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DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology. This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile…
Self-assembly is one of the most promising strategies for making functional materials at the nanoscale, yet new design principles for making self-limiting architectures, rather than spatially unlimited periodic lattice structures, are…
A challenge of molecular self-assembly is to understand how to design particles that self-assemble into a desired structure and not any of a potentially large number of undesired structures. Here we use simulation to show that a strategy of…
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…
DNA nanostructures are made using synthetic DNA strands, the sequences of which are designed such that they will self-assemble into the desired form by hybridization of complementary domains. Various structures and devices have been…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
By exploiting the exquisite selectivity of DNA hybridization, DNA-Coated Colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the…
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 introduce allostery-mimetic building blocks model for self-assembly of 3D structures. We represent the building blocks as patchy particles, where each binding site (patch) can be irreversibly activated or deactivated by binding of the…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
The Pattern self-Assembly Tile set Synthesis (PATS) problem, which arises in the theory of structured DNA self-assembly, is to determine a set of coloured tiles that, starting from a bordering seed structure, self-assembles to a given…
We develop algorithms capable of tackling robust black-box optimisation problems, where the number of model runs is limited. When a desired solution cannot be implemented exactly the aim is to find a robust one, where the worst case in an…
Sophisticated statistical mechanics approaches and human intuition have demonstrated the possibility to self-assemble complex lattices or finite size constructs, but have mostly only been successful in silico. The proposed strategies quite…
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…
The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of…
We study a fundamental problem in structure-based drug design -- generating molecules that bind to specific protein binding sites. While we have witnessed the great success of deep generative models in drug design, the existing methods are…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
Complex networks have become powerful mechanisms for studying a variety of realworld systems. Consequently, many human-designed network models are proposed that reproduce nontrivial properties of complex networks, such as long-tail degree…
Fabrication of DNA nanostructures primarily follows two fundamental rules. First, DNA oligonucleotides mutually combine by Watson-Crick base pairing rules between complementary base sequences. Second, the geometrical compatibility of the…
A structural optimization scheme for a single-layer nonnegative adaptive tensor tree (NATT) that models a target probability distribution is proposed as an alternative paradigm for generative modeling. The NATT scheme, by construction,…