The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
From A to B in free energy space
Open accessAbstract
The authors present a new method for searching low free energy paths in complex molecular systems at finite temperature. They introduce two variables that are able to describe the position of a point in configurational space relative to a preassigned path. With the help of these two variables the authors combine features of approaches such as metadynamics or umbrella sampling with those of path based methods. This allows global searches in the space of paths to be performed and a new variational principle for the determination of low free energy paths to be established. Contrary to metadynamics or umbrella sampling the path can be described by an arbitrary large number of variables, still the energy profile along the path can be calculated. The authors exemplify the method numerically by studying the conformational changes of alanine dipeptide.
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Cites
Laio, A., & Parrinello, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202427399 · Cited by 5,626
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Bolhuis, P. G., Chandler, D., Dellago, C., & Geissler, P. L. (2002) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.53.082301.113146 · Cited by 1,972
Assessing the Accuracy of Metadynamics
Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045424k · Cited by 517
Self-citationReaction coordinates of biomolecular isomerization
Bolhuis, P. G., Dellago, C., & Chandler, D. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.100127697 · Cited by 426
Automatic Method for Identifying Reaction Coordinates in Complex Systems
Ma, A., & Dinner, A. R. (2005) · The Journal of Physical Chemistry B · doi:10.1021/jp045546c · Cited by 400
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Barducci, A., Bussi, G., & Parrinello, M. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.020603 · Cited by 3,184
Self-citationLaio, A., & Gervasio, F. L. (2008) · Reports on Progress in Physics · doi:10.1088/0034-4885/71/12/126601 · Cited by 1,619
Self-citationFribourg, M., Moreno, J. L., Holloway, T., Provasi, D., Baki, L., Mahajan, R., Park, G., Adney, S. K., Hatcher, C., Eltit, J. M., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.055 · Cited by 311
Spectral gap optimization of order parameters for sampling complex molecular systems
Tiwary, P., & Berne, B. J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1600917113 · Cited by 259
Using sketch-map coordinates to analyze and bias molecular dynamics simulations
Tribello, G. A., Ceriotti, M., & Parrinello, M. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1201152109 · Cited by 202
Self-citationPietrucci, F., & Saitta, A. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1512486112 · Cited by 144
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed
Hwang, W., Austin, S. L., Blondel, A., Boittier, E. D., Boresch, S., Buck, M., Buckner, J., Caflisch, A., Chang, H.-T., Cheng, X., et al. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04100 · Cited by 136
Demonstrating the Transferability and the Descriptive Power of Sketch-Map
Ceriotti, M., Tribello, G. A., & Parrinello, M. (2013) · Journal of Chemical Theory and Computation · doi:10.1021/ct3010563 · Cited by 126
Self-citationChoreographing an enzyme's dance
Villali, J., & Kern, D. (2010) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2010.08.007 · Cited by 98
The Unfolded Ensemble and Folding Mechanism of the C-Terminal GB1 β-Hairpin
Bonomi, M., Branduardi, D., Gervasio, F. L., & Parrinello, M. (2008) · Journal of the American Chemical Society · doi:10.1021/ja803652f · Cited by 97
Self-citationMetadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
Spiwok, V., & Králová, B. (2011) · The Journal of Chemical Physics · doi:10.1063/1.3660208 · Cited by 70
Structural basis for lipid transfer by the ATG2A–ATG9A complex
(2024) · doi:10.1038/s41594-024-01376-6 · Cited by 50
Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study
Manna, R. N., Zinovjev, K., Tuñón, I., & Dybala-Defratyka, A. (2015) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5b07538 · Cited by 21
DynaMate: Leveraging AI-agents for customized research workflows
Mendible-Barreto, O. A., Díaz-Maldonado, M., Carmona Esteva, F. J., Torres, J. E., Córdova-Figueroa, U. M., & Colón, Y. J. (2025) · Molecular Systems Design & Engineering · doi:10.1039/d5me00062a · Cited by 12
Data-driven enhanced sampling of mechanistic pathways
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Metadata
- Authors
- Branduardi, D., Gervasio, F. L., & Parrinello, M.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2007-02-07
- Volume
- 126
- Issue
- 5
- Pages
- 054103-054103
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W1998404217
- Cited by
- 605
- References
- 5
- FWCI
- 10.18
- Type
- journal article
- Language
- en
- Open access
- hybrid
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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.
