Defects in crystalline packings of twisted filament bundles. I. Continuum theory of disclinations

Statistical Mechanics of Frustrated Assemblies and Incompatible Graphs

Geometrically frustrated assemblies where building blocks misfit have been shown to generate intriguing phenomena from self-limited growth, fiber formation, to structural complexity. We introduce a graph theory formulation of geometrically frustrated assemblies, capturing frustrated interactions through the concept of incompatible flows, providing a direct link between structural connectivity and frustration. This theory offers a minimal yet comprehensive framework for the fundamental statistical mechanics of frustrated assemblies, and connects it to tensor gauge theory formulations of amorphous solids. Through numerical simulations, the theory reveals new characteristics of frustrated assemblies, including two distinct percolation transitions for structure and incompatible flows, a crossover between cumulative and noncumulative frustration controlled by disorder, and a divergent length scale in their response.

Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra

We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.

Energetics of twisted elastic filament pairs

We investigate the elastic energy stored in a filament pair as a function of applied twist by measuring torque under prescribed end-to-end separation conditions. We show that the torque increases rapidly to a peak with applied twist when the filaments are initially separate, then decreases to a minimum as the filaments cross and come into contact. The torque then increases again while the filaments form a double helix with increasing twist. A nonlinear elasto-geometric model that combines the effect of geometrical nonlinearities with large stretching and self-twist is shown to capture the evolution of the helical geometry, torque profile, and stored energy with twist. We find that a large fraction of the total energy is stored in stretching the filaments, which increases with separation distance and applied tension. We find that only a small fraction of energy is stored in the form of bending energy, and that the contribution due to contact energy is negligible. Further, we provide analytical formulas for the torque observed as a function of the applied twist and the inverse relation of the observed angle for a given applied torque in the Hookean limit. Our study highlights the consequences of stretchablility on filament twisting, which is a fundamental topological transformation relevant to making ropes, tying shoelaces, actuating robots, and the physical properties of entangled polymers.

Cumulative geometric frustration and superextensive energy scaling in a nonlinear classical XY-spin model

Geometric frustration results from a discrepancy between the locally favored arrangement of the constituents of a system and the geometry of the embedding space. Geometric frustration can be either noncumulative, which implies an extensive energy growth, or cumulative, which implies superextensive energy scaling and highly cooperative ground-state configurations which may depend on the dimensions of the system. Cumulative geometric frustration was identified in a variety of continuous systems including liquid crystals, filament bundles, and molecular crystals. However, a spin-lattice model which clearly demonstrates cumulative geometric frustration was lacking. In this paper we describe a nonlinear variation of the XY-spin model on a triangular lattice that displays cumulative geometric frustration. The model is studied numerically and analyzed in three distinct parameter regimes, which are associated with different energy minimizing configurations. We show that, despite the difference in the ground-state structure in the different regimes, in all cases the superextensive power-law growth of the frustration energy for small domains grows with the same universal exponent that is predicted from the structure of the underlying compatibility condition.

Cumulative geometric frustration in physical assemblies

Geometric frustration arises whenever the constituents of a physical assembly locally favor an arrangement that cannot be realized globally. Recently, such frustrated assemblies were shown to exhibit filamentation, size limitation, large morphological variations and other exotic response properties. While these unique characteristics can be shown to be a direct outcome of the geometric frustration, some geometrically frustrated systems do not exhibit any of the above phenomena. In this work we exploit the intrinsic approach to provide a framework for directly addressing the frustration in physical assemblies. The framework highlights the role of the compatibility conditions associated with the intrinsic fields describing the physical assembly. We show that the structure of the compatibility conditions determines the behavior of small assemblies and in particular predicts their superextensive energy growth exponent. We illustrate the use of this framework to several well-known frustrated assemblies.

Stiffness heterogeneity of small viral capsids

Nanoindentation of viral capsids provides an efficient tool in order to probe their elastic properties. We investigate in the present work the various sources of stiffness heterogeneity as observed in atomic force microscopy experiments. By combining experimental results with both numerical and analytical modeling, we first show that for small viruses, a position-dependent stiffness is observed. This effect is strong and has not been properly taken into account previously. Moreover, we show that a geometrical model is able to reproduce this effect quantitatively. Our work suggests alternative ways of measuring stiffness heterogeneities on small viral capsids. This is illustrated on two different viral capsids: Adeno associated virus serotype 8 (AAV8) and hepatitis B virus (HBV with T=4). We discuss our results in light of continuous elasticity modeling.

