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Polarizable Force Field Development, and Applications to Conformational Sampling and Free Energy Calculation
Başlık:
Polarizable Force Field Development, and Applications to Conformational Sampling and Free Energy Calculation
Yazar:
Wang, Zhi, author. (orcid)0000-0001-7851-4843
ISBN:
9780355981650
Yazar Ek Girişi:
Fiziksel Tanımlama:
1 electronic resource (166 pages)
Genel Not:
Source: Dissertation Abstracts International, Volume: 79-10(E), Section: B.
Advisors: Jay W. Ponder Committee members: Gregory R. Bowman; Richard Mabbs; Garland R. Marshall; Lee G. Sobotka.
Özet:
The parameters of monovalent ions for the AMOEBA force field were revised. High level quantum mechanics results, relative solvation free energies of monovalent ions, lattice energies and lattice constants of salt crystals were used to calibrate the parameters. The revised parameters were validated against the quantum optimized structures and energies of ion-water dimers and ion-water clusters, and against thermodynamic properties of salt solutions at different concentrations measured in experiments, e.g. mean ionic activity coefficients, self-diffusion coefficients of water. In the simulations the sodium ion is found to qualitatively differ from larger cations in aqueous solution. Direct ionic interactions are predominant for potassium and larger cations, while sodium salt solutions at similar concentrations are dominated by ion-water interactions.
A novel stochastic isokinetic integrator proposed by Tuckerman, et al. was extended and generalized in three respects. First, the Nose-Hoover chain algorithm was implemented in the original integrator. Next, the functional form of the isokinetic constraint was generalized so that it was no longer restricted to multiples of kBT. Finally, the isokinetic constraint was extended to be able to constrain the kinetic energies of multi-dimensional velocities, instead of only one degree of freedom as in its original form.
An application of conformational sampling with molecular dynamics method, predictions of the binding free energies of cucurbit[8]uril and ligands in the SAMPL6 challenge, is presented. A great improvement in the prediction accuracy was made by more accurate torsional parameters of cucurbit[8]uril and by revised protocols annihilating the intra-molecular van der Waals and key torsions in the ligands.
Corresponding methods for all portions of this work have been implemented in the Tinker software package, some of which are also available in the Tinker-OpenMM library.
Notlar:
School code: 0252
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Yer Numarası | Demirbaş Numarası | Shelf Location | Lokasyon / Statüsü / İade Tarihi |
---|---|---|---|
XX(681388.1) | 681388-1001 | Proquest E-Tez Koleksiyonu | Arıyor... |
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