Macromolecular crowding: how shape and interactions affect diffusion

T Skóra, F Vaghefikia, J Fitter… - The Journal of Physical …, 2020 - ACS Publications
A significant fraction of the cell volume is occupied by various proteins, polysaccharides,
nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical …

Universal features of the shape of elastic fibres in shear flow

PJ Żuk, AM Słowicka, ML Ekiel-Jeżewska… - Journal of Fluid …, 2021 - cambridge.org
We present a numerical study of the dynamics of an elastic fibre in a shear flow at low
Reynolds number, and seek to understand several aspects of the fibre's motion using the …

The hydrodynamics of colloidal gelation

Z Varga, G Wang, J Swan - Soft Matter, 2015 - pubs.rsc.org
Colloidal gels are formed during arrested phase separation. Sub-micron, mutually attractive
particles aggregate to form a system spanning network with high interfacial area, far from …

Fast simulation of particulate suspensions enabled by graph neural network

Z Ma, Z Ye, W Pan - Computer Methods in Applied Mechanics and …, 2022 - Elsevier
Predicting the dynamic behaviors of particles in suspension subject to hydrodynamic
interaction (HI) and external drive can be critical for many applications. By harvesting …

How macromolecules softness affects diffusion under crowding

E Słyk, T Skóra, S Kondrat - Soft Matter, 2022 - pubs.rsc.org
Diffusion in a macromolecularly crowded environment is essential for many intracellular
processes, from metabolism and catalysis to gene transcription and translation. So far …

Hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow

O Maxian, B Sprinkle, CS Peskin, A Donev - Physical Review Fluids, 2022 - APS
In swimming microorganisms and the cell cytoskeleton, inextensible fibers resist bending
and twisting, and interact with the surrounding fluid to cause or resist large-scale fluid …

A scalable computational platform for particulate Stokes suspensions

W Yan, E Corona, D Malhotra, S Veerapaneni… - Journal of …, 2020 - Elsevier
We describe a computational framework for simulating suspensions of rigid particles in
Newtonian Stokes flow. One central building block is a collision-resolution algorithm that …

Methods for suspensions of passive and active filaments

SF Schoeller, AK Townsend, TA Westwood… - Journal of …, 2021 - Elsevier
Flexible filaments and fibres are essential components of important complex fluids that
appear in many biological and industrial settings. Direct simulations of these systems that …

Rapid calculation of hydrodynamic and transport properties in concentrated solutions of colloidal particles and macromolecules

JW Swan, G Wang - Physics of Fluids, 2016 - pubs.aip.org
A new method for calculating the resistance tensors of arbitrarily shaped particles and the
translational and rotational self-diffusivity in suspensions of such particles is developed. This …

Hydrodynamic radii of intrinsically disordered proteins: fast prediction by minimum dissipation approximation and experimental validation

R Waszkiewicz, A Michaś… - The Journal of …, 2024 - ACS Publications
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high
accuracy solely from their mass or chain length. However, this approach fails for intrinsically …