1
|
Vuorte M, Lokka A, Scacchi A, Sammalkorpi M. Dioctyl sodium sulfosuccinate surfactant self-assembly dependency of solvent hydrophilicity: a modelling study. Phys Chem Chem Phys 2023; 25:27250-27263. [PMID: 37791412 DOI: 10.1039/d3cp02173d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The self-assembly of dioctyl sodium sulfosuccinate (AOT) model surfactant in solvent environments of differing polarity is examined by means of dissipative particle dynamics (DPD) bead model parametrized against Hildebrand solubility parameters from atomistic molecular dynamics (MD) simulations. The model predicts that in hydrophobic solvents (e.g. dodecane) the surfactant forms small (Nagg ∼ 8) reverse micellar aggregates, while in a solvent corresponding to water lamellar assembly takes place, in good agreement with literature structural parameters. Interestingly, solvents of intermediate polarity lead to formation of large, internally structured aggregates. In these, the surfactant headgroups cluster within the aggregate, surrounded by a continuous phase formed by the hydrocarbon tails. We show that the partitioning of the headgroups between the aggregate surface layer and the inner clustered phase depends primarily on solvent polarity, and can be controlled by the solvent, but also system composition. Finally, we compare the DPD assembly response to simplified effective interaction potentials derived at dilute concentration limit for the interactions. The comparison reveals that the simplified effective potential descriptions provide good level of insight on the assembly morphologies, despite drastic, isotropic interactions simplification involved.
Collapse
Affiliation(s)
- Maisa Vuorte
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Aapo Lokka
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| | - Alberto Scacchi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Applied Physics, School of Science, Aalto University, P.O. Box 11000, FI-00076 Aalto, Finland
| | - Maria Sammalkorpi
- Department of Chemistry and Materials Science, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
- Academy of Finland Center of Excellence in Life-Inspired Hybrid Materials (LIBER), Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
- Department of Bioproducts and Biosystems, School of Chemical Engineering, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland
| |
Collapse
|
2
|
Santo KP, Neimark AV. Dissipative particle dynamics simulations in colloid and Interface science: a review. Adv Colloid Interface Sci 2021; 298:102545. [PMID: 34757286 DOI: 10.1016/j.cis.2021.102545] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Dissipative particle dynamics (DPD) is one of the most efficient mesoscale coarse-grained methodologies for modeling soft matter systems. Here, we comprehensively review the progress in theoretical formulations, parametrization strategies, and applications of DPD over the last two decades. DPD bridges the gap between the microscopic atomistic and macroscopic continuum length and time scales. Numerous efforts have been performed to improve the computational efficiency and to develop advanced versions and modifications of the original DPD framework. The progress in the parametrization techniques that can reproduce the engineering properties of experimental systems attracted a lot of interest from the industrial community longing to use DPD to characterize, help design and optimize the practical products. While there are still areas for improvements, DPD has been efficiently applied to numerous colloidal and interfacial phenomena involving phase separations, self-assembly, and transport in polymeric, surfactant, nanoparticle, and biomolecules systems.
Collapse
Affiliation(s)
- Kolattukudy P Santo
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Alexander V Neimark
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States.
| |
Collapse
|
3
|
Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations. Polymers (Basel) 2021; 13:polym13224044. [PMID: 34833344 PMCID: PMC8626026 DOI: 10.3390/polym13224044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0-32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.
Collapse
|
4
|
Biagi S, Rovigatti L, Abbasi M, Bureau L, Sciortino F, Misbah C. Hydrodynamic instability and flow reduction in polymer brush coated channels. SOFT MATTER 2021; 17:9235-9245. [PMID: 34596648 DOI: 10.1039/d1sm00638j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A polymer brush is a passive medium. At equilibrium the knowledge of its chemical composition and thickness is enough for a full system characterization. However, when the brush is exposed to fluid flow it reveals a much more intriguing nature, in which filamentous protrusions and the way they interact among themselves and with the surrounding fluid are of outmost importance. Here we investigate such a rich behavior via numerical simulations. We focus on the brush hydrodynamic response at low Reynolds numbers, observing a significant fluid flow reduction inside a polymer-brush coated channel. We find that the reduction of the flow inside the channel is significantly larger than what would happen if the brush effect consisted only in reducing the effective channel width. This amplified reduction is understood as being due to the morphological instability of the brush-liquid interface which is shown to have an elastic origin: the mechanical stress acting on the brush due to the imposed flow is partially released by the interface modulation. In turn, this modulation dissipates more energy than a flat interface in the surrounding fluid, causing a reduction of flow velocity. Our results and interpretations provide an explanation for recent experimental measurements.
