Phase diagram of hard tetrahedra

Mesoscale simulations of diffusion and sedimentation in shape-anisotropic nanoparticle suspensions

We determine the long-time self-diffusion coefficient and sedimentation coefficient for suspensions of nanoparticles with anisotropic shapes (octahedra, cubes, tetrahedra, and spherocylinders) as a function of nanoparticle concentration using mesoscale simulations. We use a discrete particle model for the nanoparticles, and we account for solvent-mediated hydrodynamic interactions between nanoparticles using the multiparticle collision dynamics method. Our simulations are compared to theoretical predictions and experimental data from existing literature, demonstrating good agreement in the majority of cases. Further, we find that the self-diffusion coefficient of the regular polyhedral shapes can be estimated from that of a sphere whose diameter is the average of their inscribed and circumscribed sphere diameters.

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).

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.

Controlled Self-Assembly of Gold Nanotetrahedra into Quasicrystals and Complex Periodic Supracrystals

The self-assembly of shape-anisotropic nanocrystals into large-scale structures is a versatile and scalable approach to creating multifunctional materials. The tetrahedral geometry is ubiquitous in natural and manmade materials, yet regular tetrahedra present a formidable challenge in understanding their self-assembly behavior as they do not tile space. Here, we report diverse supracrystals from gold nanotetrahedra including the quasicrystal (QC) and the dimer packing predicted more than a decade ago and hitherto unknown phases. We solve the complex three-dimensional (3D) structure of the QC by a combination of electron microscopy, tomography, and synchrotron X-ray scattering. Nanotetrahedron vertex sharpness, surface ligands, and assembly conditions work in concert to regulate supracrystal structure. We also discover that the surface curvature of supracrystals can induce structural changes of the QC tiling and eventually, for small supracrystals with high curvature, stabilize a hexagonal approximant. Our findings bridge the gap between computational design and experimental realization of soft matter assemblies and demonstrate the importance of accurate control over nanocrystal attributes and the assembly conditions to realize increasingly complex nanopolyhedron supracrystals.

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.

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.

Phase diagrams-Why they matter and how to predict them

Understanding the thermodynamic stability and metastability of materials can help us to, for example, gauge whether crystalline polymorphs in pharmaceutical formulations are likely to be durable. It can also help us to design experimental routes to novel phases with potentially interesting properties. In this Perspective, we provide an overview of how thermodynamic phase behavior can be quantified both in computer simulations and machine-learning approaches to determine phase diagrams, as well as combinations of the two. We review the basic workflow of free-energy computations for condensed phases, including some practical implementation advice, ranging from the Frenkel-Ladd approach to thermodynamic integration and to direct-coexistence simulations. We illustrate the applications of such methods on a range of systems from materials chemistry to biological phase separation. Finally, we outline some challenges, questions, and practical applications of phase-diagram determination which we believe are likely to be possible to address in the near future using such state-of-the-art free-energy calculations, which may provide fundamental insight into separation processes using multicomponent solvents.

Chiral assemblies of pinwheel superlattices on substrates

The unique topology and physics of chiral superlattices make their self-assembly from nanoparticles highly sought after yet challenging in regard to (meta)materials^1-3. Here we show that tetrahedral gold nanoparticles can transform from a perovskite-like, low-density phase with corner-to-corner connections into pinwheel assemblies with corner-to-edge connections and denser packing. Whereas corner-sharing assemblies are achiral, pinwheel superlattices become strongly mirror asymmetric on solid substrates as demonstrated by chirality measures. Liquid-phase transmission electron microscopy and computational models show that van der Waals and electrostatic interactions between nanoparticles control thermodynamic equilibrium. Variable corner-to-edge connections among tetrahedra enable fine-tuning of chirality. The domains of the bilayer superlattices show strong chiroptical activity as identified by photon-induced near-field electron microscopy and finite-difference time-domain simulations. The simplicity and versatility of substrate-supported chiral superlattices facilitate the manufacture of metastructured coatings with unusual optical, mechanical and electronic characteristics.

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.

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.

