Name :Daan Frenkel
Email :D.FrenkelATamolf.nl
Group :Computational physics
Publications :Hide publication list

Publications for Daan Frenkel


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Article(s) published in 2012

T. Curk, A. de Hoogh, F.J. Martinez-Veracoechea, E. Eiser, D. Frenkel, J. Dobnikar and M.E. Leunissen, Layering, freezing, and re-entrant melting of hard spheres in soft confinement, Phys. Rev. E 85, 021502 1-5 (2012).

Article(s) published in 2011

N. Xu, D. Frenkel and A.J. Liu, Direct determination of the size of basins of attraction of jammed solids, Phys. Rev. Lett. 106, 245502 1-4 (2011).

Article(s) published in 2010

J.A. van Meel, R.P. Sear and D. Frenkel, Design principles for broad-spectrum protein-crystal nucleants with nanoscale pits, Phys. Rev. Lett. 105, 205501 1-4 (2010).
A. Vila Verde and D. Frenkel, Simulation study of micelle formation by bile salts, Soft Matter 6, 3815-3825 (2010).
B. Rotenberg, I. Pagonabarraga and D. Frenkel, Coarse-grained simulations of charge, current and flow in heterogeneous media, Faraday Discuss. 144, 223-243 (2010).

Article(s) published in 2009

J.C. Pámies, A. Cacciuto and D. Frenkel, Phase diagram of Hertzian spheres, J. Chem. Phys. 131, 044514 1-9 (2009).
N.V. Gribova, Y.D. Fomin, D. Frenkel and V.N. Ryzhov, Waterlike thermodynamic anomalies in a repulsive-shoulder potential system, Physical Review E 79, 051202 1-6 (2009).
Z.-J. Wang, C. Valeriani and D. Frenkel, Homogeneous bubble nucleation driven by local hot spots: a molecular dynamics study, J. Phys. Chem. B 113, 3776-3784 (2009).

Article(s) published in 2008

R.N. Frese, J.C. Pámies, J.D. Olsen, S. Bahatyrova, Chantal D. van der Weij-de Wit, T.J. Aartsma, C. Otto, C.N. Hunter, D. Frenkel and R. van Grondelle, Protein shape and crowding drive domain formation and curvature in biological membranes, Biophys. J. 94, 640--647 (2008).
I. Coluzza, A. De Simone, F. Fraternali and D. Frenkel, Multi-scale simulation provide supporting evidence for the hypothesis of intramolecular protein translocation in GroEL/GroES complexes, PLoS Computational Biology 4, e1000006 1--7 (2008).
B. Bozorgui and D. Frenkel, Liquid-vapor transition driven by bond disorder, Phys. Rev. Lett. 101, 045701 1-4 (2008).
P. Charbonneau, C. Das and D. Frenkel, Dynamical heterogeneity in a glass-forming ideal gas, Physical Review B 78, 011505 1--11 (2008).
Y.D. Fomin, N.V. Gribova, V.N. Ryzhov, S.M. Stishov and D. Frenkel, Quasibinary amorphous phase in a three-dimensional system of particles with repulsive-shoulder interactions, J. Chem. Phys. 129, 064512 1--6 (2008).
R.J. Allen, C. Valeriani, S. Tanase-Nicola, P.R. ten Wolde and D. Frenkel, Homogeneous nucleation under shear in a two-dimensional ising model : cluster growth, coalescence and breakup, J. Chem. Phys. 129, 134704 1--11 (2008).
E. Sanz, C. Valeriani, Teun Vissers, A. Fortini, M.E. Leunissen, A. van Blaaderen, D. Frenkel and M. Dijkstra, Out-of-equilibrium processes in suspensions of oppositely charged colloids : liquid-to-crystal nucleation and gel formation, J. Phys.: Condens. Matter 20, 494247 1-10 (2008).
B.M. Mladek, P. Charbonneau, C.N. Likos, D. Frenkel and G. Kahl, Multiple occupancy crystals formed by purely repulsive soft particles, J. Phys.: Condens. Matter 20, 494245 1-9 (2008).
S. Abeln and D. Frenkel, Disordered flanks prevent peptide aggregation, PLoS Computational Biology 4, e1000241 1--7 (2008).

