27 research outputs found
Self-subdiffusion in solutions of star-shaped crowders: non-monotonic effects of inter-particle interactions
We examine by extensive computer simulations the self-diffusion of
anisotropic star like particles in crowded two-dimensional solutions. We
investigate the implications of the area coverage fraction of the
crowders and the crowder-crowder adhesion properties on the regime of transient
anomalous diffusion. We systematically compute the mean squared displacement
(MSD) of the particles, their time averaged MSD, as well as the effective
diffusion coefficient. The diffusion appears ergodic in the limit of long
traces, such that the time averaged MSD converges towards the ensemble averaged
MSD and features a small residual amplitude spread of the time averaged MSD
from individual trajectories. At intermediate time scales we quantify the
anomalous diffusion in the system. Also, we show that the translational---but
not rotational---diffusivity of the particles is a non-monotonic function
of the attraction strength between them. Both diffusion coefficients decrease
as with the area fraction occupied by
the crowders. Our results might be applicable to rationalising the experimental
observations of non-Brownian diffusion for a number of standard macromolecular
crowders used in vitro to mimic the cytoplasmic conditions of living cells.Comment: 16 pages, 7 figure
Sensing viruses by mechanical tension of DNA in responsive hydrogels
The rapid worldwide spread of severe viral infections, often involving novel
modifications of viruses, poses major challenges to our health care systems.
This means that tools that can efficiently and specifically diagnose viruses
are much needed. To be relevant for a broad application in local health care
centers, such tools should be relatively cheap and easy to use. Here we discuss
the biophysical potential for the macroscopic detection of viruses based on the
induction of a mechanical stress in a bundle of pre-stretched DNA molecules
upon binding of viruses to the DNA. We show that the affinity of the DNA to the
charged virus surface induces a local melting of the double-helix into two
single-stranded DNA. This process effects a mechanical stress along the DNA
chains leading to an overall contraction of the DNA. Our results suggest that
when such DNA bundles are incorporated in a supporting matrix such as a
responsive hydrogel, the presence of viruses may indeed lead to a significant,
macroscopic mechanical deformation of the matrix. We discuss the biophysical
basis for this effect and characterize the physical properties of the
associated DNA melting transition. In particular, we reveal several scaling
relations between the relevant physical parameters of the system. We promote
this DNA-based assay for efficient and specific virus screening.Comment: 11 pages, 7 figures, supplementary material included in the source
file
Elasticity-based polymer sorting in active fluids: A Brownian dynamics study
While the dynamics of polymer chains in equilibrium media is well understood
by now, the polymer dynamics in active non-equilibrium environments can be very
different. Here we study the dynamics of polymers in a viscous medium
containing self-propelled particles in two dimensions by using Brownian
dynamics simulations. We find that the polymer center of mass exhibits a
superdiffusive motion at short to intermediate times and the motion turns
normal at long times, but with a greatly enhanced diffusivity. Interestingly,
the long time diffusivity shows a non-monotonic behavior as a function of the
chain length and stiffness. We analyze how the polymer conformation and the
accumulation of the self-propelled particles, and therefore the directed motion
of the polymer, are correlated. At the point of maximal polymer diffusivity,
the polymer has preferentially bent conformations maintained by the balance
between the chain elasticity and the propelling force generated by the active
particles. We also consider the barrier crossing dynamics of actively-driven
polymers in a double-well potential. The barrier crossing times are
demonstrated to have a peculiar non-monotonic dependence, related to that of
the diffusivity. This effect can be potentially utilized for sorting of
polymers from solutions in \textit{in vitro} experiments.Comment: 11 pages, 7 figure
Effects of static and temporally fluctuating tensions on semiflexible polymer looping
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for
gene regulation, protein folding, etc. In cellular environments, biopolymers
are often subject to tensions which are either static, or temporally
fluctuating far away from equilibrium. We study the dynamics of semiflexible
polymer looping in the presence of such tensions by using Brownian dynamics
simulation combined with an analytical theory. We show a minute tension
dramatically changes the looping time, especially for long chains. Considering
a dichotomically flipping noise as a simple example of the nonequilibrium
tension, we find the phenomenon of resonant activation, where the looping time
can be the minimum at an optimal flipping time. We discuss our results in
connection with recent experiments.Comment: 7 pages, 8 figures, accepted in the Journal of Chemical Physic