Structure of Simple Dipolar Water-Like Fluids: Primitive Model and Hard Tetrahedra

Dipolar versions of two qualitatively different types of simple short range model fluids which exhibit the phenomenon of hydrogen bonding and which could thus serve as a reference in equations of state for associating fluids have been considered: the primitive model of water descending from the TIP4P model and the fluid of hard tetrahedra. The hydrogen bonding structure exhibited by the latter model results from purely repulsive interactions whereas in the first model the "hydrogen bonding interaction" is explicitly incorporated in the model. Since the water molecules bear a strong dipole moment, the effect of the added dipole-dipole interaction on the structure of the two short-range models is therefore examined considering them both in the full and screened dipole-dipole modifications. It is found that the hydrogen bonding structure in the primitive model resulting from the site-site interactions is so strong that the additional dipole-dipole interaction has only a marginal effect on its structure and contributes thus only to the internal energy. On the contrary, even only a weak dipole-dipole interaction destroys the original hydrogen bonding structure of the hard tetrahedron fluid; to preserve it, a screened dipole-dipole interaction has to be used in the equation of state development.

Entropic formation of a thermodynamically stable colloidal quasicrystal with negligible phason strain

Quasicrystals have been discovered in a variety of materials ranging from metals to polymers. Yet, why and how they form is incompletely understood. In situ transmission electron microscopy of alloy quasicrystal formation in metals suggests an error-and-repair mechanism, whereby quasiperiodic crystals grow imperfectly with phason strain present, and only perfect themselves later into a high-quality quasicrystal with negligible phason strain. The growth mechanism has not been investigated for other types of quasicrystals, such as dendrimeric, polymeric, or colloidal quasicrystals. Soft-matter quasicrystals typically result from entropic, rather than energetic, interactions, and are not usually grown (either in laboratories or in silico) into large-volume quasicrystals. Consequently, it is unknown whether soft-matter quasicrystals form with the high degree of structural quality found in metal alloy quasicrystals. Here, we investigate the entropically driven growth of colloidal dodecagonal quasicrystals (DQCs) via computer simulation of systems of hard tetrahedra, which are simple models for anisotropic colloidal particles that form a quasicrystal. Using a pattern recognition algorithm applied to particle trajectories during DQC growth, we analyze phason strain to follow the evolution of quasiperiodic order. As in alloys, we observe high structural quality; DQCs with low phason strain crystallize directly from the melt and only require minimal further reduction of phason strain. We also observe transformation from a denser approximant to the DQC via continuous phason strain relaxation. Our results demonstrate that soft-matter quasicrystals dominated by entropy can be thermodynamically stable and grown with high structural quality--just like their alloy quasicrystal counterparts.

Low Interfacial Free Energy Describes the Bulk Ordering Transition in Colloidal Cubes

Many hard faceted nanoparticles are known to undergo disorder-to-order phase transitions following a classical nucleation and growth mechanism. In a previous study [J. Phys. Chem. B 2018, 122, 9264-9273], it was shown that hard cubes undergo a nonclassical phase transition with a bulk character instead of originating from consolidated nuclei. Significantly, an unusually high fraction of ordered particles was observed in the metastable basin of the disordered phase, even for very low degrees of supersaturation. This work aims to substantiate the conjecture that these unique properties originate from a comparatively low interfacial free energy between the disordered and ordered phases for hard cubes relative to other hard particle systems. Using the cleaving wall method to directly measure the interfacial free energy for cubes, it is found that its values are indeed small; e.g., at phase coexistence conditions, it is only one-fifth that for hard spheres. A theoretical nucleation model is used to explore the broader implications of low interfacial tension values and how this could result in a bulk ordering mechanism.

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.

Classifying Crystals of Rounded Tetrahedra and Determining Their Order Parameters Using Dimensionality Reduction

