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Macromolecular crowding: how shape and interactions affect diffusion
A significant fraction of the cell volume is occupied by various proteins, polysaccharides,
nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical …
nucleic acids, etc., which considerably reduces the mobility of macromolecules. Theoretical …
Universal features of the shape of elastic fibres in shear flow
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 …
Reynolds number, and seek to understand several aspects of the fibre's motion using the …
The hydrodynamics of colloidal gelation
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 …
particles aggregate to form a system spanning network with high interfacial area, far from …
Fast simulation of particulate suspensions enabled by graph neural network
Predicting the dynamic behaviors of particles in suspension subject to hydrodynamic
interaction (HI) and external drive can be critical for many applications. By harvesting …
interaction (HI) and external drive can be critical for many applications. By harvesting …
How macromolecules softness affects diffusion under crowding
Diffusion in a macromolecularly crowded environment is essential for many intracellular
processes, from metabolism and catalysis to gene transcription and translation. So far …
processes, from metabolism and catalysis to gene transcription and translation. So far …
Hydrodynamics of a twisting, bending, inextensible fiber in Stokes flow
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 …
and twisting, and interact with the surrounding fluid to cause or resist large-scale fluid …
A scalable computational platform for particulate Stokes suspensions
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 …
Newtonian Stokes flow. One central building block is a collision-resolution algorithm that …
Methods for suspensions of passive and active filaments
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 …
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
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 …
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 …
accuracy solely from their mass or chain length. However, this approach fails for intrinsically …