Classification of complex local environments in systems of particle shapes through shape symmetry-encoded data augmentation

Detecting and analyzing the local environment is crucial for investigating the dynamical processes of crystal nucleation and shape colloidal particle self-assembly. Recent developments in machine learning provide a promising avenue for better order parameters in complex systems that are challenging to study using traditional approaches. However, the application of machine learning to self-assembly on systems of particle shapes is still underexplored. To address this gap, we propose a simple, physics-agnostic, yet powerful approach that involves training a multilayer perceptron (MLP) as a local environment classifier for systems of particle shapes, using input features such as particle distances and orientations. Our MLP classifier is trained in a supervised manner with a shape symmetry-encoded data augmentation technique without the need for any conventional roto-translations invariant symmetry functions. We evaluate the performance of our classifiers on four different scenarios involving self-assembly of cubic structures, two-dimensional and three-dimensional patchy particle shape systems, hexagonal bipyramids with varying aspect ratios, and truncated shapes with different degrees of truncation. The proposed training process and data augmentation technique are both straightforward and flexible, enabling easy application of the classifier to other processes involving particle orientations. Our work thus presents a valuable tool for investigating self-assembly processes on systems of particle shapes, with potential applications in structure identification of any particle-based or molecular system where orientations can be defined.

Colloidal quasicrystals engineered with DNA

In principle, designing and synthesizing almost any class of colloidal crystal is possible. Nonetheless, the deliberate and rational formation of colloidal quasicrystals has been difficult to achieve. Here we describe the assembly of colloidal quasicrystals by exploiting the geometry of nanoscale decahedra and the programmable bonding characteristics of DNA immobilized on their facets. This process is enthalpy-driven, works over a range of particle sizes and DNA lengths, and is made possible by the energetic preference of the system to maximize DNA duplex formation and favour facet alignment, generating local five- and six-coordinated motifs. This class of axial structures is defined by a square-triangle tiling with rhombus defects and successive on-average quasiperiodic layers exhibiting stacking disorder which provides the entropy necessary for thermodynamic stability. Taken together, these results establish an engineering milestone in the deliberate design of programmable matter.

Rationalizing Euclidean Assemblies of Hard Polyhedra from Tessellations in Curved Space

Entropic self-assembly is governed by the shape of the constituent particles, yet a priori prediction of crystal structures from particle shape alone is nontrivial for anything but the simplest of space-filling shapes. At the same time, most polyhedra are not space filling due to geometric constraints, but these constraints can be relaxed or even eliminated by sufficiently curving space. We show using Monte Carlo simulations that the majority of hard Platonic solids self-assemble entropically into space-filling crystals when constrained to the surface volume of a 3-sphere. As we gradually decrease curvature to "flatten" space and compare the local morphologies of crystals assembling in curved and flat space, we show that the Euclidean assemblies can be categorized as either remnants of tessellations in curved space (tetrahedra and dodecahedra) or nontessellation-based assemblies caused by large-scale geometric frustration (octahedra and icosahedra).

Complex motion of steerable vesicular robots filled with active colloidal rods

While the collective motion of active particles has been studied extensively, effective strategies to navigate particle swarms without external guidance remain elusive. We introduce a method to control the trajectories of two-dimensional swarms of active rod-like particles by confining the particles to rigid bounding membranes (vesicles) with non-uniform curvature. We show that the propelling agents spontaneously form clusters at the membrane wall and collectively propel the vesicle, turning it into an active superstructure. To further guide the motion of the superstructure, we add discontinuous features to the rigid membrane boundary in the form of a kinked tip, which acts as a steering component to direct the motion of the vesicle. We report that the system's geometrical and material properties, such as the aspect ratio and Péclet number of the active rods as well as the kink angle and flexibility of the membrane, determine the stacking of active particles close to the kinked confinement and induce a diverse set of dynamical behaviors of the superstructure, including linear and circular motion both in the direction of, and opposite to, the kink. From a systematic study of these various behaviors, we design vesicles with switchable and reversible locomotions by tuning the confinement parameters. The observed phenomena suggest a promising mechanism for particle transportation and could be used as a basic element to navigate active matter through complex and tortuous environments.

Tunable assembly of host-guest colloidal crystals

Entropy compartmentalization provides new self-assembly routes to colloidal host-guest (HG) structures. Leveraging host particle shape to drive the assembly of HG structures has only recently been proposed and demonstrated. However, the extent to which the guest particles can dictate the structure of the porous network of host particles has not been explored. In this work, by modifying only the guest shape, we show athermal, binary mixtures of star-shaped host particles and convex polygon-shaped guest particles assemble as many as five distinct crystal structures, including rotator and discrete rotator guest crystals, two homoporous host crystals, and one heteroporous host crystal. Edge-to-edge alignment of neighboring stars results in the formation of three distinct pore motifs, whose preferential formation is controlled by the size and shape of the guest particles. Finally, we confirm, via free volume calculations, that assembly is driven by entropy compartmentalization, where the hosts and guests contribute differently to the free energy of the system; free volume calculations also explain differences in assembly based on guest shape. These results provide guest design rules for assembling colloidal HG structures, especially on surfaces and interfaces.

