prof. dr. P.G. (Peter) Bolhuis
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Faculty of Science
HIMS
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POSTBUS
94157
1090 GD Amsterdam
Room number: C2.222
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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.
2015
- R. Ni, J.M. Kleijn, S. Abeln, M.A. Cohen Stuart & P.G. Bolhuis (2015). Competition between surface adsorption and folding of fibril-forming polypeptides. Physical Review E, 91 (2). doi: 10.1103/PhysRevE.91.022711
- J.A. Luiken & P.G. Bolhuis (2015). Prediction of a stable associated liquid of short amyloidogenic peptides. Physical Chemistry Chemical Physics. doi: 10.1039/C5CP00284B
- R. Ni, M.A. Cohen Stuart & P.G. Bolhuis (2015). Tunable Long Range Forces Mediated by Self-Propelled Colloidal Hard Spheres. Physical Review Letters, 114 (1). doi: 10.1103/PhysRevLett.114.018302
- W. Du & P.G. Bolhuis (2015). Equilibrium Kinetic Network of the Villin Headpiece in Implicit Solvent. Biophysical Journal, 108 (2), 368-378. doi: 10.1016/j.bpj.2014.11.3476
- R.N.W. Zeiler & P.G. Bolhuis (2015). Exposure of thiol groups in the heat-induced denaturation of β-lactoglobulin. Molecular Simulation. doi: 10.1080/08927022.2014.926547
2014
- E. Mani, W. Lechner, W.K. Kegel & P.G. Bolhuis (2014). Equilibrium and non-equilibrium cluster phases in colloids with competing interactions. Soft Matter, 10 (25), 4479-4486. doi: 10.1039/c3sm53058b[go to publisher's site]
- D.W.H. Swenson & P.G. Bolhuis (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[go to publisher's site]
- R. Ni, M.A. Cohen Stuart, M. Dijkstra & P.G. Bolhuis (2014). Crystallizing hard-sphere glasses by doping with active particles. Soft Matter, 10 (35), 6609-6613. doi: 10.1039/c4sm01015a[go to publisher's site]
- W. Du & P.G. Bolhuis (2014). Sampling the equilibrium kinetic network of Trp-cage in explicit solvent. Journal of Chemical Physics, 140 (19), 195102. doi: 10.1063/1.4874299[go to publisher's site]
2013
- W. Du & P.G. Bolhuis (2013). Adaptive single replica multiple state transition interface sampling. Journal of Chemical Physics, 139 (4), 044105. doi: 10.1063/1.4813777[go to publisher's site]
- R. Ni, S. Abeln, M. Schor, M.A. Cohen Stuart & P.G. Bolhuis (2013). Interplay between Folding and Assembly of Fibril-Forming Polypeptides. Physical Review Letters, 111 (5). doi: 10.1103/PhysRevLett.111.058101[go to publisher's site]
- M.T. Dang, A.C. Vila Verde, V.D. Nguyen, P.G. Bolhuis & P. Schall (2013). Temperature-sensitive colloidal phase behavior induced by critical Casimir forces. Journal of Chemical Physics, 139 (9), 094903. doi: 10.1063/1.4819896[go to publisher's site]
- H. Meuzelaar, K.A. Marino, A. Huerta-Viga, M.R. Panman, L.E.J. Smeenk, A.J. Kettelarij, J.H. van Maarseveen, P. Timmerman, P.G. Bolhuis & S. Woutersen (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
- L. Zhu, P.G. Bolhuis & J. Vreede (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[go to publisher's site]
- K. Singhal, J. Vreede, A. Mashaghi, S.J. Tans & P.G. Bolhuis (2013). Hydrophobic Collapse of Trigger Factor Monomer in Solution. PLoS One, 8 (4), e59683. doi: 10.1371/journal.pone.0059683[go to publisher's site]
- J.A. Luiken & P.G. Bolhuis (2013). Anisotropic aggregation in a simple model of isotropically polymer-coated nanoparticles. Physical Review E, 88 (1), 012303. doi: 10.1103/PhysRevE.88.012303[go to publisher's site]
- B. Peters, P.G. Bolhuis, R.G. Mullen & J.E. Shea (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[go to publisher's site]
2012
- J. Juraszek, J. Vreede & P.G. Bolhuis (2012). Transition path sampling of protein conformational changes. Chemical Physics, 396, 30-44. doi: 10.1016/j.chemphys.2011.04.032
- M. Schor, J. Vreede & P.G. Bolhuis (2012). Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling. Biophysical Journal, 103 (6), 1296-1304. doi: 10.1016/j.bpj.2012.07.056[go to publisher's site]
- R.N.W. Zeiler & P.G. Bolhuis (2012). Numerical study of the effect of thiol-disulfide exchange in the cluster phase of beta-lactoglobulin aggregation. Faraday Discussions, 158, 461-477. doi: 10.1039/c2fd20030a
- K.A. Marino & P.G. Bolhuis (2012). Confinement-Induced States in the Folding Landscape of the Trp-cage Miniprotein. The journal of physical chemistry. B, 116 (39), 11872-11880. doi: 10.1021/jp306727r[go to publisher's site]
- A. Vila Verde, P.G. Bolhuis & R. Kramer Campen (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. doi: 10.1021/jp304151e
