Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control such assemblies remain poorly understood, nevertheless. Using classical density functional theory we demonstrate how the intrinsic length scales and their interplay in terms of interspecies molecular interactions can be used to tune soft matter self-assembly. We apply our strategy to two different soft binary mixtures to create guidelines for tuning intermolecular interactions that lead to transitions from fully miscible, liquid-like uniform state to formation of simple and core-shell aggregates, and mixed aggregate structures. Furthermore, we demonstrate how the interspecies interactions and system composition can be used to control concentration gradients of component species within these assemblies. The insight generated by this work contributes towards understanding and controlling soft multi-component self-assembly systems. Additionally, our results aid in understanding complex biological assemblies and their function and provide tools to engineer molecular interactions in order to control polymeric and protein-based materials, pharmaceutical formulations, and nanoparticle assemblies.
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. No additional crystalline phases were observed.
We outline a basic strategy of how self-propulsion can be used to improve the yield of a typical colloidal self-assembly process. The success of this approach is predicated on the thoughtful design of the colloidal building block as well as how self-propulsion is endowed to the particle. As long as a set of criteria are satisfied, it is possible to significantly increase the rate of self-assembly, and greatly expand the window in parameter space where self-assembly can occur. In addition, we show that by tuning the relative on/off time of the self-propelling force it is possible to modulate th…
Self-assembly is the mechanism that controls the formation of well defined structures from disordered pre-existing parts. Despite the importance of self-assembly as a manufacturing method and the increasingly large number of experimental realizations of complex self-assembled nano aggregates, theoretical predictions are lagging behind. Here we show that for a non-trivial self-assembly phenomenon, originating branched loop-less clusters, it is possible to derive a fully predictive parameter-free theory of equilibrium self-assembly by combining the Wertheim theory for associating liquids with th…
Review paper. Chapter 6 in Janus Particles Synthesis, Self-Assembly, and Applications pages 108-137, Edited by Steve Granick and Shan Jiang (RCS Publishing 2012) http://www.rsc.org/Shop/books/2012/9781849734233.asp
Self-assembly dynamics in binary surfactant mixtures and structure changes of lipid vesicles induced by detergent solution are studied using coarse-grained molecular simulations. Disk-shaped micelles, the bicelles, are stabilized by detergents surrounding the rim of a bilayer disk of lipids. The self-assembled bicelles are considerably smaller than bicelles formed from vesicle rupture, and their size is determined by the concentrations of lipids and detergents and the interactions between the two species. The detergent-adsorption induces spontaneous curvature of the vesicle bilayer and results…
We use computer simulation to investigate the self-assembly of Janus-like amphiphilic peanut-shaped nanoparticles, finding phases of clusters, bilayers and micelles in accord with ideas of packing familiar from the study of molecular surfactants. However, packing arguments do not explain the hierarchical self-assembly dynamics that we observe, nor the coexistence of bilayers and faceted polyhedra. This coexistence suggests that experimental realizations of our model can achieve multipotent assembly of either of two competing ordered structures.
This is the unedited authors' version of Chapter 3 appearing in the following book: Self-Assembly Systems: Theory and Simulations Ed. Li-Tang Yan John Wiley & Sons, Ltd, Chichester, pp. 53-84 (2017)
The self-assembly of amphiphilic molecules usually takes place in a liquid phase, near room temperature. Here, using small angle X-ray scattering (SAXS) experiments performed in real time, we show that freezing of aqueous solutions of copolymer amphiphilic molecules can induce self-assembly below 0°C.
We simulate crystallisation of hard spheres with short-ranged attractive potentials, as a model self-assembling system. We show how measurements of correlation and response functions during assembly can be used to tune the interaction parameters as assembly proceeds, in order to obtain high-quality crystals. The method we use is independent of details of the interaction potential and of the structure of the final crystal - we propose that it could be applied to a wide range of self-assembling systems.