Collapse
Affiliation(s)
- Sofia Biagi
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Mehdi Abbasi
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
| | - Lionel Bureau
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza-Universitá di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
- Istituto Sistemi Complessi (ISC), Via dei Taurini 19, 00185 Roma, Italy
| | - Chaouqi Misbah
- Université Grenoble Alpes/CNRS, LIPhy UMR 5588, Grenoble, F-38401, France.
| |
Collapse
|
5
|
Tzorín A, Zamarripa AL, Goicochea AG, Vallejo-Montesinos J. Effect of increasing the number of amino groups in the solubility of Copolysiloxanes using dissipative particle dynamics. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1800006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Amanda Tzorín
- Edificio T-12, Facultad de Ciencias Químicas y Farmacia, Ciudad Universitaria, Guatemala, Guatemala
| | - Ana L. Zamarripa
- División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Armando Gama Goicochea
- División de Ingeniería Química y Bioquímica, Tecnológico de Estudios Superiores de Ecatepec, Ecatepec, Estado de México, Mexico
| | | |
Collapse
|
6
|
Goodarzi F, Zendehboudi S. Effects of Salt and Surfactant on Interfacial Characteristics of Water/Oil Systems: Molecular Dynamic Simulations and Dissipative Particle Dynamics. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b00504] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Fatemeh Goodarzi
- Faculty of Engineering and Applied Science, Memorial University, St. John’s, NL A1B 3X5, Canada
| | - Sohrab Zendehboudi
- Faculty of Engineering and Applied Science, Memorial University, St. John’s, NL A1B 3X5, Canada
| |
Collapse
|
7
|
Khedr A, Striolo A. DPD Parameters Estimation for Simultaneously Simulating Water–Oil Interfaces and Aqueous Nonionic Surfactants. J Chem Theory Comput 2018; 14:6460-6471. [DOI: 10.1021/acs.jctc.8b00476] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abeer Khedr
- Chemical Engineering Department, University College London, London, United Kingdom
| | - Alberto Striolo
- Chemical Engineering Department, University College London, London, United Kingdom
| |
Collapse
|
8
|
Vallejo-Montesinos J, Villegas A, Cervantes J, Pérez E, Goicochea AG. Study of Polymer-Solvent Interactions of Complex Polysiloxanes Using Dissipative Particle Dynamics. J MACROMOL SCI B 2018. [DOI: 10.1080/00222348.2018.1503336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | - Antonio Villegas
- División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Jorge Cervantes
- División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Mexico
| | - Elías Pérez
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Armando Gama Goicochea
- División de Ingeniería Química y Bioquímica, Tecnológico de Estudios Superiores de Ecatepec, Ecatepec, Mexico
| |
Collapse
|
9
|
Kacar G. Characterizing the structure and properties of dry and wet polyethylene glycol using multi-scale simulations. Phys Chem Chem Phys 2018; 20:12303-12311. [DOI: 10.1039/c8cp01802b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multi-scale simulations to study the structure and material properties of PEG in dry and wet conditions.
Collapse
Affiliation(s)
- Gokhan Kacar
- Department of Genetics and Bioengineering
- Faculty of Engineering
- Trakya University
- Edirne
- Turkey
| |
Collapse
|
10
|
Kos PI, Chertovich AA. Concentrated dispersions and melts from block-copolymer micelles: Computer simulation. POLYMER SCIENCE SERIES A 2016. [DOI: 10.1134/s0965545x16050096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
11
|
Dissipative Particle Dynamics: A Method to Simulate Soft Matter Systems in Equilibrium and Under Flow. SELECTED TOPICS OF COMPUTATIONAL AND EXPERIMENTAL FLUID MECHANICS 2015. [DOI: 10.1007/978-3-319-11487-3_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
12
|
Terrón-Mejía KA, López-Rendón R, Gama Goicochea A. Mesoscopic modeling of structural and thermodynamic properties of fluids confined by rough surfaces. Phys Chem Chem Phys 2015; 17:26403-16. [DOI: 10.1039/c5cp03823e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simulations show that the ordering of particles confined by rough surfaces induces a structural phase transition while the interfacial tension is insensitive to it.