Entropy compartmentalization stabilizes open host-guest colloidal clathrates

Clathrates are open crystals in which molecules are arranged in a hierarchy of polyhedral cages that encapsulate guest molecules and ions. As well as holding fundamental interest, molecular clathrates serve practical purposes, such as for gas storage, and their colloidal counterparts also appear promising for host-guest applications. Here using Monte Carlo simulations, we report the entropy-driven self-assembly of hard truncated triangular bipyramids into seven different host-guest colloidal clathrate crystals with unit cells ranging from 84 to 364 particles. The structures consist of cages that are either empty or occupied by guest particles, which can be different from or identical to the host particles. The simulations point to crystallization occurring through the compartmentalization of entropy between low- and high-entropy subsystems for the host and the guest particles, respectively. We use entropic bonding theory to design host-guest colloidal clathrates with explicit interparticle attraction, providing a route to realize such systems in the laboratory.

Inverse design of triblock Janus spheres for self-assembly of complex structures in the crystallization slot via digital alchemy

The digital alchemy framework is an extended ensemble simulation technique that incorporates particle attributes as thermodynamic variables, enabling the inverse design of colloidal particles for desired behavior. Here, we extend the digital alchemy framework for the inverse design of patchy spheres that self-assemble into target crystal structures. To constrain the potentials to non-trivial solutions, we conduct digital alchemy simulations with constant second virial coefficient. We optimize the size, range, and strength of patchy interactions in model triblock Janus spheres to self-assemble the 2D kagome and snub square lattices and the 3D pyrochlore lattice, and demonstrate self-assembly of all three target structures with the designed models. The particles designed for the kagome and snub square lattices assemble into high quality clusters of their target structures, while competition from similar polymorphs lower the yield of the pyrochlore assemblies. We find that the alchemically designed potentials do not always match physical intuition, illustrating the ability of the method to find nontrivial solutions to the optimization problem. We identify a window of second virial coefficients that result in self-assembly of the target structures, analogous to the crystallization slot in protein crystallization.

Self-Assembly of Atomically Aligned Nanoparticle Superlattices from Pt-Fe3O4 Heterodimer Nanoparticles

Multicomponent nanoparticle superlattices (SLs) promise the integration of nanoparticles (NPs) with remarkable electronic, magnetic, and optical properties into a single structure. Here, we demonstrate that heterodimers consisting of two conjoined NPs can self-assemble into novel multicomponent SLs with a high degree of alignment between the atomic lattices of individual NPs, which has been theorized to lead to a wide variety of remarkable properties. Specifically, by using simulations and experiments, we show that heterodimers composed of larger Fe₃O₄ domains decorated with a Pt domain at one vertex can self-assemble into an SL with long-range atomic alignment between the Fe₃O₄ domains of different NPs across the SL. The SLs show an unanticipated decreased coercivity relative to nonassembled NPs. In situ scattering of the self-assembly reveals a two-stage mechanism of self-assembly: translational ordering between NPs develops before atomic alignment. Our experiments and simulation indicate that atomic alignment requires selective epitaxial growth of the smaller domain during heterodimer synthesis and specific size ratios of the heterodimer domains as opposed to specific chemical composition. This composition independence makes the self-assembly principles elucidated here applicable to the future preparation of multicomponent materials with fine structural control.

Engineering the Thermodynamic Stability and Metastability of Mesophases of Colloidal Bipyramids through Shape Entropy

We report several types of entropy-driven phase transition behaviors in hard bipyramid systems using Monte Carlo simulations. Bipyramidal nanoparticle shapes are synthesizable from gold and silver, with sizes ranging from tens to hundreds of nanometers. We report numerous colloidal crystalline phases with varying symmetries and complexities as the bipyramid aspect ratio and base polygon are varied. Some bipyramids are mesogenic and undergo either monotropic or enantiotropic phase transitions. We show that such mesophase behavior can be modulated by tuning the bipyramid aspect ratio. In addition, we report stepwise kinetic crystallization and melting pathways that occur via an intermediate mesophase as the system gains or loses order in successive stages. Our results demonstrate that complex phase transition behavior involving mesophases can be driven by entropy alone. Importantly, our results can guide the synthesis of bipyramid shapes able to assemble target structures and can be used to engineer the kinetic pathways to and from those structures to involve or avoid mesophases.

Arrays of Colloidal Single Crystals Engineered with DNA in Lithographically Defined Microwells

Lithographically defined microwell templates are used to study DNA-guided colloidal crystal assembly parameters, including superlattice position, habit orientation, and size, in an effort to increase our understanding of the crystallization process. In addition to enabling the synthesis of arrays of individual superlattices in arbitrary predefined patterns, the technique allows one to study the growth pathways of the crystals via ex situ scanning electron microscopy. Importantly, a Volmer-Weber (VM) (island formation)-like growth mode is identified, which has been reproduced via simulations. Notably, both experiment and simulation reveal that the crystallites merge and reorient within the microwells that defined the crystal growth to form single-crystalline structures, an observation not common for VM pathways. The control afforded by this platform will facilitate efforts in constructing metamaterials from colloidal crystals as well as their integration into optical devices and applications.

