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Phillip L. Geissler made important contributions to the statistical mechanics of biological polymers, heterogeneous materials, and chemical dynamics in aqueous environments. He devised analytical and computational methods that revealed the underlying organization of complex systems at the frontiers of biology, chemistry, and materials science. In this retrospective we celebrate his work at these frontiers.

The propagation of chirality across scales is a common but poorly understood phenomenon in soft matter. In this work, we use computer simulations to study chiral monolayer assemblies formed by hard rod-like colloidal particles in the presence of non-adsorbing polymer and characterize the thermodynamic driving forces responsible for the twisting. Simulations show that straight (achiral) rods assemble into monolayers with a spontaneous twist that is either left- or right-handed, while helical (chiral) rods lead to assemblies with preferential chiral features that depend on their handedness and curliness. The onset of chirality in these monolayers can be traced back to small clusters formed at the initial stage of the self-assembly. In these microscopic monolayers, entropy drives twisting in ways that differ from the assumptions on which existing continuum theory is built. Depending on the geometry of the constituent rods, the preferred chiral twist can be driven by entropy gain of the polymers, or of the rods, or both. In addition, the variation of the polymer entropy with twist depends on changes in both the surface area and the volume of the monolayer. Rod fluctuations perpendicular to the monolayer also play an important role in stabilising the twisting., 14 pages, 12 figures

Large magnetic optical rotary dispersion (Faraday rotation) has been demonstrated recently in methylammonium lead bromide. Here, we investigate the prospect of extending the active spectral range by altering the halogen. We also investigate the origins of large Faraday rotation in these diamagnetic materials using magnetic circular dichroism (MCD) spectroscopy and the Kramers-Kronig relations. We find that, while MAPbCl3 (MA = methylammonium) single crystals exhibit a large Verdet constant in the blue, no appreciable Faraday rotation is observed in the red/near infra-red for MAPbI3 single crystals. However, in all film samples, we find clear evidence of large MCD resulting from the Zeeman splitting of the highly resonant 1s exciton state. Our Kramers-Kronig calculations of Faraday rotation based on MCD data matches well with the dispersion of our experimental data for MAPbCl3 and MAPbBr3 , with some deviation in magnitude-demonstrating the excitonic nature of Faraday rotation in these materials. However, our calculations predict significant Faraday rotation in MAPbI3 , contrary to our experimental results, indicating a potential discrepancy between the properties of the thin film and single crystal.

In this study, we developed a coarse-grained model based on the dissipative particle dynamics (DPD) method to investigate the aggregates of the cetyltrimethylammonium bromide (CTAB) molecules on go...

We report on the colloidal stability of nanoparticles with alkanethiol shells in apolar solvents. Small-angle X-ray scattering and molecular dynamics simulations were used to characterize the interaction between nanoparticles in linear alkane solvents ranging from hexane to hexadecane, including 4 nm gold cores with hexadecanethiol shells and 6 nm cadmium selenide cores with octadecanethiol shells. We find that the agglomeration is enthalpically driven and that, contrary to what one would expect from classical colloid theory, the temperature at which the particles agglomerate increases with increasing solvent chain length. We demonstrate that the inverted trend correlates with the temperatures at which the ligands order in the different solvents and show that the inversion is due to a combination of enthalpic and entropic effects that enhance the stability of the ordered ligand state as the solvent length increases. We also explain why cyclohexane is a better solvent than hexadecane despite the two having very similar solvation parameters.

Self-assembly of nanoscale structures at liquid–solid interfaces occurs in a broad range of industrial processes and is found in various phenomena in nature. Conventional theory assumes spherical particles and homogeneous surfaces, but that model is oversimplified, and nanoscale in situ observations are needed for a more complete understanding. Liquid-phase scanning transmission electron microscopy (LP-STEM) is used to examine the interactions that direct the self-assembly of superlattices formed by gold nanoparticles (AuNPs) in nonpolar liquids. Varying the molecular coating of the substrate modulates short-range attraction and leads to switching between a range of different geometric structures, including hexagonal close-packed (hcp), simple hexagonal (sh), dodecahedral quasi-crystal (dqc), and body-centered cubic (bcc) lattices, as well as random distributions. Langevin dynamics simulations explain the experimental results in terms of the interplay between nanoparticle faceting, ligand shell structure, and substrate–NP interactions.

