PUBLICATIONS

Books

2011

Articles

  1. On the Relation Between Projections of the Reweighted Path Ensemble Peter G. Bolhuis and Wolfgang Lechner
    J. Stat. Phys. 145, 841-859 (2011).
  2. Reaction coordinates for the crystal nucleation of colloidal suspensions extracted from the reweighted path ensemble
    Wolfgang Lechner; Christoph Dellago; Peter G.Bolhuis
    J. Chem.. Phys. 135, 154110 (2011).
  3. Multiple state transition interface sampling of alanine dipeptide in explicit solvent
    Wei-Na Du ; Kristen A. Marino; Peter G Bolhuis.
    J. Chem. Phys. 135, 145102 (2011).
  4. Ultrafast Reorientation of Dangling OH Groups at the Air-Water Interface Using Femtosecond Vibrational Spectroscopy
    Cho-Shuen Hsieh; R. Kramer Campen; Ana Celia Vila Verde ; P.G. Bolhuis; Han-Kwang Nienhuys, Mischa Bonn
    Phys. Rev. Lett. 107, 116102 (2011).
  5. Role of Fluctuations in Ligand Binding Cooperativity of Membrane Receptors
    Lizhe Zhu; Daan Frenkel; Peter G. Bolhuis
    Phys. Rev. Lett. 106, 168103 (2011).
  6. Role of the Prestructured Surface Cloud in Crystal Nucleation
    Wolfgang Lechner; Christoph Dellago; Peter G.Bolhuis
    Phys. Rev. Lett. 106, 085701 (2011).
  7. Multiscale modelling
    Lucas Visscher; Peter G. Bolhuis; F. Matthias Bickelhaupt
    Phys. Chem. Chem. Phys. 13, 10399-10400 (2011).
  8. The self-assembly mechanism of fibril-forming silk-based block copolymers
    Marieke Schor;Peter G. Bolhuis
    Phys. Chem. Chem. Phys. 13, 10457-10467 (2011).
  9. A Reply to the Comment by M. Praprotnik et al.
    Steven O. Nielsen, Preston B. Moore, and Bernd Ensing,
    Phys. Rev. Lett. 107, 099802 (2011).
  10. Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (φ, ψ) Space
    Zhiwei Liu, Bernd Ensing, and Preston B. Moore
    J. Chem. Theory. Comput.7, 402-419 (2011).

2010

Articles

  1. The influence of micelle formation on the stability of colloid surfactant mixtures
    René Pool and Peter G. Bolhuis
    Phys. Chem. Chem. Phys. 44, 14789-14797 (2010).
  2. On the efficiency of biased sampling of the multiple state path ensemble
    Jutta Rogal and Peter G. Bolhuis
    J. Chem. Phys. 133, 034101 (2010).
  3. Stabilization of Nanoparticle Shells by Competing Interactions
    Ethayaraja Mani, Eduardo Sanz, Peter Bolhuis, and Willem Kegel
    J. Phys. Chem. C 114, 7780-7786 (2010).
  4. (Un)Folding Mechanisms of the FBP28 WW Domain in Explicit Solvent Revealed by Multiple Rare Event Simulation Methods
    Jarek Juraszek and Peter Bolhuis
    Biophys. J. 98, 646-656 (2010).
  5. Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
    Joecelyne Vreede, Jarek Juraszek and Peter Bolhuis
    Proc. Nat. Acad. Sci. USA 107, 397-2402 (2010).
  6. Performance of Chiral Zeolites for Enantiomeric Separation Revealed by Molecular Simulation
    J.M. Castillo, T.J.H. Vlugt, D. Dubbeldam, S. Hamad and S. Calero,
    J. Phys. Chem. C in press, (2010).
  7. Steric Effects on Enantioselective Epoxidation Catalyzed by (Salen)Mn in Metal-Organic Frameworks
    G.A.E. Oxford, D. Dubbeldam, L.J. Broadbelt and R.Q. Snurr,
    J. Phys. Chem. C in press, (2010).
  8. On the application of chiral amplification via adsorption
    Titus S. van Erp, David Dubbeldam, Sofia Calero and Johan A. Martens,
    Chem. Eng. Sci. 65, 6478-6485 (2010).
  9. Modeling Adsorption and Self-Diffusion of Methane in LTA Zeolites: the Influence of Framework Flexibility
    A. Garcia-Sanchez, D. Dubbeldam, and S. Calero,
    J. Phys. Chem. C 114(35), 15068-15074 (2010).
  10. Analysis of the ITQ-12 Zeolite Performance in Propane-Propylene Separations Using a Combination of Experiments and Molecular Simulations
    J.J. Guitierrez-Sevillano , D. Dubbeldam, F. Rey, S. Valencia, M. Palomino, A. Martin-Calvo, and S. Calero,
    J. Phys. Chem. C 114(35), 14907-14914 (2010).



  11. Recent progress in multiscale molecular dynamics simulation of soft matter
    Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore, Bernd Ensing,
    Phys. Chem. Chem. Phys. 12, 12401-12412 (2010).



  12. Adaptive multiscale molecular dynamics of macromolecular fluids
    Steven O. Nielsen, Preston B. Moore, and Bernd Ensing,
    Phys. Rev. Lett. 105, 237802 (2010).
  13. Smooth capping of short-range repulsive forces in hybrid atomistic/coarse-grain molecular dynamics simulation
    Bernd Ensing,
    Proceedings of Multiscale Materials Modeling in press (2010).
  14. Non-linear reaction coordinate analysis in the reweighted path ensemble
    Wolfgang Lechner, Jutta Rogal, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis,
    J. Chem. Phys. 133, 174110 (2010).
  15. The reweighted path ensemble
    Jutta Rogal, Wolfgang Lechner, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis,
    J. Chem. Phys. 133, 174109 (2010).
  16. High-pressure high-temperature equation of state of graphite from Monte Carlo simulations
    F. Colonna, A. Fasolino, and E.J. Meijer,
    To be published in Carbon (2010).
  17. Liquid carbon: Freezing line and structure near freezing
    L.M. Ghiringhelli and E.J. Meijer,
    in L. Colombo and A. Fasolino, eds., Computer-based modeling of novel carbon systems (other than nanotubes), and their properties, Springer Series on Carbon Materials: Chemistry and Physics Vol. 3, 1 - 36 (Springer, 2010)
  18. Hydration mechanisms of Cu2+: tetra-, penta- or hexa-coordinated?
    X. Liu, X. Lu, E.J. Meijer, and R. Wang,
    Phys. Chem. Chem. Phys. 1210801-10804 (2010).
  19. Enantioselective Adsorption Characteristics of Aluminum Substituted MFI Zeolites
    T.P. Caremans, T. van Erp, D. Dubbeldam, J.M. Castillo, J.A. Martens, and S. Calero,
    Chem. Mat. accepted, (2010).
  20. On the Connection between the Relevant Site Model and Dynamically Corrected Transition State Theory
    T.J.H. Vlugt, J. van den Bergh, D. Dubbeldam, and F. Kapteijn,
    J. Phys. Chem. Lett. accepted, (2010).
  21. Effective Monte Carlo Scheme for Multicomponent Gas Adsorption and Enantioselectivity in Nanoporous Materials
    T. van Erp, D. Dubbeldam, T.P. Caremans, S. Calero, and J.A. Martens,
    J. Phys. Chem. Lett. accepted, (2010).
  22. Self-diffusion studies in CuBTC by PFG NMR and MD simulations
    M. Wehring, J. Gascon, D. Dubbeldam, F. Kapteijn, R.Q. Snurr, and F. Stallmach,
    J. Phys. Chem. C 114, 10527-10534 (2010).
  23. Distance and Angular Holonomic Constraints in Molecular Simulations
    D. Dubbeldam, G.A.E. Oxford, R. Krishna, R.Q. Snurr, and L. Broadbelt,
    J. Chem. Phys. accepted, (2010).
  24. Enantioselective adsorption in achiral zeolites
    T. van Erp, T.P. Caremans, D. Dubbeldam, A. Martin-Calvo, S. Calero, and J.A. Martens,
    Angew. Chem. Int. Ed. 49, 3010-3013 (2010).
  25. Erratum: Adsorption and Diffusion of Water, Methanol, and Ethanol in All-Silica DD3R: Experiments and Simulation
    J. Kuhn, J.M. Castillo-Sanchez, J. Gascon, S. Calero, D. Dubbeldam, T.J.H. Vlugt, F. Kapteijn, and J. Gross,
    J. Phys. Chem. C 114, 6877-6878 (2010).
  26. Hydrolysis of cisplatin - a first-principles metadynamics study
    Justin Kai-Chi Lau and Bernd Ensing,
    Phys. Chem. Chem. Phys. 12, 10348-10355 (2010).
  27. Acid dissociation mechanism of SiOH4 and Al(H2O)63+ in aqueous solution
    X. Liu, X. Lu, E.J. Meijer, R. Wang, and H. Zhou,
    Geochimica et Cosmochimica Acta 74, 510-516 (2010).
  28. Ab initio molecular dynamics study of iron-containing smectites
    X. Liu, E.J. Meijer, X. Lu, and R. Wang,
    Clays and Clay Minerals 58, 89-96 (2010).
  29. A simple coarse-grained model for self-assembling silk-like protein fibers
    M. Schor, B. Ensing and P.G. Bolhuis,
    Faraday Discuss. 144, 127-141 (2010).

