Prof. dr. P.G. (Peter) Bolhuis
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Van 't Hoff Institute for Molecular Sciences
Bezoekadres
- Science Park 904
- Kamernummer: C2.222
Postadres
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Postbus 94157
1090 GD Amsterdam
Contactgegevens
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Research Interest
Our group is interested in studying rare events in complex systems such as folding of proteins, biomolecular isomerisation, self-assembly and nucleation events. To achieve insight in these processes we conduct multiscale modeling simulations of biomolecular systems using rare event- and coarse graining techniques. In addition we continue developing new and advanced simulation techniques.
Signal Transduction in Photoactive Proteins
Photoactive proteins are light sensors that allow plants to turn their leafs toward the sun and allow animals (and people) to see. They form the perfect study ground to understand how (sensor) proteins work, because they can simply be activated with a flash of (laser) light, after which their functioning is probed. Using molecular simulation we study the confromational changes in a model protein, Photoactive Yellow Protein, that follow the light activation, and lead to the signal.
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Publicaties
- refereed (102)
- wetenschappelijk (5)
- vakpublicatie (1)
- erkenning (3)
- supervised theses (3)
- datasets (8)
2024
Jonas, H. J., Schall, P., & Bolhuis, P. G. (2024). Activity affects the stability, deformation and breakage dynamics of colloidal architectures. Soft Matter, 20(9), 2162-2177. https://doi.org/10.1039/d3sm01255g [details]- Keller, B. G., & Bolhuis, P. G. (2024). Dynamical Reweighting for Biased Rare Event Simulations. Annual Review of Physical Chemistry, 75, 137-162. https://doi.org/10.1146/annurev-physchem-083122-124538 [details]
- del Razo, M. J., Crommelin, D., & Bolhuis, P. G. (2024). Data-driven dynamical coarse-graining for condensed matter systems. Journal of Chemical Physics, 160(2), Article 024108. https://doi.org/10.1063/5.0177553 [details]
2023
- Arjun, A., & Bolhuis, P. G. (2023). Homogeneous nucleation of crystalline methane hydrate in molecular dynamics transition paths sampled under realistic conditions. Journal of Chemical Physics, 158(4), Article 044504. https://doi.org/10.1063/5.0124852 [details]
- Bolhuis, P. G., Brotzakis, Z. F., & Keller, B. K. (2023). Optimizing molecular potential models by imposing kinetic constraints with path reweighting. Journal of Chemical Physics, 159(7), Article 074102. https://doi.org/10.1063/5.0151166 [details]
- Jung, H., Covino, R., Arjun, A., Leitold, C., Dellago, C., Bolhuis, P. G., & Hummer, G. (2023). Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science, 3(4), 334-345. https://doi.org/10.1038/s43588-023-00428-z [details]
- Lazzeri, G., Jung, H., Bolhuis, P. G., & Covino, R. (2023). Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations. Journal of Chemical Theory and Computation, 19(24), 9060–9076. https://doi.org/10.1021/acs.jctc.3c00821 [details]
- van Heesch, T., Bolhuis, P. G., & Vreede, J. (2023). Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations. Nucleic Acids Research, 51(22), 12150-12160. https://doi.org/10.1093/nar/gkad1014 [details]
2022
- Jonas, H. J., Schall, P., & Bolhuis, P. G. (2022). Extended Wertheim theory predicts the anomalous chain length distributions of divalent patchy particles under extreme confinement. Journal of Chemical Physics, 157(9), Article 094903. https://doi.org/10.1063/5.0098882 [details]
