Advanced Computational Methods for Macromolecular Modeling and Structure Determination

Simple item page
dc.contributor.advisorMa, Jianpengen_US
dc.contributor.committeeMemberNordlander, Peter J.en_US
dc.contributor.committeeMemberKiang, Ching-Hwaen_US
dc.contributor.committeeMemberRaphael, Robert M.en_US
dc.creatorZhang, Chongen_US
dc.date.accessioned2014-10-17T16:12:11Zen_US
dc.date.available2014-10-17T16:12:11Zen_US
dc.date.created2013-12en_US
dc.date.issued2013-12-05en_US
dc.date.submittedDecember 2013en_US
dc.date.updated2014-10-17T16:12:11Zen_US
dc.description.abstractAs volume and complexity of macromolecules increase, theories and algorithms that deal with structure determination at low X-ray resolution are of particular importance. With limited diffraction data in hand, experimentalists rely on advanced computational tools to extract and utilize useful information, seeking to determinate a three dimensional model that best fits the experiment data. Success of further studies on the property and function of a specific molecule - the key to practical applications - is therefore heavily dependent on the validity and accuracy of the solved structure. In this thesis I propose Deformable Complex Network (DCN) and introduce Normal Mode Analysis (NMA), which are designed to model the average coordinates of atoms and associated fluctuations, respectively. Their applications on structure determination target two major branches ? the positional refinement and temperature factor refinement. I demonstrate their remarkable performance in structure improvements based on several criteria, such as the free R value, overfitting effect and Ramachandran Statistics, with tests carried out across a broad range of real systems for generality and consistency.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationZhang, Chong. "Advanced Computational Methods for Macromolecular Modeling and Structure Determination." (2013) Diss., Rice University. <a href="https://hdl.handle.net/1911/77596">https://hdl.handle.net/1911/77596</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/77596en_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.subjectDeformable complex networken_US
dc.subjectX-ray refinementen_US
dc.subjectHigh-performance computingen_US
dc.subjectStructure determinationen_US
dc.subjectMacromolecular modelingen_US
dc.subjectAlgorithmsen_US
dc.subjectLow resolutionen_US
dc.titleAdvanced Computational Methods for Macromolecular Modeling and Structure Determinationen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentApplied Physicsen_US
thesis.degree.disciplineNatural Sciencesen_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
No Thumbnail Available
Name:
Chong revised abstract PhD_Thesis_Final (1).pdf
Size:
15.42 MB
Format:
Adobe Portable Document Format
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
935 B
Format:
Plain Text
Description:
Download
Collections
Rice University Theses and Dissertations
Center for Research Computing