We present a theoretical and computational framework to compute the symmetry number of a flexible sphere cluster in $mathbb{R}^3$, using a definition of symmetry that arises naturally when calculating the equilibrium probability of a cluster of spher
es in the sticky-sphere limit. We define the sticky symmetry group of the cluster as the set of permutations and
In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming the capsome
rs - interact by weak forces to form a structure with exceptional mechanical resistance. The destabilization of such a structure is interesting both per se, since it is related either to infection or maturation processes, and because it yields insights into the stability of complex structures in which the constitutive elements interact by weak attractive forces. We focus here on a simplified model of a dodecahederal viral capsid, and assume that the capsomers are rigid plaquettes with one degree of freedom each. We compute the most probable transition path from the closed capsid to the final configuration using minimum energy paths, and discuss the stability of intermediate states.
We describe and analyze some Monte Carlo methods for manifolds in Euclidean space defined by equality and inequality constraints. First, we give an MCMC sampler for probability distributions defined by un-normalized densities on such manifolds. The s
ampler uses a specific orthogonal projection to the surface that requires only information about the tangent space to the manifold, obtainable from first derivatives of the constraint functions, hence avoiding the need for curvature information or second derivatives. Second, we use the sampler to develop a multi-stage algorithm to compute integrals over such manifolds. We provide single-run error estimates that avoid the need for multiple independent runs. Computational experiments on various test problems show that the algorithms and error estimates work in practice. The method is applied to compute the entropies of different sticky hard sphere systems. These predict the temperature or interaction energy at which loops of hard sticky spheres become preferable to chains.
In this paper we describe a group theoretical approach to the study of structural transitions of icosahedral quasicrystals and point arrays. We apply the concept of Schur rotations, originally proposed by Kramer, to the case of aperiodic structures w
ith icosahedral symmetry; these rotations induce a rotation of the physical and orthogonal spaces invariant under the icosahedral group, and hence, via the cut-and-project method, a continuous transformation of the corresponding model sets. We prove that this approach allows for a characterisation of such transitions in a purely group theoretical framework, and provide explicit computations and specific examples. Moreover, we prove that this approach can be used in the case of finite point sets with icosahedral symmetry, which have a wide range of applications in carbon chemistry (fullerenes) and biology (viral capsids).
The architecture of infinite structures with non-crystallographic symmetries can be modeled via aperiodic tilings, but a systematic construction method for finite structures with non-crystallographic symmetry at different radial levels is still lacki
ng. We present here a group theoretical method for the construction of finite nested point set with non-crystallographic symmetry. Akin to the construction of quasicrystals, we embed a non-crystallographic group $G$ into the point group $mathcal{P}$ of a higher dimensional lattice and construct the chains of all $G$-containing subgroups. We determine the orbits of lattice points under such subgroups, and show that their projection into a lower dimensional $G$-invariant subspace consists of nested point sets with $G$-symmetry at each radial level. The number of different radial levels is bounded by the index of $G$ in the subgroup of $mathcal{P}$. In the case of icosahedral symmetry, we determine all subgroup chains explicitly and illustrate that these point sets in projection provide blueprints that approximate the organisation of simple viral capsids, encoding information on the structural organisation of capsid proteins and the genomic material collectively, based on two case studies. Contrary to the affine extensions previously introduced, these orbits endow virus architecture with an underlying finite group structure, which lends itself better for the modelling of its dynamic properties than its infinite dimensional counterpart.
We investigate the subgroup structure of the hyperoctahedral group in six dimensions. In particular, we study the subgroups isomorphic to the icosahedral group. We classify the orthogonal crystallographic representations of the icosahedral group and
analyse their intersections and subgroups, using results from graph theory and their spectra.
We propose a Ginzburg-Landau model for the expansion of a dodecahedral viral capsid during infection or maturation. The capsid is described as a dodecahedron whose faces, meant to model rigid capsomers, are free to move independent of each other, and
has therefore twelve degrees of freedom. We assume that the energy of the system is a function of the twelve variables with icosahedral symmetry. Using techniques of the theory of invariants, we expand the energy as the sum of invariant polynomials up to fourth order, and classify its minima in dependence of the coefficients of the Ginzburg-Landau expansion. Possible conformational changes of the capsid correspond to symmetry breaking of the equilibrium closed form. The results suggest that the only generic transition from the closed state leads to icosahedral expanded form. Our approach does not allow to study the expansion pathway, which is likely to be non-icosahedral.
