Related papers: The determinism and boundedness of self-assembling…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model system for addressable, multicomponent self-assembly based on…
Addressable self-assembly is the formation of a target structure from a set of unique molecular or colloidal building-blocks, each of which occupies a defined location in the target. The requirement that each type of building-block appears…
Highly periodic structures are often said to convey the beauty of nature. However, most material properties are strongly influenced by the defects they contain. On the mesoscopic scale, molecular self-assembly exemplifies this interplay;…
Colloidal particles grafted with single-stranded DNA (ssDNA) chains can self-assemble into a number of different crystalline structures, where hybridization of the ssDNA chains creates links between colloids stabilizing their structure.…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
In the abstract Tile Assembly Model, self-assembling systems consisting of tiles of different colors can form structures on which colored patterns are ``painted.'' We explore the complexity, in terms of the numbers of unique tile types…
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…
The approach of nonequilibrium evolution thermodynamics earlier offered is developed. It helps to describe the processes of defect formation within the adiabatic approximation. The basic equations system depends on the initial defects…
We consider an important class of self-assembly problems and using the formalism of stochastic thermodynamics, we derive a set of design principles for growing controlled assemblies far from equilibrium. The design principles constrain the…
In this paper we address the characterization of the structure of condensed materials, periodic and non-periodic. Carrying out an extensive study of over 7000 different groundstate structures of a 2D lattice model of binary packing, we find…
Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization. At equilibrium, the structure is encoded through specific interactions,…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Identifying and explaining the structure of complex networks at different scales has become an important problem across disciplines. At the mesoscale, modular architecture has attracted most of the attention. At the macroscale, other…
Self-assembly in the laboratory can now yield `information-rich' nanostructures in which each component is of a distinct type and has a defined spatial position. Ensuring the thermodynamic stability of such structures requires…
We demonstrate existence of a tile assembly system that self-assembles the statistically self-similar Sierpinski Triangle in the Winfree-Rothemund Tile Assembly Model. This appears to be the first paper that considers self-assembly of a…
The self-assembly of anisotropic building blocks into complex spatial architectures is an important design strategy in material science but the mechanisms by which the anisotropic interactions influence the early-stage growth and formation…