We propose a description for the quasi-equilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA genome molecules. We describe the assembly of such viruses as the interplay between two coupled phase-transition like events: the formation of the protein shell (the capsid) by CPs and the condensation of a large ss viral RNA molecule. Electrostatic repulsion between the CPs competes with attractive hydrophobic interactions and attractive interaction between neut…
The dissipative particle dynamics (DPD) simulation method has been shown to be a promising tool to study self-assembly of soft matter systems. In particular, it has been used to study block copolymer (BCP) self-assembly. However, previous parametrizations of this model are not able to capture most of the rich phase behaviors of block copolymers in thin films nor in directed self-assembly (chemoepitaxy or graphoepitaxy). Here we extend the applicability of the DPD method for BCPs to make it applicable to thin films and directed self-assembly. Our new reparametrization is able to reproduce the b…
In this work, we use a minimal model to introduce a framework for controlling self-assembly under the influence of time-dependent driving forces. We develop a mean-field thermodynamic framework that predicts the conditions required to reliably self-assemble a desired spatial pattern under time-varying external fields. We also calculate the entropy production associated with the time-dependent self-assembly process and examine how it can be used to predict conditions under which the external time-varying signal is reliably encoded as a spatial pattern in the self-assembling material. While the …
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find that nucleation around the core particle can inhibit aggregate formation, a process which often hinders self-assembly. In particular, this new assembly pathway allows dodecahedral shells to form readily, whereas these structures never form in the absence of the template. Secondly, we consider the self-assembly of multi-shell structures, where the central ic…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully addressable limit in which each component is unique. In this paper we introduce an idealized model of cubic particles with patterned faces that allows self-assembly strategies to be compared and tested. We consider a simple octameric target, starting with the minimal requirements for successful self-assembly and comparing the benefits and limitations of more sophisti…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on a prototypical 'DNA-brick' structure. By combining temperature-dependent dynamic light scattering and atomic force microscopy with coarse-grained simulations, we show how subtle changes in the nucleation pathway profoundly affect the yield of the correctly formed structures. In particular, we can increase the range of conditions over which self-assembly occ…
We simulate the dynamics of phase assembly in binary immiscible fluids and ternary microemulsions using a three-dimensional hydrodynamic lattice gas approach. For critical spinodal decomposition we perform the scaling analysis in reduced variables introduced by Jury et al. and Kendon et al. We find a late-stage scaling exponent consistent with the inertial regime. However, as observed with the previous lattice-gas model of Appert et al. our data does not fall in the same range of reduced length and time as that of Kendon et al. For off-critical binary spinodal decomposition we observe a reduct…
In this article, we study the phenomenology of a two dimensional dilute suspension of active amphiphilic Janus particles. We analyze how the morphology of the aggregates emerging from their self-assembly depends on the strength and the direction of the active forces. We systematically explore and contrast the phenomenologies resulting from particles with a range of attractive patch coverages. Finally, we illustrate how the geometry of the colloids and the directionality of their interactions can be used to control the physical properties of the assembled active aggregates and suggest possible …
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy diffusion-limited aggregation, and the experimentally observed Amyloid-\b{eta} (A\b{eta}) fractal self-assembly using confocal microscopy. The molecular docking was used to determine the properties of the patches on A\b{eta} oligomers. Similar patch properties were used to design the particles for simulation. In agreement with the model predictions, the free energy of f…
Self-assembly at submicroscopic scales is an important but little understood phenomenon. A prominent example is virus capsid growth, whose underlying behavior can be modeled using simple particles that assemble into polyhedral shells. Molecular dynamics simulation of shell formation in the presence of an atomistic solvent provides new insight into the self-assembly mechanism, notably that growth proceeds via a cascade of strongly reversible steps and, despite the large variety of possible intermediates, only a small fraction of highly bonded forms appear on the pathway.
We report the first results of our three-dimensional, mesoscopic, amphiphilic lattice-Boltzmann model, which has been used to simulate the dynamics of self-assembly of ordered cubic and lamellar phases in binary water-surfactant systems. Our results provide insight into the mechanism of ordering of such mesophases in terms of various molecular forces acting between water and surfactant molecules and the mechanism driving the transition from the lamellar to the cubic phase.
