Advanced search options

Advanced Search Options 🞨

Browse by author name (“Author name starts with…”).

Find ETDs with:

in
/  
in
/  
in
/  
in

Written in Published in Earliest date Latest date

Sorted by

Results per page:

Sorted by: relevance · author · university · dateNew search

Dept: Biomedical Engineering  Dates: Last 2 Years

You searched for subject:(Molecular Dynamics). Showing records 1 – 2 of 2 total matches.

Search Limiters

Last 2 Years | English Only

No search limiters apply to these results.

▼ Search Limiters


Rutgers University

1. Schmidt, Kassandra L., 1992-. Computational studies of peptide self-assembly.

Degree: MS, Biomedical Engineering, 2019, Rutgers University

Research into novel biological materials for use in biomedical applications is guided by the formation of supramolecular structures which have properties resultant from the characteristics of the compositional molecules. Peptides are commonly utilized in biological material development as their properties are widely variable and highly controllable due to the sequence-specific properties of amino acids. Self-assembling peptides are of specific interest due to their spontaneous aggregation into organized morphologies with predictable characteristics based upon their constituent amino acids. Though novel peptide materials have traditionally been researched through physical experimentation, the development of Molecular Dynamics has allowed for comparable computational studies of peptide systems. In this work, coarse-grained Molecular Dynamics simulations are selected to study self-assembling peptides from two classes, aromatic and aliphatic, as these peptides have been experimentally validated to spontaneously assemble themselves into nanostructures. Computational models representative of the peptides’ chemistry are created for aromatic peptides FF (phenylalanine-phenylalanine) and FNF (phenylalanine-asparagine-phenylalanine) and aliphatic peptides A6K (alanine-alanine-alanine-alanine-alanine-alanine-lysine), V6K (valine-valine-valine-valine-valine-valine-lysine), and V6K2 (valine-valine-valine-valine-valine-valine-lysine-lysine). In the aromatic studies, the effect of varying total peptide concentrations and relative tripeptide concentrations on the morphology of the assembled structures is characterized. In the aliphatic studies, the peptide alignment in stable aggregates and nanostructures is determined. The results demonstrate the viability of these peptide systems to form stable, usable nanostructures suitable for inclusion in biological applications that require the respective specific properties of the in-scope peptides. Advisors/Committee Members: Dutt, Meenakshi (chair), Olson, Wilma (internal member), Nanda, Vikas (internal member), School of Graduate Studies.

Subjects/Keywords: Molecular Dynamics; Peptides  – Synthesis

Record DetailsSimilar RecordsGoogle PlusoneFacebookTwitterCiteULikeMendeleyreddit

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Schmidt, Kassandra L., 1. (2019). Computational studies of peptide self-assembly. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/61944/

Chicago Manual of Style (16th Edition):

Schmidt, Kassandra L., 1992-. “Computational studies of peptide self-assembly.” 2019. Masters Thesis, Rutgers University. Accessed August 10, 2020. https://rucore.libraries.rutgers.edu/rutgers-lib/61944/.

MLA Handbook (7th Edition):

Schmidt, Kassandra L., 1992-. “Computational studies of peptide self-assembly.” 2019. Web. 10 Aug 2020.

Vancouver:

Schmidt, Kassandra L. 1. Computational studies of peptide self-assembly. [Internet] [Masters thesis]. Rutgers University; 2019. [cited 2020 Aug 10]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61944/.

Council of Science Editors:

Schmidt, Kassandra L. 1. Computational studies of peptide self-assembly. [Masters Thesis]. Rutgers University; 2019. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/61944/


Washington University in St. Louis

2. Xu, Jiajing. KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences.

Degree: PhD, Biomedical Engineering, 2018, Washington University in St. Louis

Dynamic conformational changes of ion channel proteins during activation gating determine their function as carriers of current. The relationship between these molecular movements and channel function over the physiological timescale of the action potential (AP) has not been fully established due to limitations of existing techniques. We constructed a library of possible cardiac IKs protein conformations and applied a combination of protein segmentation and energy linearization to study this relationship computationally. Simulations reproduced the effects of the beta-subunit (KCNE1) on the alpha-subunit (KCNQ1) dynamics and function, observed in experiments. Mechanistically, KCNE1 increased the probability of “visiting” conducting pore conformations on activation trajectories, thereby increasing IKs current. KCNE1 slowed IKs activation by impeding the voltage sensor (VS) movement and reducing its coupling to pore opening. Conformational changes along activation trajectories determined that the S4-S5 linker (S4S5L) plays an important role in these modulatory effects by KCNE1. Integration of these molecular structure-based IKs dynamics into a model of human cardiac ventricular myocyte, revealed that KCNQ1-KCNE1 interaction is essential for normal AP repolarization. Advisors/Committee Members: Yoram Rudy, Jianmin Cui, Vitaly Klyachko, George Van Hare, Richard Schuessler.

Subjects/Keywords: Cardiac action potential; Ion channels; Molecular simulation; Protein dynamics; Protein structure-function; Biomedical Engineering and Bioengineering; Chemistry; Molecular Biology; Other Chemistry

Record DetailsSimilar RecordsGoogle PlusoneFacebookTwitterCiteULikeMendeleyreddit

APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Xu, J. (2018). KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences. (Doctoral Dissertation). Washington University in St. Louis. Retrieved from https://openscholarship.wustl.edu/eng_etds/388

Chicago Manual of Style (16th Edition):

Xu, Jiajing. “KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences.” 2018. Doctoral Dissertation, Washington University in St. Louis. Accessed August 10, 2020. https://openscholarship.wustl.edu/eng_etds/388.

MLA Handbook (7th Edition):

Xu, Jiajing. “KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences.” 2018. Web. 10 Aug 2020.

Vancouver:

Xu J. KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences. [Internet] [Doctoral dissertation]. Washington University in St. Louis; 2018. [cited 2020 Aug 10]. Available from: https://openscholarship.wustl.edu/eng_etds/388.

Council of Science Editors:

Xu J. KCNQ1/KCNE1 Interaction in the Cardiac IKs Channel and its Physiological Consequences. [Doctoral Dissertation]. Washington University in St. Louis; 2018. Available from: https://openscholarship.wustl.edu/eng_etds/388

.