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Chávez-Navarro MA, González-Tovar E, Chávez-Páez M. Enhanced charge reversal and charge amplification in a shape- and size-asymmetric electric double layer: the effect of big ions. Mol Phys 2020. [DOI: 10.1080/00268976.2020.1791368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- M. A. Chávez-Navarro
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - E. González-Tovar
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - M. Chávez-Páez
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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2
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Abstract
The accurate characterization of the electrical double layer properties of nanoparticles is of fundamental importance for optimizing their physicochemical properties for specific biotechnological and biomedical applications. In this article, we use classical solvation density functional theory and a surface complexation model to investigate the effects of the pH and the nanoparticle size on the structural and electrostatic properties of an electrolyte solution surrounding a spherical silica oxide nanoparticle. The formulation has been particularly useful for identifying dominant interactions governing the ionic driving force at a variety of pH levels and nanoparticle sizes. As a result of the energetic interplay displayed between electrostatic potential, ion-ion correlation and particle crowding effects on the nanoparticle surface titration, rich, non-trivial ion density profiles and mean electrostatic potential behavior have been found.
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Affiliation(s)
- Christian Hunley
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA.
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, TX 78249-5003, USA.
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3
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Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting. J Am Chem Soc 2015; 137:14705-15. [PMID: 26517731 PMCID: PMC4739826 DOI: 10.1021/jacs.5b08395] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that "count" the number of ions thermodynamically associated with the ion atmosphere allow dissection of energetic properties of the ion atmosphere, and thus provide direct comparison to theoretical results. Previous experiments have focused primarily on the cations that are attracted to nucleic acid polyanions, but have also showed that anions are excluded from the ion atmosphere. Herein, we have systematically explored the properties of anion exclusion, testing the zeroth-order model that anions of different identity are equally excluded due to electrostatic repulsion. Using a series of monovalent salts, we find, surprisingly, that the extent of anion exclusion and cation inclusion significantly depends on salt identity. The differences are prominent at higher concentrations and mirror trends in mean activity coefficients of the electrolyte solutions. Salts with lower activity coefficients exhibit greater accumulation of both cations and anions within the ion atmosphere, strongly suggesting that cation-anion correlation effects are present in the ion atmosphere and need to be accounted for to understand electrostatic interactions of nucleic acids. To test whether the effects of cation-anion correlations extend to nucleic acid kinetics and thermodynamics, we followed the folding of P4-P6, a domain of the Tetrahymena group I ribozyme, via single-molecule fluorescence resonance energy transfer in solutions with different salts. Solutions of identical concentration but lower activity gave slower and less favorable folding. Our results reveal hitherto unknown properties of the ion atmosphere and suggest possible roles of oriented ion pairs or anion-bridged cations in the ion atmosphere for electrolyte solutions of salts with reduced activity. Consideration of these new results leads to a reevaluation of the strengths and limitations of Poisson-Boltzmann theory and highlights the need for next-generation atomic-level models of the ion atmosphere.
