Related papers: The self-assembly and evolution of homomeric prote…
We apply a simple model system of patchy particles to study monodisperse self-assembly, using the Platonic solids as target structures. We find marked differences between the assembly behaviours of the different systems. Tetrahedra,…
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 use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
We study statistical properties of interacting protein-like surfaces and predict two strong, related effects: (i) statistically enhanced self-attraction of proteins; (ii) statistically enhanced attraction of proteins with similar…
We consider a lattice model for amphiphiles in a solvent with molecules chemically similar to one part of the amphiphilic molecule. The dependence of the interaction potential on orientation of the amphiphilic molecules is taken into…
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted…
Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…
We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We…
The hallmark feature of polymorphic systems is their ability to assemble into many possible structures at the same thermodynamic state. Designer polymorphic materials can in principle be engineered via programmable self-assembly, but the…
We consider the topology of simplicial complexes with vertices the points of a random point process and faces determined by distance relationships between the vertices. In particular, we study the Betti numbers of these complexes as the…
Understanding the protein folding process is an outstanding issue in biophysics; recent developments in molecular dynamics simulation have provided insights into this phenomenon. However, the large freedom of atomic motion hinders the…
An autocatalytic pattern matching polymer system is studied as an abstract model for chemical ecosystem evolution. Highly ordered populations with particular sequence patterns appear spontaneously out of a vast number of possible states.…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…