1
|
Fukuda I, Moritsugu K, Higo J, Fukunishi Y. A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems. J Chem Phys 2023; 159:234116. [PMID: 38112509 DOI: 10.1063/5.0172270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
We introduce a simple cutoff-based method for precise electrostatic energy calculations in the molecular dynamics (MD) simulations of point-particle systems. Our method employs a theoretically derived smooth pair potential function to define electrostatic energy, offering stability and computational efficiency in MD simulations. Instead of imposing specific physical conditions, such as dielectric environments or charge neutrality, we focus on the relationship represented by a single summation formula of charge-weighted pair potentials. This approach allows an accurate energy approximation for each particle, enabling a straightforward error analysis. The resulting particle-dependent pair potential captures the charge distribution information, making it suitable for heterogeneous systems and ensuring an enhanced accuracy through distant information inclusion. Numerical investigations of the Madelung constants of crystalline systems validate the method's accuracy.
Collapse
Affiliation(s)
- Ikuo Fukuda
- Graduate School of Science, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8231, Japan
- Japan Biological Informatics Consortium, 2-4-32 Aomi, Koto-ku, Tokyo, 135-8073, Japan
| | - Kei Moritsugu
- Graduate School of Science, Osaka Metropolitan University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8231, Japan
| | - Junichi Higo
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minamimachi, Chuo-ku, Kobe, Hyogo650-0047, Japan
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan
| |
Collapse
|
2
|
Sammüller F, Hermann S, de Las Heras D, Schmidt M. Noether-Constrained Correlations in Equilibrium Liquids. PHYSICAL REVIEW LETTERS 2023; 130:268203. [PMID: 37450808 DOI: 10.1103/physrevlett.130.268203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023]
Abstract
Liquid structure carries deep imprints of an inherent thermal invariance against a spatial transformation of the underlying classical many-body Hamiltonian. At first order in the transformation field Noether's theorem yields the local force balance. Three distinct two-body correlation functions emerge at second order, namely the standard two-body density, the localized force-force correlation function, and the localized force gradient. An exact Noether sum rule interrelates these correlators. Simulations of Lennard-Jones, Yukawa, soft-sphere dipolar, Stockmayer, Gay-Berne and Weeks-Chandler-Andersen liquids, of monatomic water and of a colloidal gel former demonstrate the fundamental role in the characterization of spatial structure.
Collapse
Affiliation(s)
- Florian Sammüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Sophie Hermann
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Daniel de Las Heras
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95447 Bayreuth, Germany
| |
Collapse
|
3
|
Elisea-Espinoza JJ, González-Tovar E, Guerrero-García GI. Theoretical description of the electrical double layer for a mixture of n ionic species with arbitrary size and charge asymmetries. I. Spherical geometry. J Chem Phys 2023; 158:2895477. [PMID: 37294907 DOI: 10.1063/5.0151140] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 05/08/2023] [Indexed: 06/11/2023] Open
Abstract
In this work, we propose a theoretical finite element description of the ionic profiles of a general mixture of n species of spherical charged particles dissolved in an implicit solvent, with arbitrary size and charge asymmetries, neutralizing a spherical macroion. This approach aims to close the gap between the nano- and the micro-scales in macroion solutions, taking into account the ion correlations and ionic excluded volume effects consistently. When these last two features are neglected, the classical non-linear Poisson-Boltzmann theory for n ionic species-with different ionic closest approach distances to the colloidal surface-is recovered as a limit case. As a proof of concept, we study the electrical double layer of an electroneutral mixture of oppositely charged colloids and small microions, with an asymmetry 1:333 in size and 1:10 in valence, in salt-free and added salt environments. Our theoretical approach displays a good agreement regarding the ionic profiles, the integrated charge, and the mean electrostatic potential obtained from molecular dynamics simulations with explicit-sized microions. Although the non-linear Poisson-Boltzmann colloid-colloid and colloid-microion profiles differ notably from those obtained via molecular dynamics simulations with explicit small-sized ions, the associated mean electrostatic potential agrees well with the corresponding explicit microion simulations.
Collapse
Affiliation(s)
| | - Enrique González-Tovar
- Instituto de Física de la Universidad Autónoma de San Luis Potosí, Álvaro Obregón 64, 78000 San Luis Potosí, Mexico
| | - Guillermo Iván Guerrero-García
- Facultad de Ciencias de la Universidad Autónoma de San Luis Potosí, Av. Chapultepec 1570, Privadas del Pedregal, 78295 San Luis Potosí, Mexico
| |
Collapse
|
4
|
Fukuda I, Nakamura H. Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference. Biophys Rev 2022; 14:1315-1340. [PMID: 36659982 PMCID: PMC9842848 DOI: 10.1007/s12551-022-01029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/30/2022] [Indexed: 01/13/2023] Open
Abstract
In molecular simulations, it is essential to properly calculate the electrostatic interactions of particles in the physical system of interest. Here we consider a method called the non-Ewald method, which does not rely on the standard Ewald method with periodic boundary conditions, but instead relies on the cutoff-based techniques. We focus on the physicochemical and mathematical conceptual aspects of the method in order to gain a deeper understanding of the simulation methodology. In particular, we take into account the reaction field (RF) method, the isotropic periodic sum (IPS) method, and the zero-multipole summation method (ZMM). These cutoff-based methods are based on different physical ideas and are completely distinguishable in their underlying concepts. The RF and IPS methods are "additive" methods that incorporate information outside the cutoff region, via dielectric medium and isotropic boundary condition, respectively. In contrast, the ZMM is a "subtraction" method that tries to remove the artificial effects, generated near the boundary, from the cutoff sphere. Nonetheless, we find physical and/or mathematical similarities between these methods. In particular, the modified RF method can be derived by the principle of neutralization utilized in the ZMM, and we also found a direct relationship between IPS and ZMM.
