Recent Progress in the Symmetric Generation of Groups

Many groups possess highly symmetric generating sets that are naturally endowed with an underlying combinatorial structure. Such generating sets can prove to be extremely useful both theoretically in providing new existence proofs for groups and practically by providing succinct means of representing group elements. We give a survey of results obtained in the study of these symmetric generating sets. In keeping with earlier surveys on this matter, we emphasize the sporadic simple groups. ADDENDUM: This is an updated version of a survey article originally accepted for inclusion in the proceedings of the 2009 `Groups St Andrews' conference. Since the article was accepted the author has become aware of other recent work in the subject that we incorporate to provide an updated version here (the most notable addition being the contents of Section 3.4.)Comment: 14 pages, 1 figure, an updated version of a survey article accepted for the proceedings of the 2009 "Groups St Andrews" conference. v2 adds McLaughlin reference and abelian groups reference

AFLOW-SYM: Platform for the complete, automatic and self-consistent symmetry analysis of crystals

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. Here, we present a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point-, factor-, space groups, site symmetries, and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space group information provided for over 54,000 entries in the Inorganic Crystal Structure Database. Subsequently, a complete symmetry analysis is applied to all 1.7$+$ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated, $\textit{ab-initio}$ framework AFLOW.Comment: 24 pages, 6 figure

Towards a combinatorial algorithm for the enumeration of isotopy classes of symmetric cellular embeddings of graphs on hyperbolic surfaces

Based on the recent mathematical theory of isotopic tilings, we present the, to the best of our knowledge, first algorithm for the enumeration of isotopy classes of cellular embeddings of graphs invariant under a given symmetry group on hyperbolic surfaces. To achieve this, we substitute the isotopy classes with combinatorial objects and propose different techniques, guided by structural results on the mapping class group of an orbifold and notions from computational group theory that ensure that the algorithm is computationally tractable. Furthermore, we extend data structures of combinatorial tiling theory to isotopy classes that lead to an actual implementation of the algorithm for symmetry groups generated by rotations. \\From the enumerated combinatorial objects, we produce a range of simple graphs on hyperbolic surfaces represented as symmetric tilings in the hyperbolic plane, illustrating the enumeration with examples and experimentally demonstrating the feasibility of the approach. These tilings are finally projected onto a family of triply-periodic surfaces that are relevant for the natural sciences

Chiral polyhedra in ordinary space, II

A chiral polyhedron has a geometric symmetry group with two orbits on the flags, such that adjacent flags are in distinct orbits. Part I of the paper described the discrete chiral polyhedra in ordinary Euclidean 3-space with finite skew faces and finite skew vertex-figures; they occur in infinite families and are of types {4,6}, {6,4} and {6,6}. Part II completes the enumeration of all discrete chiral polyhedra in 3-space. There exist several families of chiral polyhedra with infinite, helical faces. In particular, there are no discrete chiral polyhedra with finite faces in addition to those described in Part I.Comment: 48 page

On the symmetric generation of finite groups

In this thesis we discuss some uses and applications of the techniques in Symmetric generation. In Chapter 1 we introduce the notions of symmetric generation. In Chapter 2 we discuss symmetric presentations defined by symmetric generating sets that are preserved by a group acting on them transitively but imprimitively. In Chapter 3 our attention turns to Coxeter groups. We show how the Coxeter-Moser presentations traditionally associated with the families of finite Coxeter groups of types A$_n$, D$_n$ and E$_n$ (ie the “simply laced” Coxeter groups) may be interpreted as symmetric presentations and as such may be naturally arrived at by elementary means. In Chapter 4 we classify the irreducible monomial representations of the groups L$_2$(q) and use these to define symmetric generating sets of various groups

AFLOW-SYM: platform for the complete, automatic and self-consistent symmetry analysis of crystals

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW

Random generation of subgroups of the modular group with a fixed isomorphism type