Collapse
Affiliation(s)
- Ketzasmin A. Terrón-Mejía
- Laboratorio de Bioingeniería Molecular a Multiescala
- Facultad de Ciencias
- Universidad Autónoma del Estado de México
- Toluca, Mexico
| | - Roberto López-Rendón
- Laboratorio de Bioingeniería Molecular a Multiescala
- Facultad de Ciencias
- Universidad Autónoma del Estado de México
- Toluca, Mexico
| | | |
Collapse
|
13
|
Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chem Rev 2014; 114:779-814. [PMID: 23981057 PMCID: PMC3947274 DOI: 10.1021/cr300461d] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
14
|
Gavrilov AA, Chertovich AV. Computer simulation of random polymer networks: Structure and properties. POLYMER SCIENCE SERIES A 2014. [DOI: 10.1134/s0965545x14010027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
15
|
Alarcón F, Pérez-Hernández G, Pérez E, Gama Goicochea A. Coarse-grained simulations of the salt dependence of the radius of gyration of polyelectrolytes as models for biomolecules in aqueous solution. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:661-72. [DOI: 10.1007/s00249-013-0915-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/07/2013] [Accepted: 05/15/2013] [Indexed: 11/30/2022]
|
16
|
Mayoral E, Goicochea AG. Modeling the temperature dependent interfacial tension between organic solvents and water using dissipative particle dynamics. J Chem Phys 2013; 138:094703. [DOI: 10.1063/1.4793742] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
17
|
Pivkin IV, Caswell B, Karniadakisa GE. Dissipative Particle Dynamics. REVIEWS IN COMPUTATIONAL CHEMISTRY 2010. [DOI: 10.1002/9780470890905.ch2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
18
|
Sanghi T, Aluru NR. A transferable coarse-grained potential to study the structure of confined, supercritical Lennard-Jones fluids. J Chem Phys 2010; 132:044703. [DOI: 10.1063/1.3289722] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
19
|
Goujon F, Malfreyt P, Tildesley DJ. Mesoscopic Simulation of Entangled Polymer Brushes under Shear: Compression and Rheological Properties. Macromolecules 2009. [DOI: 10.1021/ma9000429] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Florent Goujon
- Laboratoire de Thermodynamique et Interactions Moléculaires FRE CNRS 3099, Université Blaise Pascal, 63177 Aubière Cedex, France
| | - Patrice Malfreyt
- Laboratoire de Thermodynamique et Interactions Moléculaires FRE CNRS 3099, Université Blaise Pascal, 63177 Aubière Cedex, France
| | | |
Collapse
|
20
|
Eriksson A, Jacobi MN, Nyström J, Tunstrøm K. Bottom-up derivation of an effective thermostat for united atoms simulations of water. J Chem Phys 2009; 130:164509. [DOI: 10.1063/1.3119922] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
21
|
Eriksson A, Jacobi MN, Nyström J, Tunstrøm K. A method for estimating the interactions in dissipative particle dynamics from particle trajectories. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:095401. [PMID: 21817387 DOI: 10.1088/0953-8984/21/9/095401] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We introduce a method for determining the functional form of the stochastic and dissipative interactions in a dissipative particle dynamics (DPD) model from projected phase space trajectories. The DPD model is viewed as a coarse graining of a detailed dynamics that displays a clear timescale separation. Based on the Mori-Zwanzig projection operator method we derive a consistency equation for the stochastic interaction in DPD. The consistency equation can be solved by an iterative bootstrapping procedure. Combined with standard techniques for estimating the conservative interaction, our method makes it possible to reconstruct all the forces in a coarse-grained DPD model. We demonstrate how the method works by recreating the interactions in a DPD model from its phase space trajectory. Furthermore, we discuss how our method can be used in realistic systems with finite timescale separation.
