Applied & Computational Mathematics seminar: Topological Data Analysis of Molecular Dynamics Simulations of Monoclonal Antibodies

Speaker: Melinda Kleczynski, National Institute of Standards and Technology (NIST)

Title:  Topological Data Analysis of Molecular Dynamics Simulations of Monoclonal Antibodies

Abstract:  A variety of medical treatments depend on artificially produced monoclonal antibodies. Measuring monoclonal antibody structure is very important due to their widespread use in biomedical applications. Similar amino acid sequences can generate biomolecules which adopt different shapes in 3-dimensional space. Molecular dynamics simulations are a valuable tool for revealing potential arrangements of the atoms in these proteins. By quantifying the structure present in each frame of a simulation, we can search for variations in the configuration of the molecule. Topological data analysis detects and quantifies structural features which are not easily measured by classical data analysis techniques. We will discuss our results from using topological data analysis to explore molecular dynamics simulations of monoclonal antibodies, with a focus on the NIST monoclonal antibody (NISTmAb) reference material. The talk will be suitable for participants without prior experience with topological data analysis.

This is joint work with Christina Bergonzo (Biomolecular Measurement Division, Material Measurement Laboratory) and Anthony Kearsley (Applied and Computational Mathematics Division, Information Technology Laboratory)

Melinda Kleczynski is a National Institute of Standards and Technology (NIST) National Research Council (NRC) Postdoctoral Associate in Gaithersburg, Maryland, where she is a member of the Mathematical Analysis and Modeling Group in the Applied and Computational Mathematics Division. Her current work focuses on using techniques from applied topology to analyze the structure of biomolecules and to improve detection of neural networks compromised by Trojan attacks.

Time:  Friday, November 15 – 1:30pm – 2:30pm
Place:  Exploratory Hall, room 4106 and Zoom