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