Understanding Self-assembly in Solution and at Interfaces Using All-atom Molecular Dynamics Simulations and Enhanced Sampling Methods

Released on by Arushi Prakash
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  • Understanding Self-assembly in Solution and at Interfaces Using All-atom Molecular Dynamics Simulations and Enhanced Sampling Methods Book Detail

  • Author : Arushi Prakash
  • Release Date : 2018
  • Publisher :
  • Genre :
  • Pages : 234
  • ISBN 13 :
  • File Size : 40,40 MB
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Understanding Self-assembly in Solution and at Interfaces Using All-atom Molecular Dynamics Simulations and Enhanced Sampling Methods by Arushi Prakash PDF Summary

Book Description: Proteins and biopolymers self-assemble to form nanostructures in solution or at interfaces. Notable examples include, the formation of plaque during Alzheimer’s disease, and the formation of protein-templates for biomineralization. Even though these assembly processes are well-studied, they remain poorly understood. The focus of this dissertation is to investigate early-stage assembly processes, including adsorption of particles on surfaces, and oligomer formation using classical molecular dynamics and enhanced sampling methods (like metadynamics and umbrella sampling). As these systems are explored, improved protocols for enhanced sampling of protein-adsorption simulations are developed to tackle the roles of ions in simulations, and to incorporate experimental data into the sampling using Bayesian inference. Further, a new sampling method is developed to make these enhanced sampling simulations more efficient.

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