1
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Santos TCB, Futerman AH. The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies. Prog Lipid Res 2023; 92:101253. [PMID: 37659458 DOI: 10.1016/j.plipres.2023.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
The unique biophysical and biochemical properties of lipids render them crucial in most models of the origin of life (OoL). Many studies have attempted to delineate the prebiotic pathways by which lipids were formed, how micelles and vesicles were generated, and how these micelles and vesicles became selectively permeable towards the chemical precursors required to initiate and support biochemistry and inheritance. Our analysis of a number of such studies highlights the extremely narrow and limited range of conditions by which an experiment is considered to have successfully modeled a role for lipids in an OoL experiment. This is in line with a recent proposal that bias is introduced into OoL studies by the extent and the kind of human intervention. It is self-evident that OoL studies can only be performed by human intervention, and we now discuss the possibility that some assumptions and simplifications inherent in such experimental approaches do not permit determination of mechanistic insight into the roles of lipids in the OoL. With these limitations in mind, we suggest that more nuanced experimental approaches than those currently pursued may be required to elucidate the generation and function of lipids, micelles and vesicles in the OoL.
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Affiliation(s)
- Tania C B Santos
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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Lodge TP, Seitzinger CL, Seeger SC, Yang S, Gupta S, Dorfman KD. Dynamics and Equilibration Mechanisms in Block Copolymer Particles. ACS POLYMERS AU 2022; 2:397-416. [PMID: 36536887 PMCID: PMC9756915 DOI: 10.1021/acspolymersau.2c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/10/2022] [Accepted: 08/10/2022] [Indexed: 06/17/2023]
Abstract
Self-assembly of block copolymers into interesting and useful nanostructures, in both solution and bulk, is a vibrant research arena. While much attention has been paid to characterization and prediction of equilibrium phases, the associated dynamic processes are far from fully understood. Here, we explore what is known and not known about the equilibration of particle phases in the bulk, and spherical micelles in solution. The presumed primary equilibration mechanisms are chain exchange, fusion, and fragmentation. These processes have been extensively studied in surfactants and lipids, where they occur on subsecond time scales. In contrast, increased chain lengths in block copolymers create much larger barriers, and time scales can become prohibitively slow. In practice, equilibration of block copolymers is achievable only in proximity to the critical micelle temperature (in solution) or the order-disorder transition (in the bulk). Detailed theories for these processes in block copolymers are few. In the bulk, the rate of chain exchange can be quantified by tracer diffusion measurements. Often the rate of equilibration, in terms of number density and aggregation number of particles, is much slower than chain exchange, and consequently observed particle phases are often metastable. This is particularly true in regions of the phase diagram where Frank-Kasper phases occur. Chain exchange in solution has been explored quantitatively by time-resolved SANS, but the results are not well captured by theory. Computer simulations, particularly via dissipative particle dynamics, are beginning to shed light on the chain escape mechanism at the molecular level. The rate of fragmentation has been quantified in a few experimental systems, and TEM images support a mechanism akin to the anaphase stage of mitosis in cells, via a thin neck that pinches off to produce two smaller micelles. Direct measurements of micelle fusion are quite rare. Suggestions for future theoretical, computational, and experimental efforts are offered.
