Austen Bernardi

Contact information
email: bernardi1@llnl.gov

 

 

Education/Experience

Ph.D., Chemical Engineering, University of California, Davis 2020

BSE, Chemical Engineering, University of Michigan, 2013

 

Research

My interests are in biophysics and computational chemistry.  I perform molecular dynamics simulations of lipid membrane systems.  I'm interested in the incorporation of simulation observables in drug discovery models and algorithms.

 

Publications

Bernardi, Austen, and Jessica MJ Swanson. "CycFlowDec: A Python module for decomposing flow networks using simple cycles." SoftwareX 14 (2021): 100676. 

Bernardi, Austen, Yihan Huang, Bradley Harris, Yongao Xiong, Somen Nandi, Karen A. McDonald, and Roland Faller. "Development and simulation of fully glycosylated molecular models of ACE2­-Fc fusion proteins and their interaction with the SARS­-CoV-­2 spike protein binding domain." PloS one 15.8 (2020): e0237295.

Bernardi, Austen. Computer Simulation of Molecular Systems: Glycoproteins and Carbon Nanotubes with Ionic Liquid. University of California, Davis (2020).

Bernardi, Austen, Eric Meshot, and Roland Faller. “Confining Liquids Inside Carbon Nanotubes: Accelerated Molecular Dynamics with Spliced, Soft­Core Potentials and Simulated Annealing.” Journal of Chemical Theory and Computation (2020).

Bernardi, Austen, Roland Faller, Dirk Reith, and Karl N. Kirschner. “ACPYPE update for nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER to GROMACS.” SoftwareX 10 (2019): 100241.

Xiong, Yongao, Kalimuthu Karuppanan, Austen Bernardi, Qiongyu Li, Vally Kommineni, Carlito Bangeles Lebrilla, Abhaya M. Dandekar, Roland Faller, Karen Ann McDonald, and Somen Nandi. “Effects of N-­glycosylation on the structure, function, and stability of a plant­made Fc­fusion anthrax decoy protein.” Frontiers in plant science 10 (2019): 768.

Bernardi, Austen, Karl N. Kirschner, and Roland Faller. “Structural analysis of human glycoprotein butyrylcholinesterase using atomistic molecular dynamics: The importance of glycosylation site ASN241.” PloS one 12.11 (2017): e0187994.