Mechanics of Metric Frustration in Contorted Filament Bundles: From Local Symmetry to Columnar Elasticity

Bundles of filaments are subject to geometric frustration: certain deformations (e.g., bending while twisted) require longitudinal variations in spacing between filaments. While bundles are common-from protein fibers to yarns-the mechanical consequences of longitudinal frustration are unknown. We derive a geometrically nonlinear formalism for bundle mechanics, using a gaugelike symmetry under reptations along filament backbones. We relate force balance to orientational geometry and assess the elastic cost of frustration in twisted-toroidal bundles.

Defects in conformal crystals: Discrete versus continuous disclination models

We study the relationship between topological defect formation and ground-state 2D packings in a model of repulsions in external confining potentials. Specifically we consider screened 2D Coulombic repulsions, which conveniently parameterizes the effects of interaction range, but also serves as simple physical model of confined, parallel arrays of polyelectrolyte filaments or vortices in type II superconductors. The countervailing tendencies of repulsions and confinement to, respectively, spread and concentrate particle density leads to an energetic preference for nonuniform densities in the clusters. Ground states in such systems have previously been modeled as conformal crystals, which are composed of locally equitriangular packings whose local areal densities exhibit long-range gradients. Here we assess two theoretical models that connect the preference for nonuniform density to the formation of disclination defects, one of which assumes a continuum distributions of defects, while the second considers the quantized and localized nature of disclinations in hexagonal conformal crystals. Comparing both theoretical descriptions to numerical simulations of discrete particles clusters, we study the influence of interaction range and confining potential on the topological charge, number, and distribution of defects in ground states. We show that treating disclinations as continuously distributable well captures the number of topological defects in the ground state in the regime of long-range interactions, while as interactions become shorter range, it dramatically overpredicts the growth in total defect charge. Detailed analysis of the discretized defect theory suggests that that failure of the continuous defect theory in this limit can be attributed to the asymmetry in the preferred placement of positive vs negative disclinations in the conformal crystal ground states, as well as a strongly asymmetric dependence of self-energy of disclinations on sign of topological charge.

Equilibrium mechanisms of self-limiting assembly

Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of equilibrium assembly processes give rise to two states: one consisting of dispersed disassociated subunits, and the other, a bulk-condensed state of unlimited size. This review focuses on the more specialized class of self-limiting assembly, which describes equilibrium assembly processes resulting in finite-size structures. These systems pose a generic and basic question, how do thermodynamic processes involving non-covalent interactions between identical subunits "measure" and select the size of assembled structures? In this review, we begin with an introduction to the basic statistical mechanical framework for assembly thermodynamics, and use this to highlight the key physical ingredients that ensure equilibrium assembly will terminate at finite dimensions. Then, we introduce examples of self-limiting assembly systems, and classify them within this framework based on two broad categories: self-closing assemblies and open-boundary assemblies. These include well-known cases in biology and synthetic soft matter - micellization of amphiphiles and shell/tubule formation of tapered subunits - as well as less widely known classes of assemblies, such as short-range attractive/long-range repulsive systems and geometrically-frustrated assemblies. For each of these self-limiting mechanisms, we describe the physical mechanisms that select equilibrium assembly size, as well as potential limitations of finite-size selection. Finally, we discuss alternative mechanisms for finite-size assemblies, and draw contrasts with the size-control that these can achieve relative to self-limitation in equilibrium, single-species assemblies.

Shape selection and mis-assembly in viral capsid formation by elastic frustration

The successful assembly of a closed protein shell (or capsid) is a key step in the replication of viruses and in the production of artificial viral cages for bio/nanotechnological applications. During self-assembly, the favorable binding energy competes with the energetic cost of the growing edge and the elastic stresses generated due to the curvature of the capsid. As a result, incomplete structures such as open caps, cylindrical or ribbon-shaped shells may emerge, preventing the successful replication of viruses. Using elasticity theory and coarse-grained simulations, we analyze the conditions required for these processes to occur and their significance for empty virus self-assembly. We find that the outcome of the assembly can be recast into a universal phase diagram showing that viruses with high mechanical resistance cannot be self-assembled directly as spherical structures. The results of our study justify the need of a maturation step and suggest promising routes to hinder viral infections by inducing mis-assembly.

