Related papers: XTile: An Error-Correction Package for DNA Self-As…
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory…
Bottom-up assembly of nanocrystals (NCs) into ordered arrays, or superlattices (SLs), is a promising route to design materials with new functionalities, but the degree of control over assembly into functional structures remains challenging.…
Self-evolution methods enhance code generation through iterative "generate-verify-refine" cycles, yet existing approaches suffer from low exploration efficiency, failing to discover solutions with superior complexity within limited budgets.…
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…
Decompilation is a well-studied area with numerous high-quality tools available. These are frequently used for security tasks and to port legacy code. However, they regularly generate difficult-to-read programs and require a large amount of…
Innovative Electronic Design Automation (EDA) solutions are important to meet the design requirements for increasingly complex electronic devices. Verilog, a hardware description language, is widely used for the design and verification of…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
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…
Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded…
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…
We ask the question of how small a self-assembling set of tiles can be yet have interesting computational behaviour. We study this question in a model where supporting walls are provided as an input structure for tiles to grow along: we…
Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
A crucial problem in genome assembly is the discovery and correction of misassembly errors in draft genomes. We develop a method that will enhance the quality of draft genomes by identifying and removing misassembly errors using paired…
This paper proposes a method for generating software components for embedded systems, integrating seamlessly into existing implementations without developer intervention. We demonstrate this by automatically generating hardware abstraction…
As synthetic data becomes higher quality and proliferates on the internet, machine learning models are increasingly trained on a mix of human- and machine-generated data. Despite the successful stories of using synthetic data for…
We introduce Compositional Imitation Learning and Execution (CompILE): a framework for learning reusable, variable-length segments of hierarchically-structured behavior from demonstration data. CompILE uses a novel unsupervised,…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
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…
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…