Related papers: Self-assembly, modularity and physical complexity
Except for crystalline or random structures, an agreed definition of complexity for intermediate and hence interesting cases does not exist. We fill this gap with a notion of complexity that characterises shapes formed by any finite number…
The structure of proteins is essential for its function. The determination of protein structures is possible by experimental or predicted by computational methods, but also a combination of both approaches is possible. Here, first an…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the…
The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3-cycles). However, many phenomena from division of labor to protein-protein…
A geometrical interpretation of the $G$-structures associated to elastic material bodies is given. In addition, characterizations of their integrability are obtained. Since the lack of integrability is a geometrical measure of the lack of…
Programmable self-assembly enables the construction of complex molecular, supramolecular, and crystalline architectures from well-designed building blocks. We introduce a hypergraph-based formalism, Blocks & Bonds (B&B), that generalizes…
We introduce a simple "patchy particle" model to study the thermodynamics and dynamics of self-assembly of homomeric protein complexes. Our calculations allow us to rationalize recent results for dihedral complexes. Namely, why evolution of…
Contemporary sensorimotor learning approaches typically start with an existing complex agent (e.g., a robotic arm), which they learn to control. In contrast, this paper investigates a modular co-evolution strategy: a collection of primitive…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
We develop a theory of aggregation using statistical mechanical methods. An example of a complicated aggregation system with several levels of structures is peptide/protein self-assembly. The problem of protein aggregation is important for…
Although atomistic simulations of proteins and other biological systems are approaching microsecond timescales, the quality of trajectories has remained difficult to assess. Such assessment is critical not only for establishing the…
A method is provided for computing an upper bound of the complexity of a module over a local ring, in terms of vanishing of certain cohomology modules. We then specialize to complete intersections, which are precisely the rings over which…
The constitutive characterization of the uniformity and homogeneity of binary elastic composites is presented in terms of a combination of the material groupoids of the individual constituents. The incorporation of these two groupoids…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
In this chapter, a statistical measure of complexity is introduced and some of its properties are discussed. Also, some straightforward applications are shown.