Computational Biophysics Group

About us

The focus of the Computational Biophysics Group at Auburn University lies on the study of mechanoactive proteins using computational biophysics/chemistry tools. Of note, mechanobiology is a vastly growing field, particularly due to the recent development of new experimental techniques, which have allowed us to better understand how cells sense and respond to mechanical stimuli, and, consequently, leverage this knowledge to develop new technologies for medical and industrial applications. Additionally, the group develops software for computational structural biology, particularly in the use of hybrid QM/MM methods, and machine learning tools for analysis of molecular simulations.
  
Mechanobiology
At the heart of many cellular processes, mechanoactive proteins are responsible for both converting mechanical cues into biochemical signals and converting these signals into force stroke. Through the employment and development of state-of-the-art computational tools, and in a collaborative effort with experimental labs, the Computational Biophysics Group explores how proteins sense and generate mechanical forces. Two of the main problems we investigate are: how bacterial adhesins are “activated” by force loads during infection; and how molecular motors produce force stroke from biochemical signals.
 
Computational Tools
To investigate biophysics problems at the atomic and subatomic level, the Computational Biophysics Group develops computational tools for Molecular Dynamics, both at the classical and the quantum level. Additionally, our group is part of the NIH Center for Macromolecular Modeling and Visualization, which is known worldwide for the development of both NAMD and VMD software. Particularly, we are on the main development team of VMD's QwikMD, a tool that simplifies the use of Molecular Dynamics tools, and the hybrid QM/MM implementation of NAMD.