Collapse
Affiliation(s)
- Anders Eriksson
- Department of Physics, University of Gothenburg, SE-41296 Göteborg, Sweden
| | | | | | | |
Collapse
|
22
|
Eriksson A, Jacobi MN, Nyström J, Tunstrøm K. Effective thermostat induced by coarse graining of simple point charge water. J Chem Phys 2008; 129:024106. [DOI: 10.1063/1.2953320] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
23
|
Noid WG, Chu JW, Ayton GS, Krishna V, Izvekov S, Voth GA, Das A, Andersen HC. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem Phys 2008; 128:244114. [PMID: 18601324 PMCID: PMC2671183 DOI: 10.1063/1.2938860] [Citation(s) in RCA: 533] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 05/13/2008] [Indexed: 01/16/2023] Open
Abstract
Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining (MS-CG) method [J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for the MS-CG models. A CG model that employs such a PMF as a "potential energy function" will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MS-CG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this many-body PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MS-CG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model.
Collapse
Affiliation(s)
- W G Noid
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Eriksson A, Jacobi MN, Nyström J, Tunstrøm K. Using force covariance to derive effective stochastic interactions in dissipative particle dynamics. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:016707. [PMID: 18351960 DOI: 10.1103/physreve.77.016707] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Indexed: 05/26/2023]
Abstract
There exist methods for determining effective conservative interactions in coarse-grained particle-based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but the model system we study does not correctly represent transport properties. We suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the RDF and a force covariance function can be used to determine all interactions in dissipative particle dynamics (DPD). Furthermore, we use the method to test whether the effective interactions in DPD can be adjusted to produce a force covariance consistent with the projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature.
Collapse
Affiliation(s)
- Anders Eriksson
- Department of Energy and Environment, Chalmers University of Technology, 41296 Göteborg, Sweden
| | | | | | | |
Collapse
|
25
|
Rao S, Li X, Liang H. Developing coarse-grained force fields for polystyrene with different chain lengths from atomistic simulation. Macromol Res 2007. [DOI: 10.1007/bf03218940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
26
|
Goicochea AG. Adsorption and disjoining pressure isotherms of confined polymers using dissipative particle dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11656-63. [PMID: 17914849 DOI: 10.1021/la701791h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The adsorption and disjoining pressure isotherms of polymers confined by planar walls are obtained using Monte Carlo (MC) simulations in the Grand Canonical (GC) ensemble in combination with the mesoscopic technique known as dissipative particle dynamics (DPD). Two models of effective potentials for the confining surfaces are used: one with both an attractive and a repulsive term and one with a purely repulsive term. As for the polymer, seven-bead linear model of polyethylene glycol (PEG) dissolved in water is used. The results indicate remarkably good agreement between the trends shown by our adsorption isotherms and those obtained from experiments of PEG on oxide surfaces. Additionally, the disjoining pressure isotherm of water shows oscillations, while those of PEG display the same trend for both wall models. Moreover, it is found that the disjoining pressure isotherms are in qualitative agreement with those from experiments on confined linear polymers.
Collapse
Affiliation(s)
- A Gama Goicochea
- Centro de Investigación en Polímeros (Grupo COMEX) Marcos Achar Lobatón No. 2, Tepexpan, 55885 Acolman, Estado de México, Mexico.
| |
Collapse
|
27
|
Goicochea AG, Romero-Bastida M, López-Rendón R. Dependence of thermodynamic properties of model systems on some dissipative particle dynamics parameters. Mol Phys 2007. [DOI: 10.1080/00268970701624679] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
28
|
Pivkin IV, Karniadakis GE. Coarse-graining limits in open and wall-bounded dissipative particle dynamics systems. J Chem Phys 2007; 124:184101. [PMID: 16709091 DOI: 10.1063/1.2191050] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse graining of dense liquid-state systems can potentially lead to fast simulation times, thus providing an effective bridge between atomistic and continuum descriptions. Dissipative particle dynamics (DPD) is a stochastic Lagrangian method that provides a simple formal procedure for coarse graining. Here we analyze some of the fundamental modeling ideas of DPD and identify three factors that limit its application at high coarse-graining levels: interparticle force magnitude, compressibility, and geometric confinement. These artifacts lead to erroneous transport properties of highly coarse-grained DPD systems and thus incorrect dynamics in simulating complex fluids, e.g., colloids and polymers.
