Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind emergence of structures with competing length scales in soft matter systems remain an open question. Examples include the droplet-inside-droplet assembly in many biomacromolecular systems undergoing liquid-liquid phase separation, analogous multiple emulsion formation in oil-surfactant-water formulations, and polymer core-shell particles with internal structure. We develop here a microscopic theoretical model based on effective interactions between the constituents of a soft matter system to explain self-organization both at single and multiple length scales. The model identifies how spatial ordering at multiple length scales emerges due to competing interactions between the system components, e.g. molecules of different sizes and different chemical properties. As an example of single and multiple-length-scale assembly, we map out a generic phase diagram for a solution with two solute species differing in their mutual and solvent interactions. By performing molecular simulations on a block-copolymer system, we further demonstrate how the phase diagram can be connected to a molecular system that has a transition from regular single-core polymer particles to multi-core aggregates that exhibit multiple structural length scales. The findings provide guidelines to understanding the length scales rising spontaneously in biological self-assembly, but also open new venues to the development and engineering of biomolecular and polymeric functional materials.
The self assembly of core-corona discs interacting via anisotropic potentials is investigated using Monte Carlo computer simulations. A minimal interaction potential that incorporates anisotropy in a simple way is introduced. It consists in a core-corona architecture in which the center of the core is shifted with respect to the center of the corona. Anisotropy can thus be tuned by progressively shifting the position of the core. Despite its simplicity, the system self organize in a rich variety of structures including stripes, triangular and rectangular lattices, and unusual plastic crystals.…
A rigid cylinder placed on a soft gel deforms its surface. When multiple cylinders are placed on the surface, they interact with each other via the topography of the deformed gel which serves as an energy landscape; as they move, the landscape changes which in turn changes their interaction. We use a combination of experiments, simple scaling estimates and numerical simulations to study the self-assembly of cylinders in this elastic analog of the Cheerios effect for capillary interactions on a fluid interface. Our results show that the effective two body interaction can be well described by an…
We use Molecular Dynamics simulations to explore the properties of dimmeric Janus nanoparticles. The nanoparticles are modeled as dumbbells. One kind of monomer interacts by a Lennard-Jones potential, while the other specie of monomer interacts though a two length scale potential. This specific two length scale potential do not present waterlike anomalies in bulk. However, our results shows that, when combined in a dimmer, the Janus nanoparticle will have waterlike anomalies. The self-assembly properties were also explored. We observe several kinds of micelles, and a liquid-crystal phase. This…
We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propos…
We study the interaction of small hydrophobic particles on the surface of an ultra-soft elastic gel, in which a small amount of elasticity of the medium balances the weights of the particles. The excess energy of the surface of the deformed gel causes them to attract as is the case with the generic capillary interactions of particles on a liquid surface. The variation of the gravitational potential energies of the particles resulting from their descents in the gel coupled with the superposition principle of Nicolson allow a fair estimation of the distance dependent attractive energy of the par…
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 intermol…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter physics to understand colloidal assembly offer some insights into the problem of crystallizing proteins. This topical review describes the various analogies that have been made between proteins and colloids in that context. We highlight the explanatory power of patchy particle models, but also the challenges of providing guidance for crystallizing specific pro…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered crystalline assemblies, and instead, disordered structures start to form when the chain length exceeds a certain threshold, which is consistent with the previous experiments. Further analysis of the simulation data suggests weakening interparticle interactions with increasing chain length, thereby shifting the suitable assembly conditions to lower temperatures …
A lattice model with soft repulsion followed by attraction is developed for a monolayer of hybrid core-shell particles self-assembling at an interface. The model is solved exactly in one dimension. One, two or three periodic structures and variety of shapes of the pressure-density isotherms may occur in different versions of the model. For strong interactions the isotherm consists of vertical segments separated by plateaus. The range of order depends strongly on the strength of attraction and on the density. Our results agree with experimental observations.