The excited-state dynamics of 6,13-bis(triisopropylsilylethynyl)pentacene is investigated to determine the role of excimer and aggregate formation in singlet fission in high-concentration solutions. Photoluminescence spectra were measured by excitation with the evanescent wave in total internal reflection, in order to avoid reabsorption effects. The spectra over nearly two magnitudes of concentration were nearly identical, with no evidence for excimer emission. Time-correlated single-photon counting measurements confirm that the fluorescence lifetime shortens with concentration. The observed rate constant grows at high concentrations, and this effect is modeled in terms of the hard-sphere radial distribution function. NMR measurements confirm that aggregation takes place with a binding constant of between 0.14 and 0.43 M-1. Transient absorption measurements are consistent with a diffusive encounter mechanism for singlet fission, with hints of more rapid singlet fission in aggregates at the highest concentration measured. These data show that excimers do not play the role of an emissive intermediate in exothermic singlet fission in solution and that, while aggregation occurs at higher concentrations, the mechanism of singlet fission remains dominated by diffusive encounters.

A dissipative particle dynamics (DPD) model is developed and demonstrated for studying dynamics in colloidal rod suspensions. The solvent is modeled as conventional DPD particles, while individual rods are represented by a rigid linear chain consisting of overlapping solid spheres, which interact with solvent particles through a hard repulsive potential. The boundary condition on the rod surface is controlled using a surface friction between the solid spheres and the solvent particles. In this work, this model is employed to study the diffusion of a single colloid in the DPD solvent and compared with theoretical predictions. Both the translational and rotational diffusion coefficients obtained at a proper surface friction show good agreement with calculations based on the rod size defined by the hard repulsive potential. In addition, the system-size dependence of the diffusion coefficients shows that the Navier–Stokes hydrodynamic interactions are correctly included in this DPD model. Comparing our results with experimental measurements of the diffusion coefficients of gold nanorods, we discuss the ability of the model to correctly describe dynamics in real nanorod suspensions. Our results provide a clear reference point from which the model could be extended to enable the study of colloid dynamics in more complex situations or for other types of particles.

The controlled positioning of spherical gold nanoparticles and gold nanorods upon self-assembly on a substrate is of great interest for the fabrication of tailored plasmonic devices. Here, an electrostatic approach with a sequential two-step assembly protocol is presented as a cost-effective and high-yield alternative to previously presented, more complex proof of concepts. Three different geometries can be separately produced in large quantities relying on electrostatic attraction and repulsion of the charge-carrying building blocks: a single gold nanoparticle at the tip, the side or on top of a gold nanorod. DLVO theory is used to explain the electrostatic assembly strategy. The process is highly efficient and assembly yields between 79% (at the tip) and 94% (for the nanoparticle at the long side of the nanorod) are achieved.

Bandgap instability due to light-induced phase segregation in mixed-halide perovskites presents a major challenge for their future commercial use. Here we demonstrate that photoinduced halide-ion segregation can be completely reversed at sufficiently high illumination intensities, enabling control of the optical bandgap of a mixed-halide perovskite single crystal by optimizing the input photogenerated carrier density. We develop a polaron-based two-dimensional lattice model that rationalizes the experimentally observed phenomena by assuming that the driving force for photoinduced halide segregation is dependent on carrier-induced strain gradients that vanish at high carrier densities. Using illumination sources with different excitation intensities, we demonstrate write–read–erase experiments showing that it is possible to store information in the form of latent images over several minutes. The ability to control the local halide-ion composition with light intensity opens opportunities for the use of mixed-halide perovskites in concentrator and tandem solar cells, as well as in high-power light-emissive devices and optical memory applications. Depending on its intensity, light irradiation is shown to induce not only segregation but also remixing of halide ions in mixed-halide perovskites, enabling in situ and localized control of chemical composition and optical bandgap in these materials.

