Computational Chemistry Group

PUBLICATIONS

Books

• Understanding Molecular Simulation. From Algorithms to Applications.
  D.Frenkel and B. Smit, Academic Press, Boston 2nd edition (2002)
  
• Computer Modelling Microporous & Mesoporous Materials
  Editors: Richard Catlow, R.A. van Santen, Berend Smit, Academic Press (2004) ISBN: 0121641376
  

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2020

Contributions to Books

1. Molecular Simulations of Adsorption and Diffusion in Crystalline Nanoporous Materials
   D. Dubbeldam, S. Calero, T.J.H. Vlugt, and R.Q. Snurr
   Book chapter in Volume 1 -- Introduction to Porous Materials edited by V. Gitis and G. Rothenberg (World Scientific Publishing Co. Pte. Ltd., 2020)

Articles

1. Adsorption of Aromatics in MFI-type Zeolites: Experiments and Framework Flexibility in Monte Carlo Simulations
   S. Caro-Ortiz, E. Zuidema, D. Dekker, M. Rigutto, D. Dubbeldam, and T.J.H. Vlugt
   J. Phys. Chem. C, Accepted, (2020)
2. Multiple Linear Regression and Thermodynamic Fluctuations are Equivalent for Computing Thermodynamic Derivatives from Molecular Simulation
   A. Rahbari, T.R. Josephson, Y. Sun, O.A. Moultos, D. Dubbeldam, J.I. Siepmann, and T.J.H. Vlugt
   Fluid Phase Equilbria, Accepted, 112785 (2020)
3. Synthesis of chiral MOF-74 frameworks by post-synthetic modification using an amino acid
   A. Gheorghe, B. Strudwick, D. M. Dawson, S. E. Ashbrook, S. Woutersen, D. Dubbeldam and S. Tanase
   Chemistry - A European J., Accepted, (2020)
4. Brick-CFCMC: open source software for Monte Carlo simulations of phase and reaction equilibria using the Continuous Fractional Component method
   R. Hens, A. Rahbari, S. Caro-Ortiz, N. Dawass, M. Erdos, A. Poursaeidesfahani, H. Salehi, A. Celebi, M. Ramdin, O. Moultos, D. Dubbeldam, and T.J.H. Vlugt
   J. Chem. Inf. Model., 60(6), 2678-2682 (2020)
5. Multiple free energy calculations from single state point Continuous Fractional Component Monte Carlo simulation using umbrella sampling
   A. Rahbari, R. Hens, O. Moultos, D. Dubbeldam, and T.J.H Vlugt
   J. Chem. Theory Comput., 16(3), 1757-1767 (2020)

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2019

Articles

1. In situ visualization of loading-dependent water effects in a stable metal-organic framework
   N. C. Burtch, I. M. Walton, J. T. Hungerford, C. R. Morelock, Y. Jiao, J. Heinen, Y.-S. Chen, A. A. Yakovenko, W. Xu, D. Dubbeldam, K. S. Walton
   Nat. Chem., 11, 1-7 (2019).
2. Water-ethanol and methanol-ethanol separations using in situ confined polymer chains in a metal-organic framework
   Y. Tang, D. Dubbeldam, and S. Tanase
   ACS Appl. Mater. Interfaces, 11(44), 41383-41393 (2019).
3. Negative Thermal Expansion Design Strategies in a Diverse Series of Metal-Organic Frameworks
   N.C. Burtch, S.J. Baxter, J. Heinen, A. Bird, A. Schneemann, D. Dubbeldam, and A. Wilkinson
   Adv. Func. Mater., 29(48), 1904669 (2019).
4. Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials
   D. Dubbeldam, K.S. Walton, T.J.H. Vlugt, and S. Calero
   Adv. Theory Simulat., 2(11), 1900135 (2019).
5. Using aliphatic alcohols to tune benzene adsorption
   A. Martin-Calvo, J.J. Gutierrez-Sevillano, D. Dubbeldam, and S. Calero
   Adv. Theory Simulat., 2(11), 1900112 (2019).
6. Improving Ammonia Production Using Zeolites
   I. Matito-Martos, J. García-Reyes, A. Martin-Calvo, D. Dubbeldam, and S. Calero
   J. Phys. Chem. C, 123(30), 18475-18481 (2019).
7. Improving the accuracy of computing chemical potentials in CFCMC simulations
   A. Rahbari, R. Hens, D. Dubbeldam, and T.J.H. Vlugt
   Mol. Phys, 117(23-24), 3493-3508 (2019).
8. Efficient separation of ethanol-methanol and ethanol-water mixtures using ZIF-8 supported on a hierarchical porous mixed-oxide substrate
   Y. Tang, D. Dubbeldam, X. Guo, G. Rothenberg and S. Tanase
   ACS Appl. Mater. Interfaces, 11(23), 21126-21136 (2019).
9. Highlights of (Bio-)Chemical Tools and Visualization Software for Computational Science
   D. Dubbeldam, J. Vreede, T J.H. Vlugt, and S. Calero
   Current Opinion in Chemical Engineering, 23C, 1-13 (2019).
10. Molecular Simulation of the Vapor-Liquid Equilibria of Xylene mixtures: Force Field performance, and Wolf vs. Ewald for Electrostatic Interactions
    S.C. Ortiz, R. Hens, E. Zuidema, M. Rigguto, D. Dubbeldam, and T J.H. Vlugt
    Fluid Phase Equilibria, 485(15), 239-247 (2019).
11. Prediction of adsorption isotherms from breakthrough curves
    A. Poursaeidesfahani, E. Andres-Garcia, M. de Lange, A. Torres-Knoop, M. Rigutto, N. Nair, F. Kapteijn, J. Gascon, D. Dubbeldam, T J.H. Vlugt
    Micropor. Mesopor. Mater., 277(15), 237-244 (2019).
12. Effect of truncating electrostatic interactions on predicting thermodynamic properties of water–methanol systems
    A. Rahbari, R. Hens, S.H. Jamali, M. Ramdin, D. Dubbeldam, T J.H. Vlugt
    Mol. Simulat., 45(4-5), 336-350 (2019).

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2018

Contributions to Books

1. Simulation of Crystalline Nanoporous Materials and the Computation of Adsorption/Diffusion Properties
   David Dubbeldam
   Book chapter in Gas Separations and Storage in Metal Organic Frameworks edited by T. Grant Glover and B. Mu (Francis and Taylor, 2018)

Articles

1. Mechanical Properties in Metal-Organic Frameworks: Emerging Opportunities and Challenges for Device Functionality and Technological Applications
   N.C. Burtch, J. Heinen, T.D. Bennett, D. Dubbeldam, and M.D. Allendorf
   Adv. Mater., 30(37), 1704124 (2018).
2. Diffusion Patterns in Zeolite MFI: the Cation Effect
   J. Perez-Carbajo, D. Dubbeldam, S. Calero, and P. Merkling
   J. Phys. Chem. C, (122)51, 29274-29284 (2018).
3. Potential of Polarizable Force Fields for Predicting the Separation Performance of Small Hydrocarbons in M- MOF-74
   T. Becker, A. Luba-Trigueo, J.M. Vicent-Luna, L.-C. Lin, D. Dubbeldam, S. Calero, T.J.H. Vlugt
   Phys. Chem. Chem. Phys., 20, 28848-28859 (2018).
4. Elucidating the Variable-Temperature Mechanical Properties of a Negative Thermal Expansion Metal–Organic Framework
   J. Heinen, A.D. Ready, T.D. Bennett, D. Dubbeldam, R.W. Friddle, and N.C. Burtch
   ACS Appl. Mater. Interfaces, 10(25), 21079-21083 (2018).
5. Polarizable Force Field for CO2 in M-MOF-74 Derived from Quantum Mechanics
   T. Becker, L.-C. Lin, D. Dubbeldam, T.J.H. Vlugt
   J. Phys. Chem. B., 122(42), 24488-24498 (2018).
6. Cis to trans isomerization of azobenzene derivatives studied with transition path sampling and quantum mechanical molecular mechanical molecular dynamics
   A. Muzdalo, P. Saalfrank, J. Vreede, and M. Santer
   J. Chem. Theory Comput., 14, (2018).
7. Absorption Refrigeration Cycles with Ammonia - Ionic Liquid Working Pairs studied by Molecular Simulation
   T. Becker, M. Wang, A. Kabra, S.H. Jamali, M. Ramdin, D. Dubbeldam, C. I. Ferreira, and T.J.H. Vlugt
   Industrial & Engineering Chemistry Research, 57(15), 5442-5452 (2018).
8. Computation of Partial Molar Properties Using Continuous Fractional Component Monte Carlo
   A. Rahbari, R. Hens, I.K. Nikolaidis, A. Poursaeidesfahani, M. Ramdin, I. G. Economou, O. A. Moultos, D. Dubbeldam and T.J.H. Vlugt Mol. Phys., 116(21-22), 3331-3344 (2018).
9. Selective CO2 adsorption in water-stable alkaline-earth based metal-organic frameworks
   Y. Tang, A. Kourtellaris, A. Tasiopoulos, S. Teat, D. Dubbeldam, G. Rothenberg and S. Tanase
   Inorganic Chemistry Frontiers, 5, 541-549 (2018).
10. iRASPA: GPU-Accelerated Visualization Software for Materials Scientists
    D. Dubbeldam, S. Calero, and T.J.H. Vlugt
    Mol. Simulat., 44(8), 653-676 (2018).
11. Adsorption equilbrium of nitrogen dioxide in porous materials
    I. Matito-Martos, A. Rahbari, A. Martin-Calvo, D. Dubbeldam, T.J.H. Vlugt, and S. Calero
    Phys. Chem. Chem. Phys., 20, 4189-4199 (2018).
12. On flexible force fields for metal-organic frameworks: recent developments and future prospects
    J. Heinen and D. Dubbeldam
    WIREs Comput. Mol. Sci., 8(4), e1363 (2018).
13. Chemical Potentials of Water, Methanol, Carbon Dioxide, and Hydrogen Sulfide at Low Temperatures using Continuous Fractional Component Gibbs Ensemble Monte Carlo
    A. Rahbari, A. Poursaeidesfahani, A. Torres-Knoop, D. Dubbeldam, and T.J.H. Vlugt
    Mol. Simulat., 44(5), 405-414 (2018).

