Computational Biophysics Group

News from our group

• Jun 2025 - We are in the cover of Biochemistry
  Published in ACS' Biochemistry, we built a 1.44‑million‑atom model of the Trypanosoma cruzi gp82:LAMP2 complex and ran microsecond‑scale simulations. Our computational network analysis mapped critical interactions—including novel contact regions and the stabilizing role of LAMP2’s transmembrane domain—revealing potential therapeutic targets to block Chagas disease invasion. Read More.
  
  
• Apr 2025 - Uncovering a Bacterial Pathway That Fuels Prostate Cancer
  In collaboration with Jason Ridlon's group at the University of Illinois, we used computational modeling to help identify microbial enzymes involved in a newly expanded pathway of androgen production by commensal bacteria. Published in Nature Microbiology, our work shows how bacterial steroid metabolism, through enzymes such as DesF and DesG, can impact prostate cancer cell growth and resistance to hormone therapies. Read More.
  
  
• Feb 2025 - VMD 2 Alpha Released at Biophysical Society Meeting
  The alpha version of VMD 2, the long-anticipated next generation of the popular molecular visualization software, was officially released during the 2025 Biophysical Society Meeting. This major update introduces a modernized interface and powerful new tools for analyzing molecular simulations. Together with the University of Illinois we have been working hard to make a new and modern VMD for the molecular biophysics community. Read More.
  
  
• Jan 2025 - Disulfide-Linked Viral Anchors and Cholesterol Dependence
  Now published in Nature Communications, we investigated how a membrane-binding peptide from the virus spike protein interacts with host membranes using AFM force spectroscopy and simulations. Our results show that the these peptides favors cholesterol-rich membranes and relies on a disulfide bridge for stability, suggesting new therapeutic strategies targeting viral entry. Read More.
  
  
• Dec 2024 - 62nd Computational Biophysics Workshop
  We hosted the 62nd Hands-On Computational Biophysics Workshop this winter, with participants from across the U.S. and instructors from the U.S. and France, all while enjoying the mild Alabama winter. Read More.
  
  
• Nov 2024 - Engineering Force Anisotropy via Anchor Point Design
  In a new article in ACS Nano, we showed that the mechanical stability of the PD-L1:Affibody complex can be tuned by changing the anchor point. Using experiments and simulations, we identified positions that greatly enhance force resistance, offering new strategies for designing stronger protein therapeutics. Read More.
  
  
• Oct 2024 - Destination STEM
  Over 900 K–12 students from across East Alabama joined the Destination STEM event, where we had fun—and a bit of trouble—organizing waves of students into our 60-person inflatable dome. With a new session every 4 to 5 minutes, it was a nonstop day of exploring molecular biophysics. Read More.
  
  
• Sept 2024 - Biophysics Dome at the GameDay Physics
  The Biophysics Dome was a huge success at the tailgate event organized by the Physics Department. Over 600 Auburn football fans experienced a planetarium-style show that offered a deep dive into molecular biophysics and showcased the power of VMD. Read More.
  
  
• Aug 2024 - Expanding Network Analysis for Epitope Mapping
  Published in JACS, we combined AI and dynamic network analysis to accurately determine the binding epitope of the PD-L1:Affibody complex, revealing interactions missed by AlphaFold alone. Read More.
  
  
• Jun 2024 - 61st Computational Biophysics Workshop
  For the second time e hosted a hands-on molecular simulation workshop with participants from across the U.S. and instructors from both the U.S. and France. Read More.
  
  
• May 2024 - Promoting Biophysics in the Mid-South
  Our group co-organized the 2024 Mid-South Biophysics Symposium, an event born out of the Mississippi Regional Biophysics Consortium. The symposium aims to strengthen collaboration and increase visibility of biophysics across Mississippi, Alabama, Arkansas, Louisiana, and Tennessee. The event brought together faculty and trainees, especially early career investigators, to build a vibrant biophysics community in the region. Read More.
  
  
• Mar 2024 - Evolution of COVID-19 virulence revealed
  Richard Feynman famously stated, "Everything that living things do can be understood in terms of the jigglings and wigglings of atoms." This week, Nature Nanotechnology features a study that sheds new light on the evolution of the coronavirus and its variants of concern by analyzing the behavior of atoms in the proteins at the interface between the virus and humans. Read More.
  
  
• Aug 2023 - 60th Computational Biophysics Workshop
  In July, as many enjoyed the hot weather at Alabama's gulf coast beaches, in the Leach Science Center, Auburn University's Department of Physics hosted an engaging scientific event. For the first time since 2016, the southern USA was home to the “Hands-On Workshop on Computational Biophysics” with Auburn University, for the first time, as its esteemed host. Read More.
  
  
• Jan 2023 - The Molecular Secrets of Bacterial Infections
  Dr. Bernardi and his team have achieved a breakthrough in combating antibiotic-resistant bacteria. Their work, featured in the cover of JACS, uses simulations to show how Staph bacteria bind strongly to human cells—a key factor in hospital infections. This discovery may opens new avenues for developing antimicrobial treatments. Read More.
  
  
• Jan 2022 - Dr. Bernardi receives the NSF Career Award
  Dr. Bernardi has won the NSF's prestigious early-career award for his "In Silico Single-Molecule Force Spectroscopy" project at Auburn University. The project aims to study mechanoactive proteins in bacteria, to understand their role in infections. It will also develop immersive technologies for visualizing these proteins and introduce the “Immersive Biophysics on the Road” program to bring biophysics education to underrepresented Alabama communities. Read More.
  
  
• Jun 2021 - Using GPUs in the fight against COVID-19
  Employing state-of-the-art molecular simulations combined with artificial intelligence tools, Dr. Rafael C. Bernardi turns millions of calculations in the study of biological molecules into visual graphics. Read More.