Degree Type

Honors Capstone Project

Date of Submission

Spring 5-1-2014

Capstone Advisor

Radhakrishna Sureshkumar, Dept. Chair & Professor

Honors Reader

Shikha Nangia, Assistant Professor

Capstone Major

Biomedical and Chemical Engineering

Capstone College

Engineering and Computer Science

Audio/Visual Component


Capstone Prize Winner


Won Capstone Funding


Honors Categories

Sciences and Engineering

Subject Categories

Chemical Engineering | Other Chemical Engineering


Bacterial biofilms are a major cause of persistent infections and diseases with known antibiotic and host immune defense resistances. The interaction of signaling factors, namely small cytokines, with the biofilm and host cell is considered vital to the survival of bacterial biofilms. In this study, molecular dynamics (MD) simulations are performed using coarse-grained biomolecular systems to provide significant insight into medical therapeutic advancements in treating persistent and chronic infections. Specifically, MD simulations of the interaction between signaling factors tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) with a model biofilm matrix with detailed description were performed. Additional simulations were used to study TNF-α interaction with dextran polymer chains of varying monomer length. In each study, resultant potential of mean force curves were analyzed to quantify the energy associated with translocation of the signaling factors through the extracellular polymeric substances, as well as to highlight the effect of chain degradation on this translocation process. In some instances, polymer intramatrix interactions were studied to better understand the translocation energy findings. The translocation of TNF-α across a lipid bilayer was also performed using MD simulation techniques, and the resultant potential of mean force curve highlights the energy barrier associated with this process. Qualitative and quantitative assessment of membrane damage was also performed.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.



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