- Roet, S., Hooft, F., Bolhuis, P. G., Swenson, D. W. H., & Vreede, J. (2022). Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas. Journal of Physical Chemistry B, 126(48), 10034-10044. https://doi.org/10.1021/acs.jpcb.2c06235 [details]
2021
- Arjun, A., & Bolhuis, P. G. (2021). Homogenous nucleation rate of CO2 hydrates using transition interface sampling. Journal of Chemical Physics, 154(16), Article 164507. https://doi.org/10.1063/5.0044883 [details]
- Arjun, A., & Bolhuis, P. G. (2021). Molecular Understanding of Homogeneous Nucleation of CO2 Hydrates Using Transition Path Sampling. Journal of Physical Chemistry B, 125(1), 338-349. Advance online publication. https://doi.org/10.1021/acs.jpcb.0c09915 [details]
- Bolhuis, P. G., & Swenson, D. W. H. (2021). Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. Advanced Theory and Simulations, 4(4), Article 2000237. https://doi.org/10.1002/adts.202000237 [details]
- Bolhuis, P. G., Brotzakis, Z. F., & Vendruscolo, M. (2021). A maximum caliber approach for continuum path ensembles. The European Physical Journal B. Condensed Matter Physics, 94(9), Article 188. https://doi.org/10.1140/epjb/s10051-021-00154-3 [details]
- Brotzakis, Z. F., Vendruscolo, M., & Bolhuis, P. G. (2021). A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America, 118(2), Article e2012423118. Advance online publication. https://doi.org/10.1073/pnas.2012423118 [details]
- Frassek, M., Arjun, A., & Bolhuis, P. G. (2021). An extended autoencoder model for reaction coordinate discovery in rare event molecular dynamics datasets. Journal of Chemical Physics, 155(6), Article 064103. Advance online publication. https://doi.org/10.1063/5.0058639 [details]
- Jonas, H. J., Stuij, S. G., Schall, P., & Bolhuis, P. G. (2021). A temperature-dependent critical Casimir patchy particle model benchmarked onto experiment. Journal of Chemical Physics, 155(3), Article 034902. https://doi.org/10.1063/5.0055012 [details]
- Stuij, S. G., Jonas, H. J., Gong, Z., Sacanna, S., Kodger, T. E., Bolhuis, P. G., & Schall, P. (2021). Revealing viscoelastic bending relaxation dynamics of isolated semiflexible colloidal polymers. Soft Matter, 17(36), 8291-8299. https://doi.org/10.1039/d1sm00556a [details]
- Stuij, S., Rouwhorst, J., Jonas, H. J., Ruffino, N., Gong, Z., Sacanna, S., Bolhuis, P. G., & Schall, P. (2021). Revealing Polymerization Kinetics with Colloidal Dipatch Particles. Physical Review Letters, 127(10), Article 108001. https://doi.org/10.1103/PhysRevLett.127.108001 [details]
- Swinkels, P. J. M., Stuij, S. G., Gong, Z., Jonas, H., Ruffino, N., van der Linden, B., Bolhuis, P. G., Sacanna, S., Woutersen, S., & Schall, P. (2021). Revealing pseudorotation and ring-opening reactions in colloidal organic molecules. Nature Communications, 12, Article 2810. https://doi.org/10.1038/s41467-021-23144-6 [details]
2020
- Arjun, A., & Bolhuis, P. G. (2020). Rate Prediction for Homogeneous Nucleation of Methane Hydrate at Moderate Supersaturation Using Transition Interface Sampling. Journal of Physical Chemistry B, 124(37), 8099-8109. https://doi.org/10.1021/acs.jpcb.0c04582 [details]
- Buijsman, P., & Bolhuis, P. G. (2020). Transition path sampling for non-equilibrium dynamics without predefined reaction coordinates. Journal of Chemical Physics, 152(4), Article 044108. https://doi.org/10.1063/1.5130760 [details]
2019
- 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 [details]
