Rafael C Bernardi
Rafael C Bernardi
Assistant Professor - Department of Physics at Auburn University
Verified email at - Homepage
Cited by
Cited by
Scalable molecular dynamics on CPU and GPU architectures with NAMD
JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ...
The Journal of Chemical Physics 153 (4), 044130, 2020
Enhanced sampling techniques in molecular dynamics simulations of biological systems
RC Bernardi, MCR Melo, K Schulten
Biochimica et Biophysica Acta (BBA)-General Subjects 1850 (5), 872-877, 2015
Molecular dynamics simulations of large macromolecular complexes
JR Perilla, BC Goh, CK Cassidy, B Liu, RC Bernardi, T Rudack, H Yu, ...
Current Opinion in Structural Biology 31, 64-74, 2015
QwikMD—integrative molecular dynamics toolkit for novices and experts
JV Ribeiro, RC Bernardi, T Rudack, JE Stone, JC Phillips, PL Freddolino, ...
Scientific Reports 6 (1), 1-14, 2016
Molecular mechanism of extreme mechanostability in a pathogen adhesin
LF Milles, K Schulten, HE Gaub, RC Bernardi
Science 359 (6383), 1527-1533, 2018
NAMD goes quantum: an integrative suite for hybrid simulations
MCR Melo, RC Bernardi, T Rudack, M Scheurer, C Riplinger, JC Phillips, ...
Nature Methods 15 (5), 351, 2018
Ultrastable cellulosome-adhesion complex tightens under load
C Schoeler, KH Malinowska, RC Bernardi, LF Milles, MA Jobst, E Durner, ...
Nature Communications 5 (1), 1-8, 2014
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
MCR Melo, RC Bernardi, C De La Fuente-Nunez, Z Luthey-Schulten
The Journal of Chemical Physics 153 (13), 2020
PyContact: Rapid, customizable, and visual analysis of noncovalent interactions in MD simulations
M Scheurer, P Rodenkirch, M Siggel, RC Bernardi, K Schulten, ...
Biophysical Journal 114 (3), 577-583, 2018
Mapping mechanical force propagation through biomolecular complexes
C Schoeler, RC Bernardi, KH Malinowska, E Durner, W Ott, EA Bayer, ...
Nano Letters 15 (11), 7370-7376, 2015
Computational methodologies for real-space structural refinement of large macromolecular complexes
BC Goh, JA Hadden, RC Bernardi, A Singharoy, R McGreevy, T Rudack, ...
Annual Review of Biophysics 45, 253-278, 2016
Streptavidin/biotin: Tethering geometry defines unbinding mechanics
SM Sedlak, LC Schendel, HE Gaub, RC Bernardi
Science advances 6 (13), eaay5999, 2020
Mechanisms of nanonewton mechanostability in a protein complex revealed by molecular dynamics simulations and single-molecule force spectroscopy
RC Bernardi, E Durner, C Schoeler, KH Malinowska, BG Carvalho, ...
Journal of the American Chemical Society 141 (37), 14752-14763, 2019
Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm
I Cann, RC Bernardi, RI Mackie
Environmental Microbiology 18 (2), 307-310, 2016
Direction Matters: Monovalent Streptavidin/Biotin Complex under Load
SM Sedlak, LC Schendel, MCR Melo, DA Pippig, Z Luthey-Schulten, ...
Nano Letters 19 (6), 3415-3421, 2019
Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics
T Verdorfer, RC Bernardi, A Meinhold, W Ott, Z Luthey-Schulten, MA Nash, ...
Journal of the American Chemical Society 139 (49), 17841-17852, 2017
High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut
Z Liu, H Liu, AM Vera, RC Bernardi, P Tinnefeld, MA Nash
Nature Communications 11, 4321, 2020
Molecular dynamics study of enhanced Man5B enzymatic activity
RC Bernardi, I Cann, K Schulten
Biotechnology for Biofuels 7 (1), 83, 2014
A tethered ligand assay to probe SARS-CoV-2: ACE2 interactions
MS Bauer, S Gruber, A Hausch, LF Milles, T Nicolaus, LC Schendel, ...
Proceedings of the National Academy of Sciences 119 (14), e2114397119, 2022
Molecular dynamics study of biomembrane/local anesthetics interactions
RC Bernardi, DEB Gomes, R Gobato, CA Taft, AT Ota, PG Pascutti
Molecular Physics 107 (14), 1437-1443, 2009
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