Contributions to Books

  1. Multiscale molecular dynamics and the reverse mapping problem
    Bernd Ensing and Steven O. Nielsen,
    Book chapter in Trends in Computational Nanomechanics (Challenges and Advances in Computational Chemistry and Physics, Volume 9) edited by T. Dumitrica (Springer, 2010), p. 25 - 60

2009

Articles

  1. In vivo mutational analysis of YtvA from bacillus subtilis. Mechanism of light activation of the general stress response
    M. Avila-Perez, J. Vreede, Y.F. Tang, O. Bende, A. Losi, W. Gartner, and K. Hellingwerf,
    J. Biol. Chem. 284, 24958-24964 (2009).
  2. Common G102S polymorphism in chitotriosidase differentially affects activity towards 4-methylumbelliferyl substrates
    A.P. Bussink M. Verhoek, J. Vreede, K. Ghauharali-van der Vlugt, W.E. Donker-Koopman R.R. Sprenger C.E. Hollak, J.M.F.G. Aerts, and R.G. Boot,
    FEBS JOURNAL 276, 5678-5688 (2009).
  3. Method for Analyzing Structural Changes of Flexible Metal-Organic Frameworks Induced by Adsorbates
    D. Dubbeldam, R. Krishna, and R.Q. Snurr,
    J. Phys. Chem. C 113, 19317-19327 (2009).
  4. Effects of a Mutation on the Folding Mechanism of beta-Hairpin
    J. Juraszek and P.G. Bolhuis,
    J. Phys. Chem. B 113, 16184-16196 (2009).
  5. Describing the Diffusion of Guest Molecules Inside Porous Structures
    R. Krishna,
    J. Phys. Chem. C 113, 19756-19781 (2009).
  6. MILCH SHAKE: An Efficient Method for Constraint Dynamics Applied to Alkanes
    A.G. Bailey and C.P. Lowe,
    J. Comp. Chem. 30, 2485-2493 (2009).
  7. Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics
    A.G. Bailey, C.P. Lowe, I. Pagonabarraga, and M.C. Lagomarsino,
    Phys. Rev. E 80, 046707 (2009).
  8. REVLD: A coarse-grained model for polymers
    A.G. Bailey, C.P. Lowe, abd A.P. Sutton,
    Comp. Phys. Comm. 180, 594-599 (2009).
  9. Properties of graphite at melting from multilayer thermodynamic integration
    F. Colonna, J.H. Los, A. Fasolino, and E.J. Meijer,
    Phys. Rev. B. 80, 134103 (2009).
  10. Effect of Counter Ions on the Silica Oligomerization Reaction
    T. T. Trinh, A. P. J. Jansen, R. A. van Santen, J. VandeVondele and E.J. Meijer,
    Chem. Phys. Chem. 10, 1775 - 1782 (2009).
  11. Toward a Practical Method for Adaptive QM/MM Simulations
    R. E. Bulo, B. Ensing, J. Sikkema, and L. Visscher,
    J. Chem. Theory Comput. 5, 2212 - 2221 (2009).
  12. Prediction of solvent dependent beta-roll formation of a self-assembling silk-like protein domain
    M. Schor, A.A. Martens, F.A. deWolf, M.A. Cohen Stuart, and P G. Bolhuis,
    Soft Matter 5, 2658 - 2665 (2009).
  13. Assessing surface permeabilities from transient guest profiles in nanoporous host materials
    D. Tzoulaki, L. Heinke, H. Lim, J. Li, D. Olson, J. Caro, R. Krishna, C. Chmelik, J. Kärger,
    Angew. Chem.-Int. Ed. 48, 3525-3528 (2009).
  14. Transferable Force Field for Carbon Dioxide Adsorption in Zeolites
    A. Garcia-Sanchez, C.O. Ania, J.B. Parra, D. Dubbeldam, T.H.J. Vlugt, R. Krishna, and S. Calero,
    J. Phys. Chem. C 113, 8814-8820 (2009).
  15. Unified Maxwell-Stefan description of binary mixture diffusion in micro- and meso-porous materials
    R. Krishna and J.M. van Baten,
    Chem. Eng. Sci. 64, 3159-3178 (2009).
  16. Diffusion of n-butane/iso-butane mixtures in silicalite-1 investigated using infrared (IR) microscopy
    C. Chmelik, L. Heinke, J.M. van Baten and R. Krishna,
    Micropor. Mesopor. Mater. 125, 11-16 (2009)
  17. A Molecular Dynamics investigation of the influence of framework flexibility on self-diffusivity of ethane in Zn(tbip) frameworks
    K. Seehamart, T. Nanok, R. Krishna, J.M. van Baten, T. Remsungnen, and S. Fritzsche,
    Micropor. Mesopor. Mater. 125, 97-100 (2009)
  18. A molecular dynamics investigation of a variety of influences of temperature on diffusion in zeolites
    R. Krishna and J.M. van Baten,
    Micropor. Mesopor. Mater. 125, 126-134 (2009)
  19. The Role of Water in Silica Oligomerization Reaction
    T.T. Trinh, A.P.J. Jansen, R.A. van Santen, and E.J. Meijer,
    Phys. Chem. Chem. Phys. 11, 5092-5099 (2009).
  20. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems
    J. Vreede, J. Wolf, M. G. de Leeuw, and P.G. Bolhuis,
    J. Phys. Chem. 113, 6484-6494 (2009).
  21. Two-state protein folding kinetics through all-atom molecular dynamics based sampling
    P.G. Bolhuis,
    Frontiers in Bioscience 14, 2801-2828 (2009).
  22. Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events
    C Dellago and P.G. Bolhuis,
    in Advanced Computer Simulation Approaches for Soft Matter Sciences III, Book Series: Advances in Polymer Science, 167-233 (2009).
  23. Mechanism of base-promoted ehydrochlorination of pentachloroethane: concerted or stepwise
    X. Liu and E.J. Meijer,
    J. Phys. Chem. C 113, 3542~3544 (2009).
  24. Role of Water in Silica Oligomerization
    T.T. Trinh, A.P.J. Jansen, R.A. van Santen, and E.J. Meijer,
    J. Phys. Chem. C 113, 2647-2652 (2009).
  25. Assessing guest diffusivities in porous hosts from transient concentration profiles
    L. Heinke, D. Tzoulaki, C. Chmelik, F. Hibbe, J.M. van Baten, H. Lim, J. Li, R. Krishna, J. Kärger,
    Phys. Rev. Lett. 102, 065901 (2009)
  26. Adsorption and diffusion of alkanes in CuBTC crystals investigated using infra-red microscopy and molecular simulations
    C. Chmelik, J. Kärger, M. Wiebcke, J. Caro, J.M. van Baten, and R. Krishna,
    Microporous Mesoporous Mater. 117, 22-32 (2009)
  27. Analysis of Diffusion Limitation in the Alkylation of Benzene over H-ZSM-5 by Combining Quantum Chemical Calculations, Molecular Simulations, and a Continuum Approach
    N. Hansen, R. Krishna, J.M. van Baten, A.T. Bell, F.J. Keil,
    J. Phys. Chem. C 113, 235-246 (2009).
  28. An investigation of the characteristics of Maxwell-Stefan diffusivities of binary mixtures in silica nanopores
    R. Krishna, and J.M. van Baten,
    Chem. Eng. Sci. 64, 870-882 (2009).
  29. Strategies for Characterization of Large-Pore Metal-Organic Frameworks by Combined Experimental and Computational Methods
    Y.S. Bae, D. Dubbeldam, A. Nelson, K.S. Walton, J.T. Hupp and R.Q. Snurr,
    Chem. Mat. 21(20), 4768-4777 (2009).
  30. A new perspective on the order-n algorithm for computing correlation functions
    D. Dubbeldam, D. Ford, D.E. Ellis, and R.Q. Snurr,
    Mol. Sim. 35(12/13), 1084-1097 (2009).
  31. The Effect of Framework Flexibility on Diffusion of Small Molecules in the Metal-Organic Framework IRMOF-1
    D. Ford, D. Dubbeldam and R.Q. Snurr,
    Diffusion Fundamentals III, Eds. C. Chmelik, N. Kanellopoulos, J. Karger, D. Theodorou, Leipziger Universitatsverlag, Germany,, 459-466 (2009).
  32. Evaluation of various water models for simulation of adsorption in hydrophobic zeolites
    J.M. Castillo, D. Dubbeldam, T.J.H. Vlugt, B. Smit, and S. Calero,
    Mol. Sim. 35(12/13), 1067-1076 (2009).
  33. Adsorption and Diffusion of Water, Methanol, and Ethanol in All-Silica DD3R: Experiments and Simulation
    J. Kuhn, J.M. Castillo-Sanchez, J. Gascon, S. Calero, D. Dubbeldam, T.J.H. Vlugt, F. Kapteijn, and J. Gross,
    J. Phys. Chem. C. 113(32), 14290-14301 (2009).
  34. Heats of Adsorption for Seven Gases in Three Metal-Organic Frameworks: Systematic Comparison of Experiment and Simulation
    D. Farrusseng, C. Daniel, C. Gaudillere, U. Ravon, Y. Schuurman, C. Mirodatos, D. Dubbeldam, H. Frost, R.Q. Snurr,
    Langmuir 25(14), 7383-7388 (2009).

