arXiv subjects
Publications and source records attributed to Jonathan Doye.
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.
We show that the vibrational entropy can play a crucial role in determining the equilibrium structure of clusters by constructing structural phase diagrams showing how the structure depends upon both size and temperature. These phase diagrams are obtained for example rare gas and metal clusters.
In this chapter the physical aspects of the global optimization of the geometry of atomic clusters are elucidated. In particular, I examine the structural principles that determine the nature of the lowest-energy structure, the physical reasons why some clusters are especially difficult to optimize and how the basin-hopping transformation of the potential energy surface enables these difficult clusters to be optimized.
The global minima of clusters bound by a Dzugutov potential form non-compact polytetrahedral clusters mainly composed of interpenetrating and face-sharing 13-atom icosahedra. As the size increases, these icosahedral units first form linear arrays, then two-dimensional rings, then three-dimensional networks. Characterization of the energy landscapes of these clusters shows that they are particularly rough and generally exhibit a multiple-funnel topography. These results provide new insights into the structure and dynamics of bulk supercooled Dzugutov liquids and the form of the bulk phase diagram.
Recently, Locatelli and Schoen proposed a transformation of the potential energy that aids the global optimization of Lennard-Jones clusters with non-icosahedral global minima. These cases are particularly difficult to optimize because the potential energy surface has a double funnel topography with the global minimum at the bottom of the narrower funnel. Here we analyse the effect of this type of transformation on the topography of the potential energy surface. The transformation, which physically corresponds to a compression of the cluster, firstly reduces the number of stationary points on the potential energy surface. Secondly, we show that for a 38-atom cluster with a face-centred-cubic global minimum the transformation causes the potential energy surface to become increasingly dominated by the funnel associated with the global minimum. The transformation has been incorporated in the basin-hopping algorithm using a two-phase approach.
In this paper I describe the computer simulations that I have performed to critically examine the Lauritzen-Hoffman and the Sadler-Gilmer theories of polymer crystallization. In particular, I have computed the free energy profile for nucleation of a new crystalline layer on the growth face to compare with that assumed by the Lauritzen-Hoffman theory, I have analysed the mechanism of thickness selection in a multi-pathway model in which some of the constraints in the Lauritzen-Hoffman theory are relaxed, and I have re-examined the model used by Sadler-Gilmer. These investigations have lead to a mechanism of thickness selection of lamellar polymer crystals that differs from the two theories that I set out to examine.
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.
In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we presents results for the thermodynamics and dynamics of one of these clusters, (NaCl)35Cl-. As the time scales for the structural transitions can be much longer than those accessible by conventional dynamics simulations, we use a master equation to describe the probability flow within a large sample of potential energy minima. We characterize the processes contributing to probability flow between the different nanocrystals, and obtain rate constants and activation energies for comparison with the experimental values.
Disconnectivity graphs are used to characterize the potential energy surfaces of Lennard-Jones clusters containing 13, 19, 31, 38, 55 and 75 atoms. This set includes members which exhibit either one or two `funnels' whose low-energy regions may be dominated by a single deep minimum or contain a number of competing structures. The graphs evolve in size due to these specific size effects and an exponential increase in the number of local minima with the number of atoms. To combat the vast number of minima we investigate the use of monotonic sequence basins as the fundamental topographical unit. Finally, we examine disconnectivity graphs for a transformed energy landscape to explain why the transformation provides a useful approach to the global optimization problem.
Temperature changes during the growth of lamellar polymer crystals give rise to steps on the surface of the crystals. It has recently been suggested that these steps could provide important insights into the mechanism of polymer crystallization. In particular, a characterization of the profiles of these steps might reveal the fixed-point attractor that underlies a recently proposed crystallization mechanism. Here we examine this hypothesis by performing simulations of such temperature jumps using the Sadler-Gilmer model. We find that for this model the step profiles do reveal the fixed-point attractor. However, for temperature decreases they also reflect the rounding of the crystal edge that occurs in this model and for temperature increases they also reflect the fluctuations in the thickness present in the crystal. We discuss the implications of these results for the interpretation of experimental step profiles.
