Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Variational Methods for Biomolecular Modeling   Structure, function and dynamics of many biomolecular systems can be
characterized by the energetic variational principle and the corresponding
systems of partial differential equations (PDEs). This principle allows us to
focus on the identification of essential energetic components, the optimal
parametrization of energies, and the efficient computational implementation of
energy variation or minimization. Given the fact that complex biomolecular
systems are structurally non-uniform and their interactions occur through
contact interfaces, their free energies are associated with various interfaces
as well, such as solute-solvent interface, molecular binding interface, lipid
domain interface, and membrane surfaces. This fact motivates the inclusion of
interface geometry, particular its curvatures, to the parametrization of free
energies. Applications of such interface geometry based energetic variational
principles are illustrated through three concrete topics: the multiscale
modeling of biomolecular electrostatics and solvation that includes the
curvature energy of the molecular surface, the formation of microdomains on
lipid membrane due to the geometric and molecular mechanics at the lipid
interface, and the mean curvature driven protein localization on membrane
surfaces. By further implicitly representing the interface using a phase field
function over the entire domain, one can simulate the dynamics of the interface
and the corresponding energy variation by evolving the phase field function,
achieving significant reduction of the number of degrees of freedom and
computational complexity. Strategies for improving the efficiency of
computational implementations and for extending applications to coarse-graining
or multiscale molecular simulations are outlined.

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The categories of this paper are: cond-mat
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The categories of this paper are: solv-int
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The categories of this paper are: hep-ex
22
The categories of this paper are: chao-dyn
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The categories of this paper are: quant-ph
11
The categories of this paper are: hep-lat
30
The categories of this paper are: q-alg
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The categories of this paper are: stat
25
The categories of this paper are: patt-sol
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The categories of this paper are: astro-ph
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The categories of this paper are: comp-gas
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The categories of this paper are: adap-org
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The categories of this paper are: atom-ph
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The categories of this paper are: q-fin
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The categories of this paper are: alg-geom
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The categories of this paper are: cs