Showing papers by "Anand Yethiraj published in 2022"
TL;DR: In this paper , an effective volume fraction for Ficoll-bound water was derived from NMR diffusion measurements, and it was shown that only a combination of particle softness and interparticle attractions, quantified using a computational model, can replicate the experimental S(0).
Abstract: The in-cell environment is crowded with macromolecules, and the consequent reduction in free volume, based on the hard-sphere paradigm, is central to understanding macromolecular motions. A much-used model crowder, Ficoll, often assumed to be a compact, if not rigid, colloidal particle, is studied by rheology, small-angle neutron scattering, nuclear magnetic resonance diffusometry, and relaxometry. We find that the Ficoll suspension viscosity scales linearly with concentration cF in the dilute limit and as ∼cF3.8 at high cF, i.e, consistent with the 15/4 (de Gennes) scaling for a reptating polymer. The form factor of Ficoll, obtained via small-angle neutron scattering (SANS), resembles either a Gaussian polymer or a soft polymer blob. From NMR diffusion measurements, we obtain an effective volume fraction for Ficoll that accounts for Ficoll-bound water in two ways and show that each results in a volume occupancy of 60% to 70% in the crowding limit, much larger than the traditionally reported values of around 30%. If we persist with the colloid paradigm and examine the dependence of the zero-q structure factor obtained via SANS in terms of this effective volume fraction, we find that only a combination of particle softness and interparticle attractions, quantified using a computational model, can replicate the experimental S(0). The stark difference between effective and traditional volume occupancies affects the interpretation of previous experiments on macromolecular crowding and might explain the intriguing non-monotonicity observed in the dependence of protein relaxation rates on crowder concentration.
6 citations
TL;DR:
Abstract: Gamete-level sexual selection of externally fertilising species is usually achieved by modifying sperm behaviour with mechanisms thought to alter the chemical environment in which gametes perform. In fish this can be accomplished through the ovarian fluid, a substance released with the eggs at spawning. While its biochemical effects in relation to sperm energetics have been investigated, the influence of the physical environment in which sperm compete remains poorly explored. Our objective was therefore to gain insights on the physical structure of this fluid and potential impacts on reproduction. Using soft-matter physics approaches of steady-state and oscillatory viscosity measurements, we subjected salmon ovarian fluids to variable shear stresses and frequencies resembling those exerted by sperm swimming through the fluid near eggs. We show that this fluid, which in its relaxed state is a gel-like substance, displays a non-Newtonian viscoelastic and shear-thinning profile, where the viscosity decreases with increasing shear rates. We concurrently find that this fluid obeys the Cox-Merz rule below 7.6 Hz and infringes it above, thus indicating a shear-thickening phase where viscosity increases provided it is probed gently enough. This suggests the presence of a unique frequency-dependant structural network with relevant implications on sperm energetics and fertilisation dynamics.
1 citations
TL;DR: Theoretical models of macromolecular crowding necessarily introduce simplifications in order to elucidate the most features of the environment, the starting point being the role of excluded volume.
Abstract: have complex and multiscale non-equilibrium environments, with 30 to 40% (by weight) of the cells being composed of macromolecular components: this macromolecular crowding can affect stability, translational motions and chemical kinetics. Theoretical models of macromolecular crowding necessarily introduce simplifications in order to elucidate the most features of the environment, the starting point being the role of excluded volume. model they the
TL;DR: The introduction of two interactions (polymers and electric fields) to a colloidal system provides fine control over its phase transitions and tunable control over transformation kinetics as mentioned in this paper , and the introduction of polymers induced by polymers, and electric field induced by an electric field, provides fine controlling over phase transitions.
Abstract: The introduction of two interactions---one induced by polymers, the other by an electric field---to a colloidal system provides fine control over its phase transitions and tunable control over transformation kinetics.