J
Julio D.C. Maia
Researcher at University of Illinois at Urbana–Champaign
Publications - 7
Citations - 1740
Julio D.C. Maia is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: MOPAC & Linear algebra. The author has an hindex of 6, co-authored 7 publications receiving 715 citations. Previous affiliations of Julio D.C. Maia include Federal University of Paraíba.
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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.
Journal ArticleDOI
GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations
Julio D.C. Maia,Gabriel A.U. Carvalho,Carlos Peixoto Mangueira,Sidney Ramos Santana,Lucídio dos Anjos Formiga Cabral,Gerd B. Rocha +5 more
TL;DR: This study presents some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size molecular systems using GPU coprocessors and multithreaded shared-memory CPUs.
Journal ArticleDOI
NAMD goes quantum: an integrative suite for hybrid simulations.
Marcelo C. R. Melo,Rafael C. Bernardi,Till Rudack,Till Rudack,Maximilian Scheurer,Maximilian Scheurer,Christoph Riplinger,James C. Phillips,Julio D.C. Maia,Gerd B. Rocha,João V. Ribeiro,John E. Stone,Frank Neese,Klaus Schulten,Zaida Luthey-Schulten +14 more
TL;DR: By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry packages ORCA and MOPAC, this work has created an integrated, comprehensive, customizable, and easy-to-use suite.
Journal ArticleDOI
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
Lorenzo Casalino,Abigail C. Dommer,Zied Gaieb,Emilia P. Barros,Terra Sztain,Surl-Hee Ahn,Anda Trifan,Anda Trifan,Alexander Brace,Anthony T. Bogetti,Austin Clyde,Austin Clyde,Heng Ma,Hyungro Lee,Matteo Turilli,Syma Khalid,Lillian T. Chong,Carlos Simmerling,David J. Hardy,Julio D.C. Maia,James C. Phillips,Thorsten Kurth,Abraham C. Stern,Lei Huang,John McCalpin,Mahidhar Tatineni,Tom Gibbs,John E. Stone,Shantenu Jha,Shantenu Jha,Arvind Ramanathan,Rommie E. Amaro +31 more
TL;DR: In this article, a generalizable AI-driven workflow that leverages heterogeneous HPC resources was developed to explore the time-dependent dynamics of molecular systems. But their work focused on the SARS-CoV-2 spike protein, the main viral infection machinery.
Posted ContentDOI
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics
Lorenzo Casalino,Abigail C. Dommer,Zied Gaieb,Emilia P. Barros,Terra Sztain,Surl-Hee Ahn,Anda Trifan,Anda Trifan,Alexander Brace,Anthony T. Bogetti,Heng Ma,Hyungro Lee,Matteo Turilli,Syma Khalid,Lillian T. Chong,Carlos Simmerling,David J. Hardy,Julio D.C. Maia,James C. Phillips,Thorsten Kurth,Abraham C. Stern,Lei Huang,John McCalpin,Mahidhar Tatineni,Tom Gibbs,John E. Stone,Shantenu Jha,Arvind Ramanathan,Rommie E. Amaro +28 more
TL;DR: A generalizable AI-driven workflow is developed that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems and demonstrates how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.