The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
Open accessAbstract
Bayesian inference is used to obtain self-consistent estimates of free energies and position-dependent diffusion coefficients along complex reaction coordinates from molecular dynamics simulation trajectories. Effectively, exact solutions for the dynamics of a diffusive model are matched globally to the observed molecular dynamics data. The approach is first tested for a simple one-dimensional diffusion model, and then applied to the dihedral-angle dynamics of a peptide fragment dissolved in water. Both long equilibrium molecular dynamics simulations and short, appropriately initialized, replica simulations are used to sample the short-time dynamics of the peptide–water system. In both cases, accurate estimates of free energies and diffusion coefficients are obtained.
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Cited by
Coarse master equations for peptide folding dynamics
Buchete, N.-V., & Hummer, G. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp0761665 · Cited by 477
Self-citationMolecular Dynamics Simulations of Membrane Permeability
Venable, R. M., Krämer, A., & Pastor, R. W. (2019) · Chemical Reviews · doi:10.1021/acs.chemrev.8b00486 · Cited by 394
Carpenter, T. S., Kirshner, D. A., Lau, E. Y., Wong, S. E., Nilmeier, J. P., & Lightstone, F. C. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.06.024 · Cited by 306
Determination of reaction coordinates via locally scaled diffusion map
Rohrdanz, M. A., Zheng, W., Maggioni, M., & Clementi, C. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3569857 · Cited by 292
Coordinate-dependent diffusion in protein folding
Best, R. B., & Hummer, G. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910390107 · Cited by 289
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Metadata
- Authors
- Hummer, G.
- Venue
- New Journal of Physics
- Publisher
- IOP Publishing
- Published
- 2005-02-01
- Volume
- 7
- Pages
- 34-34
- ISSN
- 1367-2630 (ISSN-L)
- OpenAlex
- W2011189520
- Cited by
- 527
- References
- 24
- FWCI
- 5.38
- Type
- journal article
- Language
- en
- Open access
- gold
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
