2024/03/12 by Marco Giulini, Giulini, Marco, Raffaele Fiorentini +7 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Biological Physics (physics.bio-ph) #Cell Image Analysis Techniques #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft) #Statistical Mechanics (cond-mat.stat-mech)
paper · pdf · doi:10.48550/arxiv.2403.08097
openalex publication_date 2024/03/12 · openalex created_date 2024/03/15 · openalex updated_date 2026/07/28
Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules. The development of low-resolution models takes the moves from the reduction of the degrees of freedom employed, that is, the definition of a mapping between a system's high-resolution description and its simplified counterpart. Even in the absence of an explicit parametrisation and simulation of a CG model, the observation of the atomistic system in simpler terms can be informative: this idea is leveraged by the mapping entropy, a measure of the information loss inherent to the process of coarsening. Mapping entropy lies at the heart of the extensible coarse-graining toolbox, or EXCOGITO, developed to perform a number of operations and analyses on molecular systems pivoting around the properties of mappings. EXCOGITO can process an all-atom trajectory to compute the mapping entropy, identify the mapping that minimizes it, and establish quantitative relations between a low-resolution representation and the geometrical, structural, and energetic features of the system. Here, the software, which is available free of charge under an open-source licence, is presented and showcased to introduce potential users to its capabilities and usage. Published on the J. Chem. Inf. Model. on June 11, 2024. DOI: https://doi.org/10.1021/acs.jcim.4c00490