Diffusion in crowded environments
Principal investigator: Dr. Svyatoslav Kondrat
We harness Brownian dynamics simulations to reveal the generic effects of macromolecules’ properties, e.g., shape and activity, on the diffusion coefficients in cells.
On the importance of the diffusivity gradient term in Brownian dynamics simulations
Skóra, T. On the importance of the diffusivity gradient term in Brownian dynamics simulations. Biophysical Journal 123, 2638-2640 (2024)
Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds
Raczyłło, E., Gołowicz, D., Skóra, T., Kazimierczuk, K., & Kondrat, S. Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds. Nano Letters 24, 4801–4809 (2024)
Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding
Skóra, T., Słyk, E., & Kondrat, S. Minimal Coarse-Grained Model for Immunoglobulin G: Diffusion and Binding under Crowding. The Journal of Physical Chemistry B 127, 7442–7448 (2023)
Crowding-regulated binding of divalent biomolecules
Skóra, T., Janssen, M., Carlson, A., & Kondrat, S. Crowding-regulated binding of divalent biomolecules. Physical Review Letters 130, 258401 (2023)
Diffusion and reactions under crowding: Theory and simulations
Skóra, T. Diffusion and reactions under crowding: Theory and simulations. PhD Thesis (2023)
How macromolecules softness affects diffusion under crowding
Słyk, E., Skóra T., & Kondrat, S. How macromolecules’ softness affects diffusion under crowding. Soft Matter 18, 5366–5370 (2022)
Conformation-changing enzymes and macromolecular crowding
Skóra, T., Popescu, M. N., & Kondrat, S. Conformation-changing enzymes and macromolecular crowding. Physical Chemistry Chemical Physics 23, 9065–9069 (2021)
Macromolecular crowding: how shape and interactions affect diffusion
Skóra, T., Vaghefikia, F., Fitter, J., & Kondrat, S. Macromolecular crowding: how shape and interactions affect diffusion. The Journal of Physical Chemistry B 124, 7537–7543 (2020)
One of my current aims is to develop a versatile software – pyBrown, for simulations of diffusion and reactions accounting for the hydrodynamic interactions. You can find the code here, and its documentation here.