Extreme deformation of soft matter is central to our understanding of the effects of shock, fracture, and phase change in a variety of systems. Yet, despite, the increasing interest in this area, far-from-equilibrium behaviours of soft matter remain challenging to probe. Colloidal suspensions are often used to visualise emergent behaviours in soft matter, as they offer precise control of interparticle interactions, and ease of visualisation by optical microscopy. However, previous studies have been limited to deformations that are orders of magnitude too slow to be representative of extreme de…
We report a single step synthesis of a polyisobutene with a bis-urea moiety in the middle of the chain. In low polarity solvents, this polymer self-assembles by hydrogen bonding to form a combshaped polymer with a central hydrogen bonded backbone and polyisobutene arms. The comb backbone can be reversibly broken, and consequently, its length can be tuned by changing the solvent, the concentration or the temperature. Moreover, we have proved that the bulkiness of the side-chains have a strong influence on both the self-assembly pattern and the length of the backbone. Finally, the density of arm…
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),…
We elucidate the molecular forces leading to assembly of two dimensional membrane-like structures composed of a one rod-length thick monolayer of aligned rods from an immiscible suspension of hard rods and depleting polymers. We perform simulations which predict that monolayer membranes are thermodynamically stable above a critical rod aspect ratio and below a critical depletion interaction length scale. Outside of these conditions alternative structures such as stacked smectic columns or nematic droplets are thermodynamically stable. These predictions are confirmed using an experimental model…
Skyrmions have attracted rapidly growing interest due to their topological properties and unique aspects for potential novel applications such as data storage and soft robotics. They can also serve as key elements for materials by design, self-assembly, and functional soft materials. While not real particles, these skyrmions behave like particles-they interact with each other and can be actuated by means of electric field, surface anchoring, and light. On the other hand, they are field configurations which have properties not possessed by real particles. Here, we show that, by means of alignme…
Self-assembled monolayers of microparticles encoding Archimedean and non-regular tessellations promise unprecedented structure-property relationships for a wide spectrum of applications in fields ranging from optoelectronics to surface technology. Yet, despite numerous computational studies predicting the emergence of exotic structures from simple interparticle interactions, the experimental realization of non-hexagonal patterns remains challenging. Not only kinetic limitations often hinder structural relaxation, but also programming the inteparticle interactions during assembly, and hence the…
We explore the pressure versus temperature phase diagram of dimeric Janus nanoparticles using Molecular Dynamics simulations. The nanoparticle was modeled as a dumbbells particle, and have one monomer that interacts by a standard Lennard Jones potential and another monomer that is modeled using a two-length scale shoulder potential. Monomeric and dimeric systems modeled by this shoulder potential show waterlike anomalies, and we investigate if a Janus nanoparticle composed by one anomalous monomer will exhibit anomalous behavior and self-assembly structures. The influence of the non-anomalous …
Monolayers of soft colloidal particles confined at fluid interfaces have been attracting increasing interest for fundamental studies and applications alike. However, establishing the relation between their internal architecture, which is controlled during synthesis, and their structural and mechanical properties upon interfacial confinement, which define the monolayer's properties, remains an elusive task. Here, we propose a comprehensive study elucidating this relation for a system of microgels with tunable architecture. We synthesize core-shell microgels, whose soft core can be chemically de…
The ability to design and synthesize ever more complicated colloidal particles opens the possibility of self-assembling a zoo of complex structures, including those with one or more self-limited length scales. An undesirable feature of systems with self-limited length scales is that thermal fluctuations can lead to the assembly of nearby, off-target states. We investigate strategies for limiting off-target assembly by using multiple types of subunits. Using simulations and energetics calculations, we explore this concept by considering the assembly of tubules built from triangular subunits tha…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes their aggregation into poly-disperse chains with a significant persistence length. Experiments show that liquid crystals phases form above a critical volume fraction depending on the duplex length. We introduce and investigate via numerical simulations, a coarse-grained model of DNA double-helical duplexes. Each duplex is represented as an hard quasi-cylinder wh…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of water at bio-interfaces (e.g., proteins or membranes) and nano-interfaces (e.g., nanoparticles or graphene sheets) and coarse-grain models of hydration water for protein folding and protein design. We study protein self-assembly and crystallization, in bulk or under confinement, and the kinetics of protein adsorption onto nanoparticles, verify- ing our predict…
We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying el…
The synthesis of complex materials through the self-assembly of particles at the nanoscale provides opportunities for the realization of novel material properties. However, the inverse design process to create experimentally feasible interparticle interaction strategies is uniquely challenging. Standard methods for the optimization of isotropic pair potentials tend toward overfitting, resulting in solutions with too many features and length scales that are challenging to map to mechanistic models. Here we introduce a method for the optimization of simple pair potentials that minimizes the rela…
