The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization

Recent work on the mechanism of polymer crystallization has led to a proposal for the mechanism of thickness selection which differs from those proposed by the surface nucleation theory of Lauritzen and Hoffman and the entropic barrier model of Sadler and Gilmer. This has motivated us to reexamine the model used by Sadler and Gilmer. We again find a fixed-point attractor which describes the dynamical convergence of the crystal thickness to a value just larger than the minimum stable thickness, l_min. This convergence arises from the combined effect of two constraints on the length of stems in a layer: it is unfavourable for a stem to be shorter than l_min and for a stem to overhang the edge of the previous layer. The relationship between this new mechanism and the explanation given by Sadler and Gilmer in terms of an entropic barrier is discussed. We also examine the behaviour of the Sadler-Gilmer model when an energetic contribution from chain folds is included.Comment: 15 pages, 13 figures, revte

The structure of binary Lennard-Jones clusters: The effects of atomic size ratio

We introduce a global optimization approach for binary clusters that for a given cluster size is able to directly search for the structure and composition that has the greatest stability. We apply this approach to binary Lennard-Jones clusters, where the strength of the interactions between the two atom types is the same, but where the atoms have different sizes. We map out how the most stable structure depends on the cluster size and the atomic size ratio for clusters with up to 100 atoms and up to 30% difference in atom size. A substantial portion of this parameter space is occupied by structures that are polytetrahedral, both those that are polyicosahedral and those that involve disclination lines. Such structures involve substantial strains for one-component Lennard-Jones clusters, but can be stabilized by the different-sized atoms in the binary clusters. These structures often have a `core-shell' geometry, where the larger atoms are on the surface, and the smaller atoms are in the core.Comment: 13 pages, 9 figure

CO Oxidation Catalysed by Pd-based Bimetallic Nanoalloys

Density functional theory based global geometry optimization has been used to demonstrate the crucial influence of the geometry of the catalytic cluster on the energy barriers for the CO oxidation reaction over Pd-based bimetallic nanoalloys. We show that dramatic geometry change between the reaction intermediates can lead to very high energy barriers and thus be prohibitive for the whole process. This introduces challenges for both the design of new catalysts, and theoretical methods employed. On the theory side, a careful choice of geometric configurations of all reaction intermediates is crucial for an adequate description of a possible reaction path. From the point of view of the catalyst design, the cluster geometry can be controlled by adjusting the level of interaction between the cluster and the dopant metal, as well as between the adsorbate molecules and the catalyst cluster by mixing different metals in a single nanoalloy particle. We show that substitution of a Pd atom in the Pd$_{5}$ cluster with a single Ag atom to form Pd$_{4}$Ag$_{1}$ leads to a potential improvement of the catalytic properties of the cluster for the CO oxidation reaction. On the other hand, a single Au atom does not enhance the properties of the catalyst, which is attributed to a weaker hybridization between the cluster's constituent metals and the adsorbate molecules. Such flexibility of properties of bimetallic nanoalloy clusters illustrates the possibility of fine-tuning, which might be used for design of novel efficient catalytic materials.Comment: 12 pages, 8 figure

Homogeneous TIP4P/2005 ice nucleation at low supercooling

We present a partial free energy profile for the homogeneous nucleation of ice using an all-atom model of water at low supercooling, at which ice growth dynamics are reasonably accessible to simulation. We demonstrate that the free energy profile is well described by classical nucleation theory, and that the nucleation barrier is entropic in origin. We also estimate to first order the temperature dependence of the interfacial free energy

Effects of surface interactions on heterogeneous ice nucleation for a monatomic water model

Despite its importance in atmospheric science, much remains unknown about the microscopic mechanism of heterogeneous ice nucleation. In this work, we perform hybrid Monte Carlo simulations of the heterogeneous nucleation of ice on a range of generic surfaces, both flat and structured, in order to probe the underlying factors affecting the nucleation process. The structured surfaces we study comprise one basal plane bilayer of ice with varying lattice parameters and interaction strengths. We show that what determines the propensity for nucleation is not just the surface attraction, but also the orientational ordering imposed on liquid water near a surface. In particular, varying the ratio of the surface's attraction and orientational ordering can change the mechanism by which nucleation occurs: ice can nucleate on the structured surface even when the orientational ordering imposed by the surface is weak, as the water molecules that interact strongly with the surface are themselves a good template for further growth. We also show that lattice matching is important for heterogeneous nucleation on the structured surface we study. We rationalise these brute-force simulation results by explicitly calculating the interfacial free energies of ice and liquid water in contact with the nucleating surface and their variation with surface interaction parameters

Thermodynamics of Community Structure

We introduce an approach to partitioning networks into communities that not only determines the best community structure, but also provides a range of characterization techniques to assess how significant that structure is. We study the thermodynamics of community structure by producing equilibrium ensembles of partitions, in which each partition is represented with a well-defined statistical weight. Thus we are able to study the temperature dependence of thermodynamic properties, namely the modularity $Q$ and heat capacity, with particular emphasis on the transition between high-temperature, essentially random partitions and low-temperature partitions with high modularity. We also look at frequency matrices that measure the likelihood that two nodes belong to the same community, and introduce an order parameter to measure the `blockiness' of the frequency matrix, and therefore the uniqueness of the community structure. These methods have been applied to a number of model networks in order to understand the effects of the degree distribution, spatial embedding and randomization. Finally, we apply these methods to a metabolic network known to have strong community structure and find hierarchical community structure, with some communities being more robust than others.Comment: 12 pages, 16 figure

Energy landscapes, scale-free networks and Apollonian packings

We review recent results on the topological properties of two spatial scale-free networks, the inherent structure and Apollonian networks. The similarities between these two types of network suggest an explanation for the scale-free character of the inherent structure networks. Namely, that the energy landscape can be viewed as a fractal packing of basins of attraction.Comment: 10 pages, 8 figure

Protein crystallization in vivo

Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the crystals thatare exploited. Where known, we emphasize how the nature of the protein-protein interactions leads to control of the crystallization behaviour.Comment: 17 pages, 1 figur