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Cited by 465Advanced Physical and Chemical Molecular InteractionsMaterial Dynamics and PropertiesAdvanced Mathematical Modeling in Engineering

Multiscale simulation of soft matter systems–from the atomistic to the coarse-grained level and back

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Peter, Christine, Kremer, Kurt·2009·Soft Matter
DOI 10.1039/b912027k
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Abstract

Many physical phenomena and properties of soft matter systems such as synthetic or biological materials are governed by interactions and processes on a wide range of length- and time-scales. Computer simulation approaches that are targeted at questions in these systems require models which cover these scales and the respective levels of resolution. Multiscale simulation methods combine and systematically link several simulation hierarchies so that they can address phenomena at multiple levels of resolution. In order to reach the mesoscopic time- and length-scales important for many material properties, methods that bridge from the atomistic (microscopic) to a coarser (mesocopic) level are developed. Here, we review coarse-grained simulation models that are linked to a higher resolution atomistic description. In particular, we focus on structure-based coarse-graining methods which are used for a variety of soft matter problems – ranging from structure-formation in amorphous polymers to biomolecular aggregation. It is shown that by coarse-grained simulation in combination with an efficient backmapping methodology one can obtain well-equilibrated long time- and large length-scale atomistic structures of polymeric melts or biomolecular aggregates which can be used for comparison to experimental data. Methodological aspects are addressed such as the question of the time-scales and dynamics in the different simulation hierarchies and an outlook to future challenges in the area of resolution exchange approaches and adaptive resolution models is presented.

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  • Well-equilibrated coarse-grained models can be mapped back onto an atomistic model.

    “Conversely, the well-equilibrated coarse-grained models can be mapped back onto an atomistic model, as reviewed by Müller-Plathe [38] and Peter and Kremer [340].”

    From Challenges in Multiscale Modeling of Polymer Dynamics (2013) · cites this paper as [340]

