Group

Dr. Bernardi is an Associate 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

Associate Professor of Physics

Diego E. B. Gomes

Biophysics

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

Biophysics

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.

Raissa S. L. Rosa

Chemistry and Biochemistry

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 H. L. Ribeiro

Physics

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

Walter F. dos Santos Filho

Physics

Walter has a B.S. in Physics. He is interested in theory of force spectroscopy simulations.

Former Members:

Maggie Pace: worked on using molecular dynamics to investigate mechanical properties of proteins from staph bacteria. Obtained a Biomedical Sciences degree and left for UAB School of Dentistry.
Meredith Forrester: worked on investigating how proteins from staph bacteria interacts with the human proteins. Obtained a Biomedical Sciences degree and left for UAB School of Dentistry.
Toby Sizemore. worked on investigating mechanical properties of proteins involved in Duchenne Muscular Dystrophy. Obtained a Chemistry degree and left for Medical University of South Carolina.
Dr. Marcelo C. R. Melo. worked on applying network analysis and artificial intelligence (AI) tools to analyze molecular dynamics trajectories. Dr. Melo left the group in 2024 for a faculty position at Colorado State University.

Visitors:

Dr. Maria Fernanda Ribeiro Dias: Spring 2023 - visiting faculty from SEDU-ES, Brazil.
Gabriel Cathoud Pinheiro: Summer 2023 - visiting graduate student Universidade de Coimbra, Portugal.
William O. Soté: Fall 2024 - visiting graduate student from Universidade Federal de Uberlandia, Brazil.
Dr. Manuela Leal da Silva: Spring 2025 - visiting faculty from Universidade Federal do Rio de Janeiro, Brazil.
Suchandra Roy Acharyya. Summer 2025 - visiting graduate student from Technical University of Dortmund, Germany.