Molecular simulation of biomaterials and biomolecules at the solid-liquid interface

Biomaterials and biomineralization have been successfully utilized in a broad variety of technical applications. Properties of natural biopolymers, such as the ability to control the nucleation, growth, and organization of crystals, have been extended to a much wider array of technologically applicable materials through combinatorial selection techniques. However, detailed mechanisms of peptide adsorption on inorganic surfaces have largely escaped characterization. This knowledge would open new routes for the rational design of nanostructures and composite biomaterials. The development of accurate and computationally efficient methods for the simulation of biopolymer-inorganic surface adsorption could provide a more detailed understanding of adsorption mechanisms. While simple models involving reduced solvent representations and polymer flexibility have found some success in limited applications, robust performance for systems of varying size and composition can generally be expected only through accurate inclusion of these key details. Fully atomistic representations of biopolymer and surface are necessary for detailed molecular recognition, while polymer flexibility is required to capture structural rearrangement and the resulting free energy contributions. Finally, electrostatic interactions between the adsorbing biopolymer and inorganic surface, as well as interactions of the polymer and surface with the surrounding solvent environment will play a dominant role in the adsorption process, and an accurate representation of the solvated system is inherently necessary. Computational efficiency can be increased through the application of implicit solvent models, which replace the numerous solvent molecules with a continuum dielectric, and seek to capture the average effects of the statistical solvent environment. The Poisson-Boltzmann model represents the most rigorous treatment of implicit solvent.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Chemistry.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2008

Author dc:creator

• Kottmann, Stephen Thomas

Advisor dc:contributor.advisor

• Angela M. Belcher.

• Chemistry.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/43088

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/43088