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All-atom molecular dynamic simulations for peptoids: a procedure and implementation
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TitleInfo
Title
All-atom molecular dynamic simulations for peptoids: a procedure and implementation
Name
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Shovlin
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Joseph
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Joseph Shovlin
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author
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Dutt
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Meenakshi
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Meenakshi Dutt
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Advisory Committee
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chair
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Dutt
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Meenakshi
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Meenakshi Dutt
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Advisory Committee
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member
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Celik
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Fuat Celik
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Advisory Committee
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member
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Olson
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Wilma
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Wilma Olson
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Advisory Committee
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member
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Rutgers University
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School of Graduate Studies
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theses
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2022
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2022-01
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English
Abstract
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Peptoids (poly-N-substituted glycines) are a special class of synthetic biopolymer. Peptoids have the same backbone structure as peptides, but have sidechains attached to backbone Nitrogens as opposed to α-carbons. This conformational change gives peptoids useful properties that make them candidates for practical application, but work is needed to determine how the sidechain composition and sidechain sequence of a peptoid infleunces its overall behavior.
Molecular Dynamics (MD) simulations are a promising tool that can be used to learn how a peptoid’s structure determines its behavior. MD simulations can be used to determine how a peptoid’s secondary structure influences its three-dimensional structure in solvated environments, as well as a peptoid’s ability to aggregate with other peptoids in solvated environments. The ability to understand aggregation behavior of peptoid’s has large implications for understanding the practical application of peptoids. Therefore, there is significant interest surrounding the development of MD simulations to simulate the aggregation behavior of peptoids.
This work aims to develop a specific process for performing all-atom MD simulations on peptoids, and use the developed approach to explore the three-dimensional conformation and aggregation behavior of a 12-monomer peptoid unit. This work demonstrates how changes and additions can be made to already existing simulation forcefields to adapt them to peptoid simulations. This work will outline specifically how to set up a peptoid MD simulation by making specific changes to commonly used forcefields. After developing the process for creating a peptoid MD simulation, this work will use the process to simulate the molecular dynamics of a 12-monomer peptoid. It will show that the peptoid attains a helical three-dimensional conformation, and that the peptoid forms aggregates in solvated environments.
Molecular Dynamics (MD) simulations are a promising tool that can be used to learn how a peptoid’s structure determines its behavior. MD simulations can be used to determine how a peptoid’s secondary structure influences its three-dimensional structure in solvated environments, as well as a peptoid’s ability to aggregate with other peptoids in solvated environments. The ability to understand aggregation behavior of peptoid’s has large implications for understanding the practical application of peptoids. Therefore, there is significant interest surrounding the development of MD simulations to simulate the aggregation behavior of peptoids.
This work aims to develop a specific process for performing all-atom MD simulations on peptoids, and use the developed approach to explore the three-dimensional conformation and aggregation behavior of a 12-monomer peptoid unit. This work demonstrates how changes and additions can be made to already existing simulation forcefields to adapt them to peptoid simulations. This work will outline specifically how to set up a peptoid MD simulation by making specific changes to commonly used forcefields. After developing the process for creating a peptoid MD simulation, this work will use the process to simulate the molecular dynamics of a 12-monomer peptoid. It will show that the peptoid attains a helical three-dimensional conformation, and that the peptoid forms aggregates in solvated environments.
Subject
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Topic
Chemical engineering
Subject
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Topic
Biopolymers
Subject
(authority = LCSH)
Topic
Molecular dynamics -- Computer simulation
Subject
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Topic
Peptoids
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Rutgers University Electronic Theses and Dissertations
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http://dissertations.umi.com/gsnb.rutgers:11773
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39 pages : illustrations
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M.S.
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Includes bibliographical references
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School of Graduate Studies Electronic Theses and Dissertations
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rucore10001600001
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Identifier
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doi:10.7282/t3-gvea-wb03
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Rights
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The author owns the copyright to this work.
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Shovlin
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Joseph
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Permission or license
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2022-02-04T17:41:25
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Joseph Shovlin
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Rutgers University. School of Graduate Studies
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Author Agreement License
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I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
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2022-02-04
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2023-02-03
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after February 3, 2023
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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2022-01-20T19:48:00
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2022-01-20T19:48:00
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