

FOLLOWUS
a.Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
b.University of Chinese Academy of Sciences, Beijing 100049, China
jiangj@iccas.ac.cn
Received:05 August 2021,
Revised:2021-8-27,
Accepted:01 September 2021,
Online First:09 November 2021,
Published:01 February 2022
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Jiang, J. Software package: an advanced theoretical tool for inhomogeneous fluids (Atif). Chinese J. Polym. Sci. 2022, 40, 220–230
Jian Jiang. Software Package: An Advanced Theoretical Tool for Inhomogeneous Fluids (
Jiang, J. Software package: an advanced theoretical tool for inhomogeneous fluids (Atif). Chinese J. Polym. Sci. 2022, 40, 220–230 DOI: 10.1007/s10118-021-2646-4.
Jian Jiang. Software Package: An Advanced Theoretical Tool for Inhomogeneous Fluids (
In spite of the impending flattening of Moore's law
the complexity and size of the systems we are interested in keep on increasing. This challenges the computer simulation tools due to the expensive computational cost. Fortunately
advanced theoretical methods can be considered as alternatives to accurately and efficiently capture the structural and thermodynamic properties of complex inhomogeneous fluids. In the last decades
classical density functional theory (cDFT) has proven to be a sophisticated
robust
and efficient approach for studying complex inhomogeneous fluids. In this work
we present a pedagogical introduction to a broadly accessible open-source density functional theory software package named "an advanced theoretical tool for inhomogeneous fluids" (
Atif
) and of the underlying theory. To demonstrate
Atif
we take three cases as examples using a typical laptop computer: (i) electric double-layer of asymmetric electrolytes; (ii) adsorptions of sequence-defined semiflexible polyelectrolytes on an oppositely charged surface; and (iii) interactions between surfaces mediated by polyelectrolytes. We believe that this pedagogical introduction will lower the barrier to entry to the use of
Atif
by experimental as well as theoretical groups. A companion website
which provides all of the relevant sources including codes and examples
is attached.
Yu, Y. X.; Wu, J.; Gao, G. H . Density-functional theory of spherical electric double layers and Zeta potentials of colloidal particles in restricted-primitive-model electrolyte solutions . J. Chem. Phys. , 2004 . 120 7223 - 7233 . DOI: 10.1063/1.1676121 http://doi.org/10.1063/1.1676121 .
Wu, J . Density functional theory for chemical engineering: from capillarity to soft materials . AIChE J. , 2006 . 52 1169 - 1193 . DOI: 10.1002/aic.10713 http://doi.org/10.1002/aic.10713 .
Wu, J.; Li, Z . Density-functional theory for complex fluids . Annu. Rev. Phys. Chem. , 2007 . 58 85 - 112 . DOI: 10.1146/annurev.physchem.58.032806.104650 http://doi.org/10.1146/annurev.physchem.58.032806.104650 .
Hohenberg, P.; Kohn, W . Inhomogeneous electron gas . Phys. Rev. , 1964 . 136 B864 - B871 . DOI: 10.1103/PhysRev.136.B864 http://doi.org/10.1103/PhysRev.136.B864 .
Mermin, N. D . Thermal properties of the inhomogeneous electron gas . Phys. Rev. , 1965 . 137 A1441 - A1443 . DOI: 10.1103/PhysRev.137.A1441 http://doi.org/10.1103/PhysRev.137.A1441 .
Evans, R . The nature of the liquid-vapour interface and other topics in the statistical mechanics of non-uniform, classical fluids . Adv. Phys. , 1979 . 28 143 - 200 . DOI: 10.1080/00018737900101365 http://doi.org/10.1080/00018737900101365 .
Tarazona, P . A density functional theory of melting . Mol. Phys. , 1984 . 52 81 - 96 . DOI: 10.1080/00268978400101071 http://doi.org/10.1080/00268978400101071 .
Rosenfeld, Y . Free-energy model for the inhomogeneous hard-sphere fluid mixture and density-functional theory of freezing . Phys. Rev. Lett. , 1989 . 63 980 - 983 . DOI: 10.1103/PhysRevLett.63.980 http://doi.org/10.1103/PhysRevLett.63.980 .