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Affiliation(s)
- Magdalena Gebala
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - George M. Giambasu
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Jan Lipfert
- Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, Ludwig Maximilian University of Munich, 80799 Munich, Germany
| | - Namita Bisaria
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Steve Bonilla
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Guangchao Li
- School of Earth, Energy and Environment Sciences, Stanford University, Stanford, California 94305, United States
| | - Darrin M. York
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Barrios-Contreras EA, González-Tovar E, Guerrero-García GI. The dominance of small ions in the electric double layer of size- and charge-asymmetric electrolytes: a mean-field study on the charge reversal and surface charge amplification. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1018853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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5
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Ovanesyan Z, Medasani B, Fenley MO, Guerrero-García GI, de la Cruz MO, Marucho M. Excluded volume and ion-ion correlation effects on the ionic atmosphere around B-DNA: theory, simulations, and experiments. J Chem Phys 2014; 141:225103. [PMID: 25494770 PMCID: PMC4265039 DOI: 10.1063/1.4902407] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 11/12/2014] [Indexed: 12/19/2022] Open
Abstract
The ionic atmosphere around a nucleic acid regulates its stability in aqueous salt solutions. One major source of complexity in biological activities involving nucleic acids arises from the strong influence of the surrounding ions and water molecules on their structural and thermodynamic properties. Here, we implement a classical density functional theory for cylindrical polyelectrolytes embedded in aqueous electrolytes containing explicit (neutral hard sphere) water molecules at experimental solvent concentrations. Our approach allows us to include ion correlations as well as solvent and ion excluded volume effects for studying the structural and thermodynamic properties of highly charged cylindrical polyelectrolytes. Several models of size and charge asymmetric mixtures of aqueous electrolytes at physiological concentrations are studied. Our results are in good agreement with Monte Carlo simulations. Our numerical calculations display significant differences in the ion density profiles for the different aqueous electrolyte models studied. However, similar results regarding the excess number of ions adsorbed to the B-DNA molecule are predicted by our theoretical approach for different aqueous electrolyte models. These findings suggest that ion counting experimental data should not be used alone to validate the performance of aqueous DNA-electrolyte models.
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Affiliation(s)
- Zaven Ovanesyan
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
| | - Bharat Medasani
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
| | - Marcia O Fenley
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | - Guillermo Iván Guerrero-García
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, San Luis Potosí, Mexico
| | - Mónica Olvera de la Cruz
- Department of Chemistry and Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
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6
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Naji A, Ghodrat M, Komaie-Moghaddam H, Podgornik R. Asymmetric Coulomb fluids at randomly charged dielectric interfaces: Anti-fragility, overcharging and charge inversion. J Chem Phys 2014; 141:174704. [DOI: 10.1063/1.4898663] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Malihe Ghodrat
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Haniyeh Komaie-Moghaddam
- School of Physics, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute, SI-1000 Ljubljana, Slovenia
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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7
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Medasani B, Ovanesyan Z, Thomas DG, Sushko ML, Marucho M. Ionic asymmetry and solvent excluded volume effects on spherical electric double layers: a density functional approach. J Chem Phys 2014; 140:204510. [PMID: 24880304 PMCID: PMC4039739 DOI: 10.1063/1.4876002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/29/2014] [Indexed: 02/06/2023] Open
Abstract
In this article, we present a classical density functional theory for electrical double layers of spherical macroions that extends the capabilities of conventional approaches by accounting for electrostatic ion correlations, size asymmetry, and excluded volume effects. The approach is based on a recent approximation introduced by Hansen-Goos and Roth for the hard sphere excess free energy of inhomogeneous fluids [J. Chem. Phys. 124, 154506 (2006); Hansen-Goos and Roth, J. Phys.: Condens. Matter 18, 8413 (2006)]. It accounts for the proper and efficient description of the effects of ionic asymmetry and solvent excluded volume, especially at high ion concentrations and size asymmetry ratios including those observed in experimental studies. Additionally, we utilize a leading functional Taylor expansion approximation of the ion density profiles. In addition, we use the mean spherical approximation for multi-component charged hard sphere fluids to account for the electrostatic ion correlation effects. These approximations are implemented in our theoretical formulation into a suitable decomposition of the excess free energy which plays a key role in capturing the complex interplay between charge correlations and excluded volume effects. We perform Monte Carlo simulations in various scenarios to validate the proposed approach, obtaining a good compromise between accuracy and computational cost. We use the proposed computational approach to study the effects of ion size, ion size asymmetry, and solvent excluded volume on the ion profiles, integrated charge, mean electrostatic potential, and ionic coordination number around spherical macroions in various electrolyte mixtures. Our results show that both solvent hard sphere diameter and density play a dominant role in the distribution of ions around spherical macroions, mainly for experimental water molarity and size values where the counterion distribution is characterized by a tight binding to the macroion, similar to that predicted by the Stern model.