Inorganic nanoparticle cores are often coated with organic ligands to render them dispersible in apolar solvents. However, the effect of the ligand shell on the colloidal stability of the overall hybrid particle is not fully understood. In particular, it is not known how the length of an apolar alkyl ligand chain affects the stability of a nanoparticle dispersion against agglomeration. Here, small-angle X-ray scattering and molecular dynamics simulations have been used to study the interactions between gold nanoparticles and between cadmium selenide nanoparticles passivated by alkanethiol ligands with 12-18 carbons in the solvent decane. We find that increasing the ligand length increases colloidal stability in the core-dominated regime but decreases it in the ligand-dominated regime. This unexpected inversion is connected to the transition from ligand-dominated to core-dominated agglomeration when the core diameter increases at constant ligand length. Our results provide a microscopic picture of the forces that determine the colloidal stability of apolar nanoparticles and explain why classical colloid theory fails.

Dewetting of polymer thin films has been extensively studied in the past two decades as an approach to produce patterned surfaces. Here we report a novel phenomenon where dewetted polymer droplets spontaneously align on a substrate, and the alignment extends over a large scale (millimeters). The patterns are formed by dewetting a bilayer system formed by poly(4-vinylpyridine) (P4VP) thin film (80 nm) on a polystyrene (PS) thin film (100 nm) prepared by spin-coating. We investigated the mechanism of the spontaneous droplet alignment and concluded that the final aligned pattern results from series of aligned defects on the P4VP, which are formed during spin-coating. We identified experimental parameters that control the appearance and the order of the resulting aligned droplets.

Here, we present an implicit-solvent model for dynamic simulations of hard-rod and rod-polymer suspensions. Individual rods are represented by a rigid linear chain consisting of overlapping spheres which interact through a pseudohard-core potential based on the cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). In the rod-polymer suspensions, the polymers are modeled as freely interpenetrable spheres with respect to each other, while there is the pseudohard-core repulsion between the polymer and rod spheres. Dynamic simulations with this model are carried out with a dissipative particle dynamics (DPD) thermostat-each sphere is put in a larger DPD sphere and thus interacts with others via additional pairwise frictional and random forces-which captures the effects of Brownian forces due to the solvent while conserving local momentum. The phase behavior of these models, obtained from continuous compression and expansion simulations, reproduces previous predictions based on theoretical calculations and Monte Carlo simulations. Our method is suited to study dynamic processes in these suspensions, including nucleation and self-assembly, and can be readily extended to colloidal particles of different shapes and chemistry.

In order to better control the assembly of nanorods, knowledge of the pathways by which they form ordered structures is desirable. In this paper, we characterize crystal nucleation in suspensions of spherocylindrical rods with aspect ratio L/D = 2.3 in the presence of both small and large polymer depletants. Using a combination of Langevin dynamics and Monte Carlo simulations, together with biased sampling techniques, we show that the preferred pathway always involves the formation of monolayer assemblies irrespective of the volume fraction of the initial isotropic phase and the diameter of the depletants. This includes the previously neglected case of nucleation from the colloidal liquid phase and shows that the presence of depletion attraction can alter nucleation pathways even when the initial phase is dense.

Although many nanoscale materials such as quantum dots and metallic nanocrystals exhibit size dependent optical properties, it has been difficult to incorporate them into optical or electronic devices because there are currently no methods for precise, large‐scale deposition of single nanocrystals. Of particular interest is the need to control the orientation of single nanocrystals since the optical properties are usually strongly anisotropic. Here a method based on electrophoretic deposition (EPD) is reported to precisely assemble vertically oriented, single gold nanorods. It is demonstrated that the orientation of gold nanorods during deposition is controlled by the electric dipole moment induced along the rod by the electric field. Dissipative particle dynamics simulations indicate that the magnitude of this dipole moment is dominated by the polarizability of the solution phase electric double layer around the nanorod. The resulting vertical gold nanorod arrays exhibit reflected colors due to selective excitation of the transverse surface plasmon mode. The EPD method allows assembly of arrays with a density of over one million, visually resolvable, vertical nanorods per square millimeter.

While growth and dissolution of surface nanobubbles has been widely studied in recent years, their stability under pressure changes or a temperature increase has not received the same level of scrutiny. Here, we present theoretical predictions based on classical theory for pressure and temperature thresholds ($p_c$ and $T_c$) at which unstable growth occurs for the case of air nanobubbles on a solid surface in water. We show that bubbles subjected to pinning have much lower $p_c$ and higher $T_c$ compared to both unpinned and bulk bubbles of similar size, indicating that pinned bubbles can withstand a larger tensile stress (negative pressure) and higher temperatures. The values of $p_c$ and $T_c$ obtained from many-body dissipative particle dynamics (MDPD) simulations of quasi-two-dimensional (quasi-2D) surface nanobubbles are consistent with the theoretical predictions, provided that the lateral expansion during growth is taken into account. This suggests that the modified classical thermodynamic description is valid for pinned bubbles as small as several nanometers. While some discrepancies still exist between our theoretical results and previous experiments, further experimental data is needed before a comprehensive understanding of the stability of surface nanobubbles can be achieved., Comment: 12 pages, 9 figures