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Affiliation(s)
- Timothy P. Lodge
- Department
of Chemistry, University of Minnesota 207 Pleasant St SE, Minneapolis, Minnesota 55455, United States
- Department
of Chemical Engineering & Materials Science, University of Minnesota 451 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Claire L. Seitzinger
- Department
of Chemistry, University of Minnesota 207 Pleasant St SE, Minneapolis, Minnesota 55455, United States
| | - Sarah C. Seeger
- Department
of Chemical Engineering & Materials Science, University of Minnesota 451 Washington Ave SE, Minneapolis, Minnesota 55455, United States
| | - Sanghee Yang
- Department
of Chemistry, University of Minnesota 207 Pleasant St SE, Minneapolis, Minnesota 55455, United States
| | - Supriya Gupta
- Department
of Chemistry, University of Minnesota 207 Pleasant St SE, Minneapolis, Minnesota 55455, United States
| | - Kevin D. Dorfman
- Department
of Chemical Engineering & Materials Science, University of Minnesota 451 Washington Ave SE, Minneapolis, Minnesota 55455, United States
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3
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Jamadagni SN, Ko X, Thomas JB, Eike DM. Salt- and pH-Dependent Viscosity of SDS/LAPB Solutions: Experiments and a Semiempirical Thermodynamic Model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:8714-8725. [PMID: 34270265 DOI: 10.1021/acs.langmuir.1c00964] [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
We present novel data on the composition-, pH-, and salt-dependent zero shear viscosity of the commercially important mixture of anionic sodium dodecyl sulfate (SDS) and zwitterionic lauramidopropyl betaine (LAPB). We show via proton NMR experiments that the notionally zwitterionic LAPB exhibits a large pKa shift in the presence of SDS and can become partially cationic at formulation-relevant pH ranges of 4.5-6.0-that is, the binary system is effectively a ternary system. This has a pronounced effect on the viscosity of the system at low pH, especially if the fraction of LAPB is high. We use theoretical arguments to motivate a semiempirical but practical approach to model the viscosity of the mixtures using thermodynamic parameters such as the excess chemical potentials or activity coefficients of the surfactants. We demonstrate this using an augmented regular solution theory-based mixed micelle thermodynamic model and develop robust regression models using Bayesian approaches. We also show how the pKa shift from NMR experiments can be used to parameterize the thermodynamic model. This framework should be extensible to other arbitrary surfactant mixtures in the future and hence will be of broad interest for the development of surfactant formulations for household, personal care, and other applications.
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Affiliation(s)
- Sumanth N Jamadagni
- The Procter & Gamble Company, 8700 Mason Montgomery Road, Mason, Ohio 45040, United States
| | - Xueying Ko
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701, United States
| | - Jacqueline B Thomas
- The Procter & Gamble Company, 8700 Mason Montgomery Road, Mason, Ohio 45040, United States
| | - David M Eike
- The Procter & Gamble Company, 8700 Mason Montgomery Road, Mason, Ohio 45040, United States
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4
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021; 12:1936. [PMID: 33782395 PMCID: PMC8007728 DOI: 10.1038/s41467-021-21953-3] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jason A Wagoner
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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5
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Bolhuis PG, Swenson DWH. Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. ADVANCED THEORY AND SIMULATIONS 2021. [DOI: 10.1002/adts.202000237] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Peter G. Bolhuis
- Amsterdam Center for Multiscale Modeling van 't Hoff Institute for Molecular Sciences University of Amsterdam PO Box 94157 1090 GD Amsterdam The Netherlands
| | - David W. H. Swenson
- Centre Blaise Pascal Ecole Normale Superieure 46, allée d'Italie 69364 Lyon Cedex 07 France
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6
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.158121. [PMID: 32587966 PMCID: PMC7310622 DOI: 10.1101/2020.06.17.158121] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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7
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Mysona JA, McCormick AV, Morse DC. Simulation of diblock copolymer surfactants. II. Micelle kinetics. Phys Rev E 2019; 100:012603. [PMID: 31499829 DOI: 10.1103/physreve.100.012603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Indexed: 06/10/2023]
Abstract
Molecular dynamics (MD) simulations are used to measure dynamical properties of a simple bead-spring model of A-B diblock copolymer molecules, and to characterize rates and mechanisms of several dynamical processes. Dynamical properties are analyzed within the context of a kinetic population model that allows for both stepwise insertion and expulsion of individual free molecules and occasional fission and fusion of micelles. Kinetic coefficients for stepwise processes and micelle fission have been extracted from MD simulations of individual micelles. Insertion of a free surfactant molecule into a preexisting micelle is shown to be a completely diffusion-controlled process for the model studied here. Estimates are given for rates of rare events that create and destroy entire micelles by competing mechanisms involving stepwise association and dissociation or fission and fusion. Both mechanisms are shown to be relevant over the range of parameters studied here, with association and dissociation dominating in systems with more soluble surfactants and fission and fusion dominating in systems with less soluble surfactants.
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Affiliation(s)
- Joshua A Mysona
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Alon V McCormick
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - David C Morse
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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8
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Kahana A, Lancet D. Protobiotic Systems Chemistry Analyzed by Molecular Dynamics. Life (Basel) 2019; 9:E38. [PMID: 31083329 PMCID: PMC6617412 DOI: 10.3390/life9020038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
Systems chemistry has been a key component of origin of life research, invoking models of life's inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD's kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.
