Physics-Biology interface seminar: Fernando Luis Barroso Da Silva


11:00 - 12:00

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Developing and applying fast constant pH methods in biological systems: From biomaterials to virus

Fernando Luis Barroso Da Silva (University of São Paulo, Brazil)


pH is a key parameter for biological and technological processes. Different numerical schemes were developed during the last years for such simulations ranging from Poisson-Boltzmann approaches to explicit solvent based methods. Ideally, the proton equilibria should correctly describe the experimental system without hampering the calculation time. A fast proton titration scheme (FPTS), rooted in the Kirkwood model of impenetrable spheres, where salt is treated at the Debye-Huckel level, was specially developed for proteins and nucleic acids. This method has now been coupled with OPEP5 force field for constant pH molecular dynamics simulations. A benchmark study will be presented. Despite our approximations, both the robustness and its ability to proper describe the system physics by these numerical methods can be confirmed. FPTS was also applied to quantify protein stability and biomolecular interactions. In this talk, I will present results for some protein systems with importance in different applied fields from biomaterials to public health.

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