Simulation of a Complete Model of a Cellular Membrane

Emad Tajkhorshid, University of Illinois at Urbana-Champaign

Usage Details

John Stone, Emad Tajkhorshid, Po-Chao Wen, Paween Mahinthichaichan, Yuhang Wang, Rezvan Shahoei, Mrinal Shekhar, Noah Trebesch, Muyun Lihan, Melanie Muller, Tao Jiang, Zhiyu Zhao, Moeen Meigooni, Eric Shinn, Kin Lam, Shashank Pant, Nandan Haloi, Chang Sun, Sepehr Dehghanighahnaviyeh, Anda Trifan, Aaron Chan, Karanpal Kapoor, Jimmy Do, Giuseppe Leonardo Licari, Julio Maia, Ali Rasouli, Mariano Spivak, Chun Kit Chan

Computational biology research has been critical in achieving a molecular level understanding of protein, nucleic acid, and lipid dynamics and function. Most research in this field has been limited to single protein characterization due to limits in computational power and analytical methods. However, to truly understand the behavior and mechanics of biological systems, proteins need to be studied in the broader context of a cellular environment that allows for the complex molecular interactions between the diverse components of cell. This project aims to spearhead a new generation of computational biology research that seeks insight from molecular dynamics (MD) simulations that encompass cellular-scale processes with atomistic detail. The immensely complex nature of a cell belies the elementary physics that govern it and by using MD simulations, a rigorous connection can be made between the underlying physical laws and the emergent phenomena they generate. By pioneering new large molecular simulations, we can begin to form insight into how biological mesoscopic phenomena may be quantified, such as vesicle-budding/-fusion, lipid-composition dependent membrane curvature effects, and curvature-dependent protein behavior. Due the massive nature of these bleeding-edge simulations, they can only be performed on computational platforms such as Blue Waters which meet the requisite capacity and infrastructure specifications.