Mier-y-Teran, L.; Suh, S. H.; White, H. S.; Davis, H. T . A nonlocal free-energy density-functional approximation for the electrical double layer . J. Chem. Phys. , 1990 . 92 5087 - 5098 . DOI: 10.1063/1.458542 http://doi.org/10.1063/1.458542 .
Tang, Z.; Scriven, L. E.; Davis, H. T . A three-component model of the electrical double layer . J. Chem. Phys. , 1992 . 97 494 - 503 . DOI: 10.1063/1.463595 http://doi.org/10.1063/1.463595 .
Kierlik, E.; Rosinberg, M. L . Free-energy density functional for the inhomogeneous hard-sphere fluid: application to interfacial adsorption . Phys. Rev. A , 1990 . 42 3382 - 3387 . DOI: 10.1103/PhysRevA.42.3382 http://doi.org/10.1103/PhysRevA.42.3382 .
Woodward, C. E.; Yethiraj, A . Density functional theory for inhomogeneous polymer solutions . J. Chem. Phys. , 1994 . 100 3181 - 3186 . DOI: 10.1063/1.466409 http://doi.org/10.1063/1.466409 .
Li, Z.; Wu, J . Density functional theory for polyelectrolytes near oppositely charged surfaces . Phys. Rev. Lett. , 2006 . 96 048302 - 048305 . DOI: 10.1103/PhysRevLett.96.048302 http://doi.org/10.1103/PhysRevLett.96.048302 .
Wertheim, M. S . Fluids with highly directional attractive forces. I. Statistical thermodynamics . J. Stat. Phys. , 1984 . 35 19 - 34 . DOI: 10.1007/BF01017362 http://doi.org/10.1007/BF01017362 .
Wertheim, M. S . Fluids with highly directional attractive forces. II. Thermodynamic perturbation theory and integral equations . J. Stat. Phys. , 1984 . 35 35 - 47 . DOI: 10.1007/BF01017363 http://doi.org/10.1007/BF01017363 .
Wertheim, M. S . Fluids with highly directional attractive forces. III. Multiple attraction sites . J. Stat. Phys. , 1986 . 42 459 - 476 . DOI: 10.1007/BF01127721 http://doi.org/10.1007/BF01127721 .
Wertheim, M. S . Fluids with highly directional attractive forces. IV. Equilibrium polymerization . J. Stat. Phys. , 1986 . 42 477 - 492 . DOI: 10.1007/BF01127722 http://doi.org/10.1007/BF01127722 .
Wertheim, M. S . Fluids of dimerizing hard spheres, and fluid mixtures of hard spheres and dispheres . J. Chem. Phys. , 1986 . 85 2929 - 2936 . DOI: 10.1063/1.451002 http://doi.org/10.1063/1.451002 .
Wertheim, M. S . Thermodynamic perturbation theory of polymerization . J. Chem. Phys. , 1987 . 87 7323 - 7331 . DOI: 10.1063/1.453326 http://doi.org/10.1063/1.453326 .
Wertheim, M. S . Integral equation for the Smith-Nezbeda model of associated fluids . J. Chem. Phys. , 1988 . 88 1145 - 1155 . DOI: 10.1063/1.454233 http://doi.org/10.1063/1.454233 .
Jiang, J. W.; Liu, H.; Hu, Y.; Prausnitz, J. M . A molecular-thermodynamic model for polyelectrolyte solutions . J. Chem. Phys. , 1998 . 108 780 - 784 . DOI: 10.1063/1.475438 http://doi.org/10.1063/1.475438 .
Jiang, J. W.; Blum, L.; Bernard, O.; Prausnitz, J. M . Thermodynamic properties and phase equilibria of charged hard sphere chain model for polyelectrolyte solutions . Mol. Phys. , 2001 . 99 1121 - 1128 . DOI: 10.1080/00268970110043414 http://doi.org/10.1080/00268970110043414 .
