570 research outputs found
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water
We present a local order parameter based on the standard Steinhardt-Ten Wolde
approach that is capable both of tracking and of driving homogeneous ice
nucleation in simulations of all-atom models of water. We demonstrate that it
is capable of forcing the growth of ice nuclei in supercooled liquid water
simulated using the TIP4P/2005 model using overbiassed umbrella sampling Monte
Carlo simulations. However, even with such an order parameter, the dynamics of
ice growth in deeply supercooled liquid water in all-atom models of water are
shown to be very slow, and so the computation of free energy landscapes and
nucleation rates remains extremely challenging.Comment: This version incorporates the minor changes made to the paper
following peer revie
Melting of aluminium clusters
The melting of Al clusters in the size range 49 <= N <= 62 has been studied
using two model interatomic potentials. The results for the two models are
significantly different. The glue potential exhibits a smooth relatively
featureless heat capacity curve for all sizes except for N = 54 and N = 55,
sizes at which icosahedral structures are favoured over the polytetrahedral.
Gupta heat capacity curves, instead, show a well-defined peak that is
indicative of a first-order-like transition. The differences between the two
models reflect the different ground-state structures, and neither potential is
able to reproduce or explain the size dependence of the melting transition
recently observed in experiments
Structural relaxation in Morse clusters: Energy landscapes
We perform a comprehensive survey of the potential energy landscapes of
13-atom Morse clusters, and describe how they can be characterized and
visualized. Our aim is to detail how the global features of the funnel-like
surface change with the range of the potential, and to relate these changes to
the dynamics of structural relaxation. We find that the landscape becomes
rougher and less steep as the range of the potential decreases, and that
relaxation paths to the global minimum become more complicated.Comment: 21 pages, 3 tables, 5 figure
New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster
A new atomic cluster structure corresponding to the global minimum of the
98-atom Lennard-Jones cluster has been found using a variant of the
basin-hopping global optimization algorithm. The new structure has an unusual
tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower
than the previous putative global minimum. The new LJ_98 structure is of
particular interest because its tetrahedral symmetry establishes it as one of
only three types of exceptions to the general pattern of icosahedral structural
motifs for optimal LJ microclusters. Similar to the other exceptions the global
minimum is difficult to find because it is at the bottom of a narrow funnel
which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte
Modelling the Self-Assembly of Virus Capsids
We use computer simulations to study a model, first proposed by Wales [1],
for the reversible and monodisperse self-assembly of simple icosahedral virus
capsid structures. The success and efficiency of assembly as a function of
thermodynamic and geometric factors can be qualitatively related to the
potential energy landscape structure of the assembling system. Even though the
model is strongly coarse-grained, it exhibits a number of features also
observed in experiments, such as sigmoidal assembly dynamics, hysteresis in
capsid formation and numerous kinetic traps. We also investigate the effect of
macromolecular crowding on the assembly dynamics. Crowding agents generally
reduce capsid yields at optimal conditions for non-crowded assembly, but may
increase yields for parameter regimes away from the optimum. Finally, we
generalize the model to a larger triangulation number T = 3, and observe more
complex assembly dynamics than that seen for the original T = 1 model.Comment: 16 pages, 11 figure
Evolutionary Dynamics in a Simple Model of Self-Assembly
We investigate the evolutionary dynamics of an idealised model for the robust
self-assembly of two-dimensional structures called polyominoes. The model
includes rules that encode interactions between sets of square tiles that drive
the self-assembly process. The relationship between the model's rule set and
its resulting self-assembled structure can be viewed as a genotype-phenotype
map and incorporated into a genetic algorithm. The rule sets evolve under
selection for specified target structures. The corresponding, complex fitness
landscape generates rich evolutionary dynamics as a function of parameters such
as the population size, search space size, mutation rate, and method of
recombination. Furthermore, these systems are simple enough that in some cases
the associated model genome space can be completely characterised, shedding
light on how the evolutionary dynamics depends on the detailed structure of the
fitness landscape. Finally, we apply the model to study the emergence of the
preference for dihedral over cyclic symmetry observed for homomeric protein
tetramers
Force-induced rupture of a DNA duplex
The rupture of double-stranded DNA under stress is a key process in
biophysics and nanotechnology. In this article we consider the shear-induced
rupture of short DNA duplexes, a system that has been given new importance by
recently designed force sensors and nanotechnological devices. We argue that
rupture must be understood as an activated process, where the duplex state is
metastable and the strands will separate in a finite time that depends on the
duplex length and the force applied. Thus, the critical shearing force required
to rupture a duplex within a given experiment depends strongly on the time
scale of observation. We use simple models of DNA to demonstrate that this
approach naturally captures the experimentally observed dependence of the
critical force on duplex length for a given observation time. In particular,
the critical force is zero for the shortest duplexes, before rising sharply and
then plateauing in the long length limit. The prevailing approach, based on
identifying when the presence of each additional base pair within the duplex is
thermodynamically unfavorable rather than allowing for metastability, does not
predict a time-scale-dependent critical force and does not naturally
incorporate a critical force of zero for the shortest duplexes. Additionally,
motivated by a recently proposed force sensor, we investigate application of
stress to a duplex in a mixed mode that interpolates between shearing and
unzipping. As with pure shearing, the critical force depends on the time scale
of observation; at a fixed time scale and duplex length, the critical force
exhibits a sigmoidal dependence on the fraction of the duplex that is subject
to shearing.Comment: 10 pages, 6 figure
Close-Packing of Clusters: Application to Al_100
The lowest energy configurations of close-packed clusters up to N=110 atoms
with stacking faults are studied using the Monte Carlo method with Metropolis
algorithm. Two types of contact interactions, a pair-potential and a many-atom
interaction, are used. Enhanced stability is shown for N=12, 26, 38, 50, 59,
61, 68, 75, 79, 86, 100 and 102, of which only the sizes 38, 75, 79, 86, and
102 are pure FCC clusters, the others having stacking faults. A connection
between the model potential and density functional calculations is studied in
the case of Al_100. The density functional calculations are consistent with the
experimental fact that there exist epitaxially grown FCC clusters starting from
relatively small cluster sizes. Calculations also show that several other
close-packed motifs existwith comparable total energies.Comment: 9 pages, 7 figure
Thermodynamics and the Global Optimization of Lennard-Jones clusters
Theoretical design of global optimization algorithms can profitably utilize
recent statistical mechanical treatments of potential energy surfaces (PES's).
Here we analyze the basin-hopping algorithm to explain its success in locating
the global minima of Lennard-Jones (LJ) clusters, even those such as \LJ{38}
for which the PES has a multiple-funnel topography, where trapping in local
minima with different morphologies is expected. We find that a key factor in
overcoming trapping is the transformation applied to the PES which broadens the
thermodynamic transitions. The global minimum then has a significant
probability of occupation at temperatures where the free energy barriers
between funnels are surmountable.Comment: 13 pages, 13 figures, revte
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