Dr. Bernardi is an Assistant Professor of Biophysics at the Department of Physics at Auburn University. Before joining Auburn's faculty, Dr. Bernardi was a Postdoc (2012-2017), and then a Research Scientist (2017-2020), at the Beckman Institute at the University of Illinois. Dr. Bernardi is co-Investigator of the NIH Center for Macromolecular Modeling and Visualization, which is known worldwide for the development of NAMD and VMD software. Dr. Bernardi main research interest is on protein mechanics, and how protein complexes behave under mechanical load. Such problem is very important in many areas of biomedicine, including bacterial adhesion during infection, viruses interaction with human proteins, and enzymatic activity in the gut microbiome.

Awards: Casimiro Montenegro Filho Thesis Award (2010), NSF Career Award (2022). 

Rafael C. Bernardi

Assistant Professor of Physics


Diego E. B. Gomes

Diego holds a PhD in Biophysics from the Universidade Federal do Rio de Janeiro (Brazil). He current working on developing QwikFold, a VMD interface for AI-based structural biology software. QwikFold will be integrated to a new version of QwikMD, which is also under development by Dr. Gomes. Besides that, he is working on mechanical properties of nanobodies, proteins that are under development for diagnosing and fighting cancer. 

Priscila S. F. C. Gomes

Priscila holds a dual-PhD in Biophysics from the École Normale Supérieure de Cachan (France) and the Universidade Federal do Rio de Janeiro (Brazil). Her main research interest is on the use of bioinformatics and molecular dynamics tools to investigate bacteria and virus adhesion. Dr. Gomes has recently contributed to understanding how mechanical properties of the COVID spike protein has evolved since the SARS-CoV-1 outbreak in early 2000s. 

Marcelo C. R. Melo

Dr. Melo holds a PhD in Biophysics from the University of Illinois at Urbana-Champaign. His main research interest is on applying artificial intelligence (AI) tools to analyze molecular dynamics trajectories. Dr. Melo is currently using these tools to investigate amino acid residues that are key players in the stabilization of the COVID spike interaction with human proteins.

Graduate Students

Raissa Lima
Raissa S. L. Rosa
Computational Biology (FIOCRUZ)

Raissa has a B.S. in Biomedical Sciences. She is investigating the mechanical properties of proteins that mediate the interaction between Trypanosoma cruzi and their human host. She received a prestigious CAPES fellowship to perform her PhD research at Auburn University. 

Bruno Ribeiro
Bruno H. L. Ribeiro

Bruno has a B.A. in Physics. He is interested in quantum mechanical calculations of mechanoactive proteins.  

Undergraduate Students

Meredith Forrester
Biomedical Sciences

Ms. Forrester is investigating how proteins from staph bacteria interacts with the human proteins.

Maggie Pace
Biomedical Sciences

Ms. Pace is using molecular dynamics to investigate mechanical properties of proteins from staph bacteria.

Toby Sizemore

Mr. Sizemore is investigating mechanical properties of proteins involved in Duchenne Muscular Dystrophy.

NIH Center
Computational Biophysics Group

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

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