Publications (99)
A parameter-free, solid-angle based, nearest-neighbor algorithm
Jacobus A. van Meel, Laura Filion, Chantal Valeriani +1
Point Defects in Hard Sphere Crystals
Sander Pronk, Daan Frenkel
Discrete solution of the electrokinetic equations
Fabrizio Capuani, Ignacio Pagonabarraga, Daan Frenkel
Lattice models and Monte Carlo methods for simulating DNA origami self-assembly
Alexander Cumberworth, Aleks Reinhardt, Daan Frenkel
Rational design of self-assembly pathways for complex multicomponent structures
William M. Jacobs, Aleks Reinhardt, Daan Frenkel
Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids
Eduardo Sanz, Chantal Valeriani, Daan Frenkel +1
The effect of temperature jumps during polymer crystallization
Jonathan Doye, Daan Frenkel
Gibbs, Boltzmann, and negative temperatures
Daan Frenkel, Patrick B Warren
Design principles for super selectivity using multivalent interactions
Tine Curk, Jure Dobnikar, Daan Frenkel
Kinetic Monte Carlo simulations of the growth of polymer crystals
Jonathan Doye, Daan Frenkel
Probing ergodicity in granular matter
Fabien Paillusson, Daan Frenkel
The physical determinants of the thickness of lamellar polymer crystals
Jonathan Doye, Daan Frenkel
Designing stimulus-sensitive colloidal walkers
Francisco J. Martinez-Veracoechea, Bortolo M. Mognetti, Stefano Angioletti-Uberti +3
Simple approach for calculating the binding free energy of a multivalent particle
Nicholas B. Tito, Stefano Angioletti-Uberti, Daan Frenkel
Running faster together: huge speed up of thermal ratchets due to hydrodynamic coupling
Paolo Malgaretti, Ignacio Pagonabarraga, Daan Frenkel
Quantitative prediction of the phase diagram of DNA-functionalized nano-colloids
Bianca M. Mladek, Julia Fornleitner, Francisco J. Martinez-Veracoechea +2
High pressure diamond-like liquid carbon
Luca M. Ghiringhelli, Jan H. Los, Evert Jan Meijer +2
Do cylinders exhibit a cubatic phase?
Ronald Blaak, Daan Frenkel, Bela M. Mulder
Consistent treatment of hydrophobicity in protein lattice models accounts for cold denaturation
Erik van Dijk, Patrick Varilly, Tuomas Knowles +2
Monte Carlo sampling for stochastic weight functions
Daan Frenkel, K. Julian Schrenk, Stefano Martiniani
Mobile linkers on DNA-coated colloids: valency without patches
Stefano Angioletti-Uberti, Patrick Varilly, Bortolo M. Mognetti +1
Controlling cargo trafficking in multicomponent membranes
Tine Curk, Peter Wirnsberger, Jure Dobnikar +2
Hamiltonian transformation to compute Thermo-osmotic Forces
Raman Ganti, Yawei Liu, Daan Frenkel
Phase Behavior and Selectivity of DNA-linked Nanoparticle Assemblies
D. B. Lukatsky, Daan Frenkel
Microscopic Marangoni flows cannot be predicted on the basis of pressure gradients
Yawei Liu, Raman Ganti, Hugh G. A. Burton +3
Forward Flux Sampling-type schemes for simulating rare events: Efficiency analysis
Rosalind J. Allen, Daan Frenkel, Pieter Rein ten Wolde
Numerical Evidence for Thermally Induced Monopoles
Peter Wirnsberger, Domagoj Fijan, Roger Adam Lightwood +3
Dynamical heterogeneity in a glass forming ideal gas
Patrick Charbonneau, Chinmay Das, Daan Frenkel
Large difference in the elastic properties of fcc and hcp hard-sphere crystals
Sander Pronk, Daan Frenkel
Homogeneous Bubble Nucleation driven by local hot spots: a Molecular Dynamics Study
Zun-Jing Wang, Chantal Valeriani, Daan Frenkel
Pair interactions between complex mesoscopic particles from Widom's particle-insertion method
Bianca M. Mladek, Daan Frenkel
The effect of chain stiffness on the phase behaviour of isolated homopolymers
Jonathan Doye, Richard Sear, Daan Frenkel
Multiple stalk formation as a pathway of defect-induced membrane fusion
D. B. Lukatsky, Daan Frenkel
Lattice simulation method to model diffusion and NMR spectra in porous materials
Céline Merlet, Alexander C. Forse, John M. Griffin +2
