Welcome to the Knotts Simulation Group
In recent decades, advancements in technology have reduced the length scales over which biological molecules are manipulated. The drive towards the nanoscale comes in part because the behavior of biological molecules often occurs on the single-molecule or two-molecule level. Individual enzymes catalyze reactions in the body without regard to the presence of the same type of enzyme nearby. Hybridization of DNA is two-molecule event, and proteins fold into distinct three-dimensional structures based upon their own amino-acid sequence.

While the bulk behavior of these processes can be measured experimentally, such techniques do not probe the fundamental biophysics involved. Molecular simulation provides an adept tool with which to investigate the behavior of large molecules at the single-molecule level, and with atomic-level resolution, that currently cannot be achieved experimentally. Our research group makes use of molecular dynamics, Monte Carlo, and other advanced simulation techniques. We employ both atomistic and coarse-grain models to investigate the thermodynamics of biological and chemical systems. We have a specific focus on the behavior of such molecules in inhomogeneous environments such as on surfaces.

See our research page for the specific areas of our research.