Resumo:

Neste seminário vou apresentar trabalho recente sobre um tipo de nanopartículas microbicidas. Vou detalhar como conseguimos simular estas nanopartículas utilizando o modelo coarse-grain Martini 3, o que envolveu bastante trabalho bottom-up, incluindo modelação quântica e atomística.
Vou mostrar como os modelos obtidos foram usados para observar um possível mecanismo de seletividade e de ação, e, finalmente, como puderam ser usados para prever computacionalmente modificações potenciadoras da atividade microbicida.
Este seminário servirá também como exemplo do processo de parameterização coarse-grain de moléculas poliméricas usando o modelo Martini 3.
Sobre o palestrante:
Manuel is the head of the Multiscale Modeling lab within the MOSTMICRO unit of ITQB NOVA. His work is centered on elucidating the molecular-level details of lipid-lipid, lipid-protein, and protein-protein interactions; recent collaborations also focus on modeling bacterial structures. Manuel’s research employs coarse-grained, atomistic, and hybrid molecular dynamic simulations, and tackles both the construction of models (as a developer within the Martini coarse-grain framework) and their application to biological questions. Additionally, Manuel actively develops simulation and analysis software (he is a core developer of the MDAnalysis Python package), with emphasis on large-scale parallelization of analysis. Manuel’s work, both in method development and in applied multidisciplinary research — often in collaboration with experimental biochemistry and biology — has ensured an impactful output, currently at an h-index of 26. As a Marie Curie Fellow, and later as a Dutch NWO VENI Fellow, Manuel carried out postdoctoral work at the Marrink lab, at the University of Groningen — where he became involved in the development and application of Martini. Manuel pursued his Ph.D. on the molecular level interactions of antimicrobial peptides with cellular membranes, using spectroscopic techniques coupled to mathematical modeling, connecting biophysics to microbiology.