2011
- W. Du, K.A. Marino & P.G. Bolhuis (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[go to publisher's site]
- P.G. Bolhuis & W. Lechner (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
- L. Zhu, D. Frenkel & P.G. Bolhuis (2011). Role of fluctuations in ligand binding cooperativity of membrane receptors. Physical Review Letters, 106 (16), 168103. doi: 10.1103/PhysRevLett.106.168103[go to publisher's site]
- M. Schor & P.G. Bolhuis (2011). The self-assembly mechanism of fibril-forming silk-based block copolymers. Physical Chemistry Chemical Physics, 13 (22), 10457-10467. doi: 10.1039/c0cp02842h
- W. Lechner, C. Dellago & P.G. Bolhuis (2011). Role of the prestructured surface cloud in crystal nucleation. Physical Review Letters, 106 (8), 085701. doi: 10.1103/PhysRevLett.106.085701[go to publisher's site]
- L. Visscher, P. Bolhuis & F.M. Bickelhaupt (2011). Multiscale modelling. Physical Chemistry Chemical Physics, 13 (22), 10399-10400. doi: 10.1039/c1cp90072b
- C.S. Hsieh, R. Kramer Campen, A.C. Vila Verde, P. Bolhuis, H.K. Nienhuys & M. Bonn (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
- W. Lechner, C. Dellago & P.G. Bolhuis (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[go to publisher's site]
2010
- E. Mani, E. Sanz, P.G. Bolhuis & W.K. Kegel (2010). Stabilization of nanoparticle shells by competing interactions. The Journal of Physical Chemistry. C, 114 (17), 7780-7786.
- W. Lechner, J. Rogal, J. Juraszek, B. Ensing & P.G. Bolhuis (2010). Nonlinear reaction coordinate analysis in the reweighted path ensemble. Journal of Chemical Physics, 133 (17), 174110.[go to publisher's site]
- J. Rogal & P.G. Bolhuis (2010). On the efficiency of biased sampling of the multiple state path ensemble. Journal of Chemical Physics, 133 (3), 034101.[go to publisher's site]
- J. Rogal, W. Lechner, J. Juraszek, B. Ensing & P.G. Bolhuis (2010). The reweighted path ensemble. Journal of Chemical Physics, 133 (17), 174109.[go to publisher's site]
- R. Pool & P.G. Bolhuis (2010). The influence of micelle formation on the stability of colloid surfactant mixtures. Physical Chemistry Chemical Physics, 12 (44), 14789-14797.
- J. Juraszek & P.G. Bolhuis (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.[go to publisher's site]
- J. Vreede, J. Juraszek & P.G. Bolhuis (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.
- M. Schor, B. Ensing & P.G. Bolhuis (2010). A simple coarse-grained model for self-assembling silk-like protein fibers. Faraday Discussions, 144, 127-141.
2009
- M. Schor, A.A. Martens, F.A. de Wolf, M.A. Cohen Stuart & P.G. Bolhuis (2009). Prediction of solvent dependent beta-roll formation of a self-assembling silk-like protein domain. Soft Matter, 5 (13), 2658-2665.
- C. Dellago & P.G. Bolhuis (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 (Advances in polymer science, 221) (pp. 167-233). Berlin: Springer.
- J. Juraszek & P.G. Bolhuis (2009). Effects of a mutation on the folding mechanism of a β-hairpin. The journal of physical chemistry. B, 113 (50), 16184-16196.
- J. Vreede, M.G. Wolf, S.W. de Leeuw & P.G. Bolhuis (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.
2008
- J. Rogal & P.G. Bolhuis (2008). Multiple state transition path sampling. Journal of Chemical Physics, 129 (22), 224107.[go to publisher's site]
- J. Vreede, K.J. Hellingwerf & P.G. Bolhuis (2008). Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein. Proteins, 72 (1), 136-149.
- B.A.H. Huisman, P.G. Bolhuis & A. Fasolino (2008). Phase transition to bundles of flexible supramolecular polymers. Physical Review Letters, 100 (18), 188301.[go to publisher's site]
- E.J.M. Leenders, P.G. Bolhuis & E.J. Meijer (2008). Microscopic picture of the aqueous solvation of glutamic acid. Journal of Chemical Theory and Computation, 4 (6), 898-907.
- P.G. Bolhuis (2008). Rare events via multiple reaction channels sampled by path replica exchange. Journal of Chemical Physics, 129 (11), 114108.[go to publisher's site]
- J. Juraszek & P.G. Bolhuis (2008). Rate constant and reaction coordinate of Trp-cage folding in explicit water. Biophysical Journal, 95 (9), 4246-4257.[go to publisher's site]
- A. Fortini, P.G. Bolhuis & M. Dijkstra (2008). Effect of excluded volume interactions on the interfacial properties of colloid-polymer mixtures. Journal of Chemical Physics, 128 (2), 024904.[go to publisher's site]
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