Publications

Journal Covers

Nano Letters

June 2019

Direction Matters: Monovalent Streptavidin/Biotin Complex under Load.

Biophysical Journal

February 2018

PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

JACS

December 2017

Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics.

Nano Letters

November 2015

Mapping Mechanical Force Propagation through Biomolecular Complexes.

List of Publications

DEB Gomes, B Yang, R Vanella, MA Nash‡, RC Bernardi‡; Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions; bioRxiv, 2024
MS Bauer*, S Gruber*, A Hausch*, MCR Melo*, PSFC Gomes*, LF Milles, HE Gaub, RC Bernardi‡, J Lipfert‡; Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern; Nature Nanotechnology, 2023
S Marru, M Pierce, B Plale, S Pamidighantam, D Wannipurage, M Christie, I Ranawaka, E Abeysinghe, R Quick, E Tajkhorshid, S Koric, J Basney, M Spivak, B Isralewitz, RC Bernardi, DEB Gomes, G Krishnan, M Bazhenov, S Smallen, A Majumdar, A Arkhipov, K Dai, XP Liu; Cybershuttle: An end-to-end Cyberinfrastructure Continuum to accelerate Discovery in Science and Engineering; Practice and Experience in Advanced Research Computing, 2023
M Spivak, JE Stone, J Ribeiro, J Saam, J Maia, P Freddolino, RC Bernardi, E Tajkhorshid; VMD as a platform for interactive small molecule preparation and visualization for quantum and classical simulations; Journal of Chemical Information and Modeling, 2023
RS Natividade, M Koehler, PSFC Gomes, JD Simpson, SC Smith, DEB Gomes, J Lhoneux, J Yang, A Ray, TS Dermody, RC Bernardi‡, KM Ogden‡, D Alsteens‡; Deciphering the molecular mechanisms behind the reovirus entry binding complex; PNAS, 120 (21), e2220741120, 2023
MCR Melo, RC Bernardi‡; Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike; Biophysical Journal, 122 (14), 2833-2840, 2023 – Cover Article
PSFC Gomes, M Forrester, M Pace, DEB Gomes, RC Bernardi‡; May the force be with you: the role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections; Frontiers in Chemistry, 11, 2023.1107427, 2023
MCR Melo, DEB Gomes, RC Bernardi‡; Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections; Journal of the American Chemical Society, 145 (1), 70-77, 2023 – Cover Article
PSFC Gomes, DEB Gomes, RC Bernardi‡; Protein structure prediction in the era of AI: challenges and limitations when applying to in-silico force spectroscopy; Frontiers in Bioinformatics, 2, 983306, 2022
MS Bauer, S Gruber, A Hausch, PSFC Gomes, LF Milles, T Nicolaus, P López-Navajas, LC Schendel, E Procko, D Lietha, MCR Melo, RC Bernardi, HE Gaub, J Lipfert; A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions; PNAS, 119 (14), e2114397119, 2022
RC Bernardi*, HL Doden*, MCR Melo, S Devendran RM Pollet, SM Mythen, S Bhowmik, SA Lesley, I Cann, Z Luthey-Schulten, NM Koropatkin, JM Ridlon; Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome; bioRxiv, 2020.
MCR Melo, RC Bernardi, C Fuente-Nunez, Z Luthey-Schulten; Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories; The Journal of Chemical Physics, 153 (4), 134104, 2020.
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.
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.
SM Sedlak*, LC Schendel*, HE Gaub‡, RC Bernardi‡; Streptavidin/biotin: tethering geometry defines unbinding mechanics; Science Advances, 6 (13), eaay5999, 2020.
I Cann, GV Pereira, AM Abdel-Hamid, H Kim, D Wefers, BB Kayang, T Kanai, T Sato, RC Bernardi, H Atomi, RI Mackie; Thermophilic degradation of hemicellulose, a critical feedstock in the production of bioenergy and other value-added products; Applied Environmental Microbiology, 86 (7), e02296-19, 2020.
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.
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.
TJK Haataja, RC Bernardi, S Lecointe, R Capoulade, J Merot, U Pentikäinen; Non-syndromic Mitral Valve Dysplasia Mutation Changes the Force Resilience and Interaction of Human Filamin A; Structure, 27(1), 102-112, 2019.
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.
LF Milles, K Schulten, HE Gaub, RC Bernardi‡; Molecular mechanism of extreme mechanostability in a pathogen surface anchor; Science, 359 (6383), 1527-1533, 2018.