Chiral and achiral mechanisms of self-limiting assembly of twisted bundles

A generalized theory of the self-limiting assembly of twisted bundles of filaments and columns is presented. Bundles and fibers form in a broad variety of supramolecular systems, from biological to synthetic materials. A widely-invoked mechanism to explain their finite diameter relies on chirality transfer from the molecular constituents to collective twist of the assembly, the effect of which frustrates the lateral assembly and can select equilibrium, finite diameters of bundles. In this article, the thermodynamics of twisted-bundle assembly is analyzed to understand if chirality transfer is necessary for self-limitation, or instead, if spontaneously-twisting, achiral bundles also exhibit self-limited assembly. A generalized description is invoked for the elastic costs imposed by twist for bundles of various states of intra-bundle order from nematic to crystalline, as well as a generic mechanism for generating twist, classified both by chirality but also the twist susceptibility of inter-filament alignment. The theory provides a comprehensive set of predictions for the equilibrium twist and size of bundles as a function of surface energy as well as chirality, twist susceptibility, and elasticity of bundles. Moreover, it shows that while spontaneous twist can lead to self-limitation, assembly of twisted achiral bundles can be distinguished qualitatively in terms of their range of equilibrium sizes and thermodynamic stability relative to bulk (untwisted) states.

Ground States of Crystalline Caps: Generalized Jellium on Curved Space

We study the ground states of crystals on spherical surfaces. These ground states consist of positive disclination defects in structures spanning from flat and weakly curved caps to closed shells. Comparing two continuum theories and one discrete-lattice simulation, we first investigate the transition between defect-free caps to single-disclination ground states and show it to be continuous and symmetry breaking. Further, we show that ground states adopt icosahedral subgroup symmetries across the full range of curvatures, even far from the closure of complete shells. While superficially similar to other models of 2D "jellium" (e.g., superconducting disks and 2D Wigner crystals), the interplay between the free edge of caps and the non-Euclidean geometry of its embedding leads to nontrivial ground state behavior that is without counterpart in planar jellium models.

Mechanical stress relaxation in molecular self-assembly

Molecular self-assembly on a curved substrate leads to the spontaneous inclusion of topological defects in the growing bidimensional crystal, unlike assembly on a flat substrate. We propose in this work a quantitative mechanism for this phenomenon by using standard thin shell elasticity. The Gaussian curvature of the substrate induces large in-plane compressive stress as the surface grows, in particular at the rim of the assembly, and the addition of a single defect relaxes this mechanical stress. We found out that the value of azimuthal stress at the rim of the assembly determines the preferred directions for defect nucleation. These results are also discussed as a function of different defect combinations, like dislocations and grain boundaries or scars. In particular, the elastic model permits us to compare quantitatively the ability of various defects to relax mechanical stress. Moreover, these findings allow us to understand the progressive building-up of the typical disclination and grain boundary pattern observed for ground states of large 2D spherical crystals.

Elasticity in curved topographies: Exact theories and linear approximations

Almost all available results in elasticity on curved topographies are obtained within either a small curvature expansion or an empirical covariant generalization that accounts for screening between Gaussian curvature and disclinations. In this paper, we present a formulation of elasticity theory in curved geometries that unifies its underlying geometric and topological content with the theory of defects. The two different linear approximations widely used in the literature are shown to arise as systematic expansions in reference and actual space. Taking the concrete example of a two-dimensional crystal, with and without a central disclination, constrained on a spherical cap, we compare the exact results with different approximations and evaluate their range of validity. We conclude with some general discussion about the universality of nonlinear elasticity.

Why large icosahedral viruses need scaffolding proteins

While small single-stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the herpes simplex virus or infectious bursal disease virus (IBDV), typically require a template, consisting of either scaffolding proteins or an inner core. Despite the proliferation of large viruses in nature, the mechanisms by which hundreds or thousands of proteins assemble to form structures with icosahedral order (IO) is completely unknown. Using continuum elasticity theory, we study the growth of large viral shells (capsids) and show that a nonspecific template not only selects the radius of the capsid, but also leads to the error-free assembly of protein subunits into capsids with universal IO. We prove that as a spherical cap grows, there is a deep potential well at the locations of disclinations that later in the assembly process will become the vertices of an icosahedron. Furthermore, we introduce a minimal model and simulate the assembly of a viral shell around a template under nonequilibrium conditions and find a perfect match between the results of continuum elasticity theory and the numerical simulations. Besides explaining available experimental results, we provide a number of predictions. Implications for other problems in spherical crystals are also discussed.

