820 research outputs found
Interview with Daan Frenkel, Boltzmann Medallist 2016
No full textDaan Frenkel has been awarded the most important prize in the field of statistical mechanics, the 2016 Boltzmann Medal, named after the Austrian physicist and philosopher Ludwig Boltzmann. The award recognises Frenkel’s seminal contributions to the statistical-mechanical understanding of the kinetics, self-assembly and phase behaviour of soft matter. The honour recognises Frenkel’s highly creative large-scale simulations of soft matter capable of explaining the self-assembly of complex macromolecular systems, colloidal and biomolecular systems. Frenkel is Professor of Theoretical Chemistry at the University of Cambridge, UK and has been Editor in Chief of EPJE between 2010 and 2014. The award will be given to both Frenkel and his French colleague Yves Pomeau, during the StatPhys Conference on 20th July 2016 in Lyon, France. In this interview with Sabine Louët, Frenkel gives his views on statistical physics, which has become more relevant than ever for interdisciplinary research. He also offers some pearls of wisdom for the next generation Statistical Mechanics experts
Daan Frenkel - An entropic career
No full textInternational audienceThe editors are very pleased to be able to celebrate the 70th birthday of Daan Frenkel (Figure 1) with this Special Issue of Molecular Physics. The large number and the quality of the scientific contributions, accompanied by heartfelt acknowledgements to Daan, reflect his influence on a very broad field ranging across fundamental statistical thermodynamics, computer simulation, and phase transitions. Moreover, these attest to his continuing influence on current practitioners. This is testament to the enormous respect and admiration in which Daan is held, not only for his seminal and world-leading scientific publications, but also as a true gentleman of science, friend, and colleague
Effect of the interaction strength and anisotropy on the diffusio-phoresis of spherical colloids
No full textGradients in temperature, concentration or electrostatic potential cannot exert forces on a bulk fluid; they can, however, exert forces on a fluid in a microscopic boundary layer surrounding a (nano)colloidal solute, resulting in so-called phoretic flow. Here we present a simulation study of phoretic flow around a spherical colloid held fixed in a concentration gradient. We show that the resulting flow velocity depends non-monotonically on the strength of the colloid-fluid interaction. The reason for this non-monotonic dependence is that solute particles are effectively trapped in a shell around the colloid and cannot contribute to diffusio-phoresis. We also observe that the flow depends sensitively on the anisotropy of solute-colloid interaction
Computer simulation of the phase behavior of a model membrane protein: Annexin V
No full textThe bulk thermodynamic properties of membrane proteins originate from a complex combination of molecular interactions. We propose a simple model based on the pair interactions between a model membrane protein, annexin V. The experimental observations of a honeycomb (p6) and a triangular (p3) phase are successfully reproduced with Monte Carlo computer simulations. Grand canonical simulations and a newly developed "strip"-move constant pressure technique reveal the stability of a dilute fluid phase and a dense solid phase, not observed with the current experimental technology. While this model is extremely simple in that it relies only on hard-body and short-range directional interactions, it nevertheless captures the essential physics of the interactions between the protein molecules and reproduces the phase behavior observed in experiments
Modeling the phase behavior of the membrane binding protein annexin V
No full textThe bulk thermodynamic properties of proteins originate from a varied and complex combination of interactions. We propose a simple model for the formation of ordered two-dimensional aggregates based on the interactions between pairs of annexin V molecules. Simulations of this model are shown to reproduce the experimental observations of a honeycomb (p6) and a triangular (p3) crystalline phase. The simulations indicate that the transition between these two phases is first order. While this model is extremely simple in that it relies only on hard body and short-range directional interactions, it nevertheless captures the essential physics of the interactions between the protein molecules and reproduces the phase behavior observed in electron microscopy and atomic force microscopy experiments
Superselective targeting using multivalent polymers.
No full textDespite their importance for material and life sciences, multivalent interactions between polymers and surfaces remain poorly understood. Combining recent achievements of synthetic chemistry and surface characterization, we have developed a well-defined and highly specific model system based on host/guest interactions. We use this model to study the binding of hyaluronic acid functionalized with host molecules to tunable surfaces displaying different densities of guest molecules. Remarkably, we find that the surface density of bound polymer increases faster than linearly with the surface density of binding sites. Based on predictions from a simple analytical model, we propose that this superselective behavior arises from a combination of enthalpic and entropic effects upon binding of nanoobjects to surfaces, accentuated by the ability of polymer chains to interpenetrate.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe
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Direct computation of the packing entropy of granular materials
No full textGranular materials are the second most manipulated material in industry after
water and their properties are of great importance for the pharmaceutical,
food, mechanosynthesis and semiconductor industries. Up to 60% of the
capacity of some industrial plants is used to process them.
This thesis describes computer simulations that aim to evaluate the number
of distinct packings of a granular material or, more generally, the socalled
‘granular entropy’. Monte Carlo simulations are used to probe the energy
landscape of jammed systems of disks interacting via a repulsive, finiterange
potential. In these simulations we make use of a soft-sphere model
with a hard core that approaches the hard-sphere model as the width of the
soft shell is decreased.
To compute the packing entropy, we use and develop Monte Carlo techniques
to determine the volumes of the basins of attraction of the potential energy
minima at different system sizes. Such Monte Carlo simulations require
energy minimisation after every trial move to make sure that all accepted
moves keep the system within the same basin of attraction. Hence efficient
energy minimisation is a point of paramount significance in this work. A first
objective was to find a suitable minimisation algorithm.
We report a study of the basins of attraction for potential energy minima
defined by different minimisation algorithms for an atomic system. The findings
indicate that whereas some minimisation algorithms produce compact
basins, others produce basins with complex boundaries or basins consisting
of disconnected parts. For the remainder of our work, the FIRE algorithm
was chosen because it produces compact basins at a reasonable computational
cost.
Once the minimisation algorithm is chosen a numerical approach is used
to compute the number of ways in which N particles can pack into a given
volume V . This technique extends the existing methods in such a way that
it can be applied to much larger systems than before (over 100 particles instead
of 16). Many of the caveats of previous methods are addressed. Using
this novel approach, the system size dependence of the number of distinct
packings of a system of poly-disperse soft disks is studied. Our simulations
enable us to validate a more than 20 years old conjecture due to Edwards.
The distribution of jamming densities produced by different protocols has
been studied. We found that the distribution of jamming volumes that are generated
by starting from different initial densities cannot be characterised by an
Edwards’-style compactivity although it is possible to construct an ensemble
where compactivity is well defined
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