M Scheurer, P Rodenkirch, M Siggel, RC Bernardi, K Schulten, E Tajkhorshid, T Rudack; PyContact: Rapid, Customizable and Visual Analysis of Non-Covalent Interactions in MD Simulations; Biophysical Journal, 114(3), 577-583, 2018 – Cover Article.
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.
J Seppälä, RC Bernardi, TJK Haataja, M Hellman, OT Pentikäinen, K Schulten, P Permi, J Ylänne, U Pentikäinen; Skeletal Dysplasia Mutations Effect on Human Filamins’ Structure and Mechanosensing; Scientific Reports, 7 (1), 4218, 2017.
JV Ribeiro*, RC Bernardi*, T Rudack*, JE Stone, JC Phillips,PL Freddolino, K Schulten; QwikMD Integrative Molecular Dynamics Toolkit for Novices and Experts; Scientific Reports, 6, 26536, 2016.
BC Goh*, JA Hadden*, RC Bernardi, A Singharoy, R McGreevy, T Rudack, CK Cassidy, K Schulten; Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes; Annual Review of Biophysics, 45, 253-278, 2016.
I Cann, RC Bernardi, RI Mackie; Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm; Environmental Microbiology, 18 (2), 307-310, 2016.
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.
RC Bernardi, MCR Melo, K Schulten; Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems; Biochimica et Biophysica Acta (BBA) – General Subjects, 1850 (5), 872-877, 2015.
JR Perilla, BC Goh, CK Cassidy, B Liu, RC Bernardi, T Rudack, H Yu, Z Wu, K Schulten; Molecular dynamics simulations of large macromolecular complexes; Current Opinion in Structural Biology, 31, 64-74, 2015.
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.
RC Bernardi, I Cann, K Schulten; Molecular dynamics study of enhanced Man5B enzymatic activity; Biotechnology for Biofuels, 7 (1), 83, 2014.
YS Mendes*, NS Alves*, TLF Souza, IP Sousa, ML Bianconi, RC Bernardi, PG Pascutti, JL Silva, AMO Gomes, AC Oliveira; The Structural Dynamics of the Flavivirus Fusion Peptide-Membrane Interaction; PloS one, 7 (10), e47596, 2012.
MCR Melo, RC Bernardi‡, TVA Fernandes, PG Pascutti; GSAFold: A new application of GSA to protein structure prediction; Proteins: Structure, Function, and Bioinformatics, 80 (9), 2305-2310, 2012.
RC Bernardi‡, PG Pascutti; Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction; Journal of Chemical Theory and Computation, 8 (7), 2797-2203, 2012.
LVB Hoelz, AAST Ribeiro, RC Bernardi, BAC Horta, MG Albuquerque, JFM Silva, PG Pascutti, RB Alencastro; The role of helices 5 and 6 on the human 1-adrenoceptor activation mechanism; Molecular Simulation, 38 (3), 236-240, 2012.
LVB Hoelz, RC Bernardi, BAC Horta, JQ Araújo, MG Albuquerque, JFM Silva, PG Pascutti, RB Alencastro; Dynamical behaviour of the human 1-adrenoceptor under agonist binding; Molecular Simulation, 37 (11), 907-913, 2011.
RC Bernardi, DEB Gomes, R Gobato, CA Taft, AT Ota, PG Pascutti; Molecular dynamics study of biomembrane/local anesthetics interactions; Molecular Physics, 107 (14), 1437-1443, 2009.
RC Bernardi, DEB Gomes, AS Ito, AT Ota, PG Pascutti, C Taft; Density functional and molecular dynamics simulations of local anesthetics in 0.9% NaCl solution; Molecular Simulation, 33 (14), 1135-1141, 2007.
RC Bernardi, DEB Gomes, PG Pascutti, AS Ito, CA Taft, AT Ota; Water solvent and local anesthetics: A computational study; International Journal of Quantum Chemistry, 107 (7), 1642-1649, 2007.
RC Bernardi, DEB Gomes, PG Pascutti, AS Ito, AT Ota; Theoretical studies on water-tetracaine interaction; International Journal of Quantum Chemistry, 106 (5), 1277-1282, 2006.

Research Highlights

PNAS
2022

Science Advances
2020

Science
2018

Nature Methods
2018

Journal Covers

Nano Letters

June 2019

Biophysical Journal

February 2018

JACS

December 2017

Nano Letters

November 2015

List of Publications

Research Highlights

PNAS2022

Science Advances2020

Science2018

Nature Methods2018

Journal Covers

Nano Letters

June 2019

Biophysical Journal

February 2018

JACS

December 2017

Nano Letters

November 2015

List of Publications

PNAS
2022

Science Advances
2020

Science
2018

Nature Methods
2018