Collapse
Affiliation(s)
- Igor V Pivkin
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA
| | | |
Collapse
|
29
|
Noid WG, Chu JW, Ayton GS, Voth GA. Multiscale coarse-graining and structural correlations: connections to liquid-state theory. J Phys Chem B 2007; 111:4116-27. [PMID: 17394308 PMCID: PMC2642678 DOI: 10.1021/jp068549t] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method (Izvekov, S.; Voth, G. A. J. Phys. Chem. B 2005, 109, 2469; J. Chem. Phys. 2005, 123, 134105). If no approximations are made, then the MS-CG method yields a many-body multidimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe nonbonded interactions. The analogy between coarse-graining and the inverse problem of liquid-state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.
Collapse
Affiliation(s)
- W. G. Noid
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112-0850
| | - Jhih-Wei Chu
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112-0850
| | - Gary S. Ayton
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112-0850
| | - Gregory A. Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, 315 S. 1400 E. Rm 2020, Salt Lake City, Utah 84112-0850
| |
Collapse
|
30
|
Jakobsen AF, Mouritsen OG, Besold G. Artifacts in dynamical simulations of coarse-grained model lipid bilayers. J Chem Phys 2007; 122:204901. [PMID: 15945771 DOI: 10.1063/1.1900725] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With special focus on dissipative particle dynamics simulations of anisotropic and complex soft matter, such as lipid bilayers in water, we have investigated the occurrence of artifacts in the results obtained from dynamical simulations of coarse-grained particle-based models. The particles are modeled by beads that interact via soft repulsive conservative forces (as defined in dissipative particle dynamics simulations), harmonic bond potentials, as well as bending potentials imparting stiffness to the lipid tails. Two different update schemes are investigated: dissipative particle dynamics with a velocity-Verlet-like integration scheme [G. Besold, I. Vattulainen, M. Karttunen, and J. M. Polson, Phys. Rev. E 63, R7611 (2000)] and Lowe-Andersen thermostatting [C. P. Lowe, Europhys. Lett. 47, 145 (1999)] with the standard velocity-Verlet integration algorithm. By varying the integration time step, we examine various physical quantities, in particular pressure profiles and kinetic bead temperatures, for their sensitivity to artifacts caused by the specific combination of integration technique and the thermostat. We then propose a simple fingerprint method that allows monitoring the presence of simulation artifacts.
Collapse
Affiliation(s)
- Ask F Jakobsen
- MEMPHYS-Center for Biomembrane Physics, Physics Department, University of Southern Denmark, Odense, Denmark
| | | | | |
Collapse
|
31
|
Fellermann H, Rasmussen S, Ziock HJ, Solé RV. Life cycle of a minimal protocell--a dissipative particle dynamics study. ARTIFICIAL LIFE 2007; 13:319-45. [PMID: 17716015 DOI: 10.1162/artl.2007.13.4.319] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Cross-reactions and other systematic difficulties generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key issues as we represent and analyze in simulation a full implementation of a minimal protocell. Using a 3D dissipative particle dynamics simulation method, we are able to address the coupled diffusion, self-assembly, and chemical reaction processes required to model a full life cycle of a protocell composed of coupled genetic, metabolic, and container subsystems. Utilizing this minimal structural and functional representation of the constituent molecules, their interactions, and their reactions, we identify and explore the nature of the many linked processes for the full protocellular system. Obviously the simplicity of this simulation method combined with the inherent system complexity prevents us from expecting quantitative simulation predictions from these investigations. However, we report important findings on systemic processes, some previously predicted and some newly discovered, as we couple the protocellular self-assembly processes and chemical reactions.