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  1. [1]1. H. J. C. Berendsen, Simulating the Physical World, Cambridge University Press, Cambridge, UK, 2007.
  2. [2]2. Coarse-Graining of Condensed Phase and Biomolecular Systems, ed. G. A. Voth, Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  3. [3]3. B. Dunweg and A. J. C. Ladd, Advanced Computer Simulation Approaches for Soft Matter Sciences III (Advances in Polymer Science, vol. 221), 2009, pp. 89-166.
  4. [4]4. W. Tsch€ op, K. Kremer, J. Batoulis, T. Burger and O. Hahn, Acta Polym., 1998, 49, 61-74.
  5. [5]5. W. Tsch€ op, K. Kremer, O. Hahn, J. Batoulis and T. Burger, Acta Polym., 1998, 49, 75-79.
  6. [6]6. G. S. Ayton, W. G. Noid and G. A. Voth, Curr. Opin. Struct. Biol., 2007, 17, 192-198.
  7. [7]7. P. L. Freddolino, A. Arkhipov, A. Y. Shih, Y. Yin, Z. Chen and K. Schulten, Coarse-Graining of Condensed Phase and Biomolecular Systems, Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  8. [8]8. S. J. Marrink, M. Fuhrmans, H. J. Risselada and X. Periole, Coarse- Graining of Condensed Phase and Biomolecular Systems, Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  9. [9]9. N. F. A. van der Vegt, C. Peter and K. Kremer, Coarse-Graining of Condensed Phase and Biomolecular Systems, Chapman and Hall/ CRC Press, Taylor and Francis Group, 2008.
  10. [10]10. K. Kremer and G. S. Grest, J. Chem. Phys., 1990, 92, 5057-5086.
  11. [11]11. M. Muller, K. Katsov and M. Schick, Phys. Rep., 2006, 434, 113-176.
  12. [12]12. B. J. Reynwar, G. Illya, V. A. Harmandaris, M. M. M€ uller, K. Kremer and M. Deserno, Nature, 2007, 447, 461-464.
  13. [13]13. T. C. B. McLeish, Adv. Phys., 2002, 51, 1379.
  14. [14]14. R. Everaers, S. K. Sukumaran, G. S. Grest, C. Svaneborg, A. Sivasubramanian and K. Kremer, Science, 2004, 303, 823-826.
  15. [15]15. K. Kremer, Simulations in Condensed Matter: From Materials to Chemical Biology, Springer, 2006, vol. 704.
  16. [16]16. S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman and A. H. de Vries, J. Phys. Chem. B, 2007, 111, 7812-7824.
  17. [17]17. L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman and S. J. Marrink, J. Chem. Theory Comput., 2008, 4, 819-834.
  18. [18]18. S. J. Marrink, A. H. de Vries and A. E. Mark, J. Phys. Chem. B, 2004, 108, 750-760.
  19. [19]19. R. Baron, D. Trzesniak, A. H. de Vries, A. Elsener, S. J. Marrink and W. F. van Gunsteren, ChemPhysChem, 2007, 8, 452-461.
  20. [20]20. A. P. Lyubartsev and A. Laaksonen, Phys. Rev. E, 1995, 52, 3730- 3737.
  21. [21]21. F. M€ uller-Plathe, ChemPhysChem, 2002, 3, 754-769.
  22. [22]22. C. Peter, L. Delle Site and K. Kremer, Soft Matter, 2008, 4, 859-869.
  23. [23]23. M. E. Johnson, T. Head-Gordon and A. A. Louis, J. Chem. Phys., 2007, 126, 144509.
  24. [24]24. S. Izvekov and G. A. Voth, J. Phys. Chem. B, 2005, 109, 2469-2473.
  25. [25]25. W. Noid, J. Chu, G. Ayton and G. Voth, J. Phys. Chem. B, 2007, 111, 4116-4127.
  26. [27]27. C. F. Abrams and K. Kremer, Macromolecules, 2003, 36, 260-267.
  27. [28]28. V. A. Harmandaris, N. P. Adhikari, N. F. A. van der Vegt and K. Kremer, Macromolecules, 2006, 39, 6708-6719.
  28. [29]29. V. A. Harmandaris, D. Reith, N. F. A. van der Vegt and K. Kremer, Macromol. Chem. Phys., 2007, 208, 2109-2120.
  29. [30]30. V. A. Harmandaris and K. Kremer, Macromolecules, 2009, 42, 791-802.
  30. [31]31. D. Fritz, V. A. Harmandaris, K. Kremer and N. F. A. van der Vegt, Macromolecules, submitted. 32 A. Villa, C. Peter and N. F. A. van der Vegt, Phys. Chem. Chem. Phys., 2009, 11, 2077.
  31. [32]32. A. Villa, N. F. A. van der Vegt and C. Peter, Phys. Chem. Chem. Phys., 2009, 11, 2068.
  32. [33]33. P. Schravendijk, L. M. Ghiringhelli, L. Delle Site and N. F. A. van der Vegt, J. Phys. Chem. C, 2007, 111, 2631-2642.
  33. [34]34. L. M. Ghiringhelli, B. Hess, N. F. A. Van der Vegt and L. Delle Site, J. Am. Chem. Soc., 2008, 130, 13460-13464.
  34. [35]35. L. Delle Site, S. Leon and K. Kremer, J. Am. Chem. Soc., 2004, 126, 2944-2955.
  35. [36]36. D. Andrienko, S. Leon, L. Delle Site and K. Kremer, Macromolecules, 2005, 38, 5810-5816.
  36. [37]37. G. Milano, S. Goudeau and F. Muller-Plathe, J. Polym. Sci., Part B: Polym. Phys., 2005, 43, 871-885.
  37. [38]38. W. Paul, K. Binder, K. Kremer and D. W. Heermann, Macromolecules, 1991, 24, 6332-6334.
  38. [39]39. P. Doruker and W. L. Mattice, Macromolecules, 1997, 30, 5520-5526.
  39. [40]40. V. Tries, W. Paul, J. Baschnagel and K. Binder, J. Chem. Phys., 1997, 106, 738-748.
  40. [41]41. D. Reith, M. Putz and F. Muller-Plathe, J. Comput. Chem., 2003, 24, 1624-1636.
  41. [42]42. R. L. Henderson, Phys. Lett., 1974, 49, 197-198.
  42. [43]43. M. Praprotnik, L. Delle Site and K. Kremer, Phys. Rev. E, 2006, 73, 066701.
  43. [44]44. S. Jain, S. Garde and S. K. Kumar, Ind. Eng. Chem. Res., 2006, 45, 5614-5618.
  44. [45]45. H. Wang, C. Junghans and K. Kremer, Eur. Phys. J. E, 2009, 28, 221- 229.
  45. [46]46. J. D. McCoy and J. G. Curro, Macromolecules, 1998, 31, 9362-9368.
  46. [47]47. B. Hess, S. Leon, N. van der Vegt and K. Kremer, Soft Matter, 2006, 2, 409-414.
  47. [48]48. G. Santangelo, A. Di Matteo, F. Muller-Plathe and G. Milano, J. Phys. Chem. B, 2007, 111, 2765-2773.
  48. [49]49. F. Thorpe, J. Zhou and G. A. Voth, J. Phys. Chem. B, 2008, 112, 13079-13090.
  49. [50]50. X. Chen, P. Carbone, G. Santangelo, A. Di Matteo, G. Milano and F. Muller-Plathe, Phys. Chem. Chem. Phys., 2009, 11, 1977-88.
  50. [52]52. B. Hess, C. Peter, T. Ozal and N. F. A. van der Vegt, Macromolecules, 2008, 41, 2283-2289.
  51. [53]53. T. Ozal, C. Peter, B. Hess and N. F. A. van der Vegt, Macromolecules, 2008, 41, 5055-5061.
  52. [54]54. B. Hess and N. F. A. Van der Vegt, Macromolecules, 2008, 41, 7281- 7283.
  53. [55]55. O. Hahn, D. A. Mooney, F. Muller-Plathe and K. Kremer, J. Chem. Phys., 1999, 111, 6061-6068.
  54. [56]56. S. Leon, N. F. A. van der Vegt, L. Delle Site and K. Kremer, Macromolecules, 2005, 38, 8078-8092.
  55. [58]58. V. A. Harmandaris, N. P. Adhikari, N. F. A. van der Vegt, K. Kremer, B. A. Mann, R. Voelkel, H. Weiss and C. C. Liew, Macromolecules, 2007, 40, 7026-7035.
  56. [60]60. E. Lyman, F. M. Ytreberg and D. M. Zuckerman, Phys. Rev. Lett., 2006, 96, 028105.
  57. [61]61. D. M. Zuckerman, Coarse-Graining of Condensed Phase and Biomolecular Systems, Chapman and Hall/CRC Press, Taylor and Francis Group, 2008.
  58. [62]62. M. Christen and W. F. van Gunsteren, J. Chem. Phys., 2006, 124, 154106.
  59. [63]63. M. Praprotnik, L. Delle Site and K. Kremer, J. Chem. Phys., 2005, 123, 224106.
  60. [64]64. M. Praprotnik, L. Delle Site and K. Kremer, Annu. Rev. Phys. Chem., 2008, 59, 545-571.
  61. [65]65. R. Delgado-Buscalioni, K. Kremer and M. Praprotnik, J. Chem. Phys., 2008, 128, 114110.
  62. [66]66. H. J. Limbach, A. Arnold, B. A. Mann and C. Holm, Comput. Phys. Commun., 2006, 174, 704-727.
  63. [67]67. D. Van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C. Berendsen, J. Comput. Chem., 2005, 26, 1701-1718.