We report a novel class of polymer nanocomposite composed of organic nanoparticles dispersed in polymer matrix, with the particle sizes of 30-120 nm in radius. The organic nanoparticles were formed by the self-assembly of protonated poly(4-vinyl-pyridine)-r-poly(acrylonitrile) and amphiphilic metanil yellow dye molecules through electrostatic interactions in aqueous solution. A strongly broadened Raman shift band was probed, suggesting the presence of enhanced optoelectronic property from the polymer nanocomposite. Here, using random-copolymer polyelectrolytes and mesogenic amphiphiles as the …
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building-blocks, each of which occupies a defined location in the target. The requirement that each type of building-block appears exactly once in each copy of the target introduces severe restrictions on the combinations of particles and on the pathways that lead to successful self-assembly. These restrictions can limit the efficiency of self-assembly and the final yield of the product. In particular, partially formed fragments may compete with each other if their compositions overlap,…
In this paper we introduce a new method to design interparticle interactions to target arbitrary crystal structures via the process of self-assembly. We show that it is possible to exploit the curvature of the crystal nucleation free-energy barrier to sample and select optimal interparticle interactions for self-assembly into a desired structure. We apply this method to find interactions to target two simple crystal structures: a crystal with simple cubic symmetry and a two-dimensional plane with square symmetry embedded in a three-dimensional space. Finally, we discuss the potential and limit…
The self-assembly of submerged cold-plasma-treated polyethylene beads is reported. The plasma-treated immersed millimetrically-sized polyethylene beads formed well-ordered 2D quasi-crystalline structures. The submerged floating of light polyethylene beads is possible due to the energy gain achieved by the wetting of the high-energy plasma-treated polymer surface prevailing over the energy loss due to the upward climb of the liquid over the beads. The capillary immersion attraction force is responsible for the observed self-assembly. The observed 2D quasi-crystalline structures demonstrate disl…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most protein crystals are open structures stabilized by anisotropic interactions. Here, we use theory and simulation to show that assembly of one such structure is not predicted by the second virial coefficient or enhanced by the critical point. Instead, good assembly requires that the thermodynamic driving force be on the order of the thermal energy and that in…
The assembly of filamentous bundles with controlled diameters is common in biological systems and desirable for the development of nanomaterials. We discuss dynamical simulations and free energy calculations on patchy spheres with chiral pair interactions that spontaneously assemble into filamentous bundles. The chirality frustrates long-range crystal order by introducing twist between interacting subunits. For some ranges of system parameters this constraint leads to bundles with a finite diameter as the equilibrium state, and in other cases frustration is relieved by the formation of defects…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA tethered nanoparticles.
Recent developments in the synthesis of colloidal particles allow for control over shape and inter-particle interaction. One example, among others, is the so-called "Mickey Mouse" (MM) particle for which the self-assembly properties have been previously studied yielding a stable cluster phase together with elongated, tube-like structures. Here, we investigate under which conditions a fluid of Mickey Mouse particles can yield phase separation and how the self-assembly behaviour affects the gas-liquid coexistence. We vary the distance between the repulsive and the attractive lobes (bond length),…
Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are needed. To address this challenge, we explore the trade-offs between addressable assembly and self-closing assembly of a specific class of self-limiting structures: cylindrical tubules. We make triangular subunits using DNA origami that have specific, valence-limited interactions and designed binding angles, and study their assembly into tubules that have a self-…
Recent studies of dynamic self-assembly in ferromagnetic colloids suspended in liquid-air or liquid-liquid interfaces revealed a rich variety of dynamic structures ranging from linear snakes to axisymmetric asters, which exhibit novel morphology of the magnetic ordering accompanied by large-scale hydrodynamic flows. Based on controlled experiments and first principle theory, we argue that the transition from snakes to asters is governed by the viscosity of the suspending liquid where less viscous liquids favor snakes and more viscous, asters. By obtaining analytic solutions of the time-average…