Entropically engineered formation of fivefold and icosahedral twinned clusters of colloidal shapes

Fivefold and icosahedral symmetries induced by multiply twinned crystal structures have been studied extensively for their role in influencing the shape of synthetic nanoparticles, and solution chemistry or geometric confinement are widely considered to be essential. Here we report the purely entropy-driven formation of fivefold and icosahedral twinned clusters of particles in molecular simulation without geometric confinement or chemistry. Hard truncated tetrahedra self-assemble into cubic or hexagonal diamond colloidal crystals depending on the amount of edge and vertex truncation. By engineering particle shape to achieve a negligible entropy difference between the two diamond phases, we show that the formation of the multiply twinned clusters is easily induced. The twinned clusters are entropically stabilized within a dense fluid by a strong fluid-crystal interfacial tension arising from strong entropic bonding. Our findings provide a strategy for engineering twinning behavior in colloidal systems with and without explicit bonding elements between particles.

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

In many biological systems, the curvature of the surfaces cells live on influences their collective properties. Curvature should likewise influence the behavior of active colloidal particles. We show using molecular simulation of self-propelled active particles on surfaces of Gaussian curvature (both positive and negative) how curvature sign and magnitude can alter the system's collective behavior. Curvature acts as a geometrical lens and shifts the critical density of motility-induced phase separation (MIPS) to lower values for positive curvature and higher values for negative curvature, which we explain theoretically by the nature of parallel lines in spherical and hyperbolic space. Curvature also fluidizes dense MIPS clusters due to the emergence of defect patterns disrupting the crystalline order inside the clusters. Using our findings, we engineer three confining surfaces that strategically combine regions of different curvature to produce a host of novel dynamical behaviors, including cyclic MIPS on spherocylinders, directionally biased cyclic MIPS on spherocones, and position dependent cluster fluctuations on metaballs.

Symmetry-breaking in patch formation on triangular gold nanoparticles by asymmetric polymer grafting

Synthesizing patchy particles with predictive control over patch size, shape, placement and number has been highly sought-after for nanoparticle assembly research, but is fraught with challenges. Here we show that polymers can be designed to selectively adsorb onto nanoparticle surfaces already partially coated by other chains to drive the formation of patchy nanoparticles with broken symmetry. In our model system of triangular gold nanoparticles and polystyrene-b-polyacrylic acid patch, single- and double-patch nanoparticles are produced at high yield. These asymmetric single-patch nanoparticles are shown to assemble into self-limited patch‒patch connected bowties exhibiting intriguing plasmonic properties. To unveil the mechanism of symmetry-breaking patch formation, we develop a theory that accurately predicts our experimental observations at all scales—from patch patterning on nanoparticles, to the size/shape of the patches, to the particle assemblies driven by patch‒patch interactions. Both the experimental strategy and theoretical prediction extend to nanoparticles of other shapes such as octahedra and bipyramids. Our work provides an approach to leverage polymer interactions with nanoscale curved surfaces for asymmetric grafting in nanomaterials engineering.

Shape memory in self-adapting colloidal crystals

Reconfigurable, mechanically responsive crystalline materials are central components in many sensing, soft robotic, and energy conversion and storage devices^1-4. Crystalline materials can readily deform under various stimuli and the extent of recoverable deformation is highly dependent upon bond type^1,2,5-10. Indeed, for structures held together via simple electrostatic interactions, minimal deformations are tolerated. By contrast, structures held together by molecular bonds can, in principle, sustain much larger deformations and more easily recover their original configurations. Here we study the deformation properties of well-faceted colloidal crystals engineered with DNA. These crystals are large in size (greater than 100 µm) and have a body-centred cubic (bcc) structure with a high viscoelastic volume fraction (of more than 97%). Therefore, they can be compressed into irregular shapes with wrinkles and creases, and, notably, these deformed crystals, upon rehydration, assume their initial well-formed crystalline morphology and internal nanoscale order within seconds. For most crystals, such compression and deformation would lead to permanent, irreversible damage. The substantial structural changes to the colloidal crystals are accompanied by notable and reversible optical property changes. For example, whereas the original and structurally recovered crystals exhibit near-perfect (over 98%) broadband absorption in the ultraviolet-visible region, the deformed crystals exhibit significantly increased reflection (up to 50% of incident light at certain wavelengths), mainly because of increases in their refractive index and inhomogeneity.

Tuning Stoichiometry to Promote Formation of Binary Colloidal Superlattices

The self-assembly of binary nanoparticle superlattices from colloidal mixtures is a promising method for the fabrication of complex colloidal cocrystal structures. However, binary mixtures often form amorphous or metastable phases instead of the thermodynamically stable phase. Here we show that in binary mixtures of differently sized spherical particles, an excess of the smaller component can promote-and, in some cases, may be necessary for-the self-assembly of a binary cocrystal. Using computer simulations, we identify two mechanisms responsible for this phenomenon. First, excess small particles act like plasticizers and enable systems to reach a greater supersaturation before kinetic arrest occurs. Second, they can disfavor competing structures that may interfere with the growth of the target structure. We find the phase behavior of simulated mixtures of nearly hard spheres closely matches published experimental results. We demonstrate the generality of our findings for mixtures of particles of arbitrary shape by presenting a binary mixture of hard shapes that only self-assembles with an excess of the smaller component.