Being able to predict and tune the colloidal stability of nanoparticles is essential for a wide range of applications, yet our ability to do so is currently poor due to a lack of understanding of how they interact with one another. Here, we show that the agglomeration of apolar particles is dominated by either the core or the ligand shell, depending on the particle size and materials. We do this by using Small-Angle X-ray Scattering and molecular dynamics simulations to characterize the interaction between hexadecanethiol passivated gold nanoparticles in decane solvent. For smaller particles, the agglomeration temperature and interparticle spacing are determined by ordering of the ligand shell into bundles of aligned ligands that attract one another and interlock. In contrast, the agglomeration of larger particles is driven by van der Waals attraction between the gold cores, which eventually becomes strong enough to compress the ligand shell. Our results provide a microscopic description of the forces that determine the colloidal stability of apolar nanoparticles and explain why classical colloid theory fails., 26 pages, 4 figures, plus SI

Nanoparticles are often covered in ligand monolayers, which can undergo a temperature-dependent order-disorder transition that switches the particle-particle interaction from repulsive to attractive in solution. In this work, we examine how changes in the ligand surface coverage and facet dimensions affect the ordering of ligands, the arrangement of nearby solvent molecules, and the interaction between ligand monolayers on different particles. In particular, we consider the case of strongly bound octadecyl ligands on the (100) facet of CdS in the presence of an explicit n-hexane solvent. Depending on the facet dimensions and surface coverage, we observe three distinct ordered states that differ in how the ligands are packed together, and which affect the thickness of the ligand shell and the structure of the ligand-solvent interface. The temperature dependence of the order-disorder transition also broadens and shifts to lower temperature in a nonlinear manner as the nanoscale is approached from above. We find that ligands on nanoscale facets can behave very similarly to those on macroscopic surfaces in solution, and that some facet dimensions affect the ligand alignment more strongly than others. As the ligands order, the interaction between opposing monolayers becomes attractive, even well below full surface coverage. The strength of attraction per unit surface area is strongly affected by ligand coverage, but only weakly by facet width. Conversely, we find that bringing two monolayers together just above the order-disorder transition temperature can induce ordering and attraction., Comment: 32 pages, 9 figures

In this article, we develop a modelling approach which examines selected drivers of ecosystem functioning and agricultural productivity. In particular, we develop linkages between land use and biodiversity and between biodiversity and agricultural productivity. We review the literature for quantitative estimates of key relationships and their parameters for modelling human consumption, land use, energy use, and greenhouse gas emissions on biodiversity and agricultural productivity. We assemble these specifications into an iterative causal model and carry out a number of scenario projections of country-level consumption, production, land use, energy use, greenhouse gas emissions, species diversity, and agricultural production up to 2050. Finally, we dissect the projections into key drivers using structural decomposition and sensitivity analyses.

Understanding how polyhedra pack into extended arrangements is integral to the design and discovery of crystalline materials at all length scales. Much progress has been made in enumerating and characterizing the packing of polyhedral shapes, and the self-assembly of polyhedral nanocrystals into ordered superstructures. However, directing the self-assembly of polyhedral nanocrystals into densest packings requires precise control of particle shape, polydispersity, interactions and driving forces. Here we show with experiment and computer simulation that a range of nanoscale Ag polyhedra can self-assemble into their conjectured densest packings. When passivated with adsorbing polymer, the polyhedra behave as quasi-hard particles and assemble into millimetre-sized three-dimensional supercrystals by sedimentation. We also show, by inducing depletion attraction through excess polymer in solution, that octahedra form an exotic superstructure with complex helical motifs rather than the densest Minkowski lattice. Such large-scale Ag supercrystals may facilitate the design of scalable three-dimensional plasmonic metamaterials for sensing, nanophotonics and photocatalysis.