- 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 [details]
- 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 [details]
- 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 [details]
- 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 [details]
- 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 [details]
- 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 [details]
2018
- Bolhuis, P. G., & Csányi, G. (2018). Nested Transition Path Sampling. Physical Review Letters, 120(25), Article 250601. https://doi.org/10.1103/PhysRevLett.120.250601 [details]
- Brotzakis, Z. F., Voets, I. K., Bakker, H. J., & Bolhuis, P. G. (2018). Water structure and dynamics in the hydration layer of a type III anti-freeze protein. Physical Chemistry Chemical Physics, 20(10), 6996-7006. Advance online publication. https://doi.org/10.1039/c8cp00170g [details]
- Michaels, T. C. T., Liu, L. X., Curk, S., Bolhuis, P. G., Šarić, A., & Knowles, T. P. J. (2018). Reaction rate theory for supramolecular kinetics: application to protein aggregation. Molecular Physics, 116(21-22), 3055-3065. https://doi.org/10.1080/00268976.2018.1474280 [details]
- 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 [details]
- Vijaykumar, A., ten Wolde, P. R., & Bolhuis, P. G. (2018). Generalised expressions for the association and dissociation rate constants of molecules with multiple binding sites. Molecular Physics, 116(21-22), 3042-3054. https://doi.org/10.1080/00268976.2018.1473653 [details]
- 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 [details]
2017
- Brotzakis, Z. F., Gehre, M., Voets, I. K., & Bolhuis, P. G. (2017). Stability and growth mechanism of self-assembling putative antifreeze cyclic peptides. Physical Chemistry Chemical Physics, 19(29), 19032-19042. https://doi.org/10.1039/c7cp02465g [details]
- Cabriolu, R., Refsnes, K. M. S., Bolhuis, P. G., & van Erp, T. S. (2017). Foundations and latest advances in replica exchange transition interface sampling. Journal of Chemical Physics, 147(15), Article 152722. https://doi.org/10.1063/1.4989844 [details]
- Newton, A. C., Groenewold, J., Kegel, W. K., & Bolhuis, P. G. (2017). The role of multivalency in the association kinetics of patchy particle complexes. Journal of Chemical Physics, 146(23), Article 234901. https://doi.org/10.1063/1.4984966 [details]
- Newton, A. C., Kools, R., Swenson, D. W. H., & Bolhuis, P. G. (2017). The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids. Journal of Chemical Physics, 147(15), Article 155101. https://doi.org/10.1063/1.5006485 [details]
- Newton, A. C., Nguyen, T. A., Veen, S. J., Kraft, D. J., Schall, P., & Bolhuis, P. G. (2017). Modelling critical Casimir force induced self-assembly experiments on patchy colloidal dumbbells. Soft Matter, 13(28), 4903-4915. https://doi.org/10.1039/c7sm00668c [details]
- Nguyen, T. A., Newton, A., Kraft, D. J., Bolhuis, P. G., & Schall, P. (2017). Tuning patchy bonds induced by critical Casimir forces. Materials, 10(11), Article 1265. https://doi.org/10.3390/ma10111265 [details]
- Nguyen, T. A., Newton, A., Veen, S. J., Kraft, D. J., Bolhuis, P. G., & Schall, P. (2017). Switching Colloidal Superstructures by Critical Casimir Forces. Advanced materials, 29(34), Article 1700819. https://doi.org/10.1002/adma.201700819 [details]
- Smit, F. X., Luiken, J. A., & Bolhuis, P. G. (2017). Primary Fibril Nucleation of Aggregation Prone Tau Fragments PHF6 and PHF6*. The journal of Physical Chemistry. B, 121(15), 3250-3261. Advance online publication. https://doi.org/10.1021/acs.jpcb.6b07045 [details]
