Related papers: Programmable Control of Nucleation for Algorithmic…
Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental building blocks. We aim to explore how efficiently sequence…
Within simulations of molecules deposited on a surface we show that neuroevolutionary learning can design particles and time-dependent protocols to promote self-assembly, without input from physical concepts such as thermal equilibrium or…
Moving nanoparticles/atoms to study the nearfield interaction between them is one of the many approaches to explore the optical and electrical properties of these assemblies. Traditional approach included the self assembly by spinning or…
Molecular self-organization driven by concerted many-body interactions produces the ordered structures that define both inanimate and living matter. Understanding the physical mechanisms that govern the formation of molecular complexes and…
The possibility of prescribing local interactions between nano- and microscopic components that direct them to assemble in a predictable fashion is a central goal of nanotechnology research. In this article we advance a new paradigm in…
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-assembly of addressable structures comprising hundreds of distinct component types. The nucleation behaviour, in the form of free-energy barriers to…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
We survey our research on modeling the mechanisms of control of uniformity in growth of nanosize and colloid particles. The former are produced as nanocrystals, by burst-nucleation from solution. The latter, colloid-size particles, are…
Self-assembly of granular particles is of great interest in both applied and basic research. It is commonly observed that when randomly packed into a container, granular particles form disordered structures like glass. As the particles are…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
In this paper we explore the power of tile self-assembly models that extend the well-studied abstract Tile Assembly Model (aTAM) by permitting tiles of shapes beyond unit squares. Our main result shows the surprising fact that any aTAM…
The ability to control forces between sub-micron-scale building blocks offers considerable potential for designing new materials through self-assembly. A typical paradigm is to first identify a particular (crystal) structure that has some…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant.…
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…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
In the standard DNA brick set-up, distinct 32-nucleotide strands of single-stranded DNA are each designed to bind specifically to four other such molecules. Experimentally, it has been demonstrated that the overall yield is increased if…
The field of algorithmic self-assembly is concerned with the design and analysis of self-assembly systems from a computational perspective, that is, from the perspective of mathematical problems whose study may give insight into the natural…