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2017

Articles

1. Mechanism of environmentally driven conformational changes that modulate H-NS DNA bridging activity
   R.A. van der Valk, J. Vreede, L. Qin, G.F. Moolenaar, A. Hofmann, N. Goosen, and R.T. Dame
   eLife27369 (2017)
2. Efficient application of Continuous Fractional Component Monte Carlo in the Reaction Ensemble
   A. Poursaeidesfahani, R. Hens, A. Rahbari, M. Ramdin, D. Dubbeldam, and T.J.H. Vlugt
   J. Chem. Theory. Comput, 13(9), 4452-4466 (2017).
3. Product Shape Selectivity of MFI, MEL, and BEA-type Zeolites in the Catalytic Hydroconversion of Heptane
   A. Poursaeidesfahani, M. de Lange, F. Khodadadian, D. Dubbeldam, M. Rigutto, N. Nair, and T.J.H. Vlugt
   J. Catal., 353, 54-62 (2017).
4. Flexible Force Field Parameterization through Fitting on the Ab Initio derived Elastic Tensor
   J. Heinen, N.C. Burtch, K.S. Walton, and D. Dubbeldam
   J. Chem. Theory. Comput., 13(8), 3722-3730 (2017).
5. Behavior of the Enthalpy of Adsorption in Nanoporous Materials close to Saturation Conditions
   A. Torres-Knoop, A. Poursaeidesfahani, D. Dubbeldam, and T.J.H. Vlugt
   J. Chem. Theory. Comput., 13(7), 3326-3339 (2017).
6. Polarizable Force Fields for CO₂ and CH₄ Adsorption in M-MOF-74
   T.M. Becker, J. Heinen, D. Dubbeldam, L.-C. Lin, and T.J.H. Vlugt
   J. Phys. Chem. C, 121(8), 4659-4673, (2017).
7. Effective model for Olefin/Paraffin separation using (Co, Fe, Mn, Ni)-MOF-74
   A. Luna-Triguero, J.M. Vicent-Luna, T.M. Becker, T.J.H. Vlugt, D. Dubbeldam, P. Gómez-Álvarez, and S. Calero
   ChemistrySelect, 2(2), 665-672, (2017).
8. Computation of Thermodynamic Properties in the Continuous Fractional Component Monte Carlo Gibbs Ensemble
   A. Poursaeidesfahani, R. Rahbari, A. Torres-Knoop, D. Dubbeldam, and T.J.H. Vlugt
   Mol. Simulat., 43(3), 189-195, (2017).
9. Solubility of sulfur compounds in commercial physical solvents and an ionic liquid from Monte Carlo simulations
   S.H. Jamali, M. Ramdin, T.M. Becker, A. Torres-Knoop, D. Dubbeldam, W. Buijs, and T.J.H. Vlugt
   Fluid Phase Equilbr., 433, 50-55, (2017).

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2016

Theses

• Entropy-driven separations in nanoporous materials
  Ariana Torres-Knoop , Ph.D. thesis ("cum laude", with honors), University of Amsterdam, 2016.
  Thesis.pdf (26 MB)
  
  

Articles

1. Controlling Thermal Expansion: a Metal Organic Frameworks Route
   S. Balestra; R. Bueno-Pérez, S. Hamad, D. Dubbeldam, A.R. Ruiz-Salvador, and S. Calero
   Chem. Mater., 28(22), 8296-8304, (2016).
2. Predicting Multicomponent Adsorption Isotherms in Open-Metal Site Materials using Force Field Calculations based on Energy Decomposed Density Functional Theory
   J. Heinen, N. Burtch, C.F. Guerra, K.S. Walton, and D. Dubbeldam
   Chemistry - A European Journal, 22(50), 18045-18050, (2016).
3. Optimization of Particle Transfers in the Gibbs Ensemble for Systems With Strong and Directional Interactions Using CBMC, CFCMC, and CB/CFCMC
   A. Torres-Knoop, N. Burtch, A. Poursaeidesfahani, S.P. Balaji, R. Kools, F. Smit, K.S. Walton, T.J.H. Vlugt, D. Dubbeldam
   J. Phys. Chem. C, 120(17), 9148-9159, (2016).
4. Direct Free Energy Calculation in the Continuous Fractional Component Gibbs Ensemble
   A. Poursaeidesfahani, A. Torres-Knoop, D. Dubbeldam, and T.J.H. Vlugt
   J. Chem. Theory. Comput., 12(4), 1481-1490, (2016).
5. Computation of the Heat and Entropy of Adsorption in Proximity of Inflection Points
   A. Poursaeidesfahani, A. Torres-Knoop, M. Rigutto, N. Nair, D. Dubbeldam, and T.J.H. Vlugt
   J. Phys. Chem. C, 120(3), 1727-1738 (2016).
6. Microscopic assembly of aqueous solutions of Ionic Liquids
   J.M. Vicent-Luna, D. Dubbeldam, P. Gomez-Alvarez, and S. Calero
   Chem. Phys. Chem., 17(3), 380-386, (2016).
7. Understanding and Solving Disorder in Substitution Pattern of Amino Functionalized MIL-47(V)
   Jurn Heinen and David Dubbeldam
   Dalton Transactions, 45, 4309-4315, (2016).
8. RASPA: Molecular Simulation Software for Adsorption and Diffusion in Flexible Nanoporous Materials
   David Dubbeldam, Sofia Calero, Donald E. Ellis, and Randall Q. Snurr
   Mol. Simulat., 42(2) , 81-101, (2016).

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2015

Contributions to Books

1. On the Application of Classical Molecular Simulations of Adsorption in Metal-Organic Frameworks
   David Dubbeldam and Krista S. Walton,
   Book chapter in Metal-Organic Frameworks: Materials Modeling towards Engineering Applications edited by Jiang Jianwen (Pan Stanford Publishing Pte Ltd, 2015)

Articles

1. Computing bubble-points of CO2/CH4 gas mixtures in ionic liquids from Monte Carlo simulations
   M. Ramdin, S.-P. Balaji, J.-M. Vicent-Luna, A. Torres-Knoop, Q. Chen, D. Dubbeldam, S. Calero, T. de Loos, and T.J.H. Vlugt
   Fluid Phase Equilbria, 418, 100-107, (2015).
2. Solubilities of CO2, CH4, C2H6, and SO2 in Ionic Liquids and Selexol from Monte Carlo Simulations
   M. Ramdin, Q. Chen, S.-P. Balaji, J.-M. Vicent-Luna, A. Torres-Knoop, D. Dubbeldam, S. Calero, T. de Loos, and T.J.H. Vlugt
   J. Comput. Sci., 15, 74-80, (2015).
3. Investigating polarization effects of CO2 adsorption in MgMOF-74
   T.M. Becker, D. Dubbeldam, L.-C. Lin, and T. Vlugt
   J. Comput. Sci., 15, 86-94, (2015).
4. Solubility of Natural Gas Species in Ionic Liquids and Commercial Solvents: Experiments and Monte Carlo Simulations
   M. Ramdin, S.-P. Balaji, A. Torres-Knoop, D. Dubbeldam, T. De Loos, and T. Vlugt
   J. Chem. Eng. Data, 60(10),3039-3045 (2015).
5. Understanding and Exploiting Window-Effects for Adsorption and Separations of Hydrocarbons
   A. Luna-Triguero, J.-M.Vicent-Luna, D. Dubbeldam, P. Gómez-Álvarez, S. Calero
   J. Phys. Chem. C, 119(33), 19236–19243 (2015).
6. Understanding nanopore window distortions in the reversible molecular valve zeolite RHO
   S. Balestra, S. Hamad, A. Rabdel Ruiz-Salvador, V. Domínguez-García, P. Merkling, D. Dubbeldam and S. Calero
   Chem. Mater., 27(16), 5657–5667 (2015).
7. Separation of amyl alcohol isomers in ZIF-77
   R.B. Perez, J.J. Gutierez Sevillano, D. Dubbeldam, P. Merkling, and S. Calero
   Chem. Phys. Chem., 16(13), 2735-2738 (2015)
8. Simulating the reactions of CO2 in aqueous monoethanolamine solution by Reaction Ensemble Monte Carlo using the Continuous Fractional Component method
   S.P. Balaji, S. Gangarapu, M. Ramdin, A. Torres-Knoop, H. Zuilhof, E. Goetheer, D. Dubbeldam, and T.J.H. Vlugt
   J. Chem. Theory. Comput., 11(6), 2661-2669 (2015).
9. Exploiting Large-Pore Metal-Organic Frameworks for Separations using Entropic Molecular Mechanisms
   Ariana Torres-Knoop and David Dubbeldam
   Chem. Phys. Chem., 16(10), 2046-2067 (2015).
10. Investigating Water and Framework Dynamics in Pillared MOFs
    Nicholas C. Burtch, David Dubbeldam, and Krista S. Walton
    Mol. Simulat., 41(16-17), 1379-1387, (2015).
11. Entropic Separation of Styrene/Ethylbenzene Mixtures by Exploitation of Subtle Differences in Molecular Configurations in Ordered Crystalline Nanoporous Adsorbents
    Ariana Torres-Knoop, Jurn Heinen, Rajamani Krishna, and David Dubbeldam
    Langmuir, 31(12), 3771-3778 (2015).
12. Understanding DABCO Nanorotor Dynamics in Isostructural Metal-Organic Frameworks
    Nicholas Burtch, Ariana Torres-Knoop, Guo Shiou Foo, Johannes Leisen, Carsten Sievers, Bernd Ensing, David Dubbeldam, Krista Walton
    J. Phys. Chem. Letters, 6, 812-816 (2015).

