Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Origin of Scaling Behavior of Protein Packing Density: A Sequential
  Monte Carlo Study of Compact Long Chain Polymers   Single domain proteins are thought to be tightly packed. The introduction of
voids by mutations is often regarded as destabilizing. In this study we show
that packing density for single domain proteins decreases with chain length. We
find that the radius of gyration provides poor description of protein packing
but the alpha contact number we introduce here characterize proteins well. We
further demonstrate that protein-like scaling relationship between packing
density and chain length is observed in off-lattice self-avoiding walks. A key
problem in studying compact chain polymer is the attrition problem: It is
difficult to generate independent samples of compact long self-avoiding walks.
We develop an algorithm based on the framework of sequential Monte Carlo and
succeed in generating populations of compact long chain off-lattice polymers up
to length $N=2,000$. Results based on analysis of these chain polymers suggest
that maintaining high packing density is only characteristic of short chain
proteins. We found that the scaling behavior of packing density with chain
length of proteins is a generic feature of random polymers satisfying loose
constraint in compactness. We conclude that proteins are not optimized by
evolution to eliminate packing voids.

23
The categories of this paper are: solv-int
17
The categories of this paper are: q-fin
33
The categories of this paper are: plasm-ph
29
The categories of this paper are: funct-an
7
The categories of this paper are: hep-th
12
The categories of this paper are: nucl-th
35
The categories of this paper are: mtrl-th
21
The categories of this paper are: adap-org
34
The categories of this paper are: chem-ph
16
The categories of this paper are: stat
14
The categories of this paper are: math-ph
5
The categories of this paper are: gr-qc
13
The categories of this paper are: quant-ph
0
The categories of this paper are: hep-ph
28
The categories of this paper are: alg-geom
27
The categories of this paper are: comp-gas