227 research outputs found
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
Controlling crystallization and its absence: Proteins, colloids and patchy models
The ability to control the crystallization behaviour (including its absence)
of particles, be they biomolecules such as globular proteins, inorganic
colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and
technological importance. Much can be learnt from the exquisite control that
biological systems exert over the behaviour of proteins, where protein
crystallization and aggregation are generally suppressed, but where in
particular instances complex crystalline assemblies can be formed that have a
functional purpose. We also explore the insights that can be obtained from
computational modelling, focussing on the subtle interplay between the
interparticle interactions, the preferred local order and the resulting
crystallization kinetics. In particular, we highlight the role played by
``frustration'', where there is an incompatibility between the preferred local
order and the global crystalline order, using examples from atomic glass
formers and model anisotropic particles.Comment: 11 pages, 7 figure
Polytetrahedral Clusters
By studying the structures of clusters bound by a model potential that
favours polytetrahedral order, we find a previously unknown series of `magic
numbers' (i.e. sizes of special stability) whose polytetrahedral structures are
characterized by disclination networks that are analogous to hydrocarbons.Comment: 4 pages, 4 figure
The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry
The phase diagram of model anisotropic particles with four attractive patches
in a tetrahedral arrangement has been computed at two different values for the
range of the potential, with the aim of investigating the conditions under
which a diamond crystal can be formed. We find that the diamond phase is never
stable for our longer-ranged potential. At low temperatures and pressures, the
fluid freezes into a body-centred-cubic solid that can be viewed as two
interpenetrating diamond lattices with a weak interaction between the two
sublattices. Upon compression, an orientationally ordered face-centred-cubic
crystal becomes more stable than the body-centred-cubic crystal, and at higher
temperatures a plastic face-centered-cubic phase is stabilized by the increased
entropy due to orientational disorder. A similar phase diagram is found for the
shorter-ranged potential, but at low temperatures and pressures, we also find a
region over which the diamond phase is thermodynamically favored over the
body-centred-cubic phase. The higher vibrational entropy of the diamond
structure with respect to the body-centred-cubic solid explains why it is
stable even though the enthalpy of the latter phase is lower. Some preliminary
studies on the growth of the diamond structure starting from a crystal seed
were performed. Even though the diamond phase is never thermodynamically stable
for the longer-ranged model, direct coexistence simulations of the interface
between the fluid and the body-centred-cubic crystal and between the fluid and
the diamond crystal show that, at sufficiently low pressures, it is quite
probable that in both cases the solid grows into a diamond crystal, albeit
involving some defects. These results highlight the importance of kinetic
effects in the formation of diamond crystals in systems of patchy particles.Comment: 15 pages, 13 figure
A molecular dynamics simulation of polymer crystallization from oriented amorphous state
Molecular process of crystallization from an oriented amorphous state was
reproduced by molecular dynamics simulation for a realistic polyethylene model.
Initial oriented amorphous state was obtained by uniaxial drawing an isotropic
glassy state at 100 K. By the temperature jump from 100 K to 330 K, there
occurred the crystallization into the fiber structure, during the process of
which we observed the developments of various order parameters. The real space
image and its Fourier transform revealed that a hexagonally ordered domain was
initially formed, and then highly ordered crystalline state with stacked
lamellae developed after further adjustment of the relative heights of the
chains along their axes.Comment: 4 pages, 3 figure
A simple physical model for scaling in protein-protein interaction networks
It has recently been demonstrated that many biological networks exhibit a
scale-free topology where the probability of observing a node with a certain
number of edges (k) follows a power law: i.e. p(k) ~ k^-g. This observation has
been reproduced by evolutionary models. Here we consider the network of
protein-protein interactions and demonstrate that two published independent
measurements of these interactions produce graphs that are only weakly
correlated with one another despite their strikingly similar topology. We then
propose a physical model based on the fundamental principle that (de)solvation
is a major physical factor in protein-protein interactions. This model
reproduces not only the scale-free nature of such graphs but also a number of
higher-order correlations in these networks. A key support of the model is
provided by the discovery of a significant correlation between number of
interactions made by a protein and the fraction of hydrophobic residues on its
surface. The model presented in this paper represents the first physical model
for experimentally determined protein-protein interactions that comprehensively
reproduces the topological features of interaction networks. These results have
profound implications for understanding not only protein-protein interactions
but also other types of scale-free networks.Comment: 50 pages, 17 figure
Self-similar disk packings as model spatial scale-free networks
The network of contacts in space-filling disk packings, such as the
Apollonian packing, are examined. These networks provide an interesting example
of spatial scale-free networks, where the topology reflects the broad
distribution of disk areas. A wide variety of topological and spatial
properties of these systems are characterized. Their potential as models for
networks of connected minima on energy landscapes is discussed.Comment: 13 pages, 12 figures; some bugs fixed and further discussion of
higher-dimensional packing
Self-assembly, modularity and physical complexity
We present a quantitative measure of physical complexity, based on the amount
of information required to build a given physical structure through
self-assembly. Our procedure can be adapted to any given geometry, and thus to
any given type of physical system. We illustrate our approach using
self-assembling polyominoes, and demonstrate the breadth of its potential
applications by quantifying the physical complexity of molecules and protein
complexes. This measure is particularly well suited for the detection of
symmetry and modularity in the underlying structure, and allows for a
quantitative definition of structural modularity. Furthermore we use our
approach to show that symmetric and modular structures are favoured in
biological self-assembly, for example of protein complexes. Lastly, we also
introduce the notions of joint, mutual and conditional complexity, which
provide a useful distance measure between physical structures.Comment: 9 pages, submitted for publicatio
The network topology of a potential energy landscape: A static scale-free network
Here we analyze the topology of the network formed by the minima and
transition states on the potential energy landscape of small clusters. We find
that this network has both a small-world and scale-free character. In contrast
to other scale-free networks, where the topology results from the dynamics of
the network growth, the potential energy landscape is a static entity.
Therefore, a fundamentally different organizing principle underlies this
behaviour: The potential energy landscape is highly heterogeneous with the
low-energy minima having large basins of attraction and acting as the
highly-connected hubs in the network.Comment: 4 pages, 4 figures, revtex
Decoupling of diffusion from structural relaxation and spatial heterogeneity in a supercooled simple liquid
We report a molecular dynamics simulation of a supercooled simple monatomic
glass-forming liquid. It is found that the onset of the supercooled regime
results in formation of distinct domains of slow diffusion which are confined
to the long-lived icosahedrally structured clusters associated with deeper
minima in the energy landscape. As these domains, possessing a low-dimensional
geometry, grow with cooling and percolate below , the critical temperature
of the mode coupling theory, a sharp slowing down of the structural relaxation
relative to diffusion is observed. It is concluded that this latter anomaly
cannot be accounted for by the spatial variation in atomic mobility; instead,
we explain it as a direct result of the configuration-space constraints imposed
by the transient structural correlations. We also conjecture that the observed
tendency for low-dimensional clustering may be regarded as a possible mechanism
of fragility.Comment: To be published in PR
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