Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Single molecule simulations in complex geometries with embedded dynamic
  one-dimensional structures   Stochastic models of reaction-diffusion systems are important for the study
of biochemical reaction networks where species are present in low copy numbers
or if reactions are highly diffusion limited. In living cells many such systems
include reactions and transport on one-dimensional structures, such as DNA and
microtubules. The cytoskeleton is a dynamic structure where individual fibers
move, grow and shrink. In this paper we present a simulation algorithm that
combines single molecule simulations in three-dimensional space with single
molecule simulations on one-dimensional structures of arbitrary shape.
Molecules diffuse and react with each other in space, they associate to and
dissociate from one-dimensional structures as well as diffuse and react with
each other on the one-dimensional structure. A general curve embedded in space
can be approximated by a piecewise linear curve to arbitrary accuracy. The
resulting algorithm is hence very flexible. Molecules bound to a curve can move
by pure diffusion or via active transport, and the curve can move in space as
well as grow and shrink. The flexibility and accuracy of the algorithm is
demonstrated in four numerical examples.

4
The categories of this paper are: cond-mat
9
The categories of this paper are: nlin
15
The categories of this paper are: nucl-ex
7
The categories of this paper are: hep-th
5
The categories of this paper are: gr-qc
32
The categories of this paper are: atom-ph
22
The categories of this paper are: chao-dyn
18
The categories of this paper are: econ
20
The categories of this paper are: acc-phys
31
The categories of this paper are: ao-sci
27
The categories of this paper are: comp-gas
23
The categories of this paper are: solv-int
12
The categories of this paper are: nucl-th
16
The categories of this paper are: stat
6
The categories of this paper are: astro-ph
1
The categories of this paper are: cs