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Affiliation(s)
- Bharat Medasani
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
| | - Zaven Ovanesyan
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
| | - Dennis G Thomas
- Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA
| | - Maria L Sushko
- Pacific Northwest National Laboratory, Richland, Washington 99352-0999, USA
| | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio, San Antonio, Texas 78249-5003, USA
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8
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Wei GW. Multiscale Multiphysics and Multidomain Models I: Basic Theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013; 12:10.1142/S021963361341006X. [PMID: 25382892 PMCID: PMC4220694 DOI: 10.1142/s021963361341006x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA Department of Biochemistry and Molecular Biology Michigan State University, MI 48824, USA
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9
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Simulation study on dynamics of A- to B-form transition in aqueous DNA solution: Effect of alkali metal counterions. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4959-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Yu Y, Fujimoto S. Molecular dynamics simulation of the A-DNA to B-DNA transition in aqueous RbCl solution. Sci China Chem 2013. [DOI: 10.1007/s11426-012-4825-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Tang WY, Hu GH. Prediction of the effective force on DNA in a nanopore based on density functional theory. RSC Adv 2013. [DOI: 10.1039/c3ra43325k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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13
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Magnico P. Ion size effects on electric double layers and ionic transport through ion-exchange membrane systems. J Memb Sci 2012. [DOI: 10.1016/j.memsci.2012.05.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Jin Z, Wu J. Density functional theory for encapsidated polyelectrolytes: a comparison with Monte Carlo simulation. J Chem Phys 2012; 137:044905. [PMID: 22852653 DOI: 10.1063/1.4737931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Genome packaging inside viral capsids is strongly influenced by the molecular size and the backbone structure of RNA∕DNA chains and their electrostatic affinity with the capsid proteins. Coarse-grained models are able to capture the generic features of non-specific interactions and provide a useful testing ground for theoretical developments. In this work, we use the classical density functional theory (DFT) within the framework of an extended primitive model for electrolyte solutions to investigate the self-organization of flexible and semi-flexible linear polyelectrolytes in spherical capsids that are permeable to small ions but not polymer segments. We compare the DFT predictions with Monte Carlo (MC) simulation for the density distributions of polymer segments and small ions at different backbone flexibilities and several solution conditions. In general, the agreement between DFT and MC is near quantitative except when the simulation results are noticeably influenced by the boundary effects. The numerical efficiency of the DFT calculations makes it promising as a useful tool for quantification of the structural and thermodynamic properties of viral nucleocapsids in vivo and at conditions pertinent to experiments.
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Affiliation(s)
- Zhehui Jin
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
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15
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Goel T, Patra CN, Ghosh SK, Mukherjee T. Effect of Ionic Size on the Structure of Cylindrical Electric Double Layers: A Systematic Study by Monte Carlo Simulations and Density Functional Theory. J Phys Chem B 2011; 115:10903-10. [DOI: 10.1021/jp203779t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Teena Goel
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Chandra N. Patra
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tulsi Mukherjee
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India
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16
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Bulyha A, Heitzinger C. An algorithm for three-dimensional Monte-Carlo simulation of charge distribution at biofunctionalized surfaces. NANOSCALE 2011; 3:1608-1617. [PMID: 21301731 DOI: 10.1039/c0nr00791a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this work, a Monte-Carlo algorithm in the constant-voltage ensemble for the calculation of 3d charge concentrations at charged surfaces functionalized with biomolecules is presented. The motivation for this work is the theoretical understanding of biofunctionalized surfaces in nanowire field-effect biosensors (BioFETs). This work provides the simulation capability for the boundary layer that is crucial in the detection mechanism of these sensors; slight changes in the charge concentration in the boundary layer upon binding of analyte molecules modulate the conductance of nanowire transducers. The simulation of biofunctionalized surfaces poses special requirements on the Monte-Carlo simulations and these are addressed by the algorithm. The constant-voltage ensemble enables us to include the right boundary conditions; the dna strands can be rotated with respect to the surface; and several molecules can be placed in a single simulation box to achieve good statistics in the case of low ionic concentrations relevant in experiments. Simulation results are presented for the leading example of surfaces functionalized with pna and with single- and double-stranded dna in a sodium-chloride electrolyte. These quantitative results make it possible to quantify the screening of the biomolecule charge due to the counter-ions around the biomolecules and the electrical double layer. The resulting concentration profiles show a three-layer structure and non-trivial interactions between the electric double layer and the counter-ions. The numerical results are also important as a reference for the development of simpler screening models.
