Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Green's Function Reaction Dynamics: a new approach to simulate
  biochemical networks at the particle level and in time and space   Biochemical networks are the analog computers of life. They allow living
cells to control a large number of biological processes, such as gene
expression and cell signalling. In biochemical networks, the concentrations of
the components are often low. This means that the discrete nature of the
reactants and the stochastic character of their interactions have to be taken
into account. Moreover, the spatial distribution of the components can be of
crucial importance. However, the current numerical techniques for simulating
biochemical networks either ignore the particulate nature of matter or treat
the spatial fluctuations in a mean-field manner. We have developed a new
technique, called Green's Function Reaction Dynamics (GFRD), that makes it
possible to simulate biochemical networks at the particle level and in both
time and space. In this scheme, a maximum time step is chosen such that only
single particles or pairs of particles have to be considered. For these
particles, the Smoluchowski equation can be solved analytically using Green's
functions. The main idea of GFRD is to exploit the exact solution of the
Smoluchoswki equation to set up an event-driven algorithm. This allows GFRD to
make large jumps in time when the particles are far apart from each other.
Here, we apply the technique to a simple model of gene expression. The
simulations reveal that the scheme is highly efficient. Under biologically
relevant conditions, GFRD is up to six orders of magnitude faster than
conventional particle-based techniques for simulating biochemical networks in
time and space.

5
The categories of this paper are: gr-qc
6
The categories of this paper are: astro-ph
23
The categories of this paper are: solv-int
32
The categories of this paper are: atom-ph
3
The categories of this paper are: physics
17
The categories of this paper are: q-fin
13
The categories of this paper are: quant-ph
14
The categories of this paper are: math-ph
1
The categories of this paper are: cs
19
The categories of this paper are: eess
15
The categories of this paper are: nucl-ex
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The categories of this paper are: acc-phys
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The categories of this paper are: patt-sol
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The categories of this paper are: dg-ga
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The categories of this paper are: cond-mat
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The categories of this paper are: hep-th