Related papers: Analysis and Algorithmic Construction of Self-Asse…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Graphs are used to represent and analyze data in domains as diverse as physics, biology, chemistry, planetary science, and the social sciences. Across domains, random graph models relate generative processes to expected graph properties,…
It has been argued that a central objective of nanotechnology is to make products inexpensively, and that self-replication is an effective approach to very low-cost manufacturing. The research presented here is intended to be a step towards…
Graph classification is an important problem with applications across many domains, like chemistry and bioinformatics, for which graph neural networks (GNNs) have been state-of-the-art (SOTA) methods. GNNs are designed to learn node-level…
We have functionalized the sides of fd bacteriophage virions with oligonucleotides to induce DNA hybridization driven self-assembly of high aspect ratio filamentous particles. Potential impacts of this new structure range from an entirely…
Manually authoring 3D shapes is difficult and time consuming; generative models of 3D shapes offer compelling alternatives. Procedural representations are one such possibility: they offer high-quality and editable results but are difficult…
We consider the problem of approximating a two-dimensional shape contour (or curve segment) using discrete assembly systems, which allow to build geometric structures based on limited sets of node and edge types subject to edge length and…
In micro- and nano-scale systems, particles can be moved by using an external force like gravity or a magnetic field. In the presence of adhesive particles that can attach to each other, the challenge is to decide whether a shape is…
When designing new molecules with particular properties, it is not only important what to make but crucially how to make it. These instructions form a synthesis directed acyclic graph (DAG), describing how a large vocabulary of simple…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…
We consider the problem of reconstructing graphs or labeled graphs from neighborhoods of a given radius r. Special instances of this problem include the well known: DNA shotgun assembly; the lesser-known: neural network reconstruction; and…
We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
In computational molecular biology, gene regulatory binding sites prediction in whole genome remains a challenge for the researchers. Now a days, the genome wide regulatory binding site prediction tools required either direct pattern…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
Self-assembly is one of the prevalent strategies used by living systems to fabricate ensembles of precision nanometer-scale structures and devices. The push for analogous approaches to create synthetic nanomaterials has led to the…
Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…