Using simulations we study the phase behavior of a family of hard spherotetrahedra, a shape that interpolates between tetrahedra and spheres. We identify 13 close-packed structures, some with packings that are significantly denser than previously reported. Twelve of these are crystals with unit cells of N = 2 or N = 4 particles, but in the shape regime of slightly rounded tetrahedra we find that the densest structure is a quasicrystal approximant with a unit cell of N = 82 particles. All 13 structures are also stable below close packing, together with an additional 14th plastic crystal phase at the sphere side of the phase diagram, and upon sufficient dilution to packing fractions below 50-60% all structures melt. Interestingly, however, upon compressing the fluid phase, self-assembly takes place spontaneously only at the tetrahedron and the sphere side of the family but not in an intermediate regime of tetrahedra with rounded edges. We describe the local environment of each particle by a set of l-fold bond orientational order parameters q̅l, which we use in an extensive principal component analysis. We find that the total packing fraction as well as several particular linear combinations of q̅l rather than individual q̅l's are optimally distinctive, specifically the differences q̅4 - q̅6 for separating tetragonal from hexagonal structures and q̅4-q̅8 for distinguishing tetragonal structures. We argue that these characteristic combinations are also useful as reliable order parameters in nucleation studies, enhanced sampling techniques, or inverse-design methods involving odd-shaped particles in general.

Self-assembly and entropic effects in pear-shaped colloid systems. I. Shape sensitivity of bilayer phases in colloidal pear-shaped particle systems

The role of particle shape in self-assembly processes is a double-edged sword. On the one hand, particle shape and particle elongation are often considered the most fundamental determinants of soft matter structure formation. On the other hand, structure formation is often highly sensitive to details of shape. Here, we address the question of particle shape sensitivity for the self-assembly of hard pear-shaped particles by studying two models for this system: (a) the pear hard Gaussian overlap (PHGO) and (b) the hard pears of revolution (HPR) model. Hard pear-shaped particles, given by the PHGO model, are known to form a bicontinuous gyroid phase spontaneously. However, this model does not replicate an additive object perfectly and, hence, varies slightly in shape from a "true" pear-shape. Therefore, we investigate in the first part of this series the stability of the gyroid phase in pear-shaped particle systems. We show, based on the HPR phase diagram, that the gyroid phase does not form in pears with such a "true" hard pear-shaped potential. Moreover, we acquire first indications from the HPR and PHGO pair-correlation functions that the formation of the gyroid is probably attributed to the small non-additive properties of the PHGO potential.

Self-assembly of anisotropic nanoparticles into functional superstructures

Self-assembly of colloidal nanoparticles (NPs) into superstructures offers a flexible and promising pathway to manipulate the nanometer-sized particles and thus make full use of their unique properties. This bottom-up strategy builds a bridge between the NP regime and a new class of transformative materials across multiple length scales for technological applications. In this field, anisotropic NPs with size- and shape-dependent physical properties as self-assembly building blocks have long fascinated scientists. Self-assembly of anisotropic NPs not only opens up exciting opportunities to engineer a variety of intriguing and complex superlattice architectures, but also provides access to discover emergent collective properties that stem from their ordered arrangement. Thus, this has stimulated enormous research interests in both fundamental science and technological applications. This present review comprehensively summarizes the latest advances in this area, and highlights their rich packing behaviors from the viewpoint of NP shape. We provide the basics of the experimental techniques to produce NP superstructures and structural characterization tools, and detail the delicate assembled structures. Then the current understanding of the assembly dynamics is discussed with the assistance of in situ studies, followed by emergent collective properties from these NP assemblies. Finally, we end this article with the remaining challenges and outlook, hoping to encourage further research in this field.

Performance of the asymptotic expansion method to derive equations of state for hard polyhedron fluids

The asymptotic expansion method is used to derive analytical expressions for the equations of state of 14 hard polyhedron fluids such as cube, octahedron, rhombic dodecahedron, etc., by knowing the values of only the first eight virial coefficients.

Topological order in densely packed anisotropic colloids

The existence of topological order is frequently associated with strongly coupled quantum matter. Here, we demonstrate the existence of topological phases in classical systems of densely packed, hard, anisotropic polyhedrally shaped colloidal particles. We show that previously reported transitions in dense packings lead to the existence of topologically ordered thermodynamic phases, which we show are stable away from the dense packing limit. Our work expands the library of known topological phases, whose experimental realization could provide new means for constructing plasmonic materials that are robust in the presence of fluctuations.

