R. Abel, R. A. Friesner, T. Young, B. Kim, and B. J. Berne, Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding, Proc. Natl. Acad. Sci, vol.104, pp.808-813, 2007.

R. Abel, T. Young, R. Farid, B. J. Berne, and R. A. Friesner, Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding, J. Am. Chem. Soc, pp.2817-2831, 2008.

C. N. Nguyen, T. Young, and M. K. Gilson, Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril, J. Chem. Phys, vol.137, pp.973-980, 2012.

H. T. Nguyen, S. A. Pabit, S. P. Meisburger, L. Pollack, and D. A. Case, Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids, J. Chem. Phys, p.141, 2014.

M. Marchi, A first principle particle mesh method for solution SAXS of large bio-molecular systems, J. Chem. Phys, vol.145, 2016.

I. Altan, D. Fusco, P. V. Afonine, and P. Charbonneau, Learning about Biomolecular Solvation from Water in Protein Crystals, J. Phys. Chem. B, vol.122, pp.2475-2486, 2018.

M. E. Wall, G. Calabró, C. I. Bayly, D. L. Mobley, and G. L. Warren, Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations, J. Am. Chem. Soc, vol.141, pp.4711-4720, 2019.

L. H. Klausen, T. Fuhs, and M. Dong, Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy, Nature Communications, vol.7, p.12447, 2016.

J. Segura, A. Elbourne, E. J. Wanless, G. G. Warr, K. Voïtchovsky et al., Adsorbed and near surface structure of ionic liquids at a solid interface, Physical Chemistry Chemical Physics, vol.15, pp.3320-3328, 2013.

A. Elbourne, S. Mcdonald, K. Voïchovsky, F. Endres, G. G. Warr et al., Nanostructure of the Ionic Liquid-Graphite Stern Layer, ACS Nano, vol.9, pp.7608-7620, 2015.

B. Docampo-Álvarez, V. Gómez-gonzález, H. Montes-campos, J. M. Otero-mato, T. Méndez-morales et al., Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures, J. Phys.: Condens. Matter, vol.28, p.464001, 2016.

A. A. Kornyshev and R. Qiao, Three-Dimensional Double Layers, J. Phys. Chem. C, vol.118, pp.18285-18290, 2014.

C. Merlet, D. T. Limmer, M. Salanne, R. Van-roij, P. A. Madden et al., The Electric Double Layer Has a Life of Its Own, J. Phys. Chem. C, vol.118, pp.18291-18298, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00968897

G. Jeanmairet, B. Rotenberg, M. Levesque, D. Borgis, and M. Salanne, A molecular density functional theory approach to electron transfer reactions, Chemical Science, vol.10, pp.2130-2143, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02055678

C. Merlet, B. Rotenberg, P. A. Madden, P. Taberna, P. Simon et al., On the molecular origin of supercapacitance in nanoporous carbon electrodes, Nature Materials, vol.11, pp.306-310, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00853251

C. Merlet, C. Péan, B. Rotenberg, P. A. Madden, B. Daffos et al., Highly confined ions store charge more efficiently in supercapacitors, Nature Communications, vol.4, p.2701, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00909161

S. Kondrat, C. R. Pérez, V. Presser, Y. Gogotsi, and A. A. Kornyshev, Effect of pore size and its dispersity on the energy storage in nanoporous supercapacitors, Energy & Environmental Science, vol.5, pp.6474-6479, 2012.

M. Simoncelli, N. Ganfoud, A. Sene, M. Haefele, B. Daffos et al., Blue Energy and Desalination with Nanoporous Carbon Electrodes: Capacitance from Molecular Simulations to Continuous Models, Phys. Rev. X, vol.8, p.21024, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01826410

N. Yoshida, T. Imai, S. Phongphanphanee, A. Kovalenko, and F. Hirata, Molecular recognition in biomolecules studied by statistical-mechanical integral-equation theory of liquids, J. Phys. Chem. B, vol.113, pp.873-886, 2009.

M. C. Stumpe, N. Blinov, D. Wishart, A. Kovalenko, and V. S. Pande, Calculation of local water densities in biological systems: A comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation, J. Phys. Chem. B, vol.115, pp.319-328, 2011.

L. Ding, M. Levesque, D. Borgis, and L. Belloni, Efficient molecular density functional theory using generalized spherical harmonics expansions, J. Chem. Phys, p.147, 2017.
URL : https://hal.archives-ouvertes.fr/cea-01564512

S. Zhao, R. Ramirez, R. Vuilleumier, and D. Borgis, Molecular density functional theory of solvation: From polar solvents to water, J. Chem. Phys, vol.134, 2011.

G. Jeanmairet, M. Levesque, R. Vuilleumier, and D. Borgis, Molecular density functional theory of water, J. Phys. Chem. Lett, vol.4, pp.619-624, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01308802

D. Borgis, R. Assaraf, B. Rotenberg, and R. Vuilleumier, Computation of pair distribution functions and three-dimensional densities with a reduced variance principle, Molecular Physics, vol.111, pp.3486-3492, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01078958

D. De-las-heras and M. Schmidt, Better Than Counting: Density Profiles from Force Sampling, Phys. Rev. Lett, vol.120, p.218001, 2018.

A. Purohit, A. J. Schultz, and D. A. Kofke, Force-sampling methods for density distributions as instances of mapped averaging, Molecular Physics, vol.0, pp.1-8, 2019.

A. J. Schultz and D. A. Kofke, Current Opinion in Chemical Engineering Frontiers of Chemical Engineering: Molecular Modeling, vol.23, pp.70-76, 2019.

G. Ciccotti, R. Kapral, and E. Vanden-eijnden, Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics, ChemPhysChem, vol.6, pp.1809-1814, 2005.

H. J. Berendsen, J. R. Grigera, and T. P. Straatsma, The missing term in effective pair potentials, The Journal of Physical Chemistry, vol.91, pp.6269-6271, 1987.

M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith et al., GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers, 2015.

L. Martìnez, R. Andrade, E. G. Birgin, and J. M. Martínez, PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations, Journal of Computational Chemistry, vol.30, pp.2157-2164, 2009.

T. Darden, D. York, and L. Pedersen, Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems, J. Chem. Phys, vol.98, pp.10089-10092, 1993.

H. A. Posch, W. G. Hoover, and F. J. Vesely, Canonical dynamics of the Nos\'e oscillator: Stability, order, and chaos, Phys. Rev. A, vol.33, pp.4253-4265, 1986.

J. , From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package, Living Journal of Computational Molecular Science, vol.1, p.5068, 2018.

W. L. Jorgensen, D. S. Maxwell, and J. Tirado-rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, J. Am. Chem. Soc, vol.118, pp.11225-11236, 1996.

G. Bussi, D. Donadio, and M. Parrinello, Canonical sampling through velocity rescaling, J. Chem. Phys, vol.126, p.14101, 2007.

H. J. Berendsen, J. P. Postma, W. F. Van-gunsteren, A. Dinola, and J. R. Haak, Molecular dynamics with coupling to an external bath, J. Chem. Phys, vol.81, pp.3684-3690, 1984.

R. J. Gowers, M. Linke, J. Barnoud, J. E. Tyler, M. N. Reddy et al., MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations, Proceedings of the 15th Python in Science Conference, pp.98-105, 2016.

N. Michaud-agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein, MDAnalysis: A toolkit for the analysis of molecular dynamics simulations, Journal of Computational Chemistry, vol.32, pp.2319-2327, 2011.