SOP-GPU: influence of solvent-induced hydrodynamic interactions on dynamic structural transitions in protein assemblies. - Andrey Alekseenko; Olga Kononova; Yaroslav Kholodov; Kenneth A. Marx; Valeri Barsegov (J. Comput. Chem., 2016)

Fluctuating Nonlinear Spring Model of Mechanical Deformation of Biological Particles. - Olga Kononova; Joost Snijder; Yaroslav Kholodov; Kenneth A. Marx; Gijs J. L. Wuite; Wouter H. Roos; Valeri Barsegov (PLoS Comput. Biol., 2016)

CellDynaMo-stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly. - Evgenii Kliuchnikov; Artem A. Zhmurov; Kenneth A. Marx; Alex Mogilner; Valeri Barsegov (PLoS Comput. Biol., 2022)