Computational Studies of Nanomaterials
F. Marty Ytreberg
Perhaps the best example of functional nano-machines are proteins. Proteins are responsible for nearly all functions performed in a cell, such as transport (right figure), creation and destruction (left figure) of materials. Using primarily computational techniques, the Ytreberg research group is interested in developing a fundamental understanding how proteins, and other nanomaterials, function.
Knowledge of binding affinities is vital to a fundamental understanding of any binding event. The binding could be between a protein and a ligand, a protein and a nanowire, or two proteins. In spite of the importance, these binding affinity computations remain one of the most challenging tasks in computational biophysics. An ongoing effort in the group is to develop novel methodologies capable of fast and accurate binding free energy difference calculation, and to apply state-of-the-art approaches to estimate binding affinities.
Nanomaterials, such as proteins are constantly in motion. Small-scale fluctuations are most likely, but occasionally large-scale conformational changes can occur. Unfortunately, atomically-detailed molecular simulation is limited to nanosecond to microsecond timescales, while large-scale changes typically happen on much longer timescales. Due to the time scale discrepancy, a valuable tool for simulating long time scales is to "coarse-grain." A project in the Ytreberg group is to develop and maintain coarse-grained software for rapid simulation of molecular systems.
