From viral capsids to self-assembling nanoparticles
2nd June 2021
University of York
Viruses are examples of biological nanoparticles. They are made of a highly symmetric protein container, the capsid, that contains the nucleic acid and self-assembles from several copies of a single protein. The relative position of the proteins in the capsids is conventionally described by the Caspar-Klug scheme, that was inspired by techniques developed by Fuller to construct geodetic domes.
Much interest has recently arisen in the engineering of self-assembling protein nanoparticles. In general, these nanoparticles do not fit into the Caspar-Klug framework, and conventional experimental methods only yield partial information on their structure: therefore, an original approach is needed to provide blueprints for the determination of their structure.
In this talk I will discuss a mathematical framework that enables the investigation of a specific class of self-assembling protein nanoparticles (SAPNs) which have been designed to act as antigen display systems for vaccines.
I will show that graph-theoretical tools, combined with symmetry methods based on the Goldberg construction for symmetric polyhedra, allow to study the topology of the protein networks. This approach unveils a hidden relation with fullerene geometries and enables the classification of the high and low symmetry particles seen in experiments.
Braiding wires using capillary forces
19th May 2021
Vinothan N. Manoharan
Electrical conductors that can carry frequencies of tens of GHz are needed for next-generation telecommunications networks. In principle, such conductors can be made from braided conducting filaments. However, maximizing the current-carrying capacity and minimizing loss requires each filament to have a diameter approximately equal to the skin depth, which is on the order of 1 micrometer at 10 GHz. Because such small filaments break easily, current manufacturing techniques cannot braid them. We have developed a technique to braid such small filaments using repulsive capillary forces. We attach microscale filaments to polymer “floats” that sit at a water-air interface such that the capillary force between the floats and the container walls is repulsive. As a result, the floats – and therefore the filaments – can be translated or rotated by moving the walls of the container. I will explain how the containers can be designed using principles of braid theory, and I will show how they can be used to braid wires into arbitrary topologies.
This research is in collaboration with Cheng Zeng, John Miles Faaborg, Ahmed Sherif, Ming Xiao, Martin Falk. Rozhin Hajian, Yohai Bar Sinai, and Michael P. Brenner
Biological tissues as mechanical metamaterials
5th May 2021
M. Lisa Manning
In multicellular organisms, properly programmed collective motion is required to form tissues and organs, and this programming breaks down in diseases like cancer. Recent experimental work highlights that some organisms tune the global mechanical properties of a tissue across a fluid-solid transition to allow or prohibit cell motion and control processes such as body axis elongation. What is the physical origin of such rigidity transitions? Is it similar to zero-temperature jamming transitions in particulate matter, or glass transitions in molecular or colloidal materials? Over the past decade, our group and others have shown that models for confluent tissues, where there are no gaps or overlaps between cells, exhibit a rigidity transition that depends on cell shape. A similar transition is also seen in models for biopolymer networks. I will use the framework of “higher-order rigidity”, recently implicated in origami rigidification, to discuss similarities and differences between rigidity in particulate matter and rigidity in confluent tissues and fiber networks. This suggests that many biological tissues may tune their rigidity using the same mechanisms as mechanical metamaterials. I will also discuss recent work to test which mechanisms are operating in real biological systems.
Placement and Symmetry of Singularities on Curved Surfaces
21st April 2021
University of Illinois
In various contexts, biological structures resemble regular two-dimensional lattices made from smaller units like macromolecules (on the nanoscale) or cells (on the tissue scale). This regularity carries an inherent elastic energy penalty when the 2D manifold is also required to have intrinsic curvature: Virus capsids have to close, and arthropod eyes need to reconcile the periodicity of ommatidia with eye curvature, both of which are crucial for proper function. We derive a new theoretical criterion directly from the shape properties of the manifold that predicts whether in its ground state of mechanical energy a curved structure can be regular (defect-free) or whether defects are energetically favorable. In contrast to previous approaches, the criterion does not prescribe local or globally integrated curvature, but sets a universal value for a specific weighted integral Gaussian curvature. Verified against direct numerical computation, this formalism is simple, easy to employ, and accurate for a vast variety of curved surfaces.