Javier Reguera, Christophe Petit, Leonardo Scarabelli, Xiaoying Liu, Edward Malachosky, Matthew Martin, Bruce Law, Xiao-Min Lin, Helmuth Moehwald, Peter Schurtenberger, Heiko Wolf, Vicki Meli, Damien Faivre, Eser Metin Akinoglu, Dhanavel Ganeshan, Fernando Bresme, Yangwei Liu, Casper Kunstmann-Olsen, Christopher Sorensen, Suvojit Ghosh, Asanka Yapa, Asaph WidmerCooper, M. Fernanda Cardinal, Almudena Gallego, Ozgur Tarhan, Gunadhor Okram, Andreas Fery, Emanuela Del Gado, Lucio Isa, Regine Perzynski and Brian Korgel

Colloidal gel networks are disordered elastic solids that can form even in extremely dilute particle suspensions. With interaction strengths comparable to the thermal energy, their stress-bearing network can locally restructure via breaking and reforming interparticle bonds. This allows for yielding, self-healing, and adaptive mechanics under deformation. Designing such features requires controlling stress transmission through the complex structure of the gel and this is challenging because the link between local restructuring and overall response of the network is still missing. Here, we use a space resolved analysis of dynamical processes and numerical simulations of a model gel to gain insight into this link. We show that consequences of local bond breaking propagate along the gel network over distances larger than the average mesh size. This provides the missing microscopic explanation for why nonlocal constitutive relations are necessary to rationalize the nontrivial mechanical response of colloidal gels., 8 pages, 12 figures

Potentiometric titration in 95% methanol (I = 0.1 mol dm−3, Et4NClO4) has been employed to investigate the effect of N-methylation and N-benzylation of 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane 1 on the binding of all three rings to cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II), silver(I) and lead(II). The results show that enhanced selectivity for silver(I) is exhibited by the di-N-benzylated derivative 3 while the analogous dimethylated derivative 2 discriminates for both silver(I) and lead(II). The crystal structures of [Ag(1)]PF6, [Ag(2)]PF6, [Ag(3)]PF6 and [Pb(1)(NO3)2] have been determined. In the silver complexes the NH hydrogens of 1 and the N-methyl and N-benzyl substituents of the dialkylated derivatives 2 and 3 were found to lie on the same side of the mean donor planes of the co-ordinated macrocycles (‘cis’ arrangements). Density functional theory has been employed to model the silver complexes in both their energy-minimised ‘cis’ and ‘trans’ configurations. In accordance with the X-ray evidence, the calculations predict that the ‘cis’ arrangement is the more stable in each case. The crystal structure of the lead complex of 1 shows a ‘trans’ arrangement of its NH groups.

NMR offers the possibility of accurate secondary structure for proteins that would be too large for structure determination. In the absence of an X-ray crystal structure, this information should be useful as an adjunct to protein fold recognition methods based on low resolution force fields. The value of this information has been tested by adding varying amounts of artificial secondary structure data and threading a sequence through a library of candidate folds. Using a literature test set, the threading method alone has only a one-third chance of producing a correct answer among the top ten guesses. With realistic secondary structure information, one can expect a 60-80% chance of finding a homologous structure. The method has then been applied to examples with published estimates of secondary structure. This implementation is completely independent of sequence homology, and sequences are optimally aligned to candidate structures with gaps and insertions allowed. Unlike work using predicted secondary structure, we test the effect of differing amounts of relatively reliable data.

We present the first nearly atomistic molecular dynamics study of nanorod-nanorod association in explicit solvent, showing that inter-rod forces can be dominated by microscopic factors absent in common continuum descriptions. Specifically, we find that alkane ligands on faceted CdS nanorods in n-hexane undergo a temperature-dependent order-disorder transition akin to that of self-assembled monolayers on macroscopic substrates. This collective ligand alignment organizes nearby solvent molecules, strongly influencing the statistics of rod-rod separation. The strong temperature-dependence of this mechanism could be exploited in the laboratory to manipulate and optimize the assembly of ordered structures., Comment: 25 pages, 6 figures

Relaxation of the additivity condition on the interaction length between unlike species in a binary mixture of soft disks opens up a rich variety of structures in both crystal and amorphous states with an associated diverse range of relaxation dynamics. We report on MD simulation studies of binary soft disks with negative deviations from additivity that include evidence of accumulation of crystal-like structures in metastable liquids prior to crystallization and the occurrence of a liquid to random-tiling transition., 24 pages, 21 figures. Corrected error in pdf conversion

