Global ETD Search
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Showing 1 to 8 of 8 for “"transition path sampling"”.
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Transition path sampling in organometallic catalysis: Overcoming the rare event problem in ab initio molecular dynamics
… typically limited to identifying the minima and transition states on the potential energy surface (PES) of a reaction and calculating free energies using the harmonic approximation. Ab initio molecular dynamics (AIMD) is an obvious strategy to address these issues. Within these simulations, the …
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Computing the energetic component of the charge-transfer symmetry factor
… and quantitatively predicts the location of the transition state and activation parameters. The knowledge of the reaction coordinate is exploited in two ways: to compute activation parameters from umbrella integration (UI) and Marcus theory (MT) based simulations assuming linear response and to …
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The Dynamics of Dehydrogenases - A Phase Space Odyssey
… isotope effects from first principles, using transition path sampling and centroid molecular dynamics. This method allows for the calculation of kinetic isotope effects without the assumptions necessitated by transition state theory or free energy perturbation methods. It was found that this …
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Artificial intelligence and protein engineering : information theoretical approaches to modeling enzymatic catalysis
… static molecular structures. Using computational sampling techniques, especially rare-event sampling methods like Transition Path Sampling, we can now generate large datasets of reactive and non-reactive enzyme trajectories. However, due to the high dimensionality of phase space, as well as the …
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Large scale simulation and analysis to understand enzymatic chemical mechanisms
… function of up to 6 dimensions, along a reaction path determined through a combination of knowledge from physical organic chemistry, local energetic optimizations, and experimental information. The activation barriers were converted to reaction rates and simulated with mass action kinetics. The …
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Ensemble methods in computational protein and ligand design : applications to the Fc[gamma] immunoglobulin, HIV-1 protease, and ketol-acid reductoisomerase systems
… KARI mutants. Our analysis reveals that this transition-state theory based approach is effective at reducing the enthalpy of activation, but also increases entropic activation penalties that ultimately overpower the enthalpic gains. A dynamic analysis of these KARI variants is also presented, …
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Thermal cis-trans isomerization of azobenzene studied by path sampling and QM/MM stochastic dynamics
… incorporated. Fast switching can be induced via transitions to excited electronic states and fine-tuned by a large number of different substituents at the phenyl rings. But a rational design of tailor-made azo groups also requires control of their stability in the dark, the half-lifetime of the …
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Competitive Nucleation in Nanoclusters
… the different stable phases are calculated using transition state theory and compared with the rates obtained from the mean first passage time and survival probability methods. Transition state theory is shown to predict the rates to the different structures under various conditions when the …