A5074108666- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Advanced NMR Techniques and Applications
- Bacteriophages and microbial interactions
- Machine Learning in Materials Science
- SARS-CoV-2 and COVID-19 Research
- Microbial Metabolic Engineering and Bioproduction
- Bacterial Genetics and Biotechnology
- Mass Spectrometry Techniques and Applications
- Photosynthetic Processes and Mechanisms
- Microbial infections and disease research
- Nanopore and Nanochannel Transport Studies
- Parallel Computing and Optimization Techniques
Urbana University
2021
University of Illinois Urbana-Champaign
2020
Universidade Federal da Paraíba
2012-2020
NAMDis a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance petascale parallel supercomputers consisting hundreds thousands cores, as well inexpensive commodity clusters commonly found in academic environments. It is written C++ leans Charm++ optimal low-latency versatile, multipurpose code that gathers state-of-the-art algorithms to carry out apt thermodynamic ensembles,...
In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our consisted a combination highly optimized linear algebra libraries for both CPU (LAPACK BLAS from Intel MKL) (MAGMA CUBLAS) hasten time-consuming parts MOPAC such as pseudodiagonalization, full diagonalization, density matrix...
Harnessing the power of graphics processing units (GPUs) to accelerate molecular dynamics (MD) simulations in context free-energy calculations has been a longstanding effort toward development versatile, high-performance MD engines. We report new GPU-based implementation NAMD perturbation (FEP), one oldest, most popular importance-sampling approaches for determination differences that underlie alchemical transformations. Compared CPU available since 2001 NAMD, our benchmarks indicate FEP...
ABSTRACT We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. use this investigate mechanisms infectivity SARS-CoV-2 spike protein, main viral infection machinery. Our enables more efficient investigation in variety complex environments, including within complete envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. present several novel...