468 citations · 8.1k across the 126 of their papers we have counts for
10 papers · 1 filter
Layering, freezing and re-entrant melting of hard spheres in soft confinement
Tine Curk, Anouk de Hoogh, Francisco J. Martinez-Veracoechea +4
Confinement can have a dramatic effect on the behavior of all sorts of particulate systems and it therefore is an important phenomenon in many different areas of physics and techno…
Simulations: the dark side
Daan Frenkel
This paper discusses the Monte Carlo and Molecular Dynamics methods. Both methods are, in principle, simple. However, simple does not mean risk-free. In the literature, many of the…
A simple analytical formula for the free-energy of ligand-receptor mediated interactions
Stefano Angioletti-Uberti, Patrick Varilly, Bortolo Matteo Mognetti +2
Recently \1, we presented a general theory for calculat- ing the strength and properties of colloidal interactions mediated by ligand-receptor bonds (such as those that bind DNA-co…
Probing ergodicity in granular matter
Fabien Paillusson, Daan Frenkel
When a granular system is tapped, its volume changes. Here, using a well-defined macroscopic protocol, we prepare an ensemble of granular systems and track the statistics of volume…
Collective sedimentation of colloids in grafted polymer layers
Tine Curk, Francisco J. Martinez-Veracoechea, Daan Frenkel +1
We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by external fields. The insertion free energy of a single colloid into the polymer laye…
Running faster together: huge speed up of thermal ratchets due to hydrodynamic coupling
Paolo Malgaretti, Ignacio Pagonabarraga, Daan Frenkel
We present simulations that reveal a surprisingly large effect of hydrodynamic coupling on the speed of thermal ratchet motors. The model that we use considers particles performing…
Emergence of Critical Phenomena in Full Configuration Interaction Quantum Monte Carlo
James J. Shepherd, Lauretta R. Schwarz, Robert E. Thomas +3
There has been recent literature discussion on the origin and severity of the `sign problem' in full configuration interaction quantum Monte Carlo (FCIQMC) and its `initiator' adap…
Quantitative prediction of the phase diagram of DNA-functionalized nano-colloids
Bianca M. Mladek, Julia Fornleitner, Francisco J. Martinez-Veracoechea +2
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using t…
A general theory of DNA-mediated and other valence-limited interactions
Patrick Varilly, Stefano Angioletti-Uberti, Bortolo M. Mognetti +1
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor…
A parameter-free, solid-angle based, nearest-neighbor algorithm
Jacobus A. van Meel, Laura Filion, Chantal Valeriani +1
We propose a parameter-free algorithm for the identification of nearest neighbors. The algorithm is very easy to use and has a number of advantages over existing algorithms to iden…