Crystallization Without Geometrical Frustration: a Study of 4d hard spheres (2008)
Van Meel, J. A., Frenkel, D., Charbonneau, P.
Geometrical frustration has been suggested to ease the supercooling of a liquid. For instance, in 3d hard spheres the preferred local order is icosahedral, but no periodic lattice is consistent with...
Random organization. Ordered chaos (2008)
When we speak about self-organizing systems, we intuitively think of situations where an initially disordered state spontaneously evolves into an ordered one. On page 420 of this issue, Corté and...
State-of-the-art models for the phase diagram of carbon and diamond nucleation (2008)
Ghiringhelli, Luca M., Valeriani, C., Los, J. H., Meijer, E. J., Fasolino, A., Frenkel, D.
e review recent developments in the modelling of the phase diagram and the kinetics of crystallization of carbon. In particular, we show that a particular class of bond-order potentials (the...
Harvesting graphics power for MD simulations (2008)
Meel, J.A. Van, Arnold, A., Frenkel, D., Portegies Zwart, S.F., Belleman, R.G.
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX....
Protein shape and crowding drive domain formation and curvature in biological membranes (2008)
Frese, R.N., Pàmies, J.C., Olsen, J.D., Bahatyrova, S., Aartsma, T.J., ...
Folding, curvature, and domain formation are characteristics of many biological membranes. Yet the mechanisms that drive both curvature and the formation of specialized domains enriched in particular...
Harvesting graphics power for MD simulations (2008)
Meel, J.A. Van, Arnold, A., Frenkel, D., Portegies Zwart, S.F., Belleman, R.G.
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX....
Harvesting graphics power for MD simulations (2007)
Van Meel, J. A., Arnold, A., Frenkel, D., Zwart, S. F. Portegies, Belleman, R. G.
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX....
Protein shape and crowding drive domain formation and curvature in biological membranes (2007)
Frese, R.N., Pàmies, J.C., Olsen, J.D., Bahatyrova, S., Aartsma, T.J., ...
Folding, curvature and domain formation are characteristics of many biological membranes. Yet the mechanisms that drive both curvature and the formation of specialized domains enriched in particular...
Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement (2007)
Arnold, A., Bozorgui, B., Frenkel, D., Jun, S.
We report extensive simulations of the relaxation dynamics of a self-avoiding polymer confined inside a cylindrical pore. In particular, we concentrate on examining how confinement influences the...
Gas-solid coexistence of adhesive spheres (2007)
In this note we investigate using basic free energy considerations the location of the gas-liquid critical point with respect to solidification for narrow attractive interactions down to the Baxter...
Valeriani, C., Allen, R.J., Morelli, M.J., Frenkel, D., Wolde, P.R. Ten
We present a method for computing stationary distributions for activated processes in equilibrium and nonequilibrium systems using forward flux sampling. In this method, the stationary distributions...
Sanz, E., Valeriani, C., Frenkel, D., Dijkstra, M.
We report a numerical study of the rate of crystal nucleation in a binary suspension of oppositely charged colloids. Two different crystal structures compete in the thermodynamic conditions under...
Lattice-based Monte Carlo method for telechelic chain molecules (2007)
We present a Monte Carlo (MC) scheme that makes it possible to perform efficient simulations of dense systems of self-avoiding polymers on a lattice.We show that the method is particularly useful to...
Local Structure of Liquid Carbon Controls Diamond Nucleation (2007)
Ghiringhelli, L.M., Valeriani, C., Meijer, E.J., Frenkel, D.
Diamonds melt at temperatures above 4000 K. There are no measurements of the steady-state rate of the reverse process, i.e., diamond nucleation from the melt, because experiments are difficult at...
Monte Carlo Study of Substrate-Induced Folding and Refolding of Lattice Proteins (2007)
Many proteins can switch from one conformation to another under the influence of an external driving force, such as the binding to a specific substrate. Using a simple lattice model we show that it...
Simple off-lattice model to study the folding and aggregation of peptides (2007)
We present a numerical study of a new protein model. This off-lattice model takes into account both the hydrogen bonds and the amino-acid interactions. It reproduces the folding of a small protein...
A finite-cluster phase in ¿ -DNA-coated colloids (2007)
Schmatko, T., Bozorgui, B., Geerts, N., Frenkel, D., Eiser, E., Poon, W.C.K.
Local Structure of Liquid Carbon Controls Diamond Nucleation (2007)
Ghiringhelli, L.M., Valeriani, C., Meijer, E.J., Frenkel, D.
A finite-cluster phase in ¿ -DNA-coated colloids (2007)
Schmatko, T., Bozorgui, B., Geerts, N., Frenkel, D., Eiser, E., Poon, W.C.K.
Local Structure of Liquid Carbon Controls Diamond Nucleation (2007)
Ghiringhelli, L.M., Valeriani, C., Meijer, E.J., Frenkel, D.
A finite-cluster phase in lambda-DNA-coated colloids (2007)
Schmatko, T., Bozorgui, B., Geerts, N., Frenkel, D., Eiser, E., Poon, W.C.K.
Application of the Optimized Baxter Model to the hard-core attractive Yukawa system (2006)
Prinsen, P., Pamies, J.C., Odijk, Th., Frenkel, D.
We perform Monte Carlo simulations on the hard-core attractive Yukawa system to test the Optimized Baxter Model that was introduced in [P.Prinsen and T. Odijk, J. Chem. Phys. 121, p.6525 (2004)] to...
Simulating rare events in equilibrium or nonequilibrium stochastic systems (2006)
Allen, R.J., Frenkel, D., Wolde, P.R. Ten
We present three algorithms for calculating rate constants and sampling transition paths for rare events in simulations with stochastic dynamics. The methods do not require a priori knowledge of the...