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Affiliation(s)
- Alena Bulyha
- Department of Mathematics and Wolfgang Pauli Institute, University of Vienna, A-1090, Vienna, Austria.
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17
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Keshavarzi E(T, Taghizadeh A. How Wall Curvature Affects the Structure of Fluid around a Cylindrical Nanoparticle: A DFT Approach. J Phys Chem B 2010; 114:10126-32. [DOI: 10.1021/jp101801w] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Ameneh Taghizadeh
- Department of Chemistry, Isfahan University of Technology, Isfahan, Iran 8415683111
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18
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Goel T, Patra CN, Ghosh SK, Mukherjee T. Three component model of cylindrical electric double layers containing mixed electrolytes: A systematic study by Monte Carlo simulations and density functional theory. J Chem Phys 2010; 132:194706. [DOI: 10.1063/1.3428702] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Patra CN. Molecular solvent model of spherical electric double layers: a systematic study by Monte Carlo simulations and density functional theory. J Phys Chem B 2010; 113:13980-7. [PMID: 19778069 DOI: 10.1021/jp907790t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure of spherical electric double layers is studied using Monte Carlo simulation and density functional theory by considering solvent as the third component. In this molecular solvent model (MSM), ions and solvent molecules are considered as charged and neutral hard spheres, respectively, having equal diameter. The macroion is considered as an isolated hard sphere having uniform surface charge density surrounded by the electrolyte and the solvent. The theory is partially perturbative as the hard-sphere contribution to the one particle correlation function is evaluated using suitably averaged weighted density, and the ionic part is obtained through a second-order functional Taylor expansion around the bulk electrolyte. The Monte Carlo simulations have been performed in a canonical ensemble. The system is studied at varying concentrations of electrolytes, and the solvent molecules, at different valences of the electrolyte, at different macroion radii, and at varying surface charge densities. The theory is found to be in good agreement with the simulation results over a wide range of parametric conditions. The excluded volume effects due to the molecular nature of the solvent are shown to have much richer features in diffuse layer phenomena like layering and charge inversion.
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Affiliation(s)
- Chandra N Patra
- Theoretical Chemistry Section, Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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20
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Peng B, Yu YX. Ion distributions, exclusion coefficients, and separation factors of electrolytes in a charged cylindrical nanopore: A partially perturbative density functional theory study. J Chem Phys 2009; 131:134703. [DOI: 10.1063/1.3243873] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Peng B, Yu YX. A Density Functional Theory with a Mean-field Weight Function: Applications to Surface Tension, Adsorption, and Phase Transition of a Lennard-Jones Fluid in a Slit-like Pore. J Phys Chem B 2008; 112:15407-16. [DOI: 10.1021/jp805697p] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bo Peng
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China, and State Key Laboratory of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
| | - Yang-Xin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China, and State Key Laboratory of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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22
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Goel T, Patra CN, Ghosh SK, Mukherjee T. Molecular solvent model of cylindrical electric double layers: A systematic study by Monte Carlo simulations and density functional theory. J Chem Phys 2008; 129:154707. [DOI: 10.1063/1.2981057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Goel T, Patra CN, Ghosh SK, Mukherjee T. Structure of cylindrical electric double layers: A systematic study by Monte Carlo simulations and density functional theory. J Chem Phys 2008; 129:154906. [DOI: 10.1063/1.2992525] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Wang K, Yu YX, Gao GH. Density functional study on the structural and thermodynamic properties of aqueous DNA-electrolyte solution in the framework of cell model. J Chem Phys 2008; 128:185101. [PMID: 18532848 DOI: 10.1063/1.2918342] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic functional Taylor expansion around a uniform fluid. The electroneutrality in the cell leads to a variational equation with a constraint. Since the reference fluid is selected to be a bulk phase, the Lagrange multiplier proves to be the potential drop across the cell boundary (Donnan potential). The ion profiles and electrostatic potential profiles in the cell are calculated from the present DFT-cell model. Our DFT-cell model gives better prediction of ion profiles than the Poisson-Boltzmann (PB)- or modified PB-cell models when compared to the molecular simulation data. The effects of polyelectrolyte concentration, ion size, and added-salt concentration on the electrostatic potential difference between the DNA surface and the cell boundary are investigated. The expression of osmotic coefficient is derived from the general formula of grand potential. The osmotic coefficients predicted by the DFT are lower than the PB results and are closer to the simulation results and experimental data.