Collapse
Affiliation(s)
- Harold Fellermann
- Self-Organizing Systems, EES-6 MS-D462, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | | | | | | |
Collapse
|
32
|
Symeonidis V, Karniadakis GE, Caswell B. Schmidt number effects in dissipative particle dynamics simulation of polymers. J Chem Phys 2006; 125:184902. [PMID: 17115790 DOI: 10.1063/1.2360274] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Simulation studies for dilute polymeric systems are presented using the dissipative particle dynamics method. By employing two different thermostats, the velocity-Verlet and Lowe's scheme, we show that the Schmidt number (S(c)) of the solvent strongly affects nonequilibrium polymeric quantities. The fractional extension of wormlike chains subjected to steady shear is obtained as a function of S(c). Poiseuille flow in microchannels for fixed polymer concentration and varying number of repeated units within a chain is simulated. The nonuniform concentration profiles and their dependence on S(c) are computed. We show the effect of the bounce-forward wall boundary condition on the depletion layer thickness. A power law fit of the velocity profile in stratified Poiseuille flow in a microchannel yields wall viscosities different from bulk values derived from uniform, steady plane Couette flow. The form of the velocity profiles indicates that the slip flow model is not useful for the conditions of these calculations.
Collapse
Affiliation(s)
- Vasileios Symeonidis
- Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA.
| | | | | |
Collapse
|
33
|
Abstract
A methodology is described to systematically derive coarse-grained (CG) force fields for molecular liquids from the underlying atomistic-scale forces. The coarse graining of an interparticle force field is accomplished by the application of a force-matching method to the trajectories and forces obtained from the atomistic trajectory and force data for the CG sites of the targeted system. The CG sites can be associated with the centers of mass of atomic groups because of the simplicity in the evaluation of forces acting on these sites from the atomistic data. The resulting system is called a multiscale coarse-grained (MS-CG) representation. The MS-CG method for liquids is applied here to water and methanol. For both liquids one-site and two-site CG representations without an explicit treatment of the long-ranged electrostatics have been derived. In addition, for water a two-site model having the explicit long-ranged electrostatics has been developed. To improve the thermodynamic properties (e.g., pressure and density) for the MS-CG models, the constraint for the instantaneous virial was included into the force-match procedure. The performance of the resulting models was evaluated against the underlying atomistic simulations and experiment. In contrast with existing approaches for coarse graining of liquid systems, the MS-CG approach is general, relies only on the interatomic interactions in the reference atomistic system.
Collapse
Affiliation(s)
- Sergei Izvekov
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA
| | | |
Collapse
|
34
|
Milano G, Müller-Plathe F. Mapping Atomistic Simulations to Mesoscopic Models: A Systematic Coarse-Graining Procedure for Vinyl Polymer Chains. J Phys Chem B 2005; 109:18609-19. [PMID: 16853395 DOI: 10.1021/jp0523571] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The paper introduces a systematic procedure to coarse-grain atomistic models of the largest family of synthetic polymers into a mesoscopic model that is able to keep detailed information about chain stereosequences. The mesoscopic model consists of sequences of superatoms centered on methylene carbons of two different types according to the kind of diad (m or r) they belong to. The corresponding force-field contains three different bonds, six angle and three nonbonded terms. Recently developed analytical potentials, based on sums of Gaussians for bond and angle terms of the mesoscale force field have been used. For the nonbonded part, numerical potentials optimized by pressure-corrected iterative Boltzmann inversion have been used. As test case we coarse-grained an atomistic all-atom model of atactic polystyrene. The proposed mesoscale model has been successfully tested against structural and dynamical properties for different chain lengths and opens the possibility of relaxing melts of high molecular weight vinyl polymers.