In previous approaches to form quasicrystals, multiple competing length scales involved in particle size, shape or interaction potential are believed to be necessary. It is unexpected that quasicrystals can be self-assembled by monodisperse, isotropic particles interacting via a simple potential without multiple length scales. Here we report the surprising finding of the self-assembly of such quasicrystals in two dimensional systems of soft-core disks interacting via repulsions. We find not only dodecagonal but also octagonal quasicrystals, which have not been found yet in soft quasicrystals. …
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide statistical evidence for the involvement of highly mobile and disordered regions in complex assembly. We ordered the entire set of X-ray crystallographic structures in the PDB into hierarchies of progressive interactions involving identical or very similar protein chains, yielding 40205 hierarchies of complexes with increasing numbers of partners. We then examine th…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to parametrize a coarser kinetic model that can reach the time and length scales needed to study the assembly mechanisms of these structures. We test the model by performing a detailed study of the assembly pathways for a two-dimensional target structure made up of 334 unique strands each of which are 42 nucleotides long. Without adjustable parameters, the model repro…
Soft particles are known to overlap and form stable clusters that self-assemble into periodic crystalline phases with density-independent lattice constants. We use molecular dynamics simulations in two dimensions to demonstrate that, through a judicious design of an isotropic pair potential, one can control the ordering of the clusters and generate a variety of phases, including decagonal and dodecagonal quasicrystals. Our results confirm analytical predictions based on a mean-field approximation, providing insight into the stabilization of quasicrystals in soft macromolecular systems, and sug…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins and NAs with which we investigate assembly dynamics and thermodynamics. In contrast to recent theoretical models, we find that capsids spontaneously `overcharge'; i.e., the negative charge of the NA exceeds the positive charge on capsid. When applied to specific viruses, the optimal NA lengths closely correspond to the natural genome lengths. Calculations base…
Soft materials can self-assemble into highly structured phases which replicate at the mesoscopic scale the symmetry of atomic crystals. As such, they offer an unparalleled platform to design mesostructured materials for light and sound. Here, we present a bottom-up approach based on self-assembly to engineer three-dimensional photonic and phononic crystals with topologically protected Weyl points. In addition to angular and frequency selectivity of their bulk optical response, Weyl materials are endowed with topological surface states, which allows for the existence of one-way channels even in…
The surprising recent discoveries of quasicrystals and their approximants in soft matter systems poses the intriguing possibility that these structures can be realized in a broad range of nano- and micro-scale assemblies. It has been theorized that soft matter quasicrystals and approximants are largely entropically stabilized, but the thermodynamic mechanism underlying their formation remains elusive. Here, we use computer simulation and free energy calculations to demonstrate a simple design heuristic for assembling quasicrystals and approximants in soft matter systems. Our study builds on pr…
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…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure. Depending on the geometry and the size of the particles, the grafting density of the ssDNA chains, and the length and choice of DNA sequences, a number of different crystalline structures can be fabricated. However, understanding how these factors contribute synergistically to the self-assembly process of DNA-functionalized nano- or micro-sized particles remain…
The Ground State Dominance Approximation(GSDA) has been extensively used to study the assembly of viral shells. In this work we employ the self-consistent field theory (SCFT) to investigate the adsorption of RNA onto positively charged spherical viral shells and examine the conditions when GSDA does not apply and SCFT has to be used to obtain a reliable solution. We find that there are two regimes in which GSDA does work. First, when the genomic RNA length is long enough compared to the capsid radius, and second, when the interaction between the genome and capsid is so strong that the genome i…
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…
Aqueous self-assembly of a wide range of sophorolipid and glucolipid microbial bioamphiphiles (biosurfactants): considerations on the structure-properties relationship
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.
We simulate a densely jammed, athermal assembly of repulsive soft particles immersed in a solvent. Starting from an initial condition corresponding to a quench from a high temperature, we find non-trivial slow dynamics driven by a gradual release of stored elastic energy, with the root mean squared particle speed decaying as a power law in time with a fractional exponent. This decay is accompanied by the presence within the assembly of spatially localised and temporally intermittent `hot-spots' of non-affine deformation, connected by long-ranged swirls in the velocity field, reminiscent of the…
Controlling the assembly of polyelectrolytes and surfactant at liquid-liquid interfaces offers new ways to fabricate soft materials with specific physical properties. However, little is known of the relationships between the kinetics of interfacial assembly, structural and rheological properties of such interfaces. We studied the kinetics at water-oil interface of the assembly of a positively charged biopolymer, chitosan, with an anionic fatty acid using a multi-scale approach. The growth kinetics of the membrane was followed by interfacial rheometry and space- and time- resolved dynamic light…
