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Molecular dynamics simulations are often used to provide feedback in the design workflow of DNA nanostructures. However, even with coarse-grained models, convergence of distributions from unbiased simulation is slow, limiting applications…
Metasurfaces are key to the development of flat optics and nanophotonic devices, offering significant advantages in creating structural colors and high-quality factor cavities. Multi-layer metasurfaces (MLMs) further amplify these benefits…
A general method for obtaining highly efficient factorial designs of relatively small sizes is developed for cDNA microarray experiments. The method allows the main effects and interactions of successive orders to be of possibly unequal…
The early promises of DNA computing to deliver a massively parallel architecture well-suited to computationally hard problems have so far been largely unkept. Indeed, it is probably fair to say that only toy problems have been addressed…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain…
Neural Architecture Search (NAS), aiming at automatically designing neural architectures by machines, has been considered a key step toward automatic machine learning. One notable NAS branch is the weight-sharing NAS, which significantly…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
Lightweight design, as a key approach to mitigate disparity between computational requirements of deep learning models and hardware performance, plays a pivotal role in advancing application of deep learning technologies on mobile and…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Recent advances in materials discovery have been driven by structure-based models, particularly those using crystal graphs. While effective for computational datasets, these models are impractical for real-world applications where atomic…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…
The increasing demands of sustainable energy, electronics, and biomedical applications call for next-generation functional materials with unprecedented properties. Of particular interest are emerging materials that display exceptional…
Domain-specific languages (DSLs) play an increasingly important role in the generation of high performing software. They allow the user to exploit specific knowledge encoded in the constructs for the generation of code adapted to a…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Designer manipulation of light at the nanoscale is key to several next-generation technologies, from sensing to optical computing. One way to manipulate light is to design a material structured at the sub-wavelength scale, a metamaterial,…