2008

Cover Articles

  1. Molecular simulation of hydrogen diffusion in interpenetrated metal-organic frameworks
    B. Liu, Q. Yang, C. Xue, C. Zhong and B. Smit,
    Phys. Chem. Chem. Phys. 10, 3244 - 3249 (2008)
  2. State-of-the-art models for the phase diagram of carbon and diamond nucleation
    L. M. Ghiringhelli, C. Valeriani, J. H. Los, E. J. Meijer, A. Fasolino, D. Frenkel,
    Mol. Phys. 106, 2011 - 2038 (2008)

Articles

  1. Multiple state transition path sampling
    J. Rogal and P.G. Bolhuis,
    J. Chem. Phys. 129, 224107 (2008).
  2. Effect of excluded volume interactions on the interfacial properties of colloid-polymer mixtures
    A. Fortini, P.G Bolhuis, M. Dijkstra,
    J. Chem. Phys. 128, 024904 (2008).
  3. Phase transition to bundles of flexible supra-molecular polymers
    B.A.H. Huisman, P.G Bolhuis, and A. Fasolino,
    Phys. Rev. Lett. 100, 188301 (2008).
  4. Rare events via multiple reaction channels sampled by path replica exchange
    P.G Bolhuis,
    J. Chem. Phys. 129, 114108 (2008).
  5. Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
    J. Juraszek and P.G. Bolhuis,
    Biophys. J. 95, 4246-4257 (2008).
  6. A single histidine residue modulates enzymatic activity in acidic mammalian chitinase
    A.P. Bussink, J. Vreede, J.M. Aerts, R.G. Boot,
    FEBS Lett 582, 931-935 (2008).
  7. TraR auto-inducer enhances protein backbone fluctuations in DNA binding domain
    J. Vreede, K.J. Hellingwerf, W. Crielaard,
    FEBS Lett 582, 805-809 (2008).
  8. Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein
    J. Vreede, K.J. Hellingwerf, P.G. Bolhuis,
    Proteins 72, 136-149 (2008).
  9. Sedimentation of pairs of hydrodynamically interacting semiflexible filaments
    I. Llopis, M. Cosentino Lagomarsino, I. Pagonabarraga and C.P. Lowe,
    Phys. Rev. E 76, 061901 (2008).
  10. Diffusion of alkane mixtures in MFI zeolite
    R. Krishna and J.M. van Baten,
    Microporous Mesoporous Mater. 107, 296-298 (2008).
  11. Insights into diffusion of gases in zeolites gained from molecular dynamics simulations
    R. Krishna and J.M. van Baten,
    Microporous Mesoporous Mater. 109, 91-108 (2008).
  12. Investigation of slowing-down and speeding-up effects in binary mixture permeation across SAPO-34 and MFI membranes
    R. Krishna, S. Li, J.M. van Baten, J.L. Falconer, and R.D. Noble,
    Sep. Purif. Technol. 60, 230-236 (2008).
  13. Separating n-alkane mixtures by exploiting differences in the adsorption capacity within cages of CHA, AFX and ERI zeolites
    R. Krishna, J.M. van Baten,
    Sep. Purif. Technol. 60, 315-320 (2008).
  14. Segregation effects in adsorption of CO2 containing mixtures and their consequences for separation selectivities in cage-type zeolites
    R. Krishna, J.M. van Baten,
    Sep. Purif. Technol. 61, 414-423 (2008).
  15. Onsager coefficients for binary mixture diffusion in nanopores
    R. Krishna, J.M. van Baten,
    Chem. Eng. Sci. 63, 3120-3140 (2008).
  16. Diffusion of hydrocarbon mixtures in MFI zeolite: Influence of intersection blocking
    R. Krishna, J.M. van Baten,
    Chem. Eng. J. 140, 614-620 (2008).
  17. Inflection in the loading dependence of the Maxwell-Stefan diffusivity of iso-butane in MFI zeolite
    C. Chmelik, L. Heinke, J. Kärger, W. Schmidt, D.B. Shah, J.M. van Baten, and R. Krishna,
    Chem. Phys. Lett.459, 141-145 (2008).
  18. 1H NMR signal broadening in spectra of alkane molecules adsorbed on MFI type zeolites
    E.E. Romanova, C.B. Krause, A.G. Stepanov, W. Schmidt, J.M. van Baten, R. Krishna, A. Pampel, J. Kärger, D. Freude,
    Solid State Nucl. Magn. Reson. 33, 65-71 (2008).
  19. Cooperativity and hydrodynamic interactions in externally driven semiflexible filaments
    I. Llopis, M. Cosentino Lagomarsino, I. Pagonabarraga and C.P. Lowe,
    Comp. Phys. Comm. 179, 150-154 (2008).
  20. Efficient constraint dynamics using MILC SHAKE
    A.G. Bailey, C.P. Lowe, and A.P. Sutton,
    J. Comp. Phys. 227, 8949-8959 (2008).
  21. Simplicity and Scaling - size of a polymer in three (or any) dimensions
    C.P. Lowe, and M.W. Dreischor,
    arXiv:0809.3666v1, [cond-mat.soft] (2008).
  22. Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity
    B. Smit, and T.L.M. Maesen,
    Chem. Rev. 108, 4125-4184 (2008).
  23. Enhanced Adsorption Selectivity of Hydrogen/Methane Mixtures in Metal-Organic Frameworks with Interpenetration: A Molecular Simulation Study
    B. Liu, Q. Yang, C. Xue, C. Zhong, B. Chen, and B. Smit,
    J. Phys. Chem. C 112, 9854-9860 (2008).
  24. Molecular Simulations of Lipid-Mediated Protein-Protein Interactions
    F.J-M. de Meyer, M. Ventuoli, and B. Smit,
    Biophys. J. 95, 1851-1865 (2008).
  25. Microscopic picture of the aqueous solvation of glutamic acid
    E.J.M. Leenders, P.G. Bolhuis, and E.J. Meijer,
    J. Chem. Theory Comput. 4, 898-907 (2008).
  26. Towards a molecular understanding of shape selectivity
    B. Smit and T. L. M. Maesen,
    Nature 451, 671 (2008).
  27. A New United Atom Force Field for Adsorption of Alkenes in Zeolites
    B. Liu, B. Smit, F. Rey, S. Valencia, and S. Calero,
    J. Phys. Chem. C. 112, 2492 (2008)
  28. Shape selective n-alkane hydroconversion at exterior zeolite surfaces
    Theo Maesen, Rajamani Krishna, Jasper M Van Baten, Berend Smit, Sofia Calero, and J. M. Castillo-Sanchez,
    J. Cat. 256, 95 (2008)
  29. Accurate method for including solid-fluid boundary interactions in mesoscopic model fluids
    A. Berkenbos and C.P. Lowe,
    J. Comp. Phys. 227, 4589-4599 (2008)

Theses

  • Molecular simulation studies of adsorption and diffusion. Phenomena of gases in porous materials
    Bei Liu , Ph.D. thesis, University of Amsterdam, 2008.
  • Dynamical and structural self-organization;A study of friction, liquid-crystal nucleau growth, and supramolecular polymers through simple models
    Bastiaan Huisman, Ph.D. thesis, University of Amsterdam, 2008.
  • Proton transfer in the photocycle of the photoactive yellow protein
    Elske J.M. Leenders, Ph.D. thesis, University of Amsterdam, 2008.
  • Dynamics of Polymers by Novel Mesoscopic Methods
    Arjen Berkenbos, Ph.D. thesis, University of Amsterdam, 2008.
  • Flow and flexibility; applications in biophysics
    R. Argentini, Ph.D. thesis, University of Amsterdam, 2008.
  • Proteins in Action; Simulations of Conformational changes in small proteins
    J. Juraszek, Ph.D. thesis, University of Amsterdam, 2008.