Forward flux sampling-type schemes for simulating rare events: Efficiency analysis (2006)
Allen, R.J., Frenkel, D., Wolde, P.R. Ten
We analyze the efficiency of several simulation methods which we have recently proposed for calculating rate constants for rare events in stochastic dynamical systems in or out of equilibrium. We...
Lattice-Boltzmann simulation of the sedimentation of charged disks (2006)
Capuani, F., Pagonabarraga, I., Frenkel, D.
We report a series of lattice-Boltzmann simulations of the sedimentation velocity of charged disks. In these simulations, we explicitly account for the hydrodynamic and electrostatic forces on disks...
Translocation Boost Protein-Folding Efficiency of Double-Barreled Chaperonins (2006)
Incorrect folding of proteins in living cells may lead to malfunctioning of the cell machinery. To prevent such cellular disasters from happening, all cells contain molecular chaperones that assist...
Designing ordered DNA-linked nanoparticle assemblies (2006)
Lukatsky, D.B., Mulder, B.M., Frenkel, D.
We present a model study of a multi-component system that can form low-symmetry ordered phases, even though all pair interactions between the constituent particles are spherically symmetric. Using...
The rate of crystal nucleation of colloids and globular proteins can be enhanced by critical density fluctuations. It has been argued that a closely related phenomenon influences the rate of...
Modeling flexible amphiphilic bilayers: A solvent-free off-lattice Monte Carlo study (2005)
We present a simple, implicit-solvent model for fluid bilayer membranes. The model was designed to reproduce the elastic properties of real bilayer membranes. For this model, we observed the...
Novel Monte Carlo scheme for systems with short-ranged interactions (2005)
Boulougouris, G.C., Frenkel, D.
We propose a Monte Carlo (MC) sampling algorithm to simulate systems of particles interacting via very short-ranged discontinuous potentials. Such models are often used to describe protein solutions...
Rate of homogeneous crystal nucleation in molten NaCl (2005)
Valeriani, C., Sanz, E., Frenkel, D.
We report a numerical simulation of the rate of crystal nucleation of sodium chloride from its melt at moderate supercooling. In this regime nucleation is too slow to be studied with "brute force"...
Using a simple mean-field model, we analyze the surface and bulk dissolution properties of DNA-linked nanoparticle assemblies. We find that the dissolution temperature and the sharpness of the...
Pore nucleation in mechanically stretched bilayer membranes (2005)
We report a computer-simulation study of the free-energy barrier for the nucleation of pores in the bilayer membrane under constant stretching lateral pressure. We find that incipient pores are...
Nucleation in suspensions of anisotropic colloids (2005)
We report Monte Carlo studies of liquid crystal nucleation in two types of anisotropic colloidal systems: hard rods and hard ellipsoids. In both cases we find that nucleation pathways differ strongly...
Mesoscopic lattice modeling of electrokinetic phenomena (2005)
Pagonabarraga, I., Capuani, F., Frenkel, D.
The development of models for electrolytes is challenging due to the long-range nature of electric interactions. We propose a novel implementation of a lattice Boltzmann model that solves a number of...
Monte Carlo Sampling of a Markov Web (2005)
Boulougouris, G.C., Frenkel, D.
The efficiency of Markov-Chain Monte Carlo simulations can be enhanced by exploiting information about trial moves that would normally be rejected. The original presentation of this approach was...
Liquid carbon: structure near the freezing line (2005)
Ghiringhelli, L.M., Los, J.H., Meijer, E.J., Fasolino, A., Frenkel, D.
We present a detailed analysis of the structure of liquid carbon near the freezing line. The results are obtained by molecular simulation using a recently developed state-of-the-art bond order...
Force barriers for membrane tube formation (2005)
Koster, G., Cacciuto, A., Derényi, I., Frenkel, D., Dogterom, M.
We used optical tweezers to measure the force-extension curve for the formation of tubes from giant vesicles. We show that a significant force barrier exists for the formation of tubes, which...
Simulation of colloidal crystallization on finite structured templates (2005)
We present a numerical study of colloidal crystal growth on finite templates. Specifically, we consider planar, crystalline templates with the structure of the 100, 110, and 100 faces of a fcc...
Oriented primary crystal nucleation in lamellar diblock copolymer systems (2005)
We report a numerical study of the primary crystal nucleation of diblock copolymers in a lamellar phase. Only one of two polymer blocks is crystallizable; the other is maintained in a glassy state....
Monte Carlo study of hard pentagons (2005)
Schilling, T., Pronk, S., Mulder, B., Frenkel, D.
How does a liquid freeze if the geometry of its particles conflicts with the symmetry of the crystal it should naturally form? We study this question in the simplest model system of particles...
Structural arrest in an ideal gas (2005)
Ketel, W. Van, Das, C., Frenkel, D.
We report a molecular dynamics study of a simple model system that has the static properties of an ideal gas, yet exhibits nontrivial "glassy" dynamics behavior at high densities. The constituent...
Modeling the phase diagram of carbon (2005)
Ghiringhelli, L.M., Los, J.H., Meijer, E.J., Fasolino, A., Frenkel, D.
We determined the phase diagram involving diamond, graphite, and liquid carbon using a recently developed semiempirical potential. Using accurate free-energy calculations, we computed the solid-solid...
Stresses inside critical nuclei (2005)
The usual derivation of classical nucleation theory is inappropriate for crystal nucleation. In particular, it leads to a seriously flawed estimate of the pressure inside a critical nucleus. This has...
Length, protein–protein interactions, and complexity (2005)
Tan, T., Frenkel, D., Gupta, V., Deem, M.W.
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large-scale genome sequencing efforts has been unclear. We propose here that the...