Related papers: The determinism and boundedness of self-assembling…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
During the last decade, self-affine geometrical properties of many growing aggregates, originated in a wide variety of processes, have been well characterized. However, little progress has been achieved in the search of a unified…
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…
We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…
The process of protein synthesis in biological systems resembles a one dimensional driven lattice gas in which the particles have spatial extent, covering more than one lattice site. We expand the well studied Totally Asymmetric Exclusion…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that…
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA `bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective…
We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a…
Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study…
Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…
Molecular self-assembly on surfaces constitutes a powerful method for creating tailor-made surface structures with dedicated functionalities. Varying the intermolecular interactions allows for tuning the resulting molecular structures in a…
Structural quantities such as order parameters and correlation functions are often employed to gain insight into the physical behavior and properties of condensed matter systems. While standard quantities for characterizing structure exist,…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
Both biological and artificial self-assembly processes can take place by a range of different schemes, from the successive addition of identical building blocks, to hierarchical sequences of intermediates, all the way to the fully…
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.…