1
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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: 32] [Impact Index Per Article: 10.7] [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.
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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.
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2
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Heyes D. Second virial coefficient of bounded repulsive potentials. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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3
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Santos AP, Pȩkalski J, Panagiotopoulos AZ. Thermodynamic signatures and cluster properties of self-assembly in systems with competing interactions. SOFT MATTER 2017; 13:8055-8063. [PMID: 29052681 DOI: 10.1039/c7sm01721a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Colloidal particles, amphiphiles and functionalized nanoparticles are examples of systems that frequently exhibit short-range attraction coupled with long-range repulsion. We vary the ratio of attraction and repulsion in a simple isotropic model with competing interactions, using molecular simulations, and observe significant differences in the properties of the self-assembled clusters that form. We report conditions that lead to the self-assembly of clusters of a preferred size, accompanied by a change in the slope of the pressure with respect to density, similar to micelles formed by amphiphilic molecules. We also report conditions where repulsion dominates, clusters of a preferred size form and the pressure vs. density slope is unaffected by self-assembly. We investigate cluster structure by calculating the size distributions, free colloid density, cluster shape and density profiles. The system dynamics are characterized by cluster life-times. We do not find qualitative differences in structure or dynamics of the clusters, regardless the pressure behavior. Therefore, thermodynamic and structural quantities are required to classify the different clustering characteristics that are observable in systems with competing interactions. Our results have implications in terms of development of design principles for stable cluster self-assembly.
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Affiliation(s)
- Andrew P Santos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA.
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4
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Müter D, Rother G, Bock H, Schoen M, Findenegg GH. Adsorption and Depletion Regimes of a Nonionic Surfactant in Hydrophilic Mesopores: An Experimental and Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11406-11416. [PMID: 28810734 DOI: 10.1021/acs.langmuir.7b02262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Adsorption and aggregation of nonionic surfactants at oxide surfaces has been studied extensively in the past, but only for concentrations below and near the critical micelle concentration. Here we report an adsorption study of a short-chain surfactant (C6E3) in porous silica glass of different pore sizes (7.5 to 50 nm), covering a wide composition range up to 50 wt % in a temperature range from 20 °C to the LCST. Aggregative adsorption is observed at low concentrations, but the excess concentration of C6E3 in the pores decreases and approaches zero at higher bulk concentrations. Strong depletion of surfactant (corresponding to enrichment of water in the pores) is observed in materials with wide pores at high bulk concentrations. We propose an explanation for the observed pore-size dependence of the azeotropic point. Mesoscale simulations based on dissipative particle dynamics (DPD) were performed to reveal the structural origin of this transition from the adsorption to the depletion regime. The simulated adsorption isotherms reproduce the behavior found in the 7.5 nm pores. The calculated bead density profiles indicate that the repulsive interaction of surfactant head groups causes a depletion of surfactant in the region around the corona of the surface micelles.
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Affiliation(s)
- Dirk Müter
- Nano-Science Center, Department of Chemistry, University of Copenhagen , 2100 Copenhagen, Denmark
| | - Gernot Rother
- Stranski Laboratory of Physical and Theoretical Chemistry, Department of Chemistry, Technical University Berlin , 10623 Berlin, Germany
- Geochemistry & Interfacial Science Group, Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831-6110, United States
| | - Henry Bock
- Institute of Chemical Sciences, Heriot-Watt University , Edinburgh, EH14 4AS, United Kingdom
| | - Martin Schoen
- Stranski Laboratory of Physical and Theoretical Chemistry, Department of Chemistry, Technical University Berlin , 10623 Berlin, Germany
| | - Gerhard H Findenegg
- Stranski Laboratory of Physical and Theoretical Chemistry, Department of Chemistry, Technical University Berlin , 10623 Berlin, Germany
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5
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Surfactant chain length and concentration influence on the interfacial tension of two immiscible model liquids: a coarse-grained approach. J Mol Model 2017; 23:306. [PMID: 28986687 DOI: 10.1007/s00894-017-3474-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/17/2017] [Indexed: 10/18/2022]
Abstract
The interfacial tension between immiscible liquids is studied as a function of a model linear surfactant length and concentration using coarse-grained, dissipative particle dynamics numerical simulations. The adsorption isotherms obtained from the simulations are found to be in agreement with Langmuir's model. The reduction of the interfacial tension with increasing surfactant concentration is found to display some common characteristics for all the values of chain length modeled, with our predictions being in agreement with Szyszkowski's equation. Lastly, the critical micelle concentration is predicted for all surfactant lengths, finding exponentially decaying behavior, in agreement with Kleven's model. It is argued that these findings can be helpful guiding tools in the interpretation of available experiments and in the design of new ones with new surfactants and polymers.
