Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 7 of 7 for “"Polarizable Force field"”.
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Fast Polarizable Force Field Computation in Biomolecular Simulations
Polarizable force fields are considered to be the single most significant development in the next-generation force fields used in biomolecular simulations. The self-consistent computation of induced atomic dipoles in a polarizable force field is expensive due to the cost of solving a large dense …
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Structural Dynamics and Electrostatic Properties of the VEGF and PIM-1 Oncogenic Promoter G-Quadruplexes from Polarizable Molecular Dynamics Simulations
… on two oncogenic GQ structures with the Drude polarizable force field to gain crucial insights into structural and electrostatic properties contributing to overall GQ stability and potential small-molecule binding sites. In addition to these simulations, we also subjected these structures to …
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Polarizable Simulations of the bcl-2 DNA G-Quadruplex and FMRP RNA G-Quadruplex:Duplex Junction Binding Protein
… molecular dynamics simulations using the Drude polarizable force field (FF) to gain insight into factors contributing to the stability of two GQs. One is the bcl-2 promoter region GQ, which is implicated in several types of cancer including B-cell lymphoma, and the second is the sc1 RNA GQ, …
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Development of polarizable force fields for proteins
This work describes the development of the polarizable force field for proteins based on classical mechanics, electronic structure theory and the combined quantum mechanical molecular mechanical method. In the first model, the classical force field is augmented with the explicit polarization energy …
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Investigating the Electrostatic Properties and Dynamics of Amyloidogenic Proteins with Polarizable Molecular Dynamics Simulations
… gaining greater insight into the stabilizing forces and initial unfolding events is crucial to our understanding of these amyloidogenic diseases. This work uses molecular dynamics (MD) simulations to study the secondary, tertiary, and quaternary structure of Aβ, tau, and IAPP. Specifically, …
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Computer-Aided Drug Design of G-quadruplex Structures: Harnessing Polarization for Rational Drug Design
… is the use of the classical Drude oscillator polarizable force field model to more accurately describe GQ dynamics, ion interactions, and ligand binding ener- getics. Through an in-depth characterization of the HIV-1 LTR-III GQ, we reveal how local electric fields and base dipole moments …
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Modeling of Electrostatic Interactions inside Human Voltage-Gated Sodium Channels
… molecular level. Here, we calculated electric fields inside the channel pore of Nav1.5, 1.6, and 1.7 to gain insights into the components that control the selectivity and permeation of Nav channels. We found that water inside the channel pore aligns vertically in response to the electric fields …