The emergence of valency in colloidal crystals through electron equivalents

Colloidal crystal engineering of complex, low-symmetry architectures is challenging when isotropic building blocks are assembled. Here we describe an approach to generating such structures based upon programmable atom equivalents (nanoparticles functionalized with many DNA strands) and mobile electron equivalents (small particles functionalized with a low number of DNA strands complementary to the programmable atom equivalents). Under appropriate conditions, the spatial distribution of the electron equivalents breaks the symmetry of isotropic programmable atom equivalents, akin to the anisotropic distribution of valence electrons or coordination sites around a metal atom, leading to a set of well-defined coordination geometries and access to three new low-symmetry crystalline phases. All three phases represent the first examples of colloidal crystals, with two of them having elemental analogues (body-centred tetragonal and high-pressure gallium), while the third (triple double-gyroid structure) has no known natural equivalent. This approach enables the creation of complex, low-symmetry colloidal crystals that might find use in various technologies.

Evaporation-Driven Coassembly of Hierarchical, Multicomponent Networks

Self-assembly is an increasingly popular approach to systematically control the formation of complex, multicomponent materials with structural features orders of magnitude larger than the constituent colloidal nanocrystals. Common approaches often involve templating via prefabricated patterns to control particle organization- or programming-specific interactions between individual building blocks. While effective, such fabrication methods suffer from major bottlenecks due to the complexity required in mask creation for patterning or surface modification techniques needed to program directed interactions between particles. Here, we propose an alternative strategy that aims to bypass such limitations. First, we design a ligand structure that can bridge two distinct nanocrystal types. Then, by leveraging the solvent's evaporative dynamics to drive particle organization, we direct a cross-linked, multicomponent system of nanocrystals to organize hierarchically into ordered, open-network structures with domain sizes orders of magnitude larger than the constituent building blocks. We employ simulation and theory to rationalize the driving forces governing this evaporation-driven process, showing excellent agreement across theory, simulations, and experiments. These results suggest that evaporation-driven organization can be a powerful approach to designing and fabricating hierarchical, multifunctional materials.

Structural Color Spectral Response of Dense Structures of Discoidal Particles Generated by Evaporative Assembly

Structural color─optical response due to light diffraction or scattering from submicrometer-scale structures─is a promising means for sustainable coloration. To expand the functionality of structural color, we introduce discoidal shape anisotropy into colloidal particles and characterize how structural color reflection can be engineered. Uniaxial compression of spheres is used to prepare discoids with varying shape anisotropy and particle size. Discoids are assembled into thin films by evaporation. We find that structural color of assembled films displays components due to diffuse backscattering and multilayer reflection. As discoids become more anisotropic, the assembled structure is more disordered. The multilayer reflection is suppressed─peak height becomes smaller and peak width broader; thus, the color is predominantly from diffuse backscattering. Finally, the discoid structural color can be tuned by varying particle size and has low dependence on viewing angle. We corroborate our results by comparing experimental microstructures and measured reflection spectra with Monte Carlo simulations and calculated spectra by finite-difference time-domain simulation. Our findings demonstrate that the two tunable geometries of discoids─size and aspect ratio─generate different effects on spectral response and therefore can function as independent design parameters that expand possibilities for producing noniridescent structural color.

Particle anisotropy tunes emergent behavior in active colloidal systems

Studies of active particle systems have demonstrated that particle anisotropy can impact the collective behavior of a system, motivating a systematic study. Here, we report a systematic computational investigation of the role of anisotropy in shape and active force director on the collective behavior of a two-dimensional active colloidal system. We find that shape and force anisotropy can combine to produce critical densities both lower and higher than those of disks. We demonstrate that changing particle anisotropy tunes what we define as a "collision efficiency" of inter-particle collisions in leading to motility-induced phase separation (MIPS) of the system. We use this efficiency to determine the relative critical density across systems. Additionally, we observe that local structure in phase-separated clusters is the same as the particle's equilibrium densest packing, suggesting a general connection between equilibrium behavior and non-equilibrium cluster structure of self-propelled anisotropic particles. In engineering applications for active colloidal systems, shape-controlled steric interactions such as those described here may offer a simple route for tailoring emergent behaviors.

A theory of entropic bonding

Entropy alone can self-assemble hard nanoparticles into colloidal crystals of remarkable complexity whose structures are the same as atomic and molecular crystals, but with larger lattice spacings. Molecular simulation is a powerful tool used extensively to study the self-assembly of ordered phases from disordered fluid phases of atoms, molecules, or nanoparticles. However, it is not yet possible to predict colloidal crystal structures a priori from particle shape as we can for atomic crystals from electronic valency. Here, we present such a first-principles theory. By calculating and minimizing excluded volume within the framework of statistical mechanics, we describe the directional entropic forces that collectively emerge between hard shapes, in familiar terms used to describe chemical bonds. We validate our theory by demonstrating that it predicts thermodynamically preferred structures for four families of hard polyhedra that match, in every instance, previous simulation results. The success of this first-principles approach to entropic colloidal crystal structure prediction furthers fundamental understanding of both entropically driven crystallization and conceptual pictures of bonding in matter.