2007

Cover Article

  1. Local structure of liquid carbon controls diamond nucleation
    L.M. Ghiringhelli, C. Valeriani, E.J. Meijer, and D. Frenkel, Phys. Rev. Lett. 99, 055702 (2007). [pdf-file (internal only)]

Articles

  1. In-depth study of the influence of host-framework flexibility on the diffusion of small gas molecules in one-dimensional zeolitic pore systems
    N.E.R Zimmermann, S. Jakobtorweihen, E. Beerdsen, B. Smit, and F. J. Keil J. Phys. Chem. C 111 17370 (2007)
  2. Mesoscopic simulations of accelerated polymer drift in microfluidic capillaries
    A. Berkenbos and C. P. Lowe, J. Chem. Phys. 127 164902 (2007) [pdf-file (internal only)]
  3. Understanding diffusion in nanoporous materials
    E. Beerdsen and B. Smit, Stud. Surf. Scien. Catal. 170 1646 (2007)
  4. Molecular simulations of the adsorption and diffusion of hydrocarbons in molecular sieves
    B. Smit, Stud. Surf. Scien. Catal. 170 121 (2007)
  5. Sampling the kinetic pathways of a micelle fusion and fission transition
    R. Pool and P.G. Bolhuis, J. Chem. Phys. 126, 244703 (2007)
  6. Simulating the phosphorus fluid-liquid phase transition transition up to the critical point
    L.M. Ghiringhelli and E. J. Meijer J. Phys.: Condens. Matter 19 416104 (2007) [pdf-file (internal only)]
  7. Solvation of p-Coumaric Acid in water
    Elske J. M. Leenders, Joost VandeVondele, Peter G. Bolhuis, and Evert Jan Meijer, J. Phys. Chem. B, 111 13591-13599 (2007) [pdf-file (internal only)]
  8. Hydrodynamic flow caused by active transport along cytoskeletal elements
    D. Houtman, I. Pagonabarraga, C. P. Lowe, A. Esseling-Ozdoba, A. M. C. Emons and E. Eiser, EPL 78, 18001 (2007) [pdf-file (internal only)]
  9. Diffusion of chain molecules and mixtures in carbon nanotubes: The effect of host lattice flexibility and theory of diffusion in the Knudsen regime
    S. Jakobtorweihen, C. P. Lowe, F. J. Keil, B. Smit, J. Chem. Phys. 127, 024904 (2007) [pdf-file (internal only)]
  10. Understanding Aluminum Location and Non-framework Ions Effects on Alkane Adsorption in Aluminosilicates: A Molecular Simulation Study
    Bei Liu, Elena García-Pérez, David Dubbeldam, Berend Smit, and Sofia Calero, J. Phys. Chem. C. 111, 10419-10426 (2007) [pdf-file (internal only)]
  11. Influence of latent heat and thermal diffusion on the growth of nematic liquid crystal nuclei
    B.A.H. Huisman and A. Fasolino, Phys. Rev. E. 76, 021706(2007) [pdf-file (internal only)]
  12. Protonation of the Chromophore in the Photoactive Yellow Protein
    Elske J. M. Leenders, Leonardo Guidoni, Ursula Röthlisberger, Jocelyne Vreede, Peter G. Bolhuis, and Evert Jan Meijer, J. Phys. Chem. B, 111 (14), 3765 -3773, 2007 [pdf-file (internal only)]
  13. A computational method to characterize framework aluminum in aluminosilicates
    E. García-Pérez, D. Dubbeldam, B. Liu, B. Smit, and S. Calero, Angew. Chem.-Int. Edit. 46 (1-2), 276 (2007). [pdf-file (internal only)]
  14. Realistic Modeling of Ruthenium-Catalyzed Transfer Hydrogenation
    Jan-Willem Handgraaf and Evert Jan Meijer, J. Am. Chem. Soc. 129, 3099-3103 (2007)
  15. Interpreting unary, binary and ternary mixture permeation across a SAPO-34 membrane with loading-dependent Maxwell-Stefan diffusivities
    S. Li, J.L. Falconer, R.D. Noble, and R. Krishna, J.Phys.Chem. C111, 5075-5082 (2007)
  16. Modeling Transient Permeation of Polar Organic Mixtures through a MFI Zeolite Membrane using the Maxwell-Stefan Equations
    Yu, M., J.L. Falconer, R.D. Noble, and R. Krishna, Journal of Membrane Science 293, 167-173 (2007)
  17. Screening of zeolite adsorbents for separation of hexane isomers: A molecular simulation study
    R. Krishna and J.M. van Baten, Separation and Purification Technology, 55, 246-255 (2007)
  18. Incorporating the loading dependence of the Maxwell-Stefan diffusivity in the modeling of CH4 and CO2 permeation across zeolite membranes
    R. Krishna, J.M. van Baten, E. García-Pérez, and S. Calero, Ind.Eng.Chem. Research, 46, 2974 -2986 (2007)
  19. Modeling permeation of CO2/CH4, CO2/N2, and N2/CH4 mixtures across SAPO-34 membrane with the Maxwell-Stefan equations
    S. Li, J.L. Falconer, R.D. Noble, and R. Krishna, Ind.Eng.Chem. Research, 46, 3904-3911 (2007)
  20. Using molecular simulations for screening of zeolites for separation of CO2/CH4 mixtures
    R. Krishna and J.M. van Baten, Chemical Engineering Journal, 133, 121-131 (2007)
  21. Levitation of air bubbles in liquid under low frequency vibration excitement
    J. Ellenberger and R. Krishna, Chemical Engineering Science, 62, 5669 - 5673 (2007)
  22. Loading dependence of self-diffusivities of gases in zeolites
    R. Krishna and J.M. van Baten, Chemical Engineering & Technology, 30, 1235 - 1241 (2007)
  23. Mixture diffusion in zeolites studied by MAS PFG NMR and molecular simulation
    M. Fernandez, J. Kärger, D. Freude, A. Pampel, J.M. van Baten and R. Krishna, Microporous and Mesoporous Materials, 105, 124-131 (2007)
  24. Influence of segregated adsorption on mixture diffusion in DDR zeolite
    R. Krishna and J.M. van Baten, Chemical Physics Letters, 446, 344 - 349 (2007)
  25. Levitation of air bubbles and slugs in liquids under low frequency vibration excitement
    J. Ellenberger and R. Krishna, Chemical Engineering Science, 62, 7548 - 7553 (2007)
  26. A computational study of CO2, N2 and CH4 adsorption in zeolites
    E. García-Pérez, J.B. Parra, C.O. Ania, A. Garcia-Sanchez, J.M. Van Baten, R. Krishna, D. Dubbeldam, S. Calero, Adsorption 13, 469-476 (2007)
  27. A Simulation Study of Alkanes in Linde Type A Zeolites
    A.Garcia-Sanchez, E. García-Pérez, D. Dubbeldam, R. Krishna and S. Calero, Adsorption Science and Technology 25, 419-427 (2007)
  28. Theoretical calculation of diffusivity in binary liquid mixtures
    Yan, J.M., Lee, S.L., Krishna, R., Journal Of Chemical Engineering Of Chinese Universities, 21(6), 919-923 (2007)
  29. Sedimentation of pairs of hydrodynamically interacting semi flexible filament
    I. Lopis, I. Pagonabarraga, M. Cosentino Lagomarsino and C.P. Lowe, Phys. Rev. E76, 061901 (2007)

