Work in our lab involves using computer models to study biological systems at atomic resolution. This approach allows us to conduct “experiments” that would be very difficult or even impossible to do at the laboratory bench. The principal type of model we use is called an all-atom force field. “Force field” refers to the fact that the model assigns the forces in the system according to the positions of the atoms, and “all-atom” refers to the fact that every atom in a biological system is individually considered. A force field is a combination of a mathematical equation and parameters, describing properties like bond lengths or the attraction between atoms with opposite charge. The process of force field parameter development has been ongoing for several decades and has benefitted from the contributions of many scientists around the world. As a result, contemporary all-atom force fields provide accurate representation of the forces between atoms in diverse biological systems including proteins, DNA and RNA, lipids, and carbohydrates.
We use a variety of specialized software for doing simulations, analyzing the simulation data, and visualizing the three-dimensional structures of the biological molecules under study. Much of this software requires high-performance computing resources hundreds to thousands of times more powerful than everyday laptop computers.
We are grateful to the National Science Foundation, the National Institutes of Health, and the University of New England for their support of our research.