Theory and simulation of amyloid aggregation process: sequence effects and defects

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dc.contributor.author Ghanati, Elaheh
dc.date.accessioned 2016-07-13T20:49:24Z
dc.date.available 2016-07-13T20:49:24Z
dc.date.issued 2016-08-01 en_US
dc.identifier.uri http://hdl.handle.net/2097/32816
dc.description.abstract In this work, we present a model for the kinetics of amyloid fibril aggregation. In the model we mapped the process of Hydrogen bond (H-bond) formation and breakage to a random-walk. we captured the effect of side chains using position dependent H-bonds free energies which allows us to calculated the residence time for different binding alignments with the fibril. The residence time can be compared to the diffusion-limited attachment rate to give net aggregation stability. This stability increases exponentially with increasing number of bonds or binding energy in homopolymer chains, however for chains with patterned sequences, the residence time shows strong effects of the binding alignment. Using the residence time for uniform structures combined with estimate of the diffusion rate, we modeled and simulated the kinetics of amyloid aggregation. Results of the simulations gives the bond energies and concentrations required for the onset of growth of aggregates. en_US
dc.description.sponsorship National Institute of Health, Kansas State University en_US
dc.language.iso en_US en_US
dc.publisher Kansas State University en
dc.subject Theory simulation en_US
dc.subject amyloid aggregation
dc.subject sequence effects
dc.title Theory and simulation of amyloid aggregation process: sequence effects and defects en_US
dc.type Thesis en_US
dc.description.degree Master of Science en_US
dc.description.level Masters en_US
dc.description.department Department of Physics en_US
dc.description.advisor Jeremy Schmit en_US
dc.date.published 2016 en_US
dc.date.graduationmonth August en_US


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