A route to hierarchical assembly of colloidal diamond

Photonic crystals, appealing for their ability to control light, are constructed from periodic regions of different dielectric constants. Yet, the structural holy grail in photonic materials, diamond, remains challenging to synthesize at the colloidal length scale. Here we explore new ways to assemble diamond using modified gyrobifastigial (mGBF) nanoparticles, a shape that resembles two anti-aligned triangular prisms. We investigate the parameter space that leads to the self-assembly of diamond, and we compare the likelihood of defects in diamond self-assembled via mGBF vs. the nanoparticle shape that is the current focus for assembling diamond, the truncated tetrahedra. We introduce a potential route for realizing mGBF particles by dimerizing triangular prisms using attractive patches, and we report the impact of this superstructure on the photonic properties.

Self-Assembly Mechanism of Complex Corrugated Particles

A variety of inorganic nanoscale materials produce microscale particles with highly corrugated geometries, but the mechanism of their formation remains unknown. Here we found that uniformly sized CdS-based hedgehog particles (HPs) self-assemble from polydisperse nanoparticles (NPs) with diameters of 1.0-4.0 nm. The typical diameters of HPs and spikes are 1770 ± 180 and 28 ± 3 nm, respectively. Depending on the temperature, solvent, and reaction times, the NPs self-assemble into nanorods, nanorod aggregates, low-corrugation particles, and other HP-related particles with complexity indexes ranging from 0 to 23.7. We show that "hedgehog", other geometries, and topologies of highly corrugated particles originate from the thermodynamic preference of polydisperse NPs to attach to the growing nanoscale cluster when electrostatic repulsion competes with van der Waals attraction. Theoretical models and simulations of the self-assembly accounting for the competition of attractive and repulsive interactions in electrolytes accurately describe particle morphology, growth stages, and the spectrum of observed products. When kinetic parameters are included in the models, the formation of corrugated particles with surfaces decorated by nanosheets, known as flower-like particles, were theoretically predicted and experimentally observed. The generality of the proposed mechanism was demonstrated for the formation of mixed HPs via a combination of CdS and Co₃O₄ NPs. With unusually high dispersion stability of HPs in unfavorable solvents including liquid CO₂, mechanistic insights into HP formation are essential for their structural adaptation for applications from energy storage, catalysis, water treatment, and others.

Effect of Particles of Irregular Size on the Microstructure and Structural Color of Self-Assembled Colloidal Crystals

Self-assembled colloidal crystals can exhibit structural colors, a phenomenon of intense reflection within a range of wavelengths caused by constructive interference. Such diffraction effects are most intense for highly uniform crystals; however, in practice, colloidal crystals may include particles of irregular size, which can reduce the quality of the crystal. Despite its importance in realizing high-quality structural colors, a quantitative relationship between particles of irregular size, crystal quality, and the resultant structural color response remains unclear. This study systematically and quantitatively investigates the effect of adding particles of irregular size on the microstructural quality and structural color reflectivity of colloidal crystals formed by evaporative self-assembly via experiment and simulation. We examine two sizes of irregular particles─those which are 1.9 times larger and 0.4 times smaller than the host crystal. We find that small irregular particles are more detrimental to surface crystal quality and structural color reflectivity than large irregular particles. When incorporated with 10% volume fraction of irregularly sized particles, the reflectivity of crystal films with large (small) irregularly sized particles decreases by 18.4 ± 5.6% (27.5 ± 5.8%), and a measure of surface crystal quality derived from Fourier analysis of scanning electron microscopy images reduces by 40.0 ± 4.5% (48.8 ± 6.0%). By modeling colloidal films incorporated with irregular particles via molecular dynamics simulation and computing the reflection spectra of the modeled crystals via the finite-difference time-domain method, we find that the peak reflectivity of the assembled structures increases monotonically with overall crystallinity, and that overall crystallinity is correlated with the volume fraction of incorporated irregular particles. The quantitative relationships developed in this study can be applied to predict the level of irregularly sized particles that can be tolerated in colloidal films before significant degradation in crystal quality and reflectivity occurs.

Synthesizable nanoparticle eigenshapes for colloidal crystals

The gulf between the complexity and diversity of colloidal crystal phases predicted to form in computer simulation and that realized to date in experiment is narrowing, but is still wide. Prior work shows that many synthesized particles are far from optimal "eigenshapes" for target superlattice structures. We use digital alchemy to determine eigenshapes for possible target colloidal crystal structures for eight families of polyhedral nanoparticle shapes already synthesized in the laboratory. Within each family we predict optimal building block shapes to obtain several target superlattice structures, as a guide for future experiments. For three target crystal structures common to multiple families, we identify which of the optimal shapes is most optimal under the same thermodynamic conditions.

The role of complementary shape in protein dimerization

Shape guides colloidal nanoparticles to form complex assemblies, but its role in defining interfaces in biomolecular complexes is less clear. In this work, we isolate the role of shape in protein complexes by studying the reversible binding processes of 46 protein dimer pairs, and investigate when entropic effects from shape complementarity alone are sufficient to predict the native protein binding interface. We employ depletants using a generic, implicit depletion model to amplify the magnitude of the entropic forces arising from lock-and-key binding and isolate the effect of shape complementarity in protein dimerization. For 13% of the complexes studied here, protein shape is sufficient to predict native complexes as equilibrium assemblies. We elucidate the results by analyzing the importance of competing binding configurations and how it affects the assembly. A machine learning classifier, with a precision of 89.14% and a recall of 77.11%, is able to identify the cases where shape alone predicts the native protein interface.