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Affiliation(s)
- Ke Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, People's Republic of China
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25
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Abstract
Density-functional theory (DFT) and its variations provide a fruitful approach to the computational modeling of the microscopic structures and phase behavior of soft-condensed matter. The methodology takes deep root in quantum mechanics but shares a mathematical similarity with a number of classical approaches in statistical mechanics. This review discusses different strategies commonly used to formulate the free-energy functional of complex fluids for either phenomena-oriented applications or as a generic description of the thermodynamic nonideality owing to various components of intermolecular forces. We emphasize the connections among different schemes of DFT approximations, their underlying assumptions, and inherent limitations. We also address extensions of equilibrium DFT to phenomenological theories for the dynamic properties of complex fluids and for the kinetics of phase transitions. In addition, we highlight the recent literature concerning applications of DFT to diverse static and time-dependent phenomena in complex fluids.
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Affiliation(s)
- Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
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26
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Li Z, Wu J. Density functional theory for planar electric double layers: closing the gap between simple and polyelectrolytes. J Phys Chem B 2007; 110:7473-84. [PMID: 16599527 DOI: 10.1021/jp060127w] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a nonlocal density functional theory (NLDFT) for polyelectrolyte solutions within the primitive model; i.e., the solvent is represented by a continuous dielectric medium, and the small ions and polyions by single and tangentially connected charged hard spheres, respectively. The excess Helmholtz energy functional is derived from a modified fundamental measure theory for hard-sphere repulsion, an extended first-order thermodynamic perturbation theory for chain connectivity, and a quadratic functional Taylor expansion for electrostatic correlations. With the direct and cavity correlation functions of the corresponding monomeric systems as inputs, the NLDFT predicts the segment-level microscopic structures and adsorption isotherms of polyelectrolytes at oppositely charged surfaces in good agreement with molecular simulations. In particular, it faithfully reproduces the layering structures of polyions, charge inversion, and overcharging that cannot be captured by alternative methods including the polyelectrolyte Poisson-Boltzmann equation and an earlier version of DFT. The NLDFT has also been used to investigate the influences of the small ion valence, polyion chain length, and size disparity between polyion segments and counterions on the microscopic structure, mean electrostatic potential, and overcharging in planar electric double layers containing polyelectrolytes.