Collapse
Affiliation(s)
- Giuseppe Milano
- School of Engineering and Science, International University Bremen, D-28759, Bremen, Germany.
| | | |
Collapse
|
35
|
Symeonidis V, Karniadakis G, Caswell B. A Seamless Approach to Multiscale Complex Fluid Simulation. Comput Sci Eng 2005. [DOI: 10.1109/mcse.2005.44] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
36
|
Milano G, Goudeau S, Müller-Plathe F. Multicentered Gaussian-based potentials for coarse-grained polymer simulations: Linking atomistic and mesoscopic scales. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/polb.20380] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
37
|
Hafskjold B, Liew † CC, Shinoda ‡ W. Can such Long Time Steps Really be used in Dissipative Particle Dynamics Simulations? MOLECULAR SIMULATION 2004. [DOI: 10.1080/08927020410001709370] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
38
|
Kalikmanov VI. Soft depletion in binary fluids. PHYSICAL REVIEW E 2003; 68:010101. [PMID: 12935117 DOI: 10.1103/physreve.68.010101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2003] [Indexed: 11/07/2022]
Abstract
We show theoretically that a binary fluid characterized on a mesoscopic scale by purely repulsive short-range interactions without cores possesses an effective attraction between like particles. This "soft depletion effect" is a generic phenomenon driving a mixing-demixing transition in a binary system with pure repulsions.
Collapse
Affiliation(s)
- V I Kalikmanov
- Department of Applied Physics, Computational Physics Section, University of Delft, Lorentzweg 1, 2628 CJ Delft, The Netherlands.
| |
Collapse
|
39
|
Liew CC, Mikami M. A coarse-grained model for particle dynamics simulations of complex fluids. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(02)01856-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
40
|
Reith D, Müller B, Müller-Plathe F, Wiegand S. How does the chain extension of poly (acrylic acid) scale in aqueous solution? A combined study with light scattering and computer simulation. J Chem Phys 2002. [DOI: 10.1063/1.1471901] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
41
|
Vattulainen I, Karttunen M, Besold G, Polson JM. Integration schemes for dissipative particle dynamics simulations: From softly interacting systems towards hybrid models. J Chem Phys 2002. [DOI: 10.1063/1.1450554] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
42
|
|
43
|
Neyertz S, Brown D. Preparation of bulk melt chain configurations of polycyclic polymers. J Chem Phys 2001. [DOI: 10.1063/1.1379073] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
44
|
Padding JT, Briels WJ. Zero-shear stress relaxation and long time dynamics of a linear polyethylene melt: A test of Rouse theory. J Chem Phys 2001. [DOI: 10.1063/1.1368135] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
45
|
Reith D, Meyer H, Müller-Plathe F. Mapping Atomistic to Coarse-Grained Polymer Models Using Automatic Simplex Optimization To Fit Structural Properties. Macromolecules 2001. [DOI: 10.1021/ma001499k] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dirk Reith
- Max-Planck-Institut für Polymerforschung, D-55128 Mainz, Germany; and CNRS, Institut Charles Sadron, 6, rue Boussingault, F-67083 Strasbourg Cedex, France
| | - Hendrik Meyer
- Max-Planck-Institut für Polymerforschung, D-55128 Mainz, Germany; and CNRS, Institut Charles Sadron, 6, rue Boussingault, F-67083 Strasbourg Cedex, France
| | - Florian Müller-Plathe
- Max-Planck-Institut für Polymerforschung, D-55128 Mainz, Germany; and CNRS, Institut Charles Sadron, 6, rue Boussingault, F-67083 Strasbourg Cedex, France
| |
Collapse
|
46
|
Akkermans RLC, Briels WJ. A structure-based coarse-grained model for polymer melts. J Chem Phys 2001. [DOI: 10.1063/1.1330744] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
47
|
Meyer H, Biermann O, Faller R, Reith D, Müller-Plathe F. Coarse graining of nonbonded inter-particle potentials using automatic simplex optimization to fit structural properties. J Chem Phys 2000. [DOI: 10.1063/1.1308542] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
48
|
Akkermans RLC, Briels WJ. Coarse-grained dynamics of one chain in a polymer melt. J Chem Phys 2000. [DOI: 10.1063/1.1308513] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
49
|
A multiple chain Monte Carlo method for atomistic simulation of high molecular weight polymer melts. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1089-3156(99)00030-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
50
|
Gibson JB, Zhang K, Chen K, Chynoweth S, Manke CW. Simulation of Colloid-Polymer Systems using Dissipative Particle Dynamics. MOLECULAR SIMULATION 1999. [DOI: 10.1080/08927029908022109] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|