Presenter: Dr. Mohammad Hassan Khatami, University of Ontario Institute for Technology
Topic: Large Scale Atomistic Molecular Dynamics Simulations of PhytospherixTM Nanoparticles
PhytoSpherixTM is a dendritic biodegradable nanoparticle naturally found in sweet corn, produced by Mirexus Biotechnologies. The building blocks of this particle are simple glucose molecules, which form chains and branches, acting as energy storage units in plants. These properties, along with high water solubility and water absorbance make PhytoSpherix a great candidate for a variety of applications from additives in cosmetics to possible drug delivery particles. However, despite the extensive experimental studies, the detailed structure of this particle is unknown yet. Thus, the aim of this project is to get insights into the properties of this particle to reveal possible new applications for PhytoSpherix, with the help of molecular dynamics simulations.
First, a simple glucose-chain structure is used as a base to construct PhytoSpherix. Then, the particle is solvated with explicit water molecules and simulated using the GROMACS MD package. After the production run, the final carbohydrate structure is fed as an input to our home-made C++ code to grow the particle. Here, the glucose units are added to the ends of each chain and/or start new branches, based on our algorithm. Next, we solvate the grown particle and simulate the system. This process resumes until the full-sized particle (~22,000 glucose units) is built. We have implemented the first few cycles and built up to ~1000 glucose units particle, where the simulation box contains almost a million atoms. Our estimations indicate that the final sets of simulations will have roughly 10 million atoms.
About Dr. Khatami
Received a BSc in Physics from Zanjan University and a MSc in soft matter Physics at Institute for Advanced Studies in Basic Sciences (IASBS), both in Zanjan, Iran. Obtained a PhD in Physics from the Memorial University of Newfoundland, where he conducted Molecular Dynamics simulations of membrane-active proteins in lipid bilayers. Currently a Post-doctoral researcher under the supervision of Dr. Hendrick W. de Haan at University of Ontario Institute of Technology with focus on “Large Scale Atomistic Molecular Dynamics Simulations of PhytospherixTM Nanoparticles”.
© 2018 Compute Ontario