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We characterize the self-assembly and phase behavior of Janus rods over a broad range of temperatures and volume fractions, using Langevin dynamics simulations and free energy calculations. The Janus rods consist of a line of fused overlapping spheres that interact via a soft-core repulsive potential, with the addition of an attractive pseudo-square-well tail to a fraction of the spheres (the coverage) ranging from 5\% to 100\% of sites. Competition between the stability of liquid crystal phases originating from shape anisotropy and assembly driven by directional interactions gives rise to a rich polymorphism that depends on the coverage. At low density near the Boyle temperature, we observe the formation of spherical and tubular micelles at low coverage, while at higher coverage randomly oriented monolayers form as the attractive parts of the rods overlap. At higher density, bilayer structures appear and merge to form smectic and crystalline lamellar phases. All of these structures gradually become unstable as the temperature is increased until eventually regular nematic and smectic phases appear, consistent with the hard rod limit. Our results indicate that the intermediate regime where shape-entropic effects compete with anisotropic attractions provided by site specificity is rich in structural possibilities, and should help guide the design of rod-like colloids for specific applications., Comment: 13 pages, 13 figures, SI not included

In this work, we compare existing non-polarizable force fields developed to study the solid or solution phases of hybrid organic-inorganic halide perovskites with the AMOEBA polarizable force field. The aim is to test whether more computationally expensive polarizable force fields like AMOEBA offer better transferability between solution and solid phases, with the ultimate goal being the study of crystal nucleation, growth and other interfacial phenomena involving these ionic compounds. In the context of hybrid perovskites, AMOEBA force field parameters already exist for several elements in solution and we decided to leave them unchanged and to only parameterize the missing ones (Pb\textsuperscript{2+} and CH\textsubscript{3}NH\textsubscript{3}\textsuperscript{+} ions) in order to maximise transferability and avoid over-fitting to the specific examples studied here. Overall, we find that AMOEBA yields accurate hydration free energies (within 5\%) for typical ionic species while showing the correct ordering of stability for the different crystal polymorphs of CsPbI\textsubscript{3} and CH\textsubscript{3}NH\textsubscript{3}PbI\textsubscript{3}. While the existing parameters do not accurately reproduce all transition temperatures and lattice parameters, AMOEBA offers better transferability between solution and solid states than existing non-polarizable force fields.

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 \SI{4}{\nano\meter} gold cores with hexadecanethiol shells and \SI{6}{\nano\meter} 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 hexane, despite having very similar solvation parameters to hexadecane., Comment: SI + main manuscript

The phase diagram of hard helices differs from its hard rods counterpart by the presence of chiral "screw" phases stemming from the characteristic helical shape, in addition to the conventional liquid crystal phases also found for rod-like particles. Using extensive Monte Carlo and Molecular Dynamics simulations, we study the effect of the addition of a short-range attractive tail representing solvent-induced interactions to a fraction of the sites forming the hard helices, ranging from a single-site attraction to fully attractive helices for a specific helical shape. Different temperature regimes exist for different fractions of the attractive sites, as assessed in terms of the relative Boyle temperatures, that are found to be rather insensitive to the specific shape of the helical particle. The temperature range probed by the present study is well above the corresponding Boyle temperatures, with the phase behaviour still mainly entropically dominated and with the existence and location of the various liquid crystal phases only marginally affected. The pressure in the equation of state is found to decrease upon increasing the fraction of attractive beads and/or on lowering the temperature at fixed volume fraction, as expected on physical grounds. All screw phases are found to be stable within the considered range of temperatures with the smectic phase becoming more stable on lowering the temperature. By contrast, the location of the transition lines do not display a simple dependence on the fraction of attractive beads in the considered range of temperatures., Comment: 17 pages, 13 figures, JCP in press, SI not included

The ability of thin materials to shape-shift is a common occurrence that leads to dynamic pattern formation and function in natural and man-made structures. However, harnessing this concept to design inorganic structures at the nanoscale rationally has remained far from reach due to a lack of fundamental understanding of the essential physical components. Here, we show that the interaction between organic ligands and the nanocrystal surface is responsible for the full range of chiral shapes seen in colloidal nanoplatelets. The adsorption of ligands results in incompatible curvatures on the top and bottom surfaces of NPL, causing them to deform into helico\"ids, helical ribbons, or tubes depending on the lateral dimensions and crystallographic orientation of the NPL. We demonstrate that nanoplatelets belong to the broad class of geometrically frustrated assemblies and exhibit one of their hallmark features: a transition between helico\"ids and helical ribbons at a critical width. The effective curvature $\bar{\kappa}$ is the single aggregate parameter that encodes the details of the ligand/surface interaction, determining the nanoplatelets' geometry for a given width and crystallographic orientation. The conceptual framework described here will aid the rational design of dynamic, chiral nanostructures with high fundamental and practical relevance., Comment: 16 pages, 8 figures

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., Comment: 14 pages, 12 figures

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

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 to 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- 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., Comment: manuscript + SI in one file

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., Comment: 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

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., Comment: 8 pages, 12 figures

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 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

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., Comment: 6 pages, 5 figures, to appear in Phys. Rev. Lett

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., Comment: 24 pages, 21 figures. Corrected error in pdf conversion

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 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., Comment: 23 pages, 9 figures, expanded discussion, additional references

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., Comment: Published, see below or http://www.iop.org/EJ/abstract/0953-8984/17/49/001/ Editing comments have been removed

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 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