Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Bimolecular binding rates for pairs of spherical molecules with small
  binding sites   Bimolecular binding rate constants are often used to describe the association
of large molecules, such as proteins. In this paper, we analyze a model for
such binding rates that includes the fact that pairs of molecules can bind only
in certain orientations. The model considers two spherical molecules, each with
an arbitrary number of small binding sites on their surface, and the two
molecules bind if and only if their binding sites come into contact (such
molecules are often called "patchy particles" in the biochemistry literature).
The molecules undergo translational and rotational diffusion, and the binding
sites are allowed to diffuse on their surfaces. Mathematically, the model takes
the form of a high-dimensional, anisotropic diffusion equation with mixed
boundary conditions. We apply matched asymptotic analysis to derive the
bimolecular binding rate in the limit of small, well-separated binding sites.
The resulting binding rate formula involves a factor that depends on the
electrostatic capacitance of a certain four-dimensional region embedded in five
dimensions. We compute this factor numerically by modifying a recent kinetic
Monte Carlo algorithm. We then apply a quasi chemical formalism to obtain a
simple analytical approximation for this factor and find a binding rate formula
that includes the effects of binding site competition/saturation. We verify our
results by numerical simulation.

14
The categories of this paper are: math-ph
30
The categories of this paper are: q-alg
27
The categories of this paper are: comp-gas
11
The categories of this paper are: hep-lat
8
The categories of this paper are: hep-ex
19
The categories of this paper are: eess
5
The categories of this paper are: gr-qc
25
The categories of this paper are: patt-sol
23
The categories of this paper are: solv-int
1
The categories of this paper are: cs
33
The categories of this paper are: plasm-ph
35
The categories of this paper are: mtrl-th
16
The categories of this paper are: stat
15
The categories of this paper are: nucl-ex
9
The categories of this paper are: nlin
7
The categories of this paper are: hep-th