Computational Biophysics Group

Building knowledge at the interface of Biology, Chemistry, and Physics.

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News Highlights

NSF Career Award

January 2022

Dr. Bernardi receives the most prestigious early-career award of the National Science Foundation (NSF). The project "In Silico Single-Molecule Force Spectroscopy" was selected among thousands of projects that are submitted yearly to the NSF. In this project, the Computational Biophysics Group at Auburn University will investigate the intriguing behavior of proteins that are mechanoactive, that is, that react differently depending on the forces applied on them. Not only that, the group will also work on developing computational tools that make it possible to study these proteins with atomic detail. Particularly, mechanoactive proteins that are found in the surface of both good and bad bacteria will be investigated to elucidate how they become extremally resilient to shear forces and allow infections to take place within our bodies. Additionally, new immersive technologies will be developed to observe these proteins under shear-force load, powering the “Immersive Biophysics on the Road” program, where tools and knowledge developed in this project will be taken to areas in Alabama that are historically underrepresented in STEM. An inflatable projection dome will then be used to teach the molecular mechanisms of life.
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Using GPUs in the fight against COVID-19

June 2021

Employing state-of-the-art molecular simulations combined with artificial intelligence tools, Prof. Rafael C. Bernardi turns millions of calculations in the study of biological molecules into visual graphics.
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Recent Publications

Read more about our recent contributions
January, 2022
Mechanical Properties of
Coronavirus Proteins

Comparing the mechanical properties of SARS-CoV-1 spike protein with that of SARS-CoV-2 spike protein, we were able to determine the mutations that were key in the elevated mechanical stability of the proteins of the COVID-19 outbreak compared to that of the early 2000s outbreak. 

October, 2020
Network Analysis

Dynamical Network Analysis can be used to identify important residues and information pathways within molecular complexes. The package described in this work allows users to analyze MD trajectories and produce high-quality biomolecular images.

September, 2020
Protein Mechanostability
in the Gut Microbiome

Bacterial colonization of the human intestine requires firm adhesion of bacteria to insoluble substrates under hydrodynamic flow. Here we report the molecular mechanism behind an ultrastable protein complex responsible for resisting shear forces in the human gut.

August, 2020
Molecular Dynamics with NAMD 3

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. In this new reference paper for NAMD, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance.

NIH Center
Computational Biophysics Group

Leach Science Center
380 Duncan Dr. 
Room 3180 / 3182
Auburn, AL

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