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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…
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress…
Majumder, Reif and Sahu have presented a stochastic model of reversible, error-permitting, two-dimensional tile self-assembly, and showed that restricted classes of tile assembly systems achieved equilibrium in (expected) polynomial time.…
We show that neural networks trained by evolutionary reinforcement learning can enact efficient molecular self-assembly protocols. Presented with molecular simulation trajectories, networks learn to change temperature and chemical potential…
We show the first non-trivial positive algorithmic results (i.e. programs whose output is larger than their size), in a model of self-assembly that has so far resisted many attempts of formal analysis or programming: the planar…
Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…
Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
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…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
A physically-motivated genetic algorithm (GA) and full enumeration for a tile-based model of self-assembly (JaTAM) is implemented using a graphics processing unit (GPU). We observe performance gains with respect to state-of-the-art…
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.…
In this work we propose a generalization of Winfree's abstract Tile Assembly Model (aTAM) in which tile types are assigned rigid shapes, or geometries, along each tile face. We examine the number of distinct tile types needed to assemble…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Submodularity is an important concept in integer and combinatorial optimization. A classical submodular set function models the utility of selecting homogenous items from a single ground set, and such selections can be represented by binary…
Traditionally, computation within self-assembly models is hard to conceal because the self-assembly process generates a crystalline assembly whose computational history is inherently part of the structure itself. With no way to remove…
Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for all $N \in \mathbb{N}$, there is a tile set that uniquely self-assembles into an $N \times N$ square shape at temperature 1 with optimal…
The Tile Automata (TA) model describes self-assembly systems in which monomers can build structures and transition with an adjacent monomer to change their states. This paper shows that seeded TA is a non-committal intrinsically universal…