Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Hairpins Participating in Folding of Human Telomeric Sequence
  Quadruplexes Studied by Standard and T-REMD Simulations   DNA G-hairpins are potential key structures participating in folding of human
telomeric guanine quadruplexes (GQ). We examined their properties by standard
MD simulations starting from the folded state and long T-REMD starting from the
unfolded state, accumulating ~130 {\mu}s of atomistic simulations. Antiparallel
G-hairpins should spontaneously form in all stages of the folding to support
lateral and diagonal loops, with sub-{\mu}s scale rearrangements between them.
We found no clear predisposition for direct folding into specific GQ topologies
with specific syn/anti patterns. Our key prediction stemming from the T-REMD is
that an ideal unfolded ensemble of the full GQ sequence populates all 4096
syn/anti combinations of its four G-stretches. The simulations can propose
idealized folding pathways but we explain that such few-state pathways may be
misleading. In the context of the available experimental data, the simulations
strongly suggest that the GQ folding could be best understood by the kinetic
partitioning mechanism with a set of deep competing minima on the folding
landscape, with only a small fraction of molecules directly folding to the
native fold. The landscape should further include nonspecific collapse
processes where the molecules move via diffusion and consecutive random rare
transitions, which could, e.g., structure the propeller loops.

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The categories of this paper are: hep-ex
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The categories of this paper are: solv-int
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The categories of this paper are: adap-org
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The categories of this paper are: stat
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The categories of this paper are: econ
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The categories of this paper are: gr-qc
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The categories of this paper are: math
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The categories of this paper are: hep-lat
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The categories of this paper are: plasm-ph
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The categories of this paper are: q-fin
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The categories of this paper are: comp-gas
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The categories of this paper are: atom-ph
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The categories of this paper are: hep-th
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The categories of this paper are: cond-mat
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The categories of this paper are: acc-phys
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The categories of this paper are: cmp-lg