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2014

Articles

1. Entropic Separations of Mixtures of Aromatics by Selective Face-to-Face Molecular Stacking in One-Dimensional Channels of Metal-Organic Frameworks and Zeolites
   Ariana Torres-Knoop, Salvador R.G. Balestra, Rajamani Krishna, Sofia Calero, and David Dubbeldam
   Chem. Phys. Chem., 16(3), 532-535 (2014).
2. Local orientational ordering in liquids revealed by resonant vibrational energy transfer
   Matthijs R. Panman, Daniel J. Shaw, Bernd Ensing, and Sander Woutersen
   Phys. Rev. Lett., accepted, (2014).
3. Acidity constants of lumiflavin from first principles molecular dynamics simulations.
   Murat Kılıç and Bernd Ensing
   Phys. Chem. Chem. Phys., 16, 18993 - 19000 (2014).
4. Interaction of H₂ with a double walled armchair nanotube by first principles calculations.
   Francesca Costanzo, Bernd Ensing, Roberto Scipioni, Francesco Ancilotto, and Pier Luigi Silvestrelli
   J. Phys. Chem. C, 118, 15816 - 15824 (2014).
5. Comment on Communication: Benzene dimer - The free energy landscape [J. Chem. Phys. 139, 201102 (2013)]
   Ad van der Avoird, Rafal Podeszwa, Bernd Ensing and Krzysztof Szalewicz
   J. Chem. Phys., 140, 227101 (2014).
6. CO2/CH4 Solubility and Selectivity in Ionic Liquids
   Mahinder Ramdin, Sayee Prasaad Balaji, Ariana Torres-Knoop, David Dubbeldam, Theo W. de Loos, and Thijs J.H. Vlugt
   Proceedings of the 4th International Gas Processing Symposium, 2014, Qatar, accepted, (2014).
7. Enantioselective Adsorption of Ibuprofen and Lysine in Metal-Organic Frameworks
   Rocio Bueno-Perez, Ana Martin-Calvo, Paula Gomez-Alvarez, Juan J. Gutierrez-Sevillano, Patrick J. Merkling, Thijs J. H. Vlugt, Titus van Erp, David Dubbeldam and Sofia Calero
   Chem. Commun., 50, 10849-10852 (2014).
8. Separating Xylene Isomers by Commensurate Stacking of p-Xylene within Channels of MAF-X8
   Ariana Torres-Knoop, Rajamani Krishna and David Dubbeldam
   Angew. Chem. Int. Ed., 53(30), 7774-7778 (2014).
9. Advanced Monte Carlo Simulations of the Adsorption of Chiral Alcohols in a Homochiral Metal-Organic Framework
   Zhiwei Qiao, Ariana Torres-Knoop, David Fairen-Jimenez, David Dubbeldam, Jian Zhou and Randall Q. Snurr
   AIChE Journal, 60(6), 2324-2334 (2014).
10. A Comparison of Advanced Monte Carlo Methods for Open Systems: CFCMC vs. CBMC
    Ariana Torres-Knoop, Sayee Prasaad Balaji, Thijs Vlugt and David Dubbeldam
    J. Chem. Theory. Comput., 10(3), 942-952 (2014).
11. Review: Exploring New Methods and Materials for Enantioselective Separations and Catalysis
    D. Dubbeldam, S. Calero, and T.J.H. Vlugt
    Mol. Sim. (special issue) 40(7-9), 585-598 (2014).

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2013

Articles

1. First and Second One-Electron Reduction of Lumiflavin in Water - A First Principles Molecular Dynamics Study
   Murat Kılıç and Bernd Ensing
   J. Chem. Theory Comput. 9, 3889 - 3899 (2013).
2. On the "Tertiary Structure" of Poly-Carbenes; Self-assembly of sp3-Carbon Based Polymers into Liquid-Crystalline Aggregates
   Nicole M. G. Franssen, Bernd Ensing, Maruti Hegde, Theo Dingemans, Ben Norder, Stephen J. Picken, Gert O. R. Alberda van Ekenstein, Ernst van Eck, Johannes A. A. W. Elemans, Mark Vis, Joost N. H. Reek and Bas de Bruin
   Chem. Eur. J. 19, 11577 - 11589 (2013).
3. Anisotropic aggregation in a simple model of isotropically polymer-coated nanoparticles
   Jurriaan A. Luiken and Peter G. Bolhuis
   Phys. Rev. E 88, 012303 (2013).
4. Controlling Molecular Tautomerism Through Supramolecular Selectivity
   K. Epa, C. Aakeroy, J. Desper, S. Rayat, K. Chandra and A.J. Cruz-Cabeza
   Chem. Commun. 49, 2013, 7929-7931.
5. Hydrogen bond landscapes, geometry and energetics of squaric acid and its mono- and di-anions: a Cambridge Structural Database, IsoStar and ab initio computational study
   P.A. Wood, A.J. Cruz-Cabeza, D.A. Bardwell and F.H. Allen
   Acta Crystallogr. B69, 2013, 514-523.
6. Transition metal exchanged β zeolites: Characterization of the metal state and catalytic application in the methanol conversion to hydrocarbons
   D. Esquivel, A.J. Cruz-Cabeza, C. Jimenez-Sanchidrian and F. Romero-Salguero
   Micropor. Mesopor. Mat., 179, 2013, 30-39.
7. Separation of Hexane Isomers in a Metal-Organic Framework with Triangular Channels
   Herm, Z.R., Wiers, B.M., van Baten, J.M., Hudson, M.R., Zajdel,
   P., Brown, C.M., Maschiocchi, N., Krishna, R. and Long, J.R.,
   Science 340, 960-964 (2013).
8. Investigating the Influence of Diffusional Coupling on Mixture Permeation across Porous Membranes
   Krishna, R., van Baten, J.M.,
   J. Membr. Sci. 430, 113-128 (2013).
9. A microporous metal-organic framework assembled from an aromatic tetracarboxylate for H2 purification
   He, Y., Xiang, S., Zhang, Z., Xiong, S., Wu, C., Zhou, W., Yildirim, T., Krishna, R., Chen, B.,
   J. Mater. Chem. A 1, 2543-2551(2013).
10. Carbon Dioxide Capture from Air Using Amine-Grafted Porous Polymer Networks
    Lu, W., Sculley, J.P., Yuan, D., Krishna, R., Wei, Z., Zhou, H.C.,
    J. Phys. Chem. C 117, 4057-4061 (2013).
11. Influence of Adsorption Thermodynamics on Guest Diffusivities in Nanoporous Crystalline Materials
    Krishna, R., van Baten, J.M.,
    Phys. Chem. Chem. Phys. 15, 7994-8016 (2013).
12. Metal-Organic Framework with Functional Amide Groups for Highly Selective Gas Separation
    Xiong, S., He, Y., Krishna, R., Chen, B., Wang, Z.,
    Cryst. Growth Des. 13, 2670-2674(2013).
13. Low-energy regeneration and high productivity in a lanthanide-hexacarboxylate framework for high-pressure CO2/CH4/H2 separation
    He, Y., Furukawa, H., Wu, C., O'Keefe, M., Krishna, R., Chen, B.
    Chem. Commun. 49, 6773-6775 (2013).
14. A Cationic Microporous Metal-Organic Framework for Highly Selective Separation of Small Hydrocarbons at Room Temperature
    Xu, H., Cai, J., Xiang, S., Zhang, Z., Xiong, S., Wu, C., Rao, X.,
    Cui, Y., Yang, Y., Krishna, R., Chen, B., Qian, G.,
    J. Mater. Chem. A 1, 9916-9921 (2013).
15. Graphitization of single wall carbon nanotube bundles at extreme conditions: collapse or coalescence route
    F. Colonna, A. Fasolino, and E.J. Meijer,
    Phys. Rev. B88, 165416.
16. Acidity of edge surface sites of montmorillonite and kaolinite
    X. Liu, X. Lu, M. Sprik, J. Cheng, E.J. Meijer, R. Wang,
    Geochimica et Cosmochimica Acta 117, 180-190 (2013).
17. Strategies to Simultaneously Enhance the Hydrostability and the Alcohol-Water Separation Behavior of Cu-BTC
    J. Gutierrez-Sevillano, D. Dubbeldam, L. Bellarosa, N. Lopez, X. Liu, T.J.H. Vlugt and S. Calero
    J. Phys. Chem. C 117 20706-20714 (2013).
18. Review: On the Inner Workings of Monte Carlo Codes
    D. Dubbeldam, A. Torres-Knoop, and K.S. Walton
    Mol. Sim. (special issue on Monte Carlo) 39(14-15), 1253-1292 (2013).
19. Adsorption of hydrogen sulphide on Metal-Organic Frameworks
    J.J. Gutierrez-Sevillano, A. Martin-Calvo, D. Dubbeldam, S. Calero, and S. Hamad
    RSC Advances 3,14737-14749 (2013).
20. Simulation Study of Structural Changes in Zeolite RHO
    S. Balestra, J. Gutierrez-Sevillano, P. Merckling, D. Dubbeldam and S. Calero
    J. Phys. Chem. C 117 (22), 11592-11599 (2013).
21. Clarifying the role of sodium in the silica oligomerization reaction
    Anna Pavlova, Thuat T. Trinh, Rutger A. van Santen and Evert Jan Meijer
    Phys. Chem. Chem. Phys. 15, 1123-29 (2013).
22. Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding
    Sander Jaeqx, Weina Du, Evert Jan Meijer, Jos Oomens and Anouk M. Rijs
    J. Phys. Chem. A 117 (6), 1216-27 (2013).
23. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency
    Baron Peters, Peter G. Bolhuis, Ryan G. Mullen and Joan-Emma Shea
    J. Chem. Phys. 138, 054106 (2013).
24. On the Molecular Mechanisms for Adsorption in Cu-BTC Metal Organic Framework
    J. Gutierrez-Sevillano, J. Vicent-Luna, D. Dubbeldam and S. Calero
    J. Phys. Chem. C 117 (21), 11357-11366 (2013).
25. Molecular-level Insight into Unusual Low Pressure CO2 Affinity in Pillared Metal-Organic Frameworks
    N. Burtch, H. Jasuja, D. Dubbeldam and K. Walton
    J. Am. Chem. Soc. 135 (19), 7172-7180 (2013).
26. Hydrophobic Collapse of Trigger Factor Monomer in Solution
    K. Singhal, J. Vreede A. Mashaghi, S. Tans and P.G. Bolhuis
    PLoS One 8, 1e59683 (2013).
27. A model for H-NS mediated compaction of bacterial DNA
    M. Joyeux and J. Vreede
    Biophys. J. 104, 1615-1622 (2013).
28. The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions
    L. Zhu, P.G. Bolhuis and J. Vreede
    PLoS Comput. Biol. 9(2), e1002913 (2013).
29. Interplay between Folding and Assembly of Fibril-Forming Polypeptides
    Ran Ni, Sanne Abeln, Marieke Schor, Martien A. Cohen Stuart and Peter G. Bolhuis
    Phys. Rev. Lett. 111, 058101 (2013).