Anisotropic nanocrystal shape and ligand design for co-assembly

The use of nanocrystal (NC) building blocks to create metamaterials is a powerful approach to access emergent materials. Given the immense library of materials choices, progress in this area for anisotropic NCs is limited by the lack of co-assembly design principles. Here, we use a rational design approach to guide the co-assembly of two such anisotropic systems. We modulate the removal of geometrical incompatibilities between NCs by tuning the ligand shell, taking advantage of the lock-and-key motifs between emergent shapes of the ligand coating to subvert phase separation. Using a combination of theory, simulation, and experiments, we use our strategy to achieve co-assembly of a binary system of cubes and triangular plates and a secondary system involving two two-dimensional (2D) nanoplates. This theory-guided approach to NC assembly has the potential to direct materials choices for targeted binary co-assembly.

Accelerated annealing of colloidal crystal monolayers by means of cyclically applied electric fields

External fields are commonly applied to accelerate colloidal crystallization; however, accelerated self-assembly kinetics can negatively impact the quality of crystal structures. We show that cyclically applied electric fields can produce high quality colloidal crystals by annealing local disorder. We find that the optimal off-duration for maximum annealing is approximately one-half of the characteristic melting half lifetime of the crystalline phase. Local six-fold bond orientational order grows more rapidly than global scattering peaks, indicating that local restructuring leads global annealing. Molecular dynamics simulations of cyclically activated systems show that the ratio of optimal off-duration for maximum annealing and crystal melting time is insensitive to particle interaction details. This research provides a quantitative relationship describing how the cyclic application of fields produces high quality colloidal crystals by cycling at the fundamental time scale for local defect rearrangements; such understanding of dynamics and kinetics can be applied for reconfigurable colloidal assembly.

Unexpected Dependence of Photonic Band Gap Size on Randomness in Self-Assembled Colloidal Crystals

Using computer simulations, we explore how thermal noise-induced randomness in a self-assembled photonic crystal affects its photonic band gaps (PBGs). We consider a two-dimensional photonic crystal composed of a self-assembled array of parallel dielectric hard rods of infinite length with circular or square cross section. We find that PBGs can exist over a large range of intermediate packing densities and the largest band gap does not always appear at the highest packing density studied. Remarkably, for rods with square cross section at intermediate packing densities, the transverse magnetic (TM) band gap of the self-assembled (i.e., thermal) system can be larger than that of identical rods arranged in a perfect square lattice. By considering hollow rods, we find the band gap of transverse electric modes can be substantially increased while that of TM modes show no obvious improvement over solid rods. Our study suggests that particle shape and internal structure can be used to engineer the PBG of a self-assembled system despite the positional and orientational randomness arising from thermal noise.

Shape-driven entropic self-assembly of an open, reconfigurable, binary host-guest colloidal crystal

Entropically driven self-assembly of hard anisotropic particles, where particle shape gives rise to emergent valencies, provides a useful perspective for the design of nanoparticle and colloidal systems. Hard particles self-assemble into a rich variety of crystal structures, ranging in complexity from simple close-packed structures to structures with 432 particles in the unit cell. Entropic crystallization of open structures, however, is missing from this landscape. Here, we report the self-assembly of a two-dimensional binary mixture of hard particles into an open host-guest structure, where nonconvex, triangular host particles form a honeycomb lattice that encapsulates smaller guest particles. Notably, this open structure forms in the absence of enthalpic interactions by effectively splitting the structure into low- and high-entropy sublattices. This is the first such structure to be reported in a two-dimensional athermal system. We discuss the observed compartmentalization of entropy in this system, and show that the effect of the size of the guest particle on the stability of the structure gives rise to a reentrant phase behavior. This reentrance suggests the possibility for a reconfigurable colloidal material, and we provide a proof-of-concept by showing the assembly behavior while changing the size of the guest particles in situ. Our findings provide a strategy for designing open colloidal crystals, as well as binary systems that exhibit co-crystallization, which have been elusive thus far.

Particle shape tunes fragility in hard polyhedron glass-formers

We demonstrate that fragility, a technologically relevant characteristic of glass formation, depends on particle shape for glass-formers comprised of hard polyhedral particles. We find that hard polyhedron glass-formers become stronger (less fragile) as particle shape becomes increasingly tetrahedral. We correlate fragility with local structure, and show that stronger systems display a stronger preference for a pairwise face-to-face motif that frustrates global periodic ordering and gives rise in most systems studied to bond angle distributions that are peaked around the ideal tetrahedral bond angle. We demonstrate through mean-field-like simulations of explicit particle pairs and surrounding baths of "ghost" particles that the prevalence of this pairwise configuration can be explained via free volume exchange and emergent entropic force arguments. Our study provides a clear and direct link between the local geometry of fluid structure and the properties of glass formation, independent of interaction potential or other non-geometric tuning parameters. We ultimately demonstrate that the engineering of fragility in colloidal systems via slight changes to particle shape is possible.