2006

Cover



Articles

  1. Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations
    E.A. Koopman and C.P. Lowe J. Chem. Phys. 124, 204103 (2006)
  2. Ab-initio and experimental 1H NMR signatures of solvated ions: the case of HCl(aq)
    Tatiana Murakhtina, Jasper Heuft, Evert Jan Meijer, and Daniel Sebastiani, Chem. Phys. Chem. 7, 2578--2584 (2006). [pdf-file (internal only)]
  3. Erratum: Improved long range reactive bond order potential for carbon (LCBOPII). Part I: Construction.
    J.H. Los, L.M. Ghiringhelli, E.J. Meijer, A. Fasolino, Phys. Rev. B 73, 229901 (2006). [pdf-file (internal only)]
  4. Logarithmic relaxation due to minimization of interactions in the Burridge-Knopoff model
    B.A.H. Huisman and A. Fasolino, Phys. Rev. E. 74, 026110 (2006) [pdf-file (internal only)]
  5. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
    Juraszek, J.; Bolhuis, P. G., PNAS (2006), 103(43), 15859-15864
  6. Prediction of an Autocatalytic Replication Mechanism for Micelle Formation
    Pool, Rene; Bolhuis, Peter G., Physical Review Letters (2006), 97(1), 018302/1-018302/4
  7. Transition Path Sampling Methods
    C. Dellago P.G. Bolhuis, and P. Geissler, in Computer Simulation in Condensed Mater: from Materials to Chemical Biology, Lect. Notes Phys. 703, 349-391 (2006)
  8. Transition Path Sampling Simulations of Biological Systems
    Christoph Dellago and Peter G. Bolhuis, in Atomistic Approaches in Modern Biology: From Quantum Chemistry to Molecular Simulations, Topics in Current Chemistry, Volume 268, Pages 291-317
  9. Sampling Kinetic Protein Folding Pathways using All-Atom Models
    P.G. Bolhuis:,in Computer Simulation in Condensed Mater: from Materials to Chemical Biology Lect. Notes Phys. 703, 39433 (2006)
  10. Mesoscopic models of biological membranes
    Smit, B.; Kranenburg, M.; Sperotto, M. M.; Venturoli, M., Lect. Notes Phys 2006, 704, 259-286 [pdf-file (internal only)]
  11. MD simulations of diffusivities in methanol/n-hexane mixtures near the liquid-liquid phase splitting region
    R. Krishna and J.M. van Baten Chemical Engineering & Technology, 29, 516 - 519 (2006)
  12. Influence of isotherm inflection on the loading dependence of the diffusivities of n-hexane and n-heptane in MFI zeolite.
    Quasi-Elastic Neutron Scattering experiments supplemented by molecular simulations
    H. Jobic, N. Laloué, C. Laroche, J.M. van Baten and R. Krishna, J. Phys. Chem. B; 2006; 110 pp 2195 - 2201
  13. Linking the loading dependence of the Maxwell-Stefan diffusivity of linear alkanes in zeolites with the thermodynamic correction factor
    R. Krishna and J.M. van Baten, Chemical Physics Letters, 420, 545 - 549 (2006)
  14. Describing binary mixture diffusion in carbon nanotubes with the Maxwell-Stefan equations. An investigation using molecular dynamics simulations
    R. Krishna and J.M. van Baten, Ind.Eng.Chem. Research, 45, 2084-2093 (2006)
  15. Validating the Darken relation for diffusivities in fluid mixtures of varying densities by use of MD simulations
    R. Krishna and J.M. van Baten, Chemical Engineering & Technology, 29, 761 - 765 (2006)
  16. Vibration-induced granular segregation in a pseudo-2D column: The (reverse) Brazil-nut effect
    J. Ellenberger, C.O. Vandu and R. Krishna, Powder Technology, 164, 198- 173 (2006)
  17. Scale up of slurry bubble reactors, Oil & Gas Science and Technology
    A. Forret, J-M. Schweitzer, T. Gauthier, R. Krishna and D. Schweich, Revue de L'Institut Francais du Petrole, 61, 443 - 458 (2006)
  18. Diffusion of CH4 and CO2 in MFI, CHA and DDR zeolites
    R. Krishna, J.M. van Baten, E. García-Pérez, and S. Calero, Chemical Physics Letters, 429, 219 - 224 (2006)
  19. Reply to Letter to Editor
    R. Taylor, R. Baur and R. Krishna, A.I.Ch.E.J., 52, 1969- 1970 (2006)
  20. A Molecular Dynamics investigation of diffusion of methane-ethane and methane-propane mixtures in zeolites
    R. Krishna and J.M. van Baten, Chemical Engineering & Technology, 29, 1429 - 1437 (2006)
  21. Loading Dependence of the Diffusion Coefficient of Methane in Nanoporous Materials
    E. Beerdsen, D. Dubbeldam, and B. Smit J. Phys. Chem. B; 2006; 110(45) pp 22754 - 22772 [pdf-file (internal only)]
  22. Mesoscopic models of biological membranes
    Maddalena Venturoli, Maria Maddalena Sperotto, Marieke Kranenburg, Berend Smit, Physics Reports, 437, pp 1 - 54 (2006) [pdf-file (internal only)]
  23. Evaluation of a New Force Field for Describing the Adsorption Behavior of Alkanes in Various Pure Silica Zeolites
    Bei Liu, Berend Smit, and Sofia Calero, J. Phys. Chem. B, 110, pp 20166 - 20171 (2006) [pdf-file (internal only)]
  24. Diffusion in Confinement - Agreement Between Experiments Better than Expected
    Beerdsen, E.; Smit, B., J. Phys. Chem. B, 110, 14529 (2006) [pdf-file (internal only)]
  25. Temperature and Size Effects on Diffusion in Carbon Nanotubes
    Jakobtorweihen, S.; Keil, F. J.; Smit, B., J. Phys. Chem. B, 110, 16332 (2006) [pdf-file (internal only)]
  26. A density functional theory based study of the microscopic structure and dynamics of aqueous HCl solutions
    J. M. Heuft and E. J. Meijer, Phys. Chem. Chem. Phys. 8, 3116-3123 (2006) [pdf-file (internal only)]
  27. Molecular order and disorder of surfactants in clay nanocomposites
    Tim J. Tambach, Edo S. Boek and Berend Smit, Phys. Chem. Chem. Phys. 8, 2700-2702 (2006) [pdf-file (internal only)]
  28. A novel algorithm to model the influence of host lattice flexibility in molecular dynamics simulations: Loading dependence of self-diffusion in carbon nanotubes
    S. Jakobtorweihen, C.P. Lowe, F. J. Keil, B. Smit, J. Chem. Phys. 124, 154706 (2006) [pdf-file (internal only)]
  29. Molecular simulation of adsorption of alkanes in sodium MOR-type zeolites using a new force field
    Bei Liu and Berend Smit Phys. Chem. Chem Phys; 2006; 8 pp 1852-1857 [pdf-file (internal only)]
  30. A Coarse-Graining Approach for the Proton Complex in Protonated Aluminosilicates
    S. Calero, M. D. Lobato, E. García-Pérez, J. A. Mejías, S. Lago, T. J. H. Vlugt, T. L. M. Maesen, B. Smit, and D. Dubbeldam, J. Phys. Chem. B; 2006; 110(12) pp 5838 - 5841 [pdf-file (internal only)]
  31. Density Functional Theory Study of Tetrathiafulvalene and Thianthrene in Acetonitrile: Structure, Dynamics, and Redox Properties
    Joost VandeVondele, Ruth Lynden-Bell, Evert Jan Meijer, and Michiel Sprik, J. Phys. Chem. B 110, 3614 (2006) [pdf-file (internal only)]
  32. Dynamically Corrected Transition State Theory Calculations of Self-Diffusion in Anisotropic Nanoporous Materials
    D. Dubbeldam, E. Beerdsen, S. Calero, and B. Smit, J. Phys. Chem. B; 2006; 110(7) pp 3164 - 3172 [pdf-file (internal only)]
  33. Understanding cage effects in the n-alkane conversion on zeolites
    Theo L.M. Maesen, Edith Beerdsen, Sofia Calero, David Dubbeldam and Berend Smit, Journal of Catalysis Volume 237, Issue 2 , 25 January 2006, Pages 278-290 [pdf-file (internal only)]
  34. Understanding Diffusion in Nanoporous Materials
    E. Beerdsen, D. Dubbeldam, and B. Smit, Phys. Rev. Lettr. 96, 044501 (2006) [pdf-file (internal only)]
  35. Hysteresis in Clay Swelling Induced by Hydrogen Bonding: Accurate Prediction of Swelling States
    Tim J. Tambach, Peter G. Bolhuis, Emiel J. M. Hensen, and Berend Smit, Langmuir, 22 (3), 1223 -1234, (2006) [pdf-file (internal only)]

