Related papers: DNA-based chemical compiler
Focal-plane Sensor-processors (FPSPs) are a camera technology that enable low power, high frame rate computation, making them suitable for edge computation. Unfortunately, these devices' limited instruction sets and registers make…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
A wide variety of orthographic coding schemes and models of visual word identification have been developed to account for masked priming data that provide a measure of orthographic similarity between letter strings. These models tend to…
Efficiently solving NP-complete problems-such as protein structure prediction, cryptographic decryption, and vulnerability detection-remains a central challenge in computer science. Traditional electronic computers, constrained by the…
The recent surge in Generative Artificial Intelligence (AI) has introduced exciting possibilities for computational chemistry. Generative AI methods have made significant progress in sampling molecular structures across chemical species,…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Experimental validation of chemical processes is slow and costly, limiting exploration in materials discovery. Machine learning can prioritize promising candidates, but existing data in patents and literature is heterogeneous and difficult…
We describe a system for visualization and editing of data in a computational chemistry environment. The system is a collaborative tool allowing researchers using virtual reality and/or desktop computer displays to work together on results…
Chemical systems are interpreted through the species they contain and the reactions they may undergo, i.e., their chemical reaction network (CRN). In spite of their central importance to chemistry, the structure of CRNs continues to be…
Nanotechnology has revolutionized the fabrication of hybrid species with tailored functionalities. A milestone in this field is the DNA conjugation of nanoparticles, introduced almost 30 years ago, which typically exploits the affinity…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
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…
Inferring chemical reaction networks (CRN) from concentration time series is a challenge encouragedby the growing availability of quantitative temporal data at the cellular level. This motivates thedesign of algorithms to infer the…
Due to the redundant nature of DNA synthesis and sequencing technologies, a basic model for a DNA storage system is a multi-draw "shuffling-sampling" channel. In this model, a random number of noisy copies of each sequence is observed at…
In this work, we introduce a new type of linear classifier that is implemented in a chemical form. We propose a novel encoding technique which simultaneously represents multiple datasets in an array of microliter-scale chemical mixtures.…
We demonstrate the feasibility of quantum computing for large-scale, realistic chemical systems through the development of a new interface using a quantum circuit simulator and CP2K, a highly efficient first-principles calculation software.…
Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many potential applications and can be modelled using a…
Formal methods for software development have made great strides in the last two decades, to the point that their application in safety-critical embedded software is an undeniable success. Their extension to non-critical software is one of…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
It remains a challenging task to generate a vast variety of novel compounds with desirable pharmacological properties. In this work, a generative network complex (GNC) is proposed as a new platform for designing novel compounds, predicting…