Investigation of Geometric Landscape and Structure-Property Relations for Colloidal Superstructures Using Genetic Algorithm

Over the past two decades, colloidal particles with a variety of shapes, sizes, and compositions have been synthesized and characterized successfully. One of the most important applications for colloidal building blocks is to engineer functional structures as mechanical, electrical, and optical metamaterials. However, complex interaction dynamics between the building blocks as well as sophisticated structure-property relationships make it challenging to design structures with predictable target properties. In this paper, we implement an inverse material design framework using Genetic Algorithm (GA)-based techniques to streamline the design of colloidal structures based on target properties. We investigate spherical particles as well as colloidal molecules of different sizes and shapes and evaluate a Geometric Landscape Accessibility parameter that identifies the size of feasible domains within the geometric phase space of each structure. Considering target photonic properties, our GA-assisted framework is further utilized to identify sets of building blocks and structures that lead to various target values for the size of the photonic band gaps. The proposed framework in this study will provide new insight for predictive computational material design approaches and help establish more efficient ways of understanding structure-property relations in sub-micrometer-scale materials.

Engineering entropy for the inverse design of colloidal crystals from hard shapes

Throughout the physical sciences, entropy stands out as a pivotal but enigmatic concept that, in materials design, typically takes a backseat to energy. Here, we demonstrate how to precisely engineer entropy to achieve desired colloidal crystals via particle shapes that, importantly, can be made in the laboratory. We demonstrate the inverse design of symmetric hard particles that assemble six different target colloidal crystals due solely to entropy maximization. Our approach efficiently samples 10⁸ particle shapes from 92- and 188-dimensional design spaces to discover thermodynamically optimal shapes. We design particle shapes that self-assemble into known crystals with optimized symmetry and thermodynamic stability, as well as new crystal structures with no known atomic or other equivalent.

New equations of state for the hard polyhedron fluids

In this paper, we derived a new equation of state for hard polyhedron fluids that is obtained by the knowledge of virial coefficients and a fit to the computer simulation data for the compressibility factor, and which contains two adjustable parameters. This equation reproduces exactly the correct known virial coefficients up to the ninth one and also the compressibility factor data with high accuracy, the absolute average deviations (AADs) being 0.05% for the stable state and 1.12% for both stable and metastable states for the hard tetrahedron fluid. For 12 of the other hard polyhedron fluids, it reproduces exactly the correct known virial coefficients up to the eighth one and also the compressibility factor data in the stable state with AADs less than 0.25%, with the only exception being the triangular prism polyhedron fluid.

Free energy of conformational isomers: The case of gapped DNA duplexes

Liquid-crystalline phases in all-DNA systems have been extensively studied in the past and although nematic, cholesteric and columnar mesophases have been observed, the smectic phase remained elusive. Recently, it has been found evidence of a smectic-A ordering in an all-DNA system, where the constituent particles, which are gapped DNA duplexes, resemble chain-sticks. It has been argued that in the smectic-A phase these DNA chain-sticks should be folded as a means to suppress aggregate polydispersity and excluded volume. Nevertheless, if initial crystalline configurations are prepared in silico with gapped DNA duplexes either fully unfolded or fully folded by carrying out computer simulations one can end up with two different phases having at the same concentration and temperature the majority of gapped DNA duplexes either folded or unfolded. This result suggests that these two phases have a small free energy difference, since no transition is observed from one to the other within the simulation time span. In the present manuscript, we assess which of these two phases is thermodynamically stable through a suitable protocol based on thermodynamic integration. Our method is rather general and it can be used to discriminate stable states from metastable ones of comparable free energy.

Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT

We develop a generic coarse-grained model of soluble conjugated polymers, capable of describing their self-assembly into a lamellar mesophase. Polymer chains are described by a hindered-rotation model, where interaction centers represent entire repeat units, including side chains. We introduce soft anisotropic nonbonded interactions to mimic the potential of mean force between atomistic repeat units. The functional form of this potential reflects the symmetry of the molecular order in a lamellar mesophase. The model can generate both nematic and lamellar (sanidic smectic) molecular arrangements. We parametrize this model for a soluble conjugated polymer poly(3-hexylthiophene) (P3HT) and demonstrate that the simulated lamellar mesophase matches morphologies of low molecular weight P3HT, experimentally observed at elevated temperatures. A qualitative charge-transport model allows us to link local chain conformations and mesoscale order to charge transport. In particular, it shows how coarsening of lamellar domains and chain extension increase the charge carrier mobility. By modeling large systems and long chains, we can capture transport between lamellar layers, which is due to rare, but thermodynamically allowed, backbone bridges between neighboring layers.