The tendency of amphiphilic molecules to form micelles in aqueous solution is a consequence of the hydrophobic effect. The fundamental difference between micelle assembly and macroscopic phase separation is the stoichiometric constraint that frustrates the demixing of polar and hydrophobic groups. We present a theory for micelle assembly that combines the account of this constraint with a description of the hydrophobic driving force. The latter arises from the length scale dependence of aqueous solvation. The theoretical predictions for temperature dependence and surfactant chain length depend…
The paper compares the statistical description of physical-metallurgical processes and ceramic-polycrystalline evolutions, termed the normal grain growth (NGG), as adopted to soft- and chemically-reactive grains, with a Smoluchowski's population-constant kernel cluster-cluster aggregation (CCA) model, concerning irreversible chemical reaction kinetics. The former aiming at comprehending, in a semi-quantitative way, the volume-conservative (pressure-drifted) grain-growth process which we propose to adopt for hydrogel systems at quite low temperature (near a gel point). It has been noticed, that…
The transfer of chirality across length-scales is an intriguing and universal natural phenomenon. However, connecting the properties of individual building blocks to the emergent features of their resulting large-scale structure remains a challenge. In this work, we investigate the origins of mesophase chirality in cellulose nanocrystal suspensions, whose self-assembly into chiral photonic films has attracted significant interest. By correlating the ensemble behaviour in suspensions and films with a quantitative morphological analysis of the individual nanoparticles, we reveal an inverse relat…
Viruses self-assemble from identical capsid proteins and their genome consisting, for example, of a long single stranded (ss) RNA. For a big class of T = 3 viruses capsid proteins have long positive N-terminal tails. We explore the role played by the Coulomb interaction between the brush of positive N-terminal tails rooted at the inner surface of the capsid and the negative ss RNA molecule. We show that viruses are most stable when the total contour length of ss RNA is close to the total length of the tails. For such a structure the absolute value of the total RNA charge is approximately twice…
Understanding and engineering the self-assembly of soft colloidal particles (microgels) at liquid-liquid interfaces is broadening their use in colloidal lithography. Here, we present a new route to assemble rectangular lattices of microgels at near zero surface pressure relying on the balance between attractive quadrupolar capillary interactions and steric repulsion among the particles at water/oil interfaces. These self-assembled rectangular lattices are obtained for a broad range of particles and, after deposition, can be used as lithography masks to obtain regular arrays of vertically align…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear chains. The simplicity of the model allows for a close comparison, with no fitting parameters, between simulations and theoretical predictions based on the Wertheim perturbation theory, a unique framework for the analytic prediction of the properties of self-assembling particle systems in terms of molecular parameter and liquid state correlation functions. …
We have formulated a theory of self-assembly based on the notion of local gauge invariance at the mesoscale. Local gauge invariance at the mesoscale generates the required long- range entropic forces responsible for self-assembly in binary systems. Our theory was applied to study the onset of mesostructure formation above a critical temperature in estane, a diblock copolymer. We used diagrammatic methods to transcend the Gaussian approximation and obtain a correlation length zeta ~ (c-c*)^-gamma, where c* is the minimum concentration below which self-assembly is impossible, c is the current co…
After providing a concise overview on quasicrystals and their discovery more than a quarter of a century ago, I consider the unexpected interplay between nanotechnology and quasiperiodic crystals. Of particular relevance are efforts to fabricate artificial functional micro- or nanostructures, as well as efforts to control the self-assembly of nanostructures, where current knowledge about the possibility of having long-range order without periodicity can provide significant advantages. I discuss examples of systems ranging from artificial metamaterials for photonic applications, through self-as…
Block copolymer self-assembly is a fundamental process in which incompatible blocks spontaneously form organized microstructures with broad practical applications. Classical understanding is that the domain spacing is limited by the contour length of the polymer backbone. Here, using a combination of molecular design, chemical synthesis, small/wide-angle X-ray scattering, transmission electron microscopy, and electron tomography, we discover that this molecular picture does not hold for architecturally semiflexible block copolymers. For strongly segregated linear-semiflexible bottlebrush-linea…
School of Emergent Soft Matter, State Key Laboratory of Advanced Papermaking and Paperbased Materials, South China University of Technology（华南理工大学 emergent 软物质学院，先进造纸及纸基材料国家重点实验室）；Guangdong Provincial Key Laboratory of Functional and Intelligent Hybrid Materials and Devices, Guangdong Basic Research Center of Excellence for Energy & Information Polymer Materials, South China University of Technology（华南理工大学广东省功能与智能杂化材料与器件重点实验室，广东省能源与信息高分子材料基础研究中心）；Eindhoven University of Technology（埃因霍温理工大学）
This article reviews recent inverse statistical-mechanical methodologies that we have devised to optimize interaction potentials in soft matter systems that correspond to stable "target" structures. We are interested in finding the interaction potential, not necessarily pairwise additive or spherically symmetric, that stabilizes a targeted many-body system by generally incorporating complete configurational information. Unlike previous work, our primary interest is in the possible many-body structures that may be generated, some of which may include interesting but known structures, while othe…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed phases associated with diseases, such as amyloid fibrils. Although seemingly different, these assemblies all originate from fundamental protein interactions and are driven by similar thermodynamic and kinetic factors. Here we review recent advances in understanding protein self-assembly through a soft condensed matter perspective with an emphasis on three spec…