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2012

Articles

1. Acid-Base crystalline complexes and the pKa rule
   A.J. Cruz-Cabeza
   CrystEngComm, 14, 2012, 6362-6365.
2. Systematic conformational bias in small molecule crystal structures is rare and explicable
   A.J. Cruz-Cabeza, J.W. Liebeschuetz and F.H. Allen
   CrystEngComm, 14, 2012, 6797-6811.
3. Is the Fenamate group a polymorphophore? Contrasting the crystal energy landscapes of fenamic and tolfenamic acids
   O.G. Uzoh, A.J. Cruz-Cabeza and S.L. Price
   Cryst. Growth Des., 12, 2012, 4230-4239.
4. Observed and predicted hydrogen bond motifs in crystal structures of hydantoins, dihydrouracils and uracils
   A.J. Cruz-Cabeza and C.H. Schwalbe
   New J. Chem., 36, 2012, 1347-1354.
5. Metal-exchanged β zeolites as catalysts for the conversion of acetone to hydrocarbons
   A.J. Cruz-Cabeza, D. Esquivel, C. Jimenez-Sanchidrian and F. Romero-Salguero
   Materials, 5, 2012, 121-134.
6. Geometry and conformation of cyclopropyl derivatives having σ-acceptor and σ-donor substituents: a theoretical and crystal structure database study
   A.J. Cruz-Cabeza and Frank H. Allen
   Acta Crystallogr. B68, 2012,182-188.
7. Synthon Preferences in Cocrystals of cis-Carboxamides:Carboxylic Acids
   Alaina M. Moragues-Bartolome, William Jones and A.J. Cruz-Cabeza
   CrystEngComm, 14, 2012, 2552-2559.
8. Enhanced Concentration of Medium Strength Brönsted Acid Sites in Aluminium-Modified β zeolite
   D. Esquivel, A.J. Cruz-Cabeza, C. Jimenez-Sanchidrian and F. Romero-Salguero
   Catalysis Letters, 142, 2012, 112-117.
9. Investigating the validity of the Bosanquet formula for estimation of diffusivities in mesopores
   Krishna, R., van Baten, J.M.
   Chem. Eng. Sci. 69, 684-688 (2012).
10. CO2/CH4, CH4/H2 and CO2/CH4/H2 Separations at High Pressures Using Mg2(dobdc)
    Herm, Z.R., Krishna, R., Long, J.R.
    Microporous Mesoporous Mater. 151, 481-487 (2012).
11. A Microporous Metal-Organic Framework for Highly Selective Separation of Acetylene, Ethylene and Ethane from Methane at Room Temperature
    He, Y., Zhang, Z., Xiang, S., Fronczek, F.R., Krishna, R., Chen, B.
    Chem. Eur. J. 18, 613-619 (2012).
12. High Separation Capacity and Selectivity of C2 Hydrocarbons over Methane within a Microporous Metal-Organic Framework at Room Temperature
    He, Y., Zhang. Z., Xiang, S., Wu, H., Fronczek, F.R., Zhou, W., Krishna, R., O'Keeffe, M., Chen, B.,
    Chem. Eur. J. 18, 1901-1904 (2012).
13. A comparison of the CO2 capture characteristics of zeolites and metal-organic frameworks
    Krishna, R., van Baten, J.M.
    Separation and Purification Technology 87, 120-126(2012).
14. Hindering effects in CO2/CH4 mixture diffusion in ZIF-8 crystals
    Chmelik, C., van Baten, J.M., Krishna, R.,
    J. Membr. Sci. 397-398, 87-91(2012).
15. Adsorptive separation of CO2/CH4/CO gas mixtures,
    Krishna, R.,
    Microporous and Mesoporous Materials 156, 217-223 (2012).
16. Diffusion in porous crystalline materials
    Krishna, R.
    Chemical Society Reviews 41, 3099-311 (2012).
17. Hydrocarbon Separations in a Metal-Organic Framework with Open Iron(II) Coordination Sites
    Bloch, E.D., Queen, W.L., Krishna, R., Zadrozny, J.M., Brown, C.M., Long, J.R.,
    Science 335, 1606-1610 (2012).
18. Interplay of Metalloligand and Organic Ligand to Tune Micropores within Isostructural Mixed-Metal Organic Frameworks (M'MOFs) for Their Highly Selective Separation of Chiral and Achiral Small Molecules,
    Das, M.C., Guo, Q., He, Y., Kim, J., Zhao, C.G., Hong, K., Xiang, S., Zhang, Z., Thomas, K.M., Krishna, R., Chen, B.,
    J. Am. Chem. Soc. 134, 8703-8710 (2012).
19. A robust doubly interpenetrated metal-organic framework constructed from a novel aromatic tricarboxylate for highly selective separation of small hydrocarbons
    He, Y., Zhang, Z., Xiang, S., Fronczek, F.R., Krishna, R., Chen B.,
    Chem. Commun. 48, 6493-6495(2012).
20. Microporous Metal-Organic Framework with Potential for Carbon Dioxide Capture at Ambient Conditions
    Xiang, S.C., He, Y., Zhang, Z., Wu, H., Zhou, W., Krishna, R., Chen, B.,
    Nature Communications 954 (2012).
21. Polyamine-Tethered Porous Polymer Networks for Carbon Dioxide Capture from Flue Gas
    Lu, W., Sculley, J.P., Yuan, D., Krishna, R., Wei, Z., Zhou, H.C.,
    Angew. Chem. Int. Ed. 51, 7480-7484(2012).
22. Cu-TDPAT, an rht-type Dual-Functional Metal-Organic Framework Offering Significant Potential for Use in H2 and Natural Gas Purification Processes Operating at High Pressures
    Wu, H., Yao, K., Zhu, Y., Li, B., Shi, Z., Krishna, R., Li, J.,
    J. Phys. Chem. C 116, 16609-16618 (2012).
23. Metal-Organic Frameworks with Potential for Energy-Efficient Adsorptive Separation of Light Hydrocarbons
    He, Y., Krishna, R., Chen, B.
    Energy Environ. Sci. 5, 9107-9120 (2012).
24. A microporous lanthanide-tricarboxylate framework with the potential for purification of natural gas
    He, Y., Xiong, S., Fronczek, F.R., Krishna, R., O'Keeffe, M., Chen, B.
    Chem. Commun. 48, 10856-10858(2012).
25. Investigating the Relative Influences of Molecular Dimensions and Binding Energies on
    Diffusivities of Guest Species Inside Nanoporous Crystalline Materials
    Krishna, R., van Baten, J.M.,
    J. Phys. Chem. C 116, 23556-23568 (2012).
26. Microporous metal-organic frameworks for storage, and separation of small hydrocarbons
    He, Y., Zhou, W., Krishna, R., Chen, B.,
    Chem. Commun. 48, 11813-11831(2012).
27. Structure and thermodynamic stability of carbon clathrates: A Monte Carlo study
    F. Colonna, A. Fasolino and E.J. Meijer
    Solid State Communications 152(3), 180-84 (2012).
28. Atomic-scale structures of interfaces between phyllosilicate edges and water
    Xiandong Liu, Xiancai Lu, Evert Jan Meijer, Rucheng Wang and Huiqun Zhou
    Geochimica et Cosmochimica Acta 81, 56-68 (2012).



29. First-Principles Molecular Dynamics Insight Into Fe2+ Complexes Adsorbed on Edge Surfaces of Clay Minerals
    Xiandong Liu, Evert Jan Meijer, Xiancai Lu and Rucheng Wang
    Clays and Clay Minerals 60(4), 341-7 (2012).
    
    


30. Atomic scale structures of interfaces between kaolinite edges and water
    Xiancai Lu, Rucheng Wang, Evert Jan Meijer, Huiqun Zhou and Hongping He
    Geochimica et Cosmochimica Acta 92, 233-42 (2012).
31. Understanding the Role of Water in Aqueous Ruthenium-Catalyzed Transfer Hydrogenation of Ketones
    Anna Pavlova and Evert Jan Meijer
    ChemPhysChem 13(15), 3492-96 (2012).
32. Numerical study of the effect of thiol-disulfide exchange in the cluster phase of β-lactoglobulin aggregation
    Rosanne N. W. Zeiler and Peter G. Bolhuis
    Faraday Discuss. 158, 461-77 (2012).
33. Statics and Dynamics of Free and Hydrogen-Bonded OH Groups at the Air/Water Interface
    Ana Vila Verde, Peter G. Bolhuis and R. Kramer Campen
    J. Chem. Phys. B 116(31), 9467-81 (2012).
34. Confinement-Induced States in the Folding Landscape of the Trp-cage Miniprotein
    Kristen A. Marino and Peter G. Bolhuis
    J. Chem. Phys. B 116(39), 11872-80 (2012).
35. On the polarity of buckminsterfullerene with a water molecule inside.
    Bernd Ensing, Francesca Costanzo and Pier Luigi Silverstrelli
    J. Phys. Chem. A (2012).
36. Path Finding on High-Dimensional Free Energy Landscapes
    Grisell Díaz Leines and Bernd Ensing,
    Phys. Rev. Lett. 109, 020601 (2012).
37. Computer-assisted screening of ordered crystalline nanoporous adsorbents for separation of alkane isomers
    David Dubbeldam, Rajamani Krishna, Sofia Calero and Ozgur Yazaydin
    Angew. Chem. Int. Ed. 51(47), 11867-71 (2012).
38. Feasibility of zeolitic imidazolate framework membranes for clean energy applications
    Aaron Thornton, David Dubbeldam, Ming S. liu, Bradley P. Ladewig, Anita Hill and Matthew Hill
    Energy&Environmental Science 5(6), 7637-7646 (2012).
39. Simulation Study on the Adsorption Properties of Linear Alkanes on Closed Nanotube Bundles
    James Cannon, Thijs J.H. Vlugt, David Dubbeldam, Shigeo Maruyama and Junichiro Shiomi
    J. Phys. Chem. B 116(32), 9812-9819 (2012).
40. Self-Diffusion of Chain Molecules in the Metal-Organic Framework IRMOF-1: Simulation and Experiment
    Denice C. Ford, David Dubbeldam, Randal Q. Snurr, Volker Kunzel, Markus Stallmach and Joerg Kaerger
    J. Phys. Chem. Lett. 3(7), 930-933 (2012).
41. Zeolite Force Fields and Experimental Siliceous Frameworks in a Comparative Infrared Study
    R. Bueno-Perez, S. Calero, D. Dubbeldam, C.O. Ania, J.P. Parra, A.P. Zaderenko and P.J. Merkling
    J. Phys. Chem. C 116(49), 25797-25805 (2012).
42. Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling
    M. Schor, J. Vreede and P.G. Bolhuis
    Biophys J. 103, 1296 (2012).
43. Predicting the effect of ions on the conformation of the H-NS dimerization domain
    J. Vreede and R. Th. Dame
    Biophys. J. 103, 89 (2012).
44. Transition path sampling of protein conformational changes
    J. Juraszek, J. Vreede and P.G. Bolhuis
    Chem. Phys. 396, 30 (2012).

Patent applications

1. "Process for separating mixtures containing straight-chain and branched alkanes"
   inventors: David Dubbeldam and Rajamani Krishna,
   Filed by Universiteit van Amsterdam, 27 April 2012 European Patent Office, Application No./12165907.2-2103

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2011

Articles

1. Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test
   D.A. Bardwell, C.S. Adjiman, H.L. Ammon, Y.A. Arnautova, E.Bartashevich, S.X. M. Boerrigter, D.E. Braun, A.J. Cruz-Cabeza, G.M. Day, R.G. Della Valle, G.R. Desiraju, B.P. van Eijck, J.C. Facelli, M.B. Ferraro, D. Grillo, M. Habgood, D.W.M. Hofmann, F. Hofmann, J. Jose, P.G. Karamertzanis, A.V. Kazantsev, J.Kendrick, L.N. Kuleshova, F.J. J. Leusen, A. Maleev, A.J. Misquitta, S. Mohamed, R.J. Needs, M.A. Neumann, D. Nikylov, A.M. Orendt, R. Pal, C.C. Pantelides, C. Pickard, L.S. Price, S.L. Price, H.A. Scheraga, J. van de Streek, T.S. Thakur, S. Tiwari, E. Venuti and I. Zhitkov.
   