Pinning dislocations in colloidal crystals with active particles that seek stacking faults

There is growing interest in functional, adaptive devices built from colloidal subunits of micron size or smaller. A colloidal material with dynamic mechanical properties could facilitate such microrobotic machines. Here we study via computer simulation how active interstitial particles in small quantities can be used to modify the bulk mechanical properties of a colloidal crystal. Passive interstitial particles are known to pin dislocations in metals, thereby increasing resistance to plastic deformation. We extend this tactic by employing anisotropic active interstitials that travel super-diffusively and bind strongly to stacking faults associated with partial dislocations. We find that: (1) interstitials that are effective at reducing plasticity compromise between strong binding to stacking faults and high mobility in the crystal bulk. (2) Reorientation of active interstitials in the crystal depends upon rotational transitions between high-symmetry crystal directions. (3) The addition of certain active interstitial shapes at concentrations as low as 60 per million host particles (0.006%) can create a shear threshold for dislocation migration. This work demonstrates how active materials in a dense matrix can locally sense their environment and lead to bulk property changes.

Scale-free, programmable design of morphable chain loops of kilobots and colloidal motors

Micron-scale robots require systems that can morph into arbitrary target configurations controlled by external agents such as heat, light, electricity, and chemical environment. Achieving this behavior using conventional approaches is challenging because the available materials at these scales are not programmable like their macroscopic counterparts. To overcome this challenge, we propose a design strategy to make a robotic machine that is both programmable and compatible with colloidal-scale physics. Our strategy uses motors in the form of active colloidal particles that constantly propel forward. We sequence these motors end-to-end in a closed chain forming a two-dimensional loop that folds under its mechanical constraints. We encode the target loop shape and its motion by regulating six design parameters, each scale-invariant and achievable at the colloidal scale. We demonstrate the plausibility of our design strategy using centimeter-scale robots called kilobots We use Brownian dynamics simulation to explore the large design space beyond that possible with kilobots, and present an analytical theory to aid the design process. Multiple loops can also be fused together to achieve several complex shapes and robotic behaviors, demonstrated by folding a letter shape "M," a dynamic gripper, and a dynamic pacman The material-agnostic, scale-free, and programmable nature of our design enables building a variety of reconfigurable and autonomous robots at both colloidal scales and macroscales.

Phase separation and state oscillation of active inertial particles

Active matter systems are of great interest for their novel out-of-equilibrium collective behavior. Active Brownian particles (ABPs) are known to exhibit clustering and motility-induced phase separation, and there have been many studies revealing this rich behavior in the overdamped limit of Brownian motion, where inertial effects are insignificant. Here we simulate an Active Inertial Particle (AIP) model where we focus on the underdamped, rather than overdamped limit, to study the interplay between particle inertia and collective behavior, such as phase separation. We show that inertia reduces particle motility due to collisions and a longer time delay for particles to regain speed, thereby suppressing phase separation relative to that observed in the overdamped limit. Additionally, we observe interesting oscillatory behavior between a phase separated steady-state and a homogeneous fluid state that results from inertia-induced collective motion within active clusters due to momentum transfer. Such oscillatory behavior has been reported for ABP systems with particle shape anisotropy, where collective motion is mediated by particle shape anisotropy. Furthermore, we confirm that there is no single characteristic frequency for the oscillatory behavior. The power spectral density is a power law in the high frequency domain, with an exponent close to -2.5.

Effect of Defective Microstructure and Film Thickness on the Reflective Structural Color of Self-Assembled Colloidal Crystals

Structural color arises from geometric diffraction; it has potential applications in optical materials because it is more resistant to environmental degradation than coloration mechanisms that are of chemical origin. Structural color can be produced from self-assembled films of colloidal size particles. While the relationship between the crystal structure and structural color reflection peak wavelength is well studied, the connection between assembly quality and the degree of reflective structural color is less understood. Here, we study this connection by investigating the structural color reflection peak intensity and width as a function of defect density and film thickness using a combined experimental and computational approach. Polystyrene microspheres are self-assembled into defective colloidal crystals via solvent evaporation. Colloidal crystal growth via sedimentation is simulated with molecular dynamics, and the reflection spectra of simulated structures are calculated by using the finite-difference time-domain algorithm. We examine the impact of commonly observed defect types (vacancies, stacking fault tetrahedra, planar faults, and microcracks) on structural color peak intensity. We find that the reduction in peak intensity scales with increased defect density. The reduction is less sensitive to the type of defect than to its volume. In addition, the reflectance of structural color increases as a function of the crystal thickness, until a plateau is reached at thicknesses greater than about 9.0 μm. The maximum reflection is 78.8 ± 0.9%; this value is significantly less than the 100% reflectivity predicted for a fully crystalline, defect-free material. Furthermore, we find that colloidal crystal films with small quantities of defects may be approximated as multilayer reflective materials. These findings can guide the design of optical materials with variable structural color intensity.

