361 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
Inverted critical adsorption of polyelectrolytes in confinement
What are the fundamental laws for the adsorption of charged polymers onto
oppositely charged surfaces, for convex, planar, and concave geometries? This
question is at the heart of surface coating applications, various complex
formation phenomena, as well as in the context of cellular and viral
biophysics. It has been a long-standing challenge in theoretical polymer
physics; for realistic systems the quantitative understanding is however often
achievable only by computer simulations. In this study, we present the findings
of such extensive Monte-Carlo in silico experiments for polymer-surface
adsorption in confined domains. We study the inverted critical adsorption of
finite-length polyelectrolytes in three fundamental geometries: planar slit,
cylindrical pore, and spherical cavity. The scaling relations extracted from
simulations for the critical surface charge density -defining the
adsorption-desorption transition-are in excellent agreement with our analytical
calculations based on the ground-state analysis of the Edwards equation. In
particular, we confirm the magnitude and scaling of for the concave
interfaces versus the Debye screening length and the extent of
confinement for these three interfaces for small values. For
large the critical adsorption condition approaches the planar limit.
The transition between the two regimes takes place when the radius of surface
curvature or half of the slit thickness is of the order of . We
also rationalize how gets modified for semi-flexible versus
flexible chains under external confinement. We examine the implications of the
chain length onto critical adsorption-the effect often hard to tackle
theoretically-putting an emphasis on polymers inside attractive spherical
cavities.Comment: 12 pages, 10 figures, RevTe
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