Related papers: Tree Orbits under Permutation Group Action: Algori…
Motivated by the question of how macromolecules assemble, the notion of an {\it assembly tree} of a graph is introduced. Given a graph $G$, the paper is concerned with enumerating the number of assembly trees of $G$, a problem that applies…
An elimination tree for a connected graph $G$ is a rooted tree on the vertices of $G$ obtained by choosing a root $x$ and recursing on the connected components of $G-x$ to produce the subtrees of $x$. Elimination trees appear in many guises…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
Viruses are nanoscale entities containing a nucleic acid genome encased in a protein shell called a capsid, and in some cases surrounded by a lipid bilayer membrane. This review summarizes the physics that govern the processes by which…
Bass-Serre theory provides a powerful framework for studying group actions on trees. While extremely effective for structural questions in group theory, it is less suited to the systematic construction of group actions with prescribed local…
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.…
A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can…
A subgroup $H$ of a group $G$ is confined if the $G$-orbit of $H$ under conjugation is bounded away from the trivial subgroup in the space $\operatorname{Sub}(G)$ of subgroups of $G$. We prove a commutator lemma for confined subgroups. For…
We prove a general result about the decomposition on ergodic components of group actions on boundaries of spherically homogeneous rooted trees. Namely, we identify the space of ergodic components with the boundary of the orbit tree…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
Automorphism groups of locally finite trees provide a large class of examples of simple totally disconnected locally compact groups. It is desirable to understand the connections between the global and local structure of such a group.…
Capsids of many viruses assemble around nucleic acids or other polymers. Understanding how the properties of the packaged polymer affect the assembly process could promote biomedical efforts to prevent viral assembly or nanomaterials…
The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
We study an abstract notion of tree structure which lies at the common core of various tree-like discrete structures commonly used in combinatorics: trees in graphs, order trees, nested subsets of a set, tree-decompositions of graphs and…
We provide a systematic enumerative and combinatorial study of geometric cellular diagonals on the permutahedra. In the first part of the paper, we study the combinatorics of certain hyperplane arrangements obtained as the union of $\ell$…
We construct the ordinary irreducible representations of the group of automorphisms of a finite rooted tree and we get a natural parametrization of them. To achieve this goals, we introduce and study the combinatorics of tree compositions,…
Multi-component aggregates are being intensively researched in various fields because of their highly tunable properties and wide applications. Due to the complex configurational space of these systems, research would greatly benefit from a…