- Vijaykumar, A., Ouldridge, T. E., ten Wolde, P. R., & Bolhuis, P. G. (2017). Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics. Journal of Chemical Physics, 146(11), Article 114106. https://doi.org/10.1063/1.4977515 [details]
- Vijaykumar, A., ten Wolde, P. R., & Bolhuis, P. G. (2017). The magnitude of the intrinsic rate constant: How deep can association reactions be in the diffusion limited regime? Journal of Chemical Physics, 147(18), Article 184108. https://doi.org/10.1063/1.5009547 [details]
2016
- Brotzakis, Z. F., & Bolhuis, P. G. (2016). A one-way shooting algorithm for transition path sampling of asymmetric barriers. Journal of Chemical Physics, 145(16), Article 164112. https://doi.org/10.1063/1.4965882 [details]
- Brotzakis, Z. F., Groot, C. C. M., Brandeburgo, W. H., Bakker, H. J., & Bolhuis, P. G. (2016). Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin. The journal of Physical Chemistry. B, 120(21), 4756-4766. https://doi.org/10.1021/acs.jpcb.6b02592 [details]
- Evers, C. H. J., Luiken, J. A., Bolhuis, P. G., & Kegel, W. K. (2016). Self-assembly of microcapsules via colloidal bond hybridization and anisotropy. Nature, 534(7607), 364-368. https://doi.org/10.1038/nature17956 [details]
- Kumar, A., Lowe, C. P., Cohen Stuart, M. A., & Bolhuis, P. G. (2016). Trigger sequence can influence final morphology in the self-assembly of asymmetric telechelic polymers. Soft Matter, 12(7), 2095-2107. https://doi.org/10.1039/c5sm01453k [details]
2015
- Bolhuis, P. G., & Dellago, C. (2015). Practical and conceptual path sampling issues. The European Physical Journal - Special Topics, 224(12), 2409-2427. https://doi.org/10.1140/epjst/e2015-02419-6 [details]
- Du, W., & Bolhuis, P. G. (2015). Equilibrium Kinetic Network of the Villin Headpiece in Implicit Solvent. Biophysical Journal, 108(2), 368-378. https://doi.org/10.1016/j.bpj.2014.11.3476 [details]
- Luiken, J. A., & Bolhuis, P. G. (2015). Prediction of a stable associated liquid of short amyloidogenic peptides. Physical Chemistry Chemical Physics, 17(16), 10556-10567. https://doi.org/10.1039/c5cp00284b [details]
- Luiken, J. A., & Bolhuis, P. G. (2015). Primary Nucleation Kinetics of Short Fibril-Forming Amyloidogenic Peptides. The journal of Physical Chemistry. B, 119(39), 12568-12579. Advance online publication. https://doi.org/10.1021/acs.jpcb.5b05799 [details]
- Newton, A. C., Groenewold, J., Kegel, W. K., & Bolhuis, P. G. (2015). Rotational diffusion affects the dynamical self-assembly pathways of patchy particles. Proceedings of the National Academy of Sciences of the United States of America, 112(50), 15308-15313. https://doi.org/10.1073/pnas.1513210112 [details]
- Ni, R., Cohen Stuart, M. A., & Bolhuis, P. G. (2015). Tunable Long Range Forces Mediated by Self-Propelled Colloidal Hard Spheres. Physical Review Letters, 114(1), Article 018302. https://doi.org/10.1103/PhysRevLett.114.018302 [details]
- Ni, R., Kleijn, J. M., Abeln, S., Cohen Stuart, M. A., & Bolhuis, P. G. (2015). Competition between surface adsorption and folding of fibril-forming polypeptides. Physical Review E, 91(2), Article 022711. https://doi.org/10.1103/PhysRevE.91.022711 [details]
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. (2015). The Trigger Factor chaperone encapsulates and stabilizes partial folds of substrate proteins. PLoS Computational Biology, 11(10), Article e1004444. https://doi.org/10.1371/journal.pcbi.1004444 [details]
