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

Forward flux sampling-type schemes for simulating rare events: Efficiency analysis
RJ Allen, D Frenkel, PR ten Wolde - The Journal of Chemical Physics (2006) 124, 194111
(DOI: 10.1063/1.2198827)
Translocation boost protein-folding efficiency of double-barreled chaperonins.
I Coluzza, SM van der Vies, D Frenkel - Biophysical Journal (2006) 90, 3375
(DOI: 10.1529/biophysj.105.074898)
Designing ordered DNA-linked nanoparticle assemblies
DB Lukatsky, BM Mulder, D Frenkel - Journal of Physics: Condensed Matter (2006) 18, S567
(DOI: 10.1088/0953-8984/18/18/S05)
Lattice-Boltzmann simulations of ionic current modulation by DNA translocation
S Reboux, F Capuani, N Gonzalez-Segredo, D Frenkel - Journal of Chemical Theory and Computation (2006) 2, 495
(DOI: 10.1021/ct050340g)
Lattice-Boltzmann simulation of the sedimentation of charged disks.
F Capuani, I Pagonabarraga, D Frenkel - The Journal of Chemical Physics (2006) 124, 124903
(DOI: 10.1063/1.2178804)
Effect of the coil-globule transition on the free-energy barrier for intrachain crystal nucleation.
WB Hu, D Frenkel - J Phys Chem B (2006) 110, 3734
(DOI: 10.1021/jp056679g)
Colloidal crystals: Plenty of room at the top
D Frenkel - Nature Materials (2006) 5, 85
(DOI: 10.1038/nmat1572)
Simulating rare events in equilibrium or nonequilibrium stochastic systems
RJ Allen, D Frenkel, PR ten Wolde - The Journal of Chemical Physics (2006) 124, 024102
(DOI: 10.1063/1.2140273)
Waste-recycling Monte Carlo
D Frenkel - Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Vol 1 (2006) 703, 127
(DOI: 10.1007/3-540-35273-2_4)
Introduction to colloidal systems
D Frenkel - SOFT CONDENSED MATTER PHYSICS IN MOLECULAR AND CELL BIOLOGY (2006), 19


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