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Daan Frenkel

In Brief…

I am Emeritus Professor of Chemistry. My field was/is molecular simulation of “soft” materials and related topics.
I am an Honorary Fellow and Senior Member at Trinity. From 2008 to 2015, I was what was then called “Professorial” Fellow.
I used to hold the 1968 Chair of Chemistry, and I was Head of Department from 2011-2015. Before 2008, I was affiliated with the Universities of Utrecht and Amsterdam, and the (then) FOM Institute AMOLF in Amsterdam.

Daan Frenkel

In Brief…

I am Emeritus Professor of Chemistry. My field was/is molecular simulation of “soft” materials and related topics.
I am an Honorary Fellow and Senior Member at Trinity. From 2008 to 2015, I was what was then called “Professorial” Fellow.
I used to hold the 1968 Chair of Chemistry, and I was Head of Department from 2011-2015. Before 2008, I was affiliated with the Universities of Utrecht and Amsterdam, and the (then) FOM Institute AMOLF in Amsterdam.

Profile

I did my PhD in (Physical) Chemistry at the University of Amsterdam. My PhD research was experimental in nature: “far-infrared” (now Terahertz) spectroscopy. During my PhD I spent 5 months during the summer of 1975 at CECAM in Orsay (France) where I familiarised myself with Molecular Dynamics and Monte Carlo simulations, a field that was then just taking off in Europe. Subsequently, I was a Postdoc at UCLA and Research Scientist at Shell, before moving to back Academia in 1981.

Among the topics that I studied were: simulations of “Entropic” Phase transitions in liquid crystals, (crystal) nucleation, Complex self-assembly, and super-selective targeting of cells. For my work I developed novel algorithms, including Free-energy methods, Configurational Bias Monte Carlo for (chain molecules), and techniques to “count” uncountably large numbers of distinct (granular) packings, and the modelling of DNA-mediated self-assembly.

With my former student Berend Smit, I wrote a book about computer simulation techniques (Understanding Molecular Simulations – 3rd edition, 2023). The book is widely used.

I like to share my fascination with the giants of thermodynamics and statistical physics of the 19th century (Carnot, Gibbs, Maxwell, Boltzmann). But my interest in history goes beyond that.

Teaching

I have been teaching with much pleasure in Amsterdam and Cambridge. However, I reached many more students by teaching at a series of annual international simulation courses that Berend Smit and I started in Amsterdam in 2000. I organised satellite courses in India, China, and Switzerland.
I probably learn more from students than they learned from me.

Research

Rather than just giving a list of topics that I found (and still find) interesting, let me give two examples from my time in Cambridge.
The first is a technique to count the number of distinct packings of, say, chocolate eggs in a jar. If the number of particles exceeds 10-15, the number of packing becomes super-astronomically large and cannot be counted. By exploiting my expertise with free-energy calculations, I could translate the counting problem into a sampling problem. It then became feasible to “count” numbers of packings exceeding 10^200, or (much) larger.

A more recent example is the work that we did on super-selective targeting. The idea is that many diseased cells over-express certain peptide fragments on their surface. But often, healthy cells express the same fragments, just fewer. In such cases “monovalent” molecules target healthy cells as well as diseased cells: less strongly, but there are many more healthy cells. Super selective targeting uses particles that carry several ligands. These particles bind selectively to surfaces that express the target peptide receptors above a certain threshold concentration. The road from idea to application is long, but I am happy to see that it is now progressing well.

Selected Publications

Understanding molecular simulation: from algorithms to applications, D Frenkel, B Smit, Academic Press, (1996/2002/2023).
Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings, S. Martiniani, K.J. Schrenk, J.D. Stevenson, D.J. Wales, D. Frenkel, Phys. Rev. E, 93, 12906(2016)
Simulations: The dark side, D. Frenkel, Eur Phys J. Plus. 128, 1(2013)
Designing super-selectivity in multivalent nano-particle binding, F J. Martinez-Veracoechea and D Frenkel, Proc. Nat. Acad. Sci 108, 10963-10968 (2011)
Prediction of absolute crystal-nucleation rate in hard-sphere colloids, S. Auer and D. Frenkel, Nature, 409, 1020-1023(2001)
Enhancement of Protein Crystal Nucleation by Critical Density Fluctuations, Pieter Rein ten Wolde and Daan Frenkel, Science 277, 1975-1977(1997).
Novel scheme to compute the chemical potential of chain molecules, G.C.A.M. Mooij and D. Frenkel, Mol. Phys. 74, 41(1991)
The hard ellipsoid-of-revolution fluid. I. Monte Carlo simulations, D.Frenkel and B.M.Mulder, Mol. Phys. 55, 1171 (1985).
New Monte Carlo method to compute the free energy of arbitrary solid phases. Application to the FCC and HCP phases of hard spheres, D.Frenkel and A.J.C.Ladd, J. Chem. Phys. 81, 3188 (1984).

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