The self-assembly of nanocrystals enables new classes of materials whose properties are controlled by the periodicities of the assembly, as well as by the size, shape and composition of the nanocrystals. While self-assembly of spherical nanoparticles has advanced significantly in the last decade, assembly of rod-shaped nanocrystals has seen limited progress due to the requirement of orientational order. Here, the parameters critically relevant to self-assembly are systematically quantified using a combination of diffraction and theoretical modeling; these highlight the importance of kinetics on orientational order. Through drying-mediated self-assembly we achieve unprecedented control over orientational order (up to 96% vertically oriented rods on 1cm2 areas) on a wide range of substrates (ITO, PEDOT:PSS, Si3N4). This opens new avenues for nanocrystal-based devices competitive with thin film devices, as problems of granularity can be tackled through crystallographic orientational control over macroscopic areas., Comment: 14 pages, 5 figures

We identify the pattern of microscopic dynamical relaxation for a two-dimensional glass-forming liquid. On short time scales, bursts of irreversible particle motion, called cage jumps, aggregate into clusters. On larger time scales, clusters aggregate both spatially and temporally into avalanches. This propagation of mobility takes place along the soft regions of the systems, which have been identified by computing isoconfigurational Debye-Waller maps. Our results characterize the way in which dynamical heterogeneity evolves in moderately supercooled liquids and reveal that it is astonishingly similar to the one found for dense glassy granular media.

The spatial distribution of structural relaxation in a supercooled liquid is studied using molecular dynamics simulations of a 2D binary mixture. It is shown that the spatial heterogeneity of the relaxation along with the time scale of the relaxation is determined, not by the frequency with which particles move a distance pi/2kBragg, but by the frequency with which particles can achieve persistent displacements. We show that these persistent displacements are achieved through the coupled action of local reorganizations and unrecoverable thermal strains., 23 pages, 9 figures, expanded discussion, additional references

There is widespread agreement that biodiversity loss must be reduced, yet to alleviate threats to plant and animal species, the forces driving these losses need to be better understood. We searched for explanatory variables for threatened-species data at the country level through land-use information instead of previously used socioeconomic and demographic variables. To explain the number of threatened species in one country, we used information on land-use patterns in all neighboring countries and on the extent of the country's sea border. We carried out multiple regressions of the numbers of threatened species as a function of land-use patterns, and we tested various specifications of this function, including spatial autocorrelation. Most cross-border land-use patterns had a significant influence on the number of threatened species, and land-use patterns explained the number of threatened species better than less proximate socioeconomic variables. More specifically, our overall results showed a highly adverse influence of plantations and permanent cropland, a weaker negative influence of permanent pasture, and, for the most part, a beneficial influence of nonarable lands and natural forest. Surprisingly, built-up land also showed a conserving influence on threatened species. The adverse influences extended to distances between about 250 km (plants) and 2000 km (birds and mammals) away from where the species threat was recorded, depending on the species. Our results highlight that legislation affecting biodiversity should look beyond national boundaries.

We present the dynamic propensity distribution as an explicit measure of the degree to which the dynamics in a liquid over the time scale of structural relaxation is determined by the initial configuration. We then examine, for a binary mixture of soft discs in two dimensions, the correlation between the spatial distribution of propensity and that of two localmeasures of configuration structure: the local composition and local free volume. While the small particles dominate the high propensity population,we find no strong correlation between either the local composition or the local free volume and the propensity. It is argued that this is a generic failure of purely local structural measures to capture the inherently non-local character of collective behaviour., Published, see below or http://www.iop.org/EJ/abstract/0953-8984/17/49/001/ Editing comments have been removed

Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are strongly correlated with the irreversible structural reorganization of the particles within that configuration. Establishing this correlation constitutes the identification of the aspect of a configuration that determines the heterogeneity of the subsequent motion. We demonstrate that the spatial distribution of the summation over the soft local modes can persist in spite of particle reorganization that produces significant changes in individual modes. Along with spatial localization, the persistent influence of soft modes in particle relaxation results in anisotropy in the displacements of mobile particles over the timescale referred to as beta relaxation., Comment: 47 pages, 11 figures, 1 table