We present dynamic measurements of a lattice gas during phase separation, which we use as an analogy for self-assembly of equilibrium ordered structures. We use two approaches to quantify the degree of 'reversibility' of this process: firstly, we count events in which bonds are made and broken; secondly, we use correlation-response measurements and fluctuation-dissipation ratios to probe reversibility during different time intervals. We show how correlation and response functions can be related directly to microscopic (ir)reversibility and we discuss time-dependence and observable- dependence …
The desire to create cell-like models for fundamental science and applications has spurred extensive effort towards creating giant unilamellar vesicles (GUVs). However, a route to selectively self-assemble GUVs in bulk has remained elusive. In bulk solution, membrane-forming molecules such as phospholipids, single-tailed surfactants, and block copolymers typically self-assemble into multilamellar, onion-like structures. So although self-assembly processes can form nanoscale unilamellar vesicles, scaffolding by droplets or surfaces is required to create GUVs. Here we show that surprisingly, it …
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into account explicitly. The model is solved exactly in one dimension by the transfer-matrix method. In particular, pressure as a function of concentration, correlation function and specific heat are calculated. The model is compared with the recently introduced lattice model for colloidal self-assembly, where the particles interact with the isotropic short-range attra…
We use computational modeling to investigate the assembly thermodynamics of a particle-based model for geometrically frustrated assembly, in which the local packing geometry of subunits is incompatible with uniform, strain-free large-scale assembly. The model considers discrete triangular subunits that drive assembly towards a closed, hexagonal-ordered tubule, but have geometries that locally favor negative Gaussian curvature. We use dynamical Monte Carlo simulations and enhanced sampling methods to compute the free energy landscape and corresponding self-assembly behavior as a function of exp…
From dumbbells to FCC crystals, we study the self-assembly pathway of amphiphatic, spherical colloidal particles as a function of the size of the hydrophobic region using molecular dynamics simulations. Specifically, we analyze how local inter-particle interactions correlate to the final self-assembled aggregate and how they affect the dynamical pathway of structure formation. We present a detailed diagram separating the many phases that we find for different sizes of the hydrophobic area, and uncover a narrow region where particles self-assemble into hollow, faceted cages that could potential…
We use neuroevolutionary learning to identify time-dependent protocols for low-dissipation self-assembly in a model of generic active particles with interactions. When the time allotted for assembly is sufficiently long, low-dissipation protocols use only interparticle attractions, producing an amount of entropy that scales as the number of particles. When time is too short to allow assembly to proceed via diffusive motion, low-dissipation assembly protocols instead require particle self-propulsion, producing an amount of entropy that scales with the number of particles and the swim length req…
Electrostatic interactions play an important role in numerous self-assembly phenomena, including colloidal aggregation. Although colloids typically have a dielectric constant that differs from the surrounding solvent, the effective interactions that arise from inhomogeneous polarization charge distributions are generally neglected in theoretical and computational studies. We introduce an efficient technique to resolve polarization charges in dynamical dielectric geometries, and demonstrate that dielectric effects \emph{qualitatively} alter the predicted self-assembled structures, with surprisi…
We describe some of the important physical characteristics of the `pathways', i.e. dynamical processes, by which molecular, nanoscale and micron-scale self-assembly occurs. We highlight the fact that there exist features of self-assembly pathways that are common to a wide range of physical systems, even though those systems may be different in respect of their microscopic details. We summarize some existing theoretical descriptions of self-assembly pathways, and highlight areas -- notably, the description of self-assembly pathways that occur `far' from equilibrium -- that are likely to become …
We consider an important class of self-assembly problems and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the set of structures that can be obtained under non-equilibrium conditions. Our central result provides intuition for how equilibrium self-assembly landscapes are modified under finite non-equilibrium drive.