Real-time monitoring of complex moduli from micro-rheology
Taiki Yanagishima, Daan Frenkel, Jurij Kotar +1
The steady-state of heterogeneous catalysis, studied by first-principles statistical mechanics
Karsten Reuter, Daan Frenkel, Matthias Scheffler
Waterlike thermodynamic anomalies in a repulsive-step potential system
N. V. Gribova, Yu. D. Fomin, Daan Frenkel +1
Emergence of Critical Phenomena in Full Configuration Interaction Quantum Monte Carlo
James J. Shepherd, Lauretta R. Schwarz, Robert E. Thomas +3
Structural analysis of high-dimensional basins of attraction
Stefano Martiniani, K. Julian Schrenk, Jacob D. Stevenson +2
Computing stationary distributions in equilibrium and non-equilibrium systems with Forward Flux Sampling
Chantal Valeriani, Rosalind J. Allen, Marco J. Morelli +2
Molecular Simulation of Thermo-osmotic slip
Raman Ganti, Yawei Liu, Daan Frenkel
Superposition Enhanced Nested Sampling
Stefano Martiniani, Jacob D. Stevenson, David J. Wales +1
Crystal Nucleation of Colloidal Suspensions under Shear
Ronald Blaak, Stefan Auer, Daan Frenkel +1
Complex Phase Behavior of Repulsive Step Potential Systems in Three Dimensions
Yu. D. Fomin, Daan Frenkel, N. V. Gribova +2
Evidence for non-ergodicity in quiescent states of periodically sheared suspensions
K. Julian Schrenk, Daan Frenkel
Extended corresponding-states behavior for particles with variable range attractions
Massimo G. Noro, Daan Frenkel
Simulations: the dark side
Daan Frenkel
Pressure Gradients Fail to Predict Diffusio-Osmosis
Yawei Liu, Raman Ganti, Daan Frenkel
Kinetics of spontaneous filament nucleation via oligomers: insights from theory and simulation
AnÄela Å ariÄ, Thomas C. T. Michaels, Alessio Zaccone +2
Oligomers of heat-shock proteins: Structures that don't imply function
William M. Jacobs, Tuomas P. J. Knowles, Daan Frenkel
Turning intractable counting into sampling: computing the configurational entropy of three-dimensional jammed packings
Stefano Martiniani, K. Julian Schrenk, Jacob D. Stevenson +2
Numerical calculation of granular entropy
Daniel Asenjo, Fabien Paillusson, Daan Frenkel
Theoretical prediction of free-energy landscapes for complex self-assembly
William M. Jacobs, Aleks Reinhardt, Daan Frenkel
Large effect of polydispersity on defect concentrations in colloidal crystals
Sander Pronk, Daan Frenkel
Non-equilibrium simulations of thermally induced electric fields in water
Peter Wirnsberger, Domagoj Fijan, AnÄela Å ariÄ +3
Crucial role of non-specific interactions in amyloid nucleation
AnÄela Å ariÄ, Yassmine C. Chebaro, Tuomas P. J. Knowles +1
Collective sedimentation of colloids in grafted polymer layers
Tine Curk, Francisco J. Martinez-Veracoechea, Daan Frenkel +1
Numerical evidence for nucleated self-assembly of DNA brick structures
Aleks Reinhardt, Daan Frenkel
Application of the Optimized Baxter Model to the hard-core attractive Yukawa system
Peter Prinsen, Josep C. Pamies, Theo Odijk +1
Optimal packing of polydisperse hard-sphere fluids
Junfang Zhang, Ronald Blaak, Emmanuel Trizac +2
Modelling colloids with Baxter's adhesive hard sphere model
Mark A. Miller, Daan Frenkel
Accounting for adsorption and desorption in lattice Boltzmann simulations
Maximilien Levesque, Magali Duvail, Ignacio Pagonabarraga +2
Competition of percolation and phase separation in a fluid of adhesive hard spheres
Mark A. Miller, Daan Frenkel
A general theory of DNA-mediated and other valence-limited interactions
Patrick Varilly, Stefano Angioletti-Uberti, Bortolo M. Mognetti +1
Visualizing Basins of Attraction for Different Minimization Algorithms
Daniel Asenjo, Jacob D. Stevenson, David J. Wales +1
Direct determination of the size of basins of attraction of jammed solids
Ning Xu, Daan Frenkel, Andrea J. Liu
Layering, freezing and re-entrant melting of hard spheres in soft confinement
