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Results: 187
Number of items: 187
  • Open Access
    Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J.-P., Bolhuis, P. G., Vreede, J., ... McLeish, T. (2019). Allostery in Its Many Disguises: From Theory to Applications. Structure, 27(4), 566-578. https://doi.org/10.1016/j.str.2019.01.003
  • Open Access
    Swenson, D. W. H., Prinz, J.-H., Noe, F., Chodera, J. D., & Bolhuis, P. G. (2019). OpenPathSampling: A Python Framework for Path Sampling Simulations. 2: Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, 15(2), 837-856. https://doi.org/10.1021/acs.jctc.8b00627
  • Open Access
    Brotzakis, Z. F., & Bolhuis, P. G. (2019). Approximating free energy and committor landscapes in standard transition path sampling using virtual interface exchange. Journal of Chemical Physics, 151(17), Article 174111. https://doi.org/10.1063/1.5119252
  • Open Access
    Swenson, D. W. H., Prinz, J.-H., Noe, F., Chodera, J. D., & Bolhuis, P. G. (2019). OpenPathSampling: A Python Framework for Path Sampling Simulations. 1: Basics. Journal of Chemical Theory and Computation, 15(2), 813-836. https://doi.org/10.1021/acs.jctc.8b00626
  • Open Access
    Brotzakis, Z. F., & Bolhuis, P. G. (2019). Unbiased Atomistic Insight into the Mechanisms and Solvent Role for Globular Protein Dimer Dissociation. Journal of Physical Chemistry B, 123(9), 1883-1895. https://doi.org/10.1021/acs.jpcb.8b10005
  • Open Access
    Tiwari, A. (2019). Toward accurate simulation of electrocatalyzed water splitting: Enhanced quantum chemical dynamics simulations of proton and electron transfer reactions. [Thesis, fully internal, Universiteit van Amsterdam].
  • Open Access
    The PLUMED consortium (2019). Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods, 16(8), 670-673. https://doi.org/10.1038/s41592-019-0506-8
  • Open Access
    Vreede, J., Pérez de Alba Ortíz, A., Bolhuis, P. G., & Swenson, D. W. H. (2019). Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Research, 47(21), 11069-11076. https://doi.org/10.1093/nar/gkz837
  • Open Access
    Vijaykumar, A., ten Wolde, P. R., & Bolhuis, P. G. (2018). Rate constants for proteins binding to substrates with multiple binding sites using a generalized forward flux sampling expression. Journal of Chemical Physics, 148(12), Article 124109. https://doi.org/10.1063/1.5012854
  • Open Access
    Rodenburg, J., Paliwal, S., de Jager, M., Bolhuis, P. G., Dijkstra, M., & van Roij, R. (2018). Ratchet-induced variations in bulk states of an active ideal gas. Journal of Chemical Physics, 149(17), Article 174910. https://doi.org/10.1063/1.5048698
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