Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: The effect of the filament-obstacle interaction on the force-velocity
  relation of a growing biopolymer   We investigate the effect of filament-obstacle interactions on the
force-velocity relation of growing biopolymers, via calculations explicitly
treating obstacle diffusion and stochastic addition and subtraction of
subunits. We first show that the subunit on- and off-rates satisfy a rigorous
thermodynamic relationship determined by the filament-obstacle interaction
potential. Both the on- and off-rates depend not only on the average force on
the obstacle, but also on the shape of the potential on the nanometer length
scale. Basing obstacle-induced reduction of the on-rate entirely on the force
overestimates the stall force when there are fluctuations in the force exerted
on a filament tip. We then perform simulations and analytic calculations using
the thermodynamic relationship. We find, consistent with expectations from
general thermodynamic relations, that the "Brownian-Ratchet" model is an upper
bound to the growth velocity and that for purely repulsive potentials the
growth velocity is essentially that predicted by the Brownian-Ratchet model.
For shallow potential wells of depth ~ 5k_BT, which might correspond to
transient filament-membrane attachments, the zero-force velocity is a
substantial fraction of the free-filament velocity. In this case, the growth
velocity can depend strongly on the obstacle diffusion coefficient even when
the dimensionless diffusion coefficient is large. The velocity also drops more
rapidly than predicted by the Brownian-ratchet model, in some cases by as much
as a factor of 50 at an opposing force of 1 pN. For deep potential wells, as
might result from strong filament-membrane links, both the on- and off-rates
are reduced significantly, slowing polymerization. Such potentials can sustain
pulling forces while polymerizing, but only if the attractive well has a
"shelf" comparable to or greater than the monomer size.

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The categories of this paper are: stat
18
The categories of this paper are: econ
30
The categories of this paper are: q-alg
27
The categories of this paper are: comp-gas
4
The categories of this paper are: cond-mat
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The categories of this paper are: q-fin
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The categories of this paper are: eess
33
The categories of this paper are: plasm-ph
15
The categories of this paper are: nucl-ex
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The categories of this paper are: nlin
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The categories of this paper are: hep-th
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The categories of this paper are: math-ph
2
The categories of this paper are: math
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The categories of this paper are: quant-ph
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The categories of this paper are: supr-con
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The categories of this paper are: dg-ga