45 research outputs found
How a single stretched polymer responds coherently to a minute oscillation in fluctuating environments: An entropic stochastic resonance
Within the cell, biopolymers are often situated in constrained, fluid
environments, e.g., cytoskeletal networks, stretched DNAs in chromatin. It is
of paramount importance to understand quantitatively how they, utilizing their
flexibility, optimally respond to a minute signal, which is, in general,
temporally fluctuating far away from equilibrium. To this end, we analytically
study viscoelastic response and associated stochastic resonance in a stretched
single semi-flexible chain to an oscillatory force or electric field. Including
hydrodynamic interactions between chain segments, we evaluate dynamics of the
polymer extension in coherent response to the force or field. We find power
amplification factor of the response at a noise-strength (temperature) can
attain the maximum that grows as the chain length increases, indicative of an
entropic stochastic resonance (ESR). In particular for a charged chain under an
electric field, we find that the maximum also occurs at an optimal chain
length, a new feature of ESR. The hydrodynamic interaction is found to enhance
the power amplification, representing unique polymer cooperativity which the
fluid background imparts despite its overdamping nature. For the slow
oscillatory force, the resonance behavior is explained by the chain undulation
of the longest wavelength. This novel ESR phenomenon suggests how a biopolymer
self-organizes in an overdamping environment, utilizing its flexibility and
thermal fluctuations
Polymer translocation induced by adsorption
We study the translocation of a flexible polymer through a pore in a membrane
induced by its adsorption on \trans side of the membrane. When temperature
is higher than , the adsorption-desorption transition temperature,
attractive interaction between polymer and membrane plays little role in
affecting polymer conformation, leading to translocation time that scales as
where is the polymer contour length. When ,
however, the translocation time undergoes a sharp crossover to
for sufficiently long polymers, following the second order conformational
(adsorption) transition. The translocation time is found to exhibit the
crossover around , which is lower than for polymers shorter than
a critical length().Comment: 19 pages RevTeX, 5 postscript figures, to be published in J. Chem.
Phys. 108(7), 3013 (1998
Scaling theory of driven polymer translocation
We present a theoretical argument to derive a scaling law between the mean
translocation time and the chain length for driven polymer
translocation. This scaling law explicitly takes into account the pore-polymer
interactions, which appear as a correction term to asymptotic scaling and are
responsible for the dominant finite size effects in the process. By eliminating
the correction-to-scaling term we introduce a rescaled translocation time and
show, by employing both the Brownian Dynamics Tension Propagation theory
[Ikonen {\it et al.}, Phys. Rev. E {\bf 85}, 051803 (2012)] and molecular
dynamics simulations that the rescaled exponent reaches the asymptotic limit in
a range of chain lengths that is easily accessible to simulations and
experiments. The rescaling procedure can also be used to quantitatively
estimate the magnitude of the pore-polymer interaction from simulations or
experimental data. Finally, we also consider the case of driven translocation
with hydrodynamic interactions (HIs). We show that by augmenting the BDTP
theory with HIs one reaches a good agreement between the theory and previous
simulation results found in the literature. Our results suggest that the
scaling relation between and is retained even in this case.Comment: 5 pages, 4 figure
Polymer Release out of a Spherical Vesicle through a Pore
Translocation of a polymer out of curved surface or membrane is studied via
mean first passage time approach. Membrane curvature gives rise to a constraint
on polymer conformation, which effectively drives the polymer to the outside of
membrane where the available volume of polymer conformational fluctuation is
larger. Considering a polymer release out of spherical vesicle, polymer
translocation time is changed to the scaling behavior for
, from for , where is the polymer contour
length and , are vesicle radius and polymer radius of gyration
respectively. Also the polymer capture into a spherical budd is studied and
possible apparatus for easy capture is suggested.Comment: 14 pages RevTeX, 6 postscript figures, published in Phys. Rev. E 57,
730 (1998
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
How dsDNA breathing enhances its flexibility and instability on short length scales
We study the unexpected high flexibility of short dsDNA which recently has
been reported by a number of experiments. Via the Langevin dynamics simulation
of our Breathing DNA model, first we observe the formation of bubbles within
the duplex and also forks at the ends, with the size distributions independent
of the contour length. We find that these local denaturations at a
physiological temperature, despite their rare and transient presence, can lower
the persistence length drastically for a short DNA segment in agreement with
experiment
Stochastic Resonance of a Flexible Chain Crossing over a Barrier
We study the stochastic resonance (SR) of a flexible polymer surmounting a
bistable-potential barrier. Due to the flexibility that can enhance crossing
rate and change chain conformations at the barrier, the SR behaviors manifest
many features of an entropic SR of a new kind, such as the power amplification
peaks at optimal chain lengths and elastic constants as well as the optimal
noise strengths. The pronounced peaks that emerge depending on the chain
lengths and conformation states suggest novel means of manipulating
biopolymers, such as efficient separation methods, within undulating channels.Comment: 13 pages, 9 figure
Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions
We study the driven translocation of polymers under time-dependent driving forces using N-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.Peer reviewe