Modeling Microtubule Dynamics on Lomonosov-2 Supercomputer of Moscow State University: from Atomistic to Cellular Scale Simulations

Nikita B. Gudimchuk; Veronika V. Alexandrova; Evgeniy V. Ulyanov; Vladimir A. Fedorov; Ekaterina G. Kholina; Ilya B. Kovalenko

doi:10.14529/jsfi240307

Authors

Nikita B. Gudimchuk Department of Physics, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-7283-8959
Veronika V. Alexandrova Department of Physics, Lomonosov Moscow State University, Moscow, Russia
Evgeniy V. Ulyanov Department of Physics, Lomonosov Moscow State University, Moscow, Russia
Vladimir A. Fedorov Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-9397-1548
Ekaterina G. Kholina Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-5918-5084
Ilya B. Kovalenko Department of Biology, Lomonosov Moscow State University, Moscow, Russia https://orcid.org/0000-0002-4949-6591

DOI:

https://doi.org/10.14529/jsfi240307

Keywords:

microtubule, Lomonosov-2, computational performance, multi-scale simulations, molecular dynamics, Brownian dynamics, kinetic Monte Carlo simulations

Abstract

Cytoskeletal polymers of tubulin, the microtubules, are critically important for cellular physiology. Their remarkable non-equilibrium dynamics and unusual mechanical properties have nurtured interest in exploring microtubules with diverse experimental methods and modeling their properties at different scales. In this work, we overview the studies of microtubules from the atomistic level of detail to the cellular dimension, focusing on the computational modeling work that has been carried out by our group on Lomonosov-2 supercomputer of Moscow State University since 2015. Our computational efforts have been aimed at understanding of microtubules through a set of models at multiple spatial and temporal scales, starting from examining the properties of tubulin dimers, as the building blocks, and further elucidating how those properties enable more complex assembly/disassembly and force-generation behaviors of microtubules, emerging at larger scales. Our methodology includes different approaches, from atomistic molecular dynamics to more coarse-grained techniques, such as Brownian dynamics and Monte Carlo simulations. We describe the motivation and the context for each model, overview the major conclusions from the simulations, which we believe were instrumental in building an integrative understanding of these polymers. We also discuss some technical aspects of the modeling, such as the computational performance of different types of simulations, current limitations and potential future directions for description of the microtubule dynamics, using the multi-scale approach.

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