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Building knowledge at the interface of Biology, Chemistry, and Physics.
Nov 2023
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.
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Aug 2023
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.
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May 2023
In a groundbreaking study recently published in PNAS, scientists have made significant progress in understanding the mechanisms of reovirus attachment to host cells. The study sheds light on the intricate dynamics and cooperativity of reovirus interactions with host cell surfaces, providing a better understanding of the early binding stages crucial for infection.
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Jan 2023
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.
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Jan 2022
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.
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Jun 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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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.
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.
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.
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.
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