The transition of a fluid to a rigid glass upon cooling is a common route of transformation from liquid to solid that embodies the most poorly understood features of both phases1,2,3. From the liquid perspective, the puzzle is to understand stress relaxation in the disordered state. From the perspective of solids, the challenge is to extend our description of structure and its mechanical consequences to materials without long range order. Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are causally correlated to the irreversible structural reorganization of the particles within that configuration. We also demonstrate that the spatial distribution of these soft local modes can persist in spite of significant particle reorganization. The consequence of these two results is that it is now feasible to construct a theory of relaxation length scales in glass-forming liquids without recourse to dynamics and to explicitly relate molecular properties to their collective relaxation., Comment: Published online: 20 July 2008 | doi:10.1038/nphys1025 Available from http://www.nature.com/nphys/journal/v4/n9/abs/nphys1025.html

We report that the local Debye-Waller factor in a simulated 2D glass-forming mixture exhibits significant spatial heterogeneities and that these short-time fluctuations provide an excellent predictor of the spatial distribution of the long-time dynamic propensities [Phys. Rev. Lett. 93, 135701 (2004)]. In contrast, the potential energy per particle of the inherent structure does not correlate well with the spatially distributed dynamics.

We examine the relation between the free volume per particle and the variance of the particle position, equivalent to a local Debye-Waller (DW) factor for a 2D glass-forming alloy using molecular dynamics simulations. We find that the latter quantity exhibits significant spatial heterogeneity despite involving trajectories two orders of magnitude shorter than those typically used to measure such heterogeneities. We find that the free volume exhibits no significant spatial correlation with the local DW factor. We conclude that the spatial variation in local free volume is not the cause of the short time dynamic heterogeneity., Comment: 18 pages, 5 figures

The particle dynamics in a liquid exhibits a transient spatial distribution of dynamic heterogeneities. The relationship between this kinetic structure and the underlying particle configuration remains an outstanding problem. In this Letter, we present a general simulation technique for identifying the features of the dynamic heterogeneity which arise due to a specific configuration, as distinct from the random spatial variation due to the intermittent particle dynamics.

Near Tg the dynamics in glass‐formers vary by orders of magnitude from one region to another. The existence of such spatially heterogenous dynamics is now well established, both through simulation and experiment. However, it remains unclear to what extent this dynamic heterogeneity is a reflection of some underlying structural properties of the glass‐former. Here we provide a general theoretical tool for establishing the connection between a particle configuration and the spatial heterogeneity of the dynamics that originates from that configuration, and apply this to a model soft‐disk glass. We find that the dynamic heterogeneity in a trajectory is not completely determined by the initial configuration and establish a rigorous causal connection between a given configuration and the propensity of particles to move. Finally, we discuss a number of generalisations of this tool.

This paper describes the mechanism of defect-mediated relaxation in a dodecagonal square-triangle random tiling phase exhibited by a simulated binary mixture of soft discs in 2D. We examine the internal transitions within the elementary mobile defect (christened the 'zipper') that allow it to move, as well as the mechanisms by which the zipper is created and annihilated. The structural relaxation of the random tiling phase is quantified and we show that this relaxation is well described by a model based on the distribution of waiting times for each atom to be visited by the diffusing zipper. This system, representing one of the few instances where a well defined mobile defect is capable of structural relaxation, can provide a valuable test case for general theories of relaxation in complex and disordered materials., Comment: 30 pages, 16 figures, to appear in J. Chem. Phys

We find that the hierarchical organization of the potential energy landscape in a model supercooled liquid can be related to a change in the spatial distribution of soft normal modes. For groups of nearby minima, between which fast relaxation processes typically occur, the localization of the soft modes is very similar. The spatial distribution of soft regions changes, instead, for minima between which transitions relevant to structural relaxation occur. This may be the reason why the soft modes are able to predict spatial heterogeneities in the dynamics. Nevertheless, the very softest modes are only weakly correlated with dynamical heterogeneities, and instead show higher statistical overlap with regions in the local minima that would undergo non-affine rearrangements if subjected to a shear deformation. This feature of the supercooled liquid is reminiscent of the behavior of non-affine deformations in amorphous solids, where the very softest modes identify the {\it loci} of plastic instabilities., 6 pages, 5 figures, to appear in Phys. Rev. Lett

