Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Mapping energy transport networks in proteins   The response of proteins to chemical reactions or impulsive excitation that
occurs within the molecule has fascinated chemists for decades. In recent years
ultrafast X-ray studies have provided ever more detailed information about the
evolution of protein structural change following ligand photolysis, and
time-resolved IR and Raman techniques, e.g., have provided detailed pictures of
the nature and rate of energy transport in peptides and proteins, including
recent advances in identifying transport through individual amino acids of
several heme proteins. Computational tools to locate energy transport pathways
in proteins have also been advancing. Energy transport pathways in proteins
have since some time been identified by molecular dynamics (MD) simulations,
and more recent efforts have focused on the development of coarse graining
approaches, some of which have exploited analogies to thermal transport in
other molecular materials. With the identification of pathways in proteins and
protein complexes, network analysis has been applied to locate residues that
control protein dynamics and possibly allostery, where chemical reactions at
one binding site mediate reactions at distance sites of the protein. In this
chapter we review approaches for locating computationally energy transport
networks in proteins. We present background into energy and thermal transport
in condensed phase and macromolecules that underlies the approaches we discuss
before turning to a description of the approaches themselves. We also
illustrate the application of the computational methods for locating energy
transport networks and simulating energy dynamics in proteins with several
examples.

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The categories of this paper are: stat
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The categories of this paper are: math-ph
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The categories of this paper are: hep-ex
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The categories of this paper are: hep-lat
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The categories of this paper are: supr-con
0
The categories of this paper are: hep-ph
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The categories of this paper are: cs
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The categories of this paper are: solv-int
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The categories of this paper are: alg-geom
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The categories of this paper are: chao-dyn
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The categories of this paper are: gr-qc
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The categories of this paper are: adap-org
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The categories of this paper are: q-fin
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The categories of this paper are: patt-sol
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The categories of this paper are: comp-gas
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The categories of this paper are: eess