Dendrimer Ligand Directed Nanoplate Assembly

Many studies on nanocrystal (NC) self-assembly into ordered superlattices have focused mainly on attractive forces between the NCs, whereas the role of organic ligands on anisotropic NCs is only in its infancy. Herein, we report the use of a series of dendrimer ligands to direct the assembly of nanoplates into 2D and 3D geometries. It was found that the dendrimer-nanoplates consistently form a directionally offset architecture in 3D films. We present a theory to predict ligand surface distribution and Monte Carlo simulation results that characterize the ligand shell around the nanoplates. Bulky dendrimer ligands create a nontrivial corona around the plates that changes with ligand architecture. When this organic-inorganic effective shape is used in conjunction with thermodynamic perturbation theory to predict both lattice morphology and equilibrium relative orientations between NCs, a lock-and-key type of mechanism is found for the 3D assembly. We observe excellent agreement between our experimental results and theoretical model for 2D and 3D geometries, including the percent of offset between the layers of NCs. Such level of theoretical understanding and modeling will help guide future design frameworks to achieve targeted assemblies of NCs.

Influence of Softness on the Stability of Binary Colloidal Crystals

Mixtures of two types of nanoparticles can self-assemble into a wide variety of binary colloidal crystals (also called binary nanoparticle superlattices), which are interesting for their structural diversity and potential applications. Although so-called packing models-which usually treat the particles as "hard" with only excluded volume interactions-seem to explain many reported dense crystalline phases, these models often fail to predict the right structure. Here, we examine the role of soft repulsive interparticle interactions on binary colloidal crystals comprising two sizes of spherical particles; such "softness" can arise due to ligand shells or screened electrostatics. We determine the ground state phase diagram of binary systems of particles interacting with an additive inverse power law potential using a basin hopping algorithm to calculate the enthalpy of an extremely large pool of candidate structures. We find that a surprisingly small amount of softness can destabilize dense packings in favor of less densely packed structures, which provides further evidence that considerations beyond packing are necessary for describing many of the observed phases of binary colloidal crystals. Importantly, we find that several of the phases stabilized by softness, which are characterized by relatively few interparticle contacts and a tendency for local icosahedral order, are more likely to be observed experimentally than those predicted by packing models. We also report a previously unknown dense AB₄ phase and conduct free energy calculations to examine how the stability of several crystals will vary with temperature. Our results further our understanding of why particular binary colloidal crystals form and will be useful as a reference for experimentalists working with softly repulsive colloids.

FCC ↔ BCC Phase Transitions in Convex and Concave Hard Particle Systems

Solid-solid transitions are ubiquitous in nature and are important for technology. Understanding and exploiting transitions are complicated by the fact that multiple transition pathways can exist between small unit cell structures such as face-centered cubic (FCC) and body-centered cubic (BCC). By symmetry, FCC ↔ BCC transitions can occur via a pair of continuous transitions or via a discontinuous, first-order transition. However, how to, or whether it is possible to, select between pathways is unclear. Here, we use particle shape change to induce FCC ↔ BCC transitions in systems where particle valence is malleable. Though some particle shapes can eliminate metastable HCP stacking faults, we find that for both convex and concave particles, transitions are first-order.

Anisotropy effects on the kinetics of colloidal crystallization and melting: comparison of spheres and ellipsoids

We use alternating current (AC) electric field assisted self-assembly to produce two-dimensional, millimeter scale arrays of ellipsoidal colloids and study the kinetics of their phase reconfiguration by means of confocal microscopy, light scattering, and computer simulation. We find that the kinetics of orientational and positional ordering can be manipulated by changing the shape of the colloids: ellipsoids with aspect ratio 2.0 melt into disordered structures 5.7 times faster compared to spheres. On the other hand, ellipsoids self-assemble into ordered crystals at a similar rate to spheres. Confocal microscopy is used to directly visualize defects in the self-assembled structures. Small-angle light scattering (SALS) quantifies the light diffraction response, which is sensitive to the kinetics of positional and orientational ordering in the self-assembled anisotropic structures. We find three different light diffraction patterns: a phase with high orientational order (with chain-like structure in real space), a phase with high positional and orientational order (characteristic of a close-packed structure), and a phase that is disordered in position but with intermediate orientational order. The large influence of aspect ratio on the kinetics of the positionally and orientationally ordered phase is explored through simulation; it is found that the number of particle degrees of freedom controls the difference between the melting rates of the ellipsoids and spheres. This research contributes to the understanding of reconfiguration kinetics and optical properties of colloidal crystals produced from anisotropic colloids.

Colloidal fibers and rings by cooperative assembly

Janus colloids with one attractive patch on an otherwise repulsive particle surface serve as model systems to explore structure formation of particles with chemically heterogeneous surfaces such as proteins. While there are numerous computer studies, there are few experimental realizations due to a lack of means to produce such colloids with a well-controlled variable Janus balance. Here, we report a simple scalable method to precisely vary the Janus balance over a wide range and selectively functionalize one patch with DNA. We observe, via experiment and simulation, the dynamic formation of diverse superstructures: colloidal micelles, chains, or bilayers, depending on the Janus balance. Flexible dimer chains form through cooperative polymerization while trimer chains form by a two-stage process, first by cooperative polymerization into disordered aggregates followed by condensation into more ordered stiff trimer chains. Introducing substrate binding through depletion catalyzes dimer chains to form nonequilibrium rings that otherwise do not form.