Yu, Y. X.; Wu, J . Structures of hard-sphere fluids from a modified fundamental-measure theory . J. Chem. Phys. , 2002 . 117 10156 - 10164 . DOI: 10.1063/1.1520530 http://doi.org/10.1063/1.1520530 .
Roth, R.; Evans, R.; Lang, A.; Kahl, G . Fundamental measure theory for hard-sphere mixtures revisited: the White Bear version . J. Phys.: Condens. Matter , 2002 . 14 12063 - 12078 . DOI: 10.1088/0953-8984/14/46/313 http://doi.org/10.1088/0953-8984/14/46/313 .
Jiang, J.; Ginzburg, V. V.; Wang, Z. G . Density functional theory for charged fluids . Soft Matter , 2018 . 14 5878 - 5887 . DOI: 10.1039/C8SM00595H http://doi.org/10.1039/C8SM00595H .
Blum, L . Mean spherical model for asymmetric electrolytes . Mol. Phys. , 1975 . 30 1529 - 1535 . DOI: 10.1080/00268977500103051 http://doi.org/10.1080/00268977500103051 .
Blum, L.; Hoeye, J. S . Mean spherical model for asymmetric electrolytes. 2. Thermodynamic properties and the pair correlation function . J. Phys. Chem. , 1977 . 81 1311 - 1316 . DOI: 10.1021/j100528a019 http://doi.org/10.1021/j100528a019 .
Hiroike, K . Supplement to Blum's theory for asymmetric electrolytes . Mol. Phys. , 1977 . 33 1195 - 1198 . DOI: 10.1080/00268977700101011 http://doi.org/10.1080/00268977700101011 .
Forsman, J.; Nordholm, S . Polyelectrolyte mediated interactions in colloidal dispersions: hierarchical screening, simulations, and a new classical density functional theory . Langmuir , 2012 . 28 4069 - 4079 . DOI: 10.1021/la2045459 http://doi.org/10.1021/la2045459 .
Forsman, J . Polyelectrolyte adsorption: electrostatic mechanisms and nonmonotonic responses to salt addition . Langmuir , 2012 . 28 5138 - 5150 . DOI: 10.1021/la3000735 http://doi.org/10.1021/la3000735 .
Sandia National Laboratories, Tramonto. https://software.sandia.gov/tramonto/index.html https://software.sandia.gov/tramonto/index.html .
Jiang, J . Non-monotonic effects of intrinsic stiffness and concentration of polyelectrolytes on the electro-sorption . Macromolecules , 2021 . 54 1801 - 1810 . DOI: 10.1021/acs.macromol.0c02472 http://doi.org/10.1021/acs.macromol.0c02472 .
Chang, Q.; Jiang, J . Adsorption of block-polyelectrolytes on an oppositely charged surface . Macromolecules , 2021 . 54 4145 - 4153 . DOI: 10.1021/acs.macromol.1c00165 http://doi.org/10.1021/acs.macromol.1c00165 .
Kratky, O.; Porod, G . Röntgenuntersuchung gelöster Fadenmoleküle . Recl. Trav. Chim. Pays-Bas , 1949 . 68 1106 - 1122 . DOI: 10.1002/recl.19490681203 http://doi.org/10.1002/recl.19490681203 .
Grosberg, A. Y.; Khokhlov, A. R.; Onuchic, J. N . Statistical physics of macromolecules . Phys. Today , 1995 . 48 92 - 93 . .
Rubinstein, M.; Colby, R. In Polymer Physics ; Rubinstein, M., Colby, R., Eds.; Oxford University Press: New York: NY, USA, 2003 .
Reisner, W.; Pedersen, J. N.; Austin, R. H . DNA confinement in nanochannels: physics and biological applications . Rep. Prog. Phys. , 2012 . 75 106601 - 106634 . DOI: 10.1088/0034-4885/75/10/106601 http://doi.org/10.1088/0034-4885/75/10/106601 .
