Rafael Bernardi
Department of Physics
Assistant Professor

Research Areas:

Office: Leach Science Center 2114

Address: 380 Duncan Drive
Auburn, AL 36849

Phone: 334-844-4393

Email: rcbernardi@auburn.edu


Universidade Federal do Rio de Janeiro, Brazil - Ph.D. Biophysics
Centro Brasileiro de Pesquisas Físicas, Brazil - M.Sc. Physics
Universidade Estadual de Londrina, Brazil - B.S. Physics

Professional Employment
Assistant Professor, Auburn University
Research Scientist, University of Illinois at Urbana-Champaign
Postdoctoral Research Associate, University of Illinois at Urbana Champaign
Junior Researcher, Brazilian National Institute of Standards (INMETRO)

Honors and Awards
NSF Career Award
Casimiro Montenegro Filho National Thesis Award – Bureau of Strategic Affair of the Brazilian Presidency

Professional Activities
Peer Reviewer: ACS Catalysis, ACS Central Science, BioData Mining, Biomolecules, Biophysical Journal, Biotechnology and Bioengineering, Biotechnology for Biofuels, Computation, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Current Proteomics, Energies, International Journal of Bioinformatics Research and Applications, International Journal of Molecular Sciences, Journal of Bacteriology, Journal of Chemical Information and Modeling, Journal of Chemical Theory and Computation, Journal of Computational Physics, Journal of Molecular Modeling, Journal of Structural Biology, Langmuir, Materials, Molecular Biotechnology, Molecules, Nano Letters, Nanomaterials, Nature Communications, Pharmaceutics, PLOS One, Proceedings of the National Academy of Sciences, Protein Science, RSC Advances, Scientific Reports, Soft Matter, The Journal of Physical Chemistry
Member: Biophysical Society, American Chemical Society, Brazilian Society of Physics

Research and Teaching Interests

My research focus 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, I am interested in software development for computational structural biology, particularly in the use of hybrid QM/MM methods, and machine learning tools for analysis of molecular simulations.
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, my 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, my group develops computational tools for Molecular Dynamics, both at the classical and the quantum level. Additionally, my group is part of the NIH Center for Macromolecular Modeling and Bioinformatics, 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.

Selected Publications

  1. LF Milles, K Schulten, HE Gaub, RC Bernardi; Molecular mechanism of extreme mechanostability in a pathogen surface anchor; Science, 359 (6383), 1527-1533, 2018
  2. MCR Melo*, RC Bernardi*, T Rudack, M Scheurer, C Riplinger, JC Phillips, JDC Maia, GB Rocha, JV Ribeiro, JE Stone, F Neese, K Schulten, Z Luthey-Schulten; NAMD goes quantum: A new integrative suite for hybrid simulations; Nature Methods, 15 (5), 351-354, 2018
  3. RC Bernardi*, E Durner*, C Schoeler, KH Malinowska, BG Carvalho, EA Bayer, Z Luthey-Schulten, HE Gaub, MA Nash; Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy; Journal of the American Chemical Society, 141 (37), 14752-14763, 2019
  4. T Verdorfer, RC Bernardi, A Meinhold, W Ott, Z Luthey-Schulten, MA Nash, HE Gaub; Combining in Vitro and in Silico Single Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics; Journal of The American Chemical Society, 139 (49), 17841-17852, 2017 – Cover Article
  5. SM Sedlak*, LC Schendel*, HE Gaub, RC Bernardi; Streptavidin/biotin: tethering geometry defines unbinding mechanics; Science Advances, 6 (13), eaay5999, 2020
  6. C Schoeler*, RC Bernardi*, KH Malinowska, E Durner, W Ott; EA Bayer; K Schulten; MA Nash; HE Gaub; Mapping mechanical force propagation through biomolecular complexes; Nano Letters, 15 (11), 7370-7376, 2015 – Cover Article
  7. SM Sedlak*, LC Schendel*, MCR Melo, DA Pippig, Z Luthey-Schulten, HE Gaub, RC Bernardi‡; Direction Matters – Monovalent Streptavidin/Biotin Complex under Load; Nano Letters, 19 (6), 3415-3421, 2019 – Cover Article
  8. C Schoeler*, KH Malinowska*, RC Bernardi, LF Milles, MA Jobst, E Durner, W Ott, DB Fried, EA Bayer, K Schulten, HE Gaub, MA Nash; Ultrastable cellulosome-adhesion complex tightens under load; Nature Communications, 5, 5635, 2014
  9. Z Liu, H Liu, AM Vera, RC Bernardi, P Tinnefeld, MA Nash; High force catch bond mechanism of bacterial adhesion in the human gut; Nature Communications, 11, 4321, 2020
  10. JC Phillips, D Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, R Buch, G Fiorin, J Hénin, W Jiang, R McGreevy, MCR Melo, BK Radak, RD Skeel, A Singharoy, Y Wang, B Roux, A Aksimentiev, Z Luthey-Schulten, LV Kalé, K Schulten, C Chipot, E Tajkhorshid; Scalable Molecular Dynamics on CPU and GPU Architectures with NAMD; The Journal Chemical Physics, 153 (4), 44130, 2020

* Co-first author (equally contributing)           Corresponding Author

For full list of publication see Google Scholar.



 According to Google Scholar, my work has been cited over 2,000 times (as of 2021).


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Last updated: 02/17/2023