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6
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Yoshii N, Nimura Y, Fujimoto K, Okazaki S. Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study. J Chem Phys 2017; 147:034906. [DOI: 10.1063/1.4994698] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Noriyuki Yoshii
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Department of Applied Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Yuki Nimura
- Department of Applied Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Kazushi Fujimoto
- Department of Applied Chemistry, Nagoya University, Nagoya 464-8603, Japan
| | - Susumu Okazaki
- Department of Applied Chemistry, Nagoya University, Nagoya 464-8603, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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7
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Fujimoto K, Kubo Y, Kawada S, Yoshii N, Okazaki S. Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1328557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kazushi Fujimoto
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Yousuke Kubo
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Shinji Kawada
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
| | - Noriyuki Yoshii
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Susumu Okazaki
- Department of Materials Chemistry, Nagoya University, Nagoya, Japan
- Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Japan
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8
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Lu J, Jacobson LC, Perez Sirkin YA, Molinero V. High-Resolution Coarse-Grained Model of Hydrated Anion-Exchange Membranes that Accounts for Hydrophobic and Ionic Interactions through Short-Ranged Potentials. J Chem Theory Comput 2016; 13:245-264. [PMID: 28068769 DOI: 10.1021/acs.jctc.6b00874] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Liam C. Jacobson
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yamila A. Perez Sirkin
- Departamento
de Química Inorgánica, Analítica y Química
Física, and INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
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9
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Kawada S, Komori M, Fujimoto K, Yoshii N, Okazaki S. Molecular dynamics study of the formation mechanisms of ionic SDS and nonionic C12E8 micelles and n-dodecane droplets. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.12.062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Theoretical description of 2D-cluster formation of nonionic surfactants at the air/water interface. Colloid Polym Sci 2015. [DOI: 10.1007/s00396-015-3630-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Ren Y, Liu B, Kiryutina T, Xi H, Qian Y. Investigation of structure formation mechanism of a mesoporous ZSM-5 zeolite by mesoscopic simulation. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2014.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Kacar G, Peters EAJF, van der Ven LGJ, de With G. Hierarchical multi-scale simulations of adhesion at polymer–metal interfaces: dry and wet conditions. Phys Chem Chem Phys 2015; 17:8935-44. [DOI: 10.1039/c5cp00343a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Multi-scale simulations are performed to study the adhesion properties of different polymer–metal interfaces in the absence and presence of water.
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Affiliation(s)
- Gokhan Kacar
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Elias A. J. F. Peters
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Leendert G. J. van der Ven
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
| | - Gijsbertus de With
- Laboratory of Materials and Interface Chemistry
- Department of Chemical Engineering and Chemistry
- Eindhoven University of Technology
- Eindhoven
- The Netherlands
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13
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Jiménez-Serratos G, Gil-Villegas A, Vega C, Blas FJ. Monte Carlo simulation of flexible trimers: From square well chains to amphiphilic primitive models. J Chem Phys 2013; 139:114901. [PMID: 24070305 DOI: 10.1063/1.4820530] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Guadalupe Jiménez-Serratos
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías Campus León, Universidad de Guanajuato, Colonia Lomas del Campestre, León 37150, Mexico
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14
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Vishnyakov A, Lee MT, Neimark AV. Prediction of the Critical Micelle Concentration of Nonionic Surfactants by Dissipative Particle Dynamics Simulations. J Phys Chem Lett 2013; 4:797-802. [PMID: 26281935 DOI: 10.1021/jz400066k] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Micellization of surfactant solutions is a ubiquitous phenomenon in natural systems and technological processes, and its theoretical description represents one of the cornerstone problems in the physical chemistry of colloidal systems. However, successful attempts of quantitative modeling confirmed by experimental data remains limited. We show, for the first time, that the dissipative particle dynamics with rigorously defined soft repulsion interaction and rigidity parameters is capable of predicting micellar self-assembly of nonionic surfactants. This is achieved due to a novel approach suggested for defining the interaction parameters by fitting to the infinite dilution activity coefficients of binary solutions formed by reference compounds that represent coarse-grained fragments of surfactant molecules. Using this new parametrization scheme, we obtained quantitative agreement with the experimental critical micelle concentration and aggregation number for several typical surfactants of different chemical structures. The proposed approach can be extended to various colloidal and polymeric systems beyond nonionic surfactant solutions.
