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Showing 1 to 20 of 49 for “"QM/MM"”.
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Classical And Ab Initio Qm/mm Simulations Of Bacterial Enzymes
… calculations to ascertain the existence of a communication pathway between two subunits of GatCAB. Experimental and computational results obtained, suggest the existence of a communication pathway between the GatA and GatB subunits of H. pylori GatCAB. In Chapter 3, the snapshots sampled using …
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Thermal cis-trans isomerization of azobenzene studied by path sampling and QM/MM stochastic dynamics
… a quantum mechanical/molecular mechanics (QM/MM) description; and the isomerization process is tracked by analyzing complete dynamical pathways between stable states. The suitability of this description is validated by using two test systems, pure azo benzene and a derivative with electron …
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Direct QM/MM Simulations of the Excited State Dynamics of Retinal Protonated Schiff Base in Isolation and in Complex Environments
… is represented with an empirical force field (QM/MM). The potential energy surfaces and their couplings are determined "on the fly," i.e. simultaneously with the dynamic evolution. We compare our results in methanol and in protein environments (Rh, bR, and hR) to experimental results and find …
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Measuring the effects of reaction coordinate and electronic treatments in the QM/MM reaction dynamics of Trypanosoma cruzi trans-sialidase
… dynamics package. The resulting B3LYP/6-31G/CHARMM crossing trajectory provides a molecular orbital description of the glycosylation reaction. Direct investigation of the underlying potential energy functions for B3LYP/6-31G(d), B3LYP/6-31G and SCC-DFTB/MIO point to the minimal basis set as the …
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Cálculo de derivadas de la energía libre en disolución empleando un método quantum mechanichs/molecular mechanica (QM/MM) y la aproximación al campo medio
Se ha extendido el método ASEP/MD para permitir el cálculo teórico de diferencias de energía libre y la optimización tanto de estructuras estables como de estados de transición para sistemas en disolución. Se ha elaborado un programa informático y se ha aplicado a algunos sistemas de interés.
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The design and development of GPU accelerated algorithms for ab initio integrals and integral derivatives illustrated on ab initio quantum and hybrid QM/MM dynamics
… Units (GPUs) are highly parallel, programmable accelerators boasting high peak floating point performance. Over the last couple of years the use of GPUs for general purpose computing have revolutionized quantum chemistry. The computational bottleneck in an ab-initio quantum method is the …
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Imidazolio joninių skysčių struktūros ir BMR spektrų modeliavimas /
… molecural dynamics simulations and combined QM/MM methods, in comparison with experimental data. The parameters of the force field potential, which were taken from B. Doherty’s research article, were determined, and ionic liquids were modeled using ’’GaussView’’ software before running the …
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The development of hybrid quantum classical computational methods for carbohydrate and hypervalent phosphoric systems
… a hybrid quantum mechanics/molecular mechanics (QM/MM) dynamics framework. However, semi-empirical methods have been designed to provide accurate results for organic molecules, but often fail to treat hypervalent species accurately due to their use of an sp basis. Recently, significant …
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SEMICLASSICAL APPROACHES FOR RATE CONSTANT CALCULATIONS AND VIBRATIONAL SPECTROSCOPY
… cinetica chimica, viene sviluppato il programma FDACC per facilitare il calcolo delle costanti anarmoniche su architetture parallele, interfacciandosi con codici ab initio, permettendo così l'applicazione della teoria SCTST a livelli elevati di struttura elettronica e nello studio di sistemi …
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Beschreibung angeregter Molekülzustände in komplex strukturierter Umgebung durch einen effizienten, individuell selektierenden MRCI-Algorithmus gekoppelt an ein molekularmechanisches Kraftfeld
… by combined quantum and molecular mechanical (QM/MM) methods. The goal of this work is to extend such techniques to enable the description of photochemical reactions and to carry out case studies subsequently. In order to tackle the enormous computational demand due to the involvement of …
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Modeling cellular metabolism in multiple scales
… In order to identify essential residues for communication pathways and signaling elements in biomolecular complexes, we developed an evolution of the dynamical network analysis framework. The new implementation was applied to the leucine tRNA synthetase complexed with its cognate tRNA and …
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Computational Investigation of the Catalytic and Structural Roles of Metals in Metalloenzymes
… in metalloenzymes using quantum mechanics (QM), classical molecular mechanics (MM), and hybrid, multi-scale (QM/MM) atomistic simulations. To address the unique challenges in QM/MM simulations of metalloenzymes, we study the relative magnitude of configurational and QM-region sensitivity of …
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Computational approaches to fragment based screening
… improvement given the quality of current commercial docking programs (such as Glide use d here). This improvement is most apparent when the correct pose is known a priori, so that the extent of polarization is correctly modelled, and scoring is based on force - fields that do not scale the …
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Computational Studies Of Enzymatic Reactions And Inorganic Compounds
<p>Quantum mechanics (QM) calculations have been demonstrated to give very accurate results in studying a variety of chemical reactions. However, the current computing resources limits its use in large-size systems such as enzymes. Compared to QM, Molecular Mechanics (MM) have an advantage in …
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Berechnung molekularer Eigenschaften in komplexer Lösungsmittelumgebung
Quantenmechanische (QM) Grundzustandsrechnungen auf Basis der Dichtefunktionaltheorie (DFT) erlauben bei der derzeitigen Leistungsfähigkeit von Supercomputern die Molekulardynamik- Simulation (MD-Simulation) von molekularen Systemen mit bis zu 100 Atomen. Verwendet man nicht-lokale …
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Understanding the ATP hydrolysis mechanism in myosin using computer simulation techniques
… in myosin and of mechanical events that immediately follow hydrolysis. Three different possible reaction routes are investigated using combined quantum mechanical and molecular mechanical (QM/MM) reaction path simulations. To include solvent screening effects in the calculations, a new …
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Quantum Mechanical/molecular Mechanical Studies of F(1)-Atpase and a Plant Photoreceptor
… as photoactive elements. We have performed QM/MM simulations of the photocycle of a complete Phot-LOV1 domain from C. reinhardtii. We have investigated the electronic properties and structural changes that follow blue-light absorption. This permitted us to characterize the pathway for …
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Computational studies of the structure, dynamics, and catalysis of the hepatitis delta virus ribozyme
… Quantum mechanical/molecular mechanical (QM/MM) calculations were used to study the HDV ribozyme self-cleavage reaction and elucidate the role of the catalytic metal ion. The calculations suggested a concerted mechanism of the catalytic reaction in the presence of a divalent ion at the …
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Molecular Design and Mechanistic Characterization of Glycoside Hydrolases using Computational and Experimental Techniques
… (MD), Molecular Docking, Quantum Mechanics (QM) and hybrid Quantum Mechanics and Molecular Mechanics (QM/MM), along with several site-directed mutagenesis and in vitro assays have been applied to the study and design of the activity and stability of cellulases. Using molecular dynamics to …
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