Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: How cooperatively folding are homopolymer molecular knots?   Detailed thermodynamic analysis of complex systems with multiple stable
configurational states allows for insight into the cooperativity of each
individual transition. In this work we derive a heat capacity decomposition
comprising contributions from each individual configurational state, which
together sum to a baseline heat capacity, and contributions from each
state-to-state transition. We apply this analysis framework to a series of
replica exchange molecular dynamics simulations of linear and 1-1
coarse-grained homo-oligomer models which fold into stable, configurationally
well-defined molecular knots, in order to better understand the parameters
leading to stable and cooperative folding of these knots. We find that a stiff
harmonic backbone bending angle potential is key to achieving knots with
specific 3D structures. Tuning the backbone equilibrium angle in small
increments yields a variety of knot topologies, including $3_1$, $5_1$, $7_1$,
and $8_{19}$ types. Populations of different knotted states as functions of
temperature can also be manipulated by tuning backbone torsion stiffness or by
adding side chain beads. We find that sharp total heat capacity peaks for the
homo-oligomer knots are largely due to a coil-to-globule transition, rather
than a cooperative knotting step. However, in some cases the cooperativity of
globule-to-knot and coil-to-globule transitions are comparable, suggesting that
highly cooperative folding to knotted structures can be achieved by refining
the model parameters or adding sequence specificity.

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The categories of this paper are: astro-ph
20
The categories of this paper are: acc-phys
37
The categories of this paper are: supr-con
29
The categories of this paper are: funct-an
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The categories of this paper are: q-bio
25
The categories of this paper are: patt-sol
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The categories of this paper are: chem-ph
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The categories of this paper are: cs
35
The categories of this paper are: mtrl-th
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The categories of this paper are: plasm-ph
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The categories of this paper are: adap-org
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The categories of this paper are: physics
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The categories of this paper are: math-ph
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The categories of this paper are: gr-qc
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The categories of this paper are: solv-int
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The categories of this paper are: q-fin