Topological vacancies in spherical crystals

Understanding geometric frustration of ordered phases in two-dimensional condensed matter on curved surfaces is closely related to a host of scientific problems in condensed matter physics and materials science. Here, we show how two-dimensional Lennard-Jones crystal clusters confined on a sphere resolve geometric frustration and form pentagonal vacancy structures. These vacancies, originating from the combination of curvature and physical interaction, are found to be topological defects and they can be further classified into dislocational and disclinational types. We analyze the dual role of these crystallographic defects as both vacancies and topological defects, illustrate their formation mechanism, and present the phase diagram. The revealed dual role of the topological vacancies may find applications in the fabrication of robust nanopores. This work also shows the promising potential of exploiting richness in both physical interactions and substrate geometries to create new types of crystallographic defects, which have strong connections with the design of crystalline materials.

How geometric frustration shapes twisted fibres, inside and out: competing morphologies of chiral filament assembly

Chirality frustrates and shapes the assembly of flexible filaments in rope-like, twisted bundles and fibres by introducing gradients of both filament shape (i.e. curvature) and packing throughout the structure. Previous models of chiral filament bundle formation have shown that this frustration gives rise to several distinct morphological responses, including self-limiting bundle widths, anisotropic domain (tape-like) formation and topological defects in the lateral inter-filament order. In this paper, we employ a combination of continuum elasticity theory and discrete filament bundle simulations to explore how these distinct morphological responses compete in the broader phase diagram of chiral filament assembly. We show that the most generic model of bundle formation exhibits at least four classes of equilibrium structure-finite-width, twisted bundles with isotropic and anisotropic shapes, with and without topological defects, as well as bulk phases of untwisted, columnar assembly (i.e. 'frustration escape'). These competing equilibrium morphologies are selected by only a relatively small number of parameters describing filament assembly: bundle surface energy, preferred chiral twist and stiffness of chiral filament interactions, and mechanical stiffness of filaments and their lateral interactions. Discrete filament bundle simulations test and verify continuum theory predictions for dependence of bundle structure (shape, size and packing defects of two-dimensional cross section) on these key parameters.

Measuring geometric frustration in twisted inextensible filament bundles

We investigate with experiments and mapping the structure of a hexagonally ordered filament bundle that is held near its ends and progressively twisted around its central axis. The filaments are free to slide relative to each other and are further held under tension-free boundary conditions. Measuring the bundle packing with micro x-ray imaging, we find that the filaments develop the helical rotation Ω imposed at the boundaries. We then show that the observed structure is consistent with a mapping of the filament positions to disks packed on a dual non-Euclidean surface with a Gaussian curvature which increases with twist. We further demonstrate that the mean interfilament distance is minimal on the surface, which can be approximated by a hemisphere with an effective curvature K_{eff}=3Ω^{2}. Examining the packing on the dual surface, we analyze the geometric frustration of packing in twisted bundles and find the core to remain relatively hexagonally ordered with interfilament strains growing from the bundle center, driving the formation of defects at the exterior of highly twisted bundles.

Viral self-assembly pathway and mechanical stress relaxation

The final shape of a virus is dictated by the self-assembly pathway of its constituents. Using standard thin-shell elasticity, we highlight the prominent role of the viral shell's spontaneous curvature in determining the assembly pathway. In particular, we demonstrate that the mechanical stress inherent to the growth of a curved surface can be relaxed in two different ways in the early steps of assembly, depending on the value of the spontaneous curvature of the surface. This important result explains why most viral shells have either a compact shape with icosahedral symmetry or an elongated shape lacking this symmetry.

Neutral versus charged defect patterns in curved crystals

Characterizing the complex spectrum of topological defects in ground states of curved crystals is a long-standing problem with wide implications, from the mathematical Thomson problem to diverse physical realizations, including fullerenes and particle-coated droplets. While the excess number of "topologically charged" fivefold disclinations in a closed, spherical crystal is fixed, here we study the elementary transition from defect-free, flat crystals to curved crystals possessing an excess of "charged" disclinations in their bulk. Specifically, we consider the impact of topologically neutral patterns of defects-in the form of multidislocation chains or "scars" stable for small lattice spacing-on the transition from neutral to charged ground-state patterns of a crystalline cap bound to a spherical surface. Based on the asymptotic theory of caps in continuum limit of vanishing lattice spacing, we derive the morphological phase diagram of ground-state defect patterns, spanned by surface coverage of the sphere and forces at the cap edge. For the singular limit of zero edge forces, we find that scars reduce (by half) the threshold surface coverage for excess disclinations. Even more significant, scars flatten the geometric dependence of excess disinclination number on Gaussian curvature, leading to a transition between stable "charged" and "neutral" patterns that is, instead, critically sensitive to the compressive vs tensile nature of boundary forces on the cap.

