AUC 2022

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50 years with beads and springs. A self-review of some contributions and a few new projects
Submitter: Jose Garcia de la Torre
Authors: Jose Garcia de la Torre
Corresponding Author: Jose Garcia de la Torre
Title: 50 years with beads and springs. A self-review of some contributions and a few new projects
Contribution Type: Full Talk
Selected for Presentation Yes
Abstract: The calculation of properties – mainly hydrodynamic and scattering – of macromolecules in dilute solution and nanoparticles in colloidal suspensions is of great importance for the determination of structural features from such properties. For the calculations, coarse-grained (as they are named nowadays) models consisting of spherical beads, eventually joined by spring-like connectors are useful. This concept was pioneered in the 1950’s by Kirkwood and Zimm, among others. I begun working on this scheme in 1972, now 50 years ago. This talk is intended to be an overview of my research in the development of theory, computational tools, and applications, with some emphasis on biological macromolecules. The macromolecular or colloidal particles can be classified into two categories: rigid and flexible. Rigid particles are represented by bead models: arrays of spherical beads which reproduce the size and shape of the particle. The various procedures for building the models and calculating their properties are integrated in a series of methods, implemented in the computer programs of the HYDRO suite (HYDRO++, HYDROPRO, HYDRONMR, etc.). On other hand, we have to deal also with particles having some kind and degree of flexibility, and therefore, their treatment is more complex, as they can adopt a number of conformations. So, in addition to the procedures for the evaluation of properties for instantaneous conformations, one has to take into account the conformational variability. The generation of individual conformations can be done with a Monte Carlo simulation (program MONTEHYDRO), and one can even generate a real-time trajectory of particles as they undergo both overall and internal Brownian motion (program BROWFLEX). Basic concepts about these methods and some applications will be briefly presented.