Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Molecular jamming - the cystine slipknot mechanical clamp in all-atom
  simulations   A recent survey of 17 134 proteins has identified a new class of proteins
which are expected to yield stretching induced force-peaks in the range of 1
nN. Such high force peaks should be due to forcing of a slip-loop through a
cystine ring, i.e. by generating a cystine slipknot. The survey has been
performed in a simple coarse grained model. Here, we perform all-atom steered
molecular dynamics simulations on 15 cystine knot proteins and determine their
resistance to stretching. In agreement with previous studies within a coarse
grained structure based model, the level of resistance is found to be
substantially higher than in proteins in which the mechanical clamp operates
through shear. The large stretching forces arise through formation of the
cystine slipknot mechanical clamp and the resulting steric jamming. We
elucidate the workings of such a clamp in an atomic detail. We also study the
behavior of five top strength proteins with the shear-based mechanostability in
which no jamming is involved. We show that in the atomic model, the jamming
state is relieved by moving one amino acid at a time and there is a choice in
the selection of the amino acid that advances the first. In contrast, the
coarse grained model also allows for a simultaneous passage of two amino acids.

14
The categories of this paper are: math-ph
26
The categories of this paper are: bayes-an
15
The categories of this paper are: nucl-ex
2
The categories of this paper are: math
4
The categories of this paper are: cond-mat
6
The categories of this paper are: astro-ph
32
The categories of this paper are: atom-ph
3
The categories of this paper are: physics
16
The categories of this paper are: stat
36
The categories of this paper are: cmp-lg
18
The categories of this paper are: econ
33
The categories of this paper are: plasm-ph
13
The categories of this paper are: quant-ph
8
The categories of this paper are: hep-ex
12
The categories of this paper are: nucl-th
34
The categories of this paper are: chem-ph