   Acta Crystallogr. B, B67, 2011, 535-551.

2. Understanding hydration of Zn2+ in hydrothermal fluids with ab initio molecular dynamics
   Xiandong Liu, Xiancai Lu, Rucheng Wang and Evert Jan Meijer
   Phys. Chem. Chem. Phys. 13, 13305-9 (2011).
3. High-pressure high-temperature equation of state of graphite from Monte Carlo simulations
   F. Colonna, A. Fasolino and E.J. Meijer
   Carbon 49(2), 364-8 (2011).
4. Acidities of confined water in interlayer space of clay minerals
   Xiandong Liu, Xiancai Lu, Rucheng Wang, Evert Jan Meijer and Huiqun Zhou
   Geochimica et Cosmochimica Acta 75(17), 4978-86 (2011).
5. On the Relation Between Projections of the Reweighted Path Ensemble Peter G. Bolhuis and Wolfgang Lechner
   J. Stat. Phys. 145, 841-859 (2011).
6. 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).
7. Multiple state transition interface sampling of alanine dipeptide in explicit solvent
   Weina Du, Kristen A. Marino and Peter G Bolhuis
   J. Chem. Phys. 135, 145102 (2011).
8. 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 and Mischa Bonn
   Phys. Rev. Lett. 107, 116102 (2011).
9. Role of Fluctuations in Ligand Binding Cooperativity of Membrane Receptors
   Lizhe Zhu, Daan Frenkel and Peter G. Bolhuis
   Phys. Rev. Lett. 106, 168103 (2011).
10. Role of the Prestructured Surface Cloud in Crystal Nucleation
    Wolfgang Lechner, Christoph Dellago and Peter G.Bolhuis
    Phys. Rev. Lett. 106, 085701 (2011).
11. Multiscale modelling
    Lucas Visscher, Peter G. Bolhuis and F. Matthias Bickelhaupt
    Phys. Chem. Chem. Phys. 13, 10399-10400 (2011).
12. The self-assembly mechanism of fibril-forming silk-based block copolymers
    Marieke Schor and Peter G. Bolhuis
    Phys. Chem. Chem. Phys. 13, 10457-10467 (2011).
13. 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).
14. 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).
15. Molecular simulation investigation into the performance of Cu-BTC metal-organic frameworks for carbon dioxide-methane separations
    Juan Jose Gutierrez-Sevillano, Alejandro Caro-Perez, David Dubbeldam and Sofia Calero
    Phys. Chem. Chem. Phys. 13(45), 20453-20460 (2011).
16. External Surface Adsorption on Silicalite-1 Zeolite Studied by Molecular Simulation
    Elena Garcia-Perez, Sondre K. Schnell, Juan M. Castillo, Sofia Calero, Signe Kjelstrup, David Dubbeldam and Thijs J.H. Vlugt
    J. Phys. Chem. C 115(31), 15355-15360 (2011).
17. Elucidating steric effects on enantioselective epoxidation catalyzed by (salen)Mn in metal-organic frameworks
    Gloria A.E. Oxford, David Dubbeldam, Linda J. Broadbelt and Randall Q. Snurr
    J. Mol. Cat. A 334(1-2), 89-97 (2011).
18. Proline 68 tunes photochemistry yield in Photoactive Yellow Protein
    A.B. Rupenyan, J. Vreede, I.H.M. van Stokkum, M. Hospes, J.T.M. Kennis, K.J. Hellingwerf and M.L. Groot
    J. Phys. Chem. B 115, 6668 (2011).

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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
   Jocelyne 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 114(50), 22207–22213 (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 334(1-2), 89-97 (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. 22(16), 4591-4601 (2010).
20. Reconciling 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. 495(1-3), 77-79 (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. 1(14), 2154–2158 (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. 133(3), 034114 (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

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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, and 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).

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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

3. Multiple state transition path sampling
   J. Rogal and P.G. Bolhuis,
   J. Chem. Phys. 129, 224107 (2008).
4. 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).
5. 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).
6. Rare events via multiple reaction channels sampled by path replica exchange
   P.G Bolhuis,
   J. Chem. Phys. 129, 114108 (2008).
7. Rate Constant and Reaction Coordinate of Trp-Cage Folding in Explicit Water
   J. Juraszek and P.G. Bolhuis,
   Biophys. J. 95, 4246-4257 (2008).
8. 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).
9. TraR auto-inducer enhances protein backbone fluctuations in DNA binding domain
   J. Vreede, K.J. Hellingwerf, W. Crielaard,
   FEBS Lett 582, 805-809 (2008).
10. 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).
11. 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).
12. Diffusion of alkane mixtures in MFI zeolite
    R. Krishna and J.M. van Baten,
    Microporous Mesoporous Mater. 107, 296-298 (2008).
13. 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).
14. 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).
15. 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).
16. 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).
17. Onsager coefficients for binary mixture diffusion in nanopores
    R. Krishna, J.M. van Baten,
    Chem. Eng. Sci. 63, 3120-3140 (2008).
18. Diffusion of hydrocarbon mixtures in MFI zeolite: Influence of intersection blocking
    R. Krishna, J.M. van Baten,
    Chem. Eng. J. 140, 614-620 (2008).
19. 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).
20. 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).
21. 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).
22. Efficient constraint dynamics using MILC SHAKE
    A.G. Bailey, C.P. Lowe, and A.P. Sutton,
    J. Comp. Phys. 227, 8949-8959 (2008).
23. 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).
24. Molecular Simulations of Zeolites: Adsorption, Diffusion, and Shape Selectivity
    B. Smit, and T.L.M. Maesen,
    Chem. Rev. 108, 4125-4184 (2008).
25. 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).
26. Molecular Simulations of Lipid-Mediated Protein-Protein Interactions
    F.J-M. de Meyer, M. Ventuoli, and B. Smit,
    Biophys. J. 95, 1851-1865 (2008).
27. 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).
28. Towards a molecular understanding of shape selectivity
    B. Smit and T. L. M. Maesen,
    Nature 451, 671 (2008).
29. 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)
30. 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)
31. 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.
  

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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

2. 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)
3. 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)]
   
4. Understanding diffusion in nanoporous materials
   E. Beerdsen and B. Smit, Stud. Surf. Scien. Catal. 170 1646 (2007)
5. Molecular simulations of the adsorption and diffusion of hydrocarbons in molecular sieves
   B. Smit, Stud. Surf. Scien. Catal. 170 121 (2007)
6. Sampling the kinetic pathways of a micelle fusion and fission transition
   R. Pool and P.G. Bolhuis, J. Chem. Phys. 126, 244703 (2007)
7. 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)]
   
8. 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)]
   
9. 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)]
   
10. 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)]
    
11. 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)]
    
12. 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)]
    
13. 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)]
14. 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)]
15. Realistic Modeling of Ruthenium-Catalyzed Transfer Hydrogenation
    Jan-Willem Handgraaf and Evert Jan Meijer, J. Am. Chem. Soc. 129, 3099-3103 (2007)
16. 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)
17. 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)
18. 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)
19. 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)
20. 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)
21. 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)
22. Levitation of air bubbles in liquid under low frequency vibration excitement
    J. Ellenberger and R. Krishna, Chemical Engineering Science, 62, 5669 - 5673 (2007)
23. Loading dependence of self-diffusivities of gases in zeolites
    R. Krishna and J.M. van Baten, Chemical Engineering & Technology, 30, 1235 - 1241 (2007)
24. 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)
25. Influence of segregated adsorption on mixture diffusion in DDR zeolite
    R. Krishna and J.M. van Baten, Chemical Physics Letters, 446, 344 - 349 (2007)
26. 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)
27. 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)
28. 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)
29. 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)
30. 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)

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2006

Cover

• Can purely repulsive soft potentials predict micelle formation correctly?
  René Pool and Peter G. Bolhuis, Phys. Chem. Chem. Phys., 2006, 8, 941 [pdf-file (internal only)]
  
  

Articles

2. Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations
   E.A. Koopman and C.P. Lowe J. Chem. Phys. 124, 204103 (2006)
3. 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)]
   
4. 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)]
   
5. 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)]
   
6. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
   Juraszek, J.; Bolhuis, P. G., PNAS (2006), 103(43), 15859-15864
7. Prediction of an Autocatalytic Replication Mechanism for Micelle Formation
   Pool, Rene; Bolhuis, Peter G., Physical Review Letters (2006), 97(1), 018302/1-018302/4
8. 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)
9. 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
10. 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)
11. 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)]
    
12. 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)
13. 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
14. 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)
15. 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)
16. 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)
17. 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)
18. 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)
19. 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)
20. Reply to Letter to Editor
    R. Taylor, R. Baur and R. Krishna, A.I.Ch.E.J., 52, 1969- 1970 (2006)
21. 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)
22. 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)]
    
23. 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)]
    
24. 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)]
    
25. Diffusion in Confinement - Agreement Between Experiments Better than Expected
    Beerdsen, E.; Smit, B., J. Phys. Chem. B, 110, 14529 (2006) [pdf-file (internal only)]
    
26. 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)]
    
27. 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)]
    
28. 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)]
    
29. 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)]
    
30. 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)]
    
31. 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)]
    
32. 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)]
    
33. 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)]
    
34. 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)]
    
35. Understanding Diffusion in Nanoporous Materials
    E. Beerdsen, D. Dubbeldam, and B. Smit, Phys. Rev. Lettr. 96, 044501 (2006) [pdf-file (internal only)]
    
36. 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)]
  
  

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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)]

