Related papers: Structural and Compositional Complexities of Hiera…

A comprehensive framework of characterizing complex self-assembled structures with a set of orientational order parameters is presented. It is especially relevant in the context of using anisotropic building blocks with various symmetries.…

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…

Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…

Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…

Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for…

The compositional approach is important for reasoning about large and complex systems. In this work, we address synchronous systems with hierarchical structures, which are often used to model cyber-physical systems. We revisit the theory of…

Manipulating the way in which colloidal particles self-organise is a central challenge in the design of functional soft materials. Meeting this challenge requires the use of building blocks that interact with one another in a highly…

We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…

Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…

One of the great challenges of modern science is to faithfully model, and understand, matter at a wide range of scales. Starting with atoms, the vastness of the space of possible configurations poses a formidable challenge to any simulation…

Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Complex crystal structures are composed of multiple local environments, and how this type of order emerges spontaneously during crystal growth has yet to be fully understood. We study crystal growth across various structures and along…

Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…

Representing molecular structures effectively in chemistry remains a challenging task. Language models and graph-based models are extensively utilized within this domain, consistently achieving state-of-the-art results across an array of…

We introduce structured decompositions, category-theoretic structures which simultaneously generalize notions from graph theory (including treewidth, layered treewidth, co-treewidth, graph decomposition width, tree independence number,…

Assembly Theory, as developed by Cronin and co-workers, assigns to an object an assembly index: the minimal number of binary join operations required to build at least one copy of the object from a specified set of basic building blocks,…

Disordered proteins and nucleic acids play key roles in cellular function and disease. Here we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. We focus on hierarchical chain…

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…