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Affiliation(s)
- Aleksey Vishnyakov
- Department of Chemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway New Jersey 08854, United States
| | - Ming-Tsung Lee
- Department of Chemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway New Jersey 08854, United States
| | - Alexander V Neimark
- Department of Chemical Engineering, Rutgers, the State University of New Jersey, 98 Brett Road, Piscataway New Jersey 08854, United States
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15
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Hyodo SA. Analyses of coarse graining procedure for mesoscale simulation. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2010.536544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Knott BC, Doherty MF, Peters B. A simulation test of the optical Kerr mechanism for laser-induced nucleation. J Chem Phys 2011; 134:154501. [DOI: 10.1063/1.3574010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Pool R, Bolhuis PG. The influence of micelle formation on the stability of colloid surfactant mixtures. Phys Chem Chem Phys 2010; 12:14789-97. [PMID: 20949141 DOI: 10.1039/c0cp00912a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stability of colloidal dispersions can be severely affected by the presence of surfactants. Because surfactants can adsorb at colloidal surfaces as well as form micelles, one can expect an interplay between both phenomena. Using grand-canonical coarse-grained Monte Carlo simulations on surfactant solutions confined between two surfaces, we investigate how adsorption and micelle formation affects the effective interaction between two colloidal particles, and hence, the stability of the colloidal dispersion. For solvophilic colloidal surfaces, we observe a short-ranged oscillatory solvation pressure that is hardly affected by the presence of surfactants in the system. The effective surface-surface interaction, however, reveals a decrease in solvophilic stabilization as a function of surfactant chemical potential. For solvophobic surfaces, we find that the capillary evaporation observed in a confined pure solvent, is counteracted by the addition of surfactants. Around the critical micelle concentration (CMC), the surface-surface interaction even becomes repulsive, enhancing stabilization of the colloidal dispersion. In contrast, the formation of micelles at concentrations above the CMC causes an additional depletion effect, resulting in an effective attraction, which in turn can destabilize a colloidal dispersion.
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Affiliation(s)
- René Pool
- Centre for Integrative Bioinformatics Vrije Universiteit (IBIVU), Vrije Universiteit Amsterdam, De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands.
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18
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Evaluation of alkyl sulfate and sulfonate micellar structure at the water–surfactant interphase with simple geometrical calculations. J Colloid Interface Sci 2010; 349:230-5. [DOI: 10.1016/j.jcis.2010.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/07/2010] [Accepted: 05/08/2010] [Indexed: 11/23/2022]
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19
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Rodgers JM, Webb M, Smit B. Alcohol solubility in a lipid bilayer: Efficient grand-canonical simulation of an interfacially active molecule. J Chem Phys 2010; 132:064107. [PMID: 20151733 DOI: 10.1063/1.3314289] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We derive a new density-biased Monte Carlo technique which preserves detailed balance and improves the convergence of grand-canonical simulations of a species with a strong preference for an interfacial region as compared to the bulk. This density-biasing technique is applied to the solubility of "alcohol" molecules in a mesoscopic model of the lipid bilayer, a system which has anesthetic implications but is poorly understood.