- Zeiler, R. N. W., & Bolhuis, P. G. (2015). Exposure of thiol groups in the heat-induced denaturation of β-lactoglobulin. Molecular Simulation, 41(10-12), 1006-1014. https://doi.org/10.1080/08927022.2014.926547 [details]
2014
- Du, W., & Bolhuis, P. G. (2014). Sampling the equilibrium kinetic network of Trp-cage in explicit solvent. Journal of Chemical Physics, 140(19), 195102. https://doi.org/10.1063/1.4874299 [details]
- Mani, E., Lechner, W., Kegel, W. K., & Bolhuis, P. G. (2014). Equilibrium and non-equilibrium cluster phases in colloids with competing interactions. Soft Matter, 10(25), 4479-4486. https://doi.org/10.1039/c3sm53058b [details]
- Ni, R., Cohen Stuart, M. A., Dijkstra, M., & Bolhuis, P. G. (2014). Crystallizing hard-sphere glasses by doping with active particles. Soft Matter, 10(35), 6609-6613. https://doi.org/10.1039/c4sm01015a [details]
- Swenson, D. W. H., & Bolhuis, P. G. (2014). A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events. Journal of Chemical Physics, 141(4), 044101. https://doi.org/10.1063/1.4890037 [details]
2013
- Dang, M. T., Vila Verde, A. C., Nguyen, V. D., Bolhuis, P. G., & Schall, P. (2013). Temperature-sensitive colloidal phase behavior induced by critical Casimir forces. Journal of Chemical Physics, 139(9), 094903. https://doi.org/10.1063/1.4819896 [details]
- Du, W., & Bolhuis, P. G. (2013). Adaptive single replica multiple state transition interface sampling. Journal of Chemical Physics, 139(4), 044105. https://doi.org/10.1063/1.4813777 [details]
- Luiken, J. A., & Bolhuis, P. G. (2013). Anisotropic aggregation in a simple model of isotropically polymer-coated nanoparticles. Physical Review E, 88(1), 012303. https://doi.org/10.1103/PhysRevE.88.012303 [details]
- Meuzelaar, H., Marino, K. A., Huerta-Viga, A., Panman, M. R., Smeenk, L. E. J., Kettelarij, A. J., van Maarseveen, J. H., Timmerman, P., Bolhuis, P. G., & Woutersen, S. (2013). Folding Dynamics of the Trp-Cage Miniprotein: Evidence for a Native-Like Intermediate from Combined Time-Resolved Vibrational Spectroscopy and Molecular Dynamics Simulations. The journal of Physical Chemistry. B, 117(39), 11490-11501. https://doi.org/10.1021/jp404714c [details]
- Ni, R., Abeln, S., Schor, M., Cohen Stuart, M. A., & Bolhuis, P. G. (2013). Interplay between Folding and Assembly of Fibril-Forming Polypeptides. Physical Review Letters, 111(5). https://doi.org/10.1103/PhysRevLett.111.058101 [details]
- Peters, B., Bolhuis, P. G., Mullen, R. G., & Shea, J. E. (2013). Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency. Journal of Chemical Physics, 138(5), 054106. https://doi.org/10.1063/1.4775807 [details]
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013). Hydrophobic Collapse of Trigger Factor Monomer in Solution. PLoS ONE, 8(4), e59683. https://doi.org/10.1371/journal.pone.0059683 [details]
- Zhu, L., Bolhuis, P. G., & Vreede, J. (2013). The HAMP Signal Relay Domain Adopts Multiple Conformational States through Collective Piston and Tilt Motions. PLoS Computational Biology, 9(2), Article e1002913. https://doi.org/10.1371/journal.pcbi.1002913 [details]
2012
- Juraszek, J., Vreede, J., & Bolhuis, P. G. (2012). Transition path sampling of protein conformational changes. Chemical Physics, 396, 30-44. https://doi.org/10.1016/j.chemphys.2011.04.032 [details]
- Marino, K. A., & Bolhuis, P. G. (2012). Confinement-Induced States in the Folding Landscape of the Trp-cage Miniprotein. The journal of Physical Chemistry. B, 116(39), 11872-11880. https://doi.org/10.1021/jp306727r [details]