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Affiliation(s)
- Amit Kahana
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
| | - Doron Lancet
- Dept. Molecular Genetics, The Weizmann Institute of Science, Rehovot 7610010, Israel.
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9
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Shchekin AK, Adzhemyan LT, Babintsev IA, Volkov NA. Kinetics of Aggregation and Relaxation in Micellar Surfactant Solutions. COLLOID JOURNAL 2018. [DOI: 10.1134/s1061933x18020084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Vus K, Girych M, Trusova V, Gorbenko G, Kinnunen P, Mizuguchi C, Saito H. Fluorescence study of the effect of the oxidized phospholipids on amyloid fibril formation by the apolipoprotein A-I N-terminal fragment. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.09.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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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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12
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Rodgers TL, Magee JE, Amure T, Siperstein FR. Micelle response to changes in solvent properties. SOFT MATTER 2016; 12:9014-9024. [PMID: 27782285 DOI: 10.1039/c6sm01761d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The dynamics of co-polymer systems play an important role in the preparation and stability of formulations, as well as on their capability to function in drug delivery systems. Micelle inversion can occur as a result of a change in concentration when a solvent is very volatile and evaporates, or as a result of a change in solvent quality upon addition of another solvent to the original solution, or upon changes in pH. In this work, dissipative particle dynamics (DPD) is used to examine the dynamics of micelle inversion in concentrated systems of diblock and triblock amphiphiles, where interactions between neighboring aggregates are observed. Significant differences were observed in the inversion process of different amphiphilic molecules, with a large amount of co-polymer exchange between inverting aggregates made of diblock amphiphiles, and practically no exchange of molecules between aggregates during the inversion of triblock copolymer aggregates. Fundamental mechanisms of inversion are revealed that provide information which can be used to help design micelles for targeted drug release and allow understanding of history dependant formulations.
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Affiliation(s)
- T L Rodgers
- SCEAS, The University of Manchester, Manchester M13 9PL, UK.
| | - J E Magee
- SCEAS, The University of Manchester, Manchester M13 9PL, UK.
| | - T Amure
- SCEAS, The University of Manchester, Manchester M13 9PL, UK.
| | - F R Siperstein
- SCEAS, The University of Manchester, Manchester M13 9PL, UK.
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13
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Jensen GV, Lund R, Narayanan T, Pedersen JS. Transformation from Globular to Cylindrical Mixed Micelles through Molecular Exchange that Induces Micelle Fusion. J Phys Chem Lett 2016; 7:2039-2043. [PMID: 27181112 DOI: 10.1021/acs.jpclett.6b00767] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Transformations between different micellar morphologies in solution induced by changes in composition, salt, or temperature are well-known phenomena; however, the understanding of the associated kinetic pathways is still limited. Especially for mixed surfactant systems, the micelles can take a very wide range of structures, depending on the surfactant packing parameter and other thermodynamic conditions. Synchrotron-based small-angle X-ray scattering (SAXS) in combination with fast mixing using a stopped-flow apparatus can give direct access to the structural kinetics on a millisecond time scale. Here, this approach is used to study the formation of cylindrical micelles after mixing two solutions with globular micelles of the nonionic surfactant dodecyl maltoside (DDM) and the anionic surfactant sodium dodecyl sulfate (SDS), respectively. Two separate processes were identified: (i) a transition in micellar shell structure, interpreted as exchange of surfactant molecules resulting in mixed globular micelles, and subsequently, (ii) fusion into larger, cylindrical structures.
