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CPP: Fachverband Chemische Physik und Polymerphysik

CPP 16: Modeling and Simulation of Soft Matter II

CPP 16.1: Vortrag

Dienstag, 19. März 2024, 09:30–09:45, H 0106

pyMBE: the Molecule Brewer for ESPResSo — Paola B. Torres¹, •David Beyer², Sebastian P. Pineda³, Peter Košovan³, and Pablo M. Blanco⁴ — ¹Grupo de Bionanotecnologia y Sistemas Complejos. Infap-CONICET & Facultad Regional San Rafael, Universidad Tecnológica Nacional, 5600 San Rafael, Argentina — ²Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany — ³Department of Physical and Macromolecular Chemistry, Charles University, 128 00 Prague 2, Czechia — ⁴Department of Physics, NTNU - Norwegian University of Science and Technology, NO-7491 Trondheim, Norway

We introduce pyMBE (gitlab.com/blancoapa/pyMBE), a Python-based molecule brewer designed for ESPResSo. pyMBE provides a suite of tools aimed at streamlining the construction of coarse-grained representations for molecules characterized by complex architectures, such as polyelectrolytes, peptides, and globular proteins within the ESPResSo molecular dynamics software. Notably, the tool focuses on automating the setup and simulation of chemical reactions in charge-regulating systems, i.e. ionic soft matter with weak acid/base groups. To accommodate a broad range of systems, pyMBE supports chemical reactions in different ensembles, such as constant-pH and grand-reaction. The versatility of the software is exemplified through three practical applications: weak polyelectrolytes in dialysis, charge-regulating peptides, and globular proteins.

Keywords: Weak Polyelectrolyte; Monte Carlo; Molecular Dynamics; Peptides; Proteins