Related papers: The self-assembly and evolution of homomeric prote…
We numerically study a simple fluid composed of particles having a hard-core repulsion, complemented by two short-ranged attractive (sticky) spots at the particle poles, which provides a simple model for equilibrium polymerization of linear…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
We present simulations of a hard disc system and analyze the time evolution of the dynamic heterogeneities. We characterize the time evolution of slow regions and slow particles individually. The motion of slow clusters turns out to be very…
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…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Dipolar fluids are known to exhibit complex self-assembly at low temperatures, yet a compact thermodynamic description of their aggregate statistics has remained elusive. Using molecular dynamics simulations of Stockmayer particles with a…
Biological diversity has evolved despite the essentially infinite complexity of protein sequence space. We present a hierarchical approach to the efficient searching of this space and quantify the evolutionary potential of our approach with…
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Hierarchical granular piles composed of aggregates are key structural features in both geoscience and planetary science, from fault gouge in seismic zones to the internal structures of comets. Although experimental studies have suggested a…
New model equations are derived for dynamics of self-aggregation of finite-size particles. Differences from standard Debye-Huckel and Keller-Segel models are: a) the mobility $\mu$ of particles depends on the locally-averaged particle…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…
Colloidal patchy particles with divalent attractive interaction can self-assemble into linear polymer chains. Their equilibrium properties in 2D and 3D are well described by Wertheim's thermodynamic perturbation theory which predicts a…
Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical…
A recently proposed model of non-autocatalytic reactions in dipeptide reactions leading to spontaneous symmetry breaking and homochirality is examined. The model is governed by activation, polymerization, epimerization and depolymerization…
Hierarchical self-assembly consisting of local associations of simple building-blocks for the formation of complex structures widely exists in nature, while the essential role of local assembly remains unknown. In this work, by using…
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…
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.…