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.
The 38-atom Lennard-Jones cluster has a paradigmatic double-funnel energy landscape. One funnel ends in the global minimum, a face-centred-cubic (fcc) truncated octahedron. At the bottom of the other funnel is the second lowest energy minimum which is an incomplete Mackay icosahedron. We characterize the energy landscape in two ways. Firstly, from a large sample of minima and transition states we construct a disconnectivity tree showing which minima are connected below certain energy thresholds. Secondly we compute the free energy as a function of a bond-order parameter. The free energy profile has two minima, one which corresponds to the fcc funnel and the other which at low temperature corresponds to the icosahedral funnel and at higher temperatures to the liquid-like state. These two approaches show that the greater width of the icosahedral funnel, and the greater structural similarity between the icosahedral structures and those associated with the liquid-like state, are the cause of the smaller free energy barrier for entering the icosahedral funnel from the liquid-like state and therefore of the cluster's preferential entry into this funnel on relaxation down the energy landscape. Furthermore, the large free energy barrier between the fcc and icosahedral funnels, which is energetic in origin, causes the cluster to be trapped in one of the funnels at low temperature. These results explain in detail the link between the double-funnel energy landscape and the difficulty of global optimization for this cluster.
Based upon kinetic Monte Carlo simulations of crystallization in a simple polymer model we present a new picture of the mechanism by which the thickness of lamellar polymer crystals is constrained to a value close to the minimum thermodynamically stable thickness, l_{min}. The free energetic costs of the polymer extending beyond the edges of the previous crystalline layer and of a stem being shorter than l_{min} provide upper and lower constraints on the length of stems in a new layer. Their combined effect is to cause the crystal thickness to converge dynamically to a value close to l_{min} where growth with constant thickness then occurs. This description contrasts with those given by the two dominant theoretical approaches. However, at small supercoolings the rounding of the crystal profile does inhibit growth as suggested in Sadler and Gilmer's entropic barrier model.
In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we determine reaction pathways between the low energy isomers of one of these clusters, (NaCl)35Cl-. The key process in these structural transitions is a highly cooperative rearrangement in which two parts of the nanocrystal slip past one another on a {110} plane in a <1-10> direction. In this way the nanocrystals can plastically deform, in contrast to the brittle behaviour of bulk sodium chloride crystals at the same temperatures; the nanocrystals have mechanical properties which are a unique feature of their finite size. We also report and compare the global potential energy minima for (NaCl)NCl- using two empirical potentials, and comment on the effect of polarization.
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.
We have studied the structure and free energy landscape of a semi-flexible lattice-polymer in the presence of a surface. At low temperatures coexistence of two-dimensional integer-folded crystals is observed. As the temperature is increased there is a transition from these crystalline configurations to a disordered coil adsorbed onto the surface. The polymer then gradually develops three-dimensional character at higher temperatures. We compute the free energy as a function of increasing crystallinity and compare with the free energy profiles assumed by the Lauritizen-Hoffman surface nucleation theory of polymer crystallization. Our free energy profiles exhibit a `sawtooth' structure associated with the successive formation of chain folds. However, in the early stages of crystallization our profiles significantly deviate from those assumed by surface nucleation theory because the initial nucleus is not a single stem but two incomplete stems connected by a fold. This finding has significant implications for the theoretical description of polymer crystallization.
We describe a global optimization technique using `basin-hopping' in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features which recent work suggests must be present in an energy landscape for efficient relaxation to the global minimum. The transformation associates any point in configuration space with the local minimum obtained by a geometry optimization started from that point, effectively removing transition state regions from the problem. However, unlike other methods based upon hypersurface deformation, this transformation does not change the global minimum. The lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.
Based upon kinetic Monte Carlo simulations of crystallization in a simple polymer model we present a new picture of the mechanism by which the thickness of lamellar polymer crystals is constrained to a value close to the minimum thermodynamically stable thickness. This description contrasts with those given by the two dominant theoretical approaches.