| Texto completo | |
| Autor(es): |
Cajahuaringa, Samuel
;
Zanotto, Leandro N.
;
Rigo, Sandro
;
Yviquel, Herve
;
Skaf, Munir S.
;
Araujo, Guido
Número total de Autores: 6
|
| Tipo de documento: | Artigo Científico |
| Fonte: | JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING; v. 191, p. 12-pg., 2024-04-26. |
| Resumo | |
Ion Mobility coupled with Mass Spectrometry (IM -MS) stands as a strong analytical method for structurally characterizing complex molecules. In IM -MS, the sample under investigation is ionized and propelled by an electric field into a drift tube, which collides against a buffer gas. The separation of the ion gas phase is then measured through the differences in their rotationally averaged Collision Cross -Section (CCS) values. The effectiveness of the measured Collision Cross -Section (CCS) for structural characterization critically depends on the validation against theoretical calculations. This validation process relies on intensive molecular mechanics simulations, which can be computationally demanding, especially for large systems such as molecular assemblies and viruses. Therefore, reliable and fast CCS calculations are needed to help interpret IM -MS experimental data. This work presents the MassCCS software, which considerably increases the CCS simulation performance by implementing a linked -cell -based algorithm, incorporating High -Performance Computing (HPC) techniques. We performed extensive tests regarding the system size, shape, and number of CPU cores. Experimental results reveal speedups up to 3 orders of magnitude faster than Collision Simulator for Ion Mobility Spectrometry (CoSIMS) and High -Performance Collision Cross Section (HPCCS), optimized solutions for CCS simulations, for a single node execution. In addition, we extended MassCCS at the inter -node level by employing OpenMP Cluster (OMPC). OMPC is an innovative programming model designed for the development of HPC applications. It streamlines the development process and simplifies software maintenance using only OpenMP directives. Notably, OMPC delivers a performance level comparable to a pure MPI implementation. This enhancement enabled expensive CCS calculations using nitrogen buffer gas for large systems such as human adenovirus with -11 million atoms in just -4 min, making MassCCS the most performant software nowadays, to the best of our knowledge. MassCCS is available as free software for Academic use at https://github .com /cces -cepid /massccs. (AU) | |
| Processo FAPESP: | 13/08293-7 - CECC - Centro de Engenharia e Ciências Computacionais |
| Beneficiário: | Munir Salomao Skaf |
| Modalidade de apoio: | Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs |
| Processo FAPESP: | 12/24750-6 - Relações entre a obesidade e o receptor TLR4: Novos estudos através de simulações de dinâmica molecular |
| Beneficiário: | Paulo Cesar Telles de Souza |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 21/03224-3 - Computação de alto desempenho e dinâmica molecular |
| Beneficiário: | Oscar Samuel Cajahuaringa Macollunco |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 16/04963-6 - Dinâmica molecular de hidrólise enzimática de celulose e simulações de QM/MM de reações químicas em sistemas biomoleculares |
| Beneficiário: | Gabriel Heerdt |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |