imaging and free energy perturbation calculation." Thesis, 2018. https://doi.org/10.7916/D8PP0HKZ.
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This thesis focuses on an important aspect of protein functionality – protein-protein interactions (PPI). Three physical chemistry techniques for or derived from protein-protein interaction investigation are discussed. First, in Chapter 2, we demonstrate a new fluorescent imaging technique that creates high-order nonlinear signals by harnessing the frustrated fluorescence resonance energy transfer (FRET) – energy transfer between certain proteins close in proximity which is commonly used in PPI studies. In Chapter 3, we combine fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET), two most commonly used approaches to monitor protein-protein interactions in vivo, to create a novel hybrid strategy, bioluminescence assisted switching and fluorescence imaging (BASFI), which integrates the advantages of FRET and BRET. We demonstrate BASFI with Dronpa-RLuc8 fusion constructs and drug-inducible intermolecular FKBP-FRB protein-protein interactions in live cells with high sensitivity, resolution, and specificity. Finally, in Chapter 4, we propose a systematic free energy perturbation (FEP) protocol to computationally calculate the binding affinities between proteins. We demonstrate our protocol with the gp120 envelope glycoprotein of HIV-1 and three broadly neutralizing antibodies (bNAbs) of the VRC01 class and analyze antibody residues’ contributions to the binding which further provides insights for antibody design.
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Robin, Abel. "Trajectory and channeling effects in the scattering of ions off a metal surface - Probing the electronic density corrugation at a surface by grazing axial ion channeling." Doctoral thesis, 2003. https://repositorium.ub.uni-osnabrueck.de/handle/urn:nbn:de:gbv:700-2003112519.
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The presented work investigates planar and axial channeling effects in ion-surface collisions. Therefore, energy loss and charge state distributions depending on the crystalline surface direction are recorded and analyzed. Several additional scattering parameters, like the primary energy, the outgoing charge state, the scattering angle, and the angle of incidence are varied. Multi-peak structures in the energy spectra are observed under axial channeling conditions and attributed to different trajectory classes. Using combined trajectory and inelastic energy loss calculations we are able to unambiguously assign the different peaks in the energy spectra to the different types of trajectories found in the calculations. By this, we investigate the electronic density corrugation at different metal surfaces. Die vorliegende Arbeit untersucht den Einfluß von axialem und planarem Channeling auf den Energieverlust von oberflächengestreuten Ionen. Es werden Energieverlustspektren und Ladungsverteilungen in Abhängigkeit der Parameter Primärenergie, gestreuter Ladungszustand, Streuwinkel, Einfallswinkel und der azimuthalen Ausrichtung der Oberfläche gemessen. Im Fall von axialem Channeling beobachten wir in den Energiespektren eine Multi-Peak Struktur. Diese läßt sich auf unterschiedliche Teilchentrajektorien zurückführen. Zusammen mit theoretischen Berechnungen des inelastischen Energieverlustes kann eine eindeutige Zuordnung zwischen dem gemessenen Energieverlust und der dazugehörigen Trajektorienart gemacht werden. Diese Technik erlaubt es uns, die elektronische Dichtekorrugation an Oberflächen zu studieren.