R
Rafael C. Bernardi
Researcher at University of Illinois at Urbana–Champaign
Publications - 52
Citations - 3456
Rafael C. Bernardi is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Force spectroscopy & Biology. The author has an hindex of 17, co-authored 38 publications receiving 1946 citations. Previous affiliations of Rafael C. Bernardi include Universidade Estadual de Londrina & National Institute of Metrology Standardization and Industrial Quality.
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Journal ArticleDOI
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
James C. Phillips,David J. Hardy,Julio D.C. Maia,John E. Stone,João V. Ribeiro,Rafael C. Bernardi,Ronak Buch,Giacomo Fiorin,Jérôme Hénin,Wei Jiang,Ryan McGreevy,Marcelo C. R. Melo,Brian K. Radak,Robert D. Skeel,Abhishek Singharoy,Yi Wang,Benoît Roux,Aleksei Aksimentiev,Zaida Luthey-Schulten,Laxmikant V. Kale,Klaus Schulten,Christophe Chipot,Emad Tajkhorshid +22 more
TL;DR: The main features of NAMD are reviewed, including the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and their applicability to specific problems.
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Enhanced sampling techniques in molecular dynamics simulations of biological systems
TL;DR: An overview over theses sampling methods is presented in an attempt to shed light on which should be selected depending on the type of system property studied, and whether metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics.
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Molecular dynamics simulations of large macromolecular complexes
Juan R. Perilla,Boon Chong Goh,C. Keith Cassidy,Bo Liu,Rafael C. Bernardi,Till Rudack,Hang Yu,Zhe Wu,Klaus Schulten +8 more
TL;DR: The utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone is reviewed.
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Molecular mechanism of extreme mechanostability in a pathogen adhesin
TL;DR: Using atomic force microscopy–based single-molecule force spectroscopy, the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β, is explored.
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QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
João V. Ribeiro,Rafael C. Bernardi,Till Rudack,John E. Stone,James C. Phillips,Peter L. Freddolino,Klaus Schulten +6 more
TL;DR: QwikMD as mentioned in this paper integrates two widely used modeling programs, namely NAMD and VMD, to enable novices and experts alike to address biomedically relevant questions, where often only molecular dynamics simulations can provide answers.