Thermodynamically driven assemblies and liquid-liquid phase separations in biology

The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.

On the formation of stripe, sigma, and honeycomb phases in a core-corona system

Using Monte Carlo simulations and free-energy calculations, we investigate the phase behaviour of a two-dimensional core-corona system. We model this system as particles consisting of an impenetrable hard core of diameter σ_HD surrounded by a purely repulsive soft corona of diameter δ = 1.95σ_HD. At low densities, we observe the spontaneous formation of a phase with a stripe texture as well as a honeycomb-like phase driven by both energy and entropy considerations. At high densities, we find that a two-dimensional analogue of the periodic sigma phase, considered as an approximant of dodecagonal quasicrystals, is energetically stabilised with respect to two distinct dodecagonal quasicrystals, namely, a square-triangle tiling and a square-triangle-shield tiling. We also find the formation of stable hexagonal phases at three distinct density ranges, which are energetically driven, i.e. by minimising the overlap of coronas. Furthermore, our calculations show that the low-density dodecagonal quasicrystal that was previously reported by Dotera et al., [Nature, 2014, 506, 208] is kinetically formed in the coexistence region between the honeycomb and the medium-density hexagonal phase.

Attraction Controls the Inversion of Order by Disorder in Buckled Colloidal Monolayers

We show how including attraction in interparticle interactions reverses the effect of fluctuations in ordering of a prototypical artificial frustrated system. Buckled colloidal monolayers exhibit the same ground state as the Ising antiferromagnet on a deformable triangular lattice, but it is unclear if ordering in the two systems is driven by the same geometric mechanism. By a real-space expansion we find that, for buckled colloids, bent stripes constitute the stable phase, whereas in the Ising antiferromagnet straight stripes are favored. For generic pair potentials we show that attraction governs this selection mechanism, in a manner that is linked to local packing considerations. This supports the geometric origin of entropy in jammed sphere packings and provides a tool for designing self-assembled colloidal structures.

Enhanced Computational Sampling of Perylene and Perylothiophene Packing with Rigid-Body Models

Molecular simulations have the potential to advance the understanding of how the structure of organic materials can be engineered through the choice of chemical components but are limited by computational costs. The computational costs can be significantly lowered through the use of modeling approximations that capture the relevant features of a system, while lowering algorithmic complexity or by decreasing the degrees of freedom that must be integrated. Such methods include coarse-graining techniques, approximating long-range electrostatics with short-range potentials, and the use of rigid bodies to replace flexible bonded constraints between atoms. To understand whether and to what degree these techniques can be leveraged to enhance the understanding of planar organic molecules, we investigate the morphologies predicted by molecular dynamic simulations using simplified molecular models of perylene and perylothiophene. Approximately, 10 000 wall-clock hours of graphics processing unit-accelerated simulations are performed using both rigid and flexible models to test their efficiency and predictive capability with the two chemistries. We characterize the 1191 resulting morphologies using simulated X-ray diffraction and cluster analysis to distinguish structural transitions, summarized by four phase diagrams. We find that the morphologies generated by the rigid model of perylene and perylothiophene match with those generated by the flexible model. We find that ordered, hexagonally packed columnar phases are thermodynamically favored over a wide range of densities and temperatures for both molecules, in qualitative agreement with experiments. Furthermore, we find the rigid model to be more computationally efficient for both molecules, providing more samples per second and shorter times to equilibrium. Owing to the structural accuracy and improved computational efficiency of modeling polyaromatic groups as rigid bodies, we recommend this modeling choice for enhancing the sampling in polyaromatic molecular simulations.

Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal

We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm 'star' motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA.

Structure of a molecular liquid GeI4

A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å(-1) in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak's height is confirmed by a simulation, in which the molecular size is changed.

