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 “"molecular dynamics flexible fitting"”.
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Structural analyses of the ribosome by hybrid approach
The ribosome is the molecular machine which reads and translates genetic information into proteins in all living cells. Lack of an atomic-resolution structure of the ribosome in its actual functional states prevents our understanding of the ribosome. A hybrid approach overcomes the challenge by …
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Computational study of the structure and function of membrane transport proteins
… of H+ and the subsequent effect on the substrate dynamics is studied. Furthermore, I explored the role of lipids in regulating the conformational equilibrium in XylE. In combination with HD-MS experiments we show that the nature of lipid protein interactions determined the stability of a …
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Investigating the mechanisms of protein synthesis using multi-resolution structural data
The ribosome is a complex, dynamic molecular machine responsible for protein synthesis in all cells according to the genetic information. Recent breakthroughs in ribosome crystallography culminated with the 2009 Nobel Prize in Chemistry. Concomitantly, advances in cryo-electron microscopy (cryo-EM) …
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Methods for increasing model accuracy and simulation time scales of biological processes with molecular dynamics
… methodologies to extend the capabilities of molecular dynamics simulations in one way or another. In the first chapter, molecular dynamics simulations and the central role they play in the field of structural biology is introduced to give the reader some background on the common basis of the …
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Multiscale Modeling of Biomolecular Complexes
Macromolecular complexes carry out cellular processes that span many different length and time scales. Central to their function are both large-scale conformational changes, and atomic-atomic scale events. Molecular dynamics (MD) simulations are well suited to study the structural dynamics of such …
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Molecular modeling and simulation of bacterial chemosensory arrays
… modeling and simulation to investigate the molecular structure and function of the bacterial chemosensory array. A brief overview of each chapter follows. Chapter 1 provides an introduction to the systems-level features of chemotaxis in the model organism Escherichia coli as well as an …
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Investigating translational control of the ribosome using molecular dynamics simulations
The ribosome is one of the most basic cellular machines and is ubiquitous in all living cells, responsible for the translation of genes into functional proteins. The central task of the ribosome is to promote peptide-bond transfer reaction by precisely aligning substrates of protein synthesis in …