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Affiliation(s)
- Zhidong Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521-0425, USA
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27
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Wang K, Yu YX, Gao GH, Luo GS. Preferential interaction between DNA and small ions in mixed-size counterion systems: Monte Carlo simulation and density functional study. J Chem Phys 2007; 126:135102. [PMID: 17430070 DOI: 10.1063/1.2713105] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Competitive binding between counterions around DNA molecule is characterized using the preferential interaction coefficient of individual ion in single and mixed electrolyte solutions. The canonical Monte Carlo (MC) simulation, nonlinear Poisson-Boltzmann (PB) equation, and density functional theory (DFT) proposed in our previous work [Wang, Yu, Gao, and Luo, J. Chem. Phys. 123, 234904 (2005)] are utilized to calculate the preferential interaction coefficients. The MC simulations and theoretical results show that for single electrolyte around DNA, the preferential interaction coefficient of electrolyte decreases as the cation size is increased, indicating that the larger cation has less accumulation ability in the vicinity of DNA. For the mixed electrolyte solution, it is found that cation diameter has a significant effect on the competitive ability while anion diameter has a negligible effect. It proves that the preferential interaction coefficients of all ions decrease as the total ionic concentration is increased. The DFT generally has better performance than the PB equation does when compared to the MC simulation data. The DFT behaves quite well for the real ionic solutions such as the KCl-NaCl-H2O, NaCl-CaCl2-H2O, and CaCl2-MgCl2-H2O systems.
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Affiliation(s)
- Ke Wang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, People's Republic of China
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28
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Abascal JLF, Domercq M, Montoro JCG. Computer Simulation of the Ionic Atmosphere around Z-DNA. J Phys Chem B 2006; 110:25080-90. [PMID: 17149933 DOI: 10.1021/jp064199z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We describe a coarse-grained model for Z-DNA that mimics the DNA shape with a relatively small number of repulsive interaction sites. In addition, negative charges are placed at the phosphate positions. The ionic atmosphere around this grooved Z-DNA model is then investigated with Monte Carlo simulation. Cylindrically averaged concentration profiles as well as the spatial distribution of ions have been calculated. The results are compared to those for other DNA models differing in the repulsive core. This allows the examination of the effect of the DNA shape in the ionic distribution. It is seen that the penetrability of the ions to the DNA groove plays an important role in the ionic distribution. The results are also compared with those reported for B-DNA. In both conformers the ions are structured in alternating layers of positive and negative charge. In Z-DNA the layers are more or less concentric to the molecular axis. Besides, no coions enter into the single groove of this conformer. On the contrary, the alternating layers of B-DNA are also structured along the axial coordinate with some coions penetrating into the major groove. In both cases we have found five preferred locations of the counterions and two for the coions. The concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove and at the minor groove of B-DNA, the value of the maximum being higher in the Z conformer.
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Affiliation(s)
- J L F Abascal
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
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29
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Li Z, Wu J. Density functional theory for polyelectrolytes near oppositely charged surfaces. PHYSICAL REVIEW LETTERS 2006; 96:048302. [PMID: 16486902 DOI: 10.1103/physrevlett.96.048302] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2005] [Indexed: 05/06/2023]
Abstract
We report a nonlocal density functional theory of polyelectrolyte solutions that faithfully accounts for both short- and long-range correlations neglected in a typical mean-field method. It is shown that for systems with strong electrostatic interactions, the long-range correlations are subdued by direct Coulomb attractions, thereby manifesting strong local excluded-volume effects. The theory has also been used to describe the influence of the polyion chain length and small ion valence on charge inversion due to the adsorption of polyelectrolytes at an oppositely charged surface.
