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Bridging the scales in biomaterials: role of biophysics from atom-scale to nano-scale
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Title
Bridging the scales in biomaterials: role of biophysics from atom-scale to nano-scale
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Banerjee
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Akash
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Akash Banerjee
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author
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Dutt
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Meenakshi
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Advisory Committee
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chair
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Olson
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Wilma Dr.
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Wilma Dr. Olson
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Advisory Committee
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member
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Jha
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(type = given)
Shantenu Dr.
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Shantenu Dr. Jha
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Advisory Committee
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(authority = local)
member
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Chen
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Chun-long Dr.
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Chun-long Dr. Chen
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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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2023
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2023-05
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English
Abstract
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Biomolecules such as peptides and lipids can self-assemble to form large, ordered structures. These ordered structures form biomaterials that have applications in areas such as biomedicine and electronics. The functionality of these biomaterials can be tuned by modifying the sequence of the biomolecules. To enable the design of such tunable materials with good precision, we need to characterize the biophysics underlying the self- assembly process. At small spatiotemporal scales, the local structure of a biomolecule (for example, the secondary structure of a peptide) governs the intermolecular interactions. At larger spatiotemporal scales, the overall features of the ordered structure (for example, shape, stability, and porosity) govern the functionality of the biomaterial. In this work, a set of computational tools are built to address the self-assembly of biomolecules at multiple scales. First, spherical nanostructures, also known as vesicles, are studied at large spatiotemporal scales. These vesicles encompass polyamidoamine dendron-grafted amphiphiles (PDAs) and dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipids. The overall stability of the vesicles is determined as a function of concentration and generation (degree of branching) of PDAs. Next, the local interactions between lipid-like peptides (V6K2, V:Valine and K:Lysine) are studied at small spatiotemporal scales. A model is developed to specifically capture the local structure and chemical details of these peptides. In this way, the organization of a single peptide in a small-sized aggregate is resolved accurately. Furthermore, the model resolves the assembly of these peptides into intermediate-sized aggregates that are in qualitative agreement with experiments. This demonstrates that the technique can resolve the structure (small-scale) and assembly (intermediate-scale) of peptides. Finally, a computational workflow is developed to automate the implementation of these computational tools. This will enable the extension of these tools to different chemical systems, sizes and environmental conditions.
Subject
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Computer science
Subject
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Topic
Biophysics
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Topic
Computational chemistry
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Topic
Coarse-grained molecular dynamics
Subject
(authority = local)
Topic
Lipids
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Topic
Peptides
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Topic
Peptoids
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(authority = local)
Topic
Workflows
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Rutgers University Electronic Theses and Dissertations
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http://dissertations.umi.com/gsnb.rutgers:12363
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171 pages
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Ph.D.
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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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doi:10.7282/t3-7037-zj18
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Rights
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The author owns the copyright to this work.
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Name
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Banerjee
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Akash
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Permission or license
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2023-04-27T15:49:38
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Akash Banerjee
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Rutgers University. School of Graduate Studies
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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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2023-04-27
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2024-04-27
Type
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Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after April 27, 2024.
Copyright
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Copyright protected
Availability
Status
Open
Reason
Permission or license
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