- Schor, M., Vreede, J., & Bolhuis, P. G. (2012). Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling. Biophysical Journal, 103(6), 1296-1304. https://doi.org/10.1016/j.bpj.2012.07.056 [details]
- Vila Verde, A., Bolhuis, P. G., & Kramer Campen, R. (2012). Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface. The journal of Physical Chemistry. B, 116(31), 9467-9481. https://doi.org/10.1021/jp304151e [details]
- Zeiler, R. N. W., & Bolhuis, P. G. (2012). Numerical study of the effect of thiol-disulfide exchange in the cluster phase of beta-lactoglobulin aggregation. Faraday Discussions, 158, 461-477. https://doi.org/10.1039/c2fd20030a [details]
2011
- Bolhuis, P. G., & Lechner, W. (2011). On the relation between projections of the reweighted path ensemble. Journal of Statistical Physics, 145(4), 841-859. https://doi.org/10.1007/s10955-011-0324-6 [details]
- Du, W., Marino, K. A., & Bolhuis, P. G. (2011). Multiple state transition interface sampling of alanine dipeptide in explicit solvent. Journal of Chemical Physics, 135(14), 145102-145102. https://doi.org/10.1063/1.3644344 [details]
- Hsieh, C. S., Kramer Campen, R., Vila Verde, A. C., Bolhuis, P., Nienhuys, H. K., & Bonn, M. (2011). Ultrafast Reorientation of Dangling OH Groups at the Air-Water Interface Using Femtosecond Vibrational Spectroscopy. Physical Review Letters, 107(11). https://doi.org/10.1103/PhysRevLett.107.116102 [details]
- Lechner, W., Dellago, C., & Bolhuis, P. G. (2011). Reaction coordinates for the crystal nucleation of colloidal suspensions extracted from the reweighted path ensemble. Journal of Chemical Physics, 135(15). https://doi.org/10.1063/1.3651367 [details]
- Lechner, W., Dellago, C., & Bolhuis, P. G. (2011). Role of the prestructured surface cloud in crystal nucleation. Physical Review Letters, 106(8), 085701. https://doi.org/10.1103/PhysRevLett.106.085701 [details]
- Schor, M., & Bolhuis, P. G. (2011). The self-assembly mechanism of fibril-forming silk-based block copolymers. Physical Chemistry Chemical Physics, 13(22), 10457-10467. https://doi.org/10.1039/c0cp02842h [details]
- Visscher, L., Bolhuis, P., & Bickelhaupt, F. M. (2011). Multiscale modelling. Physical Chemistry Chemical Physics, 13(22), 10399-10400. https://doi.org/10.1039/c1cp90072b [details]
- Zhu, L., Frenkel, D., & Bolhuis, P. G. (2011). Role of fluctuations in ligand binding cooperativity of membrane receptors. Physical Review Letters, 106(16), 168103. https://doi.org/10.1103/PhysRevLett.106.168103 [details]
2010
- Juraszek, J., & Bolhuis, P. G. (2010). (Un)folding mechanisms of the FBP28 WW domain in explicit solvent revealed by multiple rare event simulation methods. Biophysical Journal, 98(4), 646-656. https://doi.org/10.1016/j.bpj.2009.10.039 [details]
- Lechner, W., Rogal, J., Juraszek, J., Ensing, B., & Bolhuis, P. G. (2010). Nonlinear reaction coordinate analysis in the reweighted path ensemble. Journal of Chemical Physics, 133(17), 174110. https://doi.org/10.1063/1.3491818 [details]
- Mani, E., Sanz, E., Bolhuis, P. G., & Kegel, W. K. (2010). Stabilization of nanoparticle shells by competing interactions. The Journal of Physical Chemistry. C, 114(17), 7780-7786. https://doi.org/10.1021/jp1004067 [details]
- Pool, R., & Bolhuis, P. G. (2010). The influence of micelle formation on the stability of colloid surfactant mixtures. Physical Chemistry Chemical Physics, 12(44), 14789-14797. https://doi.org/10.1039/c0cp00912a [details]