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2004

Articles

• Activation Energies from Transition Path Sampling Simulations
  Christoph Dellago and Peter G. Bolhuis, Molecular Simulation Volume 30, Numbers 11-12, 2004 [pdf-file (internal only)]
• Elimination of time step effects in DPD
  E. A. J. F. Peters, Europhys. Lett., 66 (3) , pp. 311-317 (2004) [pdf-file (internal only)]
• Molecular Simulations of Surface Forces and Film Rupture in Oil/Water/Surfactant Systems
  Live Rekvig, Bjørn Hafskjold, and Berend Smit, Langmuir; 2004; 20(26) pp 11583 - 11593 [pdf-file (internal only)]
• Molecular Simulation of Loading Dependent Slow Diffusion in Confined Systems
  E. Beerdsen, B. Smit, and D. Dubbeldam, Phys. Rev. Lett. 93, 248301 (2004) [pdf-file (internal only)]
• Density Functional theory-based Molecular Simulation Study of Liquid Methanol,
  Jan-Willem Handgraaf, Evert Jan Meijer, and Marie-Pierre Gaigeot, J. Chem. Phys. 121, 10111 (2004).
  Appears also in in Virtual Journal of Biological Physics Research 8 (Issue 10) (2004).
• Investigating rare events by transition interface sampling,
  D. Moroni, T.S. van Erp, and P.G. Bolhuis, Physica A 340 (1-3): 395-401 ( 2004)
• The selectivity of n-hexane hydroconversion on MOR-, MAZ-, and FAU-type zeolites
  Sofia Calero, Merijn Schenk, David Dubbeldam, Theo L.M. Maesen, and Berend Smit, Journal of Catalysis, Volume 228, Issue 1 , 15 November 2004, Pages 121-129 [pdf-file (internal only)]
• Reply to the Comment on "Computer Simulation of Incommensurate Diffusion in Zeolites: Understanding Window Effects"
  D. Dubbeldam, T. L. M. Maesen, and B. Smit, J. Phys. Chem. B; 2004; 108(41) pp 16330 - 16330; (Comment) [pdf-file (internal only)]
• Mesoscopic simulations of phase transitions in lipid bilayers
  Marieke Kranenburg, Christophe Laforge and Berend Smit, Phys. Chem. Chem. Phys., 2004, 6 (19), 4531 - 4534 [pdf-file (internal only)]
• Understanding the Role of Sodium during Adsorption: A Force Field for Alkanes in Sodium-Exchanged Faujasites
  Sofía Calero, David Dubbeldam, Rajamani Krishna, Berend Smit, Thijs J. H. Vlugt, Joeri F. M. Denayer, Johan A. Martens, and Theo L. M. Maesen, J. Am. Chem. Soc., 126 (36), 11377 -11386, 2004 [pdf-file (internal only)]
• Simulating Induced Interdigitation in Membranes
  Marieke Kranenburg, Martin Vlaar and Berend Smit, Biophysical Journal 87:1596-1605 (2004) [pdf-file (internal only)]
• Force Field Parametrization through Fitting on Inflection Points in Isotherms
  D. Dubbeldam, S. Calero, T. J. H. Vlugt, R. Krishna, T. L. M. Maesen, E. Beerdsen, and B. Smit, Phys. Rev. Lett. 93, 088302, 2004 [pdf-file (internal only)]
• United Atom Force Field for Alkanes in Nanoporous Materials
  D. Dubbeldam, S. Calero, T. J. H. Vlugt, R. Krishna, T. L. M. Maesen, and B. Smit, J. Phys. Chem. B, 108 (33), 12301 -12313, 2004 [pdf-file (internal only)]
• Comparison of mesoscopic phospholipid-water models
  Marieke Kranenburg , Jean-Pierre Nicolas and Berend Smit, Phys. Chem. Chem. Phys., 2004, 6 (16), 4142 - 4151 [pdf-file (internal only)]
• Simulating the effect of alcohol on the structure of a membrane
  Marieke Kranenburg and Berend Smit, FEBS Letters, Volume 568, Issues 1-3 , 18 June 2004, Pages 15-18 [pdf-file (internal only)]
• Molecular Simulations of Swelling Clay Minerals
  Tim J. Tambach, Emiel J. M. Hensen, and Berend Smit, J. Phys. Chem. B, 108 (23), 7586 -7596, 2004 [pdf-file (internal only)]
• A Molecular Mechanism of Hysteresis in Clay Swelling
  Tim J. Tambach, Peter G. Bolhuis, Berend Smit, Angew. Chem. Int. Ed. 43, Issue 20, Pages 2650-2652, 2004 [pdf-file (internal only)]
  
• Modelling of the Complex between a 15-Residue Peptide from mSos2 and the N-Terminal SH3 Domain of Grb2 by Molecular-Dynamics Simulation
  Sofía Calero, Santiago Lago, Wilfred F. van Gunsteren, Xavier Daura, Chemistry & Biodiversity, Volume 1, Issue 3 , Pages 505 - 519, 2004 [pdf-file (internal only)]
• Chain Length Dependencies of the Bending Modulus of Surfactant Monolayers
  Phys. Rev. Lett. 92, 116101 (2004), Live Rekvig, Bjørn Hafskjold, and Berend Smit [pdf-file (internal only)]
• Rate constants for diffusive processes by partial path sampling
  Moroni D, Bolhuis PG, van Erp TS, J. Chem. Phys. 120 (9): 4055-4065 MAR 1 2004 [pdf-file (internal only)]
• High pressure diamond-like liquid carbon
  Luca M. Ghiringhelli, Jan H. Los, Evert Jan Meijer, A. Fasolino, and Daan Frenkel, Phys. Rev. B 69 (2004), 100101(R).
• Simulating the effect of surfactant structure on bending moduli of monolayers
  Live Rekvig and Bjørn Hafskjold and Berend Smit, J. Chem. Phys., Vol. 120, No. 10, pp. 4897–4905, 2004 [pdf-file (internal only)]
• Proton-Assisted Ethylene Hydration in Aqueous Solution
  Titus S. van Erp and Evert Jan Meijer, Angew. Chem. Int. Ed. 43, 1660-1662 (2004).
  
• Molecular simulations of adsorption isotherms of small alkanes in FER-, TON-, MTW-, and DON-type zeolites
  J-M. B. Ndjaka, G. Zwanenburg, B. Smit, M. Schenk, Microporous Mesoporous Matt. 68, 2004, 38.
• Capillary Phase Transitions of n-Alkanes in a Carbon Nanotube
  Jianwen Jiang, Stanley I. Sandler, and Berend Smit, Nano Letters, 4 (2), 241 -244, 2004. [pdf-file (internal only)]
• Alkane hydrocracking: shape selectivity or kinetics?
  Theo L. M. Maesen, Sofia Calero, Merijn Schenk and Berend Smit, Journal of Catalysis Volume 221, Issue 1 , 1 January 2004, Pages 241-251 [pdf-file (internal only)]
• Molecular dynamics study of n-hexane--water interface:
  towards a better understanding of the liquid-liquid interfacial broadening
  J.P. Nicolas and N.R. de Souza, J. Chem. Phys, 2004, Volume 120, 5, pp. 2464-2469. [pdf-file (internal only)]

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)
  
  

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2003

Articles

• Rate constants for diffusive processes by partial path sampling
  Moroni D, Bolhuis PG, van Erp TS, J CHEM PHYS 120 (9): 4055-4065 MAR 1 2004
• The Asakura-Oosawa model in the protein limit: the role of many-body interactions
  Moncho-Jorda A, Louis AA, Bolhuis PG, et al. , J PHYS-CONDENS MAT 15 (48): S3429-S3442 Sp. Iss. SI DEC 10 2003 [pdf-file (internal only)]
  
• Simulation and theory of fluid-fluid interfaces in binary mixtures of hard spheres and hard rods
  Bolhuis PG, Brader JM, Schmidt M, J PHYS-CONDENS MAT 15 (48): S3421-S3428 Sp. Iss. SI DEC 10 2003
• Structure of liquids composed of shifted dipole linear molecules
  Santiago Lago, Silvia López-Vidal, Benito Garzón,2 José A. Mejías, Juan A. Anta, and Sofía Calero, Phys. Rev. E 68, 021201 (2003) [pdf-file (internal only)]
  
• Influence of charge distribution on the thermophysical and dynamical properties of polar linear molecules
  Sofía Calero, Benito Garzón, and Santiago Lago, J. Chem Phys, June 22, 2003, Volume 118, Issue 24, pp. 11079-11091 [pdf-file (internal only)]
  
• DFT-based Molecular Dynamics Study of Aqueous Chloride Solvation
  J.M. Heuft and E.J. Meijer, J. Chem. Phys. 119 (2003), 11788-11791.
• Smit, B., Krishna, R. In Handbook of Zeolite Science and Technology; Auerbach, S. M., Carrado, K. A., Dutta, P. K., Eds.; Marcel Dekker: New York, 2003 [pdf-file (internal only)]
  
• Computer Simulation of Incommensurate Diffusion in Zeolites: Understanding Window Effects
  David Dubbeldam and Berend Smit, J. Phys. Chem. B, 107 (44), 12138 -12152, 2003 [pdf-file (internal only)]
  
• Simulating the Effect of Nonframework Cations on the Adsorption of Alkanes in MFI-type Zeolites
  Edith Beerdsen, David Dubbeldam, Berend Smit, Thijs J. H. Vlugt, and Sofía Calero, J. Phys. Chem. B, 107 (44), 12088 -12096, 2003 [pdf-file (internal only)]
  
• Transition path sampling on diffusive barriers
  P.G. Bolhuis, J. Phys. Cond. Mat., 15 pp S113-S120, 2003
• A novel path sampling method for thye calculation of rate constants
  T.S. van Erp, D. Moroni and P.G. Bolhuis, J. Chem Phys. 118, pp 7762-7774, 2003
• Transition-path sampling of beta hairpin folding
  P.G. Bolhuis, Proc. Nat. Acad. Sci. USA 2003 100: 12129-12134
• High-pressure liquid phase hydroconversion of heptane/nonane mixtures on Pt/H-Y zeolite catalyst
  
• Joeri F. M. Denayer, Refik A. Ocakoglu, Ward Huybrechtsb, Bruno Dejonckheere, Pierre Jacobs, Sofia Calero, Rajamani Krishna, Berend Smit, Gino V. Baron and Johan A. Martens, Journal of Catalysis, Volume 220, Issue 1 , 15 November 2003, Pages 66-73 [pdf-file (internal only)]
  
• Phase Behavior and Induced Interdigitation in Bilayers Studied with Dissipative Particle Dynamics
  Marieke Kranenburg, Maddalena Venturoli, and Berend Smit, J. Phys. Chem. B, 107 (41), 11491 -11501, 2003 [pdf-file (internal only)]
  
• Investigation of Surfactant Efficiency Using Dissipative Particle Dynamics
  Live Rekvig, Marieke Kranenburg, Jocelyne Vreede, Bjorn Hafskjold, and Berend Smit Langmuir, 19 (20), 8195 -8205, 2003 [pdf-file (internal only)]
  
• Effect of surfactant structure on interfacial properties
  L. Rekvig, M. Kranenburg, B. Hafskjold and B. Smit Europhys. Lett., 63 (6) , pp. 902-907 (2003) [pdf-file (internal only)]
  
• Molecular Dynamics Simulation of Surfactin Molecules at the Water-Hexane Interface
  J. P. Nicolas, Biophysical Journal 85:1377-1391 (2003)
• Understanding the Window Effect in Zeolite Catalysis
  David Dubbeldam, Sofia Calero, Theo L.M. Maesen and Berend Smit, Angew. Chem. Int. Ed., 42, p3624-3626 (2003) [pdf-file (internal only)]
  
