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Interactions of Biomolecules with Nanomaterials: Insight from First Principles and Molecular Dynamics Methods

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Friday, December 2, 2016, 3 pm

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A key fundamental aspect in biophysical chemistry is the cooperative effect of molecular structure and function, which correlates to protein design, biological organization and cellular morphology. Proteins determine the cellular existence, biological functions and mediate the interaction with ligands and functional nanomaterials to form highly ordered nano assemblies. The diversity in structure and function exhibited by proteins has stimulated advancements in applications at the nanoscale as smart building blocks for self-assembled systems, drug delivery and biomedical research. 

            In the areas of human health, the diversified applications of nanotechnology depend on fundamental understanding of the mechanistic pathways through which nanomaterials affect functionality of biological molecules. In a complementary way to experiments, theory can help predict and understand the physicochemical processes that span to higher length and time scales in terms of binding strength, specificity, and thermodynamics/kinetics. In this context, we discuss approaches in achieving reliable descriptions of the physical, chemical and biophysical properties of protein conjugated nanomaterials using methods ranging from quantum mechanics to atomistic molecular dynamics (MD). For example, the potential application of carbon based prototype nanomaterials in tuberculosis (TB) and cancer chemotherapy has been envisaged using molecular docking and MD simulation with target binding proteins. The challenge lies in the task of deciphering the electronic structure of nanomaterials, while considering the bio-recognition and reactivity at the interface of the conjugated complexes.

Nabanita Saikia received her PhD at Tezpur University, India in 2014 in Theoretical Chemistry and Computational Drug Delivery.  She then worked as a postdoctoral fellow at the Indian Institute of Technology (IIT) Bombay, University of Akron and University of Colorado Boulder.  In April 2016, she joined Prof. Pandey’s research group at Michigan Tech to initiate the work on “Self-assembly of noncanonical DNA bases on 2D materials, and biomolecular recognition at the interface.” She taught courses in chemistry at IIT Bombay and University of Colorado Boulder, and is currently teaching University Chemistry-II recitation at the Department of Chemistry, Michigan Tech.  Her research interests include simulation of functional nanomaterials at the Bio-Nano interface, computational biophysics, large scale simulation of protein-nanomaterial interaction for therapeutic and drug delivery applications.

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