An extension of this approach furthermore elucidates the continuous or discontinuous character of this transition to disorder: The shape of the energy landscape determines if a transition preserves the symmetry of defect placement on surfaces of revolution because an energy barrier must be overcome, or breaks the symmetry due to stable intermediate positions. Our analytical theory predicts these transition characteristics a priori for general surface shapes, demonstrating a universal scale of energy barrier that is modified, and sometimes eliminated, by local shape properties.
Our results give practical insight into the bounds of perfect order in the growth of lattices on manifolds in many biological systems that also inspire technological applications such as microlens arrays. They inform material design considerations through geometric control, while also improving our fundamental understanding.
Packing, geometry & entropy: Crystallization of spheres in a sphere
7th April 2021
When twelve equally sized spheres are packed around a central sphere, the smallest volume of the resulting cluster and thus the highest packing is obtained for a regular icosahedron, a shape with twenty equilateral triangles as faces and a five-fold symmetry. This five-fold symmetry makes this packing interesting, because it can be proven that clusters with such a symmetry cannot fully pack 3D space.
However, it has been proven only very recently that a close-packed arrangement of equally sized spheres, composed of stackings of hexagonal layers of spheres, is the closest-packed arrangement in 3D of any single-sized sphere packing. However, if the twelve spheres are arranged in this close-packed arrangement, the local packing is less dense than the one with the icosahedral symmetry. A high local density is incompatible with a high global density.
In this talk, I will show that if spheres crystallize in a spherical confinement in experiments and simulations, clusters with icosahedral symmetry will be formed up to about 100.000 spheres . Using simulations, I will show that the free energy of these icosahedral clusters is lower than that of the close-packed crystal for as many as 100.000 spheres. With larger numbers of spheres, the system crystallizes in the close-packed bulk crystal.
In the case of a mixture of two sizes of hard spheres, with a size ratio around 0.8, I will show that such a mixture of spheres would not form the bulk equilibrium MgZn2 phase, but instead a so-called binary icosahedral cluster consisting of MgCu2 crystalline domains . The resulting clusters, a.k.a. supraparticles, can be used for a next self-assembly step in order to structure matter over multiple length scales.
 Entropy-driven formation of large icosahedral colloidal clusters by spherical confinement
B. de Nijs, S. Dussi, F. Smallenburg, J.D. Meeldijk, D.J. Groenendijk, L. Filion, A. Imhof, A. van Blaaderen, and M. Dijkstra, Nature Materials 14, 56-60 (2015).
 Binary icosahedral clusters of hard spheres in spherical confinement
D. Wang, T. Dasgupta, E.B. van der Wee, D. Zanaga, T. Altantzis, Y. Wu, G.M. Coli, C.B. Murray, S. Bals, M. Dijkstra and A. van Blaaderen, Nature Physics 17, 128–134 (2021).
Twisted topological tangles or: the knot theory of knitting
24th March 2021
Imagine a 1D curve, then use it to fill a 2D manifold that covers an arbitrary 3D object – this computationally intensive materials challenge has been realized in the ancient technology known as knitting. This process for making functional materials 2D materials from 1D portable cloth dates back to prehistory, with the oldest known examples dating from the 11th century CE. Knitted textiles are ubiquitous as they are easy and cheap to create, lightweight, portable, flexible and stretchy. As with many functional materials, the key to knitting’s extraordinary properties lies in its microstructure.
At the 1D level, knits are composed of an interlocking series of slip knots. At the most basic level there is only one manipulation that creates a knitted stitch – pulling a loop of yarn through another loop. However, there exist hundreds of books with thousands of patterns of stitches with seemingly unbounded complexity.
The topology of knitted stitches has a profound impact on the geometry and elasticity of the resulting fabric. This puts a new spin on additive manufacturing – not only can stitch pattern control the local and global geometry of a textile, but the creation process encodes mechanical properties within the material itself. Unlike standard additive manufacturing techniques, the innate properties of the yarn and the stitch microstructure has a direct effect on the global geometric and mechanical outcome of knitted fabrics.