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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Designing super selectivity in multivalent nano-particle binding
FJ Martinez-Veracoechea, D Frenkel - Proceedings of the National Academy of Sciences of the United States of America (
2011)
108, 10963
(DOI:
10.1073/pnas.1105351108)
Real-time monitoring of complex moduli from micro-rheology
D Frenkel, T Yanagishima, J Kotar, E Eiser - JOURNAL OF PHYSICS-CONDENSED MATTER (2011) 23, 194118
Direct determination of the size of basins of attraction of jammed solids
N Xu, D Frenkel, AJ Liu - Physical Review Letters (
2011)
106, 245502
(DOI:
10.1103/PhysRevLett.106.245502)
COLLOIDAL SELF-ASSEMBLY Designed to yield
D Frenkel, DJ Wales - Nature Materials (
2011)
10, 410
(DOI:
10.1038/nmat3037)
Role of fluctuations in ligand binding cooperativity of membrane receptors.
LZ Zhu, D Frenkel, PG Bolhuis - Physical Review Letters (
2011)
106, 168103
(DOI:
10.1103/PhysRevLett.106.168103)
Simulation of nucleation in almost hard-sphere colloids: the discrepancy between experiment and simulation persists.
L Filion, R Ni, D Frenkel, M Dijkstra - The Journal of Chemical Physics (
2011)
134, 134901
(DOI:
10.1063/1.3572059)
Numerical study of DNA-functionalized microparticles and nanoparticles: explicit pair potentials and their implications for phase behavior.
ME Leunissen, D Frenkel - The Journal of Chemical Physics (
2011)
134, 084702
(DOI:
10.1063/1.3557794)
Accounting for protein-solvent contacts facilitates design of nonaggregating lattice proteins
S Abeln, D Frenkel - Biophysical Journal (
2011)
100, 693
(DOI:
10.1016/j.bpj.2010.11.088)
Error analysis and correction for Lattice Boltzmann simulated flow conductance in capillaries of different shapes and alignments
A Sengupta, PS Hammond, D Frenkel, ES Boek - Journal of Computational Physics (2011)
Design principles for broad-spectrum protein-crystal nucleants with nanoscale pits.
JA van Meel, RP Sear, D Frenkel - Physical Review Letters (
2010)
105, 205501
(DOI:
10.1103/PhysRevLett.105.205501)