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Affiliation(s)
- Grethe V Jensen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
| | - Reidar Lund
- Department of Chemistry, University of Oslo , Postbox 1033 Blindern, NO-0315 Oslo, Norway
| | | | - Jan Skov Pedersen
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus, Denmark
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14
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Johnston MA, Swope WC, Jordan KE, Warren PB, Noro MG, Bray DJ, Anderson RL. Toward a Standard Protocol for Micelle Simulation. J Phys Chem B 2016; 120:6337-51. [DOI: 10.1021/acs.jpcb.6b03075] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - William C. Swope
- IBM Almaden Research Center, San Jose, California, United States
| | - Kirk E. Jordan
- IBM T.J. Watson Research, Cambridge, Massachusetts, United States
| | | | - Massimo G. Noro
- Unilever R&D Port Sunlight, Quarry Road East, Bebington, Wirral, CH63 3JW, U.K
| | - David J. Bray
- STFC
Hartree Centre, SciTech Daresbury, Warrington, Cheshire WA4
4AD, U.K
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15
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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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16
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Zakharov AI, Adzhemyan LT, Shchekin AK. Relaxation times and modes of disturbed aggregate distribution in micellar solutions with fusion and fission of micelles. J Chem Phys 2015; 143:124902. [DOI: 10.1063/1.4931413] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anatoly I. Zakharov
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
| | - Loran Ts. Adzhemyan
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
| | - Alexander K. Shchekin
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
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17
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Mullen RG, Shea JE, Peters B. Easy Transition Path Sampling Methods: Flexible-Length Aimless Shooting and Permutation Shooting. J Chem Theory Comput 2015; 11:2421-8. [DOI: 10.1021/acs.jctc.5b00032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan Gotchy Mullen
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Baron Peters
- Department of Chemical Engineering, ‡Department of Chemistry & Biochemistry, §Department of Physics, University of California, Santa Barbara, California 93106, United States
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18
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Mahfud R, Lacks D, Ishida H, Qutubuddin S. Molecular dynamic simulations of self-assembly of amphiphilic comb-like anionic polybenzoxazines. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:11858-11865. [PMID: 25222627 DOI: 10.1021/la501466z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Fully atomistic molecular dynamic simulations were performed to address the self-assembly of amphiphilic and comb-like polybenzoxazines (iBnXz) in water, with i = 3 (trimer), i = 4 (tetramer); i = 6 (hexamer), i = 8 (octamer), and i = 10 (decamer). Spontaneous aggregation of these comb-like polybenzoxazine molecules into a single micelle occurs in the simulations. The simulations show that molecular size and concentration play important roles in micellar morphology. At an iBnXz concentration of 50 mM, the 3BnXz and 4BnXz molecules aggregate into spherical micelles, whereas the 6BnXz, 8BnXz, and 10BnXz molecules aggregate into cylindrical micelles. The micellar morphology is spherical at low concentrations, but undergoes a transition to cylindrical shape as concentration increases. The transition point depends on the molecular size-both the true size as indicated by molecular weight, as well as an additional effective size dependent on molecular flexibility.
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Affiliation(s)
- Riyad Mahfud
- Department of Chemical Engineering and ‡Department of Macromolecular Science and Engineering, Case Western Reserve University , Cleveland, Ohio 44106-7202, United States
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19
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Babintsev IA, Adzhemyan LT, Shchekin AK. Multi-scale times and modes of fast and slow relaxation in solutions with coexisting spherical and cylindrical micelles according to the difference Becker-Döring kinetic equations. J Chem Phys 2014; 141:064901. [PMID: 25134593 DOI: 10.1063/1.4890531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The eigenvalues and eigenvectors of the matrix of coefficients of the linearized kinetic equations applied to aggregation in surfactant solution determine the full spectrum of characteristic times and specific modes of micellar relaxation. The dependence of these relaxation times and modes on the total surfactant concentration has been analyzed for concentrations in the vicinity and well above the second critical micelle concentration (cmc2) for systems with coexisting spherical and cylindrical micelles. The analysis has been done on the basis of a discrete form of the Becker-Döring kinetic equations employing the Smoluchowsky diffusion model for the attachment rates of surfactant monomers to surfactant aggregates with matching the rates for spherical aggregates and the rates for large cylindrical micelles. The equilibrium distribution of surfactant aggregates in solution has been modeled as having one maximum for monomers, another maximum for spherical micelles and wide slowly descending branch for cylindrical micelles. The results of computations have been compared with the analytical ones known in the limiting cases from solutions of the continuous Becker-Döring kinetic equation. They demonstrated a fair agreement even in the vicinity of the cmc2 where the analytical theory looses formally its applicability.