Collapse
Affiliation(s)
- Ikuo Fukuda
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima, Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| |
Collapse
|
5
|
Guerrero-García GI, Bhuiyan LB, Outhwaite CW, González-Tovar E. Charge asymmetric electrolytes around a rigid cylindrical polyelectrolyte: A generalization of the capacitive compactness. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
6
|
Allahyarov E, Löwen H, Denton AR. Structural correlations in highly asymmetric binary charged colloidal mixtures. Phys Chem Chem Phys 2022; 24:15439-15451. [PMID: 35708479 DOI: 10.1039/d2cp01343f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We explore structural correlations of strongly asymmetric mixtures of binary charged colloids within the primitive model of electrolytes considering large charge and size ratios of 10 and higher. Using computer simulations with explicit microions, we obtain the partial pair correlation functions between the like-charged colloidal macroions. Interestingly the big-small correlation peak amplitude is smaller than that of the big-big and small-small macroion correlation peaks, which is unfamiliar for additive repulsive interactions. Extracting optimal effective microion-averaged pair interactions between the macroions, we find that on top of non-additive Yukawa-like repulsions an additional shifted Gaussian attractive potential between the small macroions is needed to accurately reproduce their correct pair correlations. For small Coulomb couplings, the behavior is reproduced in a coarse-grained theory with microion-averaged effective interactions between the macroions. However, the accuracy of the theory deteriorates with increasing Coulomb coupling. We emphasize the relevance of entropic interactions exerted by the microions on the macroions. Our results are experimentally verifiable in binary mixtures of micron-sized colloids and like-charge nanoparticles.
Collapse
Affiliation(s)
- Elshad Allahyarov
- Theoretical Department, Joint Institute for High Temperatures, Russian Academy of Sciences (IVTAN), 13/19 Izhorskaya Street, Moscow 125412, Russia. .,Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany.,Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7202, USA
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine Universität Düsseldorf, Universitätstrasse 1, 40225 Düsseldorf, Germany
| | - Alan R Denton
- Department of Physics, North Dakota State University, Fargo, ND 58108-6050, USA
| |
Collapse
|
7
|
Cywiak D, Gil-Villegas A, Patti A. Long-time relaxation dynamics in nematic and smectic liquid crystals of soft repulsive colloidal rods. Phys Rev E 2022; 105:014703. [PMID: 35193200 DOI: 10.1103/physreve.105.014703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Understanding the relaxation dynamics of colloidal suspensions is crucial to identifying the elements that influence the mobility of their constituents, assessing their macroscopic response across the relevant time and length scales, and thus disclosing the fundamentals underpinning their exploitation in formulation engineering. In this work, we specifically assess the impact of long-ranged ordering on the relaxation dynamics of suspensions of soft repulsive rodlike particles, which are able to self-organize into nematic and smectic liquid-crystalline phases. Rods are modeled as soft repulsive spherocylinders with a length-to-diameter ratio L^{★}=5, interacting via the truncated and shifted Kihara potential. By performing dynamic Monte Carlo simulations, we analyze the effect of translational and orientational order on the diffusion of the rods along the relevant directions imposed by the morphology of the background phases. To provide a clear picture of the resulting dynamics, we assess its dependence on temperature, which can dramatically determine the response time of the system relaxation and the self-diffusion coefficients of the rods. The computation of the van Hove correlation functions allows us to identify the existence of rods that diffuse significantly faster than the average and whose concentration can be accurately adjusted by a suitable choice of temperature.
Collapse
Affiliation(s)
- Daniela Cywiak
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Campus León, Mexico
| | | | - Alessandro Patti
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
8
|
Sánchez-Monroy X, Torres-Arenas J, Gil-Villegas A. Equivalence between Wolf and Yukawa non-homogeneous fluids in a gravitational field. Mol Phys 2021. [DOI: 10.1080/00268976.2021.2002451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- X. Sánchez-Monroy
- School of Environmental and Forest Sciences, College of the Environment University of Washington, Seattle, WA, USA
| | - J. Torres-Arenas
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, León Guanajuato, México
| | - A. Gil-Villegas
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, León Guanajuato, México
| |
Collapse
|