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Affiliation(s)
- Zhidong Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521-0444, USA
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30
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Wang K, Yu YX, Gao GH, Luo GS. Density-functional theory and Monte Carlo simulation study on the electric double layer around DNA in mixed-size counterion systems. J Chem Phys 2005; 123:234904. [PMID: 16392946 DOI: 10.1063/1.2137710] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A density-functional approach and canonical Monte Carlo simulations are presented for describing the ionic microscopic structure around the DNA molecule immersed in mixed-size counterion solutions. In the density-functional approach, the hard-sphere contribution to the Helmholtz energy functional is obtained from the modified fundamental measure theory [Y.-X. Yu and J. Z. Wu, J. Chem. Phys. 117, 10156 (2002)], and the electrostatic contribution is evaluated through a quadratic functional Taylor expansion. The new theory is suitable to the systems containing ions of arbitrary sizes and valences. In the established canonical Monte Carlo simulation, an iterative self-consistent method is used to evaluate the long-range energy, and another iterative algorithm is adopted to obtain desired bulk ionic concentrations. The ion distributions from the density-functional theory (DFT) are in good agreement with those from the corresponding Monte Carlo (MC) simulations. It is found that the ratio of the bulk concentrations of two species of counterions (cations) makes significant contribution to the ion distributions in the vicinity of DNA. Comparisons with the electrostatic potential profiles from the MC simulations show that the accuracy of the DFT becomes low when a small divalent cation exists. Both the DFT and MC simulation results illustrate that the electrostatic potential at the surface of DNA increases as the anion diameter or the total cation concentration is increased and decreases as the diameter of one cation species is increased. The calculation of electrostatic potential using real ion diameters shows that the accuracy of DFT predictions for divalent ions is also acceptable.
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Affiliation(s)
- Ke Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, People's Republic of China
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31
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Guerrero-García GI, González-Tovar E, Lozada-Cassou M, de J Guevara-Rodríguez F. The electrical double layer for a fully asymmetric electrolyte around a spherical colloid: An integral equation study. J Chem Phys 2005; 123:34703. [PMID: 16080751 DOI: 10.1063/1.1949168] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hypernetted chain/mean spherical approximation (HNC/MSA) integral equation for a totally asymmetric primitive model electrolyte around a spherical macroparticle is obtained and solved numerically in the case of size-asymmetric systems. The ensuing radial distribution functions show a very good agreement when compared to our Monte Carlo and molecular-dynamics simulations for spherical geometry and with respect to previous anisotropic reference HNC calculations in the planar limit. We report an analysis of the potential versus charge relationship, radial distribution functions, mean electrostatic potential, and cumulative reduced charge for representative examples of 1:1 and 2:2 salts with a size-asymmetry ratio of 2. Our results are collated with those of the modified Gouy-Chapman (MGC) and unequal radius modified Gouy-Chapman (URMGC) theories and with those of HNC/MSA in the restricted primitive model (RPM) to assess the importance of size-asymmetry effects. One of the most striking characteristics found is that, contrary to the general belief, away from the point of zero charge the properties of an asymmetric electrical double layer (EDL) are not those corresponding to a symmetric electrolyte with the size and charge of the counterion, i.e., counterions do not always dominate. This behavior suggests the existence of a new phenomenology in the EDL that genuinely belongs to a more realistic size-asymmetric model where steric correlations are taken into account consistently. Such novel features cannot be described by traditional mean-field theories such as MGC, URMGC, or even by enhanced formalisms, such as HNC/MSA, if they are based on the RPM.
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Affiliation(s)
- G Iván Guerrero-García
- Instituto de Física, Universidad Autónoma de San Luis Potosí, Alvaro Obregón 64, San Luis Potosí, México
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32
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Delville A. Influence of the diffuse layer overcharging or undercharging on the stability of charged interfaces: a restricted grand canonical Monte Carlo study. J Phys Chem B 2005; 109:1896-902. [PMID: 16851172 DOI: 10.1021/jp045949c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have applied a restricted grand canonical Monte Carlo procedure to describe, in the framework of the primitive model, the counterion exchange mechanism between diffuse layers of counterions surrounding segregated charged lamellae. The net charge transfer between the dense and dilute domains is shown to vary as a function of the valence of the neutralizing counterions: undercharging of the dense interlayer is detected in the presence of monovalent counterions and overcharging with divalent counterions. Furthermore, no net reduction of the swelling pressure is detected for monovalent counterions, while a large enhancement of the net interlamellar attraction is found for charged lamellae neutralized by divalent counterions.
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Affiliation(s)
- Alfred Delville
- CRMD, CNRS, 1B rue de la Férollerie, 45071 Orléans Cedex 02, France.
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