Multiscale modeling of emergent materials: biological and soft matter

Teemu Murtola, Alex Bunker, Ilpo Vattulainen, Markus Deserno, Mikko Karttunen

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

In this review, we focus on four current related issues in multiscale modeling of soft and biological matter. First, we discuss how to use structural information from detailed models (or experiments) to construct coarse-grained ones in a hierarchical and systematic way. This is discussed in the context of the so-called Henderson theorem and the inverse Monte Carlo method of Lyubartsev and Laaksonen. In the second part, we take a different look at coarse graining by analyzing conformations of molecules. This is done by the application of self-organizing maps, i.e., a neural network type approach. Such an approach can be used to guide the selection of the relevant degrees of freedom. Then, we discuss technical issues related to the popular dissipative particle dynamics (DPD) method. Importantly, the potentials derived using the inverse Monte Carlo method can be used together with the DPD thermostat. In the final part we focus on solvent-free modeling which offers a different route to coarse graining by integrating out the degrees of freedom associated with solvent.
Original languageEnglish
JournalPhysical Chemistry Chemical Physics
Volume11
Issue number12
Pages (from-to)1869-92
Number of pages23
ISSN1463-9076
DOIs
Publication statusPublished - 28. Mar 2009

Fingerprint

Biological materials
Monte Carlo method
Monte Carlo methods
degrees of freedom
Thermostats
thermostats
organizing
Self organizing maps
Conformations
theorems
routes
Neural networks
Molecules
molecules
Experiments

Keywords

  • Algorithms
  • Computer Simulation
  • Lipoproteins, HDL
  • Models, Biological
  • Models, Molecular
  • Molecular Conformation
  • Monte Carlo Method
  • Thermodynamics

Cite this

Murtola, T., Bunker, A., Vattulainen, I., Deserno, M., & Karttunen, M. (2009). Multiscale modeling of emergent materials: biological and soft matter. Physical Chemistry Chemical Physics, 11(12), 1869-92. https://doi.org/10.1039/b818051b
Murtola, Teemu ; Bunker, Alex ; Vattulainen, Ilpo ; Deserno, Markus ; Karttunen, Mikko. / Multiscale modeling of emergent materials: biological and soft matter. In: Physical Chemistry Chemical Physics. 2009 ; Vol. 11, No. 12. pp. 1869-92.
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Murtola, T, Bunker, A, Vattulainen, I, Deserno, M & Karttunen, M 2009, 'Multiscale modeling of emergent materials: biological and soft matter', Physical Chemistry Chemical Physics, vol. 11, no. 12, pp. 1869-92. https://doi.org/10.1039/b818051b

Multiscale modeling of emergent materials: biological and soft matter. / Murtola, Teemu; Bunker, Alex; Vattulainen, Ilpo; Deserno, Markus; Karttunen, Mikko.

In: Physical Chemistry Chemical Physics, Vol. 11, No. 12, 28.03.2009, p. 1869-92.

Research output: Contribution to journalJournal articleResearchpeer-review

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Murtola T, Bunker A, Vattulainen I, Deserno M, Karttunen M. Multiscale modeling of emergent materials: biological and soft matter. Physical Chemistry Chemical Physics. 2009 Mar 28;11(12):1869-92. https://doi.org/10.1039/b818051b