Theses

  • An ab initio study of ion solvation in water
    J.M. Heuft , Ph.D. thesis, University of Amsterdam, 2006.
    Thesis.pdf (4 MB)

  • Coarse grained soap A molecular simulation study on Micelle formation in dilute surfactant solutions
    R. Pool, Ph.D. thesis, University of Amsterdam, 2006.
    [pdf-file (internal only)]

2005

Articles



  1. Predicting the signalling state of Photoactive Yellow Protein
    J. Vreede, W. Crielaard, K.J. Hellingwerf, and P.G. Bolhuis, Biophys. J. 88,3525-3535 (2005) [pdf-file (internal only)]
  2. Simultanous computation of free energy and kinetics of rare events
    D. Moroni, T.S. van Erp and P.G. Bolhuis, Phys. Rev. E 71, 056709 (2005) [pdf-file (internal only)]
  3. The interplay between size and structure in the critical nucleus
    D. Moroni, P.R. ten Wolde and P.G. Bolhuis, Phys. Rev. Lett, 94, 235703(2005) [pdf-file (internal only)]
  4. Combined length scales in dissipative particle dynamics
    J. A. Backer, C. P. Lowe, H. C. J. Hoefsloot, and P. D. Iedema, J. Chem. Phys. 123, 114905 (2005). [pdf-file (internal only)]
  5. Hydrodynamic induced deformation and orientation of a microscopic elastic filament
    M. Cosentino Lagomarsino, I. Pagonabarraga and C.P. Lowe, Phys. Rev. Lett. 94, 148104 (2005) [pdf-file (internal only)]
  6. Poiseuille flow to measure the viscosity of particle model fluids
    J.A. Backer, C.P. Lowe, H.C.J. Hoefsloot and P.D. Iedema, J. Chem. Phys. 122, 154503 (2005). [pdf-file (internal only)]
  7. The size of a polymer in a symmetric solvent
    C.P. Lowe and M. W. Dreischor, J. Chem. Phys. 122, 084905 (2005). [pdf-file (internal only)]
  8. Transition to strictly solitary motion in the Burridge-Knopoff model of multicontact friction
    B.A.H. Huisman and A. Fasolino, Phys. Rev. E. 72, 016107 (2005) [pdf-file (internal only)]
  9. Molecular Understanding of Diffusion in Confinement
    E. Beerdsen, D. Dubbeldam, and B. Smit, PRL 95, 164505 (2005) [pdf-file (internal only)]
  10. Elucidating alkane adsorption in sodium-exchanged zeolites from molecular simulations to empirical equations
    E. García-Pérez, I.M. Torréns, S. Lago, D. Dubbeldam, T.J.H. Vlugt, T.L.M. Maesen, B. Smit, R. Krishna, S. Calero, Applied Surface Science, 252, 716-722 (2005) [pdf-file (internal only)]
  11. A Molecular Dynamics Study of an Archaeal Tetraether Lipid Membrane: Comparison with a Dipalmitoylphosphatidylcholine Lipid Bilayer
    J.P. Niclolas, Lipids, 40, 1023-1030 (2005) [pdf-file (internal only)]
  12. Improved long range reactive bond order potential for carbon (LCBOPII). Part I: Construction.
    J.H. Los, L.M. Ghiringhelli, E.J. Meijer, A. Fasolino, Phys. Rev. B 72, 214102 (2005) [pdf-file (internal only)]
  13. Improved long range reactive bond order potential for carbon (LCBOPII). Part II: Molecular simulation of liquid carbon.
    Luca M. Ghiringhelli, Jan H. Los, A. Fasolino, and Evert Jan Meijer, Phys. Rev. B 72, 214103 (2005) [pdf-file (internal only)]
  14. Liquid Carbon: Structure near the Freezing Line,
    L.M. Ghiringhelli, J.H. Los, E.J. Meijer, A. Fasolino, and D. Frenkel, J. Phys.: Condens. Matter 17 S3619-S3624 [pdf-file (internal only)]
  15. Density functional theory based molecular dynamics study of aqueous iodide solvation,
    J.M. Heuft and E.J. Meijer, J. Chem. Phys. 123, 094506 (2005) [pdf-file (internal only)]
  16. Molecular path control in zeolite membranes
    D. Dubbeldam, E. Beerdsen, S. Calero and B. Smit, Proc. Natl. Acad. Sci. USA, 102, 35, 12317-12320 (2005) [pdf-file (internal only)]
  17. Understanding the Loading Dependence of Self-Diffsion in Carbon nanotubes
    S Jakobtorweihen, M. G. Verbeek, C. P. Lowe, F. J. Keil and B. Smit, Phys Rev. Letters, 95, 044501, (2005) [pdf-file (internal only)]
  18. Adsorption and separation of linear and branched alkanes on carbon nanotube bundles from configurational-bias Monte Carlo simulation.
    J. Jiang, S.I. Sandler, M. Schenk, and B. Smit, Phys. Rev. B 72, 045447, (2005) [pdf-file (internal only)]
  19. Molecular simulation of loading-dependent diffusion in nanoporous materials using extended dynamically corrected transition state theory
    D. Dubbeldam and E. Beerdsen T. J. H. Vlugt, B. Smit, J. Chem. Phys., 2005 122, 224712 [pdf-file (internal only)]
  20. Molecular simulations of the adsorption of cycloalkanes in MFI-type silica
    M. Schenk, B. Smit, T.L.M. Maesen, and T.J.H. Vlugt, Phys. Chem. Chem. Phys., 2005, 7, 2622 - 2628 [pdf-file (internal only)]
  21. Two-Step Catalytic Oxidative Dehydrogenation of Propane: An Alternative Route to Propene,
    E. A. de Graaf, G. Zwanenburg, G. Rothenberg, and A. Bliek, Org. Process Res. Dev.; 2005; ASAP Web Release Date: 20-May-2005. [pdf-file (internal only)]
  22. Continuous Chirality Measure in Reaction Pathways of Ruthenium-Catalyzed Transfer Hydrogenation of Ketones,
    Jan-Willem Handgraaf, Joost N. H. Reek, Luca Bellarosa, Francesco Zerbetto, Advanced Synthesis and Catalysis 347, 792-802 (2005). [pdf-file (internal only)]
  23. Phosphorus: First principle simulation of a liquid-liquid phase transition ,
    Luca M. Ghiringhelli and Evert Jan Meijer, J. Chem. Phys. 122, 184510 (2005).
  24. Accurate Free Energies of Micelle Formation
    Rene Pool and Peter G. Bolhuis, J. Phys. Chem. B, 109 (14), 6650 -6657, (2005) [pdf-file (internal only)]
  25. Phase Behavior of Model Lipid Bilayers
    Marieke Kranenburg and Berend Smit, J. Phys. Chem. B, 109 (14),pp 6553 - 6563, (2005) [pdf-file (internal only)]
  26. Kinetic Pathways of β-Hairpin (Un)folding in Explicit Solvent
    Peter G. Bolhuis, Biophysical Journal 88:50-61 (2005) [pdf-file (internal only)]
  27. Elaborating transition interface sampling methods
    Titus S. van Erp and Peter G. Bolhuis, Journal of Computational Physics, 205(1), pp 157-181, (2005) [pdf-file (internal only)]
  28. Modeling the Phase Diagram of Carbon
    Luca M. Ghiringhelli, Jan H. Los, Evert Jan Meijer, A. Fasolino, and Daan Frenkel, Phys. Rev. Lett. 94, 145701 (2005).
    Note: paper appeared as research highlight in Nature 434, 1084 (2005).
  29. Simulation Studies of Protein-Induced Bilayer Deformations, and Lipid-Induced Protein Tilting, on a Mesoscopic Model for Lipid Bilayers with Embedded Proteins
    Maddalena Venturoli, Berend Smit, and Maria Maddalena Sperotto, Biophys. J. 88: 1778-1798 (2005). [pdf-file (internal only)]
  30. Density functional theory based molecular-dynamics study of aqueous fluoride solvation
    J.M. Heuft and E.J. Meijer, J. Chem. Phys. 122, 094501 (2005). [pdf-file (internal only)]

Theses

  • On the nature of phase transitions in covalent liquids
    L.M Ghiringhelli, Ph.D. thesis, University of Amsterdam, 2005.
    Thesis.pdf (3 MB)

  • Computer-simulation of adsorption and diffusion of hydrocarbons in zeolites
    D. Dubbeldam, Ph.D. thesis, University of Amsterdam, 2005.
    Thesis.pdf (13MB(!))
  • Efficient sampling of rare event pathways
    D. Moroni, Ph.D. thesis, University of Amsterdam, 2005.
    Thesis.pdf (6.2MB)

