Towards Adaptive Resolution Modeling of Biomolecular Systems in their Environment

Simple item page
dc.contributor.advisorClementi, Ceciliaen_US
dc.contributor.committeeMemberPasquali, Matteoen_US
dc.contributor.committeeMemberScuseria, Gustavo E.en_US
dc.creatorLambeth, Bradleyen_US
dc.date.accessioned2012-09-06T03:58:54Zen_US
dc.date.accessioned2012-09-06T03:59:06Zen_US
dc.date.available2012-09-06T03:58:54Zen_US
dc.date.available2012-09-06T03:59:06Zen_US
dc.date.created2012-05en_US
dc.date.issued2012-09-05en_US
dc.date.submittedMay 2012en_US
dc.date.updated2012-09-06T03:59:06Zen_US
dc.description.abstractWater plays a critical role in the function and structure of biological systems. Current techniques to study biologically relevant events that span many length and time scales are limited by the prohibitive computational cost of including accurate effects from the aqueous environment. The aim of this work is to expand the reach of current molecular dynamics techniques by reducing the computational cost for achieving an accurate description of water and its effects on biomolecular systems. This work builds from the assumption that the “local” effect of water (e.g. the local orientational preferences and hydrogen bonding) can be effectively modelled considering only the atomistic detail in a very limited region. A recent adaptive resolution simulation technique (AdResS) has been developed to practically apply this idea; in this work it will be extended to systems of simple hydrophobic solutes to determine a characteristic length for which thermodynamic, structural, and dynamic properties are preserved near the solute. This characteristic length can then be used for simulation of biomolecular systems, specifically those involving protein dynamics in water. Before this can be done, current coarse grain models must be adapted to couple with a coarse grain model of water. This thesis is organized in to five chapters. The first will give an overview of water, and the current methodologies used to simulate water in biological systems. The second chapter will describe the AdResS technique and its application to simple test systems. The third chapter will show that this method can be used to accurately describe hydrophobic solutes in water. The fourth chapter describes the use of coarse grain models as a starting point for targeted search with all-atom models. The final chapter will describe attempts to couple a coarse grain model of a protein with a single-site model for water, and it’s implications for future multi-resolution studies.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationLambeth, Bradley. "Towards Adaptive Resolution Modeling of Biomolecular Systems in their Environment." (2012) Diss., Rice University. <a href="https://hdl.handle.net/1911/64645">https://hdl.handle.net/1911/64645</a>.en_US
dc.identifier.slug123456789/ETD-2012-05-100en_US
dc.identifier.urihttps://hdl.handle.net/1911/64645en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectAdaptive resolutionen_US
dc.subjectProtein foldingen_US
dc.subjectCoarse grainen_US
dc.subjectMultiscaleen_US
dc.subjectEnergy landscapeen_US
dc.subjectWateren_US
dc.subjectGromacsen_US
dc.titleTowards Adaptive Resolution Modeling of Biomolecular Systems in their Environmenten_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentChemical and Biomolecular Engineeringen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
LAMBETH-THESIS.pdf
Size:
13.73 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.61 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Rice University Theses and Dissertations