Particle rearrangements during transitions between local minima of the potential energy landscape of a supercooled Lennard-Jones liquid

The potential energy landscape (PEL) of supercooled binary Lennard-Jones (BLJ) mixtures exhibits local minima, or inherent structures (IS), which are organized into meta-basins (MB). We study the particle rearrangements related to transitions between both successive IS and successive MB for a small 80:20 BLJ system near the mode-coupling temperature T_MCT. The analysis includes the displacements of individual particles, the localization of the rearrangements and the relevance of string-like motion. We find that the particle rearrangements during IS and MB transitions do not change significantly at T_MCT. Further, it is demonstrated that IS and MB dynamics are spatially heterogeneous and facilitated by string-like motion. To investigate the mechanism of string-like motion, we follow the particle rearrangements during suitable sequences of IS transitions. We find that most strings observed after a series of transitions do not move coherently during a single transition, but subunits of different sizes are active at different times. Several findings suggest that the occurrence of a successful string enables the system to exit a MB. Moreover, we show that the particle rearrangements during two consecutive MB transitions are basically uncorrelated. Specifically, different groups of particles are highly mobile during subsequent MB transitions. Finally, the relation between the features of the PEL and the relaxation processes in supercooled liquids is discussed.Comment: 13 pages, 10 figure

Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

Are there localized saddles behind the heterogeneous dynamics of supercooled liquids?

We numerically study the interplay between heterogeneous dynamics and properties of negatively curved regions of the potential energy surface in a model glassy system. We find that the unstable modes of saddles and quasi-saddles undergo a localization transition close to the Mode-Coupling critical temperature. We also find evidence of a positive spatial correlation between clusters of particles having large displacements in the unstable modes and dynamical heterogeneities.Comment: 7 pages, 3 figures, submitted to Europhys. Let

Growing spatial correlations of particle displacements in a simulated liquid on cooling toward the glass transition

We define a correlation function that quantifies the spatial correlation of single-particle displacements in liquids and amorphous materials. We show for an equilibrium liquid that this function is related to fluctuations in a bulk dynamical variable. We evaluate this function using computer simulations of an equilibrium glass-forming liquid, and show that long range spatial correlations of displacements emerge and grow on cooling toward the mode coupling critical temperature

Optimal Filling of Shapes

We present filling as a type of spatial subdivision problem similar to covering and packing. Filling addresses the optimal placement of overlapping objects lying entirely inside an arbitrary shape so as to cover the most interior volume. In n-dimensional space, if the objects are polydisperse n-balls, we show that solutions correspond to sets of maximal n-balls. For polygons, we provide a heuristic for finding solutions of maximal discs. We consider the properties of ideal distributions of N discs as N approaches infinity. We note an analogy with energy landscapes.Comment: 5 page

Crystalline Assemblies and Densest Packings of a Family of Truncated Tetrahedra and the Role of Directional Entropic Forces

Polyhedra and their arrangements have intrigued humankind since the ancient Greeks and are today important motifs in condensed matter, with application to many classes of liquids and solids. Yet, little is known about the thermodynamically stable phases of polyhedrally-shaped building blocks, such as faceted nanoparticles and colloids. Although hard particles are known to organize due to entropy alone, and some unusual phases are reported in the literature, the role of entropic forces in connection with polyhedral shape is not well understood. Here, we study thermodynamic self-assembly of a family of truncated tetrahedra and report several atomic crystal isostructures, including diamond, {\beta}-tin, and high- pressure lithium, as the polyhedron shape varies from tetrahedral to octahedral. We compare our findings with the densest packings of the truncated tetrahedron family obtained by numerical compression and report a new space filling polyhedron, which has been overlooked in previous searches. Interestingly, the self-assembled structures differ from the densest packings. We show that the self-assembled crystal structures can be understood as a tendency for polyhedra to maximize face-to-face alignment, which can be generalized as directional entropic forces.Comment: Article + supplementary information. 23 pages, 10 figures, 2 table

Heterogeneous slow dynamics in a two dimensional doped classical antiferromagnet

We introduce a lattice model for a classical doped two dimensional antiferromagnet which has no quenched disorder, yet displays slow dynamics similar to those observed in supercooled liquids. We calculate two-time spatial and spin correlations via Monte Carlo simulations and find that for sufficiently low temperatures, there is anomalous diffusion and stretched-exponential relaxation of spin correlations. The relaxation times associated with spin correlations and diffusion both diverge at low temperatures in a sub-Arrhenius fashion if the fit is done over a large temperature-window or an Arrhenius fashion if only low temperatures are considered. We find evidence of spatially heterogeneous dynamics, in which vacancies created by changes in occupation facilitate spin flips on neighbouring sites. We find violations of the Stokes-Einstein relation and Debye-Stokes-Einstein relation and show that the probability distributions of local spatial correlations indicate fast and slow populations of sites, and local spin correlations indicate a wide distribution of relaxation times, similar to observ ations in other glassy systems with and without quenched disorder.Comment: 12 pages, 17 figures, corrected erroneous figure, and improved quality of manuscript, updated reference

Sticky Spheres, Entropy barriers and Non-equilibrium phase transitions

A sticky spheres model to describe slow dynamics of a non-equilibrium system is proposed. The dynamical slowing down is due to the presence of entropy barriers. We present an exact mean field analysis of the model and demonstrate that there is a non-equilibrium phase transition from an exponential cluster size distribution to a powerlaw.Comment: 10pages text and 2 figure

Time and length scales in supercooled liquids

We numerically obtain the first quantitative demonstration that development of spatial correlations of mobility as temperature is lowered is responsible for the ``decoupling'' of transport properties of supercooled liquids. This result further demonstrates the necessity of a spatial description of the glass formation and therefore seriously challenges a number of popular alternative theoretical descriptions.Comment: 4 pages, 4 figs; improved version: new refs and discussion