• Iridium(I) versus Ruthenium(II). A Computational Study of the Transition Metal Catalyzed Transfer Hydrogenation of Ketones
  Jan-Willem Handgraaf, Joost N.H. Reek, and Evert Jan Meijer, Organometallics 22, 3150--3157 (2003). (DOI: 10.1021/om030104t)
• Shape selectivity through entropy
  Merijn Schenk, Sofia Calero, Theo L. M. Maesen, Thijs J. H. Vlugt, Lucas L. van Benthem, Martijn G. Verbeek, Benoit Schnell and Berend Smit, Journal of Catalysis, Volume 214, Issue 1, Pages 1-168 [pdf-file (internal only)]
  
• Incommensurate Diffusion in Confined Systems
  D. Dubbeldam, S. Calero, T. L. M. Maesen, and B. Smit, Phys. Rev. Lett. 90, 245901 (2003) [pdf-file (internal only)]
  
• Molecular simulations of mesoscopic bilayer phases
  Marieke Kranenburg, Maddalena Venturoli, and Berend Smit, Phys Rev. E 67, 060901(R) (2003) [pdf-file (internal only)]
  
• Colloid-polymer mixtures in the protein limit
  P.G. Bolhuis, E.J. Meijer, and A.A. Louis, Phys. Rev. Lett. 90 (2003), 068304
• Ab initio molecular dynamics study of liquid methanol
  J.-W. Handgraaf, T. S. van Erp and E. J. Meijer, Chem. Phys. Lett. 367 (2003) 617-624. [pdf-file (internal only)]
  
• Molecular simulations in zeolitic process design
  B. Smit and R. Krishna, Chemical Engineering Science, Volume 58, Issues 3-6, February-March 2003, Pages 557-568 [pdf-file (internal only)]
  
• Ab Initio Molecular Dynamics Study of Aqueous Solvation of Ethanol and Ethylene
  T.S. van Erp and E.J. Meijer, J. Chem. Phys. 118 (2003) p8831-8840
  

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.

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2002

Articles

• Accurate method for the Brownian dynamics simulation of spherical particles with hard-body interactions
  Barenbrug TMAOM, Peters EAJF, Schieber JD, JOURNAL OF CHEMICAL PHYSICS 117 (20): 9202-9214 NOV 22 2002
• Efficient Brownian dynamics simulation of particles near walls. I. Reflecting and absorbing walls
  Peters EAJF, Barenbrug TMAOM, PHYSICAL REVIEW E 66 (5): art. no. 056701 NOV 2002
• Efficient Brownian dynamics simulation of particles near walls. II. Sticky walls
  Peters EAJF, Barenbrug TMAOM, PHYSICAL REVIEW E 66 (5): art. no. 056702 NOV 2002
• Why Clays Swell. [pdf-file (internal only)]
  Emiel J.M. Hensen and Berend Smit, J Phys. Chem. B, 106(49), p12664 - 12667 (2002)
• Influence of Framework Flexibility on the Adsorption Properties of Hydrocarbons in the Zeolite Silicalite.
  T.J.H. Vlugt and M. Schenk, J. Phys. Chem. B 106, p12757-12763 (2002)
• The influence of non-framework sodium cations on the adsorption of alkanes in MFI- and MOR-type zeolites.
  E. Beerdsen, B. Smit and S. Calero, J. Phys. Chem. B 106, p10659-10667 (2002)
• Aubry transition studied by direct evaluation of the modulation functions of infinite incommensurate systems
  T.S. van Erp and A. Fasolino, Europhysics Letters 59 , 330-336 (2002)
• Influence of polymer excluded volume on the phase behavior of colloid-polymer mixtures
  P.G. Bolhuis, A. A. Louis and J-P. Hansen, Phys. Rev. Lett. 89 128302 (2002)
• Transtion Path Sampling
  C.Dellago, P.G.Bolhuis and P.L. Geissler, Adv. Phys. Chem. 123: 1-78 (2002)
• Polymer induced depletion potentials in polymer-colloid mixtures
  A.A. Louis, P.G. Bolhuis, E.J. Meijer and J.P. Hansen, J. Chem. Phys. 117: 1893-1907 (2002)
• Transtion Path Sampling: throwing ropes over dark mountain passes
  P.G. Bolhuis, C.Dellago, P.L. Geissler, and D. Chandler, Annu. Rev. Chem. Phys. 53: 291-318 (2002)
• Density profiles and surface tension of polymers near colloidal surfaces
  A.A. Louis, P.G. Bolhuis, E.J. Meijer and J.P. Hansen. J. Chem. Phys. 116 (23): 10547-10556 (2002)
• Coarse-graining polymers as soft colloids
  A.A. Louis, P.G. Bolhuis, R. Finken, V. Krakoviack, E.J. Meijer and J.P. Hansen, Physica A 306 (1-4): 251-261 2002
• How to derive and parameterize effective potentials in colloid-polymer mixtures
  P.G. Bolhuis and A.A. Louis, Macromolecules 35 (5): 1860-1869 (2002)
• The influence of non-framework sodium cations on the adsorption of alkanes in MFI- and MOR-type zeolites. [pdf-file (internal only)],
  E. Beerdsen, B. Smit and S. Calero, J. Phys. Chem. B, 106 (41), 10659 -10667, 2002
• Investigation of entropy effects during sorption of mixtures of alkanes in MFI zeolite, [pdf-file (internal only)]
  R. Krishna, S. Calero and B. Smit, Chemical Engineering Journal 88, 2002, p. 81-94.
• Simulating Tethered Polymer Layers in Shear Flow with the Dissipative Particle Dynamics Technique, [pdf-file (internal only)]
  C.M. Wijmans and B. Smit, Macromolecules 35, 2002, p. 7138-7148.
• Molecular dynamics simulations of the surface tension of n-hexane, n-decane and n-hexadecane, [pdf-file (internal only)]
  J. P. Nicolas and B. Smit, Molecular Physics 100, 15, 2002, p. 2471-2475.
• Regular Binary Thermal Lattice-Gases, [pdf-file (internal only)]
  R. Blaak and D. Dubbeldam, J. Stat. Phys. 108, 1-2, 2002, p. 283-315.
• Understanding zeolite catalysis: Inverse shape selectivity revised, [pdf-file (internal only)]
  M. Schenk, S. Calero, T.L.M. Maesen, L.L. van Benthem, M.G. Verbeek and B. Smit, Angew. Chem. Int. Ed. 2002, 41, p2500-2502.
  
• Entropy effects during sorption of alkanes in zeolites., [pdf-file (internal only)]
  R. Krishna, B. Smit, S. Calero, Chem. Soc. Rev. 2002, 31, p185-194

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2001

Articles

• Monte Carlo simulations in zeolites, [pdf-file (internal only)]
  B. Smit and R. Krishna, Curr. Opin. Solid. St. M., 5(5), 2001, p455-461
• Accurate effective pair potentials for polymer solutions
  P.G. Bolhuis, A.A. Louis, J-P Hansen and E.J. Meijer, J. Chem Phys 114 (9): 4296-4311 (2001)
• Differences between MFI- and MEL-type Zeolites in Paraffin Hydrocracking, [pdf-file (internal only)]
  T.L.M. Maesen, M. Schenk, T.J.H. Vlugt and B. Smit, J. Catal., 2001, 203(2), p281-291
• Configurational Entropy Effects during Sorption of Hexane Isomers in Silicalite, [pdf-file (internal only)]
  S. Calero, B. Smit, R. Krishna, J. Catal, 2001, 202(2), p395-401
• Separation of linear, mono-methyl and di-methyl alkanes in the 5-7 carbon atom range by exploiting configurational entropy effects during sorption on silicalite-1, [pdf-file (internal only)]
  S. Calero, B. Smit and R. Krishna, Phys. Chem. Chem. Phys., 2001, 3(19), 4390 - 4398
• Adsorption isotherms of water in Li-, Na-, and K-montmorillonite by molecular simulation, [pdf-file (internal only)]
  E.J.M. Hensen, T.J. Tambach, A. Bliek, and B. Smit, J. Chem. Phys., 2001, 115, p 3322-3329
• Adsorption and Diffusion of n-Hexane/2-Methylpentane Mixtures in Zeolite Silicalite: Experiments and Modeling, [pdf-file (internal only)]
  D. Schuring, A.O. Koriabkina, A.M. de Jong, B. Smit and R.A. van Santen, J. Phys. Chem. B, 2001, 105, p 7690-7698
• Simulating shape selectivity in alkane hydroconversion by zeolites
  M. Schenk, T.L.M. Maesen, B. Smit, Proceedings of the 13th International Zeolite Conference. (Studies in surface science and catalysis 135, p155)
• Introduction to Zeolite Theory and Modelling
  Van Santen, R.A. and Smit, B. and van de Graaf, B in "Introduction to Zeolite Science and Practice" 2nd edition, p 419-466, Editors van Bekkum, H. and Flanigen, E.M. and Jacobs, P.A. and Jansen, J.C., Elsevier, Amsterdam 2001.
• Structural Transitions and Phonon Localization in Frenkel Kontorova Models with Quasi-Periodic Potentials
  T.S. van Erp, A. Fasolino and T. Janssen, Ferroelectrics 250 , 421-424 (2001)
• Phase behavior of monomeric mixtures and polymer solutions with soft interaction potentials, [pdf-file (internal only)]
  C. M. Wijmans, B. Smit and R. D. Groot, J. Chem. Phys., 2001, 114, 7644-7654
• Solvation effects on the SN2 reaction between CH3Cl and Cl- in water
  B. Ensing, E.J. Meijer, P.E. Blöchl and E.J. Baerends, J. Phys. Chem. A, 2001, 105, 3300-3310.
• Shape selectivity in alkane hydroconversion , [pdf-file (internal only)]
  M. Schenk, B. Smit, T.J.H. Vlugt, T.L.M. Maesen, Angew. Chem. Int. Ed, 2001, 40, 736-738
• Separation of alkane isomers by exploiting entropy effects during adsorption on silicalite-1: A CBMC simulation study , [pdf-file (internal only)]
  M. Schenk, S.L. Vidal, T.J.H. Vlugt, B. Smit, R. Krishna, Langmuir, 2001, 17, 1558-1570
• Exploiting entropy to separate alkane isomers
  Krishna R, Smit B, CHEMICAL INNOVATION, 31: (1) 27-33 JAN 2001
• On the efficient sampling of pathways in the transition path ensemble, [pdf-file (internal only)]
  Thijs J.H. Vlugt and Berend Smit, PhysChemComm, 2001, 2
• Hydration of Methanol in Water. A DFT-based Molecular Dynamics Study
  T.S. van Erp and E.J. Meijer, Chem. Phys. Lett., 2001, 333, 290-296.
• Boltzmann approximation of transport properties in thermal lattice gases, [pdf-file (internal only)]
  Ronald Blaak and David Dubbeldam, Phys. Rev. E, Volume 63, 021109
• Coupling of thermal and mass diffusion in regular binary thermal lattice gases, [pdf-file (internal only)]
  Ronald Blaak and David Dubbeldam, Phys. Rev. E, Volume 64, 062102

