Department of Chemistry

portrait of Professor Daan Frenkel ForMemRS

Professor Daan Frenkel ForMemRS

Trinity College

Groups: Frenkel group website, Theory

Telephone: 01223 336376
             01223 336341

E-mail: df246@cam.ac.uk

The research in my research group focuses on the numerical exploration of routes to design novel, self-assembling structures and materials. In particular, I am interested in the possibilities that bio-molecular recognition and motor action offer to create complex, nano-structured materials.

The main aspects of the research are

  • Develop novel Monte Carlo techniques to predict the thermodynamic stability of complex structures (e.g. DNA-coated colloids – fig 1).
  • Explore novel dynamical simulation techniques to predict the rate at which novel structures form from a meta-stable parent phase (e.g. crystal nucleation – fig 2).
  • Quantify the disorder in granular packings.
  • Coarse-grained models for molecular motors.

Fig.1. Snapshot of condensation of a low-density (left) to high-density (right) system of colloids (shown as red and green spheres) linked by DNA coils (shown as small spheres in left snapshot).

  

Fig.2. Heterogeneous crystal nucleation on disordered substrates is facilitated by wetting and capillary condensation.

Publications

Random organization: Ordered chaos
D Frenkel - Nature Physics (2008) 4, 345
(DOI: 10.1038/nphys973)
Multi-scale simulations provide supporting evidence for the hypothesis of intramolecular protein translocation in GroEL/GroES complexes.
I Coluzza, A De Simone, F Fraternali, D Frenkel - PLoS Comput Biol (2008) 4, e1000006
(DOI: 10.1371/journal.pcbi.1000006)
Irreducible finite-size effects in the surface free energy of NaCl crystals from crystal-nucleation data
T Zykova-Timan, C Valeriani, E Sanz, D Frenkel, E Tosatti - Physical Review Letters (2008) 100, 036103
(DOI: 10.1103/PhysRevLett.100.036103)
Protein shape and crowding drive domain formation and curvature in biological membranes
RN Frese, JC Pamies, JD Olsen, S Bahatyrova, CD van der Weij-de Wit, TJ Aartsma, C Otto, CN Hunter, D Frenkel, R van Grondelle - Biophysical Journal (2008) 94, 640
(DOI: 10.1529/biophysj.107.116913)
State-of-the-art models for the phase diagram of carbon and diamond nucleation
LM Ghiringhelli, C Valeriani, JH Los, EJ Meijer, A Fasolino, D Frenkel - Molecular Physics (2008) 106, 2011
(DOI: 10.1080/00268970802077884)
Harvesting graphics power for MD simulations
JA van Meel, A Arnold, D Frenkel, SFP Zwart, RG Belleman - Molecular Simulation (2008) 34, 259
(DOI: 10.1080/08927020701744295)
Dispersion of charged tracers in charged porous media
B Rotenberg, I Pagonabarraga, D Frenkel - Europhysics Letters (2008) 83, 34004
(DOI: 10.1209/0295-5075/83/34004)
Dispersion of charged tracers in charged porous media
B Rotenberg, I Pagonabarraga, D Frenkel - EPL (2008) 83
Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement
A Arnold, B Bozorgui, D Frenkel, BY Ha, S Jun - J Chem Phys (2007) 127, 164903
(DOI: 10.1063/1.2799513)
Molecular simulations of droplet coalescence in oil/water/surfactant systems
L Rekvig, D Frenkel - J Chem Phys (2007) 127, 134701
(DOI: 10.1063/1.2780865)


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