Related papers: DNA brick self-assembly with an off-lattice potent…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We propose a mathematical model of DNA self-assembly using 2D tiles to form 3D nanostructures. This is the first work to combine studies in self-assembly and nanotechnology in 3D, just as Rothemund and Winfree did in the 2D case. Our model…
In this study, a variational method for the inverse problem of self-assembly, i.e., a reconstruction of the interparticle interaction potential of a given structure, is applied to three-dimensional crystals. According to the method, the…
Computational methods for designing interactions between colloidal particles that induce self-assembly have received much attention for their promise to discover tailored materials. However, it often remains a challenge to translate…
Colloidal molecules are designed to mimic their molecular analogues through their anisotropic shape and interactions. However, current experimental realizations are missing the structural flexibility present in real molecules thereby…
Developing construction methods of materials tailored for given applications with absolute control over building block placement poses an immense challenge. DNA-coated colloids offer the possibility of realising programmable self-assembly,…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
Fabrication of diamond structures by self-assembly is a fundamental challenge in making three-dimensional photonic crystals. We simulate a system of model hard particles with attractive patches and show that they can self-assemble into a…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
DNA nanoparticles with three-fold coordination have been observed to self-assemble in experiment into a network equivalent to the hexagonal (6.6.6) tiling, and a network equivalent to the 4.8.8 Archimedean tiling. Both networks are built…
We propose here a method to generate random networked amorphous structure using only readily available short-range properties like bond lengths, bond angles and connectivity of the constituents. This method is a variant of Monte-Carlo (MC)…
Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…
A cornerstone of advanced materials design is establishing a framework for assembling nanoparticle superstructures with tailored symmetries. A longstanding challenge has been assembling diamond-like superstructures for photonic devices.…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
We characterize the self-assembly of colloidal particles with surface mobile DNA linkers under kinetically limited valence conditions. For this, we put forward a computer simulation model that captures quantitatively the interplay between…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…