Köster, S.; Weitz, D. A.; Goldman, R. D.; Aebi, U.; Herrmann, H . Intermediate filament mechanics in vitro and in the cell: from coiled coils to filaments, fibers and networks . Curr. Opin. Cell Biol. , 2015 . 32 82 - 91 . DOI: 10.1016/j.ceb.2015.01.001 http://doi.org/10.1016/j.ceb.2015.01.001 .
Marantan, A.; Mahadevan, L . Mechanics and statistics of the worm-like chain . Am. J. Phys. , 2018 . 86 86 DOI: 10.1119/1.5003376 http://doi.org/10.1119/1.5003376 .
Honnell, K. G.; Curro, J. G.; Schweizer, K. S . Local structure of semiflexible polymer melts . Macromolecules , 1990 . 23 3496 - 3505 . DOI: 10.1021/ma00216a018 http://doi.org/10.1021/ma00216a018 .
Phan, S.; Kierlik, E.; Rosinberg, M. L.; Yethiraj, A.; Dickman, R . Perturbation density functional theory and Monte Carlo simulations for the structure of hard triatomic fluids in slitlike pores . J. Chem. Phys. , 1995 . 102 2141 - 2150 . DOI: 10.1063/1.468735 http://doi.org/10.1063/1.468735 .
Forsman, J.; Woodward, C. E . An improved density functional description of hard sphere polymer fluids at low density . J. Chem. Phys. , 2003 . 119 1889 - 1892 . DOI: 10.1063/1.1595646 http://doi.org/10.1063/1.1595646 .
Cao, D.; Wu, J . Density functional theory for semiflexible and cyclic polyatomic fluids . J. Chem. Phys. , 2004 . 121 4210 - 4220 . DOI: 10.1063/1.1774983 http://doi.org/10.1063/1.1774983 .
Forsman, J.; Woodward, C. E . Surface forces in solutions containing rigid polymers: approaching the rod limit . Macromolecules , 2006 . 39 1269 - 1278 . DOI: 10.1021/ma052472+ http://doi.org/10.1021/ma052472+ .
Turesson, M.; Forsman, J.; Åkesson, T . Surface forces mediated by charged polymers: effects of intrinsic chain stiffness . Langmuir , 2006 . 22 5734 - 5741 . DOI: 10.1021/la0604735 http://doi.org/10.1021/la0604735 .
Turesson, M.; Woodward, C. E.; Åkesson, T.; Forsman, J . simulations of surface forces in polyelectrolyte solutions . J. Phys. Chem. B , 2008 . 112 5116 - 5125 . DOI: 10.1021/jp800632e http://doi.org/10.1021/jp800632e .
Egorov, S. A.; Milchev, A.; Virnau, P.; Binder, K . Semiflexible polymers under good solvent conditions interacting with repulsive walls . J. Chem. Phys. , 2016 . 144 174902 - 174914 . DOI: 10.1063/1.4947254 http://doi.org/10.1063/1.4947254 .
Milchev, A.; Binder, K . How does stiffness of polymer chains affect their adsorption transition? . J. Chem. Phys. , 2020 . 152 064901 DOI: 10.1063/1.5139940 http://doi.org/10.1063/1.5139940 .
Jiang, J.; Gillespie, D . Revisiting the charged shell model: a density functional theory for electrolytes . Journal of Chemical Theory and Computation , 2021 . 17 2409 - 2416 . DOI: 10.1021/acs.jctc.1c00052 http://doi.org/10.1021/acs.jctc.1c00052 .
Roth, R.; Gillespie, D . Shells of charge: a density functional theory for charged hard spheres . J. Phys.: Condens. Matter , 2016 . 28 244006 - 244015 . DOI: 10.1088/0953-8984/28/24/244006 http://doi.org/10.1088/0953-8984/28/24/244006 .
Jiang, J.; Xu, X.; Huang, J.; Cao, D . Density functional theory for rod-coil polymers with different size segments . J. Chem. Phys. , 2011 . 135 054903 - 054911 . DOI: 10.1063/1.3622488 http://doi.org/10.1063/1.3622488 .