Tine Curk, Anouk de Hoogh, Francisco J. Martinez-Veracoechea +4
A Unified Description of Colloidal Thermophoresis
Jerome Burelbach, Daan Frenkel, Ignacio Pagonabarraga +1
A Lattice-Boltzmann method for the simulation of transport phenomena in charged colloids
Juergen Horbach, Daan Frenkel
Numerical test of the Edwards conjecture shows that all packings are equally probable at jamming
Stefano Martiniani, K. Julian Schrenk, Kabir Ramola +2
Free-energy barrier to melting of single-chain polymer crystallite
Wenbing Hu, Daan Frenkel, Vincent B. F. Mathot
DNA brick self-assembly with an off-lattice potential
Aleks Reinhardt, Daan Frenkel
Why Colloidal Systems can be described by Statistical Mechanics: Some not very original comments on the Gibbs paradox
Daan Frenkel
Hot nano-particles in polar or paramagnetic liquids interact as monopoles
Daan Frenkel
Simulating rare events in equilibrium or non-equilibrium stochastic systems
Rosalind J. Allen, Daan Frenkel, Pieter Rein ten Wolde
Lattice-Boltzmmann simulations of the sedimentation of charged disks
Fabrizio Capuani, Ignacio Pagonabarraga, Daan Frenkel
Melting of Polydisperse Hard Disks
Sander Pronk, Daan Frenkel
A simple analytical formula for the free-energy of ligand-receptor mediated interactions
Stefano Angioletti-Uberti, Patrick Varilly, Bortolo Matteo Mognetti +2
Procedure to construct a multi-scale coarse-grained model of DNA-coated colloids from experimental data
Bianca M. Mladek, Julia Fornleitner, Francisco J. Martinez-Veracoechea +2
Phase diagram of Hertzian spheres
Josep C. PÃ mies, Angelo Cacciuto, Daan Frenkel
Out-of-equilibrium processes in suspensions of oppositely charged colloids: liquid-to-crystal nucleation and gel formation
Eduardo Sanz, Chantal Valeriani, Teun Vissers +5
Crystallization of a polymer on a surface
Jonathan Doye, Daan Frenkel
Phase transitions in biological systems with many components
William M. Jacobs, Daan Frenkel
Lattice model study of the thermodynamic interplay of polymer crystallization and liquid-liquid demixing
Wenbing Hu, Daan Frenkel, Vincent B. F. Mathot
Investigating the role of boundary bricks in DNA brick self-assembly
Hannah Wayment-Steele, Daan Frenkel, Aleks Reinhardt
Phase Behavior of a Simple Model for Membrane Proteins
Massimo G. Noro, Daan Frenkel
The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization
Jonathan Doye, Daan Frenkel
Effects of co-ordination number on the nucleation behaviour in many-component self-assembly
Aleks Reinhardt, Chon Pan Ho, Daan Frenkel
Homogeneous nucleation under shear in a two-dimensional Ising model: cluster growth, coalescence and breakup
Rosalind J. Allen, Chantal Valeriani, Sorin Tanase-Nicola +2
Theory and Simulation of DNA-Coated Colloids: a Guide for Rational Design
Stefano Angioletti-Uberti, Bortolo M. Mognetti, Daan Frenkel
Length, Protein-Protein Interactions, and Complexity
Taison Tan, Daan Frenkel, Vishal Gupta +1
Free energy barrier for single-chain melting and crystallization
Wenbing Hu, Daan Frenkel, Vincent B. F. Mathot
Nanoparticle ordering in sandwiched polymer brushes
Tine Curk, Francisco J. Martinez-Veracoechea, Daan Frenkel +1
Theoretical prediction of thermal polarisation
Peter Wirnsberger, Christoph Dellago, Daan Frenkel +1
Phase coexistence of cluster crystals: beyond the Gibbs phase rule
Bianca M. Mladek, Patrick Charbonneau, Daan Frenkel
Quasi-binary amorphous phase in a 3D system of particles with repulsive-shoulder interactions
Yu. D. Fomin, Daan Frenkel, N. V. Gribova +2
Homogeneous nucleation of colloidal melts under the influence of shearing fields
Ronald Blaak, Stefan Auer, Daan Frenkel +1
Cubatic phase for tetrapods
Ronald Blaak, Bela M. Mulder, Daan Frenkel
Switch-like surface binding of competing multivalent particles
Nicholas B. Tito, Daan Frenkel