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Affiliation(s)
- Ilya A Babintsev
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
| | - Loran Ts Adzhemyan
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
| | - Alexander K Shchekin
- Department of Statistical Physics, Faculty of Physics, St. Petersburg State University, Ulyanovskaya 1, Petrodvoretz, St. Petersburg 198504, Russian Federation
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Poghosyan AH, Arsenyan LH, Shahinyan AA. Long-chain alkyl sulfonate micelle fission: a molecular dynamics study. Colloid Polym Sci 2014. [DOI: 10.1007/s00396-014-3364-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Rharbi Y, Karrouch M, Richardson P. Fusion and fission inhibited by the same mechanism in electrostatically charged surfactant micelles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:7947-7952. [PMID: 24866814 DOI: 10.1021/la501465v] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper revises the general idea about the role of intermicellar and intramiceller interactions in inhibiting fusion of self-assembled surfactant micelles. Fusion and fission of micelles are usually thought to be limited by different mechanisms. While fission is accepted to be controlled by surface instabilities (intramicellar interactions), fusion is commonly thought to be rate limited by the barrier to the close approach between two micelles due to the steric or Coulombic repulsions (intramicellar interactions). Here we describe the role of electrostatic repulsions in inhibiting fusion and fission kinetics in self-assembled micelles. We use stopped flow-fluorescence technique with hydrophobic pyrene to quantify fusion and fission in ionic/nonionic mixed micelles (Triton X-100/SDS). We show that the fusion and fission rates decrease with the same tendency with increasing the fraction of the ionic charges, while their ratio remains constant. Our results are interpreted to mean that, in slightly charged micelles, fusion shares the same limiting step with fission, which most likely involves surface instabilities and intramiceller interactions.
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Affiliation(s)
- Yahya Rharbi
- Laboratoire de Rhéologie et procédés, UJF/INPG/CNRS , BP 53, Domaine universitaire, 38041 Grenoble, France
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23
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Deformation of copolymer micelles induced by amphiphilic dimer particles. CHINESE JOURNAL OF POLYMER SCIENCE 2011. [DOI: 10.1007/s10118-012-1108-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Beckham GT, Peters B. Optimizing Nucleus Size Metrics for Liquid-Solid Nucleation from Transition Paths of Near-Nanosecond Duration. J Phys Chem Lett 2011; 2:1133-1138. [PMID: 26295315 DOI: 10.1021/jz2002887] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We determine the mechanism for the liquid-solid phase transition in the Lennard-Jones fluid close to coexistence with aimless shooting and likelihood maximization. The reaction coordinate for this process is a product of a structural descriptor and the size of the nascent solid nucleus and is quantitatively verified with the committor probability histogram test. This study identifies the first accurate scalar reaction coordinate for the liquid-solid nucleation process in Lennard-Jonesium, which will likely extend to nucleation processes in other spherically symmetric fluids. On the basis of our results, we propose a structural correction factor for the commonly cited nucleus size reaction coordinate from classical nucleation theory that enables connection of simulation data to stochastic models of nucleation kinetics. In addition, we show that aimless shooting is able to obtain reasonable acceptance rates for transitions with highly diffusive characteristics, which has been problematic for transition path sampling methods for diffusive processes such as nucleation and macromolecular transitions.
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Affiliation(s)
- Gregg T Beckham
- †National Bioenergy Center, National Renewable Energy Laboratory, Golden Colorado 80401, United States
- ‡Department of Chemical Engineering, Colorado School of Mines, Golden Colorado 80401, United States
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Markvoort AJ, Marrink SJ. Lipid acrobatics in the membrane fusion arena. CURRENT TOPICS IN MEMBRANES 2011; 68:259-94. [PMID: 21771503 DOI: 10.1016/b978-0-12-385891-7.00011-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Albert J Markvoort
- Institute for Complex Molecular Systems & Biomodeling and Bioinformatics Group, Eindhoven University of Technology, Eindhoven, The Netherlands
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26
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Peters B. Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927020903536382] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Chen X, Dong W, Zhang X. Self-assembly of amphiphilic molecules: A review on the recent computer simulation results. Sci China Chem 2010. [DOI: 10.1007/s11426-010-4064-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ouldridge TE, Louis AA, Doye JPK. Extracting bulk properties of self-assembling systems from small simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:104102. [PMID: 21389436 DOI: 10.1088/0953-8984/22/10/104102] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For systems that self-assemble into finite-sized objects, it is sometimes convenient to compute the thermodynamics for a small system where a single assembly can form. However, we show that in the canonical ensemble the use of small systems can lead to significant finite-size effects due to the suppression of concentration fluctuations. We introduce methods for estimating the bulk yields from simulations of small systems and for following the convergence of yields with system size, under the assumptions that the various species behave ideally.