  • Swelling of clay minerals
    T. Tambach, Ph.D. thesis, University of Amsterdam, 2005.
    [pdf-file (internal only)]

2004

Articles

Theses

  • Phase transitions of lipid bilayers, a mesoscopic approach
    M. Kranenburg, Ph.D. thesis, University of Amsterdam, 2004.
    Thesis.pdf (4MB), if you are interested in a (paper) copy, please send an email to the secretary of HIMS.
  • Mesoscopic models of lipid bilayers and bilayers with embedded proteins
    M. Venturoli, Ph.D. thesis, University of Amsterdam, 2004.
    Thesis.pdf (4.6MB)

2003

Articles

Theses

  • A molecular dynamics study of interfaces: from pure liquids to biological membranes.
    J-P Nicolas, Ph.D. thesis, University of Amsterdam, 2003.
    Thesis.pdf (2.1MB),
  • Solvent Effects on Chemistry with Alcohols. An Ab Initio Study.
    T.S. van Erp, Ph.D. thesis, University of Amsterdam, 2003.
    Thesis.pdf (3.9MB), requires Adobe Acrobat Reader 4.05 or better.
    If you are interested in a (paper) copy, please send an email to the secretary of HIMS.
  • Homogeneous Catalyzed Hydrogenation. First-Principles Computational Studies in the Gas Phase and in Solution
    J.-W. Handgraaf, Ph.D. thesis, University of Amsterdam, 2003.
    Thesis.pdf (4.6MB), requires Adobe Acrobat Reader 4.05 or better.
    If you are interested in a (paper) copy, please send an email to the secretary of HIMS.
  • Shape selectivity in zeolites.
    M. Schenk, Ph.D. thesis, University of Amsterdam, 2003.
    Thesis.pdf (2.2MB), if you are interested in a (paper) copy, please send an email to the secretary of HIMS.

2002

Articles

2001

Articles

2000

Articles

Thesis

1999

Articles

1998

Articles

1997

Articles

1996

Articles

1995

Articles

  • Computer simulations of vapour-liquid phase equilibria of n-alkanes, , [pdf-file (internal only)]
    B. Smit, S. Karaborni, and J.I. Siepmann, J. Chem. Phys. 102:2126 (1995).
  • Molecular simulations of the vapour-liquid coexistence curve of methanol,
    M.E. van Leeuwen and B. Smit, J. Phys. Chem. 99:1831 (1995).
  • Commensurate ``freezing'' of alkanes in the channels of a zeolite,
    B. Smit and T.L.M. Maesen, Nature 374:42 (1995).
  • Parallel Monte Carlo simulations, [pdf-file (internal only)]
    K. Esselink, L.D.J.C. Loyens, and B. Smit, Phys. Rev. E 51:1560 (1995).
  • Simulating the adsorption isotherms of methane, ethane, and propane in the zeolite silicalite,
    B. Smit, J. Phys. Chem. 99:5597 (1995).
  • Simulating complex fluids,
    K. Esselink, S. Hilbers, P.A.J. Karaborni, J.I. Siepmann, and B. Smit, Mol. Sim. 14:259 (1995).
  • Grand-canonical Monte Carlo simulations of chain molecules: Adsorption isotherms of alkanes in zeolites,
    B. Smit, Mol. Phys. 85:153 (1995).
  • The condition of microscopic reversibility in the Gibbs-ensemble Monte Carlo simulations of phase equilibria,
    L.F. Rull, G. Jackson, and B. Smit, Mol. Phys. 85:435 (1995).
  • Parallel Gibbs-ensemble simulations,
    L.D.J.C. Loyens, B. Smit, and K. Esselink, Mol. Phys. 86:171 (1995).
  • Commensurate freezing of n-alkanes in silicalite,
    W.J.M. van Well, J.P. Wolthuizen, B. Smit, J.H.C. van Hooff, and R.A. van Santen, Angew. Chem. (Int. Ed.) 34:2543 (1995).
  • Kommensurate Einfrieren von n-Alkanen im Silicalit,
    W.J.M. van Well, J.P. Wolthuizen, B. Smit, J.H.C. van Hooff, and R.A. van Santen, Angew. Chem. 107:2765 (1995).
  • Molecular simulations of thermodynamic properties: from argon to long-chain paraffins,
    B. Smit, Ind. Eng. Chem. Res. 34:4166 (1995).

1994

Articles

  • Models of micelle formation,
    N.M. van Os, B. Smit, and S. Karaborni, Recl. Trav. Chim. Pays-Bas 113:181 (1994).
  • Free energies and phase equilibria of chain molecules,
    B. Smit, S. Karaborni, and J.I. Siepmann, Macromol. Symp. 81:343 (1994).
  • Simulating the adsorption of alkanes in zeolites , [pdf-file (internal only)]
    B. Smit and J.I. Siepmann, Science 264:1118 (1994).
  • Simulating surfactant self-assembly , [pdf-file (internal only)]
    S. Karaborni, K. Esselink, P.A.J. Hilbers, and B. Smit, J. Phys.: Condens. Matter 6:A351 (1994).
  • Computer simulations of the energetics and siting of n-alkanes in zeolites,
    B. Smit and J.I. Siepmann, J. Phys. Chem. 98:8442 (1994).
  • Simulating the self-assembly of gemini surfactants, [pdf-file (internal only)]
    S. Karaborni, K. Esselink, P.A.J. Hilbers, B. Smit, J. Karthauser, N.M. van Os, and R. Zana, Science 266:254 (1994).
  • Molecular dynamics simulations of model oil/water/surfactant systems,
    K. Esselink, P.A.J. Hilbers, N.M. van Os, B. Smit, and S. Karaborni, Coll. and Surfaces A 91:155 (1994).

1993

Articles

  • Computer simulations of surfactant self-assembly,
    B. Smit, K. Esselink, P.A.J. Hilbers, N.M. van Os, and I. Szleifer, Langmuir 9:9 (1993).
  • Efficient parallel implementation of molecular dynamics on a toroidal network: Part I Parallelizing Strategy, [pdf-file (internal only)]
    K. Esselink, B. Smit, and P.A.J. Hilbers, J. Comp. Phys. 106:101 (1993).
  • Computer simulations of surfactants,
    B. Smit in Computer simulation in Chemical Physics, NATO ASI, edited by M.P. Allen and D.J. Tildesley (Kluwer, Dordrecht, 1993), pp. 173-209.
  • Computer simulations in the Gibbs ensemble
    B. Smit in Computer simulation in Chemical Physics, NATO ASI ,edited by M.P. Allen and D.J. Tildesley (Kluwer, Dordrecht, 1993), pp. 461-472.
  • Vapour-liquid equilibria of Stockmayer fluids: computer simulations and perturbation theory,
    M.E. van Leeuwen, B. Smit, and E.M. Hendriks, Mol. Phys. 78:271 (1993).
  • Computer simulations of surfactant self assembly,
    B. Smit, P.A.J. Hilbers, and K. Esselink, Int. J. of Mod. Phys C 4:393 (1993).
  • Vapor-liquid equilibria of model alkanes,
    J.I. Siepmann, S. Karaborni, and B. Smit, J. Am. Chem. Soc. 115:6454 (1993).
  • Computer simulations of simple oil/water/surfactant systems,
    B. Smit, P.A.J. Hilbers, and K. Esselink, Tenside Surf. Det. 30:287 (1993).
  • Simulating the critical properties of complex fluids,
    J.I. Siepmann, S. Karaborni, and B. Smit, Nature 365:330 (1993).
  • Surfactant adsorption at liquid/liquid interfaces: comparison of experimental results with SCF calculations and molecular dynamics simulations,
    N.M. van Os, L.A.M. Rupert, B. Smit, P.A.J. Hilbers, K. Esselink, M.R. Bohmer, and L.K. Koopal, Collloids and Surfaces A 81:217 (1993).
  • What makes a polar fluid a liquid ?, [pdf-file (internal only)]
    M.E. van Leeuwen and B. Smit, Phys. Rev. Lett. 71:3991 (1993).

