9 research outputs found
Dynamics of fibers in a wide microchannel
Dynamics of single flexible non-Brownian fibers, tumbling in a Poiseuille
flow between two parallel solid plane walls, is studied with the use of the
hydromultipole numerical code, based on the multipole expansion of the Stokes
equations, corrected for lubrication. It is shown that for a wide range of the
system parameters, the migration rate towards the middle plane of the channel
increases for fibers, which are closer to a wall, or are more flexible (less
stiff), or are longer. The faster motion towards the channel center is
accompanied by a slower translation along the flow and a larger fiber
deformation.Comment: 9 pages, 16 figure
MIGRATION OF FLEXIBLE FIBERS ENTRAINED BY POISEUILLE FLOW IN A MICROCHANNEL
Summary In this work, we consider a single non-Brownian mobile and flexible fiber immersed in Poiseuille flow in a channel consisting of two parallel infinite walls. The dynamics of the fiber is evaluated numerically from the Stokes equations by a multipole code HYDROMULTIPOLE. Investigating the fiber dynamics we found out that fibers migrate to a critical position across the channel. The distance between the wall and a limiting position depends on the fiber elongation and flexibility. For more stiff fibers the critical position results from the interplay between their tendency to drift away from the channel and the repulsive hydrodynamic interaction with the wall. For less stiff fibers the limiting position is not influenced by the presence of the wall. Differences between the critical position for different fibers can be used in the process of microfibers separation by the flow
Dynamics of flexible fibers and vesicles in Poiseuille flow at low Reynolds number
International audienc
Buckling of elastic fibers in a shear flow
Three-dimensional dynamics of flexible fibers in shear flow are studied numerically, with a qualitative comparison to experiments. Initially, the fibers are straight, with different orientations with respect to the flow. By changing the rotation speed of a shear rheometer, we change the ratio A of bending to shear forces. We observe fibers in the flow-vorticity plane, which gives insight into the motion out of the shear plane. The numerical simulations of moderately flexible fibers show that they rotate along effective Jeffery orbits, and therefore the fiber orientation rapidly becomes very close to the flow-vorticity plane, on average close to the flow direction, and the fiber remains in an almost straight configuration for a long time. This ‘ordering’ of fibers is temporary since they alternately bend and straighten while tumbling. We observe numerically and experimentally that if the fibers are initially in the compressional region of the shear flow, they can undergo compressional buckling, with a pronounced deformation of shape along their whole length during a short time, which is in contrast to the typical local bending that originates over a long time from the fiber ends. We identify differences between local and compressional bending and discuss their competition, which depends on the initial orientation of the fiber and the bending stiffness ratio A . There are two main finding. First, the compressional buckling is limited to a certain small range of the initial orientations, excluding those from the flow-vorticity plane. Second, since fibers straighten in the flow-vorticity plane while tumbling, the compressional buckling is transient—it does not appear for times longer than 1/4 of the Jeffery period. For larger times, bending of fibers is always driven by their ends
Reorientation Motion and Preferential Interactions of a Peptide in Denaturants and Osmolyte
Fluorescence anisotropy decay measurements
and all atom molecular
dynamics simulations are used to characterize the orientational motion
and preferential interaction of a peptide, <i>N</i>-acetyl-tryptophan-amide
(NATA) containing two peptide bonds, in aqueous, urea, guanidinium
chloride (GdmCl), and proline solution. Anisotropy decay measurements
as a function of temperature and concentration showed moderate slowing
of reorientations in urea and GdmCl and very strong slowing in proline
solution, relative to water. These effects deviate significantly from
simple proportionality of peptide tumbling time to solvent viscosity,
leading to the investigation of microscopic preferential interaction
behavior through molecular dynamics simulations. Examination of the
interactions of denaturants and osmolyte with the peptide backbone
uncovers the presence of strongest interaction with urea, intermediate
with proline, and weakest with GdmCl. In contrast, the strongest preferential
solvation of the peptide side chain is by the nonpolar part of the
proline zwitterion, followed by urea, and GdmCl. Interestingly, the
local density of urea around the side chain is higher, but the GdmCl
distribution is more organized. Thus, the computed preferential solvation
of the side chain by the denaturants and osmolyte can account for
the trend in reorientation rates. Analysis of water structure and
its dynamics uncovered underlying differences between urea, GdmCl,
and proline. Urea exerted the smallest perturbation of water behavior.
GdmCl had a larger effect on water, slowing kinetics and stabilizing
interactions. Proline had the largest overall interactions, exhibiting
a strong stabilizing effect on both water–water and water–peptide
hydrogen bonds. The results for this elementary peptide system demonstrate
significant differences in microscopic behavior of the examined solvent
environments. For the commonly used denaturants, urea tends to form
disorganized local aggregates around the peptide groups and has little
influence on water, while GdmCl only forms specific interactions with
the side chain and tends to destabilize water structure. The protective
osmolyte proline has the strongest and most specific interactions
with the tryptophan side chain, and also stabilizes both water–water
and water–peptide hydrogen bonds. Our results strongly suggest
protein or peptide denaturation triggered by urea occurs by direct
interaction, whereas GdmCl interacts favorably with side chains and
destabilizes peptide–water hydrogen bonds. The stabilization
of biopolymers by an osmolyte such as proline is governed by favorable
preferential interaction with the side chains and stabilization of
water