Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Poster Abstracts

47-POS Board 47 PYBROWN SOFTWARE FOR DIFFUSION AND REACTIONS IN CROWDED ENVIRONMENTS INCLUDING STOKESIAN DYNAMICS Tomasz Skóra 1 ; Svyatoslav Kondrat 1,2,3 ; 1 Polish Academy of Sciences, Institute of Physical Chemistry, Warsaw, Poland 2 Max-Planck-Institut für Intelligente Systeme, Stuttgart, Germany 3 Universität Stuttgart, IV. Institut für Theoretische Physik, Stuttgart, Germany Devising a predictive computer model of a biological cell poses a grand challenge at the frontier of computer science, biology, and physics. Although cell inner workings are rooted in the microscopic dynamics of its constituents at a molecular scale, the concept of first-principle simulations of whole cells with quantum mechanics/molecular mechanics (QM/MM) methods is currently unfeasible. Roland Netz and William Eaton (PNAS February 9, 2021 118 (6)) estimated that it would take ca. 1 billion years to run a QM/MM simulation of M. genitalium cell for the duration of its doubling time (ca. 2 hours). Because of that, coarse-grained mesoscopic approaches like Brownian dynamics (BD) are of particular interest to computational biophysicists. Here, we report on a versatile software — pyBrown, enabling users to perform coarse-grained simulations in crowded environments. pyBrown allows for BD simulations with and without hydrodynamic interactions (HI). In contrast to similar existing packages, such as BDBOX or BrownMove, which use Rotne-Prager-Yamakawa description for HI, pyBrown also provides short-range HI in the form of lubrication correction, which is of great importance for crowded systems mimicking the intracellular milieu, where various macromolecules are forced to stay close to each other. In addition, pyBrown enables computations of diffusion-limited reaction rates based on the Northrup–Allison–McCammon algorithm and other features. In this contribution, we present the details of pyBrown software and show the results of using it for simple one-component systems. We show the importance of short-range HI by demonstrating that the commonly used Rotne-Prager-Yamakawa description can significantly overestimate the mobility of macromolecules in volume-occupied systems. This work was supported by NCN grant No. 2017/25/B/ST3/02456. We thank PLGrid for providing computational facilities.

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