We show how to efficiently count and generate uniformly at random finitely generated subgroups of the modular group $\textsf{PSL}(2,\mathbb{Z})$ of a given isomorphism type. The method to achieve these results relies on a natural map of independent interest, which associates with any finitely generated subgroup of $\textsf{PSL}(2,\mathbb{Z})$ a graph which we call its silhouette, and which can be interpreted as a conjugacy class of free finite index subgroups of $\textsf{PSL}(2,\mathbb{Z})$.Comment: 29 pages. This is the first part of a thorough revision of arXiv:2011.09179. The second part of this revision will be posted shortl

A treatment of stereochemistry in computer aided organic synthesis

This thesis describes the author’s contributions to a new stereochemical processing module constructed for the ARChem retrosynthesis program. The purpose of the module is to add the ability to perform enantioselective and diastereoselective retrosynthetic disconnections and generate appropriate precursor molecules. The module uses evidence based rules generated from a large database of literature reactions. Chapter 1 provides an introduction and critical review of the published body of work for computer aided synthesis design. The role of computer perception of key structural features (rings, functions groups etc.) and the construction and use of reaction transforms for generating precursors is discussed. Emphasis is also given to the application of strategies in retrosynthetic analysis. The availability of large reaction databases has enabled a new generation of retrosynthesis design programs to be developed that use automatically generated transforms assembled from published reactions. A brief description of the transform generation method employed by ARChem is given. Chapter 2 describes the algorithms devised by the author for handling the computer recognition and representation of the stereochemical features found in molecule and reaction scheme diagrams. The approach is generalised and uses flexible recognition patterns to transform information found in chemical diagrams into concise stereo descriptors for computer processing. An algorithm for efficiently comparing and classifying pairs of stereo descriptors is described. This algorithm is central for solving the stereochemical constraints in a variety of substructure matching problems addressed in chapter 3. The concise representation of reactions and transform rules as hyperstructure graphs is described. Chapter 3 is concerned with the efficient and reliable detection of stereochemical symmetry in both molecules, reactions and rules. A novel symmetry perception algorithm, based on a constraints satisfaction problem (CSP) solver, is described. The use of a CSP solver to implement an isomorph‐free matching algorithm for stereochemical substructure matching is detailed. The prime function of this algorithm is to seek out unique retron locations in target molecules and then to generate precursor molecules without duplications due to symmetry. Novel algorithms for classifying asymmetric, pseudo‐asymmetric and symmetric stereocentres; meso, centro, and C2 symmetric molecules; and the stereotopicity of trigonal (sp2) centres are described. Chapter 4 introduces and formalises the annotated structural language used to create both retrosynthetic rules and the patterns used for functional group recognition. A novel functional group recognition package is described along with its use to detect important electronic features such as electron‐withdrawing or donating groups and leaving groups. The functional groups and electronic features are used as constraints in retron rules to improve transform relevance. Chapter 5 details the approach taken to design detailed stereoselective and substrate controlled transforms from organised hierarchies of rules. The rules employ a rich set of constraints annotations that concisely describe the keying retrons. The application of the transforms for collating evidence based scoring parameters from published reaction examples is described. A survey of available reaction databases and the techniques for mining stereoselective reactions is demonstrated. A data mining tool was developed for finding the best reputable stereoselective reaction types for coding as transforms. For various reasons it was not possible during the research period to fully integrate this work with the ARChem program. Instead, Chapter 6 introduces a novel one‐step retrosynthesis module to test the developed transforms. The retrosynthesis algorithms use the organisation of the transform rule hierarchy to efficiently locate the best retron matches using all applicable stereoselective transforms. This module was tested using a small set of selected target molecules and the generated routes were ranked using a series of measured parameters including: stereocentre clearance and bond cleavage; example reputation; estimated stereoselectivity with reliability; and evidence of tolerated functional groups. In addition a method for detecting regioselectivity issues is presented. This work presents a number of algorithms using common set and graph theory operations and notations. Appendix A lists the set theory symbols and meanings. Appendix B summarises and defines the common graph theory terminology used throughout this thesis