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Affiliation(s)
- Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
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Gao J, Li S, Zhang X, Wang W. Computer simulations of micelle fission. Phys Chem Chem Phys 2010; 12:3219-28. [DOI: 10.1039/b918449j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Duff N, Peters B. Nucleation in a Potts lattice gas model of crystallization from solution. J Chem Phys 2009; 131:184101. [DOI: 10.1063/1.3250934] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Schwartz SD, Schramm VL. Enzymatic transition states and dynamic motion in barrier crossing. Nat Chem Biol 2009; 5:551-8. [PMID: 19620996 DOI: 10.1038/nchembio.202] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
What are the atomic motions at enzymatic catalytic sites on the timescale of chemical change? Combined experimental and computational chemistry approaches take advantage of transition-state analogs to reveal dynamic motions linked to transition-state formation. QM/MM transition path sampling from reactive complexes provides both temporal and dynamic information for barrier crossing. Fast (femtosecond to picosecond) dynamic motions provide essential links to enzymatic barrier crossing by local or promoting-mode dynamic searches through bond-vibrational space. Transition-state lifetimes are within the femtosecond timescales of bond vibrations and show no manifestations of stabilized, equilibrated complexes. The slow binding and protein conformational changes (microsecond to millisecond) also required for catalysis are temporally decoupled from the fast dynamic motions forming the transition state. According to this view of enzymatic catalysis, transition states are formed by fast, coincident dynamic excursions of catalytic site elements, while the binding of transition-state analogs is the conversion of the dynamic excursions to equilibrated states.
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Affiliation(s)
- Steven D Schwartz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA
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Burov SV, Vanin AA, Brodskaya EN. Principal role of the stepwise aggregation mechanism in ionic surfactant solutions near the critical micelle concentration. Molecular dynamics study. J Phys Chem B 2009; 113:10715-20. [PMID: 19591445 DOI: 10.1021/jp9025305] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The validity of the assumption on the predominant contribution of the stepwise processes to the ionic micelle formation/destruction in the vicinity of critical micelle concentration was investigated by molecular dynamics simulation. A coarse-grained model was used to describe the surfactant/water mixture. The cluster size distribution was estimated directly from molecular dynamics simulations or obtained from a reduced set of kinetic equations. The good agreement between two approaches shows that the neglect of the terms responsible for cluster fusion/fission is fully justified and that such processes are less important than stepwise aggregation.
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Affiliation(s)
- Stanislav V Burov
- Department of Chemistry, Saint Petersburg State University, Universitetskiy pr. 26, Stariy Petergof, Saint Petersburg 198504, Russia.
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33
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Fujiwara S, Itoh T, Hashimoto M, Horiuchi R. Molecular dynamics simulation of amphiphilic molecules in solution: Micelle formation and dynamic coexistence. J Chem Phys 2009; 130:144901. [DOI: 10.1063/1.3105341] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Denkova AG, Mendes E, Coppens MO. Kinetics and Mechanism of the Sphere-to-Rod Transition of Triblock Copolymer Micelles in Aqueous Solutions. J Phys Chem B 2009; 113:989-96. [DOI: 10.1021/jp807513k] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. G. Denkova
- DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York, 12180
| | - E. Mendes
- DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York, 12180
| | - M.-O. Coppens
- DelftChemTech, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands, and Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th Street, Troy New York, 12180
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FUJIWARA S, HASHIMOTO M, ITOH T. Molecular Dynamics Simulations for Structure Formation of Polymers and Self-Assembly of Amphiphilic Molecules. KOBUNSHI RONBUNSHU 2009. [DOI: 10.1295/koron.66.396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Susumu FUJIWARA
- Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Masato HASHIMOTO
- Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
| | - Takashi ITOH
- Department of Macromolecular Science and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology
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Padding JT, Boek ES, Briels WJ. Dynamics and rheology of wormlike micelles emerging from particulate computer simulations. J Chem Phys 2008; 129:074903. [DOI: 10.1063/1.2970934] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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