The use of the isoconfigurational ensemble to explore structure-dynamic correlations in supercooled liquids is examined. The statistical error of the dynamic propensity and its spatial distribution are determined. The authors present the spatial distribution of the particle non-Gaussian parameter as a measure of the intermittency with which particles exhibit their propensity for motion. The ensemble average of the direction of particle motion is introduced to establish the anisotropy of the dynamic propensity., Comment: Published - see below or http://link.aip.org/link/?JCPSA6/126/154503/1

The glass transition is the dramatic dynamical slowdown one observes when cooling down a liquid or densifying a set of particles into an amorphous state. In this thesis we explore two distinct situations related to this phenomenology, mostly in the case of granular materials. In a first part we study the strongly non-linear response of an assembly of frictional grains under vibration when they are very densely packed. To this aim we pull a probe particle - an "intruder" - through the media and follow the dynamics of the particles around. We evidence the presence of two transitions: the first one is analogous to a fluidization transition, as shown by the evolution from a continuous to a highly intermittent motion and by the appearance of a yield stress in the response~; the second one is identified as the jamming transition that occurs in several systems. We show that the reorganizations induced by the intruder display critical signatures at the transition, as previously shown by the study of the same system without drag, leading to interesting connections with recent simulations in athermal and frictionless particles systems. In a second part, we study the relations between the very short term dynamics - essentially made of vibrations of the particles around their equilibrium positions - and the long time scale dynamics where dynamical heterogeneities are responsible for the slowdown of the structural relaxations on approach to the glass transition. The dynamics of the metastable states is analyzed in two experimental granular systems (grains under cyclic shear or in a fluidized bed) as well as in simulations of repulsive particles. We show the dominant role of quasi-instantaneous cooperative displacements to build the large intermittent decorrelation patterns that one observes on longer time scales through a facilitation mechanism. Facilitation becomes less and less efficient when the packing fraction increases, leading to increasingly separated and concentrated dynamical events in space and time. The vibrational dynamics leading to the cooperative motion are also investigated, and we show that the latter are essentially driven by the structure, coarse grained at a mesoscopic scale., La transition vitreuse se caractérise par un ralentissement dramatique de la dynamique, soit lorsqu'on refroidit un liquide soit lorsque l'on compacifie une assemblée de particules dans un état amorphe. Dans cette thèse nous explorons deux situations distinctes liées à cette phénoménologie, principalement dans le cas de matériaux granulaires. Dans une première partie nous étudions la réponse fortement non-linéaire d'un système de particules frottantes vibrées à très haute densité soumis à une contrainte locale. Pour cela nous tirons une particule "intrus" à force constante dans le milieu en suivant le mouvement des particules alentour. Nous mettons en évidence deux transitions distinctes : la première est l'analogue d'une transition de fluidification et se manifeste par le passage d'un mouvement continu de l'intrus à un mouvement fortement intermittent ainsi que par l'apparition d'une contrainte seuil dans la réponse ; la deuxième est identifiée à la transition de blocage qui intervient de manière générique dans de nombreux systèmes. Nous montrons que les réorganisations induites par l'intrus ont un comportement critique à la transition, venant conforter le caractère critique de la transition de blocage mis en évidence en l'absence d'intrus, et établissant d'intéressantes connections avec des simulations récentes de systèmes athermiques de particules non-frottantes. Dans une deuxième partie nous étudions les relations entre la dynamique à très court terme - essentiellement vibratoire - et à plus longue échelle de temps, où de fortes hétérogénéités dynamiques sont responsables du ralentissement des relaxations structurales à l'approche de la transition vitreuse. La dynamique des états métastables est analysée dans plusieurs systèmes granulaires (cellule de cisaillement cyclique et lit fluidisé) ainsi que dans une simulation d'un liquide de Lennard-Jones répulsif ; nous mettons en évidence le rôle de mouvements coopératifs quasi-instantanés qui construisent à long terme par un mécanisme de facilitation de larges motifs de décorrélation intermittents. Ce mécanisme de facilitation diminue lorsque le matériau se densifie, menant à des évènements dynamiques de plus en plus séparés et concentrés dans l'espace et le temps. La dynamique vibratoire aboutissant aux mouvements coopératifs est elle aussi étudiée, et nous montrons que ces derniers sont déterminés pour une large part par la structure du matériau à un niveau mésoscopique.