Article(s) published in 2007

I. Coluzza and D. Frenkel, Monte Carlo study of substrate-induced folding and refolding of lattice proteins, Biophys. J. 92, 1150--1156 (2007).
B. Bozorgui and D. Frenkel, Lattice-based Monte Carlo method for telechelic chain molecules, Physical Review E 75, 036708 1--6 (2007).
E. Sanz, C. Valeriani, D. Frenkel and M. Dijkstra, Evidence for out-of-equilibrium crystal nucleation in suspensions of oppositely charged colloids, Phys. Rev. Lett. 99, 055501 1--5 (2007).
C. Valeriani, R.J. Allen, M.J. Morelli, D. Frenkel and P.R. ten Wolde, Computing stationary distributions in equilibrium and nonequilibrium systems with forward flux sampling, J. Chem. Phys. 127, 114109 1--11 (2007).
L. Rekvig and D. Frenkel, Molecular simulations of droplet coalescence in oil/water/surfactant systems, J. Chem. Phys. 127, 134701 1--11 (2007).
A. Arnold, B. Bozorgui, D. Frenkel, B.-Y. Ha and S. Jun, Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement, J. Chem. Phys. 127, 164903 1-9 (2007).
B.M. Mladek, P. Charbonneau and D. Frenkel, Phase coexistence of cluster crystals: beyond the Gibbs phase rule, Phys. Rev. Lett. 99, 235702 1--4 (2007).
N. Combe and D. Frenkel, Simple off-lattice model to study the folding and aggregation of peptides, Molecular Physics 105, 375--385 (2007).
T. Schmatko, B. Bozorgui, N. Geerts, D. Frenkel, E. Eiser and W.C.K. Poon, A finite-cluster phase in ?-DNA-coated colloids, Soft Matter 3, 703--706 (2007).

Article(s) published in 2006

D. Frenkel, Physical chemistry: seeds of phase change, Nature 443, 641 (2006).
S. Reboux, F. Capuani, N. González-Segredo and D. Frenkel, Lattice-Boltzmann simulations of ionic current modulation by DNA translocation, J. Chem. Theory Comput. 2, 495--503 (2006).
P. Prinsen, J.C. Pámies, T. Odijk and D. Frenkel, Application of the optimized Baxter model to the hard-core attractive Yukawa system, J. Chem. Phys. 125, 194506 1--9 (2006).
D. Frenkel, Colloidal encounters: a matter of attraction, Science 314, 768--769 (2006).

Article(s) published in 1999

S. Consta, T.J.H. Vlught, J. Wichers Hoeth, B. Smit and D. Frenkel, Recoil growth algoritm for chain molecules with continuous interactions, Mol. Phys. 97, 1243-1254 (1999).
P.R. ten Wolde, D.W. Oxtoby and D. Frenkel, Chain formation in homogeneous gas-liquid nucleation of polar fluids, J. Chem. Phys. 111, 4762-4773 (1999).
J.M. Polson and D. Frenkel, Numerical prediction of the melting curve of n-octane, J. Chem. Phys. 111, 1501-1510 (1999).
S. Pronk and D. Frenkel, Can stacking faults in hard-sphere crystals anneal out spontaneously?, J. Chem. Phys. 110, 4589-4592 (1999).
R. Blaak, D. Frenkel and B.M. Mulder, Do cylinders exhibit a cubatic phase?, J. Chem. Phys. 110, 11652-11659 (1999).
J.P.K. Doye and D. Frenkel, The mechanisms of thickness selection in the Sadler-Gilmer model of polymer crystallization, J. Chem. Phys. 110, 7073-7086 (1999).
M.A. Bates and D. Frenkel, Nematic-isotropic transition in polydisperse systems of infinitely thin hard platelets, J. Chem. Phys. 110, 6653-6659 (1999).
J. Zhang, R. Blaak, E. Trizac, J.A. Cuesta and D. Frenkel, Optimal packing of polydisperse hard-shpere fluids, J. Chem. Phys. 110, 5318-5324 (1999).
J.P.K. Doye and D. Frenkel, Kinetic Monte Carlo simulations of the growth of polymer crystals, J. Chem. Phys. 110, 2692-2702 (1999).
P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Numerical calculation of the rate of homogeneous gas-liquid nucleation in a Lennard-Jones system, J. Chem. Phys. 110, 1591-1599 (1999).
P.R. ten Wolde and D. Frenkel, Homogeneous nucleation and the Ostwald step rule, Physical Chemistry Chemical Physics 1, 2191-2196 (1999).
D. Frenkel, Entropy-driven phase transitions, Physica A 263, 26-38 (1999).

