252 research outputs found
Fluid-Fluid and Fluid-Solid transitions in the Kern-Frenkel model from Barker-Henderson thermodynamic perturbation theory
We study the Kern-Frenkel model for patchy colloids using Barker-Henderson
second-order thermodynamic perturbation theory. The model describes a fluid
where hard sphere particles are decorated with one patch, so that they interact
via a square-well (SW) potential if they are sufficiently close one another,
and if patches on each particle are properly aligned. Both the gas-liquid and
fluid-solid phase coexistences are computed and contrasted against
corresponding Monte-Carlo simulations results. We find that the perturbation
theory describes rather accurately numerical simulations all the way from a
fully covered square-well potential down to the Janus limit (half coverage). In
the region where numerical data are not available (from Janus to hard-spheres),
the method provides estimates of the location of the critical lines that could
serve as a guideline for further efficient numerical work at these low
coverages. A comparison with other techniques, such as integral equation
theory, highlights the important aspect of this methodology in the present
context.Comment: Accepted for publication in The Journal of Chemical Physics (2012
Self-assembly of two-dimensional binary quasicrystals: A possible route to a DNA quasicrystal
We use Monte Carlo simulations and free-energy techniques to show that binary
solutions of penta- and hexavalent two-dimensional patchy particles can form
thermodynamically stable quasicrystals even at very narrow patch widths,
provided their patch interactions are chosen in an appropriate way. Such patchy
particles can be thought of as a coarse-grained representation of DNA multi-arm
`star' motifs, which can be chosen to bond with one another very specifically
by tuning the DNA sequences of the protruding arms. We explore several possible
design strategies and conclude that DNA star tiles that are designed to
interact with one another in a specific but not overly constrained way could
potentially be used to construct soft quasicrystals in experiment. We verify
that such star tiles can form stable dodecagonal motifs using oxDNA, a
realistic coarse-grained model of DNA
Coarse-grained simulations of DNA overstretching
We use a recently developed coarse-grained model to simulate the
overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the
model, about 6-7 pN higher than the experimental value at equivalent salt
conditions. Furthermore, the model reproduces the temperature dependence of the
overstretching force well. The mechanism of overstretching is always
force-induced melting by unpeeling from the free ends. That we never see S-DNA
(overstretched duplex DNA), even though there is clear experimental evidence
for this mode of overstretching under certain conditions, suggests that S-DNA
is not simply an unstacked but hydrogen-bonded duplex, but instead probably has
a more exotic structure.Comment: 11 pages, 11 figure
Nucleation barriers in tetrahedral liquids spanning glassy and crystallizing regimes
Crystallization and vitrification of tetrahedral liquids are important both
from a fundamental and a technological point of view. Here, we study via
extensive umbrella sampling Monte Carlo computer simulations the nucleation
barriers for a simple model for tetrahedral patchy particles in the regime
where open tetrahedral crystal structures (namely cubic and hexagonal diamond
and their stacking hybrids) are thermodynamically stable. We show that by
changing the angular bond width, it is possible to move from a glass-forming
model to a readily crystallizing model. From the shape of the barrier we infer
the role of surface tension in the formation of the crystalline clusters.
Studying the trends of the nucleation barriers with the temperature and the
patch width, we are able to identify an optimal value of the patch size that
leads to easy nucleation. Finally, we find that the nucleation barrier is the
same, within our numerical precision, for both diamond crystals and for their
stacking forms.Comment: 12 pages, 11 figure
The effect of topology on the structure and free energy landscape of DNA kissing complexes
We use a recently developed coarse-grained model for DNA to study kissing
complexes formed by hybridization of complementary hairpin loops. The binding
of the loops is topologically constrained because their linking number must
remain constant. By studying systems with linking numbers -1, 0 or 1 we show
that the average number of interstrand base pairs is larger when the topology
is more favourable for the right-handed wrapping of strands around each other.
The thermodynamic stability of the kissing complex also decreases when the
linking number changes from -1 to 0 to 1. The structures of the kissing
complexes typically involve two intermolecular helices that coaxially stack
with the hairpin stems at a parallel four-way junction
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
We present a new method for calculating internal forces in DNA structures
using coarse-grained models and demonstrate its utility with the oxDNA model.
The instantaneous forces on individual nucleotides are explored and related to
model potentials, and using our framework, internal forces are calculated for
two simple DNA systems and for a recently-published nanoscopic force clamp. Our
results highlight some pitfalls associated with conventional methods for
estimating internal forces, which are based on elastic polymer models, and
emphasise the importance of carefully considering secondary structure and ionic
conditions when modelling the elastic behaviour of single-stranded DNA. Beyond
its relevance to the DNA nanotechnological community, we expect our approach to
be broadly applicable to calculations of internal force in a variety of
structures -- from DNA to protein -- and across other coarse-grained simulation
models.Comment: 39 pages, 9 figure
- …