- Rogal, J., & Bolhuis, P. G. (2010). On the efficiency of biased sampling of the multiple state path ensemble. Journal of Chemical Physics, 133(3), 034101. https://doi.org/10.1063/1.3449144 [details]
- Rogal, J., Lechner, W., Juraszek, J., Ensing, B., & Bolhuis, P. G. (2010). The reweighted path ensemble. Journal of Chemical Physics, 133(17), 174109. https://doi.org/10.1063/1.3491817 [details]
- Schor, M., Ensing, B., & Bolhuis, P. G. (2010). A simple coarse-grained model for self-assembling silk-like protein fibers. Faraday Discussions, 144, 127-141. https://doi.org/10.1039/b901608b [details]
- Vreede, J., Juraszek, J., & Bolhuis, P. G. (2010). Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proceedings of the National Academy of Sciences of the United States of America, 107(6), 2397-2402. https://doi.org/10.1073/pnas.0908754107 [details]
2009
- Dellago, C., & Bolhuis, P. G. (2009). Transition path sampling and other advanced simulation techniques for rare events. In C. Holm, & K. Kremer (Eds.), Advanced computer simulation approaches for soft matter sciences III (pp. 167-233). (Advances in polymer science; No. 221). Springer. https://doi.org/10.1007/978-3-540-87706-6_3 [details]
- Juraszek, J., & Bolhuis, P. G. (2009). Effects of a mutation on the folding mechanism of a β-hairpin. The journal of Physical Chemistry. B, 113(50), 16184-16196. https://doi.org/10.1021/jp904468q [details]
- Schor, M., Martens, A. A., de Wolf, F. A., Cohen Stuart, M. A., & Bolhuis, P. G. (2009). Prediction of solvent dependent beta-roll formation of a self-assembling silk-like protein domain. Soft Matter, 5(13), 2658-2665. https://doi.org/10.1039/b902952d [details]
- Vreede, J., Wolf, M. G., de Leeuw, S. W., & Bolhuis, P. G. (2009). Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems. The journal of Physical Chemistry. B, 113(18), 6484-6494. https://doi.org/10.1021/jp809641j [details]
2008
- Bolhuis, P. G. (2008). Rare events via multiple reaction channels sampled by path replica exchange. Journal of Chemical Physics, 129(11), 114108. https://doi.org/10.1063/1.2976011 [details]
- Fortini, A., Bolhuis, P. G., & Dijkstra, M. (2008). Effect of excluded volume interactions on the interfacial properties of colloid-polymer mixtures. Journal of Chemical Physics, 128(2), Article 024904. https://doi.org/10.1063/1.2818562 [details]
- Huisman, B. A. H., Bolhuis, P. G., & Fasolino, A. (2008). Phase transition to bundles of flexible supramolecular polymers. Physical Review Letters, 100(18), 188301. https://doi.org/10.1103/PhysRevLett.100.188301 [details]
- Juraszek, J., & Bolhuis, P. G. (2008). Rate constant and reaction coordinate of Trp-cage folding in explicit water. Biophysical Journal, 95(9), 4246-4257. https://doi.org/10.1529/biophysj.108.136267 [details]
- Leenders, E. J. M., Bolhuis, P. G., & Meijer, E. J. (2008). Microscopic picture of the aqueous solvation of glutamic acid. Journal of Chemical Theory and Computation, 4(6), 898-907. https://doi.org/10.1021/ct700344f [details]
- Rogal, J., & Bolhuis, P. G. (2008). Multiple state transition path sampling. Journal of Chemical Physics, 129(22), 224107. https://doi.org/10.1063/1.3029696 [details]
- Vreede, J., Hellingwerf, K. J., & Bolhuis, P. G. (2008). Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein. Proteins, 72(1), 136-149. https://doi.org/10.1002/prot.21902 [details]
2021
- Covino, R., Jung, H., Arjun, A., Bolhuis, P. G., & Hummer, G. (2021). Discovering molecular mechanisms from computer simulations with deep reinforcement learning. European Biophysics Journal with Biophysics Letters, 50(SUPPL 1, 1, SI), 74.
