Related papers: Autonomous push-down automaton built on DNA
Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
The development of self-propelled particles at the micro- and the nanoscale has sparked a huge potential for future applications in active matter physics, microsurgery, and targeted drug delivery. However, while the latter applications…
Neuro-electronic hybrid promises to bring up a model architecture for computing. Such computing architecture could help to bring the power of biological connection and electronic circuits together for better computing paradigm. Such…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
Autonomous deployment and shape reconfiguration of structures is a crucial field of research in space exploration with emerging applications in the automotive, building and biomedical industries. Challenges in achieving autonomy include:…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We propose a new method to construct an isotropic cellular automaton corresponding to a reaction-diffusion equation. The method consists of replacing the diffusion term and the reaction term of the reaction-diffusion equation with a random…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
An automaton is universal if it accepts every possible input. We study the notion of u-universality, which asserts that the automaton accepts every input starting with u. Universality and u-universality are both EXPTIME-hard for…
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
Synthesizable molecular design (also known as synthesizable molecular optimization) is a fundamental problem in drug discovery, and involves designing novel molecular structures to improve their properties according to drug-relevant oracle…
We present a DNN accelerator that allows inference at arbitrary precision with dedicated processing elements that are configurable at the bit level. Our DNN accelerator has 8 Processing Elements controlled by a RISC-V controller with a…
This study introduces EngramNCA, a neural cellular automaton (NCA) that integrates both publicly visible states and private, cell-internal memory channels, drawing inspiration from emerging biological evidence suggesting that memory storage…
Understanding the binding dynamics of liquid molecules is of fundamental importance in physical and life sciences. However, nanoscale fast dynamics pose great challenges for experimental characterization. Conventionally, the binding…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
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…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path…