1992

Articles

  • Unexpected length dependence of the solubility of chain molecules,
    D. Frenkel and B. Smit, Mol. Phys. 75:983 (1992).
  • Novel scheme to study structural and thermal properties of continuously deformable molecules, [pdf-file (internal only)]
    D. Frenkel, G.C.A.M. Mooij, and B. Smit, J. Phys.: Condens. Matter 4:3053 (1992).
  • Direct simulation of phase equilibria of chain molecules, [pdf-file (internal only)]
    G.C.A.M. Mooij, D. Frenkel, and B. Smit, J. Phys.: Condens. Matter 4:L255 (1992).
  • Phase diagrams of Lennard-Jones fluids, [pdf-file (internal only)]
    B. Smit, J. Chem. Phys. 96:8639 (1992).
  • Computer simulations of surfactants at a liquid/liquid interface,
    B. Smit, P.A.J. Hilbers, and K. Esselink in Structure and Dynamics of Strongly Interacting Colloids and Supramolecular Aggregates in Solution, Proc. NATO ASI ,edited by S-H Chen, J.S. Huang, and P. Tartaglia (Kluwer, Amsterdam, 1992).
  • Electrostatic analogy for surfactant assemblies,
    D. Wu, D. Chandler, and B. Smit, J. Phys. Chem. 96:4077 (1992).
  • Comment on ``Determination of the chemical potential of polymeric systems from Monte Carlo simulations'',
    B. Smit, G.C.A.M. Mooij, and D. Frenkel, Phys. Rev. Lett. 68:3657 (1992).
  • A simple theory of weakly inhomogeneous fluids,
    A.G. Schlijper and B. Smit, Fluid Phase Equilibria 76:11 (1992).
  • Molecular dynamics studies of polar/nonpolar fluid mixtures. II. Mixtures of Stockmayer and polarizable Lennard-Jones fluids, [pdf-file (internal only)]
    G.C.A.M. Mooij, S.W. de Leeuw, B. Smit, and C.P. Williams, J. Chem. Phys. 97:5113 (1992).
  • Effect of a density-dependent potential on the phase behavior of fluids,
    B. Smit, T. Hauschild, and J.M. Prausnitz, Mol. Phys. 77:1021 (1992).
  • Surfactants can be modelled: dynamical processes in micelles reproduced,
    B. Smit, Europhys. News 23:177 (1992).

1991

Articles

  • Introduction to zeolite theory and modelling, R.A. van Santen, D.P. de Bruyn, C.J.J. den Ouden, and B. Smit, in Introduction to Zeolite Science and Practice, Studies in Surface Science and Catalysis, edited by H. van Bekkum, E.M. Flaningen, and J.C. Jansen (Elsevier, Amsterdam, 1991).
  • The mobility of adsorbed species in zeolites: Methane, ethane and propane diffusivities,
    A.K. Nowak, C.J.J. den Ouden, S.D. Pickett, B. Smit, A.K. Cheetham, M.F.M. Post, and J.M. Thomas, J. Phys. Chem. 95:848 (1991).
  • Vapour-liquid equilibria of the two dimensional Lennard-Jones fluid(s), [pdf-file (internal only)]
    B. Smit and D. Frenkel, J. Chem. Phys. 94:5663 (1991).
  • Structure of a water/oil interface in the presence of micelles: a computer simulation study,
    B. Smit, P.A.J. Hilbers, K. Esselink, L.A.M. Rupert, N.M. van Os, and A.G. Schlijper, J. Phys. Chem. 95:6361 (1991).
  • Vapour-liquid equilibria of the hard-core Yukawa fluid,
    B. Smit and D. Frenkel, Mol. Phys. 74:35 (1991).

1990

Articles

  • A new local states method for the calculation of free energies in Monte Carlo simulations of lattice models,
    A.G. Schlijper, A.R.D. van Bergen, and B. Smit, Phys. Rev. A 41:1175 (1990).
  • The mobility of adsorbed species in zeolites: A molecular dynamics simulation of xenon in silicalite,
    S.D. Pickett, A.K. Nowak, J.M. Thomas, B.K. Peterson, J.F. Swift, A.K. Cheetham, C.J.J. den Ouden, B. Smit, and M. Post, J. Phys. Chem. 94:1233 (1990).
  • Vapour-liquid equilibria for quadrupolar Lennard-Jones fluids,
    B. Smit and C.P. Williams, J. Phys.: Condens. Matter 2:4281 (1990).
  • Molecular dynamics studies of polar/nonpolar fluid mixtures: I. Mixtures of Lennard-Jones and Stockmayer fluids,
    S.W. de Leeuw, B. Smit, and C.P. Williams, J. Chem. Phys. 93:2704 (1990).
  • Effects of chain length of surfactants on the interfacial tension: Molecular dynamics simulations and experiments,
    B. Smit, A.G. Schlijper, L.A.M. Rupert, and N.M. van Os, J. Phys. Chem. 94:6933 (1990).
  • The structure of the water/oil interface in the presence of micelles,
    B. Smit, P.A.J. Hilbers, K. Esselink, L.A.M. Rupert, N.M. van Os, and A.G. Schlijper, Nature 348:624 (1990).
  • Fluid-fluid phase separation in a Repulsive $alpha$-$exp$-6 mixture: a comparison with the full $alpha$-$exp$-6 mixture by means of computer simulations,
    A. de Kuiper, B. Smit, J.A. Schouten, and J.P.J. Michels, Europhys. Lett. 13:679 (1990).
  • Free energy computations of mixtures of Stockmayer and polerizable Lennard-Jones fluids,
    G. Mooij, S.W. De Leeuw, C.P. Williams, and B. Smit, Mol. Phys. 90:909 (1990).

1989

Articles

  • Local compositions and thermodynamics of polar/non-polar mixtures,
    S.W. de Leeuw, C.P. Williams, and B. Smit, Fluid Phase Equilibria 48:99 (1989).
  • Explicit expression for finite size corrections to the chemical potential,
    B. Smit and D. Frenkel, J.Phys.:Condens.Matter 1:8659 (1989).
  • The influence of the quality of the solvent on the properties of a polymer. (A thermodynamic model and molecular dynamics calculations),
    B. Smit, K.R. Cox, and J.P.J. Michels, Mol. Phys. 66:97 (1989).
  • Monte-Carlo-simulaties van de adsorptie vam methaan in zeolieten,
    B. Smit and C.J.J. den Ouden, Ned. Tijdschrift voor Natuurkunde A55:82 (1989).
  • Vapour-liquid equilibria for Stockmayer fluids,
    B. Smit, C.P. Williams, E.M. Hendriks, and S.W. de Leeuw, Mol. Phys. 68:765(1989).
  • Computer simulations in the Gibbs ensemble,
    B. Smit, Ph. de Smedt, and D. Frenkel, Mol. Phys. 68:931 (1989).
  • Calculation of the chemical potential in the Gibbs ensemble,
    B. Smit and D. Frenkel, Mol. Phys. 68:951 (1989).
  • Computer simulations in zeolite catalysis research,
    C.J.J. den Ouden, B. Smit, A.F.H. Wielers, R.A. Jackson, and A.K. Nowak, Molec. Sim. 4:121 (1989).
  • Two-sided bound on the free energy from local states in Monte Carlo simulations,
    A.G. Schlijper and B. Smit, J. of Stat. Phys. 56:247 (1989).

1988

Articles

  • Influence of the density of the solvent on the static and dynamic properties of star polymers,
    B. Smit, A. van der Put, C.J. Peters, J. de Swaan Arons, and J.P.J. Michels, J. Chem. Phys. 88:3372 (1988).
  • Influence of the density of the solvent on the static and dynamic properties of star polymers,
    B. Smit, A. van der Put, C.J. Peters, J. de Swaan Arons, and J.P.J. Michels, Chem. Phys. Lett. 144:555 (1988).
  • Molecular dynamics simulations of amphiphilic molecules at a liquid-liquid interface, [pdf-file (internal only)]
    B. Smit, Phys. Rev. A 37:3431 (1988).
  • A new approach for calculating the accessible volume in equations of state for mixtures I. (Theory and implementation in the van der Waals equation of state),
    B. Smit and K.R. Cox, Fluid Phase Equilibria 43:171 (1988).
  • A new approach for calculating the accessible volume in equations of state for mixtures II. (Application to Lennard-Jones mixtures),
    B. Smit and K.R. Cox, Fluid Phase Equilibria 43:181 (1988).
  • Monte Carlo simulations on the relation between the structure and properties of zeolites: The adsorption of small hydrocarbons,
    B. Smit and C.J.J. den Ouden, J. Phys. Chem. 92:7169 (1988).
  • Evidence of phase separation in mixture of Lennard-Jones and Stockmayer fluids,
    S.W. de Leeuw, C.P. Williams, and B. Smit, Mol. Phys. 65:, 1269 (1988).