Article(s) published in 1998

J.P.K. Doye and D. Frenkel, Crystallization of a polymer on a surface, J. Chem. Phys. 109, 10033-10041 (1998).
P.R. ten Wolde and D. Frenkel, Numerical study of gas-liquid nucleation in partially miscible binary mixtures, J. Chem. Phys. 109, 9919-9927 (1998).
P.R. ten Wolde and D. Frenkel, Computer simulation study of gas-liquid nucleation in a Lennard-Jones system, J. Chem. Phys. 109, 9901-9918 (1998).
J.M. Polson and D. Frenkel, Calculation of solid-fluid phase equilibria for systems of chain molecules, J. Chem. Phys. 109, 318-328 (1998).
J.P.K. Doye, R.P. Sear and D. Frenkel, The effect of chain stiffness on the phase behaviour of isolated homopolymers, J. Chem. Phys. 108, 2134-2142 (1998).
J.P.K. Doye and D. Frenkel, Mechanism of thickness determination in polymer crystals, Physical Review Letters 81, 2160-2163 (1998).
P.R. ten Wolde, D.W. Oxtoby and D. Frenkel, Coil-globule transition in gas-liquid nucleation of polar fluids, Physical Review Letters 81, 3695-3698 (1998).
M.A. Bates and D. Frenkel, Infinitely thin disks exhibit a first order nematic-columnar phase transition, Physical Review E 57, 4824-4826 (1998).

Article(s) published in 1997

P.G. Bolhuis, A. Stroobants, D. Frenkel and H.N.W. Lekkerkerker, Numerical study of the phase behavior of rodlike colloids with attractive interactions, J. Chem. Phys. 107, 1551-1564 (1997).
P.R. ten Wolde and D. Frenkel, Enhancement of protein crystal nucleation by critical density fluctuations, Science 277, 1975-1978 (1997).
D. Frenkel, Physicalezing 1997: een dronkemanswandeling met de computer, Nederlands Tijdschrift voor Natuurkunde 63, 112-115 (1997).
R.P. Sear and D. Frenkel, Phase behavior of colloid plus polydisperse polymer mixtures, Physical Review E 55, 1677-1681 (1997).

Article(s) published in 1996

P.R. ten Wolde, M.J. Ruiz-Montero and D. Frenkel, Simulation of homogeneous crystal nucleation close to coexistence, Faraday Discuss. 104, 93-110 (1996).
T. Biben, P.B. Bladon and D. Frenkel, Depletion effects in binary hard-sphere fluids, J. Phys.: Condens. Matter 8, 10799-10821 (1996).
P.L. Silvestrelli, A. Alavi, M. Parrinello and D. Frenkel, Nonmetal-metal transition in metal-molten-salt solutions, Physical Review B 53, 12750-12760 (1996).

Article(s) published in 1995

R.H.H.G. van Roij, P.G. Bolhuis, B.M. Mulder and D. Frenkel, Transverse interlayer order in lyotropic smectic liquid crystals, Phys. Rev. E 52, R1277-R1280 (1995).

Scientific career Daan Frenkel

My main affiliation has changed to:

Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge CB2 1EW, UK

Most of  my publications are on line.

My Biographical Information.