2019
- Bolhuis, P. (2019). Free energy, kinetics, and reaction coordinates of biomolecular processes from transition path sampling simulations. Abstracts2view : American Chemical Society Meeting, 257. https://tpa.acs.org/abstract/acsnm257-3126806/free-energy-kinetics-and-reaction-coordinates-of-biomolecular-processes-from-transition-path-sampling-simulations [details]
2017
- Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2017). Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA. Biophysical Journal, 112(3, Supplement 1), 214a. https://doi.org/10.1016/j.bpj.2016.11.1181 [details]
2015
- Nowosielski, M. A., & Bolhuis, P. G. (2015). Exploring the Phase Space of Alpha-Synuclein with Replica Exchange Simulations. Biophysical Journal, 108(2, suppl. 1), 63A. https://doi.org/10.1016/j.bpj.2014.11.377 [details]
2013
- Singhal, K., Vreede, J., Mashaghi, A., Tans, S. J., & Bolhuis, P. G. (2013). A Molecular Dynamics Study of the Flexibility and Protein-Binding of the Trigger Factor Chaperone in Solution. Biophysical Journal, 104(2, Suppl. 1), 571A. https://doi.org/10.1016/j.bpj.2012.11.3172
2016
- Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2016). Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition. Biophysical Journal, 110(3, suppl. 1), 563A-564A. https://doi.org/10.1016/j.bpj.2015.11.3014 [details]
Andere
- Bolhuis, P. (host) (28-6-2019). Roberto Covino (hosting a visitor).
- Bolhuis, P. G. (host) (17-1-2018). Gregory Voth (hosting a visitor).
- Bolhuis, P. (visiting researcher) (2017). University of Cambridge, UK (visiting an external institution).
2017
- Brotzakis, Z. F. (2017). Hydration layer dynamics and association mechanisms of food and antifreeze proteins: A Molecular Dynamics and Transition Path Sampling study. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
- Newton, A. C. (2017). Self-assembly via anisotropic interactions: Modeling association kinetics of patchy particle systems and self-assembly induced by critical Casimir forces. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
- Vijaykumar, A. (2017). Multi-scale simulation of reaction-diffusion systems. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
2023
- Lazzeri, G., Jung, H., Bolhuis, P. & Covino, R. (16-6-2023). Source code and data for AIMMD-TPS and PE estimate. Zenodo. https://doi.org/10.5281/zenodo.8172628
- Jung, H., Covino, R., Arjun, A., Leitold, C., Dellago, C., Bolhuis, P. G. & Hummer, G. (7-3-2023). Machine-guided path sampling to discover mechanisms of molecular self-organization (Training and validation data). Zenodo. https://doi.org/10.5281/zenodo.7704969
- van Heesch, T., Bolhuis, P. G. & Vreede, J. (2023). SMD Simulations of GC-analogue Sequence. Figshare. https://doi.org/10.6084/m9.figshare.22182562.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of ETS Inverse Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161295.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of ETS Anti Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161301.v1
- Bolhuis, P. G., Vreede, J. & van Heesch, T. (2023). SMD Simulations of ETS Consensus Sequence. Figshare. https://doi.org/10.6084/m9.figshare.24161280.v1
- van Heesch, T., Vreede, J. & Bolhuis, P. G. (2023). SMD Simulations of High Affinity Sequence. Figshare. https://doi.org/10.6084/m9.figshare.21304482.v1
2020
- Vreede, J., Roet, S., Swenson, D., Hooft, F. & Bolhuis, P. (22-2-2020). Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L. Universiteit van Amsterdam. https://doi.org/10.21942/uva.11865579.v1
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Nevenwerkzaamheden
- Geen nevenwerkzaamheden
Jonas, H. J., Schall, P., & Bolhuis, P. G. (2024). Activity affects the stability, deformation and breakage dynamics of colloidal architectures. Soft Matter, 20(9), 2162-2177.