Patra, C. N.; Yethiraj, A . Generalized van der Waals density functional theory for nonuniform polymers . J. Chem. Phys. , 2000 . 112 1579 - 1584 . DOI: 10.1063/1.480706 http://doi.org/10.1063/1.480706 .
Eyert, V . A comparative study on methods for convergence acceleration of iterative vector sequences . J. Comput. Phys. , 1996 . 124 271 - 285 . DOI: 10.1006/jcph.1996.0059 http://doi.org/10.1006/jcph.1996.0059 .
Jiang, J. Atif (an Advanced Theoretical Tool for Inhomogeneous Fluids). https://github.com/jiangj-physchem/Atif https://github.com/jiangj-physchem/Atif .
Gillespie, D.; Nonner, W.; Eisenberg, R. S . Coupling Poisson-Nernst-Planck and density functional theory to calculate ion flux . J. Phys.: Condens. Matter , 2002 . 14 12129 - 12145 . DOI: 10.1088/0953-8984/14/46/317 http://doi.org/10.1088/0953-8984/14/46/317 .
Valiskó, M.; Kristóf, T.; Gillespie, D.; Boda, D . A systematic Monte Carlo simulation study of the primitive model planar electrical double layer over an extended range of concentrations, electrode charges, cation diameters and valences . AIP Adv. , 2018 . 8 025320 - 025329 . DOI: 10.1063/1.5022036 http://doi.org/10.1063/1.5022036 .
Bates, F. S.; Hillmyer, M. A.; Lodge, T. P.; Bates, C. M.; Delaney, K. T.; Fredrickson, G. H . Multiblock polymers: Panacea or Pandora's box? . Science , 2012 . 336 434 - 440 . DOI: 10.1126/science.1215368 http://doi.org/10.1126/science.1215368 .
Lutz, J.F.; Ouchi, M.; Liu, D. R.; Sawamoto, M . Sequence-controlled polymers . Science , 2013 . 341 1238149 DOI: 10.1126/science.1238149 http://doi.org/10.1126/science.1238149 .
Lutz, J.F.; Lehn, J.M.; Meijer, E. W.; Matyjaszewski, K . From precision polymers to complex materials and systems . Nat. Rev. Mater. , 2016 . 1 16024 - 16037 . DOI: 10.1038/natrevmats.2016.24 http://doi.org/10.1038/natrevmats.2016.24 .
Bolto, B.; Gregory, J . Organic polyelectrolytes in water treatment . Water Res. , 2007 . 41 2301 - 2324 . DOI: 10.1016/j.watres.2007.03.012 http://doi.org/10.1016/j.watres.2007.03.012 .
Howe, A. M.; Wesley, R. D.; Bertrand, M.; Côte, M.; Leroy, J. . Controlled association in suspensions of charged nanoparticles with a weak polyelectrolyte . Langmuir , 2006 . 22 4518 - 4525 . DOI: 10.1021/la053327s http://doi.org/10.1021/la053327s .
Claesson, P. M.; Dedinaite, A.; Rojas, O. J . Polyelectrolytes as adhesion modifiers . Adv. Colloid Interface Sci. , 2003 . 104 53 - 74 . DOI: 10.1016/S0001-8686(03)00036-8 http://doi.org/10.1016/S0001-8686(03)00036-8 .
Jiang, J.; Ginzburg, V. V.; Wang, Z. G . On the origin of oscillatory interactions between surfaces mediated by polyelectrolyte solution . J. Chem. Phys. , 2019 . 151 214901 DOI: 10.1063/1.5123172 http://doi.org/10.1063/1.5123172 .
Balzer, C.; Jiang, J.; Marson, R. L.; Ginzburg, V. V.; Wang, Z. G . Nonelectrostatic adsorption of polyelectrolytes and mediated interactions between solid surfaces . Langmuir , 2021 . 37 5483 - 5493 . DOI: 10.1021/acs.langmuir.1c00139 http://doi.org/10.1021/acs.langmuir.1c00139 .
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