Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Reweighting of molecular simulations with explicit-solvent SAXS
  restraints elucidates ion-dependent RNA ensembles   Small-angle X-ray scattering (SAXS) experiments are increasingly used to
probe RNA structure. A number of \emph{forward models} that relate measured
SAXS intensities and structural features, and that are suitable to model either
explicit-solvent effects or solute dynamics, have been proposed in the past
years. Here we introduce an approach that integrates atomistic molecular
dynamics simulations and SAXS experiments to reconstruct RNA structural
ensembles while simultaneously accounting for both RNA conformational dynamics
and explicit-solvent effects. Our protocol exploits SAXS pure-solute forward
models and enhanced sampling methods to sample an heterogenous ensemble of
structures, with no information towards the experiments provided on-the-fly.
The generated structural ensemble is then reweighted through the maximum
entropy principle so as to match reference SAXS experimental data at multiple
ionic conditions. Importantly, accurate explicit-solvent forward models are
used at this reweighting stage. We apply this framework to the
GTPase-associated center, a relevant RNA molecule involved in protein
translation, in order to elucidate its ion-dependent conformational ensembles.
We show that (a) both solvent and dynamics are crucial to reproduce
experimental SAXS data and (b) the resulting dynamical ensembles contain an
ion-dependent fraction of extended structures.

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The categories of this paper are: nucl-th
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The categories of this paper are: funct-an
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The categories of this paper are: plasm-ph
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The categories of this paper are: gr-qc
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The categories of this paper are: math-ph
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The categories of this paper are: astro-ph
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The categories of this paper are: hep-lat
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The categories of this paper are: patt-sol
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The categories of this paper are: q-alg
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The categories of this paper are: mtrl-th
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The categories of this paper are: acc-phys
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The categories of this paper are: comp-gas
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The categories of this paper are: dg-ga
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The categories of this paper are: atom-ph
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The categories of this paper are: supr-con
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The categories of this paper are: nucl-ex