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2000

Articles

• Diffusion of isobutane in Silicalite studied by transition path sampling, [pdf-file (internal only)]
  T.J.H. Vlugt, C. Dellago and B. Smit, J. Chem. Phys., 2000, 113, 8791-8799.
• Can Polymer Coils be modeled as ``Soft Colloids''?
  A.A. Louis, P.G. Bolhuis, J.P. Hansen, and E.J. Meijer, Phys. Rev. Lett., 2000, 85, 2522-2525
• Chiral induction effects in ruthenium(II)-amino alcohol catalysed asymmetric transfer hydrogenation of ketones: An experimental and theoretical approach
  D.G.I. Petra, J.N.H. Reek, J.-W. Handgraaf, E.J. Meijer, P. Dierkes, P.C.J. Kamer, J. Brussee, H.E. Schoenmaker, and P.W.N.M. van Leeuwen, Chem. Eur. J., 2000, 15, 2818-2829.
• Advanced CBMC techniques
  T.J.H. Vlugt and B. Smit, In: Proceedings of the Workshop "Molecular Dynamics on Parallel Computers", Jülich, Germany, February 8-10 1999, Editors: R. Esser, P. Grassberger, J. Grotendorst and M. Lewerenz, World Scientific, 2000.
• Line of triple points for the hard-core Yukawa model: A computer simulation study
  F. El Azhar, M. Baus, J.-P. Ryckaert, and E.J. Meijer J. Chem. Phys, 2000, 112, 5121-5126
• Book review of: Chemical Modeling: from atoms to liquids by Alan Hinchliffe (Ed.), Wiley, 1999., [pdf-file (internal only)]
  Chemical Engineering Journal, 2000, 76, 253-254.

Thesis

• Adsorption and Diffusion in Zeolites: A Computational Study
  T.J.H. Vlugt, Ph.D. thesis, University of Amsterdam, 2000. thesis.pdf (1.0M), requires Adobe Acrobat Reader 4.05 or better. If you are interested in a (paper) copy, please send an email to the secretary of ITS. It is also possible to download a stripped version of the LaTeX source (maybe usefull as a template).

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1999

Articles

• Simulating the self-assembly of model membranes, [pdf-file (internal only)]
  M.Venturoli and B. Smit, Phys. Chem. Comm., 10, 1999.
• The Shape Selectivity of Paraffin Hydroconversion on TON-, MTT- and AEL-type Sieves, [pdf-file (internal only)]
  Th.L.M. Maesen, M. Schenk, T.J.H. Vlugt, J.P. de Jonge and Berend Smit, J. Catal., 1999, 188, 403-412.
• Recoil Growth Algorithm for Chain Molecules with continuous interactions, [pdf-file (internal only)]
  S. Consta, T.J.H. Vlugt, J. Wichers Hoeth, B.Smit and D. Frenkel, Mol. Phys., 1999, 97, 1243-1254.
• Efficiency of parallel CBMC simulations
  T.J.H. Vlugt, Molecular Simulation, 1999, 23, 63-78.
• Adsorption of linear and branched alkanes in Ferrierite: A computational study
  T.J.H. Vlugt, B. Smit, R. Krishna, Proceedings of the 12th International Zeolite Conference, Treacy, M.M.J., Marcus, B.K., Bisher, M.E., and Higgins, J.B. (eds), Materials Research Society, Vol 1, 325-332 Warrendale, (1999).
• Molecular Simulations of Adsorption Isotherms for Linear and Branched Alkanes and their Mixtures in Silicalite, [pdf-file (internal only)]
  T.J.H. Vlugt, B. Smit, R. Krishna, J. Phys. Chem. B, 1999, 103, 1102-1118.
• Influence of Isotherm inflection on diffusion in Silicalite, [pdf-file (internal only)]
  R. Krishna, T.J.H. Vlugt, B. Smit., Chem. Eng. Sci., 1999, 54, 1751-1757.

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1998

Articles

• Monte Carlo Simulations for Studying Complex Fluids
  B. Smit, in "Encyclopedia of Computational Chemistry", Schleyer, P.v.R.; Allinger, N.L; Clark T.; Gasteiger, J.; Kollman, P.A.; Schaefer III, H.F., and Schreiner P.R. (editors), John Wiley & Sons, Chichester, U.K., 1998, pg. 1742-1754
• Combining Dissipative Particle Dynamics and Monte Carlo techniques , [pdf-file (internal only)]
  S. Willemsen, T.J.H. Vlugt, H. Hoefsloot and B. Smit, Journal of Computational Physics, 1998, 147, 507-517.
• Wassen in de computer
  B. Smit, Natuur & Techniek, 1998, 66, 20-29.
• BIGMAC, a Configurational Bias Monte Carlo program.
  T.J.H. Vlugt and B. Smit, published on the web on 1-9-1998.
• Improving the efficiency of the CBMC algorithm, [pdf-file (internal only)]
  T.J.H. Vlugt, M.G. Martin., B. Smit, J.I. Siepmann, R. Krishna, Mol. Phys., 1998, 94, 727-733.
• Sorption-Induced diffusion-selective separation of hydrocarbon isomers using silicalite , [pdf-file (internal only)]
  R. Krishna, B. Smit, T.J.H. Vlugt, J. Phys. Chem. A, 1998, 102, 7727-7730.
  
• Adsorption of Short Linear Alkanes and their Mixtures in Silicalite, [pdf-file (internal only)]
  Z. Du, T.J.H. Vlugt, B. Smit, G. Manos, AIChE Journal, 1998, 44, 1756-1764.
• Simulation of alkane adsorption in the aluminophosphate molecular sieve ALPO4-5 , [pdf-file (internal only)]
  T. Maris, T.J.H. Vlugt, and B. Smit, J. Phys. Chem. B, 1998, 102, 7183-7189.
• Some applications of the configurational-bias Monte Carlo technique
  B. Smit, International School Enrico Fermi: "Classical and Quantum Dynamics in Condensed Phase Simulations" Editors: B.J. Berne,G. Ciccotti, and D.F. Coker (World Scientific, Singapore, 1998) 251-266
• Adsorption of Linear and Branched Alkanes in the Zeolite Silicalite-1 , [pdf-file (internal only)]
  T.J.H. Vlugt, W. Zhu, F. Kapteijn, J.A. Moulijn, B. Smit, R. Krishna, J. Am. Chem. Soc., 120, 5599-5600.
• Chain Length Effects of Linear Alkanes in Zeolite Ferrierite. 1. Sorption and 13C NMR Experiments , [pdf-file (internal only)]
  Willy J. M. van Well, Xavier Cottin, Jan W. de Haan, Berend Smit, Gautam Nivarthy, Johannes A. Lercher, Jan H. C. van Hooff, and Rutger A. van Santen, J. Phys. Chem. B, 102 (20), 3945 -3951, 1998.
• Chain Length Effects of Linear Alkanes in Zeolite Ferrierite. 2. Molecular Simulations , [pdf-file (internal only)]
  Willy J. M. van Well, Xavier Cottin, Berend Smit, Jan H. C. van Hooff, and Rutger A. van Santen, J. Phys. Chem. B, 102 (20), 3952 -3958, 1998.
• Effect of Chain Length on the Adsorption Behavior of n-Alkanes in Ferrierite
  W.J. M. van Well, X. Cottin, J.W. de Haan, R. A. van Santen, and B. Smit, Angew. Chem. Int. Ed. 37 (1998) 1081-1083

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1997

Articles

• Configurational-bias Monte Carlo (CB-MC) calculations of n-alkane sorption in zeolites RHO and FER
  S.P. Bates, W.J.M. Van Wel, R.A. Van Santen, and B. Smit Mol. Sim., 19 (1997) 301-318
• Simulation of adsorption and diffusion of hydrocarbons in zeolites
  Berend Smit, Daniel Loyens, and Guy Verbist, Faraday Discuss., 106 (1997) 93-104
• Commensurate freezing of hydrocarbons in silicalite,
  W.J.M. van Well, J.P. Wolthuizen, B. Smit, J.H.C. van Hooff, and R.A. van Santen, in Progress in Zeolite and Microporous Materials, Vol. 105 of Studies in Surface Science and Catalysis, edited by H. Chon, S.-K. Ihm, and Y.S. Uh (Elsevier Science B.V., Amsterdam, 1997), pp. 2347-2354.
• Understanding Molecular Simulations: Simulating Phase Coexistence,
  D. Frenkel and B. Smit, Comp. in Phys. 11:246 (1997).

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1996

Articles

• Associating lattice fluids near hard and interacting walls , [pdf-file (internal only)]
  R.H.C. Jansen, E. Nies, B. Smit, Langmuir:12:6537 (1996)
• Computational physics in industry,
  B. Smit, Europhys. News 27:189 (1996).
• Solid-solid and liquid-solid phase equilibria for the restricted primitive model , [pdf-file (internal only)]
  B. Smit, K. Esselink, and D Frenkel, Mol. Phys. 87:159 (1996).
• Le ballet mol'eculaire de l'huile et du savon,
  S. Karaborni, K. Esselink, and B. Smit, La Recherche 284:74 (1996).
• Molecular simulations of adsorption: from argon to long-chain paraffins,
  B. Smit, Rev. Int. Fran. Petr. 51:73 (1996).
• The swelling of clays: molecular simulations of the hydration of montmorillonite,
  S. Karaborni, B Smit, W. Heidug, J. Urai, and E. van Oort, Science 271:1102 (1996).
• Molecular simulations of fluid phase equilibria , [pdf-file (internal only)]
  B. Smit, Fluid Phase Equilibria 116:249 (1996).
• Energetics of n-alkanes in zeolites: a configurational-bias Monte Carlo investigation into pore size dependence , [pdf-file (internal only)]
  S.P. Bates, W.J.M. van Wel, R.A. van Santen, and B. Smit, J. Am. Chem. Soc. 118:6753 (1996).
• Location and conformation of n-alkanes in zeolites: An analysis of configurational-bias Monte Carlo calculations, , [pdf-file (internal only)]
  S.P. Bates, W.J.M. van Well, R.A. van Santen, and B. Smit, J. Phys. Chem. 100:17573 (1996).
• Computational physics in industry,
  B. Smit, Physica Scripta T66:80 (1996).
• Computer simulations of surfactant structures,
  S. Karaborni and B. Smit, Curr. Opin. Coll. Interf. Sci. 1:411 (1996).

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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).

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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).

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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).

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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).

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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).

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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).

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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).

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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).

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