Fotograaf: ?

dhr. prof. dr. P.G. (Peter) Bolhuis


  • Faculteit der Natuurwetenschappen, Wiskunde en Informatica
    HIMS
  • Bezoekadres
    Science Park A
    Science Park 904  Kamernummer: C2.222
  • Postadres:
    Postbus  94157
    1090 GD  Amsterdam
  • P.G.Bolhuis@uva.nl
    T: 0205256447

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.

2017

  • 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). DOI: 10.1063/1.5006485 
  • 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). DOI: 10.1002/adma.201700819 
  • 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. DOI: 10.1039/c7cp02465g 
  • 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. DOI: 10.1039/c7sm00668c 
  • 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), [234901]. DOI: 10.1063/1.4984966 
  • 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. DOI: 10.1021/acs.jpcb.6b07045 
  • 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). DOI: 10.1063/1.4977515 
  • 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.

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). DOI: 10.1063/1.4965882 
  • 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-+. DOI: 10.1038/nature17956 
  • Brotzakis, Z. F., Groot, C. C. M., Brandeburgo, W. H., Bakker, H. J., & Bolhuis, P. (2016). Dynamics of Hydration Water around Native and Misfolded alpha-Lactalbumin. The journal of Physical Chemistry. B, 120(21), 4756-4766. DOI: 10.1021/acs.jpcb.6b02592 
  • 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. DOI: 10.1039/c5sm01453k  [details] 

2015

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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 10.1103/PhysRevE.88.012303  [details] 
  • Meuzelaar, H., Marino, K. A., Huerta-Viga, A., Panman, M. R., Smeenk, L. E. J., Kettelarij, A. J., ... 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. DOI: 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). DOI: 10.1103/PhysRevLett.111.058101  [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. DOI: 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), e1002913. DOI: 10.1371/journal.pcbi.1002913  [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. DOI: 10.1063/1.4775807  [details] 

2012

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. DOI: 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. DOI: 10.1063/1.3644344  [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). DOI: 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. DOI: 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. DOI: 10.1039/c0cp02842h  [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. DOI: 10.1103/PhysRevLett.106.168103  [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). DOI: 10.1103/PhysRevLett.107.116102  [details] 
  • Visscher, L., Bolhuis, P., & Bickelhaupt, F. M. (2011). Multiscale modelling. Physical Chemistry Chemical Physics, 13(22), 10399-10400. DOI: 10.1039/c1cp90072b  [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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 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. DOI: 10.1073/pnas.0908754107  [details] 

2009

  • 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. DOI: 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. DOI: 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. DOI: 10.1021/jp809641j  [details] 
  • 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). Berlin: Springer. DOI: 10.1007/978-3-540-87706-6_3  [details] 

2008

  • Bolhuis, P. G. (2008). Rare events via multiple reaction channels sampled by path replica exchange. Journal of Chemical Physics, 129(11), 114108. DOI: 10.1063/1.2976011  [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. DOI: 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. DOI: 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. DOI: 10.1021/ct700344f  [details] 
  • Rogal, J., & Bolhuis, P. G. (2008). Multiple state transition path sampling. Journal of Chemical Physics, 129(22), 224107. DOI: 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. DOI: 10.1002/prot.21902  [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), [024904]. DOI: 10.1063/1.2818562  [details] 

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. DOI: 10.1016/j.bpj.2015.11.3014  [details] 

2017

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