Geometry of flexible filament cohesion: better contact through twist?

Cohesive interactions between filamentous molecules have broad implications for a range of biological and synthetic materials. While long-standing theoretical approaches have addressed the problem of inter-filament forces from the limit of infinitely rigid rods, the ability of flexible filaments to deform intra-filament shape in response to changes in inter-filament geometry has a profound affect on the nature of cohesive interactions. In this paper, we study two theoretical models of inter-filament cohesion in the opposite limit, in which filaments are sufficiently flexible to maintain cohesive contact along their contours, and address, in particular, the role played by helical-interfilament geometry in defining interactions. Specifically, we study models of featureless, tubular filaments interacting via: (1) pair-wise Lennard-Jones (LJ) interactions between surface elements and (2) depletion-induced filament binding stabilized by electrostatic surface repulsion. Analysis of these models reveals a universal preference for cohesive filament interactions for non-zero helical skew, and further, that in the asymptotic limit of vanishing interaction range relative to filament diameter, the skew-dependence of cohesion approaches a geometrically defined limit described purely by the close-packing geometry of twisted tubular filaments. We further analyze non-universal features of the skew-dependence of cohesion at small-twist for both potentials, and argue that in the LJ model the pair-wise surface attraction generically destabilizes parallel filaments, while in the second model, pair-wise electrostatic repulsion in combination with non-pairwise additivity of depletion leads to a meta-stable parallel state.

Emergent structure of multidislocation ground States in curved crystals

We study the structural features and underlying principles of multidislocation ground states of a crystalline spherical cap. In the continuum limit where the ratio of crystal size to lattice spacing W/a diverges, dislocations proliferate and ground states approach a characteristic sequence of structures composed of radial grain boundaries ("neutral scars"), extending radially from the boundary and terminating in the bulk. Employing a combination of numerical simulations and asymptotic analysis of continuum elasticity theory, we prove that an energetic hierarchy gives rise to a structural hierarchy, whereby dislocation number and scar number diverge as a/W→0 while scar length and dislocation number per scar become independent of lattice spacing. We characterize a secondary transition occurring as scar length grows, where the n-fold scar symmetry is broken and ground states are characterized by polydisperse, forked-scar morphologies.

Non-euclidean geometry of twisted filament bundle packing

Densely packed and twisted assemblies of filaments are crucial structural motifs in macroscopic materials (cables, ropes, and textiles) as well as synthetic and biological nanomaterials (fibrous proteins). We study the unique and nontrivial packing geometry of this universal material design from two perspectives. First, we show that the problem of twisted bundle packing can be mapped exactly onto the problem of disc packing on a curved surface, the geometry of which has a positive, spherical curvature close to the center of rotation and approaches the intrinsically flat geometry of a cylinder far from the bundle center. From this mapping, we find the packing of any twisted bundle is geometrically frustrated, as it makes the sixfold geometry of filament close packing impossible at the core of the fiber. This geometrical equivalence leads to a spectrum of close-packed fiber geometries, whose low symmetry (five-, four-, three-, and twofold) reflect non-euclidean packing constraints at the bundle core. Second, we explore the ground-state structure of twisted filament assemblies formed under the influence of adhesive interactions by a computational model. Here, we find that the underlying non-euclidean geometry of twisted fiber packing disrupts the regular lattice packing of filaments above a critical radius, proportional to the helical pitch. Above this critical radius, the ground-state packing includes the presence of between one and six excess fivefold disclinations in the cross-sectional order.

Defects in crystalline packings of twisted filament bundles. II. Dislocations and grain boundaries

Twisted and ropelike assemblies of filamentous molecules are common and vital structural elements in cells and tissues of living organisms. We study the intrinsic frustration occurring in these materials between the two-dimensional organization of filaments in cross section and out-of-plane interfilament twist in bundles. Using nonlinear continuum elasticity theory of columnar materials, we study the favorable coupling of twist-induced stresses to the presence of edge dislocations in the lattice packing of bundles, which leads to a restructuring of the ground-state order of these materials at intermediate twist. The stability of dislocations increases as both the degree of twist and lateral bundle size grow. We show that in ground states of large bundles, multiple dislocations pile up into linear arrays, radial grain boundaries, whose number and length grows with bundle twist, giving rise to a rich class of "polycrystalline" packings.