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Affiliation(s)
- Jocelyn M Rodgers
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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20
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Knott BC, Duff N, Doherty MF, Peters B. Estimating diffusivity along a reaction coordinate in the high friction limit: Insights on pulse times in laser-induced nucleation. J Chem Phys 2009; 131:224112. [DOI: 10.1063/1.3268704] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [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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Rekvig L, Frenkel D. Molecular simulations of droplet coalescence in oil/water/surfactant systems. J Chem Phys 2007; 127:134701. [PMID: 17919037 DOI: 10.1063/1.2780865] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report a molecular simulation study of the mechanism by which droplets covered with a surfactant monolayer coalesce. We study a model system where the rate-limiting step in coalescence is the rupture of the surfactant film. Our simulations allow us to focus on the stages at the core of the coalescence process: the initial rupture of the two surfactant monolayers, the rearrangement of the surfactant molecules to form a channel connecting the two droplets, and the expansion of the radius of the resulting channel. For our numerical study, we made use of the dissipative particle dynamics method. We used a coarse-grained description of the oil, water, and surfactant molecules. The rupture of the surfactant film is a rare event on the molecular time scale. To enhance the sampling of the rupture of the surfactant film, we used forward flux sampling (FFS). FFS not only allows us to estimate coalescence rates, it also provides insight into the molecular structure and free energy of the "transition" state. For an oil-water-oil film without surfactant, the rupture rate decreases exponentially with increasing film thickness. The critical state is different in thin and thick films: Thin films break following a large enough thickness fluctuation. Thicker films break only after a sufficiently large hole fluctuation-they can heal. Next, we designed surfactant molecules with positive, zero, and negative natural curvatures. For a water film between two surfactant-covered oil droplets, the rupture rate is highest when the surfactant has a negative natural curvature, lowest when it has zero natural curvature, and lying in between when it has a positive natural curvature. This nonmonotonic variation with curvature stems from two effects: First, the surfactants with a large absolute value of the natural curvature have lower interfacial tension and bending rigidity. This promotes the interfacial fluctuations required to nucleate a channel. Second, the sign of the natural curvature determines whether there is a critical channel radius at which the channel free energy has a maximum. The latter is in agreement with the hole-nucleation theory of Kabalnov and Wennerstrom [Langmuir 12, 276 (1996)]. Our simulations seriously overestimate the relative stability of surfactant free emulsions. We argue that this is due to the fact that our model does not allow for nanobubble formation and capillary evaporation-processes that are presumably of key importance in the coalescence of surfactant-free emulsions.
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Affiliation(s)
- Live Rekvig
- FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam, The Netherlands.
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22
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Pool R, Bolhuis PG. Sampling the kinetic pathways of a micelle fusion and fission transition. J Chem Phys 2007; 126:244703. [PMID: 17614573 DOI: 10.1063/1.2741513] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mechanism and kinetics of micellar breakup and fusion in a dilute solution of a model surfactant are investigated by path sampling techniques. Analysis of the path ensemble gives insight in the mechanism of the transition. For larger, less stable micelles the fission/fusion occurs via a clear neck formation, while for smaller micelles the mechanism is more direct. In addition, path analysis yields an appropriate order parameter to evaluate the fusion and fission rate constants using stochastic transition interface sampling. For the small, stable micelle (50 surfactants) the computed fission rate constant is a factor of 10 lower than the fusion rate constant. The procedure opens the way for accurate calculation of free energy and kinetics for, e.g., membrane fusion, and wormlike micelle endcap formation.
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Affiliation(s)
- René Pool
- Condensed Matter and Interfaces, Universiteit Utrecht, Princetonplein 1, 3584 CC Utrecht, The Netherlands.
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23
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Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. J Phys Chem B 2007; 111:7812-24. [PMID: 17569554 DOI: 10.1021/jp071097f] [Citation(s) in RCA: 3594] [Impact Index Per Article: 211.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.
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Affiliation(s)
- Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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Kinjo T, Hyodo SA. Equation of motion for coarse-grained simulation based on microscopic description. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:051109. [PMID: 17677024 DOI: 10.1103/physreve.75.051109] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Indexed: 05/16/2023]
Abstract
We have derived an equation of motion for coarse-grained particles by using a projection operator. Because the derived coarse-grained equation is based on microscopic description, it can be the basis for models of various coarse-grained simulations. We show that by substitution of random forces into fluctuating forces in the coarse-grained equation, the equations for Brownian dynamics and dissipative particle dynamics are reproduced.
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25
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Hyodo S. Hierarchical and large-scale atomistic simulations for practical materials. MOLECULAR SIMULATION 2007. [DOI: 10.1080/08927020601156400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Pool R, Bolhuis PG. Prediction of an autocatalytic replication mechanism for micelle formation. PHYSICAL REVIEW LETTERS 2006; 97:018302. [PMID: 16907417 DOI: 10.1103/physrevlett.97.018302] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Indexed: 05/11/2023]
Abstract
We report molecular simulations suggesting that the kinetics of surfactant micelle formation can be sped up significantly by a replication mechanism, in which growing micelles become unstable and split into two similar sized micelles. We argue that for certain surfactants types around the critical micelle concentration, such a mechanism becomes more dominant than the commonly accepted nucleation pathway.
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Affiliation(s)
- René Pool
- van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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