The Replica Exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. Ho...
Maria Eleftheriou, Aleksandr Rayshubskiy, Jed W. P...
— This paper presents Salsa, a novel, decentralized and asynchronous realization of the “replica exchange” algorithm for simulating the structure, function, folding, and dyna...
Li Zhang, Manish Parashar, Emilio Gallicchio, Rona...
Large-scale simulations and computational modeling using molecular dynamics (MD) continues to make significant impacts in the field of biology. It is well known that simulations...
Sadaf R. Alam, Jeffrey S. Vetter, Pratul K. Agarwa...
We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and ...
Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, ...
Given the scale of massively parallel systems, occurrence of faults is no longer an exception but a regular event. Periodic checkpointing is becoming increasingly important in the...