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Authors
Peter, C., & Kremer, K.
Affiliations
Max Planck Institute for Polymer Research (DE)
Corresponding author
Kremer, Kurt
ORCID
Venue
Soft Matter
Publisher
Royal Society of Chemistry (RSC)
Published
2009
Volume
5
Issue
22
Pages
4357
ISSN
  • 1744-683X (ISSN-L)
  • 1744-6848
DOI
10.1039/b912027k
OpenAlex
W2048754774
Cited by
465
References
57
Citations by year
2026: 18 · 2025: 28 · 2024: 15 · 2023: 16 · 2022: 35 · 2021: 35 · 2020: 32 · 2019: 27 · 2018: 32 · 2017: 41 · 2016: 42 · 2015: 23 · 2014: 26 · 2013: 32 · 2012: 27
FWCI
13.00
Type
journal article
Language
en
Open access
Locations
  • Soft Matter (publishedVersion)
  • KOPS (University of Konstanz) (submittedVersion)
  • Max Planck Institute for Plasma Physics (submittedVersion)
  • MPG.PuRe (Max Planck Society) (submittedVersion)
Funders
  • Bayer
  • University of Minnesota
  • Universität zu Köln
  • Max-Planck-Institut für Polymerforschung
  • National Institutes of Health
  • University of California, Santa Barbara
Topics
  • Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
  • Physical Sciences › Materials Science › Materials Chemistry › Material Dynamics and Properties
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Advanced Mathematical Modeling in Engineering
Keywords
multiscale modeling, coarse-grained models, polymer melts, amorphous polymers, structure formation

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