Self organizing anisotropic nematic liquid crystals (LCs) induce self-assembly on quantum dots (QDs) to form one-dimensional chains along the nematic director. Spatial ordering of QDs, achieved in the nematic LC matrix, can be controlled in a preferred direction on application of electric fields, gaining better self-assembly. Once the field goes off, the LC+QD system relaxes back to the original state, revealing the intrinsic dynamics. Due to the dielectric anisotropy of the system, this dynamic response can be captured by studying dielectric relaxation. The studied dynamic response reveals in…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter can lead to self-limiting cluster growth. Furthermore, by adjusting the relative abundance of self-assembly particles in a two-particle mixture, we are able to tune the final sizes of these clusters. We show that this is a fundamental property of asymmetric interactions, which has potential applications in bioengineering, and provides new insights into the st…
Self-assembly is one of the crucial mechanisms allowing to design multifunctional materials. Soft hybrid materials contain components of different nature and exhibit competitive interactions which drive self-organisation into structures of a particular function. Here we demonstrate a novel type of a magnetic hybrid material where the molecular tilt can be manipulated through a delicate balance between the topologically-assisted colloidal self-assembly of \rev{magnetic nanoparticles} and the anisotropic molecular interactions in a liquid crystal matrix.
A big class of viruses self-assemble from a large number of identical capsid proteins with long flexible N-terminal tails and ss RNA. We study the role of the strong Coulomb interaction of positive N-terminal tails with ss RNA in the kinetics of the in vitro virus self-assembly. Capsid proteins stick to unassembled chain of ss RNA (which we call "antenna") and slide on it towards the assembly site. We show that at excess of capsid proteins such one-dimensional diffusion accelerates self-assembly more than ten times. On the other hand at excess of ss RNA, antenna slows self-assembly down. Sever…
The self-assembly of molecules at surfaces can be caused by a range of physical mechanisms. Assembly can be driven by intermolecular forces, or molecule-surface forces, or both; it can result in structures that are in equilibrium or that are kinetically trapped. Here we review examples of self-assembly at surfaces that have been studied within the User program of the Molecular Foundry at Lawrence Berkeley National Laboratory, focusing on a physical understanding of what causes patterns seen in experiment. Some apparently disparate systems can be described in similar physical terms, indicating …
In this paper, we develop a thermodynamic perturbation theory to describe the self-assembly of patchy colloids which exhibit both patch-patch attractions as well as patch / non-patch attractions. That is, patches attract other patches as well as the no patch region. In general these attractions operate on different energy scales, which allows for controlled self-assembly as well as anomalous phase behavior. As an application we apply the model to the study of liquid water.
Controlling the topology of structures self-assembled from a set of heterogeneous building blocks is highly desirable for many applications, but is poorly understood theoretically. Here we show that the thermodynamic theory of self-assembly involves an inevitable divergence in chemical potential. The divergence and its detailed structure are controlled by the spectrum of the transfer matrix, which summarizes all of self-assembly design degrees of freedom. By analyzing the transfer matrix, we map out the phase boundary between the designable structures and the unstructured aggregates, driven by…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of minimal positive design allows the self-assembly of networks equivalent to the 8 semiregular Archimedean tilings of the plane, structures not previously realized in simulation. This strategy consists of identifying the fewest distinct types of interparticle interaction that appear in the desired structure, and does not require enumeration of the many possib…
This chapter describes the synthesis and some characteristics of magnetic iron oxide nanoparticles, mainly nanocubes, and focus on their self-assembly into crystalline cuboids in dispersion. The influence of external magnetic fields, the concentration of particles, and the temperature on the assembly process is experimentally investigated.
The generation of nanoscale square and stripe patterns is of major technological importance since they are compatible with industry-standard electronic circuitry. Recently, a blend of diblock copolymer interacting via hydrogen-bonding was shown to self-assemble in square arrays. Motivated by those experiments we study, using Monte Carlo simulations, the pattern formation in a two-dimensional binary mixture of colloidal particles interacting via isotropic core-corona potentials. We find a rich variety of patterns that can be grouped mainly in aggregates that self-assemble in regular square latt…
In present study we exploited Langmuir technique to produce self-assembled arrays composed of monodisperse iron oxide nanoparticles 10 nm and 20 nm in diameter and of their binary mixture. A combination of in-situ X-ray reflectometry and Grazing-incident small-Angle X-ray scattering was used to obtain in-plane and out-of-plane structure of the arrays directly on the water surface. Surface pressure isotherms and X-ray reflectometry analysis showed that monodisperse 10 nm nanoparticles form a highly ordered monolayer, while 20 nm particles pack in three-dimensional clusters with a short-range (n…
