ArticleThe journal of physical chemistry. B2012
Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.
Article in The journal of physical chemistry. B, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed, 18 citations in OpenAlex.
- Multiscale Modeling in the Clinic: Drug Design and Development.Annals of biomedical engineering · 2016Review
- Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision.Journal of chemical theory and computation · 2014Article
- Hierarchical Multiscale Modeling of Macromolecules and their Assemblies.Soft matter · 2013Article
- Multiscale macromolecular simulation: role of evolving ensembles.Journal of chemical information and modeling · 2012Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
Coarse-grained features of macromolecular assemblies are understood via a set of order parameters (OPs) constructed in terms of their all-atom configuration. OPs are shown to be slowly changing in time and capture the large-scale spatial features of macromolecular assemblies. The relationship of these variables to the classic notion of OPs based on symmetry breaking phase transitions is discussed. OPs based on space warping transformations are analyzed in detail as they naturally provide a connection between overall structure of an assembly and all-atom configuration. These OPs serve as the basis of a multiscale analysis that yields Langevin equations for OP dynamics. In this context, the characteristics of OPs and PCA modes are compared. The OPs enable efficient all-atom multiscale simulations of the dynamics of macromolecular assemblies in response to changes in microenvironmental conditions, as demonstrated on the structural transitions of cowpea chlorotic mottle virus capsid (CCMV) and RNA of the satellite tobacco mosaic virus (STMV).
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