Molecular dynamics study of colloidal quasicrystals

Colloidal quasicrystals have received increased interest recently due to new insight in exploring their potential for photonic materials as well as for optical devices [Vardeny et al., Nat. Photonics, 2013, 7, 177]. Colloidal quasicrystals in aqueous solutions have been found in systems of micelles with impenetrable cores [Fischer et al., Proc. Natl. Acad. Sci. U. S. A., 2011, 108, 1810]. A simple model potential for micelle-micelle interaction is the step potential, which is infinite for core overlaps and constant for shell overlaps. Dotera et al. performed Monte Carlo simulations of the step potential model and found quasicrystals for specific values of the packing fraction η and the shell-core ratio λ [Dotera et al., Nature, 2014, 506, 208 ]. However, the overlap of real micelles causes repulsive forces, which increase with decreasing core distance. We consider this by introducing a novel model potential with repulsive forces depending on a third parameter α. In a systematic manner we study this more realistic potential with two-dimensional molecular dynamics simulations. For α = 0 the model is similar to the step potential model. For the first time, we provide a comprehensive overview of crystalline, quasicrystalline, and disordered structures as a function of η and λ. Simulations performed with α > 0 show the impact of the repulsive forces. We find that quasicrystalline structures at high densities vanish while new quasicrystalline structures appear at intermediate densities. Our results help to tailor colloidal systems for today's advanced applications in photonics and optical devices.

Self-assembly of a space-tessellating structure in the binary system of hard tetrahedra and octahedra

We report the formation of a binary crystal of hard polyhedra due solely to entropic forces. Although the alternating arrangement of octahedra and tetrahedra is a known space-tessellation, it had not previously been observed in self-assembly simulations. Both known one-component phases - the dodecagonal quasicrystal of tetrahedra and the densest-packing of octahedra in the Minkowski lattice - are found to coexist with the binary phase. Apart from an alternative, monoclinic packing of octahedra, no additional crystalline phases were observed.

Using depletion to control colloidal crystal assemblies of hard cuboctahedra

Depletion interactions arise from entropic forces, and their ability to induce aggregation and even ordering of colloidal particles through self-assembly is well established, especially for spherical colloids. We vary the size and concentration of penetrable hard sphere depletants in a system of cuboctahedra, and we show how depletion changes the preferential facet alignment of the colloids and thereby selects different crystal structures. Moreover, we explain the cuboctahedra phase behavior using perturbative free energy calculations. We find that cuboctahedra can form a stable simple cubic phase, and, remarkably, that the stability of this phase can be rationalized only by considering the effects of both the colloid and depletant entropy. We corroborate our results by analyzing how the depletant concentration and size affect the emergent directional entropic forces and hence the effective particle shape. We propose the use of depletants as a means of easily changing the effective shape of self-assembling anisotropic colloids.

Graphoepitaxy for translational and orientational ordering of monolayers of rectangular nanoparticles

The combinations of particle aspect ratio and enthalpic-barrier templates that lead to translational and orientational ordering of monolayers of rectangular particles are determined using Monte Carlo simulations and density functional theory. For sufficiently high enthalpic barriers, we find that only specific combinations of particle sizes and template spacings lead to ordered arrays. The pattern multiplication factor provided by the template extends to approximately ten times the smallest dimension of the particle.

Computationally Guided Assembly of Oriented Nanocubes by Modulating Grafted Polymer-Surface Interactions

The bottom-up fabrication of ordered and oriented colloidal nanoparticle assemblies is critical for engineering functional nanomaterials beyond conventional polymer-particle composites. Here, we probe the influence of polymer surface ligands on the self-orientation of shaped metal nanoparticles for the formation of nanojunctions. We examine how polymer graft-surface interactions dictate Ag nanocube orientation into either edge-edge or face-face nanojunctions. Specifically, we investigate the effect of end-functionalized polymer grafts on nanocube assembly outcomes, such as interparticle angle and interparticle distance. Our assembly results can be directly mapped onto our theoretical phase diagrams for nanocube orientation, enabling correlation of experimental variables (such as graft length and metal binding strength) with computational parameters. These results represent an important step toward unifying modeling and experimental approaches to understanding nanoparticle-polymer self-assembly.

Evolution of the dense packings of spherotetrahedral particles: from ideal tetrahedra to spheres

Particle shape plays a crucial role in determining packing characteristics. Real particles in nature usually have rounded corners. In this work, we systematically investigate the rounded corner effect on the dense packings of spherotetrahedral particles. The evolution of dense packing structure as the particle shape continuously deforms from a regular tetrahedron to a sphere is investigated, starting both from the regular tetrahedron and the sphere packings. The dimer crystal and the quasicrystal approximant are used as initial configurations, as well as the two densest sphere packing structures. We characterize the evolution of spherotetrahedron packings from the ideal tetrahedron (s = 0) to the sphere (s = 1) via a single roundness parameter s. The evolution can be partitioned into seven regions according to the shape variation of the packing unit cell. Interestingly, a peak of the packing density Φ is first observed at s ≈ 0.16 in the Φ-s curves where the tetrahedra have small rounded corners. The maximum density of the deformed quasicrystal approximant family (Φ ≈ 0.8763) is slightly larger than that of the deformed dimer crystal family (Φ ≈ 0.8704), and both of them exceed the densest known packing of ideal tetrahedra (Φ ≈ 0.8563).

Dimer covering and percolation frustration

Covering a graph or a lattice with nonoverlapping dimers is a problem that has received considerable interest in areas, such as discrete mathematics, statistical physics, chemistry, and materials science. Yet, the problem of percolation on dimer-covered lattices has received little attention. In particular, percolation on lattices that are fully covered by nonoverlapping dimers has not evidently been considered. Here, we propose a procedure for generating random dimer coverings of a given lattice. We then compute the bond percolation threshold on random and ordered coverings of the square and the triangular lattices on the remaining bonds connecting the dimers. We obtain p_{c}=0.367713(2) and p_{c}=0.235340(1) for random coverings of the square and the triangular lattices, respectively. We observe that the percolation frustration induced as a result of dimer covering is larger in the low-coordination-number square lattice. There is also no relationship between the existence of long-range order in a covering of the square lattice and its percolation threshold. In particular, an ordered covering of the square lattice, denoted by shifted covering in this paper, has an unusually low percolation threshold and is topologically identical to the triangular lattice. This is in contrast to the other ordered dimer coverings considered in this paper, which have higher percolation thresholds than the random covering. In the case of the triangular lattice, the percolation thresholds of the ordered and random coverings are very close, suggesting the lack of sensitivity of the percolation threshold to microscopic details of the covering in highly coordinated networks.

Cluster and constraint analysis in tetrahedron packings

The disordered packings of tetrahedra often show no obvious macroscopic orientational or positional order for a wide range of packing densities, and it has been found that the local order in particle clusters is the main order form of tetrahedron packings. Therefore, a cluster analysis is carried out to investigate the local structures and properties of tetrahedron packings in this work. We obtain a cluster distribution of differently sized clusters, and peaks are observed at two special clusters, i.e., dimer and wagon wheel. We then calculate the amounts of dimers and wagon wheels, which are observed to have linear or approximate linear correlations with packing density. Following our previous work, the amount of particles participating in dimers is used as an order metric to evaluate the order degree of the hierarchical packing structure of tetrahedra, and an order map is consequently depicted. Furthermore, a constraint analysis is performed to determine the isostatic or hyperstatic region in the order map. We employ a Monte Carlo algorithm to test jamming and then suggest a new maximally random jammed packing of hard tetrahedra from the order map with a packing density of 0.6337.

Symmetry considerations for the targeted assembly of entropically stabilized colloidal crystals via Voronoi particles

The relationship between colloidal building blocks and their assemblies is an active field of research. As a strategy for targeting novel crystal structures, we examine the use of Voronoi particles, which are hard, space-filling particles in the shape of Voronoi cells of a target structure. Although Voronoi particles stabilize their target structure in the limit of high pressure by construction, the thermodynamic assembly of the same structure at moderate pressure, close to the onset of crystallization, is not guaranteed. Indeed, we find that a more symmetric crystal is often preferred due to additional entropic contributions arising from configurational or occupational degeneracy. We characterize the assembly behavior of the Voronoi particles in terms of the symmetries of the building blocks as well as the symmetries